GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Pseudomonas fluorescens FW300-N1B4

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Pf1N1B4_3216 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)

Query= uniprot:Q1MCU1
         (463 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3216
          Length = 418

 Score =  358 bits (919), Expect = e-103
 Identities = 219/442 (49%), Positives = 283/442 (64%), Gaps = 36/442 (8%)

Query: 18  KGLTEALFAAVLSFGMFVLYVGLK-TDQNISNELIIVQRWGLLAIFVAVAAIGRFAMVVF 76
           + L +ALF+A+L + +    +GLK T   I+ E+       L+ I  AV ++  F  V+F
Sbjct: 3   RNLKQALFSALLVWAVAYPVLGLKLTIVGINLEVHGTSTATLITI--AVCSVLMFLRVLF 60

Query: 77  IRPNIDRRKLSKAREGELDISTEKSFFHRHFLKIA-----LIALLLYPMVVVAIKGPQGS 131
            +      K S      L +   K+    +FL +      +I  L+   +V    G +G+
Sbjct: 61  DQQISSAWKASP----NLPVMPAKA---TNFLTLPTTQRWIIIALIIGALVWPFFGSRGA 113

Query: 132 LTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVL 191
           +    +    +LIYVML  GLNIVVGLAGLLDLGYV FYAVGAYSYALLS Y+GLSFW+ 
Sbjct: 114 V----DIATLVLIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYYGLSFWIC 169

Query: 192 LPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPK 251
           LP++G+ AA +G +LGFPVLRLRGDYLAIVTL FGEIIRL L N TD+T G  GIS+IPK
Sbjct: 170 LPIAGMMAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDLTGGPNGISNIPK 229

Query: 252 ATLFGIPFDATAGGFAKLFH----LPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIG 307
            TLFG+ FD TA    + FH    L  +S    IFL+ + + L +   +V  RL RMP+G
Sbjct: 230 PTLFGLSFDRTAAEGLQTFHEYFGLEYNSINKVIFLYLIAVLLSLFALFVINRLLRMPLG 289

Query: 308 RAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESA 367
           RAWEALREDEIACR+LG+N    KL+AF  GA FAGFAGSFFAARQG V+PESF F+ESA
Sbjct: 290 RAWEALREDEIACRALGLNPTVIKLSAFTLGACFAGFAGSFFAARQGLVTPESFTFIESA 349

Query: 368 VILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMV 427
            ILAIVVLGGMGS  G+ +AA VM+   E++RE S              YRML+FG  MV
Sbjct: 350 TILAIVVLGGMGSQLGVVLAATVMILLPEMMREFS-------------EYRMLMFGALMV 396

Query: 428 VVMLFKPRGFVGSREPTAFLRE 449
           ++M+++P+G +  + P   LR+
Sbjct: 397 LMMIWRPQGLLPMQRPHMELRK 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: 635
Number of extensions: 39
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.

Links

Downloads

Related tools

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