Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate BPHYT_RS28215 BPHYT_RS28215 D-ribose transporter ATP binding protein
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__BFirm:BPHYT_RS28215 Length = 509 Score = 425 bits (1092), Expect = e-123 Identities = 229/492 (46%), Positives = 328/492 (66%), Gaps = 3/492 (0%) Query: 3 PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62 P LE++ K F V AL + +PGEVHA++GENGAGKST++KI+AGV+QPD GE++ Sbjct: 9 PRLELRHASKSFGRVRALSDGDLALWPGEVHALLGENGAGKSTVVKILAGVHQPDTGELV 68 Query: 63 YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIF-IDYKKMYREA 121 +G R+ P+EA +AG+ ++QE ++ +LS+AENIFMG + I I Y M RE Sbjct: 69 VDGEARRFATPAEARDAGLAVIYQEPTLFFDLSIAENIFMGRQPVDRIGRIQYDAMRREV 128 Query: 122 EKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLF 181 + + G+++ ++ + SIA QQ++EIA+A+ A VLI+DEPT++L+ E E+LF Sbjct: 129 DGLLAS-LGVDLRADQLVRGLSIADQQVIEIAKALSLNANVLIMDEPTAALSLPEVERLF 187 Query: 182 EVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRK 241 +V+ L+E+ VAI+FI+HRL+E+F + +V+++RDG + +L E IV MVGR Sbjct: 188 TIVRKLRERDVAILFITHRLDEVFALTQRVTIMRDGAKVFDGLTTDLNTEAIVAKMVGRD 247 Query: 242 LEKFYIKEAHEPGEVVLEVKNLSGER-FENVSFSLRRGEILGFAGLVGAGRTELMETIFG 300 LE FY K PGEV L V+ L+ F+++SF +R GEI+ AGLVGAGR+E+ IFG Sbjct: 248 LETFYPKAERPPGEVRLSVRGLTRVGVFKDISFDVRAGEIVALAGLVGAGRSEVARAIFG 307 Query: 301 FRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIK 360 P GEI+I GKR+ P A+ G+ LVPEDR++ GL L +SI N S+ L R+ Sbjct: 308 IDPLDSGEIWIAGKRLTAGRPAAAVRAGLALVPEDRRQQGLALELSIARNASMTVLGRLV 367 Query: 361 KGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDE 420 K IS + E +LA+ ++ P+ V LSGGNQQKVVL KWLA PK+LI+DE Sbjct: 368 KHGLISARSETQLANQWGTRLRLKAGDPNAPVGTLSGGNQQKVVLGKWLATGPKVLIIDE 427 Query: 421 PTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKE 480 PTRGIDVGAKAE+Y +++L ++G+ V+MISSELPEVL M+DR+ VM G+++ I + Sbjct: 428 PTRGIDVGAKAEVYSALAELVRDGMAVLMISSELPEVLGMADRVLVMHEGRISADIARAD 487 Query: 481 ASQEKVMKLAAG 492 A +E++M A G Sbjct: 488 ADEERIMGAALG 499 Score = 86.3 bits (212), Expect = 2e-21 Identities = 63/249 (25%), Positives = 116/249 (46%), Gaps = 11/249 (4%) Query: 2 KPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEI 61 +P EV+ + V K +S + GE+ A+ G GAG+S + + I G+ D GEI Sbjct: 257 RPPGEVRLSVRGLTRVGVFKDISFDVRAGEIVALAGLVGAGRSEVARAIFGIDPLDSGEI 316 Query: 62 IYEGRGVRWNHPSEAINAGIVTVFQELSVMD---NLSVAENIFMGDEEKRGIFIDYKKMY 118 G+ + P+ A+ AG+ V ++ LS+A N M G + + + Sbjct: 317 WIAGKRLTAGRPAAAVRAGLALVPEDRRQQGLALELSIARNASM---TVLGRLVKHGLIS 373 Query: 119 REAEKFMKEEFGIEI-----DPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLT 173 +E + ++G + DP +G S QQ V + + + KVLI+DEPT + Sbjct: 374 ARSETQLANQWGTRLRLKAGDPNAPVGTLSGGNQQKVVLGKWLATGPKVLIIDEPTRGID 433 Query: 174 QKETEKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKI 233 +++ + L G+A++ IS L E+ + D+V V+ +G + + +E+I Sbjct: 434 VGAKAEVYSALAELVRDGMAVLMISSELPEVLGMADRVLVMHEGRISADIARADADEERI 493 Query: 234 VEMMVGRKL 242 + +G+ + Sbjct: 494 MGAALGQPM 502 Lambda K H 0.318 0.138 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: 630 Number of extensions: 34 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: 494 Length of database: 509 Length adjustment: 34 Effective length of query: 460 Effective length of database: 475 Effective search space: 218500 Effective search space used: 218500 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 (21.7 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