GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00900 in Erythrobacter gangjinensis K7-2

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_047005877.1 AAW01_RS03230 ABC transporter ATP-binding protein

Query= uniprot:D8IUY7
         (241 letters)



>NCBI__GCF_001010925.1:WP_047005877.1
          Length = 226

 Score = 78.6 bits (192), Expect = 1e-19
 Identities = 60/190 (31%), Positives = 94/190 (49%), Gaps = 6/190 (3%)

Query: 18  IQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHIEYLGQP---LKGK 74
           I  ++G+DL+V  GE+V L+G +G+GK+T L+A+ G L      G I   G+    L   
Sbjct: 24  IDVLRGVDLDVGPGEIVALLGQSGSGKSTMLQAV-GLLEGG-FGGSIRIAGKEASQLDAA 81

Query: 75  KSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADIDKWFAVFPRLKERA 134
           +   L ++ L  V +   +    + QEN+++       K   A    +       L+ R 
Sbjct: 82  ERTSLRREHLGFVYQFHHLLPDFTAQENVVLPQLLLGTKRAEAELRAQELLGSLGLEHRL 141

Query: 135 AQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIF-EVIRNVSAQGITI 193
                 LSGGEQQ +A+ARAL + P+L+L DEP+  L     E++  E +  V  QG   
Sbjct: 142 THRPSKLSGGEQQRVAVARALANKPQLVLADEPTGNLDEKTSERVLSEFLELVRGQGSAA 201

Query: 194 LLVEQNAKLA 203
           L+   N +LA
Sbjct: 202 LVATHNERLA 211


Lambda     K      H
   0.317    0.134    0.365 

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: 117
Number of extensions: 7
Number of successful extensions: 2
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: 241
Length of database: 226
Length adjustment: 23
Effective length of query: 218
Effective length of database: 203
Effective search space:    44254
Effective search space used:    44254
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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