GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00900 in Leptospirillum ferrooxidans C2-3

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_232502519.1 LFE_RS09120 ATP-binding cassette domain-containing protein

Query= uniprot:D8IUY7
         (241 letters)



>NCBI__GCF_000284315.1:WP_232502519.1
          Length = 588

 Score = 85.1 bits (209), Expect = 3e-21
 Identities = 60/186 (32%), Positives = 102/186 (54%), Gaps = 15/186 (8%)

Query: 16  GGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHIEYLGQ-PLKGK 74
           G + A+  I   + +G +  LIG +GAGKTT ++ ++G L      G I  +G  P K  
Sbjct: 25  GIVTALDKISFSLKKGSITGLIGPDGAGKTTLMRLLSGLLWPDG--GDIRIMGNDPSKAP 82

Query: 75  KSFELVKDKLAMVPEGRGVFTRMSIQENLLMGA----YTSDDKGQIAADIDKWFAVFPRL 130
            S   V+  L  +P+  G++  +S+QENL + A       D + ++ A +     + P  
Sbjct: 83  LS---VQGSLGYMPQKFGLYEDLSVQENLDLYANLQGVPKDRRKELYAPLLSMTGLSPFQ 139

Query: 131 KERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEVIRN-VSAQ 189
           K    ++AG LSGG +Q L +A +L+  P +LLLDEP++G+ P+   +++E++R  VS  
Sbjct: 140 K----RLAGQLSGGMKQKLGVACSLVHQPPILLLDEPTVGVDPVSRRELWEILRKLVSES 195

Query: 190 GITILL 195
           G T+ +
Sbjct: 196 GATLFV 201



 Score = 80.5 bits (197), Expect = 7e-20
 Identities = 55/227 (24%), Positives = 112/227 (49%), Gaps = 5/227 (2%)

Query: 6   LKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHIE 65
           ++V+ L   +   +AV  +   V +GE+  L+GANGAGKTTT + + G L  +   G + 
Sbjct: 342 IEVENLDRYFDSFKAVNNLTFHVKKGEVFGLLGANGAGKTTTFRMLAGLLEPT--AGKLI 399

Query: 66  YLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADIDKWFA 125
             G+ +  +K     + K+  + +   +++++++ +NL+  +      G +  +  +   
Sbjct: 400 VAGEDV--RKVAAQARGKIGYMAQKFSLYSQLTVFQNLIFYSSAYGLSGTLQKEKIQDSL 457

Query: 126 VFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEVIRN 185
            F  L+      +G L  G +Q LA++ AL+  P +L LDEP+ G+ P    + + +I  
Sbjct: 458 NFFELEPYKNVSSGILPLGFRQRLALSCALIHEPSILFLDEPTSGVDPNARREFWHIINA 517

Query: 186 VSAQGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDPR 232
           ++  G+++L+     + A E   R  +M  G +   G   ++ +  R
Sbjct: 518 LATVGVSVLVTTHFMEEA-EYCDRLLIMAQGALLAMGSPAEIKEKTR 563


Lambda     K      H
   0.317    0.134    0.365 

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: 300
Number of extensions: 10
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 241
Length of database: 588
Length adjustment: 30
Effective length of query: 211
Effective length of database: 558
Effective search space:   117738
Effective search space used:   117738
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 Apr 09 2024. 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