Align Histidine transport system permease protein HisQ (characterized)
to candidate BWI76_RS08970 BWI76_RS08970 glutamine ABC transporter permease GlnP
Query= SwissProt::P52094 (228 letters) >FitnessBrowser__Koxy:BWI76_RS08970 Length = 219 Score = 108 bits (269), Expect = 1e-28 Identities = 63/214 (29%), Positives = 111/214 (51%), Gaps = 9/214 (4%) Query: 8 VILQGALVTLELAISSVVLAVIIGLIGAGGKLSQNRLSGLIFEGYTTLIRGVPDLVLMLL 67 ++L+GA +TL +++ +V +IIGL+ + ++ I + +IRG P +V ++ Sbjct: 14 ILLEGAKMTLWISVLGLVGGLIIGLVAGFARCFGGWIANHIALVFIEIIRGTPIVVQVMF 73 Query: 68 IFYGLQIALNTVTEAMGVGQIDIDPMVAGIITLGFIYGAYFTETFRGAFMAVPKGHIEAA 127 I++ L +A + + IDP A ++T+ GAY E RGA +++ KG EA Sbjct: 74 IYFALPMAFS---------DLRIDPFSAAVVTIMINSGAYIAEITRGAVLSIHKGFREAG 124 Query: 128 TAFGFTRGQVFRRIMFPSMMRYALPGIGNNWQVILKSTALVSLLGLEDVVKATQLAGKST 187 A G +R + R ++ P +R LP +GN W + +K T+L ++G+ ++ + Q Sbjct: 125 LALGLSRRETIRYVILPLALRRMLPPLGNQWIISIKDTSLFIVIGVAELTRQGQEIIAGN 184 Query: 188 WEPFYFAIVCGVIYLVFTTVSNGVLLFLERRYSV 221 + VIYL+ T V + VL LERR + Sbjct: 185 FRALEIWSAVAVIYLIITLVLSFVLRRLERRMKI 218 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: 125 Number of extensions: 8 Number of successful extensions: 3 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: 219 Length adjustment: 22 Effective length of query: 206 Effective length of database: 197 Effective search space: 40582 Effective search space used: 40582 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