GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Pseudomonas simiae WCS417

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF523 PS417_02665 branched-chain amino acid ABC transporter permease

Query= uniprot:Q1MCU1
         (463 letters)



>FitnessBrowser__WCS417:GFF523
          Length = 425

 Score =  321 bits (823), Expect = 3e-92
 Identities = 198/436 (45%), Positives = 262/436 (60%), Gaps = 31/436 (7%)

Query: 7   SAGKPDAGLVRKGLTEALFAAVLSFGMFVLYVGLKTDQNISNELIIVQRWGLLAIFVAVA 66
           SA KP    ++K + + + A ++S  +F   VG+  D    N          +A+ VA+ 
Sbjct: 2   SAAKPID--IKKSVVDTVLAGLISLVVFGPIVGVVLDGYSFN-----LEPARVALLVAIV 54

Query: 67  AIGRFAMVVFIRPNIDRRKLSKAREGELDISTEKSFFHRHFLKIALIALLLYPMVVVAIK 126
            +GRFAM +F++      K  K  +G     +        +   + +  ++  ++V+AI 
Sbjct: 55  MVGRFAMSLFLQTP----KGVKILQGFESTGSGVHVLAPDYK--SRLRWIIPALIVIAIV 108

Query: 127 GPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGL 186
            P  +  Y+    I  LIYV+L  GLNIVVGLAGLLDLGYVAFYA+GAY  AL   Y GL
Sbjct: 109 FPIFANKYLLTVVILGLIYVLLGLGLNIVVGLAGLLDLGYVAFYAIGAYGLALGYQYLGL 168

Query: 187 SFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGI 246
            FW +LPL+ I AAL G ILGFPVLR+ GDYLAIVTL FGEIIRLVL NW   T G  G+
Sbjct: 169 GFWTVLPLAAIAAALAGCILGFPVLRMHGDYLAIVTLGFGEIIRLVLNNWLSFTGGPNGM 228

Query: 247 SSIPKATLFGIPFDATA--GG--FAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLR 302
             +P  T  G+ F   A  GG  F + F +  +     +F++ ++  + +   Y+  RL 
Sbjct: 229 -PVPSPTFLGLEFGKRAKDGGIPFHEFFGIDYNPNIKFLFIYIVLFLVVLAVLYIKHRLT 287

Query: 303 RMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFV 362
           RMP+GRAWEALREDEIACRS+G+N V  KL+AF  GA  AG AG FFA+ QGFV+P SF 
Sbjct: 288 RMPVGRAWEALREDEIACRSMGLNHVLVKLSAFTIGASTAGLAGVFFASYQGFVNPSSFT 347

Query: 363 FLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIF 422
           F ESA+ILAIVVLGGMGS  G+ IAA V+    ELLR  S              YR+L+F
Sbjct: 348 FFESALILAIVVLGGMGSTVGVVIAAFVLTVAPELLRSFS-------------EYRVLLF 394

Query: 423 GLAMVVVMLFKPRGFV 438
           G+ MVV+M+++PRG +
Sbjct: 395 GVLMVVMMIWRPRGLI 410


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: 643
Number of extensions: 38
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: 425
Length adjustment: 32
Effective length of query: 431
Effective length of database: 393
Effective search space:   169383
Effective search space used:   169383
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