BLASTP 2.2.4 [Aug-26-2002]

Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

RID: 1032870435-012785-11441

Query= gi|16763661|ref|NP_459276.1| putative periplasmic
protein [Salmonella typhimurium LT2]
         (127 letters)


Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF 
           1,172,300 sequences; 371,327,854 total letters

 
If you have any problems or questions with the results of this search 
please refer to the BLAST FAQs

Taxonomy reports




                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

ref|NP_459276.1|  (NC_003197) putative periplasmic protein [...   244   5e-65
ref|NP_405138.1|  (NC_003143) putative exported protein [Yer...    59   3e-09
ref|NP_669919.1|  (NC_004088) hypothetical [Yersinia pestis ...    59   3e-09
gb|ZP_00083414.1|  (NZ_AABA01000072) hypothetical protein [P...    31   0.86 
ref|NP_661687.1|  (NC_002932) AslB/AtsB family protein [Chlo...    30   1.5  
dbj|BAC00968.1|  (AB086390) ABC-type transporter periplasmic...    30   1.6  
ref|NP_484520.1|  (NC_003272) hypothetical protein [Nostoc s...    29   3.2  
pir||H35905  hypothetical protein 1 (Sm1) - Streptococcus mu...    29   3.8  
gb|ZP_00091876.1|  (NZ_AAAD01000090) hypothetical protein [A...    29   3.9  
ref|NP_486920.1|  (NC_003272) bicarbonate transport ATP-bind...    28   4.9  
gb|ZP_00105962.1|  (NZ_AABC01000058) hypothetical protein [N...    28   4.9  
gb|ZP_00079868.1|  (NZ_AAAS01000002) hypothetical protein [G...    28   5.5  
gb|ZP_00092565.1|  (NZ_AAAD01000091) hypothetical protein [A...    28   5.7  
gb|ZP_00085892.1|  (NZ_AABA01000138) hypothetical protein [P...    28   5.7  
pir||S46920  transcription repressor - Mycoplasma capricolum...    28   5.7  
ref|NP_249846.1|  (NC_002516) ribonucleoside reductase, smal...    28   6.7  
ref|NP_224077.1|  (NC_000921) putative [Helicobacter pylori ...    28   7.1  
gb|ZP_00065184.1|  (NZ_AAAT01000002) hypothetical protein [M...    28   7.1  

Alignments


>ref|NP_459276.1| (NC_003197) putative periplasmic protein [Salmonella typhimurium
           LT2]
 gb|AAL19235.1| (AE008707) putative periplasmic protein [Salmonella typhimurium
           LT2]
          Length = 127

 Score =  244 bits (623), Expect = 5e-65
 Identities = 127/127 (100%), Positives = 127/127 (100%)

Query: 1   MDTAVKWLILVTFSISGMLVWQPSFAQEALTTQYSQSELLKNWALSHCLALVYKDDVVKN 60
           MDTAVKWLILVTFSISGMLVWQPSFAQEALTTQYSQSELLKNWALSHCLALVYKDDVVKN
Sbjct: 1   MDTAVKWLILVTFSISGMLVWQPSFAQEALTTQYSQSELLKNWALSHCLALVYKDDVVKN 60

Query: 61  DARATASAYLEYGKQSVEIYHEIDEIAKKYSGLKYNGSISSDFNTMKCIDFIHDRELNEL 120
           DARATASAYLEYGKQSVEIYHEIDEIAKKYSGLKYNGSISSDFNTMKCIDFIHDRELNEL
Sbjct: 61  DARATASAYLEYGKQSVEIYHEIDEIAKKYSGLKYNGSISSDFNTMKCIDFIHDRELNEL 120

Query: 121 IKRRVEK 127
           IKRRVEK
Sbjct: 121 IKRRVEK 127



>ref|NP_405138.1| (NC_003143) putative exported protein [Yersinia pestis]
 emb|CAC90375.1| (AJ414149) putative exported protein [Yersinia pestis]
          Length = 144

 Score = 59.3 bits (142), Expect = 3e-09
 Identities = 41/114 (35%), Positives = 59/114 (50%), Gaps = 7/114 (6%)

Query: 12  TFSISGM--LVWQPSFAQEALTTQYSQSELLKNWALSHCLALVYKDDVVKNDARATASAY 69
           T SI+ +  L+   + A E    +  Q   L+N+ALS CLA  + D  + ++A +   AY
Sbjct: 25  TLSITSLIFLISFSTLAAEVNQNKVQQKNNLENFALSICLAEGFPDGEINSEAFSAVGAY 84

