GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Shewanella amazonensis SB2B

Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate 6938088 Sama_2209 C4-dicarboxylate-binding periplasmic protein (RefSeq)

Query= SwissProt::A3QCW5
         (336 letters)



>FitnessBrowser__SB2B:6938088
          Length = 339

 Score =  517 bits (1332), Expect = e-151
 Identities = 255/322 (79%), Positives = 291/322 (90%)

Query: 15  KMTSIAALLGASLNSWAAPTEIKFSHVVAENTPKGQMALKFKQLVEERLPGEYQVNVFPN 74
           K + +A +LG S  + A P EIKFSHVVAENTPKGQMALKFK+LVE RLPGEY+V+VFPN
Sbjct: 17  KASLLATVLGFSFGAVAEPVEIKFSHVVAENTPKGQMALKFKELVESRLPGEYKVSVFPN 76

Query: 75  SQLFGDNNELSALLLNDVQFVAPSLSKFERYTKKLQLFDLPFLFKDMDAVNRFQQSDAGQ 134
           SQLFGDNNEL+ALLLNDVQ VAPSLSKFERYTKKLQ+FDLPFLF+DMDAV+RFQQS+AGQ
Sbjct: 77  SQLFGDNNELAALLLNDVQLVAPSLSKFERYTKKLQVFDLPFLFEDMDAVDRFQQSEAGQ 136

Query: 135 QLLNSMKRKGVVGLGYLHNGMKQFSASSPLVLPEDAQGKKFRIMASDVLAAQFQAVEAIP 194
           QLLNSM RKG+VGLGYLHNGMKQFSA++ L LP DA GKKFRIM SDV+AAQF+AV AIP
Sbjct: 137 QLLNSMSRKGLVGLGYLHNGMKQFSANNALSLPGDAAGKKFRIMPSDVIAAQFEAVGAIP 196

Query: 195 VKKPFSEVFTLLQTRAIDGQENTWSNIYSKKFYEVQSNITESNHGVLDYMVVTSNTFWKS 254
           VKKPFSEVFTLLQTRAIDGQENTWSNIYSKKFYEVQ++ITESNHGVLDYM+VTS TFWKS
Sbjct: 197 VKKPFSEVFTLLQTRAIDGQENTWSNIYSKKFYEVQTHITESNHGVLDYMLVTSETFWKS 256

Query: 255 LPADKRKVIKASLDEAIAYGNEIAAAKVNKDKQAIIDSKRSEVTYLTPEQRAAWVNAMKP 314
           LP DKR++IK S+DEA+A GN++A  K N+D+Q I+DSKR E+  LTPEQR AWVNAM+P
Sbjct: 257 LPKDKREIIKQSMDEAVALGNKLALEKANEDRQLILDSKRVELVTLTPEQRQAWVNAMRP 316

Query: 315 VWAQFEDKIGKDLIDAAVASNE 336
           VW+QFEDKIGKDLI+AA ++N+
Sbjct: 317 VWSQFEDKIGKDLIEAAESANK 338


Lambda     K      H
   0.317    0.130    0.368 

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: 437
Number of extensions: 5
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 336
Length of database: 339
Length adjustment: 28
Effective length of query: 308
Effective length of database: 311
Effective search space:    95788
Effective search space used:    95788
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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