Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate BPHYT_RS16060 BPHYT_RS16060 ribonucleotide-diphosphate reductase subunit alpha
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__BFirm:BPHYT_RS16060 Length = 506 Score = 370 bits (951), Expect = e-107 Identities = 212/508 (41%), Positives = 301/508 (59%), Gaps = 11/508 (2%) Query: 13 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 72 +L L NI K+FPGV+AL+ + L GE+HAL+GENGAGKSTLMKIL G Y D G Sbjct: 4 ILKLDNITKSFPGVKALQGIHLEIERGEIHALLGENGAGKSTLMKILCGIYQPDEG-TIT 62 Query: 73 IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR-GLVARGDMVRAC 131 I+G+ A GV +++QE SL P L+ EN++LGR L+ GL+ RG M RA Sbjct: 63 IEGEARHFSNYHDAVAAGVGIVFQEFSLIPYLNAVENMFLGRELKNGLGLLERGKMRRAA 122 Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191 A RLG + + LS+AQ+Q VEI +A+ EARIL++DEPT L+ E + LFA Sbjct: 123 AAIFQRLGVTIDLSVPIRELSVAQQQFVEIGKALSLEARILILDEPTATLTPAEAEHLFA 182 Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDL 251 ++R+L+ +G+A+++ISH + EI E+ DR+TVLRDG +VG + A + LV+MMVGR + Sbjct: 183 IMRELKQQGVAMIFISHHLEEIFEVCDRITVLRDGQYVGMTEVAQSNVGHLVEMMVGRRI 242 Query: 252 SGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVF 311 + + +++L V + + SF LR GE+LG AGLVG+GRTE A V Sbjct: 243 ENSFPPKPPLRADAKIVLDVEKLQLLKDSPVLSFTLREGEILGFAGLVGSGRTETALAVI 302 Query: 312 GADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENIN 371 GAD E+RI A P A+ AG+ L E RK +GL D S+ +NI+ Sbjct: 303 GADPAYVKEIRINGTAAK-------LSDPADALRAGVGILPESRKTEGLITDFSIKQNIS 355 Query: 372 LIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEI 431 + + +++ + R T + + +G++ V LSGGNQQKV+++R L Sbjct: 356 INNLGKYRSLRFFIDQRSEARATADIMKRVGVKAPTMHTEVATLSGGNQQKVVIARWLNH 415 Query: 432 QPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGT 491 +LI DEPTRG+D+GAK+EIY L+ L G +I+MISSELPE+VG+CDRV V R+G Sbjct: 416 HTNILIFDEPTRGIDVGAKAEIYLLMRELTARGYSIIMISSELPEIVGMCDRVAVFRQGR 475 Query: 492 LAGEVRPAGSAAETQERIIALATGAAAA 519 + E G A ++ + G+ A Sbjct: 476 I--EAMLEGDAIDSNAVMTYATAGSRGA 501 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: 605 Number of extensions: 30 Number of successful extensions: 8 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: 506 Length adjustment: 35 Effective length of query: 505 Effective length of database: 471 Effective search space: 237855 Effective search space used: 237855 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