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 GFF3087 HP15_3030 histidine/lysine/arginine/ornithine transporter subunit
Query= uniprot:A0A1N7U8S3 (276 letters) >FitnessBrowser__Marino:GFF3087 Length = 256 Score = 292 bits (748), Expect = 4e-84 Identities = 156/243 (64%), Positives = 187/243 (76%), Gaps = 3/243 (1%) Query: 32 IHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGVITLDGISIE 91 I+K + + EVLKG+SL R+GDV+SLIG+SGSGKST LRCIN LE P +G I + G I Sbjct: 12 IYKTFDQLEVLKGISLETRKGDVVSLIGSSGSGKSTFLRCINLLETPTSGDIIVHGDPIR 71 Query: 92 MRQGRAGTRAPHQD-QLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRVLDVSAAEAEK 150 R G R P + Q++ +R +L+MVFQ FNLWSHMTVLENI AP VL V EA + Sbjct: 72 FTTNRKGERIPADNKQVELIRAKLSMVFQSFNLWSHMTVLENIIEAPVHVLKVPKKEAIE 131 Query: 151 RARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTSALDPELVGE 210 RA YL+KVG+ R D YPA +SGGQQQR AIARALAMEPE++LFDEPTSALDPELVGE Sbjct: 132 RAEAYLNKVGIYER-KDYYPAQMSGGQQQRAAIARALAMEPEVMLFDEPTSALDPELVGE 190 Query: 211 VLKVIQTLAEEGRTMLMVTHEMGFARQVSSQVLFLHQGRVEEHG-DARILDQPNSERLQQ 269 VLKV+Q LAEEGRTM++VTHEM FAR VSSQVLFLHQG +EE G ++ D P+SER++Q Sbjct: 191 VLKVMQGLAEEGRTMIVVTHEMAFARDVSSQVLFLHQGVIEEQGTPEKVFDHPDSERMKQ 250 Query: 270 FLS 272 FL+ Sbjct: 251 FLT 253 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: 247 Number of extensions: 9 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: 276 Length of database: 256 Length adjustment: 25 Effective length of query: 251 Effective length of database: 231 Effective search space: 57981 Effective search space used: 57981 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