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_b20673 SM_b20673 sugar uptake ABC transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__Smeli:SM_b20673 Length = 526 Score = 415 bits (1066), Expect = e-120 Identities = 229/502 (45%), Positives = 334/502 (66%), Gaps = 13/502 (2%) Query: 2 KPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEI 61 +PIL ++I K F GV ALK V E GE+HA++GENGAGKSTLMK+++GVY EG + Sbjct: 16 RPILAAEAISKSFGGVAALKDVRFELRAGEIHALMGENGAGKSTLMKVLSGVYTDYEGAV 75 Query: 62 IYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEK-RGIFIDYKKMYRE 120 +G VR+++ +A AGI + QEL+++ L VA+NIF+G E G+F+D +K E Sbjct: 76 RVDGETVRFSNVRDAEAAGIAIIHQELNLVPELGVADNIFLGRERVIAGLFVD-RKASLE 134 Query: 121 AEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKL 180 A + + GIE+DPE ++G+ + QQ+VEIA+A+ +A++LI+DEPTS+L+ E +L Sbjct: 135 AARGLLNRLGIELDPEARVGQLRVGEQQLVEIAKALSVEARILIMDEPTSALSPGECRRL 194 Query: 181 FEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240 F++++ L GV II+ISHR++E+ ++ D+V+V RDG ++ + L + I+ MVGR Sbjct: 195 FKIMRQLAADGVGIIYISHRIDEVMQLSDRVTVFRDGRHVWARPMAGLDENTIIAAMVGR 254 Query: 241 KLEKFYIKEAHE-PGEVVLEVKNLS---------GERFENVSFSLRRGEILGFAGLVGAG 290 L + ++ + GE VL V++LS + + VSF +R GEILG GL+GAG Sbjct: 255 NLLDAHRRDRGKGGGEPVLSVRDLSLAVSGRHGWRDVLKGVSFDVRAGEILGIGGLLGAG 314 Query: 291 RTELMETIFGFRP-KRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMH 349 RTE++ETIF RGGEI ++G V I P DA G LV EDRK GL L SI Sbjct: 315 RTEILETIFASNEGLRGGEIRLDGIAVNIRSPRDARRLGFALVTEDRKAKGLHLHESIRD 374 Query: 350 NVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWL 409 NV+LP + R+ + SF+ E+ LA A+ +R A + LSGGNQQKVV+ KWL Sbjct: 375 NVALPLVGRLARFGLRSFEGERALAKGAVDALGVRCAGTGQAAGTLSGGNQQKVVIGKWL 434 Query: 410 ALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSF 469 A P++L+LDEPTRGIDVGAK EIY ++ +LA +G+ ++++SSELPE+L ++DRI VM+ Sbjct: 435 ATGPRVLLLDEPTRGIDVGAKREIYDLIFKLAGDGLAIVVVSSELPELLLLADRILVMAE 494 Query: 470 GKLAGIIDAKEASQEKVMKLAA 491 G+ G+I +EAS+E++M+LAA Sbjct: 495 GRQTGLISREEASEERIMQLAA 516 Score = 73.9 bits (180), Expect = 1e-17 Identities = 63/249 (25%), Positives = 115/249 (46%), Gaps = 10/249 (4%) Query: 2 KPILEVKSIHKRFPGVHA----LKGVSMEFYPGEVHAIVGENGAGKSTLMK-IIAGVYQP 56 +P+L V+ + G H LKGVS + GE+ I G GAG++ +++ I A Sbjct: 270 EPVLSVRDLSLAVSGRHGWRDVLKGVSFDVRAGEILGIGGLLGAGRTEILETIFASNEGL 329 Query: 57 DEGEIIYEGRGVRWNHPSEAINAGIVTVFQELSVMD---NLSVAENIFMGDEEKRGIF-I 112 GEI +G V P +A G V ++ + S+ +N+ + + F + Sbjct: 330 RGGEIRLDGIAVNIRSPRDARRLGFALVTEDRKAKGLHLHESIRDNVALPLVGRLARFGL 389 Query: 113 DYKKMYREAEKFMKEEFGIEI-DPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSS 171 + R K + G+ + G S QQ V I + + +VL+LDEPT Sbjct: 390 RSFEGERALAKGAVDALGVRCAGTGQAAGTLSGGNQQKVVIGKWLATGPRVLLLDEPTRG 449 Query: 172 LTQKETEKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKE 231 + ++++++ L G+AI+ +S L E+ + D++ V+ +G G S E ++E Sbjct: 450 IDVGAKREIYDLIFKLAGDGLAIVVVSSELPELLLLADRILVMAEGRQTGLISREEASEE 509 Query: 232 KIVEMMVGR 240 +I+++ R Sbjct: 510 RIMQLAAPR 518 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: 703 Number of extensions: 43 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: 526 Length adjustment: 34 Effective length of query: 460 Effective length of database: 492 Effective search space: 226320 Effective search space used: 226320 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