RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780889|ref|YP_003065302.1| inosine 5'-monophosphate dehydrogenase [Candidatus Liberibacter asiaticus str. psy62] (493 letters) >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 = 634 bits (1638), Expect = 0.0 Identities = 259/471 (54%), Positives = 346/471 (73%), Gaps = 10/471 (2%) Query: 13 ALTFDDVLLRPEFSNVLPR--DIDISTRIAKDFTLNLPIMSAAMDQVTDSRLAIAMAQAG 70 LTFDDVLL P S VLP D+D+ST++ ++ TLN+P++SA MD VT+SR+AIAMA+ G Sbjct: 2 GLTFDDVLLLPGRS-VLPSRSDVDLSTKLTRNITLNIPLVSANMDTVTESRMAIAMAREG 60 Query: 71 GLGVIHRNFSPSEQVAQVHQVKKFESGMVVNPVTISPYATLADALALMKKYSISGIPVVE 130 G+GVIH+N S EQ +V +VK+FESG + +PVT+SP T+A+AL L ++Y ISG+PV E Sbjct: 61 GIGVIHKNMSIEEQAEEVRKVKRFESGFITDPVTVSPDTTVAEALELKERYGISGVPVTE 120 Query: 131 SDVGKLVGILTNRDVRF-ASNAQQAVGELMTRNLITVKKTVNLENAKALLHQHRIEKLLV 189 D L G++ R R ++ +V MT +L+T + + LE A +LH+H+IEKL + Sbjct: 121 -DGKLLGGLVGIRTSRDIDFLSKVSVVMTMTEDLVTAPEGITLEEANEILHEHKIEKLPI 179 Query: 190 VDDDGCCIGLITVKDIERSQLNPNATKDSKGRLRVAAAVSVAKDIADRVGPLFDVNVDLV 249 VDDDG +GLIT KDIE+++ PNA+KD++GRL V AAV D +R L + VD++ Sbjct: 180 VDDDGELVGLITRKDIEKARDYPNASKDAQGRLLVGAAVGTRDDDLERAEALVEAGVDVI 239 Query: 250 VVDTAHGHSQKVLDAVVQIKKNFPSLLVMAGNIATAEGALALIDAGADIIKVGIGPGSIC 309 V+D+AHGHS+ VL+ + IKK +P L V+AGN+ TAE A LIDAGAD +KVGIGPGSIC Sbjct: 240 VIDSAHGHSEYVLEMIKWIKKKYPDLDVIAGNVVTAEAARELIDAGADAVKVGIGPGSIC 299 Query: 310 TTRVVTGVGCPQLSAIMSVVEVAERAGVAIVADGGIRFSGDIAKAIAAGSACVMIGSLLA 369 TTR V GVG PQL+A+ V + A + GV ++ADGGIR+SGDIAKA+AAG++ VM+GSLLA Sbjct: 300 TTREVAGVGRPQLTAVYEVADAARKLGVPVIADGGIRYSGDIAKALAAGASAVMLGSLLA 359 Query: 370 GTDESPGDIFLYQGRSFKSYRGMGSVAAMER--GSSARYSQDGVTDVLKLVPEGIEGRVP 427 GT+ESPG+ GR +K YRGMGS+ AME+ GS RY Q G K VPEG+EGRVP Sbjct: 360 GTEESPGEYIERNGRRYKEYRGMGSLGAMEKHKGSKDRYFQAGDK---KGVPEGVEGRVP 416 Query: 428 YKGPIASVLHQMSGGLKSSMGYVGASNIEEFQKKANFIRVSVAGLRESHVH 478 YKG + +HQ+ GGL+SSMGYVGA++++E ++KA F+RV+ AGLRE HVH Sbjct: 417 YKGSVKDTIHQLLGGLRSSMGYVGAASLKELREKAFFVRVTSAGLREGHVH 467 >gnl|CDD|37761 KOG2550, KOG2550, KOG2550, IMP dehydrogenase/GMP reductase [Nucleotide transport and metabolism]. Length = 503 Score = 385 bits (989), Expect = e-107 Identities = 173/459 (37%), Positives = 276/459 (60%), Gaps = 5/459 (1%) Query: 11 GVALTFDDVLLRPEFSNVLPRDIDISTRIAKDFTLNLPIMSAAMDQVTDSRLAIAMAQAG 70 + LT++D L+ P F + ++ + T++ ++ TLN P++S+ MD VT+S +AIAMA G Sbjct: 27 KIGLTYNDFLILPGFIDFASDEVSLQTKLTRNITLNTPLVSSPMDTVTESEMAIAMALLG 86 Query: 71 GLGVIHRNFSPSEQVAQVHQVKKFESGMVVNPVTISPYATLADALALMKKYSISGIPVVE 130 G+G IH N +P +Q V +VK +E+G + NP+ ISP T+ + +K+ SGIPV E Sbjct: 87 GIGFIHHNCTPEDQADMVRRVKNYENGFINNPIVISPTTTVGEVKEAKEKHGFSGIPVTE 146 Query: 131 SDV--GKLVGILTNRDVRFASNAQQAVGELMTRNLITVKKTVNLENAKALLHQHRIEKLL 188 KLVGI+T+RD++F + V ++MT+N +T + + L+ A +L + + KL Sbjct: 147 DGKRGSKLVGIITSRDIQFLEDNSLLVSDVMTKNPVTGAQGITLKEANEILKKIKKGKLP 206 Query: 189 VVDDDGCCIGLITVKDIERSQLNPNATKDSKGRLRVAAAVSVAKDIADRVGPLFDVNVDL 248 VVDD G + +++ D+ +++ P A+KDS +L AA+ D +R+ L VD+ Sbjct: 207 VVDDKGELVAMLSRTDLMKNRDYPLASKDSTKQLLCGAAIGTRDDDKERLDLLVQAGVDV 266 Query: 249 VVVDTAHGHSQKVLDAVVQIKKNFPSLLVMAGNIATAEGALALIDAGADIIKVGIGPGSI 308 V++D++ G+S L+ + IK+ +P L ++AGN+ T E A LI AGAD ++VG+G GSI Sbjct: 267 VILDSSQGNSIYQLEMIKYIKETYPDLQIIAGNVVTKEQAANLIAAGADGLRVGMGSGSI 326 Query: 309 CTTRVVTGVGCPQLSAIMSVVEVAERAGVAIVADGGIRFSGDIAKAIAAGSACVMIGSLL 368 C T+ V G PQ +A+ V E A + GV +ADGGI+ G + KA+ G++ VM+G LL Sbjct: 327 CITQKVMACGRPQGTAVYKVAEFANQFGVPCIADGGIQNVGHVVKALGLGASTVMMGGLL 386 Query: 369 AGTDESPGDIFLYQGRSFKSYRGMGSVAAMERGSSARYSQDGVTDVLKLVPEGIEGRVPY 428 AGT E+PG+ F G K YRGMGS+ AME S RY + D +K + +G+ G V Sbjct: 387 AGTTEAPGEYFFRDGVRLKKYRGMGSLDAMESSSQKRYFSEV--DKVK-IAQGVSGSVQD 443 Query: 429 KGPIASVLHQMSGGLKSSMGYVGASNIEEFQKKANFIRV 467 KG + + + G++ S +GA +++E ++ V Sbjct: 444 KGSVQKFIPYLLAGIQHSCQDIGARSLKELREMMYSGEV 482 >gnl|CDD|73364 cd00381, IMPDH, IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the guanine nucleotides. There is often a CBS domain inserted in the middle of this domain, which is proposed to play a regulatory role. IMPDH is a key enzyme in the regulation of cell proliferation and differentiation. It has been identified as an attractive target for developing chemotherapeutic agents.. Length = 325 Score = 334 bits (859), Expect = 2e-92 Identities = 139/249 (55%), Positives = 180/249 (72%), Gaps = 3/249 (1%) Query: 219 KGRLRVAAAVSVAKDIADRVGPLFDVNVDLVVVDTAHGHSQKVLDAVVQIKKNFPSLLVM 