Align histidine transport ATP-binding protein hisP (characterized)
to candidate Echvi_1582 Echvi_1582 ABC-type antimicrobial peptide transport system, ATPase component
Query= CharProtDB::CH_003210 (257 letters) >FitnessBrowser__Cola:Echvi_1582 Length = 225 Score = 127 bits (320), Expect = 2e-34 Identities = 83/217 (38%), Positives = 129/217 (59%), Gaps = 19/217 (8%) Query: 20 VLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGSIVVNGQTINLVRDKDGQL 79 VL+ ++L AGD I+I+G SGSGK+T L L+ S GS+ +NG +L Sbjct: 22 VLEDINLSVKAGDSIAIVGPSGSGKTTLLGLCAGLDSASSGSVALNGH----------RL 71 Query: 80 KVADKNQLRLLRTR-LTMVFQHFNLWSHMTVLENVMEAPIQVLGLSKQEARERAVKYLAK 138 + ++Q +R++ + +FQ+F L +T LENVM P+++ +++A+++A + L + Sbjct: 72 EGLSEDQRAAVRSQEIGFIFQNFQLLPTLTALENVM-VPLELK--KRKDAKQKATELLQQ 128 Query: 139 VGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPTSALDPELVGEVLR--IMQ 196 VG+ +R YP LSGG+QQRVSIARA A EP++L DEPT LD E GE++ I Sbjct: 129 VGLGDRMT-HYPTQLSGGEQQRVSIARAFANEPKILFADEPTGNLDTE-TGELIETLIFD 186 Query: 197 QLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEE 233 G T+++VTH+ A + +I + GKI+EE Sbjct: 187 LNKALGTTLILVTHDTDLAAK-TNRIIHIKGGKIQEE 222 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: 128 Number of extensions: 10 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: 225 Length adjustment: 23 Effective length of query: 234 Effective length of database: 202 Effective search space: 47268 Effective search space used: 47268 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: 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