Align Histidine transport system permease protein HisM (characterized)
to candidate GFF3089 HP15_3032 amino acid ABC transporter, inner membrane subunit
Query= SwissProt::P0AEU3 (238 letters) >FitnessBrowser__Marino:GFF3089 Length = 247 Score = 95.5 bits (236), Expect = 9e-25 Identities = 69/213 (32%), Positives = 105/213 (49%), Gaps = 9/213 (4%) Query: 11 PLLWTDGYR---FTGVAITLWLLILSVVIGGVLALFLAIGRVSSNKYIQFPIWLFTYIFR 67 P+L GY G +T+ L LS+ + L L A ++S ++ + +T + R Sbjct: 13 PMLDLKGYGPALMDGAIVTIELAFLSLALSVALGLIGASAKLSQSRVAKGIATTYTTLIR 72 Query: 68 GTPLYVQLLVFYSG------MYTLEIVKGTEFLNAFFRSGLNCTVLALTLNTCAYTTEIF 121 G P V +L+FY G M + I + E F V+ + L AY TE F Sbjct: 73 GVPDLVMMLLFYYGGQVAVNMLSDYIWEAYEIDFFFQFDPFISGVVTIGLIFGAYMTETF 132 Query: 122 AGAIRSVPHGEIEAARAYGFSTFKMYRCIILPSALRIALPAYSNEVILMLHSTALAFTAT 181 GA +V G+IEAARAYGF+ F +R I+LP +R ALP N ++L +TAL Sbjct: 133 RGAFLAVETGQIEAARAYGFTRFHTFRRIMLPQMMRHALPGLGNNWQVLLKTTALVSIIG 192 Query: 182 VPDLLKIARDINAATYQPFTAFGIAAVLYLIIS 214 + D++++A + A PF F A +YL ++ Sbjct: 193 LTDMVRVAEEAAKAERMPFHFFIPVAFVYLALT 225 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: 135 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: 238 Length of database: 247 Length adjustment: 23 Effective length of query: 215 Effective length of database: 224 Effective search space: 48160 Effective search space used: 48160 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