Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate 8502321 DvMF_3029 ABC transporter related (RefSeq)
Query= CharProtDB::CH_003578 (501 letters) >FitnessBrowser__Miya:8502321 Length = 537 Score = 268 bits (685), Expect = 4e-76 Identities = 158/484 (32%), Positives = 268/484 (55%), Gaps = 10/484 (2%) Query: 4 LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63 +++L GI K+F V+A L++ PG + AL+GENGAGKST+M +L G +DAGT++ Sbjct: 29 VVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIVV 88 Query: 64 LGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGR--EFVNRFGKIDWKTMYAE 121 G T F P+ + AGIG+++Q L+ +T+AEN+ LG+ + + R + M E Sbjct: 89 DGVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLLGQSPDMLLRPAR-----MRDE 143 Query: 122 ADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLF 181 L + L VG LS+G++Q VEI K+L +S+V+I+DEPT LT ET+ LF Sbjct: 144 VAALAERYGLAVDPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLF 203 Query: 182 RVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDS-LIEMMVGR 240 + + QG+ +V+ISH+++E+ + D++ + R G+ + E A + + L MVGR Sbjct: 204 EAMWRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVGR 263 Query: 241 KLEDQYPHLDKAPGDIRLKVDNLCGPGVNDVSFTLRKGEILGVSGLMGAGRTELMKVLYG 300 + Q P D L V++L G G++DVS +R+GEI+ ++G+ G G+ EL++ + G Sbjct: 264 DVVLQVDAKRLTPVDTVLSVEHLSGAGLSDVSLQVRRGEIVAIAGVAGNGQKELVEAICG 323 Query: 301 ALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFS 360 +G V + G G+ YI EDR+ + + +N LT F+ Sbjct: 324 LARPEAGEVRILGRPWREFFAGPPGRRGLAYIPEDRQGLATCRHLDLVDNFLLTTRNQFA 383 Query: 361 RAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILD 420 + G L + AV + +NV+ + LSGGN QK+ I R +P+V++ + Sbjct: 384 K-GVFLDRTEATNAVKRVVWEYNVQPGDITAPARALSGGNLQKLVIGREFFRKPEVIVAE 442 Query: 421 EPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTRE 480 PT+G+D+ A +E++ + + ++ ++LV+ ++ E L ++DRI VM+ G F ++ Sbjct: 443 NPTQGLDISATEEVWGRLLEARSTS-GVLLVTGDLNEALELADRIAVMYRGRFIDVFDKD 501 Query: 481 QATQ 484 + Sbjct: 502 DTAK 505 Score = 85.9 bits (211), Expect = 3e-21 Identities = 68/255 (26%), Positives = 124/255 (48%), Gaps = 19/255 (7%) Query: 240 RKLEDQYPHLDKAPGDIRLKVDNLCGP-----GVNDVSFTLRKGEILGVSGLMGAGRTEL 294 R++ + + HL P +RL D +C +D++ +R G I + G GAG++ L Sbjct: 17 RRVRETHAHL---PPVVRL--DGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTL 71 Query: 295 MKVLYGALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLT 354 M +L G L + +G + +DG V SP+D L GI + + LV M+V EN+ L Sbjct: 72 MSILAGKLRQDAGTIVVDGVPTVFASPRDALRAGIGMVYQHFM---LVDSMTVAENVLLG 128 Query: 355 ALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRP 414 L+ A + V+ + + + +G LS G +Q+V I + L Sbjct: 129 -----QSPDMLLRPARMRDEVAALAERYGLAVDPAAR-VGGLSMGERQRVEILKLLYRDS 182 Query: 415 KVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLS 474 +VLILDEPT + ++++ + + G +++ +S ++ EVL ++D I ++ G + Sbjct: 183 RVLILDEPTAVLTPRETDQLFEAMWRMADQGKALVFISHKLQEVLTVADEIAILRRGEVV 242 Query: 475 GEFTREQATQEVLMA 489 EF+ + ++A Sbjct: 243 DEFSEADVPNQTVLA 257 Lambda K H 0.318 0.137 0.380 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: 646 Number of extensions: 28 Number of successful extensions: 10 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: 501 Length of database: 537 Length adjustment: 35 Effective length of query: 466 Effective length of database: 502 Effective search space: 233932 Effective search space used: 233932 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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