RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|255764505|ref|YP_003065248.2| polysialic acid capsule expression protein [Candidatus Liberibacter asiaticus str. psy62] (341 letters) >gnl|CDD|31137 COG0794, GutQ, Predicted sugar phosphate isomerase involved in capsule formation [Cell envelope biogenesis, outer membrane]. Length = 202 Score = 210 bits (535), Expect = 6e-55 Identities = 100/201 (49%), Positives = 124/201 (61%), Gaps = 4/201 (1%) Query: 27 ALRSIIAEKRGLSSLESSLQGELSFQFHCAVEKIKAIKGRVVITGIGKSGHIGSKLASTL 86 A ++ E L L L E F AVE I KG+V +TG+GKSG IG K A+ L Sbjct: 5 AKEILMTEAEALLELAERLDDE---DFVRAVELILECKGKVFVTGVGKSGLIGKKFAARL 61 Query: 87 ASTGTPSFFVHAAEASHGDLGMITRDDLIIVLSWSGSSDELKAILYYARRFSIPLIAITS 146 ASTGTP+FFV AEA HGDLGMIT D++I +S SG + EL + A+R LIAITS Sbjct: 62 ASTGTPAFFVGPAEALHGDLGMITPGDVVIAISGSGETKELLNLAPKAKRLGAKLIAITS 121 Query: 147 ENKSVVACHADIVLTLPKEPESCPHGLAPTTSAIMQLAIGDALAIALLESRNFSENDFYV 206 S +A AD+VL +P + E+CP GLAPTTS + LA+GDALA L E+R FS DF + Sbjct: 122 NPDSSLAKAADVVLVIPVKTEACPLGLAPTTSTTLTLALGDALAGTLFEARGFSFEDFAI 181 Query: 207 LHPGGKLG-TLFVCASDVMHS 226 HPGG LG L + D M+ Sbjct: 182 AHPGGALGAKLLLKVKDHMNL 202 >gnl|CDD|88409 cd05014, SIS_Kpsf, KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose 5-phosphate to arabinose 5-phosphate. This is the second step in the CMP-Kdo biosynthesis pathway.. Length = 128 Score = 174 bits (443), Expect = 3e-44 Identities = 73/128 (57%), Positives = 96/128 (75%) Query: 65 GRVVITGIGKSGHIGSKLASTLASTGTPSFFVHAAEASHGDLGMITRDDLIIVLSWSGSS 124 G+VV+TG+GKSGHI K+A+TL+STGTP+FF+H EA HGDLGM+T D++I +S SG + Sbjct: 1 GKVVVTGVGKSGHIARKIAATLSSTGTPAFFLHPTEALHGDLGMVTPGDVVIAISNSGET 60 Query: 125 DELKAILYYARRFSIPLIAITSENKSVVACHADIVLTLPKEPESCPHGLAPTTSAIMQLA 184 DEL +L + +R P+IAIT S +A +D+VL LP E E+CP GLAPTTS LA Sbjct: 61 DELLNLLPHLKRRGAPIIAITGNPNSTLAKLSDVVLDLPVEEEACPLGLAPTTSTTAMLA 120 Query: 185 IGDALAIA 192 +GDALA+A Sbjct: 121 LGDALAVA 128 >gnl|CDD|73104 cd04604, CBS_pair_KpsF_GutQ_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with KpsF/GutQ domains in the API [A5P (D-arabinose 5-phosphate) isomerase] protein. These APIs catalyze the conversion of the pentose pathway intermediate D-ribulose 5-phosphate into A5P, a precursor of 3-deoxy-D-manno-octulosonate, which is an integral carbohydrate component of various glycolipids coating the surface of the outer membrane of Gram-negative bacteria, including lipopolysaccharide and many group 2 K-antigen capsules. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 114 Score = 128 bits (323), Expect = 3e-30 Identities = 51/113 (45%), Positives = 70/113 (61%), Gaps = 2/113 (1%) Query: 227 GDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHK--DLNTLS 284 GD++PLV L DA+ +S K G AVVDE +L GI T+GD+ R K D+ TL Sbjct: 1 GDALPLVSPDTSLKDALLEMSRKGLGMTAVVDEDGRLVGIFTDGDLRRALEKGLDILTLP 60 Query: 285 VEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 V DVM +NPK I D L A++L+ ++ I+ L VVDD + +G++H DLLR Sbjct: 61 VADVMTRNPKTIDPDALAAEALELMEENKITALPVVDDNGRPVGVLHIHDLLR 113 >gnl|CDD|144827 pfam01380, SIS, SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars. Presumably the SIS domains bind to the end-product of the pathway. Length = 131 Score = 94.7 bits (236), Expect = 4e-20 Identities = 48/132 (36%), Positives = 66/132 (50%), Gaps = 4/132 (3%) Query: 62 AIKGRVVITGIGKSGHIGSKLASTLASTGTPSFFVH-AAEASHGDLGMITRDDLIIVLSW 120 A R+ + G G S +LA L G V A+E HG L ++ DDL+I +S Sbjct: 3 AKAKRIYVIGAGTSYAAALELALKLEEIGYIVVEVEDASEFRHGPLALVDPDDLVIAISQ 62 Query: 121 SGSSDELKAILYYARRFSIPLIAITSENKSVVACHADIVLTLPKEPESCPHGLAPTTSAI 180 SG + +L + +IAIT S +A AD VL + PE+ G+A T S Sbjct: 63 SGETRDLLEAAKLLKARGAKIIAITDSKGSPLAREADHVLYIIAGPEA---GVASTKSLT 119 Query: 181 MQLAIGDALAIA 192 +QLA+ DALAIA Sbjct: 120 LQLALLDALAIA 131 >gnl|CDD|31923 COG1737, RpiR, Transcriptional regulators [Transcription]. Length = 281 Score = 80.8 bits (199), Expect = 5e-16 Identities = 47/147 (31%), Positives = 69/147 (46%), Gaps = 3/147 (2%) Query: 52 QFHCAVEKIKAIKGRVVITGIGKSGHIGSKLASTLASTGTPSFFVHAAEASHGDLGMITR 111 AVE + + R+ G+G SG + S LA L G + L ++T Sbjct: 119 ALERAVELLAKAR-RIYFFGLGSSGLVASDLAYKLMRIGLNVVALSDTHGQLMQLALLTP 177 Query: 112 DDLIIVLSWSGSSDELKAILYYARRFSIPLIAITSENKSVVACHADIVLTLPKEPESCPH 171 D++I +S+SG + E+ A+ +IAIT S +A ADIVL +P ES Sbjct: 178 GDVVIAISFSGYTREIVEAAELAKERGAKVIAITDSADSPLAKLADIVLLVPVAEESFFR 237 Query: 172 GLAPTTSAIMQLAIGDALAIALLESRN 198 P +S I QLA+ DAL A+ + R Sbjct: 238 S--PISSRIAQLALIDALITAVAQRRG 262 >gnl|CDD|73081 cd02205, CBS_pair, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 113 Score = 80.2 bits (197), Expect = 8e-16 Identities = 35/111 (31%), Positives = 57/111 (51%), Gaps = 2/111 (1%) Query: 230 IPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNF--HKDLNTLSVED 287 + V + +A+ ++ E + VVD+ +L GI+TE D+ R ++V D Sbjct: 3 VVTVSPDDTVAEALRLMLEHGISGLPVVDDDGRLVGIVTERDLLRALAEGGLDPLVTVGD 62 Query: 288 VMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338 VM ++ + DT L A +L+ +H I L VVDD + +GIV D+LR Sbjct: 63 VMTRDVVTVSPDTSLEEAAELMLEHGIRRLPVVDDEGRLVGIVTRSDILRA 113 Score = 42.1 bits (98), Expect = 2e-04 Identities = 18/48 (37%), Positives = 28/48 (58%) Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338 ++ + D + A++L+ +H IS L VVDD + +GIV DLLR Sbjct: 1 RDVVTVSPDDTVAEALRLMLEHGISGLPVVDDDGRLVGIVTERDLLRA 48 >gnl|CDD|73122 cd04623, CBS_pair_10, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 113 Score = 72.8 bits (179), Expect = 1e-13 Identities = 33/109 (30%), Positives = 53/109 (48%), Gaps = 4/109 (3%) Query: 233 VKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFH---KDLNTLSVEDVM 289 V+ + +A +++EK G V VVD+G +L GI +E DI R V ++M Sbjct: 6 VRPDATVAEAAKLMAEKNIGAVVVVDDGGRLVGIFSERDIVRKVALRGASALDTPVSEIM 65 Query: 290 IKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338 +N + D + AM L+ + L VVD K +GIV D+++ Sbjct: 66 TRNVITVTPDDTVDEAMALMTERRFRHLPVVDG-GKLVGIVSIGDVVKA 113 Score = 32.8 bits (75), Expect = 0.13 Identities = 13/43 (30%), Positives = 24/43 (55%) Query: 295 VILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 + D + A +L+ + NI ++VVDD + +GI D++R Sbjct: 5 TVRPDATVAEAAKLMAEKNIGAVVVVDDGGRLVGIFSERDIVR 47 >gnl|CDD|88408 cd05013, SIS_RpiR, RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate isomerases that catalyze the reversible reactions of ribose 5-phosphate into ribulose 5-phosphate.. Length = 139 Score = 70.7 bits (173), Expect = 6e-13 Identities = 42/137 (30%), Positives = 62/137 (45%), Gaps = 3/137 (2%) Query: 56 AVEKIKAIKGRVVITGIGKSGHIGSKLASTLASTGTPSFFVHAAEASHGDLGMITRDDLI 115 AV+ + R+ I G+G SG + LA L G P + +T D++ Sbjct: 6 AVDLLAK-ARRIYIFGVGSSGLVAEYLAYKLLRLGKPVVLLSDPHLQLMSAANLTPGDVV 64 Query: 116 IVLSWSGSSDELKAILYYARRFSIPLIAITSENKSVVACHADIVLTLPKEPESCPHGLAP 175 I +S+SG + E A+ +IAIT S +A ADIVL + E + Sbjct: 65 IAISFSGETKETVEAAEIAKERGAKVIAITDSANSPLAKLADIVLLVSSEEG--DFRSSA 122 Query: 176 TTSAIMQLAIGDALAIA 192 +S I QLA+ DAL +A Sbjct: 123 FSSRIAQLALIDALFLA 139 >gnl|CDD|32593 COG2524, COG2524, Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]. Length = 294 Score = 69.5 bits (170), Expect = 1e-12 Identities = 34/106 (32%), Positives = 51/106 (48%), Gaps = 1/106 (0%) Query: 232 LVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIK 291 V+ L +A + EK VVD+ K+ GIIT DI + V D M K Sbjct: 184 TVRPDDTLREAAKLFYEKGIRGAPVVDDD-KIVGIITLSDIAKAIANGNLDAKVSDYMRK 242 Query: 292 NPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 N I ED + A++L+ ++N+ L+V D K +GI+ D+L Sbjct: 243 NVITINEDEDIYDAIRLMNKNNVGRLLVTDSNGKPVGIITRTDILT 288 Score = 27.5 bits (61), Expect = 5.5 Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 1/52 (1%) Query: 284 SVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDL 335 V+++M K + D L A +L + I VVDD K +GI+ D+ Sbjct: 173 KVKNLMSKKLITVRPDDTLREAAKLFYEKGIRGAPVVDD-DKIVGIITLSDI 223 >gnl|CDD|73111 cd04611, CBS_pair_PAS_GGDEF_DUF1_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with a PAS domain, a GGDEF (DiGuanylate-Cyclase (DGC) domain, and a DUF1 domain downstream. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and is thought to be involved in regulating cell surface adhesiveness in bacteria. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 111 Score = 69.1 bits (169), Expect = 2e-12 Identities = 38/110 (34%), Positives = 57/110 (51%), Gaps = 2/110 (1%) Query: 229 SIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLN-TLSVED 287 I L +A + + E+R + VVD+G+ L GI+TE DI R + V + Sbjct: 2 QILTCPPDTSLAEAASRMRERRISSIVVVDDGRPL-GIVTERDILRLLASGPDLQTPVGE 60 Query: 288 VMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 VM + DT L A QL+R+H I L+VVDD + +G++ DLL+ Sbjct: 61 VMSSPLLTVPADTSLYDARQLMREHGIRHLVVVDDDGELLGLLSQTDLLQ 110 Score = 35.2 bits (81), Expect = 0.024 Identities = 16/60 (26%), Positives = 30/60 (50%), Gaps = 6/60 (10%) Query: 218 VCASDVMHSGDSIPLVKI--GCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRN 275 +VM S PL+ + L DA ++ E + VVD+ +L G++++ D+ +N Sbjct: 56 TPVGEVMSS----PLLTVPADTSLYDARQLMREHGIRHLVVVDDDGELLGLLSQTDLLQN 111 >gnl|CDD|73123 cd04624, CBS_pair_11, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 112 Score = 68.3 bits (167), Expect = 3e-12 Identities = 30/106 (28%), Positives = 57/106 (53%), Gaps = 1/106 (0%) Query: 233 VKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLN-TLSVEDVMIK 291 V + +A +++E+ G V VVD ++ GI+TE DI R ++ V ++M + Sbjct: 6 VDPDTSIREAAKLMAEENVGSVVVVDPDERPIGIVTERDIVRAVAAGIDLDTPVSEIMTR 65 Query: 292 NPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 + + D + A +L+R++NI +VVD + +G++ DL+R Sbjct: 66 DLVTVDPDEPVAEAAKLMRKNNIRHHLVVDKGGELVGVISIRDLVR 111 Score = 29.4 bits (66), Expect = 1.4 Identities = 14/47 (29%), Positives = 27/47 (57%) Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 + + DT + A +L+ + N+ ++VVD ++ IGIV D++R Sbjct: 1 RPVVTVDPDTSIREAAKLMAEENVGSVVVVDPDERPIGIVTERDIVR 47 >gnl|CDD|30863 COG0517, COG0517, FOG: CBS domain [General function prediction only]. Length = 117 Score = 67.9 bits (165), Expect = 4e-12 Identities = 43/112 (38%), Positives = 59/112 (52%), Gaps = 4/112 (3%) Query: 228 DSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNF-HKDLNTLSVE 286 + VK + DA+ ++SE V VVD+G KL GIITE DI R L V+ Sbjct: 7 KDVITVKPDTSVRDALLLMSENGVSAVPVVDDG-KLVGIITERDILRALAAGGKRLLPVK 65 Query: 287 DVMIKNPKVILEDTLLTVAMQLLRQ-HNISVLMVVDDCQ-KAIGIVHFLDLL 336 +VM K + DT L A++L+ + H I L VVDD K +GI+ D+L Sbjct: 66 EVMTKPVVTVDPDTPLEEALELMVERHKIRRLPVVDDDGGKLVGIITLSDIL 117 Score = 39.7 bits (92), Expect = 0.001 Identities = 19/54 (35%), Positives = 33/54 (61%), Gaps = 1/54 (1%) Query: 285 VEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338 V+D+M K+ + DT + A+ L+ ++ +S + VVDD K +GI+ D+LR Sbjct: 1 VKDIMTKDVITVKPDTSVRDALLLMSENGVSAVPVVDD-GKLVGIITERDILRA 53 >gnl|CDD|73107 cd04607, CBS_pair_NTP_transferase_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain associated with the NTP (Nucleotidyl transferase) domain downstream. