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_011613066.1 TERY_RS17640 ABC transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >NCBI__GCF_000014265.1:WP_011613066.1 Length = 491 Score = 321 bits (822), Expect = 4e-92 Identities = 184/490 (37%), Positives = 284/490 (57%), Gaps = 19/490 (3%) Query: 5 LEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYE 64 L +++I K F + A +S+ G +HAI+GENGAGK+TLM I++G+YQPD G+I E Sbjct: 4 LRLENITKSFGNLIANDNISISIAAGSIHAILGENGAGKTTLMNILSGLYQPDSGQIYLE 63 Query: 65 GRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEKF 124 + ++ + PS AIN GI ++Q ++ L+ ENI +G + + K A Sbjct: 64 DKPIKISSPSRAINYGIGMIYQHFMLVPQLTATENIILGTSGNFHLNLSAKSREINA--- 120 Query: 125 MKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVV 184 M + + +EI K+ I QQ VEI + +Y++AK+LILDEPT+ LT E + L ++ Sbjct: 121 MAKAYNLEIPTNIKIANLPIGTQQRVEILKVIYRQAKILILDEPTAVLTPVEVKSLLNIL 180 Query: 185 KSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKLEK 244 + L IIFISH+LEEI ICD V+VLR G+ + T + T K+ +MM+GR++ Sbjct: 181 RKLAGNNHTIIFISHKLEEIINICDTVTVLRRGQVVDTITTAVTTTHKLAKMMLGREVNL 240 Query: 245 FYIKEAHEPGEVVLEVKNLSGER------FENVSFSLRRGEILGFAGLVGAGRTELMETI 298 K+ + G +V+EVKN+ + +++SF L GEILG AG+ G G+ EL + I Sbjct: 241 IPQKKPTQKGNIVMEVKNIEVKNDQGLSAVDDLSFQLYSGEILGVAGIDGNGQRELADGI 300 Query: 299 FGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDR 358 G R GEI N+ D + +G +PEDR+K+GLIL SI N+ L Sbjct: 301 NGLRSLEKGEIKF------TNNLTDKFQ--VGYIPEDRQKMGLILNFSIAQNLILKLFQF 352 Query: 359 IK--KGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKIL 416 + + F+ I+ FDIR ++P K LSGGNQQK++L + L+ +P ++ Sbjct: 353 LPFCRYGFLKLGAINNYGKNTIEKFDIRASHPQLKASQLSGGNQQKIILGRELSGEPNLI 412 Query: 417 ILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGII 476 + +PTRG+D+GA + +++ ++G ++ IS+EL E++ MSDRIA++ GK I+ Sbjct: 413 VAMQPTRGLDIGATEYVQQVLLAQKQKGAAILYISTELEEIMTMSDRIAIIYEGKFVDIL 472 Query: 477 DAKEASQEKV 486 DA A+ EKV Sbjct: 473 DAATATIEKV 482 Score = 86.3 bits (212), Expect = 2e-21 Identities = 63/227 (27%), Positives = 110/227 (48%), Gaps = 10/227 (4%) Query: 269 ENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQG 328 +N+S S+ G I G GAG+T LM + G G+IY+E K ++I+ P AI G Sbjct: 20 DNISISIAAGSIHAILGENGAGKTTLMNILSGLYQPDSGQIYLEDKPIKISSPSRAINYG 79 Query: 329 IGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPF-ISFKREKELADWAIKTFDIRPAY 387 IG++ + L+ ++ N+ L + G F ++ + + K +++ Sbjct: 80 IGMIYQH---FMLVPQLTATENIILGT-----SGNFHLNLSAKSREINAMAKAYNLEIP- 130 Query: 388 PDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGV 447 + K+ L G QQ+V + K + + KILILDEPT + + I+ +LA + Sbjct: 131 TNIKIANLPIGTQQRVEILKVIYRQAKILILDEPTAVLTPVEVKSLLNILRKLAGNNHTI 190 Query: 448 IMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAGLE 494 I IS +L E++ + D + V+ G++ I + K+ K+ G E Sbjct: 191 IFISHKLEEIINICDTVTVLRRGQVVDTITTAVTTTHKLAKMMLGRE 237 Score = 79.3 bits (194), Expect = 3e-19 Identities = 62/244 (25%), Positives = 122/244 (50%), Gaps = 20/244 (8%) Query: 4 ILEVKSIH-KRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62 ++EVK+I K G+ A+ +S + Y GE+ + G +G G+ L I G+ ++GEI Sbjct: 253 VMEVKNIEVKNDQGLSAVDDLSFQLYSGEILGVAGIDGNGQRELADGINGLRSLEKGEIK 312 Query: 63 YEGRGVRWNHPSEAINAGIVTVF-QELSVMDNLSVAENIFMGDEEKRGIFIDYKKM---- 117 + N+ ++ G + Q++ ++ N S+A+N+ + K F+ + + Sbjct: 313 FT------NNLTDKFQVGYIPEDRQKMGLILNFSIAQNLIL----KLFQFLPFCRYGFLK 362 Query: 118 ---YREAEKFMKEEFGIEID-PEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLT 173 K E+F I P+ K + S QQ + + R + + +++ +PT L Sbjct: 363 LGAINNYGKNTIEKFDIRASHPQLKASQLSGGNQQKIILGRELSGEPNLIVAMQPTRGLD 422 Query: 174 QKETEKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKI 233 TE + +V+ + K+KG AI++IS LEEI + D+++++ +G+++ T EK+ Sbjct: 423 IGATEYVQQVLLAQKQKGAAILYISTELEEIMTMSDRIAIIYEGKFVDILDAATATIEKV 482 Query: 234 VEMM 237 +M Sbjct: 483 GLLM 486 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: 661 Number of extensions: 34 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: 3 Length of query: 494 Length of database: 491 Length adjustment: 34 Effective length of query: 460 Effective length of database: 457 Effective search space: 210220 Effective search space used: 210220 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