Align Histidine transport ATP-binding protein HisP (characterized)
to candidate GFF3439 PS417_17605 amino acid transporter
Query= SwissProt::P02915 (258 letters) >FitnessBrowser__WCS417:GFF3439 Length = 276 Score = 318 bits (816), Expect = 6e-92 Identities = 163/253 (64%), Positives = 199/253 (78%), Gaps = 2/253 (0%) Query: 6 KLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEGAIIV 65 KL V +HKRYG HEVLKGVSL AR GDVIS+IG+SGSGKST LRCINFLE+P G I + Sbjct: 26 KLQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGVITL 85 Query: 66 NGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLS 125 +G +I + + + G + ++QL+ LRTRL MVFQHFNLWSHMTVLEN+ AP +VL +S Sbjct: 86 DGISIEMRQGRAGT-RAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRVLDVS 144 Query: 126 KHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSALD 185 +A +RA YL KVG+ R +YP LSGGQQQRV+IARALAMEP+++LFDEPTSALD Sbjct: 145 AAEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTSALD 204 Query: 186 PELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVFGNPQ 245 PELVGEVL+++Q LAEEG+TM++VTHEMGFAR VSS V+FLHQG++EE GD ++ P Sbjct: 205 PELVGEVLKVIQTLAEEGRTMLMVTHEMGFARQVSSQVLFLHQGRVEEHGD-ARILDQPN 263 Query: 246 SPRLQQFLKGSLK 258 S RLQQFL LK Sbjct: 264 SERLQQFLSNRLK 276 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: 224 Number of extensions: 5 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: 276 Length adjustment: 25 Effective length of query: 233 Effective length of database: 251 Effective search space: 58483 Effective search space used: 58483 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: 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