Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate BPHYT_RS27185 BPHYT_RS27185 D-ribose transporter ATP-binding protein
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__BFirm:BPHYT_RS27185 Length = 516 Score = 401 bits (1030), Expect = e-116 Identities = 217/494 (43%), Positives = 319/494 (64%), Gaps = 4/494 (0%) Query: 5 LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64 L+ + K FPGV ALDG+ D+ G+VH + GENGAGKSTL+KI+ G+Y+ D G V Sbjct: 24 LQLKGVSKRFPGVVALDGIDLDLCAGEVHAVCGENGAGKSTLMKIISGQYRADEGVVRYR 83 Query: 65 GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRER 124 G V+F+S + + AAGIA+IHQEL VP L+VAEN+ L + P +V+ R + Sbjct: 84 GAPVQFSSTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRGPFVDYRTLNSNAQRC 143 Query: 125 LEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVR 184 L+ +G+ + P+ + LS+AQ+QMVEI KAL +ARV+ +DEPTSSL+ ET LF+++R Sbjct: 144 LQRIGLNVSPSTLVGALSLAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQLFRIIR 203 Query: 185 DLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREISD 244 +LRA A++YISHR+DE+ E+ D T+ RDGR IA+ T + IV+ MVGR + D Sbjct: 204 ELRAGGVAILYISHRLDEMAEIVDRVTVLRDGRHIAT-SDFASTTVNEIVARMVGRPLDD 262 Query: 245 IY-NYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGAD 303 Y + P ++ + ++ + P SFE+R+GEI+GF GL+GAGR+E ++GA+ Sbjct: 263 AYPPRQSTPSNQILLRVRDLQRTGVFGPLSFELRKGEILGFAGLMGAGRTETARAIFGAE 322 Query: 304 HKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRV 363 G + L +P+ + S EAIRHGI EDRK++G+ VS NI ++ R Sbjct: 323 RPDSGSITLGDEPVTIGSPREAIRHGIAYLSEDRKKDGLALSMPVSANITLANVRAISSR 382 Query: 364 GMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDE 423 G FL +E A+R+++ L I+TP+ +Q R LSGGNQQK ++S+WL +++ DE Sbjct: 383 G-FLRFSEETAIAERYVRELGIRTPTVKQIARNLSGGNQQKIVISKWLYRGS-RILFFDE 440 Query: 424 PTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKD 483 PTRGIDVGAK+ IY ++ +LA G +V+ISSELPE+LG++DRI V +GRI+ L + Sbjct: 441 PTRGIDVGAKYAIYGLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGRITAVLETRQ 500 Query: 484 ATEQSVLSLALPQS 497 +++ +L A +S Sbjct: 501 TSQEEILHHASGRS 514 Score = 75.5 bits (184), Expect = 4e-18 Identities = 59/225 (26%), Positives = 108/225 (48%), Gaps = 8/225 (3%) Query: 250 ARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGE 309 +R + +++ +K G ++ GE+ G GAG+S LM ++ G G Sbjct: 20 SREILQLKGVSKRFPGVVALDGIDLDLCAGEVHAVCGENGAGKSTLMKIISGQYRADEGV 79 Query: 310 LLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDR 369 + G P++ S +A GI + +E +V +V+ENI ++ + G F+D Sbjct: 80 VRYRGAPVQFSSTSDAQAAGIAII---HQELNLVPHLSVAENIYLA---REPKRGPFVDY 133 Query: 370 KKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGID 429 + A R ++ + + S + LS QQ +++ L+ D +V+I+DEPT + Sbjct: 134 RTLNSNAQRCLQRIGLNV-SPSTLVGALSLAQQQMVEIAKALS-LDARVLIMDEPTSSLT 191 Query: 430 VGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGR 474 +++ +I +L G AI+ IS L E+ + DR+ V+R GR Sbjct: 192 ESETVQLFRIIRELRAGGVAILYISHRLDEMAEIVDRVTVLRDGR 236 Lambda K H 0.320 0.136 0.385 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: 641 Number of extensions: 26 Number of successful extensions: 9 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: 512 Length of database: 516 Length adjustment: 35 Effective length of query: 477 Effective length of database: 481 Effective search space: 229437 Effective search space used: 229437 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