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 GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__Phaeo:GFF2274 Length = 503 Score = 463 bits (1191), Expect = e-135 Identities = 244/494 (49%), Positives = 342/494 (69%), Gaps = 3/494 (0%) Query: 3 PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62 P+L ++ I K FPGV AL GVS+ PGEVHA++GENGAGKSTLMK++ G++QPDEG+II Sbjct: 6 PVLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEGQII 65 Query: 63 YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGD-EEKRGIFIDYKKMYREA 121 + V + P +A GIV + QELS+ D LSVAENI++G+ KR +D+ ++ + Sbjct: 66 VAEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGLVDWAELEAKT 125 Query: 122 EKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLF 181 + E+ + + + ++G SIA QQMVEIARA+ AK +I DEPT+SLT E LF Sbjct: 126 NAIL-EKLKVGFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVVLF 184 Query: 182 EVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRK 241 EV+ L+E+GV I +ISHR+EEIF+I D++SVLRDG+Y GT + +E + +MM+GRK Sbjct: 185 EVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMMIGRK 244 Query: 242 LEKFYIKEAHEPGEVVLEVKNLS-GERFENVSFSLRRGEILGFAGLVGAGRTELMETIFG 300 L+ + HE GEV LEV+ LS G FE+V+F +RRGE++GF GLVGAGRTE+ ET+FG Sbjct: 245 LDLSRNEAHHELGEVALEVRGLSCGSLFEDVNFEVRRGEVVGFYGLVGAGRTEIAETLFG 304 Query: 301 FRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIK 360 R G I+++G V I P DAIE+GI LVPEDRK GL+L M+ N++LP +D +K Sbjct: 305 LRNPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCRDNMTLPQVDDLK 364 Query: 361 KGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDE 420 GPF++ E + D DIR + V LSGGNQQK+V+ KWL+++P +LI+DE Sbjct: 365 AGPFVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGKWLSMRPNVLIVDE 424 Query: 421 PTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKE 480 PTRGIDVG+KAEI+ ++ LA +G VI+ISSE+PEVL ++DRI M G++ ++E Sbjct: 425 PTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAMYSGRIMRTFTSEE 484 Query: 481 ASQEKVMKLAAGLE 494 ++E ++ +GL+ Sbjct: 485 VTEENLIAAISGLD 498 Score = 78.6 bits (192), Expect = 5e-19 Identities = 58/236 (24%), Positives = 112/236 (47%), Gaps = 23/236 (9%) Query: 23 VSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPSEAINAGIV 82 V+ E GEV G GAG++ + + + G+ P G I +G V P +AI GI Sbjct: 275 VNFEVRRGEVVGFYGLVGAGRTEIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERGIS 334 Query: 83 TVFQE---------LSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEKFMKEEFGIEI 133 V ++ ++ DN+++ + D+ K G F+ AE + +++ ++ Sbjct: 335 LVPEDRKGQGLVLGMNCRDNMTLPQV----DDLKAGPFVA-----DGAEIAIFDQYRDKL 385 Query: 134 DP-----EEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLK 188 D ++ +G S QQ + I + + + VLI+DEPT + ++ +++ L Sbjct: 386 DIRTPGWKQLVGNLSGGNQQKIVIGKWLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLA 445 Query: 189 EKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKLEK 244 +G A+I IS + E+ + D++ + G + T + E +T+E ++ + G EK Sbjct: 446 AQGYAVIVISSEMPEVLHVADRIVAMYSGRIMRTFTSEEVTEENLIAAISGLDTEK 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: 697 Number of extensions: 33 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: 503 Length adjustment: 34 Effective length of query: 460 Effective length of database: 469 Effective search space: 215740 Effective search space used: 215740 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