GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livM in Pseudomonas fluorescens FW300-N2E2

Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate Pf6N2E2_3578 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)

Query= uniprot:A0A159ZYE0
         (418 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3578 Branched-chain amino
           acid transport system permease protein LivM (TC
           3.A.1.4.1)
          Length = 426

 Score =  412 bits (1059), Expect = e-119
 Identities = 221/413 (53%), Positives = 288/413 (69%), Gaps = 9/413 (2%)

Query: 8   ALFSALLVWAVAYPVLGLKLTIVGINLEVHGTSPAI-LATIAVCSLLMFLRVLFSTQISA 66
           A+ + L+   V  P++G+ L     NL+       + +  I   +L +FL+     +I  
Sbjct: 17  AILAGLISLIVFGPIVGVVLDGYSFNLQPARVGWLVAIVMIGRFALSLFLQTPKGLKILQ 76

Query: 67  MWKSS-PGLPVIPAKASNFLTLPTTQRWIVLALIVGALVWPFFGSRGAVDIATLILIYVM 125
            ++S+  G+ V+P    + L      RWI+ ALIV A+V+PFF ++  + +  L LIYV+
Sbjct: 77  GFESTGSGVHVLPPDYKSRL------RWIIPALIVIAIVFPFFANKYVLTVVILGLIYVL 130

Query: 126 LGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMAATFGFLLG 185
           LGLGLNIVVGLAGLLDLGYV FYA+GAY  AL   Y GL FW  LP+A + AA  G +LG
Sbjct: 131 LGLGLNIVVGLAGLLDLGYVAFYAIGAYGLALGYQYLGLGFWTVLPLAAIAAAMAGCILG 190

Query: 186 FPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLTFERKAAEGL 245
           FPVLR+ GDYLAIVTLGFGEIIRL L N    TGGPNG+  +  PTF GL F R+A +G 
Sbjct: 191 FPVLRMHGDYLAIVTLGFGEIIRLVLNNWLSFTGGPNGMP-VPSPTFLGLEFGRRAKDGG 249

Query: 246 QTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEIACRAL 305
             FHE+FG++YN   K +F+Y+V  +  L  L+V +RL RMP+GRAWEALREDEIACR++
Sbjct: 250 VPFHEFFGIDYNPNIKFLFIYIVLFITVLLVLYVKHRLTRMPVGRAWEALREDEIACRSM 309

Query: 306 GLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGMGSQLG 365
           GLN  ++KLSAFT+GA+ AG AG FFA+ QG V P SFTF ESA+ILAIVVLGGMGS +G
Sbjct: 310 GLNHVLVKLSAFTIGASTAGLAGVFFASYQGFVNPSSFTFFESALILAIVVLGGMGSTVG 369

Query: 366 VILAAIVMILLPEMMREFSEYRMLMFGALMVLMMIWRPQGLLPMQRPHMELRK 418
           V++AA V+ + PE++R FSEYR+L+FG LMVLMMIWRP+GL+ + R  +  RK
Sbjct: 370 VVIAAFVLTVAPELLRSFSEYRVLLFGVLMVLMMIWRPRGLIRISRTGVTPRK 422


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: 648
Number of extensions: 35
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: 418
Length of database: 426
Length adjustment: 32
Effective length of query: 386
Effective length of database: 394
Effective search space:   152084
Effective search space used:   152084
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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