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 16258 b2149 fused methyl-galactoside transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__Keio:16258 Length = 506 Score = 447 bits (1150), Expect = e-130 Identities = 223/492 (45%), Positives = 344/492 (69%), Gaps = 5/492 (1%) Query: 4 ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63 +LE+ I+K FPGV AL V+++ P +HA++GENGAGKSTL+K + G+YQ D G I++ Sbjct: 13 LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72 Query: 64 EGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEK 123 +G+ + ++ EA+ GI V QEL+++ SV +N+++G +G+F+D KMYRE K Sbjct: 73 QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRET-K 131 Query: 124 FMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEV 183 + +E I+IDP ++G S++ QM+EIA+A AK++I+DEPTSSLT+KE LF + Sbjct: 132 AIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTI 191 Query: 184 VKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKLE 243 ++ LKE+G I++ISH++EEIF++CD+V+VLRDG++I T+ + LT +KI+ MMVGR L Sbjct: 192 IRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLN 251 Query: 244 KFYIKEAHEPGEVVLEVKNLSGER---FENVSFSLRRGEILGFAGLVGAGRTELMETIFG 300 + + + ++PGEV+LEV+NL+ R +VSF L +GEILG AGLVGA RT+++ET+FG Sbjct: 252 QRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFG 311 Query: 301 FRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIK 360 R K G I + GK++ ++ +AI G LV E+R+ G+ + I N + ++ K Sbjct: 312 IREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYK 371 Query: 361 -KGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILD 419 K + R K W I + ++ ++ LSGGNQQKV++ +WL +P+IL+LD Sbjct: 372 NKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLD 431 Query: 420 EPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAK 479 EPTRGIDVGAK EIY+++++LAK+G G+I+ISSE+PE+L ++DRI VMS G ++GI+D K Sbjct: 432 EPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTK 491 Query: 480 EASQEKVMKLAA 491 +Q ++++LA+ Sbjct: 492 TTTQNEILRLAS 503 Score = 94.0 bits (232), Expect = 1e-23 Identities = 65/248 (26%), Positives = 120/248 (48%), Gaps = 19/248 (7%) Query: 254 GEVVLEVKNLSG-----ERFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGE 308 GE +LE+ ++ + +NV+ +R I G GAG++ L++ +FG K G Sbjct: 10 GEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGT 69 Query: 309 IYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFIS-- 366 I +GK ++ + +A+E GI +V ++ L L+L S+M N+ L KG F+ Sbjct: 70 ILFQGKEIDFHSAKEALENGISMVHQE---LNLVLQRSVMDNMWLGRYPT--KGMFVDQD 124 Query: 367 --FKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRG 424 ++ K + D D P +V LS Q + +AK + KI+I+DEPT Sbjct: 125 KMYRETKAIFDELDIDID-----PRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSS 179 Query: 425 IDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQE 484 + ++ I+ +L + G G++ IS ++ E+ Q+ D + V+ G+ + + Sbjct: 180 LTEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMD 239 Query: 485 KVMKLAAG 492 K++ + G Sbjct: 240 KIIAMMVG 247 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: 685 Number of extensions: 36 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: 506 Length adjustment: 34 Effective length of query: 460 Effective length of database: 472 Effective search space: 217120 Effective search space used: 217120 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