GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braC in Desulfovibrio vulgaris Hildenborough

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate 206137 DVU0712 amino acid ABC transporter, periplasmic-binding protein

Query= SwissProt::P21175
         (373 letters)



>lcl|MicrobesOnline__882:206137 DVU0712 amino acid ABC transporter,
           periplasmic-binding protein
          Length = 376

 Score =  204 bits (518), Expect = 4e-57
 Identities = 121/366 (33%), Positives = 197/366 (53%), Gaps = 8/366 (2%)

Query: 3   KGTQRLSRLFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINK 62
           KG  RL  +    ++   A+ + AA  +++ L  P+TG  A  G   R    +  E++NK
Sbjct: 2   KGVVRLLAVCMVTSLL-MAATAFAAGPVRVGLMCPLTGKWASEGQDMRNIVELLAEEVNK 60

Query: 63  AGGVNGAQLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVL 122
           AGG+NG ++E ++ DD  DP+ A   A K+   GV  V+G   S+ T+ + +IY++ G+ 
Sbjct: 61  AGGINGNKVELIVEDDGGDPRTAALAAQKLSTSGVTAVIGTYGSAVTEASQNIYDEAGIA 120

Query: 123 MITPSATAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIA 182
            I   +T   +T +G KL  RT   D+ QG VA K I  +   K +A+LHD   Y +G+A
Sbjct: 121 QIATGSTNVRLTEKGLKLFLRTCPRDDEQGRVAAKVIKNK-GYKAVALLHDNSSYAKGLA 179

Query: 183 TEVKKTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQ 242
            E K  ++  G K+  ++ L  G++D+ A+++KLK A    ++F GY+PE+G+LLRQ  +
Sbjct: 180 DETKALLDKDGTKIVFYDALTPGERDYTAILTKLKAANPDIIFFTGYYPEVGMLLRQKME 239

Query: 243 AGLDARFMGPEGVGNSEITAIAGDASEGMLATLPRAFEQD---PKNKALIDAFKAK-NQD 298
              +   MG +   N ++  IAG A+      L     QD    + KA + A+KAK N  
Sbjct: 240 MKWNVPMMGGDAANNLDLVKIAGKAAAKGYFFLSPPVPQDFDTAEAKAFLAAYKAKHNAL 299

Query: 299 PSGIFVLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETP--TGNLGFDEKGDLKNF 356
           P+ ++ + A  A  VI + ++K G+AD   +A  L+      P  +G + F+EKGD    
Sbjct: 300 PNSVWSVLAGDAFKVIVEAVQKGGKADGAGIATYLKTQLKNYPGLSGQISFNEKGDRVGD 359

Query: 357 DFTVYE 362
            + VY+
Sbjct: 360 LYRVYD 365


Lambda     K      H
   0.316    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: 347
Number of extensions: 15
Number of successful extensions: 4
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: 373
Length of database: 376
Length adjustment: 30
Effective length of query: 343
Effective length of database: 346
Effective search space:   118678
Effective search space used:   118678
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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