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 Pf6N2E2_1456 D-xylose transport ATP-binding protein XylG
Query= TCDB::Q7BSH4 (512 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1456 Length = 518 Score = 351 bits (900), Expect = e-101 Identities = 204/500 (40%), Positives = 306/500 (61%), Gaps = 12/500 (2%) Query: 20 ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPN--EGEI 77 +L+M GI + F GVKAL+ + I + PG L GENGAGKSTL+K+L+ +Y +GEI Sbjct: 5 LLQMNGIVKTFGGVKALNGIDIKVRPGECVGLCGENGAGKSTLMKVLSAVYPYGTWDGEI 64 Query: 78 LVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSR 137 L DG+P S AG+ IHQE L +L+VAENIF+GH +++ M R Sbjct: 65 LWDGQPLKAQSISETEAAGIVIIHQELTLVPDLSVAENIFMGHELTLPGGRMNYPAMIHR 124 Query: 138 SKALLTALE-SNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDL 196 ++AL+ L+ +++ ++ + + LV IA+AL+ +AR++I+DEP++AL+R EI+ L Sbjct: 125 AEALMRELKVPDMNVSLPVSQYGGGYQQLVEIAKALNKQARLLILDEPSSALTRSEIEVL 184 Query: 197 FRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVG 256 I+R LK +G A ++ISHK DE+ + D V R + +I+ MVG Sbjct: 185 LDIIRDLKAKGVACVYISHKLDEVAAVCDTISVI-RDGKHIATTAMADMSIPKIITQMVG 243 Query: 257 RDVENVFPKIDVAIGGPVLEIRNYS-------HRTEFRDISFTLRKGEILGVYGLIGAGR 309 R++ N++P +G + E R+++ R DISF L++GEILG+ GL+GAGR Sbjct: 244 REMSNLYPTEPHDVGEVIFEARHFTCYDVDNPRRKRVDDISFVLKRGEILGIAGLVGAGR 303 Query: 310 SELSQSLFGITKP-LSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQN 368 +EL +LFG G++ L GQ+I +P +IRAG+ VPE+R R G+ + + QN Sbjct: 304 TELVSALFGAYPGRYEGEVWLNGQQIDTRTPLKSIRAGLCMVPEDRKRQGIIPDLGVGQN 363 Query: 369 MTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLA 428 +TL L S+ + A E K R+ L+ A+ +P+ +LSGGNQQK V+ K L Sbjct: 364 ITLAVLDNYSKLTRIDAEAELGSIDKEISRMHLKTASPFLPITSLSGGNQQKAVLAKMLL 423 Query: 429 TAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEG 488 T P+V+ILDEPT+G+D+G+K ++ + LAAEG+SIIMVSSEL E++G+SDRVLV+ +G Sbjct: 424 TKPRVLILDEPTRGVDVGAKYEIYKLMGALAAEGVSIIMVSSELAEVLGVSDRVLVIGDG 483 Query: 489 LSAGIFERAELSPEALVRAA 508 G F EL+ E ++ AA Sbjct: 484 QLRGDFINHELTQEQVLAAA 503 Score = 72.4 bits (176), Expect = 4e-17 Identities = 62/227 (27%), Positives = 108/227 (47%), Gaps = 12/227 (5%) Query: 289 ISFTLRKGEILGVYGLIGAGRSELSQSLFGITK--PLSGKMVLEGQEITIHSPQDAIRAG 346 I +R GE +G+ G GAG+S L + L + G+++ +GQ + S + AG Sbjct: 24 IDIKVRPGECVGLCGENGAGKSTLMKVLSAVYPYGTWDGEILWDGQPLKAQSISETEAAG 83 Query: 347 IVYVPEERGR-HGLALPMPIFQN--MTLPSLARTSRRGFLRAANEFALARKYAERLDLRA 403 IV + +E L++ IF +TLP R + + A AL R+ L + Sbjct: 84 IVIIHQELTLVPDLSVAENIFMGHELTLPG-GRMNYPAMIHRAE--ALMRE----LKVPD 136 Query: 404 AALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGL 463 +S+PV GG QQ V I K L +++ILDEP+ + + I +L A+G+ Sbjct: 137 MNVSLPVSQYGGGYQQLVEIAKALNKQARLLILDEPSSALTRSEIEVLLDIIRDLKAKGV 196 Query: 464 SIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAATG 510 + + +S +L E+ + D + V+++G A++S ++ G Sbjct: 197 ACVYISHKLDEVAAVCDTISVIRDGKHIATTAMADMSIPKIITQMVG 243 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: 605 Number of extensions: 29 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: 512 Length of database: 518 Length adjustment: 35 Effective length of query: 477 Effective length of database: 483 Effective search space: 230391 Effective search space used: 230391 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