GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Shewanella sp. ANA-3

Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate 7024209 Shewana3_1416 TRAP dicarboxylate transporter, DctP subunit (RefSeq)

Query= reanno::SB2B:6938088
         (339 letters)



>FitnessBrowser__ANA3:7024209
          Length = 340

 Score =  525 bits (1352), Expect = e-154
 Identities = 258/327 (78%), Positives = 291/327 (88%)

Query: 12  LFTLGKASLLATVLGFSFGAVAEPVEIKFSHVVAENTPKGQMALKFKELVESRLPGEYKV 71
           L T+ K   LA+V   SF   A PVEIKFSHVVAENTPKGQMALKFKELVE RLPGEY V
Sbjct: 13  LKTVAKMLALASVFATSFNVFAAPVEIKFSHVVAENTPKGQMALKFKELVEQRLPGEYTV 72

Query: 72  SVFPNSQLFGDNNELAALLLNDVQLVAPSLSKFERYTKKLQVFDLPFLFEDMDAVDRFQQ 131
           SVFPNSQLFGDNNELAALLLNDVQ VAPSLSKFERYTK+LQVFDLPFLF DMDAV+RFQQ
Sbjct: 73  SVFPNSQLFGDNNELAALLLNDVQFVAPSLSKFERYTKRLQVFDLPFLFNDMDAVNRFQQ 132

Query: 132 SEAGQQLLNSMSRKGLVGLGYLHNGMKQFSANNALSLPGDAAGKKFRIMPSDVIAAQFEA 191
            EAGQ LLNSMSRKG+VGLGYLHNGMKQFSAN  L  P DA G KFR+M SDV+AAQF+A
Sbjct: 133 GEAGQALLNSMSRKGIVGLGYLHNGMKQFSANTPLKQPSDAKGLKFRVMASDVLAAQFDA 192

Query: 192 VGAIPVKKPFSEVFTLLQTRAIDGQENTWSNIYSKKFYEVQTHITESNHGVLDYMLVTSE 251
           VGAIPVKKPFSEVFTLLQTRAIDGQENTWSN YS+KFYEVQ+ ITESNHGVLDYM+VTS+
Sbjct: 193 VGAIPVKKPFSEVFTLLQTRAIDGQENTWSNTYSQKFYEVQSQITESNHGVLDYMVVTSD 252

Query: 252 TFWKSLPKDKREIIKQSMDEAVALGNKLALEKANEDRQLILDSKRVELVTLTPEQRQAWV 311
            FWKSLP DKR++IK+++DE++ALGNK+A EK NED+QLILDSKR +LVTLTP++RQ W+
Sbjct: 253 AFWKSLPADKRKVIKEALDESIALGNKIAAEKDNEDKQLILDSKRSQLVTLTPDERQKWI 312

Query: 312 NAMRPVWSQFEDKIGKDLIEAAESANK 338
           + M+PVW++FED++GKD+IEAA +ANK
Sbjct: 313 DVMKPVWAKFEDQVGKDVIEAAVAANK 339


Lambda     K      H
   0.316    0.132    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: 424
Number of extensions: 13
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: 339
Length of database: 340
Length adjustment: 28
Effective length of query: 311
Effective length of database: 312
Effective search space:    97032
Effective search space used:    97032
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 (21.6 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