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_003944041.1 C1M55_RS16615 ABC transporter ATP-binding protein

Query= uniprot:G8ALJ1
         (236 letters)



>NCBI__GCF_002893965.1:WP_003944041.1
          Length = 268

 Score =  167 bits (424), Expect = 1e-46
 Identities = 94/219 (42%), Positives = 134/219 (61%), Gaps = 2/219 (0%)

Query: 14  IEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITFEGQDITQMPTYEL 73
           +  L+  +  +  GEIV +IG NGAGKSTLL ++ G    R G +T    +IT  P + L
Sbjct: 43  VNILRECNFFLKEGEIVGIIGPNGAGKSTLLKSLFGLIPVREGSVTLREDNITSAPAHVL 102

Query: 74  VRLGIAQSPEGRRIFPRMSVLENLQMGSITAKPGSFANELERVLTLFPRLKERISQRAGT 133
           V+ G+   P+ + +F  +++ ENL+MG I  +P +FA     V  LFP L ER   +AG 
Sbjct: 103 VQKGVGYVPQTQNVFQTLTIEENLEMG-IYLRPKAFAERFAFVSELFPLLSERRKVKAGA 161

Query: 134 MSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAVKDINREQKMTVFMVEQN 193
           +SGGE+QM+A+GRALM  P +LLLDEPS GL+P+   ++F   K IN    ++V MVEQN
Sbjct: 162 LSGGERQMVAMGRALMMDPSVLLLDEPSAGLSPMFQDEVFIRCKKIN-AAGVSVIMVEQN 220

Query: 194 AFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYL 232
           A   L++  RGYV+  GK   + TGA L+ + +V   YL
Sbjct: 221 ARRCLQICDRGYVLDQGKNAYTDTGANLMNDPKVIELYL 259


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: 143
Number of extensions: 5
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: 268
Length adjustment: 24
Effective length of query: 212
Effective length of database: 244
Effective search space:    51728
Effective search space used:    51728
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