GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Pseudomonas simiae WCS417

Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate GFF523 PS417_02665 branched-chain amino acid ABC transporter permease

Query= uniprot:A0A159ZYE0
         (418 letters)



>FitnessBrowser__WCS417:GFF523
          Length = 425

 Score =  407 bits (1045), Expect = e-118
 Identities = 219/414 (52%), Positives = 289/414 (69%), Gaps = 13/414 (3%)

Query: 9   LFSALLVWAVAYPVLGLKLTIVGINLEVHGTSPAILATIAVC---SLLMFLRVLFSTQIS 65
           + + L+   V  P++G+ L     NLE      A+L  I +    ++ +FL+     +I 
Sbjct: 17  VLAGLISLVVFGPIVGVVLDGYSFNLEP--ARVALLVAIVMVGRFAMSLFLQTPKGVKIL 74

Query: 66  AMWKSS-PGLPVIPAKASNFLTLPTTQRWIVLALIVGALVWPFFGSRGAVDIATLILIYV 124
             ++S+  G+ V+     + L      RWI+ ALIV A+V+P F ++  + +  L LIYV
Sbjct: 75  QGFESTGSGVHVLAPDYKSRL------RWIIPALIVIAIVFPIFANKYLLTVVILGLIYV 128

Query: 125 MLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMAATFGFLL 184
           +LGLGLNIVVGLAGLLDLGYV FYA+GAY  AL   Y GL FW  LP+A + AA  G +L
Sbjct: 129 LLGLGLNIVVGLAGLLDLGYVAFYAIGAYGLALGYQYLGLGFWTVLPLAAIAAALAGCIL 188

Query: 185 GFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLTFERKAAEG 244
           GFPVLR+ GDYLAIVTLGFGEIIRL L N    TGGPNG+  +  PTF GL F ++A +G
Sbjct: 189 GFPVLRMHGDYLAIVTLGFGEIIRLVLNNWLSFTGGPNGMP-VPSPTFLGLEFGKRAKDG 247

Query: 245 LQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEIACRA 304
              FHE+FG++YN   K +F+Y+V  L+ LA L++ +RL RMP+GRAWEALREDEIACR+
Sbjct: 248 GIPFHEFFGIDYNPNIKFLFIYIVLFLVVLAVLYIKHRLTRMPVGRAWEALREDEIACRS 307

Query: 305 LGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGMGSQL 364
           +GLN  ++KLSAFT+GA+ AG AG FFA+ QG V P SFTF ESA+ILAIVVLGGMGS +
Sbjct: 308 MGLNHVLVKLSAFTIGASTAGLAGVFFASYQGFVNPSSFTFFESALILAIVVLGGMGSTV 367

Query: 365 GVILAAIVMILLPEMMREFSEYRMLMFGALMVLMMIWRPQGLLPMQRPHMELRK 418
           GV++AA V+ + PE++R FSEYR+L+FG LMV+MMIWRP+GL+ + R  +  RK
Sbjct: 368 GVVIAAFVLTVAPELLRSFSEYRVLLFGVLMVVMMIWRPRGLIRISRTGVTPRK 421


Lambda     K      H
   0.331    0.145    0.439 

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: 641
Number of extensions: 37
Number of successful extensions: 2
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: 418
Length of database: 425
Length adjustment: 32
Effective length of query: 386
Effective length of database: 393
Effective search space:   151698
Effective search space used:   151698
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 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