Align Histidine transport system permease protein HisM (characterized)
to candidate GFF3090 HP15_3033 amino acid ABC transporter, inner membrane subunit
Query= SwissProt::P0AEU3 (238 letters) >FitnessBrowser__Marino:GFF3090 Length = 240 Score = 190 bits (483), Expect = 2e-53 Identities = 101/213 (47%), Positives = 141/213 (66%), Gaps = 1/213 (0%) Query: 22 GVAITLWLLILSVVIGGVLALFLAIGRVSSNKYIQFPIWLFTYIFRGTPLYVQLLVFYSG 81 G+ T+ L+ LS+VIG ++A+ LAI R N ++ P+WL+TY+FRGTPL +QL + Y G Sbjct: 26 GMVTTVHLVFLSLVIGLLVAVPLAILRTVRNPFVSGPVWLYTYLFRGTPLLIQLYIIYYG 85 Query: 82 MYTLEIVKGTEFLNAFFRSGLNCTVLALTLNTCAYTTEIFAGAIRSVPHGEIEAARAYGF 141 + +E ++ T F FR +LA TLNT AYTTEI GAI S P+GEIEAA+AYG Sbjct: 86 LAQIEGIQET-FWWEIFREPFYPALLAFTLNTAAYTTEIIRGAIISTPNGEIEAAKAYGM 144 Query: 142 STFKMYRCIILPSALRIALPAYSNEVILMLHSTALAFTATVPDLLKIARDINAATYQPFT 201 + F R I+LPSA R A+ AYSNEVI MLH++A+A T+ DL AR+I + Y PF Sbjct: 145 NWFMRMRRIVLPSAARRAVQAYSNEVIFMLHASAIASVVTIVDLTGAARNIYSRFYAPFD 204 Query: 202 AFGIAAVLYLIISYVLISLFRRAEKRWLQHVKP 234 AF A+ Y+ ++++L+ FR+ E L+H +P Sbjct: 205 AFIFVALCYMALTFILVFAFRKLETHLLKHQRP 237 Lambda K H 0.330 0.142 0.438 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: 182 Number of extensions: 11 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: 238 Length of database: 240 Length adjustment: 23 Effective length of query: 215 Effective length of database: 217 Effective search space: 46655 Effective search space used: 46655 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