Align histidine transport ATP-binding protein hisP (characterized)
to candidate WP_011383520.1 AMB_RS05625 phosphate ABC transporter ATP-binding protein
Query= CharProtDB::CH_003210 (257 letters) >NCBI__GCF_000009985.1:WP_011383520.1 Length = 260 Score = 142 bits (359), Expect = 5e-39 Identities = 97/258 (37%), Positives = 136/258 (52%), Gaps = 12/258 (4%) Query: 1 MSENKLNVIDLHKRYGEHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEG 60 + +K++ DL+ YGE + L V+L G V ++IG SG GKSTFLRCIN + E Sbjct: 8 VGSSKISARDLNVHYGEKQALFDVNLDIPVGQVTALIGPSGCGKSTFLRCINRMNDLVEI 67 Query: 61 SIVVNGQTINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAP-IQ 119 + V ++ + +D + V LR R+ MVFQ N + ++ ENV P + Sbjct: 68 ARVSGSLFLDGIDIQDAAMDVVQ------LRARVGMVFQRPNPFPK-SIYENVAFGPRLH 120 Query: 120 VLGLSKQEARERAVKYLAKVGIDERAQ---GKYPVHLSGGQQQRVSIARALAMEPEVLLF 176 L E E + L K G+ + G+ LSGGQQQR+ IARA+A+ PEV+L Sbjct: 121 GLAAGADELDEIVISSLDKAGLWGEVKDRMGETGTSLSGGQQQRLCIARAIAVAPEVILM 180 Query: 177 DEPTSALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAP 236 DEP SALDP V ++ +L T+V+VTH M A VS F H GK+ E G Sbjct: 181 DEPCSALDPIATAAVEELIDEL-RGSYTIVIVTHSMQQAARVSQRTGFFHLGKLIEMGET 239 Query: 237 EQLFGNPQSPRLQRFLKG 254 E +F +PQ P Q ++ G Sbjct: 240 ESMFTSPQHPLTQGYITG 257 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: 156 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: 260 Length adjustment: 24 Effective length of query: 233 Effective length of database: 236 Effective search space: 54988 Effective search space used: 54988 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