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 113 Score = 67.5 bits (165), Expect = 5e-12 Identities = 31/107 (28%), Positives = 53/107 (49%), Gaps = 3/107 (2%) Query: 232 LVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNF--HKDLNTLSVEDVM 289 LV ++DA+ + + V VVDE +L G +T+GDI R L+ V +VM Sbjct: 6 LVSPDASILDALRKIDKNALRIVLVVDENGRLLGTVTDGDIRRALLKGLSLDD-PVSEVM 64 Query: 290 IKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLL 336 +NP + + L+R+ +I L ++D+ + +G+ DLL Sbjct: 65 NRNPITAKVGSSREEILALMRERSIRHLPILDEEGRVVGLATLDDLL 111 >gnl|CDD|73085 cd04585, CBS_pair_ACT_assoc2, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the acetoin utilization proteins in bacteria. Acetoin is a product of fermentative metabolism in many prokaryotic and eukaryotic microorganisms. They produce acetoin as an external carbon storage compound and then later reuse it as a carbon and energy source during their stationary phase and sporulation. In addition these CBS domains are associated with a downstream ACT domain, which is linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. Pairs of ACT domains bind specifically to a particular amino acid leading to regulation of the linked enzyme. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 122 Score = 66.4 bits (162), Expect = 1e-11 Identities = 33/112 (29%), Positives = 56/112 (50%), Gaps = 13/112 (11%) Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR------------NFHKDLNTLSV 285 L++A+ ++ E + VVD G KL GI+T+ D+ + L+ + V Sbjct: 11 SLMEALKLMKENSIRRLPVVDRG-KLVGIVTDRDLKLASPSKATTLDIWELYYLLSKIKV 69 Query: 286 EDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 D+M ++P + D + A +L+ + IS L VVDD + +GI+ DL R Sbjct: 70 SDIMTRDPITVSPDASVEEAAELMLERKISGLPVVDDQGRLVGIITESDLFR 121 Score = 36.7 bits (85), Expect = 0.009 Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 1/48 (2%) Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338 KNP + DT L A++L+++++I L VVD K +GIV DL Sbjct: 1 KNPITVTPDTSLMEALKLMKENSIRRLPVVDR-GKLVGIVTDRDLKLA 47 >gnl|CDD|73101 cd04601, CBS_pair_IMPDH, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a key role in the regulation of cell proliferation and differentiation. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain in IMPDH have been associated with retinitis pigmentosa.. Length = 110 Score = 64.3 bits (157), Expect = 4e-11 Identities = 32/101 (31%), Positives = 52/101 (51%), Gaps = 4/101 (3%) Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVIL 297 + +A+ +++E + VVD+ KL GI+T D+ F DL+ V +VM + Sbjct: 12 TVAEALELMAEYGISGLPVVDDDGKLVGIVTNRDL--RFETDLDK-PVSEVMTPENLLTT 68 Query: 298 E-DTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 T L A++LL +H I L VVDD K G++ D+ + Sbjct: 69 VEGTSLEEALELLHEHKIEKLPVVDDEGKLKGLITVKDIEK 109 Score = 38.1 bits (89), Expect = 0.003 Identities = 20/49 (40%), Positives = 30/49 (61%), Gaps = 1/49 (2%) Query: 290 IKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338 I++P + D + A++L+ ++ IS L VVDD K +GIV D LRF Sbjct: 1 IRDPITVSPDATVAEALELMAEYGISGLPVVDDDGKLVGIVTNRD-LRF 48 Score = 34.7 bits (80), Expect = 0.043 Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 1/53 (1%) Query: 220 ASDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI 272 S+VM + + G L +A+ +L E + + VVD+ KLKG+IT DI Sbjct: 56 VSEVMTPENLL-TTVEGTSLEEALELLHEHKIEKLPVVDDEGKLKGLITVKDI 107 >gnl|CDD|73105 cd04605, CBS_pair_MET2_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the MET2 domain. Met2 is a key enzyme in the biosynthesis of methionine. It encodes a homoserine transacetylase involved in converting homoserine to O-acetyl homoserine. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 110 Score = 64.1 bits (156), Expect = 5e-11 Identities = 34/97 (35%), Positives = 53/97 (54%), Gaps = 2/97 (2%) Query: 241 DAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVILEDT 300 +A ++ E+ + VVDE +L GI+T DI + +D SVED+M +N D Sbjct: 15 EAAKLMIEENINHLPVVDEDGRLVGIVTSWDISKAVARDKK--SVEDIMTRNVITATPDE 72 Query: 301 LLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 + VA + + +HNIS L VVD + IGI+ D+ + Sbjct: 73 PIDVAARKMERHNISALPVVDAENRVIGIITSEDISK 109 Score = 26.7 bits (59), Expect = 9.1 Identities = 11/37 (29%), Positives = 17/37 (45%) Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR 274 P+ A + + VVD ++ GIIT DI + Sbjct: 73 PIDVAARKMERHNISALPVVDAENRVIGIITSEDISK 109 >gnl|CDD|73087 cd04587, CBS_pair_CAP-ED_DUF294_PBI_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain. Members of CAP_ED, include CAP which binds cAMP, FNR (fumarate and nitrate reductase) which uses an iron-sulfur cluster to sense oxygen, and CooA a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. DUF294 is a putative nucleotidyltransferase with a conserved DxD motif. The PB1 domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 113 Score = 64.1 bits (156), Expect = 5e-11 Identities = 35/111 (31%), Positives = 48/111 (43%), Gaps = 4/111 (3%) Query: 228 DSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI-FRNF--HKDLNTLS 284 V + +A ++ EKR CV V+D KL GI T DI R D + Sbjct: 1 TKPATVSPTTTVQEAAKLMREKRVSCVLVMDGN-KLVGIFTSKDIALRVVAQGLDPESTL 59 Query: 285 VEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDL 335 VE VM NP DT + A+ L+ Q L VVD + +G++ L Sbjct: 60 VERVMTPNPVCATSDTPVLEALHLMVQGKFRHLPVVDKSGQVVGLLDVTKL 110 Score = 26.7 bits (59), Expect = 9.2 Identities = 7/38 (18%), Positives = 22/38 (57%) Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRN 275 P+++A+ ++ + +F + VVD+ ++ G++ + Sbjct: 76 PVLEALHLMVQGKFRHLPVVDKSGQVVGLLDVTKLTHA 113 >gnl|CDD|73121 cd04622, CBS_pair_9, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 113 Score = 64.0 bits (156), Expect = 6e-11 Identities = 34/104 (32%), Positives = 55/104 (52%), Gaps = 4/104 (3%) Query: 237 CPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI-FRNF--HKDLNTLSVEDVMIKNP 293 + +A ++ E G + V + +L GI+T+ DI R +D +T +V DVM + Sbjct: 10 DTIREAARLMREHDVGALPVCEND-RLVGIVTDRDIVVRAVAEGRDPDTTTVGDVMTRGV 68 Query: 294 KVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 + ED + A +L+R+H + L VVDD + +GIV DL R Sbjct: 69 VTVTEDDDVDEAARLMREHQVRRLPVVDDDGRLVGIVSLGDLAR 112 Score = 27.8 bits (62), Expect = 4.7 Identities = 10/40 (25%), Positives = 23/40 (57%), Gaps = 1/40 (2%) Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIV 330 ++ + D + A +L+R+H++ L V ++ + +GIV Sbjct: 1 RDVVTVSPDDTIREAARLMREHDVGALPVCEN-DRLVGIV 39 >gnl|CDD|73088 cd04588, CBS_pair_CAP-ED_DUF294_assoc_arch, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the archaeal CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain. Members of CAP_ED, include CAP which binds cAMP, FNR (fumarate and nitrate reductase) which uses an iron-sulfur cluster to sense oxygen, and CooA a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. DUF294 is a putative nucleotidyltransferase with a conserved DxD motif. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 110 Score = 62.1 bits (151), Expect = 2e-10 Identities = 36/106 (33%), Positives = 55/106 (51%), Gaps = 1/106 (0%) Query: 232 LVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIK 291 + L +A + + VVD+G KL GI+T DI + L V+DVM K Sbjct: 5 TLNPNATLREAARLFNTHHIHGAPVVDDG-KLVGIVTLSDIAHAIARGLELAKVKDVMTK 63 Query: 292 NPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 + I ED L A++L+ +HN+ L+V DD + +GI+ D+LR Sbjct: 64 DVITIDEDEQLYDAIRLMNKHNVGRLIVTDDEGRPVGIITRTDILR 109 >gnl|CDD|73135 cd04637, CBS_pair_24, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 122 Score = 60.3 bits (146), Expect = 8e-10 Identities = 33/112 (29%), Positives = 60/112 (53%), Gaps = 13/112 (11%) Query: 239 LIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNF----------HKDLNTLS--VE 286 L + I + +F + VV++ + L G+I++ D + KDL TL+ Sbjct: 12 LEEVREIFEKHKFHHLLVVEDNE-LVGVISDRDYLKAISPFLGTAGETEKDLATLNRRAH 70 Query: 287 DVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338 +M ++P + DT + A +LL +++IS L VVD+ + IGI+ + DLL++ Sbjct: 71 QIMTRDPITVSPDTPVDEASKLLLENSISCLPVVDENGQLIGIITWKDLLKY 122 Score = 39.1 bits (91), Expect = 0.002 Identities = 23/62 (37%), Positives = 32/62 (51%), Gaps = 2/62 (3%) Query: 213 LGTLFVCASDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI 272 L TL A +M + D I V P+ +A +L E C+ VVDE +L GIIT D+ Sbjct: 62 LATLNRRAHQIM-TRDPI-TVSPDTPVDEASKLLLENSISCLPVVDENGQLIGIITWKDL 119 Query: 273 FR 274 + Sbjct: 120 LK 121 >gnl|CDD|73119 cd04620, CBS_pair_7, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 115 Score = 60.2 bits (146), Expect = 9e-10 Identities = 36/104 (34%), Positives = 54/104 (51%), Gaps = 4/104 (3%) Query: 231 PLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR--NFHKDLNTLSVEDV 288 V P+ DAI ++S++ +V E +L GI TE DI R KDL+ L + +V Sbjct: 4 LTVTPDTPVADAIALMSQQGDSSCVLVVEKGRLLGIFTERDIVRLTAIGKDLSDLPIGEV 63 Query: 289 MIKNPKVILEDTLLTV--AMQLLRQHNISVLMVVDDCQKAIGIV 330 M + + E + + A+ L RQH I L V+DD + IG+V Sbjct: 64 MTQPVVTLQESEIQDIFTALSLFRQHQIRHLPVLDDQGQLIGLV 107 >gnl|CDD|73129 cd04631, CBS_pair_18, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 125 Score = 59.8 bits (145), Expect = 9e-10 Identities = 37/120 (30%), Positives = 52/120 (43%), Gaps = 14/120 (11%) Query: 233 VKIGCPLIDAITILSEKRFGCVAVVDEGQ-KLKGIITEGDIFRNFHKDLNTLS------- 284 V P+++A I+ F + VVDEG KL GIIT DI + Sbjct: 6 VPPTTPIMEAAKIMVRNGFRRLPVVDEGTGKLVGIITATDILKYLGGGEKFNKIKTGNGL 65 Query: 285 ------VEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338 V +M +N I D + A +L+ + + L VVDD K +GIV DLL+ Sbjct: 66 EAINEPVRSIMTRNVITITPDDSIKDAAELMLEKRVGGLPVVDDDGKLVGIVTERDLLKA 125 >gnl|CDD|73086 cd04586, CBS_pair_BON_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the BON (bacterial OsmY and nodulation domain) domain. BON is a putative phospholipid-binding domain found in a family of osmotic shock protection proteins. It is also found in some secretins and a group of potential haemolysins. Its likely function is attachment to phospholipid membranes. