Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF1247 PGA1_c12630 putative high-affinity branched-chain amino acid transport ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >FitnessBrowser__Phaeo:GFF1247 Length = 251 Score = 166 bits (420), Expect = 4e-46 Identities = 94/233 (40%), Positives = 143/233 (61%), Gaps = 6/233 (2%) Query: 10 LQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAI--TGTLSMNDGNIE 67 L V + YG V+G+ F V EGE+++L+G NGAGKT+T+++I TG+ + G I Sbjct: 21 LSVWDMHAYYGESYIVQGISFNVHEGEILALLGRNGAGKTSTLRSIARTGSPMVTKGEIW 80 Query: 68 YLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEKMFT 127 + + + + GL +VPE R + +T+ ENLQ+ + IE+++ Sbjct: 81 LDHQPLHKMSSHEASAAGLGLVPEDRRIIPGLTVEENLQLAQIAPP----VGWSIERLYE 136 Query: 128 IFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVRD 187 +FPRL ER+ Q T+SGGEQQMLA+ RAL KVLLLDEP GL+P++VD+I + + Sbjct: 137 LFPRLGERRKQEGVTLSGGEQQMLAIARALARDIKVLLLDEPYEGLAPVIVDEIEKTLIH 196 Query: 188 VYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYL 240 + G+T V+VEQNA RAL +ADR ++++G I G ++L + ++RA YL Sbjct: 197 IKQQGITTVIVEQNAVRALELADRAVILDTGGIVFDGAAAEVLENEELRAEYL 249 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: 164 Number of extensions: 8 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: 242 Length of database: 251 Length adjustment: 24 Effective length of query: 218 Effective length of database: 227 Effective search space: 49486 Effective search space used: 49486 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: 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