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 SM_b20713 SM_b20713 sugar uptake ABC transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__Smeli:SM_b20713 Length = 513 Score = 439 bits (1128), Expect = e-127 Identities = 234/491 (47%), Positives = 333/491 (67%), Gaps = 4/491 (0%) Query: 4 ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63 +L + + K FPGV AL V + G VHA++GENGAGKSTLMKI+AG+Y PD+GE+ Sbjct: 23 LLTAEGVRKEFPGVVALDDVEFKLKRGTVHALMGENGAGKSTLMKILAGIYYPDQGEVKL 82 Query: 64 EGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGI-FIDYKKMYREAE 122 G G+R P +A+ GI + QEL++M ++VAENI++ E K F+D+ +M R Sbjct: 83 RGAGIRLKSPLDALENGIAMIHQELNLMPFMTVAENIWIRREPKNRFGFVDHGEMRRMTA 142 Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182 K E I++DPE ++ S+A +QMVEIA+AV ++ VLI+DEPTS+LT++E LFE Sbjct: 143 KLF-ERLKIDLDPEIEVRHLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVAHLFE 201 Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242 +++ L+ +G+ I++I+H++ E+FEI D+ SV RDG+YIGT +T++ I+ MMVGR++ Sbjct: 202 IIRDLRSQGIGIVYITHKMNELFEIADEFSVFRDGKYIGTHLSNEVTRDDIIRMMVGREI 261 Query: 243 EKFYIKEAHEPGEVVLEVKNLS-GERFENVSFSLRRGEILGFAGLVGAGRTELMETIFGF 301 + + KE G+VVL VKNL+ F +VSF +R GEILG AGLVG+GR+ + ET+FG Sbjct: 262 TQMFPKEEVPIGDVVLSVKNLTLNGVFRDVSFDVRAGEILGVAGLVGSGRSNVAETLFGV 321 Query: 302 RPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSL-DRIK 360 P G I I+GK V I+ AI + + EDRK G +LI+ I+ N+ + L D+ Sbjct: 322 TPASSGTIAIDGKEVVIDSANKAIRHRMAFLTEDRKDTGCLLILDILENMQIAVLQDKFV 381 Query: 361 KGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDE 420 K F+S + + + ++ +V LSGGNQQKV++ +WL P+ILILDE Sbjct: 382 KRGFVSEREVTAACEEMSRKLRVKTPNLQERVENLSGGNQQKVLIGRWLLTNPRILILDE 441 Query: 421 PTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKE 480 PTRGIDVGAKAEI+R++++LA+ GV VIMISSE+PEVL MSDRI VM G++ GI+D E Sbjct: 442 PTRGIDVGAKAEIHRLVTELARNGVAVIMISSEMPEVLGMSDRIMVMHEGRVTGILDRAE 501 Query: 481 ASQEKVMKLAA 491 A+Q KVM+LAA Sbjct: 502 ATQIKVMELAA 512 Score = 103 bits (256), Expect = 2e-26 Identities = 61/228 (26%), Positives = 121/228 (53%), Gaps = 9/228 (3%) Query: 269 ENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQG 328 ++V F L+RG + G GAG++ LM+ + G GE+ + G + + PLDA+E G Sbjct: 40 DDVEFKLKRGTVHALMGENGAGKSTLMKILAGIYYPDQGEVKLRGAGIRLKSPLDALENG 99 Query: 329 IGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAY- 387 I ++ ++ L L+ M++ N+ + + + G F E+ K F+ Sbjct: 100 IAMIHQE---LNLMPFMTVAENIWIRREPKNRFG----FVDHGEMRRMTAKLFERLKIDL 152 Query: 388 -PDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVG 446 P+ +V +LS N+Q V +AK ++ + +LI+DEPT + A ++ I+ L +G+G Sbjct: 153 DPEIEVRHLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVAHLFEIIRDLRSQGIG 212 Query: 447 VIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAGLE 494 ++ I+ ++ E+ +++D +V GK G + E +++ ++++ G E Sbjct: 213 IVYITHKMNELFEIADEFSVFRDGKYIGTHLSNEVTRDDIIRMMVGRE 260 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: 682 Number of extensions: 37 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 494 Length of database: 513 Length adjustment: 34 Effective length of query: 460 Effective length of database: 479 Effective search space: 220340 Effective search space used: 220340 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