Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__WCS417:GFF2332 Length = 517 Score = 427 bits (1097), Expect = e-124 Identities = 223/494 (45%), Positives = 326/494 (65%), Gaps = 6/494 (1%) Query: 6 LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65 LL++ I K F +AL+D+ L +RPG + ALMGENGAGKSTLMK+++G++ PD GEI L Sbjct: 23 LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82 Query: 66 DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTD 125 G+P+ P A++ AGI +I+QEL + P++S+A N+++G E L +++H M T Sbjct: 83 RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTA 142 Query: 126 AVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNV 185 +L +L + G LSIAE+Q VEIA+A+ + S I+IMDEPT+A++E+E LF++ Sbjct: 143 ELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSI 202 Query: 186 VRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLS 245 + L+ +G I+YI+H+M EV+A+AD V V RDG ++G D ++S+ ++ MMVGR LS Sbjct: 203 IADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELS 262 Query: 246 EFYQHQRIAPADAAQLPTVMQVRALA-GGKIRPASFDVRAGEVLGFAGLVGAGRTELARL 304 + + + D ++ VR L G + SFD+ AGE+LG AGL+G+GRT +A Sbjct: 263 QLFPLRETPIGD-----LLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAET 317 Query: 305 LFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVAS 364 +FG P S G I L+G+ V I P A+ G A + EDRK GLF ++V N M V Sbjct: 318 IFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLP 377 Query: 365 RHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLI 424 +T G ++ ++L + ++L VK E + LSGGNQQK LLARWL P++LI Sbjct: 378 HYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLI 437 Query: 425 LDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELA 484 LDEPTRG+D+ AK+EIY+L+ LAS+G+AV++ISSELPEV+G+ DRV+VM EG + G L Sbjct: 438 LDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLD 497 Query: 485 GAAITQENIMRLAT 498 + TQE +M+LA+ Sbjct: 498 RSEATQEKVMQLAS 511 Score = 100 bits (249), Expect = 1e-25 Identities = 63/223 (28%), Positives = 116/223 (52%), Gaps = 5/223 (2%) Query: 24 DMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAAGI 83 D+ + GEI + G G+G++ + + + G+ G+I LDG+ V + DP + G Sbjct: 290 DVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGF 349 Query: 84 NLIYQELAVA---PNISVAANVFMGSELR-TRLGLIDHAAMRSRTDAVLRQLGAGFGASD 139 L+ ++ ++ P +SV N+ M T G I A+R+ + + ++L + + Sbjct: 350 ALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKTPSLE 409 Query: 140 LA-GRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAIIY 198 LS QQ+ +AR L+ R++I+DEPT + +++ ++ L EG+A+I Sbjct: 410 QCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIM 469 Query: 199 ISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVG 241 IS + EV ++DRV V+ +G +G L R E E+++Q+ G Sbjct: 470 ISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASG 512 Score = 97.8 bits (242), Expect = 8e-25 Identities = 68/241 (28%), Positives = 119/241 (49%), Gaps = 10/241 (4%) Query: 267 VRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHID 326 V ALA ++R VR G VL G GAG++ L +++ G G+I L G+P+ + Sbjct: 36 VVALADVQLR-----VRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKPIVFE 90 Query: 327 QPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQ 386 P AA +AGIA + ++ L M++A N + ++ L +V R + + Sbjct: 91 TPLAAQKAGIAMIHQELN---LMPHMSIAENIWIGREQLNS-LHMVNHREMHRCTAELLA 146 Query: 387 RLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHR 446 RL + + PE VG LS +Q V +A+ + +LI+DEPT + + ++ ++ Sbjct: 147 RLRINL-DPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIAD 205 Query: 447 LASQGVAVVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTA 506 L SQG +V I+ ++ EV I D V V R+G G ++ ++++ + + + Sbjct: 206 LKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELSQLF 265 Query: 507 P 507 P Sbjct: 266 P 266 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: 615 Number of extensions: 21 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 3 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 Apr 09 2024. 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