Align RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate N515DRAFT_3232 N515DRAFT_3232 xylose ABC transporter ATP-binding protein
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__Dyella79:N515DRAFT_3232 Length = 513 Score = 368 bits (944), Expect = e-106 Identities = 214/502 (42%), Positives = 315/502 (62%), Gaps = 16/502 (3%) Query: 20 ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPN--EGEI 77 + EMRGI++ F GVKALD + + L G L GENGAGKSTL+K+L+G+Y +GEI Sbjct: 7 LFEMRGIAKSFGGVKALDGIDLRLRAGECLGLCGENGAGKSTLMKVLSGVYPHGSWDGEI 66 Query: 78 LVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSR 137 L G+P S + + AG+ IHQE +L +L+VAENIFLGH +D+ M ++ Sbjct: 67 LWQGQPLRARSVRDSERAGIVIIHQELMLVPQLSVAENIFLGHEITRPGGRMDYDAMYAK 126 Query: 138 SKALLTALESNIDPTIRLKDLSIAQRH--LVAIARALSIEARIVIMDEPTAALSRKEIDD 195 + ALL L + D + L + H L IA+AL+ +A+++I+DEPT++L+ E + Sbjct: 127 ADALLQELGLH-DVNVALPAMHYGGGHQQLFEIAKALAKQAKLLILDEPTSSLTSSETEV 185 Query: 196 LFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMV 255 L IV LK +G A ++ISHK DE+ + D V R R + D ++ +MV Sbjct: 186 LLGIVEDLKRRGVACIYISHKLDEVERVCDTVCVI-RDGRHIATQPMHELDVDTLITLMV 244 Query: 256 GRDVENVFPKIDVAIGGPVLEIRNYS-------HRTEFRDISFTLRKGEILGVYGLIGAG 308 GR +EN++P+I+ AIG + E R+ + R D+SF LR+GEILG+ GL+GAG Sbjct: 245 GRKLENLYPRIEHAIGEVIFEARHATCLDPVNPQRKRVDDVSFQLRRGEILGIAGLVGAG 304 Query: 309 RSELSQSLFGI-TKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQ 367 R+EL ++FG T S ++ LEG+ + I SP DAIRAG+ VPE+R RHG+ + + Sbjct: 305 RTELVSAIFGAYTGKSSVELFLEGRPLKIRSPADAIRAGLGMVPEDRKRHGIVPLLGVGD 364 Query: 368 NMTLPSLARTSRRGFLRAANEF-ALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKW 426 N+TL +L + G + E A+ + AER ++ A+ ++P+ LSGGNQQK V+ K Sbjct: 365 NITLATLDHYAHAGHIDRQRELVAIEAQIAERR-VKTASPALPIARLSGGNQQKAVLAKM 423 Query: 427 LATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMK 486 L PKV+ILDEPT+G+D+G+KA ++ I ELAA+G++I++VSSE+PE++GM+DRVLVM Sbjct: 424 LLARPKVLILDEPTRGVDVGAKAEIYRLIFELAAQGVAIVLVSSEMPEVLGMADRVLVMG 483 Query: 487 EGLSAGIFERAELSPEALVRAA 508 EG G F L+ E ++ AA Sbjct: 484 EGRLRGDFPNQGLTQEQVLAAA 505 Score = 87.0 bits (214), Expect = 1e-21 Identities = 67/224 (29%), Positives = 108/224 (48%), Gaps = 6/224 (2%) Query: 289 ISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLS--GKMVLEGQEITIHSPQDAIRAG 346 I LR GE LG+ G GAG+S L + L G+ S G+++ +GQ + S +D+ RAG Sbjct: 26 IDLRLRAGECLGLCGENGAGKSTLMKVLSGVYPHGSWDGEILWQGQPLRARSVRDSERAG 85 Query: 347 IVYVPEERGRHGLALPMPIFQNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAAL 406 IV + +E L + + +N+ L T G + +A A + L L + Sbjct: 86 IVIIHQELM---LVPQLSVAENIFLGHEI-TRPGGRMDYDAMYAKADALLQELGLHDVNV 141 Query: 407 SVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSII 466 ++P GG+QQ I K LA K++ILDEPT + + G + +L G++ I Sbjct: 142 ALPAMHYGGGHQQLFEIAKALAKQAKLLILDEPTSSLTSSETEVLLGIVEDLKRRGVACI 201 Query: 467 MVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAATG 510 +S +L E+ + D V V+++G EL + L+ G Sbjct: 202 YISHKLDEVERVCDTVCVIRDGRHIATQPMHELDVDTLITLMVG 245 Lambda K H 0.320 0.137 0.382 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: 637 Number of extensions: 32 Number of successful extensions: 12 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: 513 Length adjustment: 35 Effective length of query: 477 Effective length of database: 478 Effective search space: 228006 Effective search space used: 228006 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