Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate HSERO_RS05250 HSERO_RS05250 D-ribose transporter ATP binding protein
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__HerbieS:HSERO_RS05250 Length = 520 Score = 436 bits (1122), Expect = e-127 Identities = 232/498 (46%), Positives = 339/498 (68%), Gaps = 8/498 (1%) Query: 14 ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73 ++ + + KRFPGV+A+DN FE+ E+ +L+GENGAGKSTL+KIL+GV + D+G+IL+ Sbjct: 22 VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81 Query: 74 NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133 +G+ VE P A GI +IHQELNL ++++ A+NIF+ E ++ + +DE+ + Sbjct: 82 DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREP----RKAMGLFIDEDEL 137 Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193 ++ + + P V LT A++QMVEI KAL + R++ MDEPT++L E Sbjct: 138 NRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIA 197 Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253 LF II L+++G+ +V++SH++DE+ +I+DR+ VMRDGK I + E +DTII MMV Sbjct: 198 ELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMV 257 Query: 254 GREVEFFPH-GIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETML 312 GR ++ +T ++ LEVR L +++VSF +RKGE+LGFAGL+GAGRTE Sbjct: 258 GRALDGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVAR 317 Query: 313 LVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSL 372 +FG + E+G+I ++G K IK+P DA+ GIG + EDRK GL + M V+ NI L S+ Sbjct: 318 AIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSM 377 Query: 373 KKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADI 432 + +R G +D+R E ++ YV++L+IKTPS+ Q LSGGNQQK+V+AKWL + DI Sbjct: 378 GRFTRVGF-MDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDI 436 Query: 433 LIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAV 492 L FDEPTRGIDVGAK+EI++++ LA QGKA++MISSELPE+L +S R++VM EG IT Sbjct: 437 LFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGE 496 Query: 493 LDNREKRVTQEEIMYYAS 510 L + TQE+IM A+ Sbjct: 497 LARAD--ATQEKIMQLAT 512 Score = 97.8 bits (242), Expect = 8e-25 Identities = 63/232 (27%), Positives = 121/232 (52%), Gaps = 8/232 (3%) Query: 29 AVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVEFHSPVDAFK 88 A+ +V F + + EI+ G GAG++ + + + G +AGEI+++G + SP DA Sbjct: 288 AIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVA 347 Query: 89 KGISVIHQE---LNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRSKELLDLIG 145 GI + ++ L M V NI L+ + T +D+ + ++ + + Sbjct: 348 HGIGYLSEDRKHFGLAVGMDVQANIALSSMG----RFTRVGFMDQRAIREAAQMYVRQLA 403 Query: 146 AKF-SPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEIIEMLKS 204 K S + R L+ +Q + I K L+++ I+F DEPT + V ++++++ L Sbjct: 404 IKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAE 463 Query: 205 RGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVGRE 256 +G ++V +S L EV+R+S R++VM +G+ GEL + + + I+++ RE Sbjct: 464 QGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLATQRE 515 Lambda K H 0.319 0.138 0.381 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: 656 Number of extensions: 26 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: 520 Length adjustment: 35 Effective length of query: 485 Effective length of database: 485 Effective search space: 235225 Effective search space used: 235225 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 (21.7 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