Align Histidine transport system permease protein HisM (characterized)
to candidate WP_086508347.1 BZY95_RS02055 ABC transporter
Query= SwissProt::P0AEU3 (238 letters) >NCBI__GCF_002151265.1:WP_086508347.1 Length = 233 Score = 119 bits (298), Expect = 5e-32 Identities = 79/235 (33%), Positives = 122/235 (51%), Gaps = 23/235 (9%) Query: 5 LHEYWKPLLWTDGYRFTGVAITLWLLILSVVIGGVLALFLAIGRVSSNKYIQFPIWLFTY 64 LH Y LL G +TL L +LS+++ +L L A ++S N + L+T Sbjct: 4 LHGYGPRLL-------EGAGVTLQLAVLSLILALILGLLTASAKMSRNWLLHKVATLYTT 56 Query: 65 IFRGTP-LYVQLLVFYSGMYTLEIVKGTEF----------LNAFFRSGLNCTVLALTLNT 113 + RG P L + LL+F+ G L + + LNAF VL + Sbjct: 57 VIRGVPDLVLMLLLFFGGQMALNVATDAIYDRFGVDWYINLNAFAAG-----VLTIGFIF 111 Query: 114 CAYTTEIFAGAIRSVPHGEIEAARAYGFSTFKMYRCIILPSALRIALPAYSNEVILMLHS 173 AY E F GA +V HG+IEA +AYG S + ++R I P +R ALP SN +++L + Sbjct: 112 GAYMGETFRGAFMAVEHGQIEAGKAYGMSPWLVFRRIRFPQMMRHALPGISNNWMVLLKT 171 Query: 174 TALAFTATVPDLLKIARDINAATYQPFTAFGIAAVLYLIISYVLISLFRRAEKRW 228 TAL + D++++A + + AT++PFT AV+YL+I+ V +F R +KR+ Sbjct: 172 TALVSVIGLSDMVRVAAEASRATHEPFTFLIPVAVVYLLIASVSEWMFARLQKRY 226 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: 129 Number of extensions: 3 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: 233 Length adjustment: 23 Effective length of query: 215 Effective length of database: 210 Effective search space: 45150 Effective search space used: 45150 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 24 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