Align Histidine transport system permease protein HisM (characterized)
to candidate WP_013981191.1 PST_RS00085 ectoine/hydroxyectoine ABC transporter permease subunit EhuC
Query= SwissProt::P0A2I7 (235 letters) >NCBI__GCF_000013785.1:WP_013981191.1 Length = 219 Score = 99.4 bits (246), Expect = 5e-26 Identities = 69/204 (33%), Positives = 104/204 (50%), Gaps = 12/204 (5%) Query: 28 WLLISSVVMGGLLAV----ILAVGRVSSNKFIRFPIWLFTYIFRGTPLYVQLLVFYSGMY 83 W+ + V G LLA+ I A+ R+S +R+ ++ +FRG+ L VQL Y + Sbjct: 13 WVTVKVTVFGSLLAIACALIAALARLSPLAPLRWLAVIYVEVFRGSSLLVQLFWLY---F 69 Query: 84 TLEIVKGTDLLNAFFRSGLNCTVLALTLNTCAYTTEIFAGAIRSVPHGEIEAARAYGFSS 143 L + ++AF V+ L LN AY E+ GAIRSV G+ EA A + Sbjct: 70 VLPLPPFNVEMSAFA-----VAVVGLGLNIGAYGAEVLRGAIRSVHRGQHEACHALNMTP 124 Query: 144 FKMYRCIILPSALRIALPAYSNEVILMLHSTALAFTATVPDLLKIARDINSATYQPFTAF 203 R IILP AL A+P +N +I +L +T+L T+ DL AR ++ AT F Sbjct: 125 LTRMRRIILPQALLAAIPPGTNLLIELLKNTSLVSLITLSDLAFRARQLDQATLMTLEIF 184 Query: 204 GIAAVLYLLISYVLISLFRRAERR 227 G+A V+Y +++ + RR E+R Sbjct: 185 GLALVIYFVLAQTINFAMRRLEQR 208 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: 131 Number of extensions: 11 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 235 Length of database: 219 Length adjustment: 22 Effective length of query: 213 Effective length of database: 197 Effective search space: 41961 Effective search space used: 41961 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