Align Histidine transport system permease protein HisQ (characterized)
to candidate 8500098 DvMF_0861 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= SwissProt::P52094 (228 letters) >FitnessBrowser__Miya:8500098 Length = 263 Score = 112 bits (280), Expect = 7e-30 Identities = 66/207 (31%), Positives = 108/207 (52%), Gaps = 13/207 (6%) Query: 12 GALVTLELAISSVVLAVIIGLIGAGGKLSQNRLSGLIFEGYTTLIRGVPDLVLMLLIFYG 71 G VT ++ + S++ ++ IGLI G+LS+NRL L+ Y ++RG+P LV + I+Y Sbjct: 62 GIAVTFKVTVLSILCSIPIGLITGLGRLSRNRLINLVASTYVEVVRGIPLLVQLFYIYYA 121 Query: 72 LQIALNTVTEAMGVGQIDIDPMVAGIITLGFIYGAYFTETFRGAFMAVPKGHIEAATAFG 131 L L + ++A II L YGAY E FR ++ KG EAA + G Sbjct: 122 LGRFLK------------VPDLLAAIIALSVCYGAYMGEVFRAGIDSISKGQTEAARSLG 169 Query: 132 FTRGQVFRRIMFPSMMRYALPGIGNNWQVILKSTALVSLLGLEDVVKATQLAGKSTWEPF 191 F R + ++ P R LP +GN + +LK T+LVS++ + D+++ + ++ F Sbjct: 170 FNRAETMFMVILPQAWRTILPPVGNEFIAMLKDTSLVSIIAVADILRRGREFASESFLYF 229 Query: 192 YFAIVCGVIYLVFTT-VSNGVLLFLER 217 + +IYL+ T +S GV + R Sbjct: 230 ETYTMVALIYLLITLFLSKGVSIMESR 256 Lambda K H 0.328 0.145 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: 139 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: 228 Length of database: 263 Length adjustment: 24 Effective length of query: 204 Effective length of database: 239 Effective search space: 48756 Effective search space used: 48756 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: 46 (22.3 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