Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 5210976 Shew_3402 ABC transporter-related protein (RefSeq)
Query= uniprot:A0A165KC78 (242 letters) >FitnessBrowser__PV4:5210976 Length = 322 Score = 103 bits (258), Expect = 3e-27 Identities = 68/216 (31%), Positives = 116/216 (53%), Gaps = 14/216 (6%) Query: 2 AEKSNKVLLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSM 61 A ++ ++ + G+ Y + A++ +DFE+ GE++ L G NGAGKTT MK I G + Sbjct: 3 ASSPSRPIVSLSGVAKRYAKVSALERIDFELFPGEVMGLFGHNGAGKTTIMKLILGIIPA 62 Query: 62 NDGNIEYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRK-DKAGILA 120 +DG ++ G+ K A++ K+ + +PE + ++T E L+ A ++ K I Sbjct: 63 SDGQVKVFGQDPLSKQAFEARKQ-VGYLPENVSFYDQLTGREVLRYFARLKSVPKQAIEQ 121 Query: 121 DIEKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDK 180 +E++ L D+ T S G +Q L + +A + PK+LLLDEP++GL PI + Sbjct: 122 LLEQV-----GLTHAMDRQVKTYSKGMRQRLGLAQAFLGSPKLLLLDEPTVGLDPIATQE 176 Query: 181 IFEVVRDVYALGVTIVL-------VEQNASRALAIA 209 + V + + G +I+L VEQ+ RAL I+ Sbjct: 177 FYASVDKLKSEGASIILCSHVLPGVEQHIDRALIIS 212 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: 168 Number of extensions: 9 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: 322 Length adjustment: 26 Effective length of query: 216 Effective length of database: 296 Effective search space: 63936 Effective search space used: 63936 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: 47 (22.7 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