Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate BWI76_RS07240 BWI76_RS07240 D-ribose transporter ATP-binding protein
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__Koxy:BWI76_RS07240 Length = 494 Score = 436 bits (1121), Expect = e-127 Identities = 228/490 (46%), Positives = 328/490 (66%), Gaps = 4/490 (0%) Query: 5 LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64 L + I K FPGV+ALD VS V G VH LMGENGAGKSTL+K L G Y+PD G + + Sbjct: 6 LEAEGISKFFPGVKALDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKGAIRVK 65 Query: 65 GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRER 124 G V+F ++ +GI++IHQEL VP +TVAEN+ LG+ P G+V+ R+ R ++ Sbjct: 66 GEPVQFQDTMDALRSGISMIHQELNLVPHMTVAENIWLGREPMKYGFVDHRQLARQTQDL 125 Query: 125 LEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVR 184 L+ + + L + + +LSIA +QMVEI KA+ NA ++ +DEPTS+L+ E LF ++R Sbjct: 126 LDKLNIRLSADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEVAHLFTIIR 185 Query: 185 DLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREISD 244 DLR +A+IYISH+MDEI+ + D ++FRDG + S T E TR +++++MVGRE++ Sbjct: 186 DLRQQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQTTE-FTRQSLITQMVGRELTQ 244 Query: 245 IYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADH 304 ++ +GE + + +F VRRGEI+G GLVGAGRSE+M ++G + Sbjct: 245 LFPKFNNAIGEEVLTVRNLSRKGAFHDINFSVRRGEILGVAGLVGAGRSEVMESLFGMEK 304 Query: 305 KKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVG 364 GE+L+DG P+ + S AI G+ L EDRK+ G+ + +V EN++I Y+ Sbjct: 305 ADSGEVLIDGMPVNIDSPSTAIEKGMALLTEDRKKSGLFLVLSVLENMSIVKMPEYIGKT 364 Query: 365 MFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRW-LAEPDLKVVILDE 423 F+ K AE I+ L IKTP+ Q I LSGGNQQK +++RW LA+P K++ILDE Sbjct: 365 GFVQHLKMAEDCMEQIRRLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQP--KILILDE 422 Query: 424 PTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKD 483 PTRGIDVGAK EIY++I +LA RG A++M+SSELPE+LG+SDR++VM +GRI+G L ++D Sbjct: 423 PTRGIDVGAKAEIYHLISELANRGVAVIMVSSELPEILGMSDRVMVMHEGRITGILDKED 482 Query: 484 ATEQSVLSLA 493 A ++++LSLA Sbjct: 483 ADQETILSLA 492 Score = 86.3 bits (212), Expect = 2e-21 Identities = 68/250 (27%), Positives = 119/250 (47%), Gaps = 14/250 (5%) Query: 255 EVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELLLDG 314 E +K G S VR G + G GAG+S LM + G G + + G Sbjct: 7 EAEGISKFFPGVKALDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKGAIRVKG 66 Query: 315 KPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDRKKEAE 374 +P++ + +A+R GI + +E +V TV+ENI + R ++ G F+D ++ A Sbjct: 67 EPVQFQDTMDALRSGISMI---HQELNLVPHMTVAENIWLG--REPMKYG-FVDHRQLAR 120 Query: 375 TADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSR---WLAEPDLKVVILDEPTRGIDVG 431 + L I+ + R + LS +QQ +++ W A+ +VI+DEPT + Sbjct: 121 QTQDLLDKLNIRLSADRL-VGELSIASQQMVEIAKAVSWNAD----IVIMDEPTSALTES 175 Query: 432 AKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQSVLS 491 ++ +I L ++G AI+ IS ++ E+ ++D I V R G G + T QS+++ Sbjct: 176 EVAHLFTIIRDLRQQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQSLIT 235 Query: 492 LALPQSSTAL 501 + + T L Sbjct: 236 QMVGRELTQL 245 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: 642 Number of extensions: 26 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: 512 Length of database: 494 Length adjustment: 34 Effective length of query: 478 Effective length of database: 460 Effective search space: 219880 Effective search space used: 219880 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