GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24015 in Phaeobacter inhibens BS107

Align ABC transporter related (characterized, see rationale)
to candidate GFF3910 PGA1_65p00130 putative amino-acid ABC transporter, ATP-binding protein

Query= uniprot:B2TBJ9
         (263 letters)



>FitnessBrowser__Phaeo:GFF3910
          Length = 251

 Score =  217 bits (553), Expect = 2e-61
 Identities = 115/253 (45%), Positives = 164/253 (64%), Gaps = 8/253 (3%)

Query: 2   NATAPVALSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPD 61
           + T   A+S+  + K+FGD  VL GI L    G+ I I+G SG+GKST LRCLN L+ PD
Sbjct: 3   DTTQGPAISITGLRKTFGDSVVLDGIDLTIQPGERIVIIGPSGTGKSTLLRCLNFLDAPD 62

Query: 62  DGSVSLAGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPM 121
            G V +   ++   R        + + ++  +R +   VFQN+ L+++ T  EN++E  +
Sbjct: 63  AGLVRIGDLDVDAAR--------ASKAEILALRRRTAFVFQNYALFANKTAAENIMEALI 114

Query: 122 RVQKRSRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEP 181
            VQK+ RAE+   A  +LA+ GLA+K   YPA LSGGQQQRV I RA+A+  ++MLFDEP
Sbjct: 115 TVQKQPRAEAEARAREILAETGLADKADAYPASLSGGQQQRVGIGRAMALGAELMLFDEP 174

Query: 182 TSALDPELVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEV 241
           TSALDPE VGEVL +M  +AEE +TML+VTHEM FAR +++RV+F+  G++   G P ++
Sbjct: 175 TSALDPEWVGEVLALMHKVAEERQTMLIVTHEMQFAREIADRVVFMEGGRIVEQGPPTQI 234

Query: 242 FVECKSDRFRQFV 254
           F   +  R R F+
Sbjct: 235 FDAPQDPRTRAFL 247


Lambda     K      H
   0.318    0.133    0.377 

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: 143
Number of extensions: 4
Number of successful extensions: 2
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: 263
Length of database: 251
Length adjustment: 24
Effective length of query: 239
Effective length of database: 227
Effective search space:    54253
Effective search space used:    54253
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 (21.7 bits)
S2: 47 (22.7 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