Align Histidine transport system permease protein HisM (characterized)
to candidate Dsui_0636 Dsui_0636 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family
Query= SwissProt::P0A2I7 (235 letters) >FitnessBrowser__PS:Dsui_0636 Length = 245 Score = 91.7 bits (226), Expect = 1e-23 Identities = 65/216 (30%), Positives = 112/216 (51%), Gaps = 8/216 (3%) Query: 17 GYRFTGVAITLWLLISSVVMGGLLAVILAVGRVSSNKFIRFPIWLFTYIFRGTPLYVQLL 76 G+ FTG+ T+ L +S+ V+ ++ I+ V R N+++ ++ FR PL VQL Sbjct: 23 GWLFTGLQWTVALSLSAWVIALVVGSIVGVLRTVPNRWLSGFAAVYVECFRNVPLLVQLF 82 Query: 77 VFYSGMYTLEIVKGTDLLNAFFRSG-----LNCTVLALTLNTCAYTTEIFAGAIRSVPHG 131 +Y + L + L NA+ +S +L L L T A E I S+P G Sbjct: 83 SWY---FVLPELLPPALGNAYKQSDPLLQQFLAAMLCLGLFTAARVAEQVRAGIESLPRG 139 Query: 132 EIEAARAYGFSSFKMYRCIILPSALRIALPAYSNEVILMLHSTALAFTATVPDLLKIARD 191 + A A GF+ ++YR ++LP A RI +P ++E + + ++A+A T + +L + A+ Sbjct: 140 QRNAGLAMGFTLAQVYRHVLLPMAFRIIVPPLTSEFLNIFKNSAVATTIGLIELSRQAQQ 199 Query: 192 INSATYQPFTAFGIAAVLYLLISYVLISLFRRAERR 227 + T QP+ AF +LY+ I+ ++ L RR E + Sbjct: 200 LVDYTAQPYEAFIAVTLLYVCINVTVMFLMRRLEEK 235 Lambda K H 0.330 0.141 0.429 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: 7 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: 235 Length of database: 245 Length adjustment: 23 Effective length of query: 212 Effective length of database: 222 Effective search space: 47064 Effective search space used: 47064 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 (21.9 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