GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Shewanella amazonensis SB2B

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate 6937828 Sama_1969 ABC transporter, ATP-binding protein (RefSeq)

Query= uniprot:D8IUD1
         (522 letters)



>FitnessBrowser__SB2B:6937828
          Length = 301

 Score = 89.4 bits (220), Expect = 2e-22
 Identities = 74/234 (31%), Positives = 114/234 (48%), Gaps = 12/234 (5%)

Query: 13  LLTLSGIGKRYAAPV-LDGIDLDLRPGQVLALTGENGAGKSTLSKIICGLVDASAGGMML 71
           L+    + KRY +   LD + L +  G  +AL G NGAGK+TL  ++CG +    G + +
Sbjct: 3   LIVTRNLTKRYGSKTALDDVSLQVEAGAPVALVGPNGAGKTTLMSLMCGYIQPDGGSLEI 62

Query: 72  DGQPYAPASRTQAEGLG-IRMVMQELNLIPTLSIAENLFLEKLPRRFGWIDRKKLAEAAR 130
            G  + P SR   + LG +  + Q+  L P  S+ E L      + F   D ++ AE   
Sbjct: 63  LG--HVPGSR---QLLGKVCALPQDALLDPNFSVGEQLSFFASLQGFSAKDARREAERV- 116

Query: 131 AQMEVVGLGELDPWTPVGDLGLGHQQMVEIARNLIGSCRCLILDEPTAMLTNREVELLFS 190
             +E+V L +     P   L  G  + V IA+ LIG+ + ++LDEPTA L       +  
Sbjct: 117 --LELVELKDAARHKPTA-LSHGMGKRVAIAQALIGTPQLVLLDEPTAGLDPANARAVRE 173

Query: 191 RIERLRAEGVAIIYISHRLEELKRIADRIVVLRDGKLVCNDDIGRYSTEQLVQL 244
            I    +E    +  SH LEEL+R+ D ++ L  GKL  +  I   S E+ + L
Sbjct: 174 LISH-ASEQTTFLISSHNLEELERLCDTVLYLDKGKLSQSLSIKSESVERFLTL 226



 Score = 57.8 bits (138), Expect = 5e-13
 Identities = 59/244 (24%), Positives = 101/244 (41%), Gaps = 28/244 (11%)

Query: 272 GRAPVVHPASLALHAGEVLGIAGLIGSGRTELLRLIFGADRAEQGEIFI-----GDSQEP 326
           G    +   SL + AG  + + G  G+G+T L+ L+ G  + + G + I     G  Q  
Sbjct: 14  GSKTALDDVSLQVEAGAPVALVGPNGAGKTTLMSLMCGYIQPDGGSLEILGHVPGSRQLL 73

Query: 327 ARIRS-PKDAVKAGIAMVTEDRKGQGLLLPQAISVNTSLANLGSVSRGGMLDHAAESSVA 385
            ++ + P+DA                 LL    SV   L+   S+      D   E+   
Sbjct: 74  GKVCALPQDA-----------------LLDPNFSVGEQLSFFASLQGFSAKDARREAERV 116

Query: 386 QDYVKKLRIRSGSVAQAAGELSGGNQQKVVIARWLYRDCPIMLFDEPTRGIDIGAKSDIY 445
            + V+       +       LS G  ++V IA+ L     ++L DEPT G+D  A +   
Sbjct: 117 LELVEL----KDAARHKPTALSHGMGKRVAIAQALIGTPQLVLLDEPTAGLD-PANARAV 171

Query: 446 RLFAELAAQGKGLLVVSSDLRELMQICDRIAVMSAGRIADTFSRDDWSQERILAAAFSGY 505
           R     A++    L+ S +L EL ++CD +  +  G+++ + S    S ER L  +    
Sbjct: 172 RELISHASEQTTFLISSHNLEELERLCDTVLYLDKGKLSQSLSIKSESVERFLTLSLQDS 231

Query: 506 VGRQ 509
            G +
Sbjct: 232 AGEE 235


Lambda     K      H
   0.320    0.137    0.390 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 349
Number of extensions: 17
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 522
Length of database: 301
Length adjustment: 31
Effective length of query: 491
Effective length of database: 270
Effective search space:   132570
Effective search space used:   132570
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory