Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 8500412 DvMF_1162 ABC transporter related (RefSeq)
Query= uniprot:A0A165KC78 (242 letters) >FitnessBrowser__Miya:8500412 Length = 241 Score = 228 bits (580), Expect = 1e-64 Identities = 116/240 (48%), Positives = 171/240 (71%), Gaps = 6/240 (2%) Query: 8 VLLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITG-----TLSMN 62 +LL ++ L V YG I+A+ G+ F V EGE+V+LIG+NGAGK+TT+K+I ++ Sbjct: 1 MLLSIENLYVKYGNIEALHGLSFHVNEGEIVTLIGANGAGKSTTLKSIMRLPPPEAPKVS 60 Query: 63 DGNIEYLGKSIKGKGAWDLV-KEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILAD 121 G+I + GKS+ D+V K + +VPEGR +F +T+ ENL + Y RK+ I D Sbjct: 61 GGDILFKGKSLLNVEPHDVVSKLHVALVPEGRHIFGNLTVMENLMLATYARKNDPAISRD 120 Query: 122 IEKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKI 181 +E++F +FPRL ER+ Q + T+SGGEQQMLA+GRALM+ +VLLLDEPSMGL+P+++ ++ Sbjct: 121 LERIFDLFPRLAERRTQRSDTLSGGEQQMLAVGRALMTSCEVLLLDEPSMGLAPLLMYEM 180 Query: 182 FEVVRDVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241 F ++++ G+TI++VEQNA AL +A RGYV+++G I GP + LLNDP+V+ AYLG Sbjct: 181 FRTLKELNREGLTIIVVEQNARLALQVASRGYVLDTGEIVAQGPSESLLNDPEVKKAYLG 240 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: 171 Number of extensions: 6 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: 241 Length adjustment: 23 Effective length of query: 219 Effective length of database: 218 Effective search space: 47742 Effective search space used: 47742 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 17 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