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 Synpcc7942_1680 Synpcc7942_1680 Sulphate transport system permease protein 1
Query= uniprot:A0A1N7U8S3 (276 letters) >FitnessBrowser__SynE:Synpcc7942_1680 Length = 338 Score = 145 bits (366), Expect = 1e-39 Identities = 94/252 (37%), Positives = 150/252 (59%), Gaps = 24/252 (9%) Query: 25 IKLQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGVIT 84 + +QV + K++G + +K V L G +++L+G SGSGKST+LR I LEQPD+G I Sbjct: 1 VGIQVSQVSKQFGSFQAVKDVDLTVETGSLVALLGPSGSGKSTLLRLIAGLEQPDSGRIF 60 Query: 85 LDGISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRVLDVS 144 L GR T +D+ ++ VFQH+ L+ H+TV +NI L++ Sbjct: 61 L--------TGRDATNESVRDR------QIGFVFQHYALFKHLTVRKNIAFG----LELR 102 Query: 145 AAEAEK-RARM--YLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTS 201 EK RAR+ L+ V L + + D+YP+ LSGGQ+QRVA+ARALA++P+++L DEP Sbjct: 103 KHTKEKVRARVEELLELVQL-TGLGDRYPSQLSGGQRQRVALARALAVQPQVLLLDEPFG 161 Query: 202 ALDPELVGEVLKVIQTLAEEGR-TMLMVTHEMGFARQVSSQVLFLHQGRVEEHGD-ARIL 259 ALD ++ ++ ++ L +E T + VTH+ A +V+ Q++ ++ G+VE+ G A I Sbjct: 162 ALDAKVRKDLRSWLRKLHDEVHVTTVFVTHDQEEAMEVADQIVVMNHGKVEQIGSPAEIY 221 Query: 260 DQPNSERLQQFL 271 D P + + F+ Sbjct: 222 DNPATPFVMSFI 233 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: 204 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: 338 Length adjustment: 27 Effective length of query: 249 Effective length of database: 311 Effective search space: 77439 Effective search space used: 77439 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