Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate PfGW456L13_483 Sulfate and thiosulfate import ATP-binding protein CysA (EC 3.6.3.25)
Query= TCDB::Q8DQH8 (254 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_483 Length = 329 Score = 143 bits (360), Expect = 5e-39 Identities = 80/240 (33%), Positives = 134/240 (55%), Gaps = 16/240 (6%) Query: 4 LEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTLD 63 +EV+ ++K+F A+ +++L++ GELV L+GP+G GKTTL ++ G+ P +G + Sbjct: 3 IEVRNVSKNFHAFKALDNISLDIQSGELVALLGPSGCGKTTLLRIIAGLETPDQGNIVFH 62 Query: 64 GHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFYK 123 G ++G + + +G FQ+ LF+ +TV DNV AFG K P + Sbjct: 63 GEDVSG---HDVRDRNVGFVFQHYALFRHMTVFDNV--AFGLRMK----------PKNQR 107 Query: 124 -SEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAGM 182 SE ++ K ELL + LD ++ + LS GQ++R+ + RALA EPK+L LDEP + Sbjct: 108 PSESQIATKVHELLNMVQLDWLSDRYPEQLSGGQRQRIALARALAVEPKVLLLDEPFGAL 167 Query: 183 NPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIKTN 242 + + EL + R+ ++ +T + + HD MEV +RI V+ G + G+P ++ N Sbjct: 168 DAKVRKELRRWLARLHEDINLTSVFVTHDQEEAMEVADRIVVMNKGVIEQIGSPGDVYEN 227 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: 196 Number of extensions: 7 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: 254 Length of database: 329 Length adjustment: 26 Effective length of query: 228 Effective length of database: 303 Effective search space: 69084 Effective search space used: 69084 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: 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