GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Nocardioides daejeonensis MJ31

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_110206118.1 DNK54_RS06375 branched-chain amino acid ABC transporter permease

Query= uniprot:Q1MCU1
         (463 letters)



>NCBI__GCF_003194585.1:WP_110206118.1
          Length = 376

 Score =  149 bits (377), Expect = 1e-40
 Identities = 100/311 (32%), Positives = 163/311 (52%), Gaps = 15/311 (4%)

Query: 140 IQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLPLSGIFA 199
           IQ  I+++ A GL ++ G+ G L LG+ AF AVG ++ A L+  FGL +WV+LPL+G+ +
Sbjct: 55  IQAQIFIVGAVGLMLLSGVTGQLSLGHAAFLAVGGFAAANLALDFGLPWWVVLPLAGLIS 114

Query: 200 ALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPKATLF---- 255
           AL GV++     RL+G YLAIVTL    +I+ VL+ WTD++ G  G +++P    F    
Sbjct: 115 ALVGVLIAPFAFRLKGLYLAIVTLGLVFVIQHVLLRWTDISGGHRG-TAVPMFNGFVDDP 173

Query: 256 --GIPFDATAGGFAK----LFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRA 309
               P +    GF +    +  + +        +F L+     L A   +R R   +GRA
Sbjct: 174 ENMTPMEKAEAGFGREPWEIGGVFMGRDVQMYVVFLLVTVAACLFARNVLRTR---MGRA 230

Query: 310 WEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPE-SFVFLESAV 368
             A+   +IA   LGI     K  AF   + +AG AG+ +  +Q +++ +  F    S  
Sbjct: 231 MAAVGSGDIAASVLGIRVKWVKTAAFGLSSFYAGVAGAMWGWKQTYLTVDPPFDLHLSME 290

Query: 369 ILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMVV 428
            +A++ +GG+G++ G  + AI+   G  L  E++ L  +           + +FG  ++V
Sbjct: 291 FVAMIFIGGLGTVMGAVLGAILFASGRPLAAELAELPFLRDSSLQEGDIVLFVFGATVIV 350

Query: 429 VMLFKPRGFVG 439
            MLF+PRG  G
Sbjct: 351 FMLFEPRGLRG 361


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: 510
Number of extensions: 34
Number of successful extensions: 3
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: 376
Length adjustment: 31
Effective length of query: 432
Effective length of database: 345
Effective search space:   149040
Effective search space used:   149040
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