Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF3203 PGA1_c32560 high-affinity branched-chain amino acid transport ATP-binding protein
Query= uniprot:A0A165KC78 (242 letters) >FitnessBrowser__Phaeo:GFF3203 Length = 278 Score = 211 bits (536), Expect = 2e-59 Identities = 113/243 (46%), Positives = 163/243 (67%), Gaps = 8/243 (3%) Query: 7 KVLLQVKGLKVAYGGIQAV-KGVDFEVREGELVSLIGSNGAGKTTTMKAITGTL-----S 60 + LL+V ++V Y + V KGV +V +G + +L+G NGAGKTTT+KA++ L Sbjct: 13 ETLLEVNNIEVIYNHVILVLKGVSLKVPKGGITALLGGNGAGKTTTLKAVSNLLHSERGE 72 Query: 61 MNDGNIEYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKD-KAGIL 119 + G+I Y G+ I+ + +LVK+G++ V EGR F +T+ ENL GAY R D A I Sbjct: 73 VTKGSISYRGERIQDRDPAELVKKGVIQVMEGRHCFEHLTVEENLLTGAYTRSDGNANIQ 132 Query: 120 ADIEKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVD 179 D+E +++ FPRL+ER+ AG SGGEQQM+AMGRALMS+P+ +LLDEPSMGL+P +V+ Sbjct: 133 RDLEMVYSYFPRLKERRRSQAGYTSGGEQQMVAMGRALMSRPETILLDEPSMGLAPQLVE 192 Query: 180 KIFEVVRDVYA-LGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAA 238 +IFE+V+ + GVT +L EQN + AL + GY++ESG + M GP +L +P V+ Sbjct: 193 QIFEIVKSINENEGVTFLLAEQNTNVALRYSHYGYILESGRVVMDGPAAELRENPDVKEF 252 Query: 239 YLG 241 YLG Sbjct: 253 YLG 255 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: 204 Number of extensions: 8 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: 242 Length of database: 278 Length adjustment: 24 Effective length of query: 218 Effective length of database: 254 Effective search space: 55372 Effective search space used: 55372 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: 47 (22.7 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