Align histidine transport ATP-binding protein hisP (characterized)
to candidate Ac3H11_4899 ABC transporter ATP-binding protein
Query= CharProtDB::CH_003210 (257 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4899 Length = 264 Score = 244 bits (624), Expect = 1e-69 Identities = 131/247 (53%), Positives = 173/247 (70%), Gaps = 11/247 (4%) Query: 6 LNVIDLHKRYGEHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGSIVVN 65 +++ L K YG +EVLKG+ L+ G+VI+IIG SGSGKST LRC+N LE+ EG++ VN Sbjct: 24 VDITALRKSYGSNEVLKGIDLKVQRGEVIAIIGKSGSGKSTLLRCVNGLEEFQEGALSVN 83 Query: 66 GQTINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSK 125 G+ L+ D +R LR ++ M+FQ FNL+ H++V N+M AP V Sbjct: 84 GK--KLLHDSP--------TAMRELRQQVGMIFQSFNLFPHLSVGRNIMLAPTLVKARDA 133 Query: 126 QEARERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPTSALDP 185 + A +A K L +VG+ E+ P LSGGQQQRV+IARALAMEP+VLL DE TSALDP Sbjct: 134 KTAETQARKLLERVGLAEKFDAM-PDQLSGGQQQRVAIARALAMEPQVLLCDEITSALDP 192 Query: 186 ELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQLFGNPQS 245 ELVGEVLR+++ LA+EG T+++VTHEM FAR V VIF+HQG++ E+G P LFGNPQ+ Sbjct: 193 ELVGEVLRVVESLAQEGMTLMMVTHEMAFARKVGDRVIFMHQGRVHEQGTPAALFGNPQT 252 Query: 246 PRLQRFL 252 P LQ+FL Sbjct: 253 PELQQFL 259 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: 215 Number of extensions: 7 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: 264 Length adjustment: 25 Effective length of query: 232 Effective length of database: 239 Effective search space: 55448 Effective search space used: 55448 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