Align Histidine transport system permease protein HisM (characterized)
to candidate BWI76_RS19230 BWI76_RS19230 polar amino acid ABC transporter inner membrane subunit
Query= SwissProt::P0A2I7 (235 letters) >FitnessBrowser__Koxy:BWI76_RS19230 Length = 241 Score = 177 bits (450), Expect = 1e-49 Identities = 97/228 (42%), Positives = 140/228 (61%), Gaps = 7/228 (3%) Query: 11 SLLWTDGY-RFTGVAITLWLLISSVVMGGLLAVILAVGRVSSNKFIRFPIWLFTYIFRGT 69 S LW+DG +G+A+T L + S+V G LA+ +AVG+V + + PI FTY FR T Sbjct: 12 SFLWSDGNGAASGLAVTAELFLLSIVPGMALAIAMAVGQVYGPRGLALPIRAFTYFFRST 71 Query: 70 PLYVQLLVFYSGMYTLEIVKGTDLLN-----AFFRSGLNCTVLALTLNTCAYTTEIFAGA 124 PLY+QL++ Y G+ +IV+ T +N FR C LAL LNT AY E+ AG Sbjct: 72 PLYLQLMLIYYGLSQFDIVQ-TGWMNDQPFWLLFRDATFCATLALVLNTAAYVAELLAGM 130 Query: 125 IRSVPHGEIEAARAYGFSSFKMYRCIILPSALRIALPAYSNEVILMLHSTALAFTATVPD 184 + + P E A AYG +++ R ++LP+ LR +PA +NE++ +LH+T+LA T T+ D Sbjct: 131 MVTFPRQEWIAGEAYGMGKWQIIRRLVLPATLRRGIPALNNEMVFLLHATSLASTVTLLD 190 Query: 185 LLKIARDINSATYQPFTAFGIAAVLYLLISYVLISLFRRAERRWLQHV 232 + +AR + TY PF F +AA LYLL +++LI F RAERRWL + Sbjct: 191 ITGVARAFYAMTYSPFIPFLMAAALYLLCTFLLIFTFARAERRWLAFI 238 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: 170 Number of extensions: 8 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: 241 Length adjustment: 23 Effective length of query: 212 Effective length of database: 218 Effective search space: 46216 Effective search space used: 46216 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