GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Paraburkholderia bryophila 376MFSha3.1

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate H281DRAFT_05513 H281DRAFT_05513 branched-chain amino acid transport system permease protein

Query= uniprot:Q1MCU1
         (463 letters)



>FitnessBrowser__Burk376:H281DRAFT_05513
          Length = 597

 Score =  130 bits (326), Expect = 2e-34
 Identities = 95/306 (31%), Positives = 148/306 (48%), Gaps = 36/306 (11%)

Query: 138 FGIQI---LIYVMLAW-GLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLP 193
           FGI I     Y  +A  G+N++VGL+G + LG  AFYA+GAY+  L S   G      + 
Sbjct: 36  FGIHIAQSFCYTAIAVIGVNLLVGLSGQMSLGQAAFYAIGAYASVLTSLKLGWPIAASVL 95

Query: 194 LSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPKAT 253
                AA  G ++G   LR RG YLA+ TLA G ++ ++   W  +T GT G+S +P+  
Sbjct: 96  FGVAVAAAVGTVVGVFALRTRGLYLAMTTLAVGFVVSILAQRWVGLTGGTMGLSGVPQ-- 153

Query: 254 LFGIPFDATAGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEAL 313
              + F  T  G              +I+  Y++    ++   +   +    IGR   A 
Sbjct: 154 ---VDFGDTIHG--------------EIWYLYVVGGTLLVVQILNDYVFDSRIGRCLLAT 196

Query: 314 REDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIV 373
           R+ E    S+GI     +   FA  A  AG +G  FA + GFV  ++F    S  +L   
Sbjct: 197 RDSEAFAASVGIKVPIVRSAIFAVSAALAGLSGGLFAHQSGFVGSDAFSVTLSLSLLIAA 256

Query: 374 VLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMVVVMLFK 433
           V+GG+G       A I  + GT +L  M+ ++L+ G D     Y ++++G  M++V+L  
Sbjct: 257 VIGGLG-------ARIGPLAGTAIL--MTIVELVAGLD----RYGLMVYGGIMLLVLLVF 303

Query: 434 PRGFVG 439
           P+G  G
Sbjct: 304 PQGAAG 309


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: 673
Number of extensions: 40
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 463
Length of database: 597
Length adjustment: 35
Effective length of query: 428
Effective length of database: 562
Effective search space:   240536
Effective search space used:   240536
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: 52 (24.6 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