Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__Dyella79:N515DRAFT_2413 Length = 505 Score = 360 bits (923), Expect = e-104 Identities = 198/495 (40%), Positives = 302/495 (61%), Gaps = 11/495 (2%) Query: 22 VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81 V+ R + KRF LALD L AGEVHALMG+NGAGKSTL+K+L+GV + D G + L Sbjct: 12 VLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGSVEL 71 Query: 82 DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQA 141 DG+ + + P +AQ GIG ++QE+NL +LS A+N++ GR PR+ ID ++ A Sbjct: 72 DGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRRRRLRMIDWRQVRDGA 131 Query: 142 AAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201 ++ ++ L++D P+G VA +QMV IA+AL +RVLI+DEPT++L+ E+ ELFR Sbjct: 132 RSLLRQLHLELDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVRELFR 191 Query: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261 +I L+ +G+ I++++H +D++ ++DR++V+RDG + + + +++ MVGR L Sbjct: 192 VIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPPAALVNAMVGRDL 251 Query: 262 ------DGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEV 315 D E+ PPD ++ +GL + V +R+GE+LG GL+G+GRTE+ Sbjct: 252 PTVAGADAERAPPPDA---PPAIDAQGLGCRGKLHPVDLQVRRGEMLGLGGLLGSGRTEL 308 Query: 316 ARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALS 375 AR +FG D E GE+ I G + +K PADAV G+ E+RK G+ + V+ NI L+ Sbjct: 309 ARLLFGLDRAERGELRIGGERVELKHPADAVVRGLALCPEERKTDGIVAELSVRENIVLA 368 Query: 376 SMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCD 435 R G M + E A+ V+ L IK +E LLSGGNQQK+++A+WL+ + Sbjct: 369 LQARQGWRG-MSRARQDELARQLVQALGIKAADIETPVGLLSGGNQQKVMLARWLVTEPR 427 Query: 436 ILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITG 495 +L DEPTRGIDV AK E+ + A G A++ IS+E E+ R R+ VM E R G Sbjct: 428 LLILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWCDRIAVMRERRKAG 487 Query: 496 ELARADATQEKIMQL 510 EL +T+ +++ + Sbjct: 488 ELP-GGSTEARVLAM 501 Score = 95.5 bits (236), Expect = 4e-24 Identities = 67/252 (26%), Positives = 119/252 (47%), Gaps = 8/252 (3%) Query: 268 PPDTSRNDVVLEVRGLNRG----RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGAD 323 P + VVL+ RGL + A+ V LR GE+ G GAG++ + + + G + Sbjct: 3 PVSPAARPVVLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVE 62 Query: 324 PLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRV 383 + G + + G +P +A GIG + ++ L + V N+ R R+ Sbjct: 63 RPDRGSVELDGRVIAPSTPMEAQRDGIGTVYQE---VNLCPNLSVAENLYAGRYPRRRRL 119 Query: 384 GFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPT 443 +D R +R+ A+ +RQL ++ V+ +Q + IA+ L +L DEPT Sbjct: 120 RMIDWRQVRDGARSLLRQLHLEL-DVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPT 178 Query: 444 RGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADAT 503 +D G E+++++ L E+G AI+ ++ L +V +S R+ V+ +G GE A AD Sbjct: 179 SSLDEGEVRELFRVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLP 238 Query: 504 QEKIMQLATQRE 515 ++ R+ Sbjct: 239 PAALVNAMVGRD 250 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: 670 Number of extensions: 37 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: 505 Length adjustment: 35 Effective length of query: 485 Effective length of database: 470 Effective search space: 227950 Effective search space used: 227950 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