GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08250 in Rhodococcus qingshengii djl-6-2

Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_003944438.1 C1M55_RS06875 ABC transporter ATP-binding protein

Query= uniprot:G8ALJ1
         (236 letters)



>NCBI__GCF_002893965.1:WP_003944438.1
          Length = 239

 Score =  163 bits (412), Expect = 3e-45
 Identities = 91/233 (39%), Positives = 141/233 (60%), Gaps = 3/233 (1%)

Query: 1   MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF 60
           +LKV  + T YG +  +  V  ++  G++ +L+G NGAGK++ L  + G  +   G +  
Sbjct: 4   ILKVRNLQTGYGDLRVVWDVSFDVYPGQVTALLGRNGAGKTSTLRALSGLNKVASGTVEM 63

Query: 61  EGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSIT--AKPGSFANELERVLT 118
           +G DIT +P ++ VR G+A   EG+R+F + +V +NL +G  T  AK G     +E +  
Sbjct: 64  DGADITGVPAHKRVRQGMAYVQEGKRVFHKQTVEQNLLLGGYTRKAKRGELMESVESMYE 123

Query: 119 LFPRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAVKD 178
           +FP L E+ S  AG+MSGG+QQMLAIG ALM+QPRLLLLDEPS GLAP++V ++   V+ 
Sbjct: 124 MFPILGEKRSLPAGSMSGGQQQMLAIGAALMAQPRLLLLDEPSGGLAPVIVGEVMDRVQQ 183

Query: 179 INREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAY 231
           + +E  + V +VEQ    A+ +A    V+  GKV +     ++     ++ AY
Sbjct: 184 L-KETGLAVLLVEQAVEAAMSVADHVTVLDIGKVVLDADAKDIDDLAVLKDAY 235


Lambda     K      H
   0.320    0.136    0.377 

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: 168
Number of extensions: 10
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: 236
Length of database: 239
Length adjustment: 23
Effective length of query: 213
Effective length of database: 216
Effective search space:    46008
Effective search space used:    46008
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 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