Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate AZOBR_RS20990 AZOBR_RS20990 amino acid ABC transporter ATPase
Query= uniprot:A0A165KC78 (242 letters) >FitnessBrowser__azobra:AZOBR_RS20990 Length = 233 Score = 233 bits (595), Expect = 2e-66 Identities = 114/233 (48%), Positives = 166/233 (71%), Gaps = 1/233 (0%) Query: 9 LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68 +L V+ L YG IQ + G+D +V EGE+VS++G+N AGKTT + AI+GT+ G + + Sbjct: 1 VLTVRKLDAFYGEIQTLHGIDLDVLEGEVVSVVGANAAGKTTLLNAISGTVERY-GRVSF 59 Query: 69 LGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEKMFTI 128 + I + + GLV VPEGR +F MT+ ENL++GA+ +A +EK+F + Sbjct: 60 FDQDIGTLPPHAIARHGLVQVPEGRRLFPFMTVRENLELGAFAPHARAHRAESLEKVFDL 119 Query: 129 FPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVRDV 188 PRLRER QLAG+MSGGEQQM A+GRALM++P+ ++ DEP++GL+PIMVD +F++VR + Sbjct: 120 MPRLRERSGQLAGSMSGGEQQMCAIGRALMAKPRAIMFDEPTLGLAPIMVDVVFKLVRSI 179 Query: 189 YALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241 G+TI+LVEQN +LA++DRGYV+E+G I ++GP LL DP+++ AYLG Sbjct: 180 KETGITILLVEQNVKHSLAMSDRGYVLENGHIVLSGPAADLLTDPRLKEAYLG 232 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: 152 Number of extensions: 4 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: 233 Length adjustment: 23 Effective length of query: 219 Effective length of database: 210 Effective search space: 45990 Effective search space used: 45990 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 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