278 KGRL V AAV +D +R L + VD++V+D+AHGHS V++ + IKK +P++ V+ Sbjct: 80 KGRLLVGAAVGTREDDKERAEALVEAGVDVIVIDSAHGHSVYVIEMIKFIKKKYPNVDVI 139 Query: 279 AGNIATAEGALALIDAGADIIKVGIGPGSICTTRVVTGVGCPQLSAIMSVVEVAERAGVA 338 AGN+ TAE A LIDAGAD +KVGIGPGSICTTR+VTGVG PQ +A+ V A GV Sbjct: 140 AGNVVTAEAARDLIDAGADGVKVGIGPGSICTTRIVTGVGVPQATAVADVAAAARDYGVP 199 Query: 339 IVADGGIRFSGDIAKAIAAGSACVMIGSLLAGTDESPGDIFLYQGRSFKSYRGMGSVAAM 398 ++ADGGIR SGDI KA+AAG+ VM+GSLLAGTDESPG+ G+ +K YRGMGS+ AM Sbjct: 200 VIADGGIRTSGDIVKALAAGADAVMLGSLLAGTDESPGEYIEINGKRYKEYRGMGSLGAM 259 Query: 399 ERGSSARYSQDGVTDVLKLVPEGIEGRVPYKGPIASVLHQMSGGLKSSMGYVGASNIEEF 458 ++G RY + KLVPEG+EG VPYKG + VL Q+ GGL+SSMGY GA +++E Sbjct: 260 KKGGGDRYFGEEAK---KLVPEGVEGIVPYKGSVKDVLPQLVGGLRSSMGYCGAKSLKEL 316 Query: 459 QKKANFIRV 467 Q+KA F+R+ Sbjct: 317 QEKARFVRI 325 Score = 113 bits (285), Expect = 9e-26 Identities = 47/81 (58%), Positives = 63/81 (77%) Query: 13 ALTFDDVLLRPEFSNVLPRDIDISTRIAKDFTLNLPIMSAAMDQVTDSRLAIAMAQAGGL 72 LTFDDVLL P +S VLP ++D+ST++ K+ TLN+P++SA MD VT+S +AIAMA+ GG+ Sbjct: 1 GLTFDDVLLVPGYSTVLPSEVDLSTKLTKNITLNIPLVSAPMDTVTESEMAIAMARLGGI 60 Query: 73 GVIHRNFSPSEQVAQVHQVKK 93 GVIHRN S EQ +V +VK Sbjct: 61 GVIHRNMSIEEQAEEVRKVKG 81 >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 = 151 bits (384), Expect = 3e-37 Identities = 63/111 (56%), Positives = 85/111 (76%), Gaps = 2/111 (1%) Query: 99 VVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASNAQQAVGEL 158 + +P+T+SP AT+A+AL LM +Y ISG+PVV+ D GKLVGI+TNRD+RF ++ + V E+ Sbjct: 1 IRDPITVSPDATVAEALELMAEYGISGLPVVDDD-GKLVGIVTNRDLRFETDLDKPVSEV 59 Query: 159 MTR-NLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERS 208 MT NL+T + +LE A LLH+H+IEKL VVDD+G GLITVKDIE+ Sbjct: 60 MTPENLLTTVEGTSLEEALELLHEHKIEKLPVVDDEGKLKGLITVKDIEKR 110 >gnl|CDD|30862 COG0516, GuaB, IMP dehydrogenase/GMP reductase [Nucleotide transport and metabolism]. Length = 170 Score = 133 bits (337), Expect = 8e-32 Identities = 68/220 (30%), Positives = 98/220 (44%), Gaps = 51/220 (23%) Query: 261 VLDAVVQIKKNFPSLLVMAGNIATAEGALALIDAGADIIKVGIGPGSICTTRVVTGVGCP 320 VL V++IKK P L ++ A + AG +K G+GPG GV P Sbjct: 1 VLMQVLKIKKARPGL--TFDDVLLLPAASDVAPAG-VDVKTGLGPG--------IGVNIP 49 Query: 321 QLSAIMSVVEVAERAGVAIVADGGIRFSGDIAKAIAAGSACVMIGSLLAGTDESPGDIFL 380 Q+SA M V A A +A+ DGGI VM G++LA +ESPG+ Sbjct: 50 QVSAAMDTVTEARMA-IAMARDGGIG---------------VMHGNMLA--EESPGEYLY 91 Query: 381 YQGRSFKSYRGMGSVAAMERGSSARYSQDGVTDVLKLVPEGIEGRVPYKGPIASVLHQMS 440 + RGMGS+ AM RY LV +G+ G V KG I + + Sbjct: 92 QK-------RGMGSIDAM-----QRYFSS------VLVAQGVSGVV-DKGSIKKFIPYLY 132 Query: 441 GGLKSSMGYVGASNIEEFQKKANFIRVSVAGLRESHVHDV 480 GGL+SS Y+G ++ ++ F + + E VH++ Sbjct: 133 GGLQSSCQYIGCRSLTLLKENVRFEFRTAS---EGGVHNL 169 Score = 90.7 bits (225), Expect = 8e-19 Identities = 37/99 (37%), Positives = 58/99 (58%) Query: 1 MARIIENNVGGVALTFDDVLLRPEFSNVLPRDIDISTRIAKDFTLNLPIMSAAMDQVTDS 60 + ++++ LTFDDVLL P S+V P +D+ T + +N+P +SAAMD VT++ Sbjct: 2 LMQVLKIKKARPGLTFDDVLLLPAASDVAPAGVDVKTGLGPGIGVNIPQVSAAMDTVTEA 61 Query: 61 RLAIAMAQAGGLGVIHRNFSPSEQVAQVHQVKKFESGMV 99 R+AIAMA+ GG+GV+H N E + K+ + Sbjct: 62 RMAIAMARDGGIGVMHGNMLAEESPGEYLYQKRGMGSID 100 >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 = 94.5 bits (235), Expect = 6e-20 Identities = 40/113 (35%), Positives = 68/113 (60%), Gaps = 4/113 (3%) Query: 99 VVNPVTISPYATLADALALMKKYSISGIPVVE--SDVGKLVGILTNRDVRFASNAQQAVG 156 + +P +SP T+AD L + +K SGIPV E GKL+GI+T+RD+ F ++++ + Sbjct: 1 ITDPSVLSPDHTVADVLEIKEKKGFSGIPVTEDGKSGGKLLGIVTSRDIDFLTDSETPLS 60 Query: 157 ELMTRN--LITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIER 207 E+MT L+ + LE A +L + + KL +V+DDG + L+T D+++ Sbjct: 61 EVMTPREVLVVAPTGITLEEANEILRESKKGKLPIVNDDGELVALVTRSDLKK 113 >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 = 88.4 bits (219), Expect = 5e-18 Identities = 43/107 (40%), Positives = 67/107 (62%), Gaps = 4/107 (3%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASNAQQAVGELMT 160 +P+TI P ++ A LM+K+ I G+PVVE GKLVGI+T+RDVR A + + V + MT Sbjct: 2 DPITIDPLDSVGRAARLMEKHRIGGLPVVED--GKLVGIITSRDVRRA-HPNRLVADAMT 58 Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIER 207 R ++T+ +L AK L+ + +IE+L V+ + +G+IT I Sbjct: 59 REVVTISPEASLLEAKRLMEEKKIERLPVLRERK-LVGIITKGTIAL 104 Score = 39.9 bits (93), Expect = 0.002 Identities = 31/105 (29%), Positives = 46/105 (43%), Gaps = 6/105 (5%) Query: 48 PIMSAAMDQVTDSRLAIAMAQAGGLGVIHRN----FSPSEQVAQVHQVKKFESGMVVNPV 103 