Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate BWI76_RS14860 BWI76_RS14860 ABC transporter
Query= uniprot:D8IZC7 (521 letters) >lcl|FitnessBrowser__Koxy:BWI76_RS14860 BWI76_RS14860 ABC transporter Length = 510 Score = 441 bits (1135), Expect = e-128 Identities = 237/500 (47%), Positives = 325/500 (65%), Gaps = 5/500 (1%) Query: 1 MTQTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQ 60 ++ PLL++ GI K +GATLAL+++ + GE+HALMGENGAGKSTLMK+LSG D Sbjct: 4 ISSPPLLRLEGISKRYGATLALNNVRFDLFAGEVHALMGENGAGKSTLMKILSGNEQRDS 63 Query: 61 GEILLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAM 120 G I +DG+ + +R P +R GI +I+QEL P+++VA N+F+G E + G++D M Sbjct: 64 GVIFIDGQAIDIRTPRDARKYGIAIIHQELNTVPDMTVAENLFLGQEPTSFAGILDRKRM 123 Query: 121 RSRTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETE 180 L ++ A G LSI QQ VEIARA+ ++++++DEPTAALS ET Sbjct: 124 HREAKEKLNRINADIDPQAPLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALSRAETL 183 Query: 181 QLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMV 240 QL+ ++ ++R +G+ ++YISHRM EV+ LA+RVTV RDG+++G + + IV+MMV Sbjct: 184 QLYRLIAQMRQDGVGMVYISHRMEEVWQLANRVTVFRDGTWIGTENLGNVSTTDIVRMMV 243 Query: 241 GRSLSEFYQHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTE 300 GR + + YQH+ P D +++VR LAG P SF+V AGEV+ +GLVG+GRTE Sbjct: 244 GRQIVDLYQHEPRTPGD-----VLLEVRDLAGSATGPVSFEVSAGEVVSMSGLVGSGRTE 298 Query: 301 LARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATM 360 +ARLLFGADPRS G + L GR P AA+ GI V EDRK QGLFL +V N + Sbjct: 299 VARLLFGADPRSQGSVRLAGRESQPSDPTAAIADGIGMVTEDRKTQGLFLGHSVEHNIDI 358 Query: 361 NVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAP 420 + G+V+ +++ ++RL ++ E PV LSGGNQQK LARWL Sbjct: 359 SSLDNFVAGGVVKRKTIRAAVLEQMRRLRLRENAVELPVSALSGGNQQKAALARWLLRDS 418 Query: 421 KVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMIT 480 ++LILDEPTRGVDI AK EIY+L+ RLA G A++VISS+LPE IGI DRVLVMR G I Sbjct: 419 RLLILDEPTRGVDIGAKREIYELIDRLARAGKAILVISSDLPEAIGISDRVLVMRGGRIV 478 Query: 481 GELAGAAITQENIMRLATDT 500 +L + T+E +M AT T Sbjct: 479 HQLPSCSATEEEVMLHATGT 498 Score = 84.3 bits (207), Expect = 9e-21 Identities = 67/253 (26%), Positives = 119/253 (47%), Gaps = 24/253 (9%) Query: 6 LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65 LL++R + S A + + GE+ ++ G G+G++ + ++L G QG + L Sbjct: 262 LLEVRDLAGS-----ATGPVSFEVSAGEVVSMSGLVGSGRTEVARLLFGADPRSQGSVRL 316 Query: 66 DGRPVALRDPGASRAAGINLIYQEL---------AVAPNISVAA--NVFMGSELRTRLGL 114 GR DP A+ A GI ++ ++ +V NI +++ N G G+ Sbjct: 317 AGRESQPSDPTAAIADGIGMVTEDRKTQGLFLGHSVEHNIDISSLDNFVAG-------GV 369 Query: 115 IDHAAMRSRTDAVLRQLGAGFGASDL-AGRLSIAEQQQVEIARALVHRSRIVIMDEPTAA 173 + +R+ +R+L A +L LS QQ+ +AR L+ SR++I+DEPT Sbjct: 370 VKRKTIRAAVLEQMRRLRLRENAVELPVSALSGGNQQKAALARWLLRDSRLLILDEPTRG 429 Query: 174 LSERETEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSE 233 + +++ ++ RL G AI+ IS + E ++DRV V+R G V +L E Sbjct: 430 VDIGAKREIYELIDRLARAGKAILVISSDLPEAIGISDRVLVMRGGRIVHQLPSCSATEE 489 Query: 234 RIVQMMVGRSLSE 246 ++ G S+ Sbjct: 490 EVMLHATGTFTSQ 502 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: 752 Number of extensions: 27 Number of successful extensions: 7 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: 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