Align histidine transport ATP-binding protein hisP (characterized)
to candidate WP_086508440.1 BZY95_RS02565 amino acid ABC transporter ATP-binding protein
Query= CharProtDB::CH_003210 (257 letters) >NCBI__GCF_002151265.1:WP_086508440.1 Length = 240 Score = 264 bits (674), Expect = 1e-75 Identities = 141/247 (57%), Positives = 176/247 (71%), Gaps = 12/247 (4%) Query: 6 LNVIDLHKRYGEHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGSIVVN 65 + V +LHK +GE VLKGV L+ +V+ +IG+SGSGKST LRC+NFLE EGSIV++ Sbjct: 2 ITVSNLHKYFGELHVLKGVDLEVRPREVVVLIGASGSGKSTLLRCLNFLELKDEGSIVID 61 Query: 66 GQTINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSK 125 GQ I+ L +R + MVFQHFNL+ HMTVLENV+EAP+ V + K Sbjct: 62 GQEIDPAT-----------TPLNKVRENVGMVFQHFNLFPHMTVLENVIEAPVHVKRIPK 110 Query: 126 QEARERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPTSALDP 185 EA ERA + L KVG+ +++ YP LSGGQ+QRV+IARALAMEP V+LFDEPTSALDP Sbjct: 111 AEAIERARQLLDKVGLGDKSDA-YPEKLSGGQKQRVAIARALAMEPSVMLFDEPTSALDP 169 Query: 186 ELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQLFGNPQS 245 ELVGEVL +M+ LA +G TMVVVTHEMGFAR V+ V+FL G I E+G P LF NPQ Sbjct: 170 ELVGEVLEVMKGLAADGMTMVVVTHEMGFAREVADRVVFLDGGTIAEQGPPGTLFSNPQH 229 Query: 246 PRLQRFL 252 P+ ++FL Sbjct: 230 PKARQFL 236 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: 211 Number of extensions: 11 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: 240 Length adjustment: 24 Effective length of query: 233 Effective length of database: 216 Effective search space: 50328 Effective search space used: 50328 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: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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