Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__Phaeo:GFF2274 Length = 503 Score = 357 bits (915), Expect = e-103 Identities = 218/508 (42%), Positives = 308/508 (60%), Gaps = 17/508 (3%) Query: 10 KAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGG 69 ++P+L L I KTFPGVRAL V LT GEVHALMGENGAGKSTLMK+L G + D G Sbjct: 4 QSPVLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEG- 62 Query: 70 ECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR-GLVARGDMV 128 + + Q V + GP A+ G+ I+QELSLA LSVAENIYLG ++R GLV ++ Sbjct: 63 QIIVAEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGLVDWAELE 122 Query: 129 RACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDR 188 L +L F+ V LSIA +Q+VEIARA+ +A+ ++ DEPT L+ E Sbjct: 123 AKTNAILEKLKVGFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVV 182 Query: 189 LFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVG 248 LF +I L+ +G+ I YISHRM EI ++ DR++VLRDG + GT++ A ++ + +MM+G Sbjct: 183 LFEVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMMIG 242 Query: 249 RDLSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELAR 308 R L + H + EV L VR ++ G + +F++R GEV+G GLVGAGRTE+A Sbjct: 243 RKLDLSRNEAHHEL--GEVALEVRGLSCGSLFEDVNFEVRRGEVVGFYGLVGAGRTEIAE 300 Query: 309 LVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHE 368 +FG T G + + G V + + P AI+ GI+ + EDRK QGL L + + Sbjct: 301 TLFGLRNPTSGSIFL-----DGAEVAITS--PHDAIERGISLVPEDRKGQGLVLGMNCRD 353 Query: 369 NINLIVAARDALGLGRLNRTAARRRTTEAI-DTLGIRVAHAQVNVGALSGGNQQKVMLSR 427 N+ L D L G A + D L IR + VG LSGGNQQK+++ + Sbjct: 354 NMTL--PQVDDLKAGPFVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGK 411 Query: 428 LLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVM 487 L ++P VLI+DEPTRG+D+G+K+EI+ L+ LA G A+++ISSE+PEV+ + DR++ M Sbjct: 412 WLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAM 471 Query: 488 REGTLAGEVRPAGSAAETQERIIALATG 515 G + +R S T+E +IA +G Sbjct: 472 YSGRI---MRTFTSEEVTEENLIAAISG 496 Score = 64.3 bits (155), Expect = 1e-14 Identities = 53/219 (24%), Positives = 98/219 (44%), Gaps = 9/219 (4%) Query: 39 GEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQSARDLGVAVIYQEL 98 GEV G GAG++ + + L G G +DG V I P A + G++++ ++ Sbjct: 282 GEVVGFYGLVGAGRTEIAETLFGLRNPT-SGSIFLDGAEVAITSPHDAIERGISLVPEDR 340 Query: 99 S---LAPNLSVAENIYLGRA--LQRRGLVARGDMVRACAPTLARLGADFSPAAN--VASL 151 L ++ +N+ L + L+ VA G + +L +P V +L Sbjct: 341 KGQGLVLGMNCRDNMTLPQVDDLKAGPFVADGAEIAIFDQYRDKLDIR-TPGWKQLVGNL 399 Query: 152 SIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRGEGMAILYISHRMA 211 S +Q + I + + +L++DEPT + + L+R L +G A++ IS M Sbjct: 400 SGGNQQKIVIGKWLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMP 459 Query: 212 EIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRD 250 E+ +ADR+ + G + T +++ L+ + G D Sbjct: 460 EVLHVADRIVAMYSGRIMRTFTSEEVTEENLIAAISGLD 498 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: 589 Number of extensions: 28 Number of successful extensions: 8 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: 540 Length of database: 503 Length adjustment: 35 Effective length of query: 505 Effective length of database: 468 Effective search space: 236340 Effective search space used: 236340 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