Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate 8502321 DvMF_3029 ABC transporter related (RefSeq)
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__Miya:8502321 Length = 537 Score = 274 bits (701), Expect = 5e-78 Identities = 165/496 (33%), Positives = 272/496 (54%), Gaps = 18/496 (3%) Query: 21 PVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDIL 80 PV+ L +CK F V A + ++ G + AL+GENGAGKSTLM IL+G ++D+G I+ Sbjct: 28 PVVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIV 87 Query: 81 LDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQ 140 +DG P PR A GIG+++Q L++ ++ A+N+ +G+ P + + + + Sbjct: 88 VDGVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLLGQSP----DMLLRPARMRDE 143 Query: 141 AAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELF 200 AA+ R L +DP+ VG L++ +Q VEI K L DSRVLI+DEPTA L E +LF Sbjct: 144 VAALAERYGLAVDPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLF 203 Query: 201 RIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYI-----ATVPMQETSMDTIISM 255 + + QG +V+ISHK+ E+ +AD ++++R G+ + A VP Q + ++ Sbjct: 204 EAMWRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVGR 263 Query: 256 MVGRALDGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEV 315 V +D ++ P DT VL V L+ G + DVS +R+GEI+ AG+ G G+ E+ Sbjct: 264 DVVLQVDAKRLTPVDT-----VLSVEHLS-GAGLSDVSLQVRRGEIVAIAGVAGNGQKEL 317 Query: 316 ARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALS 375 AI G EAGE+ I G G+ Y+ EDR+ +D+ N L+ Sbjct: 318 VEAICGLARPEAGEVRILGRPWREFFAGPPGRRGLAYIPEDRQGLATCRHLDLVDNFLLT 377 Query: 376 SMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCD 435 + +F + F+D+ A + V + ++ + AR LSGGN QK+VI + R + Sbjct: 378 TRNQFAKGVFLDRTEATNAVKRVVWEYNVQPGDITAPARALSGGNLQKLVIGREFFRKPE 437 Query: 436 ILFFDEPTRGIDVGAKSEIY-KLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRIT 494 ++ + PT+G+D+ A E++ +LL+A + G +++++ +L E L ++ R+ VM GR Sbjct: 438 VIVAENPTQGLDISATEEVWGRLLEARSTSG--VLLVTGDLNEALELADRIAVMYRGRFI 495 Query: 495 GELARADATQEKIMQL 510 + D + + + L Sbjct: 496 DVFDKDDTAKVQAIGL 511 Score = 65.1 bits (157), Expect = 6e-15 Identities = 46/224 (20%), Positives = 101/224 (45%), Gaps = 5/224 (2%) Query: 38 LDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQAL 97 L + ++ GE+ A+ G G G+ L++ + G+ + ++G++ + G+P Sbjct: 291 LSDVSLQVRRGEIVAIAGVAGNGQKELVEAICGLARPEAGEVRILGRPWREFFAGPPGRR 350 Query: 98 GIGII---HQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFARMRLDM-D 153 G+ I Q L HL N + + A G+F+D E + + D Sbjct: 351 GLAYIPEDRQGLATCRHLDLVDNFLLTTRNQFAKGVFLDRTEATNAVKRVVWEYNVQPGD 410 Query: 154 PSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGVGI 213 + P L+ Q + I + V++ + PT L+ + E++ + + ++ G+ Sbjct: 411 ITAPARALSGGNLQKLVIGREFFRKPEVIVAENPTQGLDISATEEVWGRLLEARSTS-GV 469 Query: 214 VYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMV 257 + ++ ++E ++ADR++VM G++I +T+ I +M+ Sbjct: 470 LLVTGDLNEALELADRIAVMYRGRFIDVFDKDDTAKVQAIGLMM 513 Lambda K H 0.320 0.135 0.372 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: 627 Number of extensions: 32 Number of successful extensions: 9 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: 520 Length of database: 537 Length adjustment: 35 Effective length of query: 485 Effective length of database: 502 Effective search space: 243470 Effective search space used: 243470 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