Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF2759 HP15_2703 branched-chain amino acid ABC transporter ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >FitnessBrowser__Marino:GFF2759 Length = 454 Score = 241 bits (616), Expect = 1e-68 Identities = 117/240 (48%), Positives = 176/240 (73%) Query: 2 AEKSNKVLLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSM 61 A + + +L +KGL +YG I+ + VD + GE+VSL+G+NGAGK+T + I+G Sbjct: 214 APHAKEEMLSIKGLVTSYGQIEVLHDVDIHINSGEIVSLVGANGAGKSTLLMTISGLQPT 273 Query: 62 NDGNIEYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILAD 121 + G I + GK + A V +G+V VPEGR VF +++ +NL +GAY R ++ D Sbjct: 274 DRGAITFEGKDLSKITADQRVADGIVQVPEGRQVFKDLSVHDNLLLGAYTRGKTPEVMDD 333 Query: 122 IEKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKI 181 +E+M+T FP LR+++ LAG +SGG+QQMLAMGRALM++P++LLLDEPSMGL+P+++++I Sbjct: 334 LERMYTKFPILRQKRHNLAGELSGGQQQMLAMGRALMAKPRLLLLDEPSMGLAPLIIEEI 393 Query: 182 FEVVRDVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241 F +V+++ G+TI LVEQNAS+ALA+ADRGYV+E+G + + G G++LL++ KVR AYLG Sbjct: 394 FNIVKELKEEGITIFLVEQNASQALALADRGYVLETGKVVIEGTGRELLSNEKVREAYLG 453 Lambda K H 0.317 0.136 0.373 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: 279 Number of extensions: 11 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 242 Length of database: 454 Length adjustment: 28 Effective length of query: 214 Effective length of database: 426 Effective search space: 91164 Effective search space used: 91164 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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