GapMind for catabolism of small carbon sources

 

Alignments 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)



>MicrobesOnline__882:206137
          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:

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