GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Desulfacinum hydrothermale DSM 13146

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_084055968.1 B9A12_RS01570 ABC transporter ATP-binding protein

Query= uniprot:A0A165KC78
         (242 letters)



>NCBI__GCF_900176285.1:WP_084055968.1
          Length = 247

 Score =  228 bits (580), Expect = 1e-64
 Identities = 110/236 (46%), Positives = 173/236 (73%), Gaps = 3/236 (1%)

Query: 9   LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68
           +L ++ L+  YG I+ + GV   VR GE+V+L+G+NGAGK+T +KA++G L    G + +
Sbjct: 1   MLTIRNLRGGYGRIEVLHGVSLSVRRGEVVALVGANGAGKSTLLKAVSGLLPQWTGEVLF 60

Query: 69  LGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRK---DKAGILADIEKM 125
            G+ ++GK   ++V  G+ +VPEGR +F  M++ +NL++GAY+R    D  G+  ++E++
Sbjct: 61  DGRPLQGKKPPEIVALGVGLVPEGRWIFPPMSVVDNLRLGAYLRLRRGDHKGVEEELERV 120

Query: 126 FTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVV 185
           + +FP L ER+ Q AG +SGGEQQMLAMGRALM++P++LLLDEP+ GL+P++V+KIF+++
Sbjct: 121 YELFPILAERRRQPAGILSGGEQQMLAMGRALMTRPRMLLLDEPTTGLAPLLVEKIFQII 180

Query: 186 RDVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241
             +    +T +LVEQNA  ALA+ADRGYV+E+G + + G  ++LL D +V+ AYLG
Sbjct: 181 ARLRDESLTFLLVEQNAQGALALADRGYVLETGRMVLQGRARELLEDQEVKRAYLG 236


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: 177
Number of extensions: 8
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: 247
Length adjustment: 24
Effective length of query: 218
Effective length of database: 223
Effective search space:    48614
Effective search space used:    48614
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: 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