PI +D V + + + GGL V+ S V + H + M V Sbjct: 3 PITIDPLDSVGRAARLMEKHRIGGLPVVEDGKLVGIITSRDVRRAHPNRLVADAMTREVV 62 Query: 104 TISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFA 148 TISP A+L +A LM++ I +PV+ KLVGI+T + Sbjct: 63 TISPEASLLEAKRLMEEKKIERLPVLRE--RKLVGIITKGTIALE 105 Score = 35.3 bits (81), Expect = 0.039 Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 1/51 (1%) Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERSQLN 211 R+ IT+ ++ A L+ +HRI L VV+D G+IT +D+ R+ N Sbjct: 1 RDPITIDPLDSVGRAARLMEKHRIGGLPVVEDGKLV-GIITSRDVRRAHPN 50 >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 = 86.8 bits (215), Expect = 1e-17 Identities = 48/122 (39%), Positives = 73/122 (59%), Gaps = 17/122 (13%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASN---------- 150 NP+T++P +L +AL LMK+ SI +PVV+ GKLVGI+T+RD++ AS Sbjct: 2 NPITVTPDTSLMEALKLMKENSIRRLPVVDR--GKLVGIVTDRDLKLASPSKATTLDIWE 59 Query: 151 -----AQQAVGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 ++ V ++MTR+ ITV ++E A L+ + +I L VVDD G +G+IT D+ Sbjct: 60 LYYLLSKIKVSDIMTRDPITVSPDASVEEAAELMLERKISGLPVVDDQGRLVGIITESDL 119 Query: 206 ER 207 R Sbjct: 120 FR 121 Score = 51.3 bits (123), Expect = 6e-07 Identities = 32/90 (35%), Positives = 49/90 (54%), Gaps = 10/90 (11%) Query: 57 VTDSRLAIAMA-QAGGLGVIHRNFSPSEQVAQVHQVKKFESGMVVNPVTISPYATLADAL 115 VTD L +A +A L + + S+ K M +P+T+SP A++ +A Sbjct: 39 VTDRDLKLASPSKATTLDIWELYYLLSKI--------KVSDIMTRDPITVSPDASVEEAA 90 Query: 116 ALMKKYSISGIPVVESDVGKLVGILTNRDV 145 LM + ISG+PVV+ D G+LVGI+T D+ Sbjct: 91 ELMLERKISGLPVVD-DQGRLVGIITESDL 119 Score = 38.6 bits (90), Expect = 0.003 Identities = 26/94 (27%), Positives = 45/94 (47%), Gaps = 4/94 (4%) Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERSQLNPNATKDSKG 220 +N ITV +L A L+ ++ I +L VV D G +G++T +D++ + + T D Sbjct: 1 KNPITVTPDTSLMEALKLMKENSIRRLPVV-DRGKLVGIVTDRDLKLASPSKATTLDIWE 59 Query: 221 RLRVAAAVSVAKDIADRVGPLFDVNVDLVVVDTA 254 + + + V DI R V+ D V + A Sbjct: 60 LYYLLSKIKV-SDIMTR--DPITVSPDASVEEAA 90 >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 = 85.2 bits (211), Expect = 4e-17 Identities = 47/119 (39%), Positives = 73/119 (61%), Gaps = 16/119 (13%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFAS----------- 149 + VTI+P T+A+AL LM+++ I +PVV+ + G+LVGI+T+RD+R AS Sbjct: 2 DVVTITPTTTIAEALELMREHKIRHLPVVDEE-GRLVGIVTDRDLRDASPSPFTTLSEHE 60 Query: 150 ---NAQQAVGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 + V E+MT+++ITV +E A L+ +HRI L VV +DG +G+IT D+ Sbjct: 61 LYLLLKMPVKEIMTKDVITVHPLDTVEEAALLMREHRIGCLPVV-EDGRLVGIITETDL 118 Score = 49.8 bits (119), Expect = 2e-06 Identities = 19/48 (39%), Positives = 31/48 (64%), Gaps = 2/48 (4%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 M + +T+ P T+ +A LM+++ I +PVVE G+LVGI+T D+ Sbjct: 73 MTKDVITVHPLDTVEEAALLMREHRIGCLPVVED--GRLVGIITETDL 118 Score = 44.4 bits (105), Expect = 7e-05 Identities = 15/47 (31%), Positives = 30/47 (63%) Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIER 207 R+++T+ T + A L+ +H+I L VVD++G +G++T +D+ Sbjct: 1 RDVVTITPTTTIAEALELMREHKIRHLPVVDEEGRLVGIVTDRDLRD 47 >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 = 81.4 bits (201), Expect = 5e-16 Identities = 40/109 (36%), Positives = 65/109 (59%), Gaps = 6/109 (5%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRD-VRFA---SNAQQAVG 156 +T P +LA+A + M++ IS I VV+ + +GI+T RD +R + Q VG Sbjct: 2 QILTCPPDTSLAEAASRMRERRISSIVVVDDG--RPLGIVTERDILRLLASGPDLQTPVG 59 Query: 157 ELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 E+M+ L+TV +L +A+ L+ +H I L+VVDDDG +GL++ D+ Sbjct: 60 EVMSSPLLTVPADTSLYDARQLMREHGIRHLVVVDDDGELLGLLSQTDL 108 Score = 30.5 bits (69), Expect = 1.2 Identities = 15/43 (34%), Positives = 27/43 (62%), Gaps = 1/43 (2%) Query: 104 TISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVR 146 T+ +L DA LM+++ I + VV+ D G+L+G+L+ D+ Sbjct: 68 TVPADTSLYDARQLMREHGIRHLVVVDDD-GELLGLLSQTDLL 109 Score = 28.6 bits (64), Expect = 4.1 Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 1/47 (2%) Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIER 207 ++T +L A + + + RI ++VVDD +G++T +DI R Sbjct: 1 TQILTCPPDTSLAEAASRMRERRISSIVVVDDGR-PLGIVTERDILR 46 >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 = 1e-15 Identities = 50/112 (44%), Positives = 75/112 (66%), Gaps = 6/112 (5%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFA-----SNAQQAV 155 + VT+SP T+A+AL LM ++ ISG+PVV+ D G+LVGI+T RD+ A + V