Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate AO356_23205 AO356_23205 D-ribose transporter ATP-binding protein
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_23205 Length = 517 Score = 431 bits (1107), Expect = e-125 Identities = 226/494 (45%), Positives = 328/494 (66%), Gaps = 6/494 (1%) Query: 6 LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65 LL++ + K F +ALSD+ L +RPG + ALMGENGAGKSTLMK+++G++ PD GE+ L Sbjct: 26 LLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 85 Query: 66 DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTD 125 G+PV P A+ AGI +I+QEL + P++S+A N+++G E L ++DH M T Sbjct: 86 RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMVDHGEMHRCTA 145 Query: 126 AVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNV 185 +L +L + G LSIAE+Q VEIA+A+ + S I+IMDEPT+A++E E LF++ Sbjct: 146 RLLERLRIKLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVAHLFSI 205 Query: 186 VRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLS 245 + L+ +G IIYI+H+M EV+A+AD V V RDG+++G D +D + ++ MMVGR LS Sbjct: 206 IADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 265 Query: 246 EFYQHQRIAPADAAQLPTVMQVRALA-GGKIRPASFDVRAGEVLGFAGLVGAGRTELARL 304 + + + +L V+ VR L+ G + SFD+ AGE+LG AGL+G+GRT +A Sbjct: 266 QLFP---VREQPIGEL--VLSVRDLSLDGIFKGVSFDLHAGEILGIAGLMGSGRTNVAEA 320 Query: 305 LFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVAS 364 +FG P +GG+I L+G+PV I P A+ G A + EDRK GLF ++V N M V Sbjct: 321 IFGVTPSTGGEIRLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLP 380 Query: 365 RHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLI 424 + G ++ ++L + ++L VK E + LSGGNQQK LLARWL P++LI Sbjct: 381 HYVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILI 440 Query: 425 LDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELA 484 LDEPTRG+D+ AK+EIY+L+ LAS+G+AV++ISSELPEV+G+ DRV+VM EG + G L Sbjct: 441 LDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLD 500 Query: 485 GAAITQENIMRLAT 498 + TQE +M+LA+ Sbjct: 501 RSEATQERVMQLAS 514 Score = 102 bits (254), Expect = 3e-26 Identities = 67/220 (30%), Positives = 115/220 (52%), Gaps = 5/220 (2%) Query: 29 IRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAAGINLIYQ 88 + GEI + G G+G++ + + + GV GEI LDG+PV + DP + G L+ + Sbjct: 298 LHAGEILGIAGLMGSGRTNVAEAIFGVTPSTGGEIRLDGQPVRISDPHMAIEKGFALLTE 357 Query: 89 ELAVA---PNISVAANVFMGSELR-TRLGLIDHAAMRSRTDAVLRQLGAGFGASDLA-GR 143 + ++ P +SV N+ M G I A+R+ + + ++L + + Sbjct: 358 DRKLSGLFPCLSVLENMEMAVLPHYVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDT 417 Query: 144 LSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAIIYISHRM 203 LS QQ+ +AR L+ RI+I+DEPT + +++ ++ L EG+A+I IS + Sbjct: 418 LSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSEL 477 Query: 204 AEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRS 243 EV ++DRV V+ +G +G L R E ER++Q+ G S Sbjct: 478 PEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGLS 517 Lambda K H 0.320 0.135 0.378 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: 662 Number of extensions: 23 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 521 Length of database: 517 Length adjustment: 35 Effective length of query: 486 Effective length of database: 482 Effective search space: 234252 Effective search space used: 234252 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