Align histidine transport ATP-binding protein hisP (characterized)
to candidate WP_011938227.1 GURA_RS06655 ABC transporter ATP-binding protein
Query= CharProtDB::CH_003210 (257 letters) >NCBI__GCF_000016745.1:WP_011938227.1 Length = 353 Score = 160 bits (405), Expect = 3e-44 Identities = 94/253 (37%), Positives = 151/253 (59%), Gaps = 12/253 (4%) Query: 1 MSENKLNVIDLHKRYGEHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEG 60 M+ +L+V DLH G++ +LKGVSL N G++++++G SGSGK+T LR I LE PS G Sbjct: 1 MTSIELSVHDLHVTLGKNHILKGVSLDVNKGEIVALLGPSGSGKTTLLRSIAGLELPSHG 60 Query: 61 SIVVNGQTINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV 120 SI + Q + + A K ++ + + L VFQ + LW H TV ENV +++ Sbjct: 61 SIRIGEQMV---------FESAKKIEVSVEKRCLGFVFQSYALWPHRTVYENVAYG-LKL 110 Query: 121 LGLSKQEARERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPT 180 + E R+R + LA +G+ + ++ ++P LSGGQQQRV++AR+L P+V+L DEP Sbjct: 111 RKVPDGEIRQRVQEVLANLGLGDLSE-RHPHQLSGGQQQRVALARSLVYNPQVILLDEPL 169 Query: 181 SALDPELVGEV-LRIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQL 239 S LD +L E + + Q + + + V VTH+ A ++ V+ L G IE+ G P+++ Sbjct: 170 SNLDAKLREEARIWLRQLIIDLNLSAVCVTHDQAEAMAMADKVVLLKDGVIEQAGTPQEM 229 Query: 240 FGNPQSPRLQRFL 252 +G P+S + F+ Sbjct: 230 YGAPKSLFVAEFM 242 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: 193 Number of extensions: 7 Number of successful extensions: 4 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: 353 Length adjustment: 27 Effective length of query: 230 Effective length of database: 326 Effective search space: 74980 Effective search space used: 74980 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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