GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braE in Pseudomonas fluorescens GW456-L13

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate PfGW456L13_4609 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)

Query= uniprot:Q1MCU1
         (463 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4609
           Branched-chain amino acid transport system permease
           protein LivM (TC 3.A.1.4.1)
          Length = 418

 Score =  349 bits (895), Expect = e-100
 Identities = 217/445 (48%), Positives = 285/445 (64%), Gaps = 42/445 (9%)

Query: 18  KGLTEALFAAVLSFGMFVLYVGLK-TDQNISNELIIVQRWGLLAIFVAVAAIGRFAMVVF 76
           + L +ALF+A+L + +    +GLK T   I+ E+       L+ I V        ++++F
Sbjct: 3   RNLKQALFSALLVWAVAYPVLGLKLTIVGINLEVHGTSDATLITIAVC-------SVLMF 55

Query: 77  IRPNIDRRKLSKAREGELD--ISTEKSFF-----HRHFLKIALIA-LLLYPMVVVAIKGP 128
           +R   D++  S  R       I  + S F      + ++ IALIA  L++P       G 
Sbjct: 56  LRVLFDQQISSAWRSSPSMPLIPAKASNFLTLPTTQRWIIIALIAGALVWPFF-----GS 110

Query: 129 QGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSF 188
           +G++    +    +LIYVML  GLNIVVGLAGLLDLGYV FYAVGAYSYALLS Y+GLSF
Sbjct: 111 RGAV----DIATLVLIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYYGLSF 166

Query: 189 WVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISS 248
           W+ LP++G+ AA +G +LGFPVLRLRGDYLAIVTL FGEIIRL L N T +T G  GIS+
Sbjct: 167 WICLPIAGLMAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTGLTGGPNGISN 226

Query: 249 IPKATLFGIPFDATAGGFAKLFH----LPISSAYYKIFLFYLILALCMLTAYVTIRLRRM 304
           I K T FG+ F+  A    + FH    L  +S    IFL+ + L L +   +V  RL RM
Sbjct: 227 IEKPTFFGLTFERKAAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALGALFVINRLLRM 286

Query: 305 PIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFL 364
           P+GRAWEALREDEIACR+LG+N    KL+AF  GA FAGFAGSFFAARQG V+PESF F+
Sbjct: 287 PLGRAWEALREDEIACRALGLNPTVIKLSAFTLGASFAGFAGSFFAARQGLVTPESFTFI 346

Query: 365 ESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGL 424
           ESA+ILAIVVLGGMGS  G+ +AA+VM+   E++RE S              YRML+FG 
Sbjct: 347 ESAIILAIVVLGGMGSQLGVILAAVVMILLPEMMREFS-------------EYRMLMFGA 393

Query: 425 AMVVVMLFKPRGFVGSREPTAFLRE 449
            MV++M+++P+G +  + P   LR+
Sbjct: 394 LMVLMMIWRPQGLLPMQRPHMELRK 418


Lambda     K      H
   0.330    0.145    0.432 

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: 639
Number of extensions: 42
Number of successful extensions: 4
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: 463
Length of database: 418
Length adjustment: 32
Effective length of query: 431
Effective length of database: 386
Effective search space:   166366
Effective search space used:   166366
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 (21.8 bits)
S2: 51 (24.3 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