Align Histidine transport ATP-binding protein HisP (characterized)
to candidate N515DRAFT_2216 N515DRAFT_2216 cell division transport system ATP-binding protein
Query= SwissProt::P02915 (258 letters) >FitnessBrowser__Dyella79:N515DRAFT_2216 Length = 225 Score = 132 bits (332), Expect = 6e-36 Identities = 78/228 (34%), Positives = 127/228 (55%), Gaps = 13/228 (5%) Query: 14 KRY-GGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEGAIIVNGQNINL 72 KRY GGHE L +S Q G++ + G SG+GKST L+ + +E+PS G+I ++GQ++ Sbjct: 9 KRYEGGHEALSQLSFQVAPGEMAFVTGHSGAGKSTLLKLLGLIERPSHGSISLDGQSLAK 68 Query: 73 VRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSKHDARER 132 + + + LR R+ MVFQ L TV NV E P+ + G++ + R Sbjct: 69 I----------GRGGIPKLRRRIGMVFQDHRLLMDRTVFANV-ELPLVIGGVAPAERGRR 117 Query: 133 ALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSALDPELVGEV 192 L KVG+ + + P LS G+QQRV IARA+ +P +L+ DEPT LDP+L E+ Sbjct: 118 VRAALEKVGL-LAYERQLPATLSTGEQQRVGIARAIVAKPTLLIADEPTGNLDPQLAVEI 176 Query: 193 LRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQV 240 + + + + G T++V +H++ + + V+ L G++ + E+V Sbjct: 177 MGLFAEFQQVGTTVLVASHDLPLIKRMRKRVVVLDHGRLVADIAAEEV 224 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: 123 Number of extensions: 6 Number of successful extensions: 2 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: 225 Length adjustment: 23 Effective length of query: 235 Effective length of database: 202 Effective search space: 47470 Effective search space used: 47470 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