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 135 Score = 59.4 bits (144), Expect = 1e-09 Identities = 32/133 (24%), Positives = 54/133 (40%), Gaps = 27/133 (20%) Query: 231 PLVKIG--CPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNF------------ 276 +V + + +A ++ + + VVD+ +L GI++EGD+ R Sbjct: 3 DVVTVSPETSVAEAARLMLDNHISGLPVVDDDGRLVGIVSEGDLLRRAELGTERRRARWL 62 Query: 277 ------------HKDLNTLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQ 324 + V DVM + + EDT L +L+ +H I + VV Sbjct: 63 DLLAGAEELAAAFVRSHGRKVADVMTRPVVTVGEDTPLAEVAELMEEHRIKRVPVVRG-G 121 Query: 325 KAIGIVHFLDLLR 337 + +GIV DLLR Sbjct: 122 RLVGIVSRADLLR 134 >gnl|CDD|88405 cd05008, SIS_GlmS_GlmD_1, SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal glutaminase domain and two C-terminal SIS domains and catalyzes the first step in hexosamine metabolism, converting fructose 6-phosphate into glucosamine 6-phosphate using glutamine as nitrogen source. The glutaminase domain hydrolyzes glutamine to glutamate and ammonia. Ammonia is transferred through a channel to the isomerase domain for glucosamine 6-phosphate synthesis. The end product of the pathway is N-acetylglucosamine, which plays multiple roles in eukaryotic cells including being a building block of bacterial and fungal cell walls. In the absence of glutamine, GlmS catalyzes the isomerization of fructose 6-phosphate into glucose 6- phosphate (PGI-like activity). Glucosamine-6-phosphate deaminase (GlmD) contains two SIS domains and catalyzes the deamination and isomerization of glucosamine-6-phosphate into fructose-6-phosphate with the release of ammonia; in presence of high ammonia concentration, GlmD can catalyze the reverse reaction.. Length = 126 Score = 58.6 bits (142), Expect = 2e-09 Identities = 39/128 (30%), Positives = 54/128 (42%), Gaps = 3/128 (2%) Query: 66 RVVITGIGKSGHIGSKLASTLASTGTPSFFVHAAEASHGDLGMITRDDLIIVLSWSGSSD 125 R++I G G S H L V AA ++ D L+I +S SG + Sbjct: 1 RILIVGCGTSYHAALVAKYLLERLAGIPVEVEAASEFRYRRPLLDEDTLVIAISQSGETA 60 Query: 126 ELKAILYYARRFSIPLIAITSENKSVVACHADIVLTLPKEPESCPHGLAPTTSAIMQLAI 185 + A L A+ +AIT+ S +A AD VL L PE +A T + QL Sbjct: 61 DTLAALRLAKEKGAKTVAITNVVGSTLAREADYVLYLRAGPE---ISVAATKAFTSQLLA 117 Query: 186 GDALAIAL 193 LA+AL Sbjct: 118 LLLLALAL 125 >gnl|CDD|73084 cd04584, CBS_pair_ACT_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the acetoin utilization proteins in bacteria. Acetoin is a product of fermentative metabolism in many prokaryotic and eukaryotic microorganisms. They produce acetoin as an external carbon storage compound and then later reuse it as a carbon and energy source during their stationary phase and sporulation. In addition these CBS domains are associated with a downstream ACT domain, which is linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. Pairs of ACT domains bind specifically to a particular amino acid leading to regulation of the linked enzyme. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 121 Score = 58.3 bits (141), Expect = 3e-09 Identities = 32/110 (29%), Positives = 55/110 (50%), Gaps = 12/110 (10%) Query: 239 LIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLS-----------VED 287 + +A+ ++ E + + VVDE +L GI+T+ D+ TLS V++ Sbjct: 12 IAEALELMREHKIRHLPVVDEEGRLVGIVTDRDLRDASPSPFTTLSEHELYLLLKMPVKE 71 Query: 288 VMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 +M K+ + + A L+R+H I L VV+D + +GI+ DLLR Sbjct: 72 IMTKDVITVHPLDTVEEAALLMREHRIGCLPVVED-GRLVGIITETDLLR 120 Score = 39.4 bits (92), Expect = 0.002 Identities = 16/37 (43%), Positives = 25/37 (67%), Gaps = 1/37 (2%) Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR 274 + +A ++ E R GC+ VV++G +L GIITE D+ R Sbjct: 85 TVEEAALLMREHRIGCLPVVEDG-RLVGIITETDLLR 120 Score = 31.3 bits (71), Expect = 0.39 Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 1/40 (2%) Query: 298 EDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 T+ A++L+R+H I L VVD+ + +GIV DL Sbjct: 9 TTTIAE-ALELMREHKIRHLPVVDEEGRLVGIVTDRDLRD 47 >gnl|CDD|73142 cd04800, CBS_pair_CAP-ED_DUF294_PBI_assoc2, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain. Members of CAP_ED, include CAP which binds cAMP, FNR (fumarate and nitrate reductase) which uses an iron-sulfur cluster to sense oxygen, and CooA a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. DUF294 is a putative nucleotidyltransferase with a conserved DxD motif. The PB1 domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 111 Score = 58.2 bits (141), Expect = 3e-09 Identities = 33/103 (32%), Positives = 55/103 (53%), Gaps = 4/103 (3%) Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI-FRNFHKDLN-TLSVEDVMIKNPKV 295 + +A +++E R + VVD+G +L GI+T+ D+ R + L+ V +VM P Sbjct: 11 TIREAARLMTEHRVSSLLVVDDG-RLVGIVTDRDLRNRVVAEGLDPDTPVSEVMTAPPIT 69 Query: 296 ILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338 I D + A+ L+ + I L VVDD + +G++ DLLR Sbjct: 70 IPPDATVFEALLLMLERGIHHLPVVDD-GRLVGVISATDLLRL 111 >gnl|CDD|73115 cd04615, CBS_pair_2, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 113 Score = 58.0 bits (140), Expect = 4e-09 Identities = 32/107 (29%), Positives = 50/107 (46%), Gaps = 2/107 (1%) Query: 233 VKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNF--HKDLNTLSVEDVMI 290 V + + A+ + + VVD+ ++L GIIT D+ ++L V +VM Sbjct: 6 VVLNTDIARAVAEMYTSGSRALPVVDDKKRLVGIITRYDVLSYALESEELKDAKVREVMN 65 Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 I + + A L+ +NIS L V+DD K GIV D+LR Sbjct: 66 SPVITIDANDSIAKARWLMSNNNISRLPVLDDKGKVGGIVTEDDILR 112 >gnl|CDD|73136 cd04638, CBS_pair_25, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 106 Score = 56.8 bits (137), Expect = 8e-09 Identities = 32/97 (32%), Positives = 53/97 (54%), Gaps = 5/97 (5%) Query: 241 DAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVILEDT 300 D + +L E + V VV + +L GIIT D+ RN ++ L +M ++P + D Sbjct: 14 DVLELLKEYKVSGVPVVKKSGELVGIITRKDLLRNPEEEQLAL----LMTRDPPTVSPDD 69 Query: 301 LLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 + A +L+ ++NI + VVDD K +GIV D++R Sbjct: 70 DVKEAAKLMVENNIRRVPVVDD-GKLVGIVTVADIVR 105 >gnl|CDD|73083 cd04583, CBS_pair_ABC_OpuCA_assoc2, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the ABC transporter OpuCA. OpuCA is the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment but the function of the CBS domains in OpuCA remains unknown. In the related ABC transporter, OpuA, the tandem CBS domains have been shown to function as sensors for ionic strength, whereby they control the transport activity through an electronic switching mechanism. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. They are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 109 Score = 55.6 bits (134), Expect = 2e-08 Identities = 23/92 (25%), Positives = 50/92 (54%), Gaps = 3/92 (3%) Query: 239 LIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVILE 298 L +AI ++ +K+ + VVD+ KL GI++ + + + + S+ED+M+++ + Sbjct: 13 LAEAIKLMRDKKVDSLLVVDKDNKLLGIVSLESLEQAYKEAK---SLEDIMLEDVFTVQP 69 Query: 299 DTLLTVAMQLLRQHNISVLMVVDDCQKAIGIV 330 D L + L+ + + VVD+ K +G++ Sbjct: 70 DASLRDVLGLVLKRGPKYVPVVDEDGKLVGLI 101 Score = 34.4 bits (79), Expect = 0.043 Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 2/51 (3%) Query: 220 ASDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEG 270 D+M + V+ L D + ++ ++ V VVDE KL G+IT Sbjct: 56 LEDIMLE--DVFTVQPDASLRDVLGLVLKRGPKYVPVVDEDGKLVGLITRS 104 Score = 33.2 bits (76), Expect = 0.10 Identities = 18/41 (43%), Positives = 24/41 (58%) Query: 290 IKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIV 330 IKNP I D L A++L+R + L+VVD K +GIV Sbjct: 1 IKNPVTITPDRTLAEAIKLMRDKKVDSLLVVDKDNKLLGIV 41 >gnl|CDD|73095 cd04595, CBS_pair_DHH_polyA_Pol_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with an upstream DHH domain which performs a phosphoesterase function and a downstream polyA polymerase domain. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 110 Score = 54.8 bits (132), Expect = 4e-08 Identities = 30/90 (33%), Positives = 49/90 (54%), Gaps = 2/90 (2%) Query: 250 RFGCVAV-VDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVILEDTLLTVAMQL 308 R+G A+ V EG ++ GII+ D+ + L V+D M + + DT L+ +L Sbjct: 22 RYGHTALPVVEGGRVVGIISRRDVEKALRHGLGHAPVKDYMSTDVVTVPPDTPLSEVQEL 81 Query: 309 LRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338 + +H+I + VV+D + +GIV DLLR Sbjct: 82 MVEHDIGRVPVVED-GRLVGIVTRTDLLRT 110 >gnl|CDD|73113 cd04613, CBS_pair_SpoIVFB_EriC_assoc2, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with either the SpoIVFB domain (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) or the chloride channel protein EriC. SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A ), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. EriC is involved in inorganic ion transport and metabolism. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 114 Score = 54.8 bits (132), Expect = 4e-08 Identities = 28/102 (27%), Positives = 47/102 (46%), Gaps = 3/102 (2%) Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKD--LNTLSVEDVMIKNPKV 295 PL + + +++ VVD+ +L GI++ DI + + D+M K P V Sbjct: 11 PLNELLDVIAHSPENNFPVVDDDGRLVGIVSLDDIREILFDPSLYDLVVASDIMTKPPVV 70 Query: 296 ILEDTLLTVAMQLLRQHNISVLMVVDDCQ-KAIGIVHFLDLL 336 + + L A++ + L VVDD K +GI+ DLL Sbjct: 71 VYPEDSLEDALKKFEDSDYEQLPVVDDDPGKLLGILSRSDLL 112 Score = 29.3 bits (66), Expect = 1.6 Identities = 13/48 (27%), Positives = 22/48 (45%) Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338 ++ I EDT L + ++ + VVDD + +GIV D+ Sbjct: 1 RDVVTIPEDTPLNELLDVIAHSPENNFPVVDDDGRLVGIVSLDDIREI 48 >gnl|CDD|73112 cd04612, CBS_pair_SpoIVFB_EriC_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with either the SpoIVFB domain (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) or the chloride channel protein EriC. SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A ), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. EriC is involved in inorganic ion transport and metabolism. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 111 Score = 54.5 bits (131), Expect = 4e-08 Identities = 34/102 (33%), Positives = 53/102 (51%), Gaps = 2/102 (1%) Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR-NFHKDLNTLSVEDVMIKNPKVI 296 + + + ++ +R VVD+G +L GI+T DI R T+ V DVM ++P Sbjct: 11 TVDEVLALMFGERHRGYPVVDDG-RLVGIVTLADIRRVPAEGREATVLVGDVMTRDPVTA 69 Query: 297 LEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338 D L A++ + + +I L VVDD + +GIV DLLR Sbjct: 70 SPDETLRDALKRMAERDIGRLPVVDDSGRLVGIVSRSDLLRA 111 Score = 37.9 bits (88), Expect = 0.004 Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 2/55 (3%) Query: 220 ASDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR 274 DVM L DA+ ++E+ G + VVD+ +L GI++ D+ R Sbjct: 58 VGDVMT--RDPVTASPDETLRDALKRMAERDIGRLPVVDDSGRLVGIVSRSDLLR 110 >gnl|CDD|144238 pfam00571, CBS, CBS domain. CBS domains are small intracellular modules that pair together to form a stable globular domain. This family represents a single CBS domain. Pairs of these domains have been termed a Bateman domain. CBS domains have been shown to bind ligands with an adenosyl group such as AMP, ATP and S-AdoMet. CBS domains are found attached to a wide range of other protein domains suggesting that CBS domains may play a regulatory role making proteins sensitive to adenosyl carrying ligands. The region containing the CBS domains in Cystathionine-beta synthase is involved in regulation by S-AdoMet. CBS domain pairs from AMPK bind AMP or ATP. The CBS domains from IMPDH and the chloride channel CLC2 bind ATP. Length = 57 Score = 54.5 bits (132), Expect = 4e-08 Identities = 23/54 (42%), Positives = 34/54 (62%) Query: 285 VEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338 V+D+M + + DT L A++L+R++ IS L VVD+ K +GIV DLLR Sbjct: 1 VKDIMTPDVVTVPPDTSLEEALELMRENGISRLPVVDEDGKLVGIVTLRDLLRA 54 Score = 49.9 bits (120), Expect = 1e-06 Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 2/59 (3%) Query: 220 ASDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHK 278 D+M + V L +A+ ++ E + VVDE KL GI+T D+ R Sbjct: 1 VKDIMTP--DVVTVPPDTSLEEALELMRENGISRLPVVDEDGKLVGIVTLRDLLRALLG 57 >gnl|CDD|144171 pfam00478, IMPDH, IMP dehydrogenase / GMP reductase domain. This family is involved in biosynthesis of guanosine nucleotide. Members of this family contain a TIM barrel structure. In the inosine monophosphate dehydrogenases 2 CBS domains pfam00571 are inserted in the TIM barrel. This family is a member of the common phosphate binding site TIM barrel family. Length = 467 Score = 54.2 bits (131), Expect = 6e-08 Identities = 22/100 (22%), Positives = 