Query: 70  LEYGKQSVEIYHEIDEIAKKYSGLKY---NGSISSDFNTMKCIDFIHDRELNEL 120
           +E G   VE Y E+ E+AKK+   KY   NG   S    MKCID     EL+ +
Sbjct: 85  VELGAYPVEAYEEVSELAKKFLEKKYISKNG--ESKLTVMKCIDLSQSSELSAI 136



>ref|NP_669919.1| (NC_004088) hypothetical [Yersinia pestis KIM]
 gb|AAM86170.1|AE013863_4 (AE013863) hypothetical [Yersinia pestis KIM]
          Length = 136

 Score = 59.3 bits (142), Expect = 3e-09
 Identities = 41/114 (35%), Positives = 59/114 (50%), Gaps = 7/114 (6%)

Query: 12  TFSISGM--LVWQPSFAQEALTTQYSQSELLKNWALSHCLALVYKDDVVKNDARATASAY 69
           T SI+ +  L+   + A E    +  Q   L+N+ALS CLA  + D  + ++A +   AY
Sbjct: 17  TLSITSLIFLISFSTLAAEVNQNKVQQKNNLENFALSICLAEGFPDGEINSEAFSAVGAY 76

Query: 70  LEYGKQSVEIYHEIDEIAKKYSGLKY---NGSISSDFNTMKCIDFIHDRELNEL 120
           +E G   VE Y E+ E+AKK+   KY   NG   S    MKCID     EL+ +
Sbjct: 77  VELGAYPVEAYEEVSELAKKFLEKKYISKNG--ESKLTVMKCIDLSQSSELSAI 128



>gb|ZP_00083414.1| (NZ_AABA01000072) hypothetical protein [Pseudomonas fluorescens]
          Length = 158

 Score = 31.2 bits (69), Expect = 0.86
 Identities = 20/50 (40%), Positives = 27/50 (54%), Gaps = 3/50 (6%)

Query: 26 AQEALTTQYSQSELLKNWALSHCLALVYKD-DVVKNDARATASAYLEYGK 74
          A E  T Q  Q+  LKN+ LSHC+   +K+   +K D   +A AY   GK
Sbjct: 40 ASEGRTEQARQN--LKNYGLSHCILAPFKEHSAMKKDIELSAGAYSFMGK 87



>ref|NP_661687.1| (NC_002932) AslB/AtsB family protein [Chlorobium tepidum TLS]
 gb|AAM72029.1| (AE012847) AslB/AtsB family protein [Chlorobium tepidum TLS]
          Length = 394

 Score = 30.4 bits (67), Expect = 1.5
 Identities = 13/41 (31%), Positives = 23/41 (55%), Gaps = 7/41 (17%)

Query: 77  VEIYHEIDEIAKKYSGLKYNGSISSDFNTMKCIDFIHDREL 117
           ++ Y ++D + KKY+   Y        NT++   ++HDREL
Sbjct: 81  IDFYRKVDRLQKKYATKPYA-------NTIQTSGYVHDREL 114



>dbj|BAC00968.1| (AB086390) ABC-type transporter periplasmic sulfonate-binding
           component [Pseudomonas putida]
          Length = 323

 Score = 30.4 bits (67), Expect = 1.6
 Identities = 29/90 (32%), Positives = 38/90 (42%), Gaps = 10/90 (11%)

Query: 15  ISGMLVWQPSF--AQEALTTQYSQSELLKNWALSHCLALVYKD------DVVKNDARATA 66
           I    VW P+   A+E      +  EL K  A +    +V KD      DVVK  A+ T 
Sbjct: 172 IDATYVWDPALGVAKENGKVLITSGELAKKGAPTFDAWIVRKDFAAKHPDVVKAFAKVTL 231

Query: 67  SAYLEYGKQSVEIYHEIDEIAK--KYSGLK 94
            AY +Y K         D ++K  K SG K
Sbjct: 232 DAYADYRKNPQAWLANPDNVSKLAKLSGAK 261



>ref|NP_484520.1| (NC_003272) hypothetical protein [Nostoc sp. PCC 7120]
 dbj|BAB72434.1| (AP003582) ORF_ID:all0476~hypothetical protein [Nostoc sp. PCC
          7120]
          Length = 274

 Score = 29.3 bits (64), Expect = 3.2
 Identities = 12/31 (38%), Positives = 19/31 (60%)

Query: 7  WLILVTFSISGMLVWQPSFAQEALTTQYSQS 37
          WLIL   S+  + +WQP+ A E   T+ +Q+
Sbjct: 20 WLILCILSLGLVNIWQPTQAIEVAQTRTTQN 50



