Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate GFF385 PGA1_c03960 ribose import ATP-binding protein RbsA
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__Phaeo:GFF385 Length = 509 Score = 248 bits (634), Expect = 3e-70 Identities = 170/513 (33%), Positives = 260/513 (50%), Gaps = 27/513 (5%) Query: 11 SVPVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGE 70 + P +E ++K FG A D+SIRV PG H ++G NGAGKSTL+SIL G K D GE Sbjct: 2 TAPAIELKGISKAFGPVQANKDISIRVAPGTIHGIIGENGAGKSTLMSILYGFYKADKGE 61 Query: 71 VRFSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVI--DWQAMR 128 V G + A + V+QH ++ + +V EN+ + + GG++ R Sbjct: 62 VWIHGKRTEIPDSQAAISAGIGMVFQHFKLVENFTVLENIILGAED--GGLLKPSLSKAR 119 Query: 129 RDARALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKR 188 + + L ++++V DAR ++ V +Q VEI +AL A +ILDEPT L E + Sbjct: 120 KSLKDLAAEYELNVDPDARIDEIGVGMQQRVEILKALYRQADILILDEPTGVLTPAEADQ 179 Query: 189 LFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTG 248 LFR + L+ EG T + I+H L+E+ E V+V+R + + E L E M G Sbjct: 180 LFRILDRLRAEGKTIILITHKLREIMEYTDTVSVMRRGEMTATVKTAETSPEHLAELMVG 239 Query: 249 ERGGLAVADAAARGALPADTAVALELKELTGADYEGVS------FTVKRGEVVGLTGATS 302 + L V A P LE++ L+ D GV+ TV+ GE++G+ G Sbjct: 240 RKVLLRVDKVPATPGKP-----ILEIENLSVVDEAGVARVKNIDLTVRAGEILGIAGVAG 294 Query: 303 SGRTSVAEAIAGLRAAKRGTISVDGAILP----PGDVPASLAHGIGCVPKDRHHEGLVLT 358 +G++ + E + G+R +G+I ++GA LP D A A + VP+DR EGL++ Sbjct: 295 NGQSELMEVLGGMREG-QGSIRLNGAPLPLSGAGSDARARRAAHVAHVPEDRQREGLIMD 353 Query: 359 QSVAENASMTI--ARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQK 416 EN + A + + A A + + + P SGGNQQK Sbjct: 354 FHAWENVAFGYHHAPEYQRGLLMNNAALRADTEAKMAKFDVRPPDPWLAAKNFSGGNQQK 413 Query: 417 VVMARALATNPNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCD 475 +V+AR + NP +L++ PT GVD+ + E + + +R++GKA+L+VS EL++ L D Sbjct: 414 IVVAREIERNPELLLIGQPTRGVDIGAIEFIHKQIVELRDQGKAILLVSVELEEILSLAD 473 Query: 476 RVLVMFRGRVAAEFPAGWQDHD----LIASVEG 504 RV VMF G + E PA D L+A V G Sbjct: 474 RVAVMFDGMIMGERPADQTDEKELGLLMAGVAG 506 Score = 73.2 bits (178), Expect = 2e-17 Identities = 69/254 (27%), Positives = 113/254 (44%), Gaps = 18/254 (7%) Query: 15 VEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFS 74 +E L V G A + ++ + V GE + G G G+S L+ +L G+R+ G +R + Sbjct: 260 IENLSVVDEAG-VARVKNIDLTVRAGEILGIAGVAGNGQSELMEVLGGMREGQ-GSIRLN 317 Query: 75 GAAAP-SIADRDAWRERVACVY------QHSTIIRDLSVAENLFINRQPL----RGGVID 123 GA P S A DA R A V Q +I D EN+ RG +++ Sbjct: 318 GAPLPLSGAGSDARARRAAHVAHVPEDRQREGLIMDFHAWENVAFGYHHAPEYQRGLLMN 377 Query: 124 WQAMRRDARALLDHWKIDVRED---ARAGDLSVEARQLVEIARALSYGARFIILDEPTAQ 180 A+R D A + K DVR A + S +Q + +AR + +++ +PT Sbjct: 378 NAALRADTEAKMA--KFDVRPPDPWLAAKNFSGGNQQKIVVAREIERNPELLLIGQPTRG 435 Query: 181 LDGDEIKRLFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPRE 240 +D I+ + ++I EL+ +G L +S L+E+ + V V+ D + P + Sbjct: 436 VDIGAIEFIHKQIVELRDQGKAILLVSVELEEILSLADRVAVMFDGMIMGERPADQTDEK 495 Query: 241 QLIEAMTGERGGLA 254 +L M G G A Sbjct: 496 ELGLLMAGVAGEAA 509 Lambda K H 0.318 0.134 0.377 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: 605 Number of extensions: 31 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 510 Length of database: 509 Length adjustment: 34 Effective length of query: 476 Effective length of database: 475 Effective search space: 226100 Effective search space used: 226100 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: 52 (24.6 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