GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Pseudomonas fluorescens FW300-N2C3

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate AO356_08490 AO356_08490 branched-chain amino acid ABC transporter permease

Query= uniprot:Q1MCU1
         (463 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_08490
          Length = 426

 Score =  318 bits (816), Expect = 2e-91
 Identities = 193/427 (45%), Positives = 254/427 (59%), Gaps = 29/427 (6%)

Query: 16  VRKGLTEALFAAVLSFGMFVLYVGLKTDQNISNELIIVQRWGLLAIFVAVAAIGRFAMVV 75
           +++ + +A+ A ++S  +F   VG+  D    N       W      VA+  IGRFA+ +
Sbjct: 10  IKQSVIDAILAGLISLIVFGPIVGVVLDGYSFNLQPARVGW-----LVAIVMIGRFALSL 64

Query: 76  FIRPNIDRRKLSKAREGELDISTEKSFFHRHFLKIALIALLLYPMVVVAIKGPQGSLTYV 135
           F++     + L         +      +         +  ++  ++V+AI  P  +  YV
Sbjct: 65  FLQTPKGLKILQGFESTGSGVHVLPPDYKSR------LRWIIPALIVIAIVFPFFANKYV 118

Query: 136 DNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLPLS 195
               I  LIYV+L  GLNIVVGLAGLLDLGYVAFYA+GAY  AL   Y GL FW +LPL+
Sbjct: 119 LTVVILGLIYVLLGLGLNIVVGLAGLLDLGYVAFYAIGAYGLALGYQYLGLGFWTVLPLA 178

Query: 196 GIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPKATLF 255
            I AA+ G ILGFPVLR+ GDYLAIVTL FGEIIRLVL NW   T G  G+  +P  T  
Sbjct: 179 AIAAAMAGCILGFPVLRMHGDYLAIVTLGFGEIIRLVLNNWLSFTGGPNGM-PVPSPTFL 237

Query: 256 GIPFDATA--GG--FAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWE 311
           G+ F   A  GG  F + F +  +     +F++ ++    +L  YV  RL RMP+GRAWE
Sbjct: 238 GLEFGRRAKDGGVPFHEFFGIDYNPNIKFLFIYIVLFITVLLVLYVKHRLTRMPVGRAWE 297

Query: 312 ALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILA 371
           ALREDEIACRS+G+N V  KL+AF  GA  AG AG FFA+ QGFV+P SF F ESA+ILA
Sbjct: 298 ALREDEIACRSMGLNHVLVKLSAFTIGASTAGLAGVFFASYQGFVNPSSFTFFESALILA 357

Query: 372 IVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMVVVML 431
           IVVLGGMGS  G+ IAA V+    ELLR  S              YR+L+FG+ MV++M+
Sbjct: 358 IVVLGGMGSTVGVVIAAFVLTVAPELLRSFS-------------EYRVLLFGVLMVLMMI 404

Query: 432 FKPRGFV 438
           ++PRG +
Sbjct: 405 WRPRGLI 411


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: 636
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: 426
Length adjustment: 32
Effective length of query: 431
Effective length of database: 394
Effective search space:   169814
Effective search space used:   169814
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