45/100 (45%), Gaps = 2/100 (2%) Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVIL 297 + +A+ + V V ++G+ L G++ L+ +SV M ++ Sbjct: 100 TVAEALELKERYGISGVPVTEDGKLLGGLVGIRT--SRDIDFLSKVSVVMTMTEDLVTAP 157 Query: 298 EDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 E L A ++L +H I L +VDD + +G++ D+ + Sbjct: 158 EGITLEEANEILHEHKIEKLPIVDDDGELVGLITRKDIEK 197 Score = 34.2 bits (79), Expect = 0.049 Identities = 17/55 (30%), Positives = 27/55 (49%) Query: 221 SDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRN 275 S VM + + G L +A IL E + + +VD+ +L G+IT DI + Sbjct: 144 SVVMTMTEDLVTAPEGITLEEANEILHEHKIEKLPIVDDDGELVGLITRKDIEKA 198 >gnl|CDD|73145 cd04803, CBS_pair_15, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 122 Score = 52.9 bits (127), Expect = 1e-07 Identities = 32/112 (28%), Positives = 51/112 (45%), Gaps = 11/112 (9%) Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR-----------NFHKDLNTLSVE 286 L DA ++ E R + VV+E KL G++T+ D+ R + V Sbjct: 11 SLADAEELMREHRIRHLPVVNEDGKLVGLLTQRDLLRAALSSLSDNGEESLTKERDVPVA 70 Query: 287 DVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338 +VM + + DT L A +++ ++ I L VVDD +GI+ D LR Sbjct: 71 EVMKTDVLTVTPDTPLREAAEIMVENKIGCLPVVDDKGTLVGIITRSDFLRL 122 Score = 47.1 bits (112), Expect = 6e-06 Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 2/54 (3%) Query: 221 SDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR 274 ++VM + + V PL +A I+ E + GC+ VVD+ L GIIT D R Sbjct: 70 AEVMKT--DVLTVTPDTPLREAAEIMVENKIGCLPVVDDKGTLVGIITRSDFLR 121 Score = 33.3 bits (76), Expect = 0.10 Identities = 17/50 (34%), Positives = 27/50 (54%) Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRFGI 340 + ED L A +L+R+H I L VV++ K +G++ DLLR + Sbjct: 1 SPVVTLSEDDSLADAEELMREHRIRHLPVVNEDGKLVGLLTQRDLLRAAL 50 >gnl|CDD|88402 cd05005, SIS_PHI, Hexulose-6-phosphate isomerase (PHI). PHI is a member of the SIS (Sugar ISomerase domain) superfamily. In the ribulose monophosphate pathway of formaldehyde fixation, hexulose-6-phosphate synthase catalyzes the condensation of ribulose-5-phosphate with formadelhyde to become hexulose-6-phosphate, which is then isomerized to fructose-6-phosphate by PHI.. Length = 179 Score = 52.9 bits (127), Expect = 1e-07 Identities = 38/163 (23%), Positives = 63/163 (38%), Gaps = 12/163 (7%) Query: 52 QFHCAVEKIKAIKGRVVITGIGKSGHIGSKLASTLASTGTPSFFVHAAEASHGDLGMITR 111 + + I K R+ + G G+SG + A L G + V I Sbjct: 22 ELDKLISAILNAK-RIFVYGAGRSGLVAKAFAMRLMHLGLNVYVVGETTTPA-----IGP 75 Query: 112 DDLIIVLSWSGSSDELKAILYYARRFSIPLIAITSENKSVVACHADIVLTLP----KEPE 167 DL+I +S SG + + A++ ++ ITS S +A AD+V+ +P + Sbjct: 76 GDLLIAISGSGETSSVVNAAEKAKKAGAKVVLITSNPDSPLAKLADVVVVIPAATKDDHG 135 Query: 168 SCPHGLAPTTSAIMQLA--IGDALAIALLESRNFSENDFYVLH 208 + P + Q A DA+ L+E SE + H Sbjct: 136 GEHKSIQPLGTLFEQSALVFLDAVIAKLMEELGVSEEEMKKRH 178 >gnl|CDD|73141 cd04643, CBS_pair_30, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 116 Score = 52.9 bits (127), Expect = 1e-07 Identities = 31/105 (29%), Positives = 48/105 (45%), Gaps = 9/105 (8%) Query: 233 VKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI------FRNFH-KDLNTLSV 285 V+ L A+ +L++ + + V+D+ K G I+ DI N + L L V Sbjct: 6 VQDTNTLRHALLVLTKHGYSAIPVLDKEGKYVGTISLTDILWKLKGLENLDLERLVDLKV 65 Query: 286 EDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIV 330 DVM + VI++D + + LL L VVDD IGI+ Sbjct: 66 IDVMNTDVPVIIDDADIEEILHLLIDQPF--LPVVDDDGIFIGII 108 >gnl|CDD|73099 cd04599, CBS_pair_GGDEF_assoc2, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the GGDEF (DiGuanylate-Cyclase (DGC)) domain. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and is thought to be involved in regulating cell surface adhesiveness in bacteria. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 105 Score = 52.2 bits (125), Expect = 2e-07 Identities = 30/97 (30%), Positives = 47/97 (48%), Gaps = 6/97 (6%) Query: 241 DAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVILEDT 300 A ++ + R G + VV++G KL GIIT D+ R H N L V D M + I + Sbjct: 14 RAARLMEKHRIGGLPVVEDG-KLVGIITSRDV-RRAHP--NRL-VADAMTREVVTISPEA 68 Query: 301 LLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 L A +L+ + I L V+ + K +GI+ + Sbjct: 69 SLLEAKRLMEEKKIERLPVLRER-KLVGIITKGTIAL 104 >gnl|CDD|73134 cd04636, CBS_pair_23, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 132 Score = 51.4 bits (123), Expect = 3e-07 Identities = 35/122 (28%), Positives = 55/122 (45%), Gaps = 23/122 (18%) Query: 239 LIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHK-------------------- 278 L D + IL + V VVD ++ GI++EGD+ R +K Sbjct: 12 LRDVVEILLTGKISGVPVVDNEGRVVGIVSEGDLIRKIYKGKGLFYVTLLYSVIFLDESK 71 Query: 279 --DLNTLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLL 336 L VE++M K + EDT + +++ + NI L VVDD K +GI+ D++ Sbjct: 72 IKKLLGKKVEEIMTKKVITVDEDTTIEDVARIMSKKNIKRLPVVDD-GKLVGIISRGDII 130 Query: 337 RF 338 R Sbjct: 131 RS 132 Score = 36.8 bits (85), Expect = 0.008 Identities = 18/42 (42%), Positives = 24/42 (57%), Gaps = 1/42 (2%) Query: 233 VKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR 274 V + D I+S+K + VVD+G KL GII+ GDI R Sbjct: 91 VDEDTTIEDVARIMSKKNIKRLPVVDDG-KLVGIISRGDIIR 131 Score = 34.5 bits (79), Expect = 0.039 Identities = 15/47 (31%), Positives = 26/47 (55%) Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 K+ + +D L +++L IS + VVD+ + +GIV DL+R Sbjct: 1 KDVITVKKDDTLRDVVEILLTGKISGVPVVDNEGRVVGIVSEGDLIR 47 >gnl|CDD|73100 cd04600, CBS_pair_HPP_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the HPP motif domain. These proteins are integral membrane proteins with four transmembrane spanning helices. The function of these proteins is uncertain, but they are thought to be transporters. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 124 Score = 51.4 bits (123), Expect = 4e-07 Identities = 29/111 (26%), Positives = 49/111 (44%), Gaps = 12/111 (10%) Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDL------------NTLSV 285 L +A +L R + VVD ++L GI+T+ D+ R+ D +V Sbjct: 12 SLEEAWALLRRHRIKALPVVDGDRRLVGIVTQRDLLRHARPDGRRPLRGRLRGRDKPETV 71 Query: 286 EDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLL 336 D+M + DT + + LL + VVD+ ++ +GIV DL+ Sbjct: 72 GDIMSPPVVTVRPDTPIAELVPLLADGGHHHVPVVDEDRRLVGIVTQTDLI 122 Score = 41.4 bits (97), Expect = 4e-04 Identities = 20/39 (51%), Positives = 24/39 (61%) Query: 299 DTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 DT L A LLR+H I L VVD ++ +GIV DLLR Sbjct: 10 DTSLEEAWALLRRHRIKALPVVDGDRRLVGIVTQRDLLR 48 Score = 36.7 bits (85), Expect = 0.009 Identities = 15/54 (27%), Positives = 29/54 (53%), Gaps = 2/54 (3%) Query: 219 CASDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI 272 D+M + V+ P+ + + +L++ V VVDE ++L GI+T+ D+ Sbjct: 70 TVGDIMSPP--VVTVRPDTPIAELVPLLADGGHHHVPVVDEDRRLVGIVTQTDL 121 >gnl|CDD|88401 cd04795, SIS, SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.. Length = 87 Score = 51.1 bits (122), Expect = 4e-07 Identities = 31/81 (38%), Positives = 45/81 (55%), Gaps = 2/81 (2%) Query: 67 VVITGIGKSGHIGSKLASTLAS-TGTPSFFVHAAEASHGD-LGMITRDDLIIVLSWSGSS 124 + + GIG SG I + A L TG + A E H L ++ + D++I LS+SG + Sbjct: 1 IFVIGIGGSGAIAAYFALELLELTGIEVVALIATELEHASLLSLLRKGDVVIALSYSGRT 60 Query: 125 DELKAILYYARRFSIPLIAIT 145 +EL A L A+ IP+IAIT Sbjct: 61 EELLAALEIAKELGIPVIAIT 81 >gnl|CDD|73102 cd04602, CBS_pair_IMPDH_2, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a key role in the regulation of cell proliferation and differentiation. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain in IMPDH have been associated with retinitis pigmentosa.. Length = 114 Score = 50.9 bits (122), Expect = 5e-07 Identities = 28/102 (27%), Positives = 53/102 (51%), Gaps = 8/102 (7%) Query: 241 DAITILSEKRFGCVAVVDEGQ---KLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVIL 297 D + I +K F + V ++G+ KL GI+T DI +F D + + +VM +++ Sbjct: 15 DVLEIKEKKGFSGIPVTEDGKSGGKLLGIVTSRDI--DFLTD-SETPLSEVMTPREVLVV 71 Query: 298 EDTLLTV--AMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 T +T+ A ++LR+ L +V+D + + +V DL + Sbjct: 72 APTGITLEEANEILRESKKGKLPIVNDDGELVALVTRSDLKK 113 Score = 31.7 bits (72), Expect = 0.28 Identities = 15/55 (27%), Positives = 30/55 (54%) Query: 221 SDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRN 275 S+VM + + + G L +A IL E + G + +V++ +L ++T D+ +N Sbjct: 60 SEVMTPREVLVVAPTGITLEEANEILRESKKGKLPIVNDDGELVALVTRSDLKKN 114 >gnl|CDD|73144 cd04802, CBS_pair_3, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 112 Score = 51.0 bits (122), Expect = 5e-07 Identities = 33/108 (30%), Positives = 51/108 (47%), Gaps = 5/108 (4%) Query: 233 VKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNF---HKDLNTLSVEDVM 289 V + +A I++E G + VVD K GIITE D+ + + + V +VM Sbjct: 6 VDPDTTVYEAANIMTENNIGRLIVVDNE-KPVGIITERDLVKKVVSRNLKPREVPVGEVM 64 Query: 290 IKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 I + L A +L+ +H I L VVDD + +GIV D++ Sbjct: 65 STPLITIDPNASLNEAAKLMAKHGIKRLPVVDD-DELVGIVTTTDIVM 111 Score = 29.4 bits (66), Expect = 1.4 Identities = 16/47 (34%), Positives = 29/47 (61%), Gaps = 1/47 (2%) Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 KN + DT + A ++ ++NI L+VVD+ +K +GI+ DL++ Sbjct: 1 KNVITVDPDTTVYEAANIMTENNIGRLIVVDN-EKPVGIITERDLVK 46 >gnl|CDD|32404 COG2222, AgaS, Predicted phosphosugar isomerases [Cell envelope biogenesis, outer membrane]. Length = 340 Score = 50.7 bits (121), Expect = 6e-07 Identities = 32/120 (26%), Positives = 48/120 (40%), Gaps = 4/120 (3%) Query: 66 RVVITGIGKSGHIGSKLASTLAS-TGTPSFFVHAAEASHGDLGMITRDDLIIVLSWSGSS 124 R++ G G S H + L G + A+E + D L+I S SG++ Sbjct: 41 RILFVGCGSSLHAATPAKYLLERELGLLVAAIPASEFLTNGAKYLGEDSLVIAFSQSGNT 100 Query: 125 DELKAILYYARRFSIPLIAITSENKSVVACHADIVLTLPKEPESCPHGLAPTTSAIMQLA 184 E A A+ IA+T+E S +A AD V+ E+ +A T S L Sbjct: 101 PESVAAAELAKEGGALTIALTNEEDSPLARAADYVIPYLAGEEA---SVAATKSFTASLL 157 Score = 29.9 bits (67), Expect = 0.94 Identities = 35/183 (19%), Positives = 68/183 (37%), Gaps = 22/183 (12%) Query: 26 CALRSIIAEKRGLSSLESSLQG---ELSFQFHC-AVEKIKAIKGRVVITGIGKSGHIGSK 81 AL +++AE G + L ++L E + A E + I +G G+ Sbjct: 157 LALLALLAEYDGDAQLLAALPDLPLEAAKALEEDAQEFAEEYADEDRIYTLGSGPLYGAA 216 Query: 82 LASTLAS---TGTPSFFVHAAEASHGDLGMITRDDLIIVLSWSGSSDEL-KAILYYARRF 137 + L S + + E HG ++ +++ + EL + L + + + Sbjct: 217 YEAALKLKEMQWIHSEAISSGEFRHGPKELVEEGTPVLLFVSEDETRELDERALKFLKNY 276 Query: 138 SIPLIAITSENKSVVACHADIVLTLPKEPESCPHGLAPTTSAIMQLAIGDALAIALLESR 197 ++ I ++ D L L + H LAP ++ L + LA AL +R Sbjct: 277 GAKVLVIDAK---------DAALDLIDQRVR--HDLAP---PLLSLVVAQRLAYALAVAR 322 Query: 198 NFS 200 + Sbjct: 323 GHN 325 >gnl|CDD|73103 cd04603, CBS_pair_KefB_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the KefB (Kef-type K+ transport systems) domain which is involved in inorganic ion transport and metabolism. