Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_011764862.1 AZO_RS05730 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >NCBI__GCF_000061505.1:WP_011764862.1 Length = 238 Score = 189 bits (480), Expect = 4e-53 Identities = 95/236 (40%), Positives = 153/236 (64%), Gaps = 1/236 (0%) Query: 6 NKVLLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGN 65 ++ LL GL+ YG Q + G+DFE+R GE++ L+G NG GK+TT+K+I GTL+ + G+ Sbjct: 3 HEALLSCSGLQAGYGASQVLFGLDFEIRPGEVIGLLGRNGMGKSTTIKSIVGTLAPSRGD 62 Query: 66 IEYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEKM 125 I +LGKSI G + + G+ +VPEGR F +++ E+L A R D+ +E++ Sbjct: 63 IRFLGKSIAGMRPDAIARMGVAIVPEGRHCFPNLSVREHLVAFADNRNDQRDGWT-LERI 121 Query: 126 FTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVV 185 + +FPRL+ER D L +SGGEQQMLA+GRAL + P++L+LDE + GL+P++ D+I+ + Sbjct: 122 YALFPRLKERADNLGNQLSGGEQQMLAIGRALSTNPRLLILDEATEGLAPVIRDEIWRCL 181 Query: 186 RDVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241 + A G T ++V++ R + +ADR ++E G + +GP +L D + Y+G Sbjct: 182 AQLKAEGQTTLVVDKYVDRLVGLADRHLILERGRVVWSGPSSELAADRSLWHRYMG 237 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: 174 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: 238 Length adjustment: 23 Effective length of query: 219 Effective length of database: 215 Effective search space: 47085 Effective search space used: 47085 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