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 WP_040513205.1 J416_RS08125 sugar ABC transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >NCBI__GCF_000359605.1:WP_040513205.1 Length = 506 Score = 400 bits (1028), Expect = e-116 Identities = 208/492 (42%), Positives = 321/492 (65%), Gaps = 3/492 (0%) Query: 3 PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62 P+L++ I K F G L GV +E GE+HA++GENGAGKSTLM I+ GVYQP++GEI Sbjct: 7 PVLQMSGIKKSFNGNEVLHGVDLEVKKGEIHALLGENGAGKSTLMNILGGVYQPNDGEIK 66 Query: 63 YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEK-RGIFIDYKKMYREA 121 G + P + GI + QEL+V+ +L+V EN+F+G E + R F+D K+M ++ Sbjct: 67 LSGAPIVMESPRVSQENGISFIHQELNVVTDLTVYENMFLGSEIRTRFGFLDVKEMCKQT 126 Query: 122 EKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLF 181 E+ + G++IDP+ + + +QM+EIA+++ + ++I+DEPT++LT+ E E+LF Sbjct: 127 EEVLSR-LGVQIDPKTYVRDIETSYKQMIEIAKSLLHNSNMIIMDEPTTALTENEVERLF 185 Query: 182 EVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRK 241 ++SL+ GV+II+ISH+L+EI +CD+ +VLRDG +GT ++ I + MVG+ Sbjct: 186 AFMRSLQASGVSIIYISHKLKEIQTVCDRYTVLRDGHLVGTGEVKGTDLSAITQQMVGKS 245 Query: 242 LEKFYIKEAHEPGEVVLEVKNLSGER-FENVSFSLRRGEILGFAGLVGAGRTELMETIFG 300 + GE VL VK+L+ E F +++FS+ +GE++GF GL G GRTEL E+IFG Sbjct: 246 VSTNAFYHKATKGEPVLTVKHLTSEGLFNDINFSVSKGEVVGFTGLAGDGRTELFESIFG 305 Query: 301 FRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIK 360 FR K GG I + G+ ++INHP A++ GIGLVP++RK+ ++ +S++ N+SL SL + Sbjct: 306 FRKKYGGVIEVNGQPLKINHPRKAVQGGIGLVPKNRKENAIVKDLSVIENMSLSSLGHFE 365 Query: 361 KGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDE 420 I KRE++ +I+ P + LSGGNQQKVV+AKWL + ++I D Sbjct: 366 ANGLIRSKREQKRFQEYKDQLNIKVHDPKVTIDSLSGGNQQKVVIAKWLEVDGDLIIFDN 425 Query: 421 PTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKE 480 PT+GIDVGAK EIY+ + LA+ G +I++SSE PE+L++ DR+ +M G++ G E Sbjct: 426 PTQGIDVGAKNEIYQHIMNLAEMGKAIIILSSEAPEILRVCDRVNIMFHGEITGKFTRDE 485 Query: 481 ASQEKVMKLAAG 492 ++EK+M+ A G Sbjct: 486 LTEEKIMEYATG 497 Score = 100 bits (250), Expect = 9e-26 Identities = 75/251 (29%), Positives = 127/251 (50%), Gaps = 17/251 (6%) Query: 2 KPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEI 61 +P+L VK H G+ ++ GEV G G G++ L + I G + G I Sbjct: 259 EPVLTVK--HLTSEGL--FNDINFSVSKGEVVGFTGLAGDGRTELFESIFGFRKKYGGVI 314 Query: 62 IYEGRGVRWNHPSEAINAGIVTV---FQELSVMDNLSVAENIFM---GDEEKRGIFIDYK 115 G+ ++ NHP +A+ GI V +E +++ +LSV EN+ + G E G+ Sbjct: 315 EVNGQPLKINHPRKAVQGGIGLVPKNRKENAIVKDLSVIENMSLSSLGHFEANGLI---- 370 Query: 116 KMYREAEKFM--KEEFGIEI-DPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSL 172 + RE ++F K++ I++ DP+ + S QQ V IA+ + ++I D PT + Sbjct: 371 RSKREQKRFQEYKDQLNIKVHDPKVTIDSLSGGNQQKVVIAKWLEVDGDLIIFDNPTQGI 430 Query: 173 TQKETEKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEK 232 ++++ + +L E G AII +S EI +CD+V+++ GE G + + LT+EK Sbjct: 431 DVGAKNEIYQHIMNLAEMGKAIIILSSEAPEILRVCDRVNIMFHGEITGKFTRDELTEEK 490 Query: 233 IVEMMVGRKLE 243 I+E G K E Sbjct: 491 IMEYATGSKKE 501 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: 639 Number of extensions: 32 Number of successful extensions: 6 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 24 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