Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate Synpcc7942_0513 Synpcc7942_0513 ATPase
Query= TCDB::Q8DQH8 (254 letters) >FitnessBrowser__SynE:Synpcc7942_0513 Length = 250 Score = 145 bits (365), Expect = 1e-39 Identities = 89/251 (35%), Positives = 142/251 (56%), Gaps = 19/251 (7%) Query: 4 LEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTLD 63 + ++ + K +G V V+L + +GE+VGL+GPNGAGKTT F + TG+ P EG V LD Sbjct: 11 IRLENVRKSYGKRLIVNRVSLSVAQGEVVGLLGPNGAGKTTTFYMTTGLERPDEGHVWLD 70 Query: 64 GHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFYK 123 L + A LG+G Q +F+ LTV++N+L+ L Sbjct: 71 ETELTRLPMTQRARLGIGYLAQEASIFRHLTVVENLLLV---------------LQQTGI 115 Query: 124 SEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALAT---EPKILFLDEPAA 180 +E + + ELL F L+ A T +S G++RR EI RALA PK L LDEP A Sbjct: 116 RGREQRQRVEELLSEFRLEKVAHTQGIRVSGGERRRTEIARALAVGSQGPKFLLLDEPFA 175 Query: 181 GMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIK 240 G++P AE+ E+I R++ + ++ I++ +H++ +++T+R Y+L G ++A G+ +E+ Sbjct: 176 GIDPIAVAEVQEIIARLRAQ-QMGILITDHNVRETLKITDRAYILRDGEILAAGSAEELA 234 Query: 241 TNKRVIEAYLG 251 +N V + YLG Sbjct: 235 SNPLVRQYYLG 245 Lambda K H 0.319 0.139 0.385 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: 138 Number of extensions: 5 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: 254 Length of database: 250 Length adjustment: 24 Effective length of query: 230 Effective length of database: 226 Effective search space: 51980 Effective search space used: 51980 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 (21.7 bits) S2: 46 (22.3 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