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) >FitnessBrowser__Koxy:BWI76_RS14860 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:
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