Align Histidine transport system permease protein HisQ (characterized)
to candidate BPHYT_RS24045 BPHYT_RS24045 amino acid ABC transporter
Query= SwissProt::P0A2I9 (228 letters) >FitnessBrowser__BFirm:BPHYT_RS24045 Length = 216 Score = 115 bits (289), Expect = 5e-31 Identities = 61/196 (31%), Positives = 103/196 (52%), Gaps = 11/196 (5%) Query: 8 VILQGAIVTLELALSSVVLAVLIGLVGAGAKLSQNRVTGLIFEGYTTLIRGVPDLVLMLL 67 ++L A+ T+ ++L+ +++ + + A+LS NR + Y RGVP LV +LL Sbjct: 13 LLLHAALATIGISLAGLLIGFFVAIGVCAARLSPNRAARMFGGAYVFFFRGVPMLVQLLL 72 Query: 68 IFYGLQIALNVVTDSLGIDQIDIDPMVAGIITLGFIYGAYFTETFRGAFMAVPKGHIEAA 127 ++Y L A I++ P+VA + + +Y E RG F++VP GH+EAA Sbjct: 73 VYYLLPFA-----------GINVSPIVAALSAVSLCSASYIAEILRGGFLSVPPGHLEAA 121 Query: 128 TAFGFTHGQTFRRIMFPAMMRYALPGIGNNWQVILKATALVSLLGLEDVVKATQLAGKST 187 G + RRI+ P R LP + N +++KA++L+S++G+ ++ + Q ST Sbjct: 122 RMLGLSPFDMLRRILVPQAFRLTLPSLVNEMVLLIKASSLISVVGVAELTRTAQNIAAST 181 Query: 188 WEPFYFAVVCGLIYLV 203 + P V GLIY V Sbjct: 182 YRPLEAYVAAGLIYFV 197 Lambda K H 0.328 0.144 0.422 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: 128 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: 228 Length of database: 216 Length adjustment: 22 Effective length of query: 206 Effective length of database: 194 Effective search space: 39964 Effective search space used: 39964 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 (21.7 bits) S2: 45 (21.9 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