Align histidine transport ATP-binding protein hisP (characterized)
to candidate CCNA_00294 CCNA_00294 phosphate transport ATP-binding protein pstB
Query= CharProtDB::CH_003210 (257 letters) >FitnessBrowser__Caulo:CCNA_00294 Length = 274 Score = 139 bits (351), Expect = 5e-38 Identities = 97/249 (38%), Positives = 130/249 (52%), Gaps = 22/249 (8%) Query: 15 YGEHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEK--PS---EGSIVVNGQTI 69 YG+ + L V L A V + IG SG GKSTFLRCIN + PS EGSI+++G + Sbjct: 36 YGDKQALFDVDLDIPAKSVTAFIGPSGCGKSTFLRCINRMNDTIPSARVEGSILIDGADV 95 Query: 70 NLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAP-IQVLGLSKQEA 128 N A +LR+R+ MVFQ N + T+ ENV P I L K E Sbjct: 96 N-----------AKSVDPVVLRSRVGMVFQKPNPFPK-TIFENVAYGPRIHGLATGKAEL 143 Query: 129 RERAVKYLAKVGIDERAQGKYP---VHLSGGQQQRVSIARALAMEPEVLLFDEPTSALDP 185 L K G+ + LSGGQQQR+ IARA+A+ PEV+L DEP SALDP Sbjct: 144 EAIVESSLKKAGLWNEVADRLHQPGTGLSGGQQQRLVIARAIAVSPEVILMDEPCSALDP 203 Query: 186 ELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQLFGNPQS 245 ++ ++ +L + +V+VTH M A VS F H GK+ E G E++F NP+ Sbjct: 204 IATAKIEELIDELRSQ-FCIVIVTHSMAQAARVSQRTAFFHLGKLVESGPTEEMFTNPRD 262 Query: 246 PRLQRFLKG 254 R Q ++ G Sbjct: 263 SRTQDYITG 271 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: 142 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: 274 Length adjustment: 25 Effective length of query: 232 Effective length of database: 249 Effective search space: 57768 Effective search space used: 57768 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