Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate BWI76_RS27035 BWI76_RS27035 xylose ABC transporter ATP-binding protein
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__Koxy:BWI76_RS27035 Length = 513 Score = 389 bits (999), Expect = e-112 Identities = 223/509 (43%), Positives = 323/509 (63%), Gaps = 28/509 (5%) Query: 6 LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGV--HAPDQGEI 63 LL+M+ I K+FGA A+ ++ L + GE+ +L GENG+GKSTLMKVL G+ H +GEI Sbjct: 4 LLEMKNITKTFGAVKAIDNVSLRLNAGEVVSLCGENGSGKSTLMKVLCGIYPHGSYEGEI 63 Query: 64 LLDG---RPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAM 120 + G +P +RD + GI +I+QELA+ +++V N+F+G+E+ +R GL+D+ M Sbjct: 64 IFSGETLQPGHIRD---TERKGIAIIHQELALVKHLTVLENIFLGAEI-SRHGLLDYETM 119 Query: 121 RSRTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETE 180 R + +L Q+ G L + +QQ VEIA+AL + R++I+DEPTA+L+E+ET Sbjct: 120 TLRCEKLLAQVNLAISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETA 179 Query: 181 QLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMV 240 L N++R L++ G+A IYISH++ EV A++D + V+RDG +G D + + I+ MMV Sbjct: 180 ILLNIIRDLQNHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRNADGMSEDDIITMMV 239 Query: 241 GRSLSEFYQHQRIAPADAAQLPTVMQVRALAGG--------KIRPASFDVRAGEVLGFAG 292 GR L+ Y + + D +++V L ++ SF +R GE+LG AG Sbjct: 240 GRELTALYPSEAHSCGDE-----ILRVENLTAWHPVNRHIKRVNDVSFSLRRGEILGIAG 294 Query: 293 LVGAGRTELARLLFGADP-RSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQ 351 LVGAGRTE + LFG P R G I ++G+PV I + A+ GIA VPEDRK G+ Sbjct: 295 LVGAGRTEAVQCLFGVWPGRWQGKIFIDGQPVTIHTCQQAIAQGIAMVPEDRKKDGIVPV 354 Query: 352 MAVAANATMNVASRHTRLGLVRSRSLGG---VARAAIQRLNVKVAHPETPVGKLSGGNQQ 408 MAV N T+ ++ T G + S G + +IQRL +K + PE +G+LSGGNQQ Sbjct: 355 MAVGKNITLAALNQFT--GPLSSLDDAGEQLCIQQSIQRLKIKTSSPELAIGRLSGGNQQ 412 Query: 409 KVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGIC 468 K +LAR L + P++LILDEPTRG+DI AK EIY+L+++L QG+AV+VISSELPEV+G+ Sbjct: 413 KAILARCLLLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLS 472 Query: 469 DRVLVMREGMITGELAGAAITQENIMRLA 497 DRVLVM EG + L +TQE +M A Sbjct: 473 DRVLVMHEGKLKANLINQGLTQEQVMEAA 501 Score = 84.0 bits (206), Expect = 1e-20 Identities = 65/237 (27%), Positives = 116/237 (48%), Gaps = 11/237 (4%) Query: 279 SFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSG--GDILLEGRPVHIDQPRAAMRAGI 336 S + AGEV+ G G+G++ L ++L G P G+I+ G + R R GI Sbjct: 24 SLRLNAGEVVSLCGENGSGKSTLMKVLCGIYPHGSYEGEIIFSGETLQPGHIRDTERKGI 83 Query: 337 AYVPEDRKGQGLFLQMAVAANATMNVA-SRHTRLGLVRSRSLGGVARAAIQRLNVKVAHP 395 A + ++ L + V N + SRH GL+ ++ + ++N+ ++ P Sbjct: 84 AIIHQEL---ALVKHLTVLENIFLGAEISRH---GLLDYETMTLRCEKLLAQVNLAIS-P 136 Query: 396 ETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVV 455 +T VG L G QQ V +A+ L ++LILDEPT + + + ++ L + G+A + Sbjct: 137 DTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETAILLNIIRDLQNHGIACI 196 Query: 456 VISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTAPA-SHS 511 IS +L EV I D + V+R+G G +++++I+ + + P+ +HS Sbjct: 197 YISHKLNEVKAISDTICVIRDGQHIGTRNADGMSEDDIITMMVGRELTALYPSEAHS 253 Lambda K H 0.320 0.135 0.378 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: 619 Number of extensions: 25 Number of successful extensions: 11 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: 521 Length of database: 513 Length adjustment: 35 Effective length of query: 486 Effective length of database: 478 Effective search space: 232308 Effective search space used: 232308 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