Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate RR42_RS30800 RR42_RS30800 sugar ABC transporter ATP-binding protein
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__Cup4G11:RR42_RS30800 Length = 530 Score = 272 bits (695), Expect = 3e-77 Identities = 170/494 (34%), Positives = 272/494 (55%), Gaps = 24/494 (4%) Query: 21 PVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDIL 80 P++ L + KRF ++A D+ EL GEV AL+GENGAGKSTL+ IL G Y D+G + Sbjct: 4 PILRLAGITKRFGPLVANDDISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTVE 63 Query: 81 LDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQ 140 +DG+P+ +PR A GIG++HQ L ++LS NI +G +P L D + Sbjct: 64 VDGQPLPPGQPRAALTAGIGMVHQHFTLADNLSVLDNIMLGTQPLWQWRL--DGHAARGK 121 Query: 141 AAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELF 200 A+ R L + P VGEL+V +Q VEI KAL +RVLI+DEPTA L E LF Sbjct: 122 VLALAERFGLAVRPQARVGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAETLF 181 Query: 201 RIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRA 260 + L A+G+ +++ISHK+DE+ +++DR++V+R GK +A +T+ + +MVGR Sbjct: 182 STLAQLIAEGLSVIFISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAELAELMVGRV 241 Query: 261 LDGEQRIPPDTSRND---------VVLE---VRGLNRGRAIRDVSFTLRKGEILGFAGLM 308 + +R+ ++ + + LE R N +R+VS +R GEI+G AG+ Sbjct: 242 VAMPERVARRSAEDGANGNAAPPVLALEHVGARAANGRALLREVSLQVRAGEIVGIAGVS 301 Query: 309 GAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDV 368 G G+ +A G G I + GK + P + G+ + EDR G+ + V Sbjct: 302 GNGQAALAELASGMLEASEGRITL-AGKPMSAKPRAWIGAGVARVPEDRHAIGVVGDLAV 360 Query: 369 QANIALSSMG--RFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVI 426 N + RF+R G + + A + A+ V + ++T ++ AR +SGGN QK+++ Sbjct: 361 WENAVSEQLSEPRFSRWGVIRRAAAQRFARDLVARFDVRTAGIDVPARTMSGGNMQKLIL 420 Query: 427 AKWLLRDCD-----ILFFDEPTRGIDVGAKSEI-YKLLDALAEQGKAIVMISSELPEVLR 480 + L + ++ +PT G+D+GA + + +LLDA A +G A+++IS +L E+ Sbjct: 421 GRALSVRGEGSAPRLVVASQPTWGLDIGAVAYVRARLLDA-AREGAAVLLISEDLDELHA 479 Query: 481 MSHRVLVMCEGRIT 494 ++ R+ VM G +T Sbjct: 480 LADRIAVMHAGHLT 493 Score = 94.0 bits (232), Expect = 1e-23 Identities = 68/230 (29%), Positives = 112/230 (48%), Gaps = 10/230 (4%) Query: 291 DVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGI 350 D+S L++GE+L G GAG++ + +FG +AG + + G P A+ GI Sbjct: 23 DISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTVEVDGQPLPPGQPRAALTAGI 82 Query: 351 GYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVE 410 G + + HF LA + V NI L + + +D A R + + +V Sbjct: 83 GMVHQ---HFTLADNLSVLDNIMLGTQPLWQ--WRLDGHAARGKVLALAERFGL---AVR 134 Query: 411 QQARL--LSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAI 468 QAR+ LS G +Q++ I K L R +L DEPT + ++ L L +G ++ Sbjct: 135 PQARVGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAETLFSTLAQLIAEGLSV 194 Query: 469 VMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLATQRESAV 518 + IS +L EVLR+S R+ V+ G++ A A T+ ++ +L R A+ Sbjct: 195 IFISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAELAELMVGRVVAM 244 Score = 75.1 bits (183), Expect = 6e-18 Identities = 67/262 (25%), Positives = 122/262 (46%), Gaps = 23/262 (8%) Query: 14 ASSSSSVPVIALRNVCKRFP-GVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVY 72 A+ +++ PV+AL +V R G L ++ AGE+ + G +G G++ L ++ SG+ Sbjct: 257 ANGNAAPPVLALEHVGARAANGRALLREVSLQVRAGEIVGIAGVSGNGQAALAELASGML 316 Query: 73 QRDSGDILLDGKPVEITEPRQAQALGIGIIHQE---LNLMNHLSAAQNIFIGR--EPRKA 127 + G I L GKP+ +PR G+ + ++ + ++ L+ +N + EPR Sbjct: 317 EASEGRITLAGKPMS-AKPRAWIGAGVARVPEDRHAIGVVGDLAVWENAVSEQLSEPR-- 373 Query: 128 MGLFIDEDELNRQAAAIFAR---MRLDMDPS---TPVGELTVARQQMVEIAKALSFDS-- 179 F + R AA FAR R D+ + P ++ Q + + +ALS Sbjct: 374 ---FSRWGVIRRAAAQRFARDLVARFDVRTAGIDVPARTMSGGNMQKLILGRALSVRGEG 430 Query: 180 ---RVLIMDEPTAALNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDG 236 R+++ +PT L+ +A + + D +G ++ IS +DEL +ADR++VM G Sbjct: 431 SAPRLVVASQPTWGLDIGAVAYVRARLLDAAREGAAVLLISEDLDELHALADRIAVMHAG 490 Query: 237 KYIATVPMQETSMDTIISMMVG 258 P ++ + M G Sbjct: 491 HLTEARPTAAWTLGELGLAMAG 512 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: 648 Number of extensions: 33 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 520 Length of database: 530 Length adjustment: 35 Effective length of query: 485 Effective length of database: 495 Effective search space: 240075 Effective search space used: 240075 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