Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_012281447.1 HM1_RS01335 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >NCBI__GCF_000019165.1:WP_012281447.1 Length = 259 Score = 142 bits (359), Expect = 5e-39 Identities = 88/253 (34%), Positives = 145/253 (57%), Gaps = 20/253 (7%) Query: 8 VLLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIE 67 +LL V L +GG++AV V+ E++ GELV LIG NGAGKTT +TG DG+I Sbjct: 2 ILLSVNHLSKTFGGLKAVSDVNMELKIGELVGLIGPNGAGKTTLFNLLTGVYKPTDGDIV 61 Query: 68 YLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADI----- 122 ++I G + ++G+ + +F+ +T+ +N+++ AY + +L+ I Sbjct: 62 LRRETIVGLKPHQINQKGIARTFQNIRLFSNLTVMDNVKI-AYHQHRSYNMLSAILRLPS 120 Query: 123 ------------EKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPS 170 E++ IF +L +KD+LA + GEQ+ L + RAL +QP++LLLDEP+ Sbjct: 121 YFHGEEEMDKKAERLLEIF-KLGHKKDELAKNLPYGEQRRLEIARALAAQPQLLLLDEPA 179 Query: 171 MGLSPIMVDKIFEVVRDV-YALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQL 229 G++P ++ E++R V +TI+L+E + S + I +R YV++ G I G +Q+ Sbjct: 180 AGMNPQETAELMEMIRWVRKEFDLTILLIEHDMSLVMGICERIYVLDYGQIIAEGTPEQI 239 Query: 230 LNDPKVRAAYLGE 242 ++PKV AYLGE Sbjct: 240 KSNPKVIEAYLGE 252 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: 133 Number of extensions: 7 Number of successful extensions: 3 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: 259 Length adjustment: 24 Effective length of query: 218 Effective length of database: 235 Effective search space: 51230 Effective search space used: 51230 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