Align Histidine transport ATP-binding protein HisP (characterized)
to candidate 7026313 Shewana3_3455 ABC transporter related (RefSeq)
Query= SwissProt::P02915 (258 letters) >FitnessBrowser__ANA3:7026313 Length = 656 Score = 145 bits (366), Expect = 2e-39 Identities = 91/241 (37%), Positives = 144/241 (59%), Gaps = 17/241 (7%) Query: 2 MSENKLHVIDLHKRYGGHE----VLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEK 57 MS+ L V ++ + E VLK ++L G++++I+G+SGSGKST + + L+K Sbjct: 1 MSKPLLEVSACYRSFQAGEQQLTVLKDINLSIARGEMVAIVGASGSGKSTLMNILGCLDK 60 Query: 58 PSEGAIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEA 117 PS+G+ ++GQ+ + Q+ V + +LR R +FQ ++L + + NV E Sbjct: 61 PSKGSYFIDGQDTS-------QMDVDELAKLR--REHFGFIFQRYHLLGDLNAVGNV-EV 110 Query: 118 PIQVLGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLF 177 P G + + RERA L+++G+ ER K P LSGGQQQRVS+ARAL DV+L Sbjct: 111 PAVYAGKDRLERRERAESLLSRLGLGERLDHK-PNQLSGGQQQRVSVARALMNGGDVILA 169 Query: 178 DEPTSALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGK-IEEEGD 236 DEPT ALD E++R++Q+L EG+T+++VTH+M A+H + +I + G I +E + Sbjct: 170 DEPTGALDSHSGEEMMRLLQELHREGQTIIIVTHDMHVAQH-ADRIIEIKDGVIISDEPN 228 Query: 237 P 237 P Sbjct: 229 P 229 Lambda K H 0.319 0.136 0.383 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: 337 Number of extensions: 15 Number of successful extensions: 3 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: 258 Length of database: 656 Length adjustment: 31 Effective length of query: 227 Effective length of database: 625 Effective search space: 141875 Effective search space used: 141875 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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