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 111 Score = 49.5 bits (118), Expect = 1e-06 Identities = 33/101 (32%), Positives = 54/101 (53%) Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVIL 297 PL +AI +++E V VVDE K+ G +T D+ D TL V +V I ++ Sbjct: 11 PLREAIKMINELGARAVVVVDEENKVLGQVTLSDLLEIGPNDYETLKVCEVYIVPVPIVY 70 Query: 298 EDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338 D+ +T +++ R+ V+ VVD K +G ++ +LLRF Sbjct: 71 CDSKVTDLLRIFRETEPPVVAVVDKEGKLVGTIYERELLRF 111 Score = 33.7 bits (77), Expect = 0.066 Identities = 20/64 (31%), Positives = 28/64 (43%), Gaps = 4/64 (6%) Query: 211 GKLGTLFVCASDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEG 270 TL VC + +P+V + D + I E VAVVD+ KL G I E Sbjct: 51 NDYETLKVCEVYI----VPVPIVYCDSKVTDLLRIFRETEPPVVAVVDKEGKLVGTIYER 106 Query: 271 DIFR 274 ++ R Sbjct: 107 ELLR 110 >gnl|CDD|73133 cd04635, CBS_pair_22, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 122 Score = 49.6 bits (118), Expect = 1e-06 Identities = 28/104 (26%), Positives = 50/104 (48%), Gaps = 11/104 (10%) Query: 245 ILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFH-----------KDLNTLSVEDVMIKNP 293 ++ E F + VV + +L GIIT DI R + + +VE +M Sbjct: 18 LMLESGFTGLPVVQKAGELIGIITRRDIIRAGSVRTSVEDQQRTQTKASPTVEKIMSTPV 77 Query: 294 KVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 + D + A++L+ +H+I L VV++ + +GIV D+L+ Sbjct: 78 YSVTPDDSIATAVELMLEHDIGRLPVVNEKDQLVGIVDRHDVLK 121 Score = 27.6 bits (61), Expect = 4.7 Identities = 12/51 (23%), Positives = 23/51 (45%) Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRFGII 341 + P D ++ L+ + + L VV + IGI+ D++R G + Sbjct: 1 REPVTCTPDDPVSKVWDLMLESGFTGLPVVQKAGELIGIITRRDIIRAGSV 51 >gnl|CDD|73131 cd04633, CBS_pair_20, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 121 Score = 49.4 bits (118), Expect = 2e-06 Identities = 35/117 (29%), Positives = 55/117 (47%), Gaps = 14/117 (11%) Query: 233 VKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI------------FRNFHKDL 280 V + A ++ + + V++ G KL GI+TE DI R+ + + Sbjct: 6 VSPDDRVSHARRLMLDHDISRLPVIEGG-KLVGIVTEKDIADALRSFRPLVRDRHQERRI 64 Query: 281 NTLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 L V D+M + I DT ++ L+ ++NI L VVDD K +GIV D+LR Sbjct: 65 RNLPVSDIMTRPVITIEPDTSVSDVASLMLENNIGGLPVVDD-GKLVGIVTRTDILR 120 >gnl|CDD|73127 cd04629, CBS_pair_16, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 114 Score = 49.0 bits (117), Expect = 2e-06 Identities = 27/106 (25%), Positives = 51/106 (48%), Gaps = 9/106 (8%) Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR-----NFHKDLNTLSVEDVMIKN 292 + +A+ L + + VVD+ L G ++E D + ++H D +V D+M Sbjct: 11 SVTEAVEKLLKSKISGGPVVDDNGNLVGFLSEQDCLKQLLESSYHCDG-VATVRDIMTTE 69 Query: 293 PKVI-LEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 + +D+++ +A QL+ + VVDD K +G + D+LR Sbjct: 70 VLTVSPDDSIVDLA-QLMLKAKPKRYPVVDD-GKLVGQISRRDVLR 113 Score = 31.6 bits (72), Expect = 0.33 Identities = 15/48 (31%), Positives = 23/48 (47%) Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338 +NP D +T A++ L + IS VVDD +G + D L+ Sbjct: 1 RNPVTFTPDMSVTEAVEKLLKSKISGGPVVDDNGNLVGFLSEQDCLKQ 48 >gnl|CDD|73109 cd04609, CBS_pair_PALP_assoc2, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the pyridoxal-phosphate (PALP) dependent enzyme domain upstream. The vitamin B6 complex comprises pyridoxine, pyridoxal, and pyridoxamine, as well as the 5'-phosphate esters of pyridoxal (PALP) and pyridoxamine, the last two being the biologically active coenzyme derivatives. The members of the PALP family are principally involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and other amine-containing compounds. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 110 Score = 49.0 bits (117), Expect = 2e-06 Identities = 29/103 (28%), Positives = 51/103 (49%), Gaps = 5/103 (4%) Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLN--TLSVEDVMIKNPKV 295 + AI + E + VVD+G ++ G I E D+ + +L V +VM + Sbjct: 11 TVSQAIERMREYGVSQLPVVDDG-RVVGSIDESDLLDALIEGKAKFSLPVREVMGEPLPT 69 Query: 296 ILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338 + D + +LL + N++V VVD+ K +GI+ DLL++ Sbjct: 70 VDPDAPIEELSELLDRGNVAV--VVDEGGKFVGIITRADLLKY 110 Score = 30.5 bits (69), Expect = 0.69 Identities = 15/43 (34%), Positives = 26/43 (60%), Gaps = 2/43 (4%) Query: 298 EDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRFGI 340 +DT+ A++ +R++ +S L VVDD + +G + DLL I Sbjct: 9 DDTVSQ-AIERMREYGVSQLPVVDD-GRVVGSIDESDLLDALI 49 Score = 29.4 bits (66), Expect = 1.5 Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 4/55 (7%) Query: 220 ASDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR 274 +VM G+ +P V P+ + +L R VVDEG K GIIT D+ + Sbjct: 59 VREVM--GEPLPTVDPDAPIEELSELLD--RGNVAVVVDEGGKFVGIITRADLLK 109 >gnl|CDD|73125 cd04626, CBS_pair_13, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 111 Score = 49.1 bits (117), Expect = 2e-06 Identities = 28/100 (28%), Positives = 51/100 (51%), Gaps = 4/100 (4%) Query: 239 LIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR--NFHKDLNTLSVEDVMIKNPKVI 296 + +A+ + + + V D +KLKG++T DI F L V +++ ++ + Sbjct: 12 IREALHEMLKYNTNEIIVKDNEEKLKGVVTFTDILDLDLFESFLE-KKVFNIVSQDVFYV 70 Query: 297 LEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLL 336 E+ + A+ ++R+ I L VVDD K IG+V D+L Sbjct: 71 NEEDTIDEALDIMREKQIGRLPVVDD-NKLIGVVRTKDIL 109 Score = 32.9 bits (75), Expect = 0.15 Identities = 13/45 (28%), Positives = 25/45 (55%) Query: 295 VILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRFG 339 I ED + A+ + ++N + ++V D+ +K G+V F D+L Sbjct: 5 TIDEDASIREALHEMLKYNTNEIIVKDNEEKLKGVVTFTDILDLD 49 >gnl|CDD|73143 cd04801, CBS_pair_M50_like, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the metalloprotease peptidase M50. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 114 Score = 48.7 bits (116), Expect = 2e-06 Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 4/88 (4%) Query: 254 VAVVDEGQKLKGIITEGDIFR---NFHKDLNTLSVEDVMIKNPKVILEDTLLTVAMQLLR 310 VVD + GII+ D+ + + V K V+ E++L V ++LL Sbjct: 28 FVVVDNEGRYVGIISLADLRAIPTSQWAQTTVIQVMTPAAKLVTVLSEESLAEV-LKLLE 86 Query: 311 QHNISVLMVVDDCQKAIGIVHFLDLLRF 338 + + L VV+D + IG++ DLLR Sbjct: 87 EQGLDELAVVEDSGQVIGLITEADLLRR 114 Score = 33.6 bits (77), Expect = 0.081 Identities = 15/53 (28%), Positives = 27/53 (50%) Query: 222 DVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR 274 VM + V L + + +L E+ +AVV++ ++ G+ITE D+ R Sbjct: 61 QVMTPAAKLVTVLSEESLAEVLKLLEEQGLDELAVVEDSGQVIGLITEADLLR 113 >gnl|CDD|73132 cd04634, CBS_pair_21, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 143 Score = 48.3 bits (115), Expect = 3e-06 Identities = 35/139 (25%), Positives = 52/139 (37%), Gaps = 36/139 (25%) Query: 233 VKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIF------------------- 273 + DA +L E + V+D G KL GI++E DI Sbjct: 6 CNADDTISDAARLLRENKISGAPVLDGG-KLVGIVSESDILKLLVTHDPSGNLWLPSPLE 64 Query: 274 ------RNFHK---------DLNTLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLM 318 R F D + V D+M K I D + A +L+ +H I L Sbjct: 65 LIELPLREFINWEETKRALTDAGKMKVRDIMTKKVITISPDASIEDAAELMVRHKIKRLP 124 Query: 319 VVDDCQKAIGIVHFLDLLR 337 VV+D + +GIV D++ Sbjct: 125 VVED-GRLVGIVTRGDIIE 142 Score = 30.2 bits (68), Expect = 0.90 Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 1/47 (2%) Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 KNP D ++ A +LLR++ IS V+D K +GIV D+L+ Sbjct: 1 KNPITCNADDTISDAARLLRENKISGAPVLDG-GKLVGIVSESDILK 46 >gnl|CDD|32729 COG2905, COG2905, Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]. Length = 610 Score = 48.4 bits (115), Expect = 3e-06 Identities = 27/102 (26%), Positives = 46/102 (45%), Gaps = 3/102 (2%) Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLN--TLSVEDVMIKNPKV 295 + DA + ++ + V+D+ L GI+T D+ D T V +VM Sbjct: 167 SIQDAARKMKDEGVSSLVVLDDSGPLLGIVTRKDLRSRVIADGRSKTQKVSEVMTSPVIS 226 Query: 296 ILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 + L AM ++ ++ I L V +D Q +GI+ D+LR Sbjct: 227 VDRGDFLFEAMLMMLRNRIKHLPVTEDGQ-PLGILTLTDILR 267 Score = 35.3 bits (81), Expect = 0.027 Identities = 13/61 (21%), Positives = 24/61 (39%) Query: 278 KDLNTLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 + V +V + + A + ++ +S L+V+DD +GIV DL Sbjct: 144 SEFILTRVGEVKTLPAVTVSPQASIQDAARKMKDEGVSSLVVLDDSGPLLGIVTRKDLRS 203 Query: 338 F 338 Sbjct: 204 R 204 Score = 33.7 bits (77), Expect = 0.077 Identities = 32/109 (29%), Positives = 56/109 (51%), Gaps = 17/109 (15%) Query: 220 ASDVMHSGDSIPLVKI--GCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFH 277 S+VM S P++ + G L +A+ ++ R + V ++GQ L GI+T DI R F Sbjct: 216 VSEVMTS----PVISVDRGDFLFEAMLMMLRNRIKHLPVTEDGQPL-GILTLTDILRLFS 270 Query: 278 KDLNTL--------SVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLM 318 ++ L S+E+ + N +L+D+L T+ + +R IS L+ Sbjct: 271 QNSIVLVKRIARASSIEE--LANTAELLDDSLSTLVSRGVRTEFISELI 317 >gnl|CDD|73106 cd04606, CBS_pair_Mg_transporter, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other divalent cations into the cell via two highly conserved aspartates. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 109 Score = 47.8 bits (114), Expect = 4e-06 Identities = 21/81 (25%), Positives = 41/81 (50%), Gaps = 4/81 (4%) Query: 256 VVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNIS 315 VVDE +L G+++ D+ D +T V D+M + + D +L ++++ Sbjct: 30 VVDEEGRLLGVVSLRDLLLA---DPDTP-VSDIMDTDVISVSADDDQEEVARLFEKYDLL 85 Query: 316 VLMVVDDCQKAIGIVHFLDLL 336 L VVD+ + +GI+ D++ Sbjct: 86 ALPVVDEEGRLVGIITVDDVI 106 Score = 34.7 bits (80), Expect = 0.034 Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 2/52 (3%) Query: 221 SDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI 272 SD+M + V + + + + VVDE +L GIIT D+ Sbjct: 56 SDIMD--TDVISVSADDDQEEVARLFEKYDLLALPVVDEEGRLVGIITVDDV 105 Score = 28.9 bits (65), Expect = 2.1 Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 5/48 (10%) Query: 295 VILEDTLLTVAMQLLRQH-----NISVLMVVDDCQKAIGIVHFLDLLR 337 + ED + A++ LR++ I + VVD+ + +G+V DLL Sbjct: 1 AVREDWTVGEALEYLRRNADDPETIYYIYVVDEEGRLLGVVSLRDLLL 48 >gnl|CDD|73120 cd04621, CBS_pair_8, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 135 Score = 47.6 bits (113), Expect = 4e-06 Identities = 28/124 (22%), Positives = 49/124 (39%), Gaps = 26/124 (20%) Query: 239 LIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLN----------------- 281 L+ + + + G V VVD+ K G+IT D+ +D Sbjct: 12 LLHVVDEMEKNGVGRVIVVDDNGKPVGVITYRDLAFAEFEDNERGLPKKSIKMKRKAGQK 71 Query: 282 --------TLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFL 333 L ED+M + + + + A +L+ + NIS L VVD+ +G++ Sbjct: 72 RYRYVKEVPLVAEDIMTEEIITVSPNDDVVDAAKLMLEANISGLPVVDN-DNIVGVITKT 130 Query: 334 DLLR 337 D+ R Sbjct: 131 DICR 134 >gnl|CDD|30798 COG0449, GlmS, Glucosamine 6-phosphate synthetase, contains amidotransferase and phosphosugar isomerase domains [Cell envelope biogenesis, outer membrane]. Length = 597 Score = 47.5 bits (113), Expect = 6e-06 Identities = 40/168 (23%), Positives = 66/168 (39%), Gaps = 10/168 (5%) Query: 40 SLESSLQGELSFQFHCAVE-KIKAIKGRVVITGIGKSGH---IGSKLASTLASTGTPSFF 95 +L ++LQG L ++ I R++I G S H + LA Sbjct: 258 ALRNTLQGRLDELVQNELDLDILREVDRIIIVACGTSYHAGLVAKYFFERLAKIPV---E 314 Query: 96 VHAAEASHGDLGMITRDDLIIVLSWSGSSDELKAILYYARRFSIPLIAITSENKSVVACH 155 V A + + L+I +S SG + + A L A+ +AIT+ S +A Sbjct: 315 VEEASEFRYREPALNPNTLVIAISQSGETADTLAALRLAKEQGAKTLAITNVPGSTIARE 374 Query: 156 ADIVLTLPKEPESCPHGLAPTTSAIMQLAIGDALAIALLESRNFSEND 203 +D L + PE G+A T + Q+ LA+ L + R + Sbjct: 375 SDHTLLIRAGPEI---GVASTKAFTAQVLALYLLALYLAKQRGTISEE 419 >gnl|CDD|73096 cd04596, CBS_pair_DRTGG_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with a DRTGG domain upstream. The function of the DRTGG domain, named after its conserved residues, is unknown. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 108 Score = 47.1 bits (112), Expect = 6e-06 Identities = 29/87 (33%), Positives = 43/87 (49%), Gaps = 7/87 (8%) Query: 250 RFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVILEDTLLTVAMQLL 309 RF VVDE K+ GI+T D+ ++E VM KNP + T + ++ Sbjct: 27 RF---PVVDEKNKVVGIVTSKDVA----GKDPDTTIEKVMTKNPITVNPKTSVASVAHMM 79 Query: 310 RQHNISVLMVVDDCQKAIGIVHFLDLL 336 I +L VVDD +K +GI+ D+L Sbjct: 80 IWEGIEMLPVVDDNKKLLGIISRQDVL 106 Score = 27.0 bits (60), Expect = 7.8 Identities = 9/22 (40%), Positives = 15/22 (68%) Query: 254 VAVVDEGQKLKGIITEGDIFRN 275 + VVD+ +KL GII+ D+ + Sbjct: 87 LPVVDDNKKLLGIISRQDVLKA 108 >gnl|CDD|73118 cd04619, CBS_pair_6, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 114 Score = 46.9 bits (111), Expect = 8e-06 Identities = 29/108 (26%), Positives = 50/108 (46%), Gaps = 3/108 (2%) Query: 233 VKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLN---TLSVEDVM 289 + + L A IL E V V D KL G++T+ D+ R + T VE+VM Sbjct: 6 IDVNATLQRAAKILGEPGIDLVVVCDPHGKLAGVLTKTDVVRQMGRCGGPGCTAPVENVM 65 Query: 290 IKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 + LL Q+++Q + + VVD+ + +G+++ D L+ Sbjct: 66 TRAVVSCRPGDLLHDVWQVMKQRGLKNIPVVDENARPLGVLNARDALK 113 >gnl|CDD|32420 COG2239, MgtE, Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]. Length = 451 Score = 45.6 bits (108), Expect = 2e-05 Identities = 21/89 (23%), Positives = 43/89 (48%), Gaps = 4/89 (4%) Query: 250 RFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVILEDTLLTVAMQLL 309 + VVDE KL G+++ D+ +L ++D+M + +L D +L Sbjct: 167 TIYYLYVVDEKGKLLGVVSLRDLLTAEPDEL----LKDLMEDDVVSVLADDDQEEVARLF 222 Query: 310 RQHNISVLMVVDDCQKAIGIVHFLDLLRF 338 ++++ + VVD+ + IGI+ D++ Sbjct: 223 EKYDLLAVPVVDEDNRLIGIITIDDIIDV 251 >gnl|CDD|32286 COG2103, COG2103, Predicted sugar phosphate isomerase [General function prediction only]. Length = 298 Score = 45.2 bits (107), Expect = 3e-05 Identities = 35/137 (25%), Positives = 55/137 (40%), Gaps = 25/137 (18%) Query: 56 AVEKI-KAIK--GRVVITGIGKSGHIGSKLASTLAST-------------GTPSFFVHAA 99 AV+ I A+K GR++ G G SG +G AS T G + A Sbjct: 49 AVDIIAAALKQGGRLIYIGAGTSGRLGVLDASECPPTFGVPPELVIGLIAGGEEAILKAV 108 Query: 100 EASHGDLGM---------ITRDDLIIVLSWSGSSDELKAILYYARRFSIPLIAITSENKS 150 E + D + +T D+++ ++ SG + + L YAR+ I I S Sbjct: 109 EGAEDDEELGEADLKNIGLTAKDVVVGIAASGRTPYVIGALEYARQRGATTIGIACNPGS 168 Query: 151 VVACHADIVLTLPKEPE 167 ++ ADI + PE Sbjct: 169 AISRIADIAIEPVVGPE 185 >gnl|CDD|88404 cd05007, SIS_Etherase, N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid carries a unique D-lactyl ether substituent at the C3 position. The etherase catalyzes the cleavage of the lactyl ether bond of N-acetylmuramic acid 6-phosphate.. Length = 257 Score = 45.1 bits (107), Expect = 3e-05 Identities = 41/134 (30%), Positives = 55/134 (41%), Gaps = 23/134 (17%) Query: 56 AVEKIKAIKGRVVITGIGKSGHIGSKLASTLAST-GTPSFFVHA---------------- 98 A E+++A GR++ G G SG +G AS L T GTP V Sbjct: 42 AAERLRA-GGRLIYVGAGTSGRLGVLDASELPPTFGTPPERVVGLIAGGEPALTRAVEGA 100 Query: 99 ---AEASHGDLGMI--TRDDLIIVLSWSGSSDELKAILYYARRFSIPLIAITSENKSVVA 153 EA DL I T D++I ++ SG + + L YAR I I S + Sbjct: 101 EDDEEAGAADLQAINLTERDVVIGIAASGRTPYVLGALRYARARGALTIGIACNPGSPLL 160 Query: 154 CHADIVLTLPKEPE 167 ADI + L PE Sbjct: 161 QLADIAIALITGPE 174 >gnl|CDD|33866 COG4109, COG4109, Predicted transcriptional regulator containing CBS domains [Transcription]. Length = 432 Score = 44.9 bits (106), Expect = 4e-05 Identities = 26/116 (22%), Positives = 52/116 (44%), Gaps = 4/116 (3%) Query: 222 DVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLN 281 D+M + ++ + D + ++ + VV+ K+ G++T D+ Sbjct: 192 DIMTPLEDTSYLRETDTVEDWLDLVEKTGHSRFPVVNRSMKVVGVVTMRDVLDK----KP 247 Query: 282 TLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 + ++E VM KNP + T + Q++ I +L VVD +GI+ D+L+ Sbjct: 248 STTIEKVMTKNPITVRAKTSVASVAQMMIWEGIEMLPVVDSNNTLLGIITRQDVLK 303 >gnl|CDD|33419 COG3620, COG3620, Predicted transcriptional regulator with C-terminal CBS domains [Transcription]. Length = 187 Score = 44.1 bits (104), Expect = 5e-05 Identities = 34/125 (27%), Positives = 62/125 (49%), Gaps = 9/125 (7%) Query: 218 VCASDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR--- 274 + A +MHS + V + D + ++ +K + V++E K+ G ITE DI R Sbjct: 65 ITAKTIMHS--PVVSVSPDDSISDVVNLMRDKGISQLPVIEED-KVVGSITENDIVRALL 121 Query: 275 NFHKDLNTLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLD 334 + + +L V +VM + + D L V QLL +H ++VV++ K +GI+ D Sbjct: 122 EGMESIRSLRVREVMGEPFPTVSPDESLNVISQLLEEHP--AVLVVEN-GKVVGIITKAD 178 Query: 335 LLRFG 339 +++ Sbjct: 179 IMKLL 183 >gnl|CDD|36975 KOG1764, KOG1764, KOG1764, 5'-AMP-activated protein kinase, gamma subunit [Energy production and conversion]. Length = 381 Score = 43.9 bits (103), Expect = 7e-05 Identities = 29/112 (25%), Positives = 52/112 (46%), Gaps = 12/112 (10%) Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI--------FRNFHKDLNTLSVEDVM 289 P+I+A+ I+SE+R + VVDE K G + D+ + N + ++ Sbjct: 247 PVIEALKIMSERRISALPVVDENGKKVGNYSRFDVIHLAREGTYNNLDLSCLSEALSHRP 306 Query: 290 IKNPKVIL---EDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338 I+ V+ TL V +L+ H + L VVD+ +G++ D+L + Sbjct: 307 IRFEGVVTCRPTSTLAEVIDKLVA-HRVHRLWVVDEDGVLVGVISLSDILSY 357 Score = 41.2 bits (96), Expect = 4e-04 Identities = 36/161 (22%), Positives = 67/161 (41%), Gaps = 15/161 (9%) Query: 183 LAIGDALAIALLESRNFSENDFYVLHPGGKLGTLFVCASDVMHSGDSIPLVKIGCP--LI 240 L I D + + L ++ S D + +L ++ P V I L+ Sbjct: 116 LTITDFITVLLRYYKSKSSLDNIEVLEDSQLSKR-REVECLLKETLKPPFVSISPESSLL 174 Query: 241 DAITILSEKRFGCVAVVDEGQ-KLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPK----- 294 DA+ +L + R V V+D ++ I+T+ I + + L + ++ K+ Sbjct: 175 DAVLLLIKSRIHRVPVIDPETGEVLYILTQRRILKFLWLNGRLLPLPSLLSKSLSDLGIG 234 Query: 295 ------VILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGI 329 I EDT + A++++ + IS L VVD+ K +G Sbjct: 235 TWSNIASISEDTPVIEALKIMSERRISALPVVDENGKKVGN 275 >gnl|CDD|73114 cd04614, CBS_pair_1, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 96 Score = 43.3 bits (102), Expect = 1e-04 Identities = 25/108 (23%), Positives = 48/108 (44%), Gaps = 15/108 (13%) Query: 230 IPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVM 289 +P V PL A+ I+ + V+D+ KL GIITE D+ +V+ Sbjct: 3 VPTVWEETPLPVAVRIMELANVKALPVLDDDGKLSGIITERDLIAK----------SEVV 52 Query: 290 IKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 + + + Q ++++ I + +++ K IG++ DLL+ Sbjct: 53 TATKRTTVSE-----CAQKMKRNRIEQIPIINGNDKLIGLLRDHDLLK 95 Score = 29.1 bits (65), Expect = 1.8 Identities = 16/47 (34%), Positives = 27/47 (57%) Query: 291 KNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 +N + E+T L VA++++ N+ L V+DD K GI+ DL+ Sbjct: 1 RNVPTVWEETPLPVAVRIMELANVKALPVLDDDGKLSGIITERDLIA 47 >gnl|CDD|73137 cd04639, CBS_pair_26, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 111 Score = 42.9 bits (101), Expect = 1e-04 Identities = 19/76 (25%), Positives = 34/76 (44%) Query: 255 AVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNI 314 VVD L G++T D+ R + V VM ++ + L ++L++Q Sbjct: 28 PVVDGDGHLVGLLTRDDLIRALAEGGPDAPVRGVMRRDFPTVSPSATLDAVLRLMQQGGA 87 Query: 315 SVLMVVDDCQKAIGIV 330 + VVD + +G+V Sbjct: 88 PAVPVVDGSGRLVGLV 103 Score = 30.6 bits (69), Expect = 0.61 Identities = 22/103 (21%), Positives = 38/103 (36%), Gaps = 21/103 (20%) Query: 185 IGDALAIALLESRNFSENDFYVLHPGGKL---------------GTLFVCASDVMHSGDS 229 + DA ALL + ++++F V+ G L G VM Sbjct: 12 LDDAAD-ALLAT---TQHEFPVVDGDGHLVGLLTRDDLIRALAEGGPDAPVRGVMRRD-- 65 Query: 230 IPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI 272 P V L + ++ + V VVD +L G++T ++ Sbjct: 66 FPTVSPSATLDAVLRLMQQGGAPAVPVVDGSGRLVGLVTLENV 108 >gnl|CDD|73090 cd04590, CBS_pair_CorC_HlyC_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in magnesium and cobalt efflux, and in association with some proteins of unknown function. The function of the CorC_HlyC domain is uncertain but it might be involved in modulating transport of ion substrates. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. The second CBS domain in this CD is degenerate.. Length = 111 Score = 42.4 bits (100), Expect = 2e-04 Identities = 21/100 (21%), Positives = 45/100 (45%), Gaps = 2/100 (2%) Query: 238 PLIDAITILSEKRFGCVAVVDEG-QKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVI 296 L + + +++E V D + G++ D+ R + L + D +++ P + Sbjct: 11 TLEEILELIAESGHSRFPVYDGDLDNIIGVVHVKDLLRALAEGEEDLDLRD-LLRPPLFV 69 Query: 297 LEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLL 336 E T L ++ +R+ + +VVD+ G+V D+L Sbjct: 70 PESTPLDDLLEEMRKERSHMAIVVDEYGGTAGLVTLEDIL 109 Score = 26.6 bits (59), Expect = 9.2 Identities = 13/43 (30%), Positives = 19/43 (44%) Query: 230 IPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI 272 V PL D + + ++R VVDE G++T DI Sbjct: 66 PLFVPESTPLDDLLEEMRKERSHMAIVVDEYGGTAGLVTLEDI 108 >gnl|CDD|73116 cd04617, CBS_pair_4, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 118 Score = 42.5 bits (100), Expect = 2e-04 Identities = 28/108 (25%), Positives = 54/108 (50%), Gaps = 7/108 (6%) Query: 229 SIPL-VKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNF--HKDLNTLSV 285 S P+ V+ + DAI L + G + VVDE L G+++ D+ + DL + V Sbjct: 1 SPPVVVRENTSVYDAIVTLFLEDVGSLFVVDEDGDLVGVVSRKDLLKASIGGADLQKVPV 60 Query: 286 EDVMIKNPKVIL---EDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIV 330 +M + P + E+++L A +L+ +H + L VV+ + + ++ Sbjct: 61 GVIMTRMPNITTTTPEESVLEAAKKLI-EHQVDSLPVVEKVDEGLEVI 107 Score = 28.2 bits (63), Expect = 3.6 Identities = 15/45 (33%), Positives = 25/45 (55%) Query: 293 PKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 P V+ E+T + A+ L ++ L VVD+ +G+V DLL+ Sbjct: 3 PVVVRENTSVYDAIVTLFLEDVGSLFVVDEDGDLVGVVSRKDLLK 47 >gnl|CDD|73089 cd04589, CBS_pair_CAP-ED_DUF294_assoc_bac, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the bacterial CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain. Members of CAP_ED, include CAP which binds cAMP, FNR (fumarate and nitrate reductase) which uses an iron-sulfur cluster to sense oxygen, and CooA a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. DUF294 is a putative nucleotidyltransferase with a conserved DxD motif. