Align ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale)
to candidate WP_054655718.1 CES79_RS03450 amino acid ABC transporter ATP-binding protein
Query= uniprot:A0A1N7U8S3 (276 letters) >NCBI__GCF_002217945.1:WP_054655718.1 Length = 247 Score = 213 bits (542), Expect = 3e-60 Identities = 114/252 (45%), Positives = 168/252 (66%), Gaps = 12/252 (4%) Query: 25 IKLQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGVIT 84 IK++V + K +G+++VLKG+++ +V+ +IG SGSGKST LR +N LE P +G I Sbjct: 5 IKVKVSNLVKNFGDNKVLKGINMEVHDNEVVVVIGPSGSGKSTFLRNLNRLEAPTSGSIV 64 Query: 85 LDGISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRVLDVS 144 +D + I A + + +R + MVFQHFNL+S+++V EN+ +AP + + Sbjct: 65 IDDMDI----------ADPKTDINKVRENIGMVFQHFNLFSNLSVSENVMLAPVELKKKT 114 Query: 145 AAEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTSALD 204 EA K+A L+ VGL S+ + LSGGQQQRVAIARALAM P ++LFDEPTSALD Sbjct: 115 KEEATKQAHDLLNMVGLESKFNATVQS-LSGGQQQRVAIARALAMNPNVMLFDEPTSALD 173 Query: 205 PELVGEVLKVIQTLAEEGRTMLMVTHEMGFARQVSSQVLFLHQGRVEEHGDA-RILDQPN 263 PE+VG+VL V++ LA++G TM++VTHEMGFA++V+ +V+F+ G ++E G + + P Sbjct: 174 PEMVGDVLAVMKQLAKQGMTMIVVTHEMGFAKEVADRVVFVDDGNIQEQGTPDEMFNHPQ 233 Query: 264 SERLQQFLSNRL 275 + LQ FL L Sbjct: 234 NPHLQDFLDKVL 245 Lambda K H 0.319 0.133 0.372 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: 167 Number of extensions: 6 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: 276 Length of database: 247 Length adjustment: 25 Effective length of query: 251 Effective length of database: 222 Effective search space: 55722 Effective search space used: 55722 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 (21.8 bits) S2: 47 (22.7 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