Align histidine transport ATP-binding protein hisP (characterized)
to candidate N515DRAFT_1085 N515DRAFT_1085 D-methionine transport system ATP-binding protein
Query= CharProtDB::CH_003210 (257 letters) >FitnessBrowser__Dyella79:N515DRAFT_1085 Length = 336 Score = 172 bits (435), Expect = 1e-47 Identities = 105/257 (40%), Positives = 150/257 (58%), Gaps = 18/257 (7%) Query: 6 LNVIDLHKRYG----EHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGS 61 + +D+HK Y + L+ SL G+V IIG SG+GKST +R IN LE+PS GS Sbjct: 2 IRFVDVHKSYRVDGKDIPALQPFSLDIADGEVFGIIGHSGAGKSTLIRLINLLERPSGGS 61 Query: 62 IVVNGQTINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVL 121 I+++G + + D LR R R+ M+FQHFNL S TV +N+ P+++ Sbjct: 62 ILIDGTEMTALGDA----------ALRAQRRRIGMIFQHFNLLSSQTVADNIA-FPLRLA 110 Query: 122 GLSKQ-EARERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPT 180 G + + + R + L +VG++ A KYP LSGGQ+QRV IARALA P +LL DE T Sbjct: 111 GETDAGKIKARVDELLRRVGLEAHAS-KYPAQLSGGQKQRVGIARALANRPSILLCDEAT 169 Query: 181 SALDPELVGEVLRIMQQLAEEGK-TMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQL 239 SALDP+ VL ++ ++ E K T+V++THEM R V V L G+I E GA + Sbjct: 170 SALDPQTTASVLELLAEINRELKLTIVLITHEMDVVRRVCDRVAVLDAGRIVEHGAVADV 229 Query: 240 FGNPQSPRLQRFLKGSL 256 F +P+ P +RF+ +L Sbjct: 230 FLHPRHPTTRRFVNEAL 246 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: 200 Number of extensions: 10 Number of successful extensions: 4 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: 336 Length adjustment: 26 Effective length of query: 231 Effective length of database: 310 Effective search space: 71610 Effective search space used: 71610 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: 48 (23.1 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