Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate 3609044 Dshi_2433 ABC transporter related (RefSeq)
Query= uniprot:D8IZC7 (521 letters) >lcl|FitnessBrowser__Dino:3609044 Dshi_2433 ABC transporter related (RefSeq) Length = 510 Score = 388 bits (996), Expect = e-112 Identities = 212/492 (43%), Positives = 306/492 (62%), Gaps = 6/492 (1%) Query: 7 LQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLD 66 L + I K+F ALSD+ L++ PG++ AL+GENGAGKST++K+L+G++ PD G IL+D Sbjct: 21 LALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRILVD 80 Query: 67 GRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTDA 126 G+PV P A+ G+ I+QE + +SVA N+F+G R GLID A Sbjct: 81 GQPVPFSTPQAAADHGVTAIHQETVLFDELSVAENIFLGHAPRGAFGLIDWKKTTENARA 140 Query: 127 VLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVV 186 +L +GA L IA + V IARAL +R+VIMDEPTAALS +E E+L+ +V Sbjct: 141 LLTSIGAELDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEELYELV 200 Query: 187 RRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLSE 246 L+ +G AI++ISH+ E++ +AD TV RDG +G+ ++ +V+MMVGR +S+ Sbjct: 201 ESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKMMVGRDVSQ 260 Query: 247 FYQHQRIAPADAAQLPTVMQVRALAGG-KIRPASFDVRAGEVLGFAGLVGAGRTELARLL 305 + + D TV+ V+ A + SF +R GE+LGF GLVGAGR+E + L Sbjct: 261 IFPQRAPNVGD-----TVLTVQGYAHPTEFDDISFTLREGEILGFYGLVGAGRSEFMQSL 315 Query: 306 FGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVASR 365 FG S G + + G I P A+ GI YVPEDR QG L + + N T+ R Sbjct: 316 FGITRPSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQNVTLPSLGR 375 Query: 366 HTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLIL 425 +R G +R +AR +RL+++ A +T VG LSGGNQQKV++A+WL P+V+IL Sbjct: 376 ISRKGFLRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVVIAKWLATRPRVIIL 435 Query: 426 DEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELAG 485 DEPT+GVDI +K+ ++ + LA+QG+AV+++SSE+PEV+G+ DRV+VMREG I ELAG Sbjct: 436 DEPTKGVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMREGRIVAELAG 495 Query: 486 AAITQENIMRLA 497 + E ++R A Sbjct: 496 DDLQPETLVRHA 507 Score = 105 bits (263), Expect = 3e-27 Identities = 73/254 (28%), Positives = 127/254 (50%), Gaps = 6/254 (2%) Query: 255 PADAAQLPTVMQVRALAGGK-IRPASFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSG 313 P A L + G K + S + G+V G GAG++ + ++L G G Sbjct: 15 PVSQAALALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDG 74 Query: 314 GDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVR 373 G IL++G+PV P+AA G+ + ++ LF +++VA N + A R GL+ Sbjct: 75 GRILVDGQPVPFSTPQAAADHGVTAIHQETV---LFDELSVAENIFLGHAPRGA-FGLID 130 Query: 374 SRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVD 433 + ARA + + ++ P+ + L N+ V +AR L I +V+I+DEPT + Sbjct: 131 WKKTTENARALLTSIGAEL-DPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALS 189 Query: 434 IYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENI 493 E+Y+LV L +QG A++ IS + E+ I D V R+G + G+ A A +T+ ++ Sbjct: 190 HKEIEELYELVESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADL 249 Query: 494 MRLATDTNVPRTAP 507 +++ +V + P Sbjct: 250 VKMMVGRDVSQIFP 263 Score = 93.2 bits (230), Expect = 2e-23 Identities = 66/223 (29%), Positives = 108/223 (48%), Gaps = 5/223 (2%) Query: 24 DMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAAGI 83 D+ T+R GEI G GAG+S M+ L G+ P G + + G + P + GI Sbjct: 287 DISFTLREGEILGFYGLVGAGRSEFMQSLFGITRPSAGSVEIGGARAEISSPADAVDHGI 346 Query: 84 NLIYQELA---VAPNISVAANVFMGSELR-TRLGLIDHAAMRSRTDAVLRQLGAGFGASD 139 + ++ ++ + NV + S R +R G + A + +L + D Sbjct: 347 VYVPEDRGKQGAILDLPIFQNVTLPSLGRISRKGFLRLAEEFALAREYTERLDLRAASLD 406 Query: 140 L-AGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAIIY 198 G LS QQ+V IA+ L R R++I+DEPT + + + + L +GLA+I Sbjct: 407 THVGNLSGGNQQKVVIAKWLATRPRVIILDEPTKGVDIGSKAAVHDFMAELAAQGLAVIM 466 Query: 199 ISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVG 241 +S + EV ++DRV V+R+G V EL D++ E +V+ G Sbjct: 467 VSSEIPEVLGMSDRVIVMREGRIVAELAGDDLQPETLVRHAAG 509 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: 713 Number of extensions: 41 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 521 Length of database: 510 Length adjustment: 35 Effective length of query: 486 Effective length of database: 475 Effective search space: 230850 Effective search space used: 230850 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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