Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate GFF385 PGA1_c03960 ribose import ATP-binding protein RbsA
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__Phaeo:GFF385 Length = 509 Score = 278 bits (712), Expect = 3e-79 Identities = 188/519 (36%), Positives = 280/519 (53%), Gaps = 22/519 (4%) Query: 11 APLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGE 70 AP + L+ I K F V+A + + + G +H ++GENGAGKSTLM IL G Y AD G E Sbjct: 3 APAIELKGISKAFGPVQANKDISIRVAPGTIHGIIGENGAGKSTLMSILYGFYKADKG-E 61 Query: 71 CHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRA 130 I G+R +I Q+A G+ +++Q L N +V ENI LG G + + + +A Sbjct: 62 VWIHGKRTEIPDSQAAISAGIGMVFQHFKLVENFTVLENIILGA---EDGGLLKPSLSKA 118 Query: 131 CAPTLARLGADFS----PAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHET 186 +L L A++ P A + + + +Q VEI +A++ +A IL++DEPT L+ E Sbjct: 119 -RKSLKDLAAEYELNVDPDARIDEIGVGMQQRVEILKALYRQADILILDEPTGVLTPAEA 177 Query: 187 DRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMM 246 D+LF ++ +LR EG I+ I+H++ EI E D V+V+R G T+ A S L ++M Sbjct: 178 DQLFRILDRLRAEGKTIILITHKLREIMEYTDTVSVMRRGEMTATVKTAETSPEHLAELM 237 Query: 247 VGRDLSGFYTK---THGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGR 303 VGR + K T G+ + LSV D A RVK +RAGE+LG+AG+ G G+ Sbjct: 238 VGRKVLLRVDKVPATPGKPILEIENLSVVDEAGVARVKNIDLTVRAGEILGIAGVAGNGQ 297 Query: 304 TELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGP--RQAIDAGIAYLTEDRKLQGLF 361 +EL V G +G +R+ +G + L G R A +A++ EDR+ +GL Sbjct: 298 SELME-VLGGMREGQGSIRL-----NGAPLPLSGAGSDARARRAAHVAHVPEDRQREGLI 351 Query: 362 LDQSVHENINLIVAARDALGLGRLNRTAARRRTTEA-IDTLGIRVAHAQVNVGALSGGNQ 420 +D EN+ G L AA R TEA + +R + SGGNQ Sbjct: 352 MDFHAWENVAFGYHHAPEYQRGLLMNNAALRADTEAKMAKFDVRPPDPWLAAKNFSGGNQ 411 Query: 421 QKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGL 480 QK++++R +E P +L++ +PTRGVDIGA I++ I L G AIL++S EL E++ L Sbjct: 412 QKIVVAREIERNPELLLIGQPTRGVDIGAIEFIHKQIVELRDQGKAILLVSVELEEILSL 471 Query: 481 CDRVLVMREGTLAGEVRPAGSAAETQERIIALATGAAAA 519 DRV VM +G + GE RPA E + ++ AA Sbjct: 472 ADRVAVMFDGMIMGE-RPADQTDEKELGLLMAGVAGEAA 509 Lambda K H 0.320 0.136 0.382 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: 625 Number of extensions: 34 Number of successful extensions: 9 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: 540 Length of database: 509 Length adjustment: 35 Effective length of query: 505 Effective length of database: 474 Effective search space: 239370 Effective search space used: 239370 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 (21.8 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