Align Histidine transport ATP-binding protein HisP (characterized)
to candidate 5211189 Shew_3605 cell division ATP-binding protein FtsE (RefSeq)
Query= SwissProt::P02915 (258 letters) >FitnessBrowser__PV4:5211189 Length = 233 Score = 139 bits (349), Expect = 7e-38 Identities = 75/215 (34%), Positives = 125/215 (58%), Gaps = 12/215 (5%) Query: 17 GGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEGAIIVNGQNINLVRDK 76 GG + L VS + G++ + G SG+GKST L+ I +E+ + G + +NG +I +R K Sbjct: 13 GGQKALTDVSFHLKRGEMAFLTGHSGAGKSTLLKLITVIERANAGRVAINGHDIANIRPK 72 Query: 77 DGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSKHDARERALKY 136 D + LR + M+FQ+ +L +V +N+ P+ + G + H+ ++R L Sbjct: 73 D----------VPFLRRDIGMIFQNHHLLMDRSVFDNIA-LPLVIEGFALHEIKKRVLAA 121 Query: 137 LAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSALDPELVGEVLRIM 196 L VG+ + + YP+ LSGG+QQRV IARA+ +P +LL DEPT LDP+L ++LR+ Sbjct: 122 LDMVGLYGKER-HYPIMLSGGEQQRVGIARAIVNKPPLLLADEPTGNLDPKLSMDILRLF 180 Query: 197 QQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKI 231 + + G T+++ TH++G + + L QG+I Sbjct: 181 ETFNDAGTTVLIATHDLGLIARMRYRTLTLKQGRI 215 Lambda K H 0.319 0.136 0.383 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: 146 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: 258 Length of database: 233 Length adjustment: 24 Effective length of query: 234 Effective length of database: 209 Effective search space: 48906 Effective search space used: 48906 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 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