GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00900 in Rhodococcus qingshengii djl-6-2

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_003944041.1 C1M55_RS16615 ABC transporter ATP-binding protein

Query= uniprot:A0A165KC78
         (242 letters)



>NCBI__GCF_002893965.1:WP_003944041.1
          Length = 268

 Score =  190 bits (483), Expect = 2e-53
 Identities = 105/235 (44%), Positives = 151/235 (64%), Gaps = 5/235 (2%)

Query: 9   LLQVKGLKVAY-GGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIE 67
           LL+   L   Y  G+  ++  +F ++EGE+V +IG NGAGK+T +K++ G + + +G++ 
Sbjct: 29  LLRADSLVAGYIPGVNILRECNFFLKEGEIVGIIGPNGAGKSTLLKSLFGLIPVREGSVT 88

Query: 68  YLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIR-KDKAGILADIEKMF 126
               +I    A  LV++G+  VP+ + VF  +TI ENL+MG Y+R K  A   A + ++F
Sbjct: 89  LREDNITSAPAHVLVQKGVGYVPQTQNVFQTLTIEENLEMGIYLRPKAFAERFAFVSELF 148

Query: 127 TIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVR 186
              P L ER+   AG +SGGE+QM+AMGRALM  P VLLLDEPS GLSP+  D++F   +
Sbjct: 149 ---PLLSERRKVKAGALSGGERQMVAMGRALMMDPSVLLLDEPSAGLSPMFQDEVFIRCK 205

Query: 187 DVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241
            + A GV++++VEQNA R L I DRGYV++ G    T  G  L+NDPKV   YLG
Sbjct: 206 KINAAGVSVIMVEQNARRCLQICDRGYVLDQGKNAYTDTGANLMNDPKVIELYLG 260


Lambda     K      H
   0.317    0.136    0.373 

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: 189
Number of extensions: 11
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: 242
Length of database: 268
Length adjustment: 24
Effective length of query: 218
Effective length of database: 244
Effective search space:    53192
Effective search space used:    53192
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 (21.7 bits)
S2: 47 (22.7 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