Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate H281DRAFT_02712 H281DRAFT_02712 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= TCDB::Q9X051 (523 letters) >FitnessBrowser__Burk376:H281DRAFT_02712 Length = 505 Score = 449 bits (1156), Expect = e-131 Identities = 240/499 (48%), Positives = 336/499 (67%), Gaps = 7/499 (1%) Query: 13 LEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVY-PDYEGQIFL 71 LE RNI++TFPGV A++ V L+I GEV AL GENGAGKSTLMKIL G+Y PD G I + Sbjct: 10 LEMRNISRTFPGVKALDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAPDPGGTILV 69 Query: 72 EGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMFEQAS 131 EG+EV + A+ G+ +I QEL +V NL+ ENIFL+REP G+I+ +M+ +A Sbjct: 70 EGQEVALADSHHARTLGVNIIYQELAVVGNLTVGENIFLAREPRTRLGLIDRPRMYREAR 129 Query: 132 KLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLFNI 191 ++ + + ++IDP T+V +LS QQQM+ IAKAL +K IIMDEPT+++ ET L I Sbjct: 130 EVLATIDMDIDPATRVSELSVGQQQMIEIAKALCARSKAIIMDEPTASLSHHETSVLLGI 189 Query: 192 IRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVGRSID 251 ++ L+ +V+YISHRLEEIFE+ADRV V+RDGR VG PI + + LVRLMV R + Sbjct: 190 VKRLRERNIAVVYISHRLEEIFELADRVTVLRDGRTVGTAPIADMTRETLVRLMVARELS 249 Query: 252 QFFIKERATIT-DEIFRVEGIKLWSLDRKKLLVDDVSFYVRKGEVLGIYGLVGAGRTELL 310 + + + ++ + D + V + L + + + + D+SF + +GEVLGI GLVG+GRTE++ Sbjct: 250 ELYGEPQSHASRDPVLEVRALSLKPVRKAEPRIRDISFTLHRGEVLGIAGLVGSGRTEIM 309 Query: 311 EAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLHNITLP 370 E IFG G V I GK + I +P DA+++GIG V EDRK GLIL M+V N +L Sbjct: 310 EMIFGMR--ACTGSVKIEGKPVSIRNPHDAIRSGIGFVTEDRKAQGLILGMTVRENFSLT 367 Query: 371 SVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKVVLAKWLAI 430 + F + E+E R F+ L IKTP Q V NLSGGNQQK+V+AKW+A Sbjct: 368 HLER---YSPFQFVQHARERESCRRFVRMLGIKTPGVEQKVVNLSGGNQQKIVIAKWVAR 424 Query: 431 KPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDRILVMSEGR 490 PKVL++DEPTRGIDV AK+E++ LI+ +A G+GV+++SS+L E+LA+SDRIL + EGR Sbjct: 425 SPKVLIVDEPTRGIDVGAKAEVHALIARLAAEGIGVIVISSDLLEVLAVSDRILTVREGR 484 Query: 491 KTAEFLREEVTEEDLLKAA 509 + E R + ++E ++ A Sbjct: 485 ISGELSRAQASQEKVMALA 503 Score = 90.1 bits (222), Expect = 2e-22 Identities = 59/232 (25%), Positives = 111/232 (47%), Gaps = 8/232 (3%) Query: 283 VDDVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVK 342 +D V+ +R GEVL + G GAG++ L++ + G + G + + G+E+ + A Sbjct: 25 LDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAPDPGGTILVEGQEVALADSHHART 84 Query: 343 NGIGLVPEDRKTAGLILQMSVLHNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNI 402 G+ ++ ++ G ++V NI L + GLID R + +++ Sbjct: 85 LGVNIIYQELAVVG---NLTVGENIFLAREPRT----RLGLIDRPRMYREAREVLATIDM 137 Query: 403 KTPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVS 462 P V LS G QQ + +AK L + K +++DEPT + + S + ++ + Sbjct: 138 DI-DPATRVSELSVGQQQMIEIAKALCARSKAIIMDEPTASLSHHETSVLLGIVKRLRER 196 Query: 463 GMGVVMVSSELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSV 514 + VV +S L EI ++DR+ V+ +GR ++T E L++ + R + Sbjct: 197 NIAVVYISHRLEEIFELADRVTVLRDGRTVGTAPIADMTRETLVRLMVAREL 248 Lambda K H 0.317 0.137 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: 625 Number of extensions: 22 Number of successful extensions: 10 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: 523 Length of database: 505 Length adjustment: 35 Effective length of query: 488 Effective length of database: 470 Effective search space: 229360 Effective search space used: 229360 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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