GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4609
          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:

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