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 111 Score = 41.7 bits (98), Expect = 3e-04 Identities = 26/103 (25%), Positives = 44/103 (42%), Gaps = 4/103 (3%) Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVIL 297 + DA ++ E + V D +L GI+T D+ D S I +I Sbjct: 11 SIRDAARLMREHGADALLVRDGDPRL-GIVTRTDLLDAVLLDGLPSSTPVGEIATFPLIT 69 Query: 298 --EDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338 D L A+ L+ +H I ++V + + +G++ DLL F Sbjct: 70 VDPDDFLFNALLLMTRHRIHRVVVREG-GEVVGVLEQTDLLSF 111 >gnl|CDD|88412 cd05017, SIS_PGI_PMI_1, The members of this protein family contain the SIS (Sugar ISomerase) domain and have both the phosphoglucose isomerase (PGI) and the phosphomannose isomerase (PMI) functions. These functions catalyze the reversible reactions of glucose 6-phosphate to fructose 6-phosphate, and mannose 6-phosphate to fructose 6-phosphate, respectively at an equal rate. This protein contains two SIS domains. This alignment is based on the first SIS domain.. Length = 119 Score = 41.7 bits (98), Expect = 3e-04 Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 3/81 (3%) Query: 66 RVVITGIGKSGHIGSKLASTLASTGTPSFFVHAAEASHGDLGMITRDDLIIVLSWSGSSD 125 +VI G+G SG G L S L +V + + R L+I +S+SG+++ Sbjct: 1 NIVILGMGGSGIGGDLLESLLLDEAKIPVYVVK---DYTLPAFVDRKTLVIAVSYSGNTE 57 Query: 126 ELKAILYYARRFSIPLIAITS 146 E + + A+ ++AITS Sbjct: 58 ETLSAVEQAKERGAKIVAITS 78 >gnl|CDD|73140 cd04642, CBS_pair_29, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 126 Score = 41.8 bits (98), Expect = 3e-04 Identities = 22/116 (18%), Positives = 42/116 (36%), Gaps = 15/116 (12%) Query: 238 PLIDAITILSEKRFGCVAVVDEGQK---------LKGIITEGDIFRNFHKDLNTLSVED- 287 ++DA ++ + + VVDE K LKG++ D + E Sbjct: 11 RVLDAFKLMRKNNISGLPVVDEKGKLIGNISASDLKGLLLSPDDLLLYRTITFKELSEKF 70 Query: 288 -----VMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338 V + + L + L + + + VVD+ K IG++ D++ Sbjct: 71 TDSDGVKSRPLITCTPSSTLKEVITKLVANKVHRVWVVDEEGKPIGVITLTDIISI 126 Score = 31.4 bits (71), Expect = 0.38 Identities = 17/40 (42%), Positives = 24/40 (60%) Query: 296 ILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDL 335 I D + A +L+R++NIS L VVD+ K IG + DL Sbjct: 6 IDSDERVLDAFKLMRKNNISGLPVVDEKGKLIGNISASDL 45 >gnl|CDD|73108 cd04608, CBS_pair_PALP_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the pyridoxal-phosphate (PALP) dependent enzyme domain upstream. The vitamin B6 complex comprises pyridoxine, pyridoxal, and pyridoxamine, as well as the 5'-phosphate esters of pyridoxal (PALP) and pyridoxamine, the last two being the biologically active coenzyme derivatives. The members of the PALP family are principally involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and other amine-containing compounds. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 124 Score = 41.4 bits (97), Expect = 4e-04 Identities = 32/109 (29%), Positives = 50/109 (45%), Gaps = 11/109 (10%) Query: 241 DAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLS--VEDVMIK-NPKVIL 297 +AI IL EK F + VVDE K+ G++T G++ + S V + K +V Sbjct: 15 EAIEILKEKGFDQLPVVDESGKILGMVTLGNLLSSLSSGKVQPSDPVSKALYKQFKRVNK 74 Query: 298 EDTLLTVAMQLLRQHNISVL--------MVVDDCQKAIGIVHFLDLLRF 338 DTL ++ L + V + + +K IGIV +DLL + Sbjct: 75 NDTLGKLSRILETDAFLLVFFEQISSAAIGKEKQEKPIGIVTKIDLLSY 123 Score = 28.3 bits (63), Expect = 3.1 Identities = 14/49 (28%), Positives = 25/49 (51%) Query: 290 IKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338 +K P +L A+++L++ L VVD+ K +G+V +LL Sbjct: 1 LKAPVTVLPTVTCAEAIEILKEKGFDQLPVVDESGKILGMVTLGNLLSS 49 >gnl|CDD|73139 cd04641, CBS_pair_28, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 120 Score = 41.3 bits (97), Expect = 4e-04 Identities = 27/111 (24%), Positives = 54/111 (48%), Gaps = 11/111 (9%) Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIF---RNFHKDLNTLSVEDVMIKNP- 293 PLID + +L E+R + +VDE K+ + + D+ + + L+V + + + Sbjct: 11 PLIDVLDMLVERRVSALPIVDENGKVVDVYSRFDVINLAKEGAYNNLDLTVGEALERRSQ 70 Query: 294 ------KVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRF 338 +D L T+ L+ + + L+VVD+ ++ GI+ D+L+F Sbjct: 71 DFEGVRTCSPDDCLRTI-FDLIVKARVHRLVVVDENKRVEGIISLSDILQF 120 >gnl|CDD|37761 KOG2550, KOG2550, KOG2550, IMP dehydrogenase/GMP reductase [Nucleotide transport and metabolism]. Length = 503 Score = 41.1 bits (96), Expect = 4e-04 Identities = 29/78 (37%), Positives = 42/78 (53%), Gaps = 3/78 (3%) Query: 260 GQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMV 319 G KL GIIT DI F +D + L V DVM KNP + L A ++L++ L V Sbjct: 151 GSKLVGIITSRDI--QFLEDNSLL-VSDVMTKNPVTGAQGITLKEANEILKKIKKGKLPV 207 Query: 320 VDDCQKAIGIVHFLDLLR 337 VDD + + ++ DL++ Sbjct: 208 VDDKGELVAMLSRTDLMK 225 >gnl|CDD|73097 cd04597, CBS_pair_DRTGG_assoc2, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with a DRTGG domain upstream. The function of the DRTGG domain, named after its conserved residues, is unknown. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 113 Score = 41.0 bits (96), Expect = 5e-04 Identities = 20/53 (37%), Positives = 27/53 (50%) Query: 285 VEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 V DV+ + P + L A+ L+ +HNI L VVDD GI+ LDL Sbjct: 60 VRDVINRKPVTARPNDPLREALNLMHEHNIRTLPVVDDDGTPAGIITLLDLAE 112 Score = 33.3 bits (76), Expect = 0.11 Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 2/54 (3%) Query: 222 DVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRN 275 DV++ + PL +A+ ++ E + VVD+ GIIT D+ Sbjct: 62 DVIN--RKPVTARPNDPLREALNLMHEHNIRTLPVVDDDGTPAGIITLLDLAEK 113 >gnl|CDD|73092 cd04592, CBS_pair_EriC_assoc_euk, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in eukaryotes. These ion channels are proteins with a seemingly simple task of allowing the passive flow of chloride ions across biological membranes. CIC-type chloride channels come from all kingdoms of life, have several gene families, and can be gated by voltage. The members of the CIC-type chloride channel are double-barreled: two proteins forming homodimers at a broad interface formed by four helices from each protein. The two pores are not found at this interface, but are completely contained within each subunit, as deduced from the mutational analyses, unlike many other channels, in which four or five identical or structurally related subunits jointly form one pore. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain in CLC chloride channel family members have been associated with classic Bartter syndrome, Osteopetrosis, Dent's disease, idiopathic generalized epilepsy, and myotonia.. Length = 133 Score = 40.0 bits (93), Expect = 0.001 Identities = 31/110 (28%), Positives = 44/110 (40%), Gaps = 22/110 (20%) Query: 233 VKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR-------------NFHKD 279 V L +A+ ++ +++ CV VVD L+GI+T GDI R + K Sbjct: 6 VSPTTTLKEALNLMLDEKQSCVLVVDSDDFLEGILTLGDIQRFLFTNKTTRVQPEDETKQ 65 Query: 280 LNTLSVEDVMIKN---------PKVILEDTLLTVAMQLLRQHNISVLMVV 320 NT V V K DT LT A +L+ + L VV Sbjct: 66 TNTCLVSSVCTKGISYGGQECGLWTCTPDTDLTTAKKLMEAKGVKQLPVV 115 >gnl|CDD|73110 cd04610, CBS_pair_ParBc_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with a ParBc (ParB-like nuclease) domain downstream. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 107 Score = 38.3 bits (89), Expect = 0.003 Identities = 28/97 (28%), Positives = 50/97 (51%), Gaps = 5/97 (5%) Query: 241 DAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVILEDT 300 D I ++ E VVD K+ GI++ D+ KD + VE++M K+ V + + Sbjct: 15 DVIKLIKETGHDGFPVVD-NGKVVGIVSARDLL---GKDPDET-VEEIMSKDLVVAVPEM 69 Query: 301 LLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 + A +++ + IS L VVD+ +GI+ D++R Sbjct: 70 DIMDAARVMFRTGISKLPVVDENNNLVGIITNTDVIR 106 Score = 26.8 bits (59), Expect = 9.0 Identities = 13/37 (35%), Positives = 20/37 (54%) Query: 239 LIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRN 275 ++DA ++ + VVDE L GIIT D+ R+ Sbjct: 71 IMDAARVMFRTGISKLPVVDENNNLVGIITNTDVIRS 107 >gnl|CDD|73130 cd04632, CBS_pair_19, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 128 Score = 38.4 bits (89), Expect = 0.003 Identities = 31/117 (26%), Positives = 50/117 (42%), Gaps = 17/117 (14%) Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLN---------------T 282 + AI +L E + VVD+ KL GI+T DI +D + Sbjct: 11 SVGKAINVLREHGISRLPVVDDNGKLTGIVTRHDIVDFVVRDRDKARTGDRSGEKERMLD 70 Query: 283 LSVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVV--DDCQKAIGIVHFLDLLR 337 L V D M + + A+ + +++ S ++VV DD K +GI+ D+LR Sbjct: 71 LPVYDAMSSPVITASPNDSVRDAVDRMLENDDSSVVVVTPDDDTKVVGILTKKDVLR 127 Score = 34.2 bits (78), Expect = 0.055 Identities = 19/43 (44%), Positives = 26/43 (60%) Query: 298 EDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRFGI 340 ED + A+ +LR+H IS L VVDD K GIV D++ F + Sbjct: 8 EDDSVGKAINVLREHGISRLPVVDDNGKLTGIVTRHDIVDFVV 50 >gnl|CDD|33251 COG3448, COG3448, CBS-domain-containing membrane protein [Signal transduction mechanisms]. Length = 382 Score = 38.0 bits (88), Expect = 0.003 Identities = 28/103 (27%), Positives = 47/103 (45%), Gaps = 7/103 (6%) Query: 241 DAITILSEKRFGCVAVVDEGQKLKGIITEGDIF----RNFHKDLNTL---SVEDVMIKNP 293 A +L E R + V+DE ++L GI+T+ D+ + + L L +V+ +M Sbjct: 266 HARKLLQEHRIKALPVLDEHRRLVGIVTQRDLLKHARPSPFQRLRFLRPPTVKGIMTTPV 325 Query: 294 KVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLL 336 + DT + L + L V+D K +GIV DL+ Sbjct: 326 VTVRPDTPAVELVPRLADEGLHALPVLDAAGKLVGIVSQTDLI 368 Score = 38.0 bits (88), Expect = 0.003 Identities = 19/56 (33%), Positives = 34/56 (60%) Query: 282 TLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 L+ D+M ++ + DT + A +LL++H I L V+D+ ++ +GIV DLL+ Sbjct: 244 ELTCADIMSRDVVTVSTDTSIDHARKLLQEHRIKALPVLDEHRRLVGIVTQRDLLK 299 Score = 33.0 bits (75), Expect = 0.12 Identities = 9/45 (20%), Positives = 25/45 (55%) Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNT 282 P ++ + L+++ + V+D KL GI+++ D+ +++ + Sbjct: 333 PAVELVPRLADEGLHALPVLDAAGKLVGIVSQTDLIAALYRNWSQ 377 >gnl|CDD|31445 COG1253, TlyC, Hemolysins and related proteins containing CBS domains [General function prediction only]. Length = 429 Score = 37.2 bits (86), Expect = 0.007 Identities = 21/120 (17%), Positives = 49/120 (40%), Gaps = 2/120 (1%) Query: 218 VCASDVMHSGDSIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQK-LKGIITEGDIFRNF 276 ++M I + + + + I ++ E + V D + GI+ D+ R Sbjct: 206 RTVREIMTPRTDIVALDLTDTVEELIELILESGHSRIPVYDGDLDNIIGIVHVKDLLRAL 265 Query: 277 HKDLNTLSVEDVMIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLL 336 + L + + ++ P + E L+ ++ R+ + +VVD+ G+V D++ Sbjct: 266 LDGQSDLDLRVL-VRPPLFVPETLSLSDLLEEFREERTHMAIVVDEYGGVEGLVTLEDII 324 Score = 31.8 bits (72), Expect = 0.25 Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 3/62 (4%) Query: 279 DLNTLSVEDVMIKNPKVIL--EDTLLTVAMQLLRQHNISVLMVVDDCQKAI-GIVHFLDL 335 DL+ +V ++M ++ + ++L+ + S + V D I GIVH DL Sbjct: 202 DLDDRTVREIMTPRTDIVALDLTDTVEELIELILESGHSRIPVYDGDLDNIIGIVHVKDL 261 Query: 336 LR 337 LR Sbjct: 262 LR 263 >gnl|CDD|73098 cd04598, CBS_pair_GGDEF_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the GGDEF (DiGuanylate-Cyclase (DGC)) domain. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and is thought to be involved in regulating cell surface adhesiveness in bacteria. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 119 Score = 36.3 bits (84), Expect = 0.012 Identities = 24/92 (26%), Positives = 42/92 (45%), Gaps = 9/92 (9%) Query: 254 VAVVDEGQKLKGIITEGDIFR----NFHKDLNT-LSVEDVMIKNPKVILEDTLLTVAMQL 308 +AVVD+G+ + G+I + + + L V +VM +P ++ DT L +L Sbjct: 28 LAVVDDGRPV-GLIMREALMELLSTPYGRALYGKKPVSEVMDPDPLIVEADTPLEEVSRL 86 Query: 309 L---RQHNISVLMVVDDCQKAIGIVHFLDLLR 337 N+ +V + + +GI DLLR Sbjct: 87 ATGRDSQNLYDGFIVTEEGRYLGIGTVKDLLR 118 >gnl|CDD|73093 cd04593, CBS_pair_EriC_assoc_bac_arch, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in bacteria and archaea. These ion channels are proteins with a seemingly simple task of allowing the passive flow of chloride ions across biological membranes. CIC-type chloride channels come from all kingdoms of life, have several gene families, and can be gated by voltage. The members of the CIC-type chloride channel are double-barreled: two proteins forming homodimers at a broad interface formed by four helices from each protein. The two pores are not found at this interface, but are completely contained within each subunit, as deduced from the mutational analyses, unlike many other channels, in which four or five identical or structurally related subunits jointly form one pore. