Align histidine transport ATP-binding protein hisP (characterized)
to candidate H281DRAFT_02573 H281DRAFT_02573 amino acid ABC transporter ATP-binding protein, PAAT family
Query= CharProtDB::CH_003210 (257 letters) >FitnessBrowser__Burk376:H281DRAFT_02573 Length = 252 Score = 246 bits (627), Expect = 4e-70 Identities = 135/243 (55%), Positives = 161/243 (66%), Gaps = 12/243 (4%) Query: 11 LHKRYGEHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGSIVVNGQTIN 70 +HKR+ EVLKGVSL AG+V+ +IG SGSGKST LRCIN E GSI ++G ++ Sbjct: 7 IHKRFYNQEVLKGVSLSVKAGEVVCLIGPSGSGKSTVLRCINGFETYDAGSITIDGVRVD 66 Query: 71 LVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSKQEARE 130 A+ + LR R+ MVFQ FNL++H T LENVME P+ V +ARE Sbjct: 67 -----------ANAKNIHELRMRVGMVFQRFNLFAHRTALENVMEGPVYVRRTPVAQARE 115 Query: 131 RAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPTSALDPELVGE 190 +A + L KVG+ R YP LSGGQQQRV+IARALAMEPE LLFDEPTSALDPELVGE Sbjct: 116 QARQLLDKVGLSHRMNA-YPSELSGGQQQRVAIARALAMEPEALLFDEPTSALDPELVGE 174 Query: 191 VLRIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQLFGNPQSPRLQR 250 VL +M+ LA +G TMVVVTHEM FAR V+ V FLH G I E G + PQ PR Q Sbjct: 175 VLNVMRSLARDGMTMVVVTHEMAFAREVADRVCFLHGGTICETGPARGVLTEPQHPRTQE 234 Query: 251 FLK 253 FL+ Sbjct: 235 FLR 237 Lambda K H 0.318 0.134 0.375 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: 197 Number of extensions: 8 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: 257 Length of database: 252 Length adjustment: 24 Effective length of query: 233 Effective length of database: 228 Effective search space: 53124 Effective search space used: 53124 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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