Align ABC transporter related (characterized, see rationale)
to candidate WP_011938227.1 GURA_RS06655 ABC transporter ATP-binding protein
Query= uniprot:B2TBJ9 (263 letters) >NCBI__GCF_000016745.1:WP_011938227.1 Length = 353 Score = 160 bits (406), Expect = 3e-44 Identities = 92/252 (36%), Positives = 153/252 (60%), Gaps = 11/252 (4%) Query: 7 VALSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVS 66 + LSV ++H + G +H+LKG+SLD ++G+++++LG SGSGK+T LR + LE P GS+ Sbjct: 4 IELSVHDLHVTLGKNHILKGVSLDVNKGEIVALLGPSGSGKTTLLRSIAGLELPSHGSIR 63 Query: 67 LAGEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQKR 126 + GE++ + + + +V + LG VFQ++ LW H TV EN+ G ++++K Sbjct: 64 I-GEQM--------VFESAKKIEVSVEKRCLGFVFQSYALWPHRTVYENVAYG-LKLRKV 113 Query: 127 SRAESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSALD 186 E + + +LA +GL + +P LSGGQQQRVA+AR+L +P+V+L DEP S LD Sbjct: 114 PDGEIRQRVQEVLANLGLGDLSERHPHQLSGGQQQRVALARSLVYNPQVILLDEPLSNLD 173 Query: 187 PELVGEVLRVMRSL-AEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVEC 245 +L E +R L + + + VTH+ A ++++V+ L G +E GTP E++ Sbjct: 174 AKLREEARIWLRQLIIDLNLSAVCVTHDQAEAMAMADKVVLLKDGVIEQAGTPQEMYGAP 233 Query: 246 KSDRFRQFVSSH 257 KS +F+ ++ Sbjct: 234 KSLFVAEFMGAN 245 Lambda K H 0.318 0.133 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: 200 Number of extensions: 13 Number of successful extensions: 4 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: 263 Length of database: 353 Length adjustment: 27 Effective length of query: 236 Effective length of database: 326 Effective search space: 76936 Effective search space used: 76936 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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