Align Histidine transport ATP-binding protein HisP (characterized)
to candidate WP_047094318.1 AAV99_RS11970 ABC transporter ATP-binding protein
Query= SwissProt::P02915 (258 letters) >NCBI__GCF_001013305.1:WP_047094318.1 Length = 240 Score = 132 bits (331), Expect = 9e-36 Identities = 90/230 (39%), Positives = 133/230 (57%), Gaps = 18/230 (7%) Query: 2 MSENKLHVID-LHKRYG----GHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLE 56 M+++KL ++ + K +G + LKGV ++ GD ++I+G SGSGKST + + L+ Sbjct: 1 MTQHKLIELEGITKTFGKGPAAFQALKGVDMKIDRGDFVAIMGPSGSGKSTTMNILGCLD 60 Query: 57 KPSEGAIIVNGQNINLVRDKDGQLKVADKNQLRLLRTR-LTMVFQHFNLWSHMTVLENVM 115 P++G + R + +++ ++Q LLR R L VFQ FNL + T LENV Sbjct: 61 VPTDG----------IFRFRGIEVQALTRDQRSLLRRRYLGFVFQGFNLLARTTALENV- 109 Query: 116 EAPIQVLGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVL 175 E P+ G +K R A + L KVG+ A P LSGGQQQRV+IARAL +PDVL Sbjct: 110 ELPLLYRGETKKQRRIAAERSLDKVGLLPWASHT-PAELSGGQQQRVAIARALVTDPDVL 168 Query: 176 LFDEPTSALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIF 225 L DEPT LD E E++ ++ L++ G T+++VTHE A + + V F Sbjct: 169 LADEPTGNLDTERSLEIMELLTDLSDTGITVLMVTHEEEMAEYARTIVHF 218 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: 134 Number of extensions: 9 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: 240 Length adjustment: 24 Effective length of query: 234 Effective length of database: 216 Effective search space: 50544 Effective search space used: 50544 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 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