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain in CLC chloride channel family members have been associated with classic Bartter syndrome, Osteopetrosis, Dent's disease, idiopathic generalized epilepsy, and myotonia.. Length = 115 Score = 35.7 bits (82), Expect = 0.017 Identities = 16/44 (36%), Positives = 22/44 (50%) Query: 231 PLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFR 274 P++ PL +A L E + G VVD + GIIT D+ R Sbjct: 4 PVLSATTPLREAAEQLIESKHGSALVVDRDGGVVGIITLPDLLR 47 Score = 33.4 bits (76), Expect = 0.11 Identities = 15/45 (33%), Positives = 21/45 (46%) Query: 293 PKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 P V+ T L A + L + +VVD +GI+ DLLR Sbjct: 3 PPVLSATTPLREAAEQLIESKHGSALVVDRDGGVVGIITLPDLLR 47 >gnl|CDD|73138 cd04640, CBS_pair_27, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 126 Score = 34.8 bits (80), Expect = 0.036 Identities = 18/50 (36%), Positives = 29/50 (58%) Query: 292 NPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRFGII 341 P VI DT + A++L+ +H + +L+VVD IG++ +DLL I Sbjct: 2 KPIVIPADTSIDEALELMIKHGVRLLLVVDSDDNFIGVITAVDLLGEEPI 51 >gnl|CDD|88403 cd05006, SIS_GmhA, Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of gram-negative bacteria inner core lipopolysaccharide precursor, L-glycero-D-mannoheptose (Gmh).. Length = 177 Score = 34.3 bits (79), Expect = 0.049 Identities = 15/51 (29%), Positives = 27/51 (52%) Query: 113 DLIIVLSWSGSSDELKAILYYARRFSIPLIAITSENKSVVACHADIVLTLP 163 D++I +S SG+S + L A+ + IA+T + + ADI + +P Sbjct: 103 DVLIGISTSGNSPNVLKALEAAKERGMKTIALTGRDGGKLLELADIEIHVP 153 >gnl|CDD|73082 cd04582, CBS_pair_ABC_OpuCA_assoc, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the ABC transporter OpuCA. OpuCA is the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment but the function of the CBS domains in OpuCA remains unknown. In the related ABC transporter, OpuA, the tandem CBS domains have been shown to function as sensors for ionic strength, whereby they control the transport activity through an electronic switching mechanism. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. They are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.. Length = 106 Score = 34.1 bits (78), Expect = 0.064 Identities = 20/102 (19%), Positives = 39/102 (38%), Gaps = 5/102 (4%) Query: 229 SIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDV 288 V+ PL DA+ ++ + + VVD + G +T + + D Sbjct: 2 EPITVRPDDPLSDALGLMDDSDLRALTVVDADGQPLGFVTRREA-----ARASGGCCGDH 56 Query: 289 MIKNPKVILEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIV 330 + D L + + + H++S L VD+ + +G V Sbjct: 57 AEPFKVTVSVDDDLRIVLSRMFAHDMSWLPCVDEDGRYVGEV 98 >gnl|CDD|88414 cd05710, SIS_1, A subgroup of the SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.. Length = 120 Score = 33.2 bits (76), Expect = 0.095 Identities = 22/78 (28%), Positives = 38/78 (48%) Query: 92 PSFFVHAAEASHGDLGMITRDDLIIVLSWSGSSDELKAILYYARRFSIPLIAITSENKSV 151 P F +AAE H +T ++I+ S SG++ E A +A+ +I +T + S Sbjct: 28 PVFVYNAAEFLHTGPKRLTEKSVVILASHSGNTKETVAAAKFAKEKGATVIGLTDDEDSP 87 Query: 152 VACHADIVLTLPKEPESC 169 +A AD V+ E ++ Sbjct: 88 LAKLADYVIVYGFEIDAV 105 >gnl|CDD|73128 cd04630, CBS_pair_17, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 114 Score = 33.2 bits (76), Expect = 0.11 Identities = 21/101 (20%), Positives = 43/101 (42%), Gaps = 5/101 (4%) Query: 241 DAITILSEKRFGCVAVVDEG-QKLKGIITEGDIFRNF---HKDLNTLSVEDVMIKNPKVI 296 +A+ ++ E + V GI+T DI + +D + ++V ++M K + Sbjct: 14 EALQLMKEHGVSSLVVEKRRESDAYGIVTMRDILKKVVAEGRDPDRVNVYEIMTKPLISV 73 Query: 297 LEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLR 337 D + +L+ + NI V + + IGI+ D+ Sbjct: 74 SPDMDIKYCARLMERTNI-RRAPVVENNELIGIISLTDIFL 113 >gnl|CDD|88406 cd05009, SIS_GlmS_GlmD_2, SIS (Sugar ISomerase) domain repeat 2 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal glutaminase domain and two C-terminal SIS domains and catalyzes the first step in hexosamine metabolism, converting fructose 6-phosphate into glucosamine 6-phosphate using glutamine as nitrogen source. The glutaminase domain hydrolyzes glutamine to glutamate and ammonia. Ammonia is transferred through a channel to the isomerase domain for glucosamine 6-phosphate synthesis. The end product of the pathway is N-acetylglucosamine, which plays multiple roles in eukaryotic cells including being a building block of bacterial and fungal cell walls. In the absence of glutamine, GlmS catalyzes the isomerization of fructose 6-phosphate into glucose 6- phosphate (PGI-like activity). Glucosamine-6-phosphate deaminase (GlmD) contains two SIS domains and catalyzes the deamination and isomerization of glucosamine-6-phosphate into fructose-6-phosphate with the release of ammonia; in presence of high ammonia concentration, GlmD can catalyze the reverse reaction.. Length = 153 Score = 31.4 bits (71), Expect = 0.37 Identities = 21/112 (18%), Positives = 46/112 (41%), Gaps = 11/112 (9%) Query: 89 TGTPSFFVHAAEASHGDLGMITRDDLIIVLSWSGSSDEL-KAILYYARRFSIPLIAITSE 147 + + A E HG + ++ +I L+ +E ++++ + +I IT + Sbjct: 39 SYIHAEAYSAGEFKHGPIALVDEGTPVIFLAPEDRLEEKLESLIKEVKARGAKVIVITDD 98 Query: 148 NKSVVACHADIVLTLPKEPESCPHGLAPTTSAI-MQLAIGDALAIALLESRN 198 + AD+V+ +P E L+P + +QL A +A+ + Sbjct: 99 GDA--KDLADVVIRVPATVEE----LSPLLYIVPLQL---LAYHLAVARGID 141 >gnl|CDD|34183 COG4536, CorB, Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]. Length = 423 Score = 30.9 bits (70), Expect = 0.46 Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 3/63 (4%) Query: 279 DLNTLSVEDVMIKNPKVI---LEDTLLTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDL 335 DL L+V D+M+ ++I ++D + QLL + + + DD IG++H DL Sbjct: 196 DLENLTVSDIMVPRNEIIGIDIDDPWEEIVRQLLHSPHTRIPLYRDDLDNIIGVLHVRDL 255 Query: 336 LRF 338 LR Sbjct: 256 LRL 258 >gnl|CDD|73091 cd04591, CBS_pair_EriC_assoc_euk_bac, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in eukaryotes and bacteria. These ion channels are proteins with a seemingly simple task of allowing the passive flow of chloride ions across biological membranes. CIC-type chloride channels come from all kingdoms of life, have several gene families, and can be gated by voltage. The members of the CIC-type chloride channel are double-barreled: two proteins forming homodimers at a broad interface formed by four helices from each protein. The two pores are not found at this interface, but are completely contained within each subunit, as deduced from the mutational analyses, unlike many other channels, in which four or five identical or structurally related subunits jointly form one pore. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain in CLC chloride channel family members have been associated with classic Bartter syndrome, Osteopetrosis, Dent's disease, idiopathic generalized epilepsy, and myotonia.. Length = 105 Score = 30.2 bits (68), Expect = 0.75 Identities = 20/85 (23%), Positives = 35/85 (41%), Gaps = 10/85 (11%) Query: 254 VAVVDEGQKLKGIITEGDIFRNFHKDLNTLSVEDVMIKNPKVILEDTLLTVAMQLLRQHN 313 V +E +L G I + ++ +P + T L QL R+ Sbjct: 31 VDSTEESPRLVGYILRSQLVVALKNYIDP---------SPFTVSPRTSLEKVHQLFRKLG 81 Query: 314 ISVLMVVDDCQKAIGIVHFLDLLRF 338 + L+VVD+ + +GI+ DLL+ Sbjct: 82 LRHLLVVDE-GRLVGIITRKDLLKA 105 >gnl|CDD|31322 COG1125, OpuBA, ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]. Length = 309 Score = 29.1 bits (65), Expect = 1.9 Identities = 18/68 (26%), Positives = 27/68 (39%), Gaps = 6/68 (8%) Query: 274 RNFHKDLNTLSVEDVMIKNPKVILEDTLLTVA-----MQLLRQHNISVLMVVDDCQKAIG 328 + L+ +SV D + + E L L + SVL VVD+ + +G Sbjct: 240 ERGLRLLSLVSVADAVRRGEPADGEPLLEGFVDRDALSDFLARG-RSVLPVVDEDGRPLG 298 Query: 329 IVHFLDLL 336 V DLL Sbjct: 299 TVTRADLL 306 >gnl|CDD|35695 KOG0474, KOG0474, KOG0474, Cl- channel CLC-7 and related proteins (CLC superfamily) [Inorganic ion transport and metabolism]. Length = 762 Score = 28.7 bits (64), Expect = 2.1 Identities = 21/99 (21%), Positives = 36/99 (36%), Gaps = 4/99 (4%) Query: 246 LSEKRFGCVAVVDEGQKLKGIITEGDIFRNFHK---DLN-TLSVEDVMIKNPKVILEDTL 301 + E R V + + H ++ + + M +P + E Sbjct: 649 VEESRSTFDLPVRRKFTFRDFAKREPSIEDVHLTSEEMEMYVDLHPFMNPSPYTVPETMS 708 Query: 302 LTVAMQLLRQHNISVLMVVDDCQKAIGIVHFLDLLRFGI 340 L A L RQ + L+VV + +GI+ DL R+ I Sbjct: 709 LAKAFILFRQLGLRHLLVVPKTNRVVGILTRKDLARYRI 747 >gnl|CDD|73126 cd04627, CBS_pair_14, The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase).. Length = 123 Score = 28.7 bits (64), Expect = 2.4 Identities = 14/35 (40%), Positives = 20/35 (57%) Query: 238 PLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI 272 PLIDA+ ++ + VAVVD L G I+ D+ Sbjct: 86 PLIDALHLMHNEGISSVAVVDNQGNLIGNISVTDV 120 >gnl|CDD|33915 COG4175, ProV, ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism]. Length = 386 Score = 28.4 bits (63), Expect = 2.7 Identities = 25/104 (24%), Positives = 37/104 (35%), Gaps = 7/104 (6%) Query: 176 TTSAIMQLA-------IGDALAIALLESRNFSENDFYVLHPGGKLGTLFVCASDVMHSGD 228 T IM+ GD +AL R+ Y + G K + S V + Sbjct: 275 TAKDIMRRPDLLIRKTPGDGPRVALKLLRDEGREYGYAVDRGNKFVGVVSIDSLVKAALI 334 Query: 229 SIPLVKIGCPLIDAITILSEKRFGCVAVVDEGQKLKGIITEGDI 272 L + I + VAVVDE + GII+ G++ Sbjct: 335 DDVLTVDADTPLSEILARIRQAPCPVAVVDEDGRYVGIISRGEL 378 >gnl|CDD|31264 COG1064, AdhP, Zn-dependent alcohol dehydrogenases [General function prediction only]. Length = 339 Score = 27.9 bits (62), Expect = 4.7 Identities = 9/32 (28%), Positives = 15/32 (46%), Gaps = 1/32 (3%) Query: 56 AVEKIKAIKG-RVVITGIGKSGHIGSKLASTL 86 A++K G V + G G GH+ + A + Sbjct: 158 ALKKANVKPGKWVAVVGAGGLGHMAVQYAKAM 189 >gnl|CDD|173900 cd00674, LysRS_core_class_I, catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity. Length = 353 Score = 27.3 bits (61), Expect = 6.6 Identities = 19/66 (28%), Positives = 25/66 (37%), Gaps = 15/66 (22%) Query: 57 VEKIKAIKGRVVITGIGKSG--HIGSKLASTLASTGTPSFFVHAAEASHGDLGMITRDDL 114 +E+ K + VV +GI SG HIG T A DLG R Sbjct: 12 IEERKGKEKYVVASGISPSGHIHIG-----NFREVITADLVARALR----DLGFEVR--- 59 Query: 115 IIVLSW 120 ++ SW Sbjct: 60 -LIYSW 64 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.323 0.138 0.397 Gapped Lambda K H 0.267 0.0718 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,955,295 Number of extensions: 204884 Number of successful extensions: 839 Number of sequences better than 10.0: 1 Number of HSP's gapped: 742 Number of HSP's successfully gapped: 163 Length of query: 341 Length of database: 6,263,737 Length adjustment: 94 Effective length of query: 247 Effective length of database: 4,232,491 Effective search space: 1045425277 Effective search space used: 1045425277 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 58 (26.1 bits)