Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_028999964.1 H537_RS0124585 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >NCBI__GCF_000430725.1:WP_028999964.1 Length = 237 Score = 239 bits (611), Expect = 3e-68 Identities = 120/235 (51%), Positives = 173/235 (73%), Gaps = 2/235 (0%) Query: 9 LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68 +L++ +++AYG I+AVKGV ++R+GE+V++IG+NGAGKT+ +K I G + G I + Sbjct: 1 MLKLNSVRIAYGAIEAVKGVSLQIRQGEVVTIIGANGAGKTSLLKGIAGLEPLAGGTITF 60 Query: 69 LGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILAD--IEKMF 126 G+ A V G+ + PEGRGVFA T+ +NL +GAY K + + +E+ + Sbjct: 61 DGQDCSKLPAHRRVGMGIALSPEGRGVFADQTVRDNLLLGAYAVKGRDPKRTEELMEREY 120 Query: 127 TIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVR 186 FPRLRER++Q AGT+SGGEQQMLAM RALMS+PK+LLLDEPS+GL+P+++ IF+ ++ Sbjct: 121 RRFPRLRERQNQYAGTLSGGEQQMLAMSRALMSEPKMLLLDEPSLGLAPLIIKDIFKAIQ 180 Query: 187 DVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241 + G+TI+LVEQ A +AL +ADR YV+E+G +T+ G G+QLL+DPKVRAAYLG Sbjct: 181 QLRDAGLTILLVEQMAMQALGVADRAYVLETGRVTLEGTGKQLLDDPKVRAAYLG 235 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: 232 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: 242 Length of database: 237 Length adjustment: 23 Effective length of query: 219 Effective length of database: 214 Effective search space: 46866 Effective search space used: 46866 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.
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:
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