Sbjct: 2 DVVTVSPDDTVAEALRLMLEHGISGLPVVDDD-GRLVGIVTERDLLRALAEGGLDPLVTV 60 Query: 156 GELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIER 207 G++MTR+++TV +LE A L+ +H I +L VVDD+G +G++T DI R Sbjct: 61 GDVMTRDVVTVSPDTSLEEAAELMLEHGIRRLPVVDDEGRLVGIVTRSDILR 112 Score = 43.6 bits (102), Expect = 1e-04 Identities = 20/48 (41%), Positives = 32/48 (66%), Gaps = 1/48 (2%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 M + VT+SP +L +A LM ++ I +PVV+ + G+LVGI+T D+ Sbjct: 64 MTRDVVTVSPDTSLEEAAELMLEHGIRRLPVVDDE-GRLVGIVTRSDI 110 Score = 38.2 bits (88), Expect = 0.005 Identities = 18/57 (31%), Positives = 30/57 (52%) Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERSQLNPNATKD 217 R+++TV + A L+ +H I L VVDDDG +G++T +D+ R+ Sbjct: 1 RDVVTVSPDDTVAEALRLMLEHGISGLPVVDDDGRLVGIVTERDLLRALAEGGLDPL 57 >gnl|CDD|30863 COG0517, COG0517, FOG: CBS domain [General function prediction only]. Length = 117 Score = 78.3 bits (192), Expect = 4e-15 Identities = 48/114 (42%), Positives = 69/114 (60%), Gaps = 8/114 (7%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASNAQQA--- 154 M + +T+ P ++ DAL LM + +S +PVV D GKLVGI+T RD+ A A Sbjct: 5 MTKDVITVKPDTSVRDALLLMSENGVSAVPVV--DDGKLVGIITERDILRALAAGGKRLL 62 Query: 155 -VGELMTRNLITVKKTVNLENAKALLHQ-HRIEKLLVVDDDGC-CIGLITVKDI 205 V E+MT+ ++TV LE A L+ + H+I +L VVDDDG +G+IT+ DI Sbjct: 63 PVKEVMTKPVVTVDPDTPLEEALELMVERHKIRRLPVVDDDGGKLVGIITLSDI 116 Score = 37.0 bits (85), Expect = 0.011 Identities = 22/79 (27%), Positives = 41/79 (51%), Gaps = 1/79 (1%) Query: 155 VGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERSQLNPNA 214 V ++MT+++ITVK ++ +A L+ ++ + + VVDD +G+IT +DI R+ Sbjct: 1 VKDIMTKDVITVKPDTSVRDALLLMSENGVSAVPVVDDGK-LVGIITERDILRALAAGGK 59 Query: 215 TKDSKGRLRVAAAVSVAKD 233 + V+V D Sbjct: 60 RLLPVKEVMTKPVVTVDPD 78 >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 = 78.2 bits (193), Expect = 5e-15 Identities = 40/114 (35%), Positives = 76/114 (66%), Gaps = 8/114 (7%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASNAQ------QA 154 + VT+SP T+ +A LM+++ + +PV E+D +LVGI+T+RD+ + A+ Sbjct: 2 DVVTVSPDDTIREAARLMREHDVGALPVCEND--RLVGIVTDRDIVVRAVAEGRDPDTTT 59 Query: 155 VGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERS 208 VG++MTR ++TV + +++ A L+ +H++ +L VVDDDG +G++++ D+ R+ Sbjct: 60 VGDVMTRGVVTVTEDDDVDEAARLMREHQVRRLPVVDDDGRLVGIVSLGDLARA 113 Score = 39.3 bits (92), Expect = 0.003 Identities = 16/48 (33%), Positives = 30/48 (62%), Gaps = 1/48 (2%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 M VT++ + +A LM+++ + +PVV+ D G+LVGI++ D+ Sbjct: 64 MTRGVVTVTEDDDVDEAARLMREHQVRRLPVVDDD-GRLVGIVSLGDL 110 >gnl|CDD|32729 COG2905, COG2905, Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]. Length = 610 Score = 74.9 bits (184), Expect = 4e-14 Identities = 48/178 (26%), Positives = 84/178 (47%), Gaps = 14/178 (7%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASNA-----Q 152 + VT+SP A++ DA MK +S + V++ G L+GI+T +D+R A Sbjct: 155 KTLPAVTVSPQASIQDAARKMKDEGVSSLVVLDDS-GPLLGIVTRKDLRSRVIADGRSKT 213 Query: 153 QAVGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERSQLNP 212 Q V E+MT +I+V + L A ++ ++RI+ L V +DG +G++T+ DI R + Sbjct: 214 QKVSEVMTSPVISVDRGDFLFEAMLMMLRNRIKH-LPVTEDGQPLGILTLTDILR-LFSQ 271 Query: 213 N---ATKDSKGRLRVAAAVSVAKDIADRVGPLFDVNVDLVVVDTAHGHSQKVLDAVVQ 267 N K + + A+ + D + L V + ++ D +VQ Sbjct: 272 NSIVLVKRIARASSIEELANTAELLDDSLSTLVSRGVRTEFISELI---TEINDQLVQ 326 >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 = 74.8 bits (184), Expect = 5e-14 Identities = 36/121 (29%), Positives = 62/121 (51%), Gaps = 16/121 (13%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV--------------- 145 + VT+ P + +A +M + +PVV+ GKLVGI+T D+ Sbjct: 2 DVVTVPPTTPIMEAAKIMVRNGFRRLPVVDEGTGKLVGIITATDILKYLGGGEKFNKIKT 61 Query: 146 -RFASNAQQAVGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKD 204 + V +MTRN+IT+ ++++A L+ + R+ L VVDDDG +G++T +D Sbjct: 62 GNGLEAINEPVRSIMTRNVITITPDDSIKDAAELMLEKRVGGLPVVDDDGKLVGIVTERD 121 Query: 205 I 205 + Sbjct: 122 L 122 Score = 49.4 bits (118), Expect = 2e-06 Identities = 23/48 (47%), Positives = 33/48 (68%), Gaps = 1/48 (2%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 M N +TI+P ++ DA LM + + G+PVV+ D GKLVGI+T RD+ Sbjct: 76 MTRNVITITPDDSIKDAAELMLEKRVGGLPVVDDD-GKLVGIVTERDL 122 >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 = 72.5 bits (178), Expect = 3e-13 Identities = 41/113 (36%), Positives = 61/113 (53%), Gaps = 8/113 (7%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRF-----ASNAQQAV 155 PVT SP T+ +A LM ++ +S + VV D G+LVGI+T+RD+R + V Sbjct: 2 PPVTCSPDTTIREAARLMTEHRVSSLLVV--DDGRLVGIVTDRDLRNRVVAEGLDPDTPV 59 Query: 156 GELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERS 208 E+MT IT+ + A L+ + I L VV DDG +G+I+ D+ R Sbjct: 60 SEVMTAPPITIPPDATVFEALLLMLERGIHHLPVV-DDGRLVGVISATDLLRL 111 Score = 46.7 bits (111), Expect = 2e-05 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 11/72 (15%) Query: 74 VIHRNFSPSEQVAQVHQVKKFESGMVVNPVTISPYATLADALALMKKYSISGIPVVESDV 133 V+ P V++V M P+TI P AT+ +AL LM + I +PVV+ Sbjct: 48 VVAEGLDPDTPVSEV---------MTAPPITIPPDATVFEALLLMLERGIHHLPVVDD-- 96 Query: 134 GKLVGILTNRDV 145 G+LVG+++ D+ Sbjct: 97 GRLVGVISATDL 108 Score = 28.9 bits (65), Expect = 3.4 Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 1/45 (2%) Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 R +T + A L+ +HR+ LLVVDD +G++T +D+ Sbjct: 1 RPPVTCSPDTTIREAARLMTEHRVSSLLVVDDGR-LVGIVTDRDL 44 >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 = 71.3 bits (175), Expect = 5e-13 Identities = 42/111 (37%), Positives = 66/111 (59%), Gaps = 8/111 (7%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV------RFASNAQQA 154 + +T+ P AT+A+A LM + +I + VV+ D G+LVGI + RD+ R AS Sbjct: 2 DVITVRPDATVAEAAKLMAEKNIGAVVVVD-DGGRLVGIFSERDIVRKVALRGASALDTP 60 Query: 155 VGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 V E+MTRN+ITV ++ A AL+ + R L VV D G +G++++ D+ Sbjct: 61 VSEIMTRNVITVTPDDTVDEAMALMTERRFRHLPVV-DGGKLVGIVSIGDV 110 Score = 40.9 bits (96), Expect = 0.001 Identities = 20/48 (41%), Positives = 31/48 (64%), Gaps = 2/48 (4%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 M N +T++P T+ +A+ALM + +PVV+ GKLVGI++ DV Sbjct: 65 MTRNVITVTPDDTVDEAMALMTERRFRHLPVVDG--GKLVGIVSIGDV 110 Score = 36.3 bits (84), Expect = 0.023 Identities = 16/47 (34%), Positives = 28/47 (59%) Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIER 207 R++ITV+ + A L+ + I ++VVDD G +G+ + +DI R Sbjct: 1 RDVITVRPDATVAEAAKLMAEKNIGAVVVVDDGGRLVGIFSERDIVR 47 >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 = 71.0 bits (174), Expect = 6e-13 Identities = 42/110 (38%), Positives = 66/110 (60%), Gaps = 5/110 (4%) Query: 102 PVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVR---FASNAQQAVGEL 158 +T++P ATL +A L + I G PVV D GKLVGI+T D+ V ++ Sbjct: 3 LITLNPNATLREAARLFNTHHIHGAPVV--DDGKLVGIVTLSDIAHAIARGLELAKVKDV 60 Query: 159 MTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERS 208 MT+++IT+ + L +A L+++H + +L+V DD+G +G+IT DI RS Sbjct: 61 MTKDVITIDEDEQLYDAIRLMNKHNVGRLIVTDDEGRPVGIITRTDILRS 110 Score = 34.0 bits (78), Expect = 0.097 Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 1/48 (2%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 M + +TI L DA+ LM K+++ + V + D G+ VGI+T D+ Sbjct: 61 MTKDVITIDEDEQLYDAIRLMNKHNVGRLIVTD-DEGRPVGIITRTDI 107 Score = 27.9 bits (62), Expect = 6.9 Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 1/48 (2%) Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERS 208 + LIT+ L A L + H I VVDD +G++T+ DI + Sbjct: 1 KPLITLNPNATLREAARLFNTHHIHGAPVVDDGK-LVGIVTLSDIAHA 47 >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 = 70.3 bits (172), Expect = 1e-12 Identities = 42/121 (34%), Positives = 61/121 (50%), Gaps = 15/121 (12%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV--------------R 146 VT+S +LADA LM+++ I +PVV D GKLVG+LT RD+ Sbjct: 2 PVVTLSEDDSLADAEELMREHRIRHLPVVNED-GKLVGLLTQRDLLRAALSSLSDNGEES 60 Query: 147 FASNAQQAVGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIE 206 V E+M +++TV L A ++ +++I L VVDD G +G+IT D Sbjct: 61 LTKERDVPVAEVMKTDVLTVTPDTPLREAAEIMVENKIGCLPVVDDKGTLVGIITRSDFL 120 Query: 207 R 207 R Sbjct: 121 R 121 Score = 43.3 bits (102), Expect = 2e-04 Identities = 18/50 (36%), Positives = 34/50 (68%) Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERSQL 210 ++T+ + +L +A+ L+ +HRI L VV++DG +GL+T +D+ R+ L Sbjct: 1 SPVVTLSEDDSLADAEELMREHRIRHLPVVNEDGKLVGLLTQRDLLRAAL 50 >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 = 68.7 bits (168), Expect = 4e-12 Identities = 42/108 (38%), Positives = 66/108 (61%), Gaps = 5/108 (4%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRD-VRFASNAQQAVGELM 159 N V ++ T D L L+K+Y +SG+PVV+ G+LVGI+T +D +R Q A+ LM Sbjct: 2 NVVYVTLPGTRDDVLELLKEYKVSGVPVVK-KSGELVGIITRKDLLRNPEEEQLAL--LM 58 Query: 160 TRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIER 