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 3607108 Dshi_0530 ABC transporter related (RefSeq)
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__Dino:3607108 Length = 498 Score = 322 bits (826), Expect = 1e-92 Identities = 180/480 (37%), Positives = 286/480 (59%), Gaps = 6/480 (1%) Query: 5 LEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYE 64 +++++I KR+ GV AL V PGE + GENG+GKSTL+KII+GV G + Sbjct: 10 IDLRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIA 69 Query: 65 GRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEKF 124 G+ +P + AG++ +FQ+ S+ NLSVAENI + + + R+ + Sbjct: 70 GQEHVTLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKFRAVRDIARA 129 Query: 125 MKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVV 184 + G++ID + ++ +A +Q+V I RA+ KA+++I+DEPT++LT+KE +L ++ Sbjct: 130 ALDRIGVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQGII 189 Query: 185 KSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKLEK 244 + LKE+GVA+IF+SH+L E+ E+ +KV VLR+G+ + + + M GR + + Sbjct: 190 RMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTYHMTGRDVPE 249 Query: 245 FYIKEAHEPGEVVLEVKNLS-GERFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRP 303 + + +++V+ L F ++SF LR GE+LG GL+G GRT + + +FG Sbjct: 250 VPPSDVAAGAQTLMQVQGLGKAGSFSDISFDLRTGEVLGITGLLGCGRTSVAKALFGLVT 309 Query: 304 KRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGP 363 G I ++G V + P A IG VPEDR GL L SI+ NV++ LD G Sbjct: 310 PDAGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVAVGRLDAHTSGG 369 Query: 364 FISFKR-EKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPT 422 F+ KE +DW ++ ++ + V LSGGNQQ+V LA+WL+ P++LIL+ P+ Sbjct: 370 FLDMTGLAKEASDW-LRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSRAPRVLILNGPS 428 Query: 423 RGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEAS 482 G+DVG+KA+I+ I+ +LA+EG+GVI+IS +LPE+L R+ VM G+ IIDA E + Sbjct: 429 VGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGR---IIDALEGT 485 Score = 82.0 bits (201), Expect = 4e-20 Identities = 58/220 (26%), Positives = 105/220 (47%), Gaps = 5/220 (2%) Query: 23 VSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPSEAINAGIV 82 +S + GEV I G G G++++ K + G+ PD G I+ +G V P A A I Sbjct: 277 ISFDLRTGEVLGITGLLGCGRTSVAKALFGLVTPDAGSILVDGSPVPLGDPQAASLARIG 336 Query: 83 TVFQEL---SVMDNLSVAENIFMG--DEEKRGIFIDYKKMYREAEKFMKEEFGIEIDPEE 137 V ++ + + S+ N+ +G D G F+D + +EA +++ D E Sbjct: 337 YVPEDRLTEGLFLSQSILRNVAVGRLDAHTSGGFLDMTGLAKEASDWLRRLKVKAPDVEA 396 Query: 138 KLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGVAIIFI 197 + S QQ V +AR + + +VLIL+ P+ + + ++++ L +G+ +I I Sbjct: 397 PVQSLSGGNQQRVALARWLSRAPRVLILNGPSVGVDVGSKADIHDIIRELAREGIGVIVI 456 Query: 198 SHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMM 237 S L E+ C +V V+R+G I LT++ + + Sbjct: 457 SDDLPELLATCHRVLVMREGRIIDALEGTALTEDDLAHRL 496 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: 538 Number of extensions: 22 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: 498 Length adjustment: 34 Effective length of query: 460 Effective length of database: 464 Effective search space: 213440 Effective search space used: 213440 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