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 N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein
Query= uniprot:A0A1N7U8S3 (276 letters) >FitnessBrowser__Dyella79:N515DRAFT_1562 Length = 384 Score = 134 bits (338), Expect = 2e-36 Identities = 88/259 (33%), Positives = 144/259 (55%), Gaps = 22/259 (8%) Query: 25 IKLQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGVIT 84 + L + + +RYG L SL+ +G+ ++L+G SGSGKS++LR + L+ PD G + Sbjct: 1 MSLSIRQLTRRYGAFAALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDVL 60 Query: 85 LDGISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPR---RVL 141 DG + P Q R + +VFQH+ L+ HMTV +NI R R Sbjct: 61 RDGTDL--------LALPAQ------RRDIGLVFQHYALFPHMTVADNIAFGLRVRPRAR 106 Query: 142 DVSAAEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTS 201 S + R L +V L + +YP LSGGQ+QRVA+ARALA+EP ++L DEP Sbjct: 107 RPSRRDIAARVEDLLRRVQL-EELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFG 165 Query: 202 ALDPELVGEVLKVIQTLAEE-GRTMLMVTHEMGFARQVSSQVLFLHQGRVEEHG-DARIL 259 ALD ++ G + ++ L G T ++VTH+ A +++ +V+ +++GR+E+ G + I Sbjct: 166 ALDAQVRGTLRVWLRDLQRSLGLTTVLVTHDQDEALELADRVVVMNRGRIEQVGAPSEIY 225 Query: 260 DQPNSERLQQFL--SNRLK 276 +P + + F+ +NR++ Sbjct: 226 REPATPFVHGFVGRANRIR 244 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: 243 Number of extensions: 11 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: 384 Length adjustment: 28 Effective length of query: 248 Effective length of database: 356 Effective search space: 88288 Effective search space used: 88288 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: 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