Align ABC-type sugar transport system, permease component, component of Maltose transporter, MusEFGKI (characterized)
to candidate BPHYT_RS27975 BPHYT_RS27975 ABC transporter permease
Query= TCDB::Q8NMV4 (281 letters) >FitnessBrowser__BFirm:BPHYT_RS27975 Length = 318 Score = 122 bits (306), Expect = 1e-32 Identities = 82/279 (29%), Positives = 132/279 (47%), Gaps = 18/279 (6%) Query: 11 VFVLPTLLAFMIAFLVPFIVGFFLSFTKFTT---ITNAKWVGIDNYVKAFSQREGFISAF 67 +F+LPT+L + + P I LSFT F + A++VGIDNYV + E A Sbjct: 35 LFILPTVLLLLAINIFPLIWALRLSFTNFKSNMPSVPARFVGIDNYVDILTD-EDIWYAM 93 Query: 68 GFTVLVVIVSVITVNIFAFLLAWLLTRKLRGTNFFRTVFFMPNLIGGIVLGYTWQTMINA 127 T V SV + F LA L+ R+ RG +F+ T+ +P ++ V+G W ++ Sbjct: 94 QVTARFVFWSVGLEVLLGFGLALLINRQFRGHSFWTTLILLPMMLSPAVVGNFWTFLLQP 153 Query: 128 VLSHYATTIS-----ADWKFGYAG--------LIMLLNWQLIGYMMIIYIAGLQNVPPEL 174 + + A F G ++M+ W Y+M+I +AGL+++P + Sbjct: 154 QTGLFNDIVGFFTGIAPGSFQMIGDVSLAPWTIVMVDTWMWTPYVMLICLAGLRSIPDYI 213 Query: 175 IEAAELDGVNKWEMLRHVTIPMVMPSITICLFLTLSNSFKLFDQNLALTNGAPGGQTEMV 234 EAAE+D W +T+PM +P + + + +FK+FD LT+G PG TE V Sbjct: 214 YEAAEVDRATPWRQFWSITLPMTLPFLMLAVLFRGIENFKMFDMVNLLTSGGPGSVTETV 273 Query: 235 ALNIINTLFNRMNVEGVGQAKAVIFVVVVVVIAYFQLRA 273 ++ + F + G A A+I V V A ++A Sbjct: 274 SITLKRAAFEKWQT-GYSSALAIILFVTVFGAANIYVKA 311 Lambda K H 0.331 0.142 0.431 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: 263 Number of extensions: 20 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: 281 Length of database: 318 Length adjustment: 27 Effective length of query: 254 Effective length of database: 291 Effective search space: 73914 Effective search space used: 73914 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 48 (23.1 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