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 AZOBR_RS26405 AZOBR_RS26405 amino acid ABC transporter ATP-binding protein
Query= uniprot:A0A1N7U8S3 (276 letters) >FitnessBrowser__azobra:AZOBR_RS26405 Length = 242 Score = 234 bits (596), Expect = 2e-66 Identities = 127/248 (51%), Positives = 174/248 (70%), Gaps = 12/248 (4%) Query: 27 LQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGVITLD 86 + ++ + K YG EVLKGVSL+ +G+++++IG SGSGKST+LRCIN LE+ D G IT++ Sbjct: 4 VDIKNVTKSYGSIEVLKGVSLSIDEGEIVTIIGKSGSGKSTLLRCINALERIDGGAITVE 63 Query: 87 GISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRVLDVSAA 146 G S+ T P+ L+ R R+ +VFQ FNL+ H+TV NIT+AP ++ A Sbjct: 64 GQSVR-------TDMPN---LRGFRQRVGIVFQAFNLFPHLTVERNITLAPILNKRIAKA 113 Query: 147 EAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTSALDPE 206 E A L +VGL ++ D YPA LSGGQQQRVAIAR LAM P ++LFDE TSALDPE Sbjct: 114 EGRALALDVLARVGLADKI-DAYPAQLSGGQQQRVAIARCLAMGPHLMLFDEVTSALDPE 172 Query: 207 LVGEVLKVIQTLAEEGRTMLMVTHEMGFARQVSSQVLFLHQGRVEEHG-DARILDQPNSE 265 LVGEVLKV++ +A +G TM++VTHEMGFAR V+S+++F+HQGRV E G A + P + Sbjct: 173 LVGEVLKVMEDMARQGMTMVLVTHEMGFARNVASKIVFMHQGRVWEEGPPAELFANPRTP 232 Query: 266 RLQQFLSN 273 L+ F+++ Sbjct: 233 ELRSFIAS 240 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: 219 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: 276 Length of database: 242 Length adjustment: 24 Effective length of query: 252 Effective length of database: 218 Effective search space: 54936 Effective search space used: 54936 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 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