Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__Cola:Echvi_1282 Length = 502 Score = 421 bits (1082), Expect = e-122 Identities = 233/502 (46%), Positives = 328/502 (65%), Gaps = 10/502 (1%) Query: 22 VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81 ++ ++N+ K F GV ALD+ EL AG V A++GENGAGKSTLMKILSGVY G I Sbjct: 1 MLTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYY 60 Query: 82 DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQA 141 +G PV+ R AQ GI IIHQELNL+ +LS +NIF+GREP MGL +D +++++A Sbjct: 61 NGDPVKFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPETPMGL-LDVAKMHKEA 119 Query: 142 AAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201 A + R++L++DP TPV +L V +QQ+VEIAKALS +S+V+IMDEPT+A+++ E+ LF Sbjct: 120 AQLLHRLKLNVDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFG 179 Query: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261 IIR L+A+G I YISHK+DEL IADR V+RDGK I + M+ + + +I MVGR + Sbjct: 180 IIRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMVGREI 239 Query: 262 DGEQRIPPDTSRNDVVLEVRGLNRGRA-------IRDVSFTLRKGEILGFAGLMGAGRTE 314 E R ++ VL V+ L ++D++F L KGE+LG GLMGAGRTE Sbjct: 240 VIE-RSCSGRQFDETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGAGRTE 298 Query: 315 VARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIAL 374 + A+FG P + EI + G + P +A+ G+ + EDRK GL + MD+ N +L Sbjct: 299 LMEALFGVLPHQGAEITLAGKVHEFQKPQEAMDAGLALVPEDRKQDGLVLCMDLCTNSSL 358 Query: 375 SSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDC 434 + + G +D + + AQ Y+ +L IK S Q LSGGNQQK+V+AKWL Sbjct: 359 TVVDSILSGGLLDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVVLAKWLATRP 418 Query: 435 DILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRIT 494 +L DEPTRGID+ AK+EIYKL+ LA +G ++++SSELPE+L +S RVLVM EGR+T Sbjct: 419 KVLMLDEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRVLVMAEGRLT 478 Query: 495 GEL-ARADATQEKIMQLATQRE 515 + A ++++I+Q A ++ Sbjct: 479 ANIPIDAQTSEDEILQAAIPKK 500 Score = 83.2 bits (204), Expect = 2e-20 Identities = 60/232 (25%), Positives = 107/232 (46%), Gaps = 5/232 (2%) Query: 287 RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAV 346 +A+ DVS L+ G + G GAG++ + + + G P G I +G ++ DA Sbjct: 15 KALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYYNGDPVKFQNTRDAQ 74 Query: 347 AHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKT 406 GI + ++ L + ++ NI L T +G +D + + A + +L + Sbjct: 75 EKGINIIHQE---LNLIPYLSIRENIFLGREPE-TPMGLLDVAKMHKEAAQLLHRLKLNV 130 Query: 407 PSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGK 466 E L G QQ + IAK L + ++ DEPT I ++ ++ AL +GK Sbjct: 131 DP-ETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFGIIRALRAEGK 189 Query: 467 AIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLATQRESAV 518 AI IS +L E+ ++ R +V+ +G++ T+E ++Q RE + Sbjct: 190 AIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMVGREIVI 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: 652 Number of extensions: 38 Number of successful extensions: 7 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: 502 Length adjustment: 35 Effective length of query: 485 Effective length of database: 467 Effective search space: 226495 Effective search space used: 226495 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