207 TR+ TV +++ A L+ ++ I ++ VVDD +G++TV DI R Sbjct: 59 TRDPPTVSPDDDVKEAAKLMVENNIRRVPVVDDGK-LVGIVTVADIVR 105 Score = 41.4 bits (97), Expect = 6e-04 Identities = 20/48 (41%), Positives = 30/48 (62%), Gaps = 2/48 (4%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 M +P T+SP + +A LM + +I +PVV+ GKLVGI+T D+ Sbjct: 58 MTRDPPTVSPDDDVKEAAKLMVENNIRRVPVVDD--GKLVGIVTVADI 103 >gnl|CDD|32593 COG2524, COG2524, Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]. Length = 294 Score = 68.4 bits (167), Expect = 5e-12 Identities = 38/120 (31%), Positives = 66/120 (55%), Gaps = 5/120 (4%) Query: 92 KKFESGMVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVR---FA 148 +K ++ M +T+ P TL +A L + I G PVV+ D K+VGI+T D+ Sbjct: 172 EKVKNLMSKKLITVRPDDTLREAAKLFYEKGIRGAPVVDDD--KIVGIITLSDIAKAIAN 229 Query: 149 SNAQQAVGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERS 208 N V + M +N+IT+ + ++ +A L++++ + +LLV D +G +G+IT DI Sbjct: 230 GNLDAKVSDYMRKNVITINEDEDIYDAIRLMNKNNVGRLLVTDSNGKPVGIITRTDILTR 289 Score = 36.0 bits (83), Expect = 0.021 Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 1/64 (1%) Query: 82 SEQVAQVHQVKKFESGMVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILT 141 ++ +A + K M N +TI+ + DA+ LM K ++ G +V GK VGI+T Sbjct: 224 AKAIANGNLDAKVSDYMRKNVITINEDEDIYDAIRLMNKNNV-GRLLVTDSNGKPVGIIT 282 Query: 142 NRDV 145 D+ Sbjct: 283 RTDI 286 >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 = 67.2 bits (164), Expect = 1e-11 Identities = 41/108 (37%), Positives = 68/108 (62%), Gaps = 2/108 (1%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFA-SNAQQAVGELM 159 VTIS A++ +A LM + +I+ +PVV+ D G+LVGI+T+ D+ A + +++V ++M Sbjct: 3 PVVTISEDASIKEAAKLMIEENINHLPVVDED-GRLVGIVTSWDISKAVARDKKSVEDIM 61 Query: 160 TRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIER 207 TRN+IT ++ A + +H I L VVD + IG+IT +DI + Sbjct: 62 TRNVITATPDEPIDVAARKMERHNISALPVVDAENRVIGIITSEDISK 109 Score = 38.7 bits (90), Expect = 0.004 Identities = 20/64 (31%), Positives = 39/64 (60%), Gaps = 3/64 (4%) Query: 82 SEQVAQVHQVKKFESGMVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILT 141 S+ VA+ K E M N +T +P + A M++++IS +PVV+++ +++GI+T Sbjct: 47 SKAVAR--DKKSVEDIMTRNVITATPDEPIDVAARKMERHNISALPVVDAE-NRVIGIIT 103 Query: 142 NRDV 145 + D+ Sbjct: 104 SEDI 107 Score = 37.1 bits (86), Expect = 0.010 Identities = 15/49 (30%), Positives = 31/49 (63%) Query: 160 TRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERS 208 +R ++T+ + +++ A L+ + I L VVD+DG +G++T DI ++ Sbjct: 1 SRPVVTISEDASIKEAAKLMIEENINHLPVVDEDGRLVGIVTSWDISKA 49 >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 = 66.8 bits (163), Expect = 1e-11 Identities = 42/114 (36%), Positives = 70/114 (61%), Gaps = 10/114 (8%) Query: 102 PVTISPYATLADALALMKKYSISG-IPVVESDVGKLVGILTNRD-VRFASN----AQQAV 155 P+T++P +ADA+ALM + S + VVE G+L+GI T RD VR + + + Sbjct: 3 PLTVTPDTPVADAIALMSQQGDSSCVLVVEK--GRLLGIFTERDIVRLTAIGKDLSDLPI 60 Query: 156 GELMTRNLITVKKT--VNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIER 207 GE+MT+ ++T++++ ++ A +L QH+I L V+DD G IGL+T + I + Sbjct: 61 GEVMTQPVVTLQESEIQDIFTALSLFRQHQIRHLPVLDDQGQLIGLVTAESIRQ 114 >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 = 66.4 bits (162), Expect = 2e-11 Identities = 36/111 (32%), Positives = 62/111 (55%), Gaps = 5/111 (4%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASNAQQA----VG 156 VT+ P ++ +A LM + ++ + VV+ D + +GI+T RD+ A A V Sbjct: 2 PVVTVDPDTSIREAAKLMAEENVGSVVVVDPD-ERPIGIVTERDIVRAVAAGIDLDTPVS 60 Query: 157 ELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIER 207 E+MTR+L+TV + A L+ ++ I LVVD G +G+I+++D+ R Sbjct: 61 EIMTRDLVTVDPDEPVAEAAKLMRKNNIRHHLVVDKGGELVGVISIRDLVR 111 Score = 35.9 bits (83), Expect = 0.027 Identities = 18/51 (35%), Positives = 30/51 (58%), Gaps = 1/51 (1%) Query: 95 ESGMVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 M + VT+ P +A+A LM+K +I VV+ G+LVG+++ RD+ Sbjct: 60 SEIMTRDLVTVDPDEPVAEAAKLMRKNNIRHHLVVDKG-GELVGVISIRDL 109 Score = 31.3 bits (71), Expect = 0.55 Identities = 15/48 (31%), Positives = 28/48 (58%) Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERS 208 R ++TV ++ A L+ + + ++VVD D IG++T +DI R+ Sbjct: 1 RPVVTVDPDTSIREAAKLMAEENVGSVVVVDPDERPIGIVTERDIVRA 48 >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 = 66.3 bits (162), Expect = 2e-11 Identities = 37/108 (34%), Positives = 58/108 (53%), Gaps = 6/108 (5%) Query: 105 ISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFA-----SNAQQAVGELM 159 +SP +L DAL M + + VV+ D G+LVGI T+ D+R A V ++M Sbjct: 7 VSPDTSLKDALLEMSRKGLGMTAVVDED-GRLVGIFTDGDLRRALEKGLDILTLPVADVM 65 Query: 160 TRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIER 207 TRN T+ A L+ +++I L VVDD+G +G++ + D+ R Sbjct: 66 TRNPKTIDPDALAAEALELMEENKITALPVVDDNGRPVGVLHIHDLLR 113 Score = 45.5 bits (108), Expect = 4e-05 Identities = 20/43 (46%), Positives = 29/43 (67%), Gaps = 1/43 (2%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGIL 140 M NP TI P A A+AL LM++ I+ +PVV+ + G+ VG+L Sbjct: 65 MTRNPKTIDPDALAAEALELMEENKITALPVVDDN-GRPVGVL 106 >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 = 66.0 bits (161), Expect = 2e-11 Identities = 38/111 (34%), Positives = 59/111 (53%), Gaps = 6/111 (5%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASN----AQQAVG 156 + VT+ T+ + LALM G PVV+ G+LVGI+T D+R A VG Sbjct: 2 DVVTVPVDLTVDEVLALMFGERHRGYPVVDD--GRLVGIVTLADIRRVPAEGREATVLVG 59 Query: 157 ELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIER 207 ++MTR+ +T L +A + + I +L VVDD G +G+++ D+ R Sbjct: 60 DVMTRDPVTASPDETLRDALKRMAERDIGRLPVVDDSGRLVGIVSRSDLLR 110 Score = 42.1 bits (99), Expect = 3e-04 Identities = 23/48 (47%), Positives = 31/48 (64%), Gaps = 1/48 (2%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 M +PVT SP TL DAL M + I +PVV+ D G+LVGI++ D+ Sbjct: 62 MTRDPVTASPDETLRDALKRMAERDIGRLPVVD-DSGRLVGIVSRSDL 108 >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 = 66.0 bits (161), Expect = 3e-11 Identities = 34/101 (33%), Positives = 61/101 (60%), Gaps = 1/101 (0%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASNAQQAVGELMT 160 NPVTI+P TLA+A+ LM+ + + VV+ D KL+GI++ + A +++ ++M Sbjct: 3 NPVTITPDRTLAEAIKLMRDKKVDSLLVVDKD-NKLLGIVSLESLEQAYKEAKSLEDIML 61 Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLIT 201 ++ TV+ +L + L+ + + + VVD+DG +GLIT Sbjct: 62 EDVFTVQPDASLRDVLGLVLKRGPKYVPVVDEDGKLVGLIT 102 Score = 39.4 bits (92), Expect = 0.002 Identities = 21/50 (42%), Positives = 30/50 (60%), Gaps = 1/50 (2%) Query: 92 KKFESGMVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILT 141 K E M+ + T+ P A+L D L L+ K +PVV+ D GKLVG++T Sbjct: 54 KSLEDIMLEDVFTVQPDASLRDVLGLVLKRGPKYVPVVDED-GKLVGLIT 102 Score = 34.0 bits (78), Expect = 0.086 Identities = 14/56 (25%), Positives = 31/56 (55%) Query: 162 NLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERSQLNPNATKD 217 N +T+ L A L+ +++ LLVVD D +G+++++ +E++ + +D Sbjct: 3 NPVTITPDRTLAEAIKLMRDKKVDSLLVVDKDNKLLGIVSLESLEQAYKEAKSLED 58 >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 = 65.2 bits (159), Expect = 3e-11 Identities = 36/111 (32%), Positives = 62/111 (55%), Gaps = 7/111 (6%) Query: 102 PV-TISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASN---AQQAVGE 157 PV T+ P AT+ +A L+ +Y + +PVVE G++VGI++ RDV A V + Sbjct: 3 PVKTVRPEATIEEARELLLRYGHTALPVVEG--GRVVGIISRRDVEKALRHGLGHAPVKD 60 Query: 158 LMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERS 208 M+ +++TV L + L+ +H I + V +DG +G++T D+ R+ Sbjct: 61 YMSTDVVTVPPDTPLSEVQELMVEHDI-GRVPVVEDGRLVGIVTRTDLLRT 110 Score = 38.2 bits (89), Expect = 0.005 Identities = 19/50 (38%), Positives = 29/50 (58%), Gaps = 2/50 (4%) Query: 96 SGMVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 M + VT+ P L++ LM ++ I +PVVE G+LVGI+T D+ Sbjct: 60 DYMSTDVVTVPPDTPLSEVQELMVEHDIGRVPVVED--GRLVGIVTRTDL 107 >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 = 64.5 bits (157), Expect = 7e-11 Identities = 33/121 (27%), Positives = 60/121 (49%), Gaps = 17/121 (14%) Query: 102 PVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV---------------R 146 VT+ L + + +K+ + VVE + +LVG++++RD + Sbjct: 3 VVTVEMDDRLEEVREIFEKHKFHHLLVVEDN--ELVGVISDRDYLKAISPFLGTAGETEK 60 Query: 147 FASNAQQAVGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIE 206 + + ++MTR+ ITV ++ A LL ++ I L VVD++G IG+IT KD+ Sbjct: 61 DLATLNRRAHQIMTRDPITVSPDTPVDEASKLLLENSISCLPVVDENGQLIGIITWKDLL 120 Query: 207 R 207 + Sbjct: 121 K 121 Score = 52.2 bits (125), Expect = 3e-07 Identities = 21/59 (35%), Positives = 38/59 (64%), Gaps = 7/59 (11%) Query: 87 QVHQVKKFESGMVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 + HQ+ M +P+T+SP + +A L+ + SIS +PVV+ + G+L+GI+T +D+ Sbjct: 68 RAHQI------MTRDPITVSPDTPVDEASKLLLENSISCLPVVDEN-GQLIGIITWKDL 119 Score = 30.6 bits (69), Expect = 1.00 Identities = 14/53 (26%), Positives = 29/53 (54%), Gaps = 2/53 (3%) Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERSQLNPN 