GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Caldicellulosiruptor hydrothermalis 108

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_013403236.1 CALHY_RS06830 branched-chain amino acid ABC transporter permease

Query= uniprot:Q1MCU1
         (463 letters)



>NCBI__GCF_000166355.1:WP_013403236.1
          Length = 312

 Score =  192 bits (487), Expect = 2e-53
 Identities = 115/302 (38%), Positives = 178/302 (58%), Gaps = 44/302 (14%)

Query: 142 ILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFG-LSFWVLLPLSGIFAA 200
           I++ ++LA  LN++ G+ G   LG+  F A+GAY+ A+L++    + F++ + + G+FA 
Sbjct: 39  IMLNIILAVSLNLINGITGQFSLGHAGFMAIGAYTTAVLTTLEKPVPFYLTVLIGGLFAM 98

Query: 201 LWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPKATLFGIPFD 260
           + G+I+G PVLRLRGDYLAI TL FGEIIR+++ N  D   G  GIS IP+    GI + 
Sbjct: 99  ICGLIIGLPVLRLRGDYLAIATLGFGEIIRVIIQN-IDYLGGASGISDIPQ----GIDW- 152

Query: 261 ATAGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEALREDEIAC 320
                          + Y+ I          +L+  V + +     GRA  A+REDEIA 
Sbjct: 153 ---------------TGYFVI---------TVLSVVVILNIINSSFGRAMIAIREDEIAA 188

Query: 321 RSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIVVLGGMGS 380
            ++GINT   K+ AF  GA FAG AGS ++   GF+ P+ F F +S  IL IVVLGG+GS
Sbjct: 189 EAMGINTTLYKVLAFMIGAFFAGVAGSIYSGSFGFIQPDMFNFFKSIDILVIVVLGGLGS 248

Query: 381 LTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMVVVMLFKPRGFVGS 440
           ++G  I+AIV+   + LL++   +             RM+++ L ++++MLF+P+G +G+
Sbjct: 249 ISGSIISAIVLTIISALLQDYPAV-------------RMVLYSLILIIIMLFRPQGLMGT 295

Query: 441 RE 442
           +E
Sbjct: 296 KE 297


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: 416
Number of extensions: 29
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: 312
Length adjustment: 30
Effective length of query: 433
Effective length of database: 282
Effective search space:   122106
Effective search space used:   122106
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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