>pir||H35905 hypothetical protein 1 (Sm1) - Streptococcus mutans  (fragment)
          Length = 159

 Score = 28.9 bits (63), Expect = 3.8
 Identities = 16/56 (28%), Positives = 27/56 (47%)

Query: 43 WALSHCLALVYKDDVVKNDARATASAYLEYGKQSVEIYHEIDEIAKKYSGLKYNGS 98
          W  SH L L +  D V     A A A + +  +S  I  ++ E  +K++  + NG+
Sbjct: 4  WQTSHWLFLFFGADSVGKTELAKALAEVLFDDESALIRFDMSEYMEKFAASRLNGA 59



>gb|ZP_00091876.1| (NZ_AAAD01000090) hypothetical protein [Azotobacter vinelandii]
          Length = 517

 Score = 28.9 bits (63), Expect = 3.9
 Identities = 26/107 (24%), Positives = 45/107 (41%), Gaps = 7/107 (6%)

Query: 21  WQPSFAQEALTTQYSQSELLKNWALSHCLALVYKDDVVKNDARATASAYLEYGKQSVEIY 80
           + PS+A+  L +Q S S  L        L  +    V +    A A AYL   +   +  
Sbjct: 147 YNPSYAEMGLRSQVSGSVDLD-------LEALIDRKVYRFMGDAAAFAYLSMEQAIKDAG 199

Query: 81  HEIDEIAKKYSGLKYNGSISSDFNTMKCIDFIHDRELNELIKRRVEK 127
              ++I+    GL      +S FN M+ +D + D+ +  +   RV +
Sbjct: 200 LTAEQISDPRVGLIAGSGGASTFNQMEAMDILRDKGVKRVGPYRVPR 246



>ref|NP_486920.1| (NC_003272) bicarbonate transport ATP-binding protein [Nostoc sp.
           PCC 7120]
 dbj|BAB74579.1| (AP003591) bicarbonate transport ATP-binding protein [Nostoc sp.
           PCC 7120]
          Length = 289

 Score = 28.5 bits (62), Expect = 4.9
 Identities = 13/40 (32%), Positives = 23/40 (57%)

Query: 18  MLVWQPSFAQEALTTQYSQSELLKNWALSHCLALVYKDDV 57
           +++ +P  A +A+T +  Q ELLK W  + C  L+   D+
Sbjct: 185 LILDEPFGALDAITKEELQEELLKIWGDNRCTVLMITHDI 224



>gb|ZP_00105962.1| (NZ_AABC01000058) hypothetical protein [Nostoc punctiforme]
          Length = 245

 Score = 28.5 bits (62), Expect = 4.9
 Identities = 13/40 (32%), Positives = 23/40 (57%)

Query: 18  MLVWQPSFAQEALTTQYSQSELLKNWALSHCLALVYKDDV 57
           +++ +P  A +A+T +  Q ELLK W  + C  L+   D+
Sbjct: 141 LILDEPFGALDAITKEELQEELLKIWGDNRCTVLMITHDI 180



>gb|ZP_00079868.1| (NZ_AAAS01000002) hypothetical protein [Geobacter metallireducens]
          Length = 752

 Score = 28.5 bits (62), Expect = 5.5
 Identities = 19/57 (33%), Positives = 28/57 (48%), Gaps = 1/57 (1%)

Query: 38  ELLKNWALSHCL-ALVYKDDVVKNDARATASAYLEYGKQSVEIYHEIDEIAKKYSGL 93
           E  + W LS    A  YKD+V+KND    A  Y   G  +V++     ++ +  SGL
Sbjct: 202 ETKEKWFLSWLTGAGTYKDEVLKNDVNLIADLYFNNGYVNVKVGEPDVKVLEDRSGL 258



>gb|ZP_00092565.1| (NZ_AAAD01000091) hypothetical protein [Azotobacter vinelandii]
          Length = 416

 Score = 28.5 bits (62), Expect = 5.7
 Identities = 15/23 (65%), Positives = 17/23 (73%), Gaps = 1/23 (4%)

Query: 79  IYHEIDEIAKKYS-GLKYNGSIS 100
           +YHEI  +AKK S GLKY  SIS
Sbjct: 212 MYHEIPSVAKKASWGLKYTRSIS 234



>gb|ZP_00085892.1| (NZ_AABA01000138) hypothetical protein [Pseudomonas fluorescens]
          Length = 416

