GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Dechlorosoma suillum PS

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate Dsui_0630 Dsui_0630 ABC-type branched-chain amino acid transport system, periplasmic component

Query= SwissProt::P21175
         (373 letters)



>FitnessBrowser__PS:Dsui_0630
          Length = 434

 Score =  209 bits (531), Expect = 2e-58
 Identities = 118/339 (34%), Positives = 181/339 (53%), Gaps = 4/339 (1%)

Query: 29  TIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAG-GVNGAQL--EGVIYDDACDPKQA 85
           T+KI  A P+TGP A  G     GA +AIE++N  G  + GA++  E +  DD  DPKQ 
Sbjct: 45  TVKIGHASPLTGPQAHIGKDNEYGATLAIEELNAKGLEIGGAKVKFELISDDDQADPKQG 104

Query: 86  VAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSATAPEITSRGYKLIFRTI 145
             VA K V+  V  V+GH+ S +T PA+ IY D G+  I+ SAT P  T +G+   FR +
Sbjct: 105 TTVAQKFVDAKVNGVIGHLNSGTTIPASKIYFDAGIPQISGSATNPTYTKQGFATAFRVM 164

Query: 146 GLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTVEDAGIKVAVFEGLNAG 205
             D  QG    +F A+    K++A++ D+  YG+G+A E KK  E AG+KV   E  N  
Sbjct: 165 ANDEQQGKALAQFAAKTLAAKSVAIIDDRTAYGQGLADEFKKAAEAAGLKVVASEYTNDK 224

Query: 206 DKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARFMGPEGVGNSEITAIAG 265
             DF A+++K+K      +++GG  P+ G + +Q K+ GL A+F+  +G        +AG
Sbjct: 225 ATDFKAILTKIKSKKPDLIFYGGMDPQGGPMAKQMKELGLKAKFLTGDGGCTPNFITLAG 284

Query: 266 DASEGMLATLPRA-FEQDPKNKALIDAFKAKNQDPSGIFVLPAYSAVTVIAKGIEKAGEA 324
            A+EG   +LP    ++ P      D F  K +    ++    Y A  V+   +++A   
Sbjct: 285 AAAEGQYCSLPGVPLDKMPGGTVFKDKFVGKFKTEIQLYAPYVYDATMVLVDAMKRANSV 344

Query: 325 DPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEW 363
           +P K    +   +F+  T  +GFDE GDLK+   + YE+
Sbjct: 345 EPAKYLPEIGKTSFQGVTAKIGFDEFGDLKDGAISFYEY 383


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: 425
Number of extensions: 27
Number of successful extensions: 3
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: 434
Length adjustment: 31
Effective length of query: 342
Effective length of database: 403
Effective search space:   137826
Effective search space used:   137826
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