GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1694 in Pseudomonas simiae WCS417

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF1300 PS417_06605 leucine/isoleucine/valine transporter permease subunit

Query= uniprot:A0A165KER0
         (358 letters)



>FitnessBrowser__WCS417:GFF1300
          Length = 417

 Score =  267 bits (682), Expect = 4e-76
 Identities = 158/346 (45%), Positives = 213/346 (61%), Gaps = 45/346 (13%)

Query: 13  VALLVLPLILQSFGNAW-VRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLF 71
           +AL++  LI   FG+   V IA L L+YVLL LGLNIVVG AGLLDLGYV FYAVGAY +
Sbjct: 95  IALIIAALIWPFFGSRGAVDIATLILIYVLLGLGLNIVVGLAGLLDLGYVGFYAVGAYTY 154

Query: 72  ALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIV 131
           AL++                + L  S WI +P+A + AA FG +LG P L+LRGDYLAIV
Sbjct: 155 ALLS----------------HYLGWSFWICLPLAGMAAATFGFLLGFPVLRLRGDYLAIV 198

Query: 132 TLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRL--------EVFGFDI 183
           TLGFGEIIR+FL NL    ++T GP G+  I     FGL   +          E FG D 
Sbjct: 199 TLGFGEIIRLFLRNL---TDITGGPNGISSIPKPTFFGLSFDRTAAEGMQTFHEYFGIDY 255

Query: 184 NSVTLYYYLFLV---LVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLA 240
           N V+   +L+LV   L + ++ +  RL    IGRAW A+REDEIA +A+G+N   +KL A
Sbjct: 256 NPVSKVVFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEIACRALGLNPTIIKLSA 315

Query: 241 FGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSAL 300
           F +GA+F G +G+ F A QG V+PESF+ +ES +I+A+VVLGG+G   GVIL A+++  L
Sbjct: 316 FTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGMGSQLGVILAAIVMILL 375

Query: 301 PEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWP 346
           PE++R              + +  R L+    M+++M+ RP+GL P
Sbjct: 376 PEMMR--------------EFSEYRMLMFGAMMVLMMIWRPQGLLP 407


Lambda     K      H
   0.328    0.144    0.430 

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: 409
Number of extensions: 20
Number of successful extensions: 5
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: 358
Length of database: 417
Length adjustment: 30
Effective length of query: 328
Effective length of database: 387
Effective search space:   126936
Effective search space used:   126936
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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