Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate 3607108 Dshi_0530 ABC transporter related (RefSeq)
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__Dino:3607108 Length = 498 Score = 326 bits (836), Expect = 1e-93 Identities = 182/495 (36%), Positives = 288/495 (58%), Gaps = 6/495 (1%) Query: 15 SSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQR 74 SS I LR + KR+ GV ALD+ F + GE L GENG+GKSTL+KI+SGV Sbjct: 2 SSDHDTAFIDLRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPA 61 Query: 75 DSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDE 134 +G + + G+ PR + A G+ +I Q+ +L +LS A+NI + LF Sbjct: 62 TAGTVQIAGQEHVTLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKFR 121 Query: 135 DELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNA 194 + A A R+ + +D V L VA++Q+V I +AL+ ++++IMDEPT AL Sbjct: 122 -AVRDIARAALDRIGVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEK 180 Query: 195 EIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIIS 254 E+ L IIR L+ +GV ++++SHK+ E+ +++++V V+R+GK +A P E ++ Sbjct: 181 EVRRLQGIIRMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTY 240 Query: 255 MMVGRALDGEQRIPPD--TSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGR 312 M GR + +PP + +++V+GL + + D+SF LR GE+LG GL+G GR Sbjct: 241 HMTGRDVP---EVPPSDVAAGAQTLMQVQGLGKAGSFSDISFDLRTGEVLGITGLLGCGR 297 Query: 313 TEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANI 372 T VA+A+FG +AG I++ G + P A IGY+ EDR GL + + N+ Sbjct: 298 TSVAKALFGLVTPDAGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNV 357 Query: 373 ALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLR 432 A+ + T GF+D + + A ++R+L +K P VE + LSGGNQQ++ +A+WL R Sbjct: 358 AVGRLDAHTSGGFLDMTGLAKEASDWLRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSR 417 Query: 433 DCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGR 492 +L + P+ G+DVG+K++I+ ++ LA +G +++IS +LPE+L HRVLVM EGR Sbjct: 418 APRVLILNGPSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGR 477 Query: 493 ITGELARADATQEKI 507 I L T++ + Sbjct: 478 IIDALEGTALTEDDL 492 Score = 87.4 bits (215), Expect = 1e-21 Identities = 58/228 (25%), Positives = 113/228 (49%), Gaps = 5/228 (2%) Query: 288 AIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVA 347 A+ V FT++ GE + AG G+G++ + + I G +P AG + I G + V +P + A Sbjct: 24 ALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIAGQEHVTLNPRISAA 83 Query: 348 HGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTP 407 G+ + +D F L + V NIA ++ TR RA+R+ A+ + ++ ++ Sbjct: 84 AGVMVIFQD---FSLFPNLSVAENIAFTTQ-LSTRQRLFKFRAVRDIARAALDRIGVQI- 138 Query: 408 SVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKA 467 ++ + L +Q + I + L ++ DEPT + + ++ L E+G A Sbjct: 139 DLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQGIIRMLKEEGVA 198 Query: 468 IVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLATQRE 515 ++ +S +L EVL +S +V+V+ G+ E ++ + + T R+ Sbjct: 199 VIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTYHMTGRD 246 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: 562 Number of extensions: 34 Number of successful extensions: 8 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: 498 Length adjustment: 34 Effective length of query: 486 Effective length of database: 464 Effective search space: 225504 Effective search space used: 225504 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