Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate HSERO_RS22220 HSERO_RS22220 D-ribose transporter ATP-binding protein
Query= TCDB::Q9X051 (523 letters) >FitnessBrowser__HerbieS:HSERO_RS22220 Length = 505 Score = 408 bits (1048), Expect = e-118 Identities = 220/500 (44%), Positives = 325/500 (65%), Gaps = 10/500 (2%) Query: 12 LLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQIFL 71 +L I K F GV+A+ +V + GEV AL+GENGAGKSTL+KIL G++ EG I L Sbjct: 12 VLSLSGIGKRFQGVVALQDVGFTVRPGEVMALLGENGAGKSTLVKILTGIHQPDEGSIHL 71 Query: 72 EGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPV-NEFGVIEYQKMFEQA 130 G+EVRF + ++A GI + QE + LS AENI++ R+P+ I++++M ++A Sbjct: 72 GGREVRFASAQDAMRGGITAVHQETVMFEELSVAENIWIGRQPLCGTPRRIDWRRMEDEA 131 Query: 131 SKLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLFN 190 LF++L V++ + +V+DLS +Q+ V IA+ALS A+++IMDEPT+A+ E +L+ Sbjct: 132 RALFARLEVDLPVRARVKDLSVAQRHFVEIARALSQQAQVVIMDEPTAALSHHEIGELYR 191 Query: 191 IIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVGRSI 250 II L+ G +VI+ISH+ +EI+ +ADR V+RDGR + G + + +LV LMVGR + Sbjct: 192 IIGQLRRAGTAVIFISHKFDEIYAVADRYTVLRDGRFIASGELADITEQQLVALMVGREV 251 Query: 251 DQFFIKERATITDEIFRVEGIKLWSLDRKKLLVDDVSFYVRKGEVLGIYGLVGAGRTELL 310 Q F + + D+ V +K S + DDVSF VR GE+LG YGLVGAGR+E++ Sbjct: 252 GQVFSRAASNTEDQTAPVLEVKHLSHPSE---FDDVSFAVRPGEILGFYGLVGAGRSEVM 308 Query: 311 EAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLHNITLP 370 A+FG P +G V+I G+E+K+ SP A+ +G+ VPEDR+ G +L + + NITLP Sbjct: 309 HALFGLSP-EAQGAVWIDGREVKLCSPAQAIAHGLAYVPEDRQRQGALLSLPIFQNITLP 367 Query: 371 SVV-MKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKVVLAKWLA 429 + + +R+ + E +I R E+L +K +Q V LSGGNQQKVVLAKWLA Sbjct: 368 VLPGIGFFLRRH----RRREIDIARRLCEQLELKASHFHQHVAQLSGGNQQKVVLAKWLA 423 Query: 430 IKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDRILVMSEG 489 +P+VL+LDEPT+GID+ +K+ +++ I E+ G+ V++VSSELPE++ MSDRI+VM +G Sbjct: 424 TQPRVLILDEPTKGIDIGSKAAVHRFIGELVAQGLAVILVSSELPEVMGMSDRIVVMHQG 483 Query: 490 RKTAEFLREEVTEEDLLKAA 509 R F R E + E L AA Sbjct: 484 RVQQVFSRAEASAEALAAAA 503 Score = 105 bits (263), Expect = 3e-27 Identities = 67/232 (28%), Positives = 129/232 (55%), Gaps = 8/232 (3%) Query: 283 VDDVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVK 342 + DV F VR GEV+ + G GAG++ L++ + G H EG + +GG+E++ S +DA++ Sbjct: 28 LQDVGFTVRPGEVMALLGENGAGKSTLVKILTGIHQP-DEGSIHLGGREVRFASAQDAMR 86 Query: 343 NGIGLVPEDRKTAGLILQMSVLHNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNI 402 GI V ++ + ++SV NI + + R+ ID + ++ R+ +L + Sbjct: 87 GGITAVHQETV---MFEELSVAENIWIGRQPLCGTPRR---IDWRRMEDEARALFARLEV 140 Query: 403 KTPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVS 462 P + V++LS + V +A+ L+ + +V+++DEPT + + E+Y++I ++ + Sbjct: 141 DLPVRAR-VKDLSVAQRHFVEIARALSQQAQVVIMDEPTAALSHHEIGELYRIIGQLRRA 199 Query: 463 GMGVVMVSSELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSV 514 G V+ +S + EI A++DR V+ +GR A ++TE+ L+ + R V Sbjct: 200 GTAVIFISHKFDEIYAVADRYTVLRDGRFIASGELADITEQQLVALMVGREV 251 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: 561 Number of extensions: 24 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