Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate BWI76_RS07240 BWI76_RS07240 D-ribose transporter ATP-binding protein
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__Koxy:BWI76_RS07240 Length = 494 Score = 443 bits (1139), Expect = e-129 Identities = 237/487 (48%), Positives = 331/487 (67%), Gaps = 6/487 (1%) Query: 28 VCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVE 87 + K FPGV ALDN + G VHALMGENGAGKSTLMK L G+Y+ D G I + G+PV+ Sbjct: 11 ISKFFPGVKALDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKGAIRVKGEPVQ 70 Query: 88 ITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFAR 147 + A GI +IHQELNL+ H++ A+NI++GREP K F+D +L RQ + + Sbjct: 71 FQDTMDALRSGISMIHQELNLVPHMTVAENIWLGREPMKYG--FVDHRQLARQTQDLLDK 128 Query: 148 MRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQ 207 + + + VGEL++A QQMVEIAKA+S+++ ++IMDEPT+AL +E+A LF IIRDL+ Sbjct: 129 LNIRLSADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEVAHLFTIIRDLR 188 Query: 208 AQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRALDGEQRI 267 QG I+YISHKMDE+ I D +SV RDG ++ + E + ++I+ MVGR L Q Sbjct: 189 QQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQSLITQMVGRELT--QLF 246 Query: 268 PP-DTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLE 326 P + + + VL VR L+R A D++F++R+GEILG AGL+GAGR+EV ++FG + + Sbjct: 247 PKFNNAIGEEVLTVRNLSRKGAFHDINFSVRRGEILGVAGLVGAGRSEVMESLFGMEKAD 306 Query: 327 AGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFT-RVGF 385 +GE++I G I SP+ A+ G+ L+EDRK GL + + V N+++ M + + GF Sbjct: 307 SGEVLIDGMPVNIDSPSTAIEKGMALLTEDRKKSGLFLVLSVLENMSIVKMPEYIGKTGF 366 Query: 386 MDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRG 445 + + E +R+L IKTP+++Q LSGGNQQK++IA+WLL IL DEPTRG Sbjct: 367 VQHLKMAEDCMEQIRRLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQPKILILDEPTRG 426 Query: 446 IDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQE 505 IDVGAK+EIY L+ LA +G A++M+SSELPE+L MS RV+VM EGRITG L + DA QE Sbjct: 427 IDVGAKAEIYHLISELANRGVAVIMVSSELPEILGMSDRVMVMHEGRITGILDKEDADQE 486 Query: 506 KIMQLAT 512 I+ LA+ Sbjct: 487 TILSLAS 493 Score = 85.9 bits (211), Expect = 3e-21 Identities = 63/246 (25%), Positives = 116/246 (47%), Gaps = 10/246 (4%) Query: 274 NDVVLEVRGLNRG----RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGE 329 N LE G+++ +A+ +VS +R G + G GAG++ + + + G + G Sbjct: 2 NAFALEAEGISKFFPGVKALDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKGA 61 Query: 330 IIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQR 389 I + G + DA+ GI + ++ L M V NI L + GF+D R Sbjct: 62 IRVKGEPVQFQDTMDALRSGISMIHQE---LNLVPHMTVAENIWLGREPM--KYGFVDHR 116 Query: 390 AIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVG 449 + Q + +L I+ S ++ LS +QQ + IAK + + DI+ DEPT + Sbjct: 117 QLARQTQDLLDKLNIRL-SADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTES 175 Query: 450 AKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQ 509 + ++ ++ L +QGKAI+ IS ++ E+ ++ + V +G G + T++ ++ Sbjct: 176 EVAHLFTIIRDLRQQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQSLIT 235 Query: 510 LATQRE 515 RE Sbjct: 236 QMVGRE 241 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: 637 Number of extensions: 23 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: 494 Length adjustment: 34 Effective length of query: 486 Effective length of database: 460 Effective search space: 223560 Effective search space used: 223560 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