Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate BPHYT_RS28215 BPHYT_RS28215 D-ribose transporter ATP binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__BFirm:BPHYT_RS28215 Length = 509 Score = 386 bits (991), Expect = e-111 Identities = 233/532 (43%), Positives = 323/532 (60%), Gaps = 25/532 (4%) Query: 4 MSDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAY 63 M ++ P L LR+ K+F VRAL +L + GEVHAL+GENGAGKST++KIL+G + Sbjct: 1 MQQPTSAVPRLELRHASKSFGRVRALSDGDLALWPGEVHALLGENGAGKSTVVKILAGVH 60 Query: 64 TADPGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRA-LQRRGLV 122 D G E +DG+ + P ARD G+AVIYQE +L +LS+AENI++GR + R G + Sbjct: 61 QPDTG-ELVVDGEARRFATPAEARDAGLAVIYQEPTLFFDLSIAENIFMGRQPVDRIGRI 119 Query: 123 ARGDMVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLS 182 M R LA LG D V LSIA +Q++EIA+A+ A +L+MDEPT LS Sbjct: 120 QYDAMRREVDGLLASLGVDLRADQLVRGLSIADQQVIEIAKALSLNANVLIMDEPTAALS 179 Query: 183 THETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAAL 242 E +RLF ++R+LR +AIL+I+HR+ E+ L RVT++RDG V L+ A+ Sbjct: 180 LPEVERLFTIVRKLRERDVAILFITHRLDEVFALTQRVTIMRDGAKVFDGLTTDLNTEAI 239 Query: 243 VKMMVGRDLSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAG 302 V MVGRDL FY K + EV LSVR + K SFD+RAGE++ LAGLVGAG Sbjct: 240 VAKMVGRDLETFYPKA--ERPPGEVRLSVRGLTRVGVFKDISFDVRAGEIVALAGLVGAG 297 Query: 303 RTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFL 362 R+E+AR +FG D GE+ IA L AG P A+ AG+A + EDR+ QGL L Sbjct: 298 RSEVARAIFGIDPLDSGEIWIAGKR-------LTAGRPAAAVRAGLALVPEDRRQQGLAL 350 Query: 363 DQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQK 422 + S+ N ++ V R + G ++ + + + L ++ VG LSGGNQQK Sbjct: 351 ELSIARNASMTVLGR-LVKHGLISARSETQLANQWGTRLRLKAGDPNAPVGTLSGGNQQK 409 Query: 423 VMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCD 482 V+L + L P+VLI+DEPTRG+D+GAK+E+Y + L + G+A+LMISSELPEV+G+ D Sbjct: 410 VVLGKWLATGPKVLIIDEPTRGIDVGAKAEVYSALAELVRDGMAVLMISSELPEVLGMAD 469 Query: 483 RVLVMREGTLAGEVRPAGSAAETQERIIALATGAAAAAPAWVDVPLPGAGNA 534 RVLVM EG ++ ++ A + +ERI+ A G P+P G+A Sbjct: 470 RVLVMHEGRISADIARADA---DEERIMGAALGQ----------PMPPLGHA 508 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: 723 Number of extensions: 46 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