 Score = 28.5 bits (62), Expect = 5.7
 Identities = 16/29 (55%), Positives = 21/29 (72%), Gaps = 2/29 (6%)

Query: 79  IYHEIDEIAKKYS-GLKYNGSISS-DFNT 105
           +YHEI  +AKK + GLKY  +IS  +FNT
Sbjct: 212 MYHEIPSVAKKAAWGLKYTRAISDPEFNT 240



>pir||S46920 transcription repressor - Mycoplasma capricolum (SGC3) (fragment)
 pir||S77828 probable transcription repressor MC063 - Mycoplasma capricolum
           (fragment)
 emb|CAA83725.1| (Z33052) transcription repressor [Mycoplasma capricolum]
          Length = 224

 Score = 28.5 bits (62), Expect = 5.7
 Identities = 25/77 (32%), Positives = 37/77 (47%), Gaps = 9/77 (11%)

Query: 52  VYKDDVVKNDARATASAYLEYGKQSVEIYHEIDEIAKKYSGLKYNGSISSDFNTMKC--- 108
           VY  D+  ND +    A+LEY K+  E Y E++E+    +   Y+        T  C   
Sbjct: 11  VYYTDI--NDKKVIELAFLEYKKKYDEFYVELEELKNYMTAEDYHQDYLDKNPTGYCHVN 68

Query: 109 --IDF-IHDRELNELIK 122
             +DF + D+E  ELIK
Sbjct: 69  LNVDFNLTDKE-QELIK 84



>ref|NP_249846.1| (NC_002516) ribonucleoside reductase, small chain [Pseudomonas
           aeruginosa]
 pir||A83502 ribonucleoside reductase, small chain PA1155 [imported] -
           Pseudomonas aeruginosa (strain PAO1)
 gb|AAG04544.1|AE004545_7 (AE004545) ribonucleoside reductase, small chain [Pseudomonas
           aeruginosa]
          Length = 415

 Score = 28.1 bits (61), Expect = 6.7
 Identities = 15/23 (65%), Positives = 17/23 (73%), Gaps = 1/23 (4%)

Query: 79  IYHEIDEIAKKYS-GLKYNGSIS 100
           +YHEI  +AKK S GLKY  SIS
Sbjct: 211 MYHEIPSVAKKASWGLKYTRSIS 233



>ref|NP_224077.1| (NC_000921) putative [Helicobacter pylori J99]
 pir||A71818 hypothetical protein jhp1359 - Helicobacter pylori (strain J99)
 gb|AAD06935.1| (AE001558) putative [Helicobacter pylori J99]
          Length = 377

 Score = 28.1 bits (61), Expect = 7.1
 Identities = 15/42 (35%), Positives = 24/42 (56%), Gaps = 2/42 (4%)

Query: 83  IDEIAKKYSGLKYNGSISSDFNTMKCIDFIHDRELNELIKRR 124
           +DE+ K    L + GS+  DF+  + IDF+    L +L+K R
Sbjct: 35  LDELKKNL--LDHQGSLKMDFSGCQKIDFVFGMFLFDLVKER 74



>gb|ZP_00065184.1| (NZ_AAAT01000002) hypothetical protein [Microbulbifer degradans
          2-40]
          Length = 168

 Score = 28.1 bits (61), Expect = 7.1
 Identities = 13/49 (26%), Positives = 25/49 (50%), Gaps = 8/49 (16%)

Query: 7  WLILVTFSISGMLVWQPSFAQEALTTQYSQSELLKNWALSHCLALVYKD 55
          W IL    +S ++  +  F +EAL+        + NW ++  +A+ +KD
Sbjct: 6  WAILAILLVSSLISLKRGFVKEALS--------MLNWVIAFFIAMSFKD 46






  Database: All non-redundant GenBank CDS
  translations+PDB+SwissProt+PIR+PRF
    Posted date:  Sep 22, 2002  1:02 PM
  Number of letters in database: 371,327,854
  Number of sequences in database:  1,172,300
  
Lambda     K      H
   0.318    0.132    0.382 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 27,815,718
Number of Sequences: 1172300
Number of extensions: 952650
Number of successful extensions: 2875
Number of sequences better than 10.0: 38
Number of HSP's better than 10.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 26
Number of HSP's that attempted gapping in prelim test: 2863
Number of HSP's gapped (non-prelim): 38
length of query: 127
length of database: 126,083,458
effective HSP length: 103
effective length of query: 24
effective length of database: 83,891,671
effective search space: 2013400104
effective search space used: 2013400104
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (27.7 bits)