Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate BWI76_RS05985 BWI76_RS05985 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQH9 (318 letters) >FitnessBrowser__Koxy:BWI76_RS05985 Length = 349 Score = 167 bits (424), Expect = 3e-46 Identities = 114/331 (34%), Positives = 179/331 (54%), Gaps = 44/331 (13%) Query: 7 VNILWLLLLLAGYSLISVLVSVGVLNLFYVQILQQIGINIILAVGLNLIVGFSGQFSLGH 66 V I+ + LLAG ++ V N + ++++ I + +ILAV NLI G +GQ SL Sbjct: 16 VIIVLCVALLAGINV--------VFNDYIIRVISTIFVFMILAVSYNLINGVTGQLSLEP 67 Query: 67 AGFMAIGAYAAAII-------------GSKSP----TYGAFFGAMLVGALLSGAVALLVG 109 GF+A+GAY A++ + SP + F A+L+ L + A+A+ + Sbjct: 68 NGFVAVGAYVTALLILSSDSKLDMFEMAAPSPWILVLHAGFLPALLISGLCAAALAVCLA 127 Query: 110 IPTLRLKGDYLAVATLGVSEIIRIFIINGGSLTNGAAGILGIP---NFTTWQMVYFFVVI 166 +P R++GDYLA+ TLG II+I IN +TNGA G+ IP + W F ++ Sbjct: 128 LPVFRVRGDYLAIVTLGFGFIIKILAINNPQITNGAIGLNDIPQQPHLLFW--CGLFALL 185 Query: 167 TTIATLNFLRSPIGRSTLSVREDEIAAESVGVNTTKIKIIAFVFGAITASIAGSLQAGFI 226 T L + S GR +VR+DE AA ++GVNT +IK AF A I G L A + Sbjct: 186 ATGMILQLVWSKYGRMMKAVRDDEDAAIAMGVNTFRIKTCAFATSAFFEGIGGGLLASLL 245 Query: 227 GSVVPKDYTFINSINVLIIVVFGGLGSITGAIVSAIV-------LGILNMLLQ----DVA 275 ++ P + F+ + +LII+V GGLGS TGA++ ++ L L+ LQ D+ Sbjct: 246 TTISPGLFDFMLTFQLLIIIVLGGLGSTTGALLGTVLVVGSGEWLRFLDQPLQFFGHDLG 305 Query: 276 S---VRMIIYALALVLVMIFRPGGLLGTWEL 303 + +RM++++L L+++M+F GLLG E+ Sbjct: 306 AYPGLRMVVFSLLLLIIMLFAREGLLGKKEI 336 Lambda K H 0.327 0.143 0.403 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: 221 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: 318 Length of database: 349 Length adjustment: 28 Effective length of query: 290 Effective length of database: 321 Effective search space: 93090 Effective search space used: 93090 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 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