213 ++TV+ LE + + +H+ LLVV+D+ G+I+ +D + ++P Sbjct: 1 TRVVTVEMDDRLEEVREIFEKHKFHHLLVVEDNELV-GVISDRDYLK-AISPF 51 >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 = 61.8 bits (150), Expect = 4e-10 Identities = 39/142 (27%), Positives = 71/142 (50%), Gaps = 40/142 (28%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV--------------- 145 NP+T + T++DA L+++ ISG PV++ GKLVGI++ D+ Sbjct: 2 NPITCNADDTISDAARLLRENKISGAPVLDG--GKLVGIVSESDILKLLVTHDPSGNLWL 59 Query: 146 ---------------------RFASNA-QQAVGELMTRNLITVKKTVNLENAKALLHQHR 183 R ++A + V ++MT+ +IT+ ++E+A L+ +H+ Sbjct: 60 PSPLELIELPLREFINWEETKRALTDAGKMKVRDIMTKKVITISPDASIEDAAELMVRHK 119 Query: 184 IEKLLVVDDDGCCIGLITVKDI 205 I++L VV+D +G++T DI Sbjct: 120 IKRLPVVEDGR-LVGIVTRGDI 140 Score = 41.8 bits (98), Expect = 4e-04 Identities = 23/55 (41%), Positives = 32/55 (58%), Gaps = 2/55 (3%) Query: 91 VKKFESGMVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 K M +TISP A++ DA LM ++ I +PVVE G+LVGI+T D+ Sbjct: 88 KMKVRDIMTKKVITISPDASIEDAAELMVRHKIKRLPVVED--GRLVGIVTRGDI 140 >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 = 60.2 bits (146), Expect = 1e-09 Identities = 40/123 (32%), Positives = 66/123 (53%), Gaps = 18/123 (14%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFA--------SNAQ 152 +T+SP ++ A LM + IS +PV+E GKLVGI+T +D+ A + Sbjct: 2 PVITVSPDDRVSHARRLMLDHDISRLPVIEG--GKLVGIVTEKDIADALRSFRPLVRDRH 59 Query: 153 QA-------VGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 Q V ++MTR +IT++ ++ + +L+ ++ I L VV DDG +G++T DI Sbjct: 60 QERRIRNLPVSDIMTRPVITIEPDTSVSDVASLMLENNIGGLPVV-DDGKLVGIVTRTDI 118 Query: 206 ERS 208 R Sbjct: 119 LRY 121 Score = 45.9 bits (109), Expect = 2e-05 Identities = 20/48 (41%), Positives = 31/48 (64%), Gaps = 2/48 (4%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 M +TI P +++D +LM + +I G+PVV+ GKLVGI+T D+ Sbjct: 73 MTRPVITIEPDTSVSDVASLMLENNIGGLPVVDD--GKLVGIVTRTDI 118 Score = 30.1 bits (68), Expect = 1.4 Identities = 14/45 (31%), Positives = 26/45 (57%), Gaps = 1/45 (2%) Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 + +ITV + +A+ L+ H I +L V++ +G++T KDI Sbjct: 1 KPVITVSPDDRVSHARRLMLDHDISRLPVIEGGK-LVGIVTEKDI 44 >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 = 60.1 bits (146), Expect = 1e-09 Identities = 25/105 (23%), Positives = 51/105 (48%), Gaps = 2/105 (1%) Query: 103 VTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV--RFASNAQQAVGELMT 160 V + TL + L L+ + S PV + D+ ++G++ +D+ A + + Sbjct: 4 VALDADDTLEEILELIAESGHSRFPVYDGDLDNIIGVVHVKDLLRALAEGEEDLDLRDLL 63 Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 R + V ++ L++ + + R +VVD+ G GL+T++DI Sbjct: 64 RPPLFVPESTPLDDLLEEMRKERSHMAIVVDEYGGTAGLVTLEDI 108 Score = 29.3 bits (66), Expect = 2.8 Identities = 17/76 (22%), Positives = 31/76 (40%), Gaps = 1/76 (1%) Query: 162 NLITVKKTVNLENAKALLHQHRIEKLLVVDDD-GCCIGLITVKDIERSQLNPNATKDSKG 220 +++ + LE L+ + + V D D IG++ VKD+ R+ D + Sbjct: 2 DIVALDADDTLEEILELIAESGHSRFPVYDGDLDNIIGVVHVKDLLRALAEGEEDLDLRD 61 Query: 221 RLRVAAAVSVAKDIAD 236 LR V + + D Sbjct: 62 LLRPPLFVPESTPLDD 77 >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 = 59.8 bits (145), Expect = 2e-09 Identities = 35/113 (30%), Positives = 61/113 (53%), Gaps = 5/113 (4%) Query: 100 VNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFA----SNAQQAV 155 + + +SP A++ DAL + K + I +V + G+L+G +T+ D+R A + V Sbjct: 2 IKQLLVSPDASILDALRKIDK-NALRIVLVVDENGRLLGTVTDGDIRRALLKGLSLDDPV 60 Query: 156 GELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERS 208 E+M RN IT K + E AL+ + I L ++D++G +GL T+ D+ Sbjct: 61 SEVMNRNPITAKVGSSREEILALMRERSIRHLPILDEEGRVVGLATLDDLLSK 113 Score = 39.0 bits (91), Expect = 0.003 Identities = 16/47 (34%), Positives = 30/47 (63%), Gaps = 1/47 (2%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRD 144 M NP+T ++ + LALM++ SI +P+++ + G++VG+ T D Sbjct: 64 MNRNPITAKVGSSREEILALMRERSIRHLPILDEE-GRVVGLATLDD 109 Score = 31.7 bits (72), Expect = 0.44 Identities = 13/48 (27%), Positives = 27/48 (56%) Query: 164 ITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERSQLN 211 + V ++ +A + ++ + +LVVD++G +G +T DI R+ L Sbjct: 5 LLVSPDASILDALRKIDKNALRIVLVVDENGRLLGTVTDGDIRRALLK 52 >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 = 59.1 bits (143), Expect = 3e-09 Identities = 35/122 (28%), Positives = 59/122 (48%), Gaps = 19/122 (15%) Query: 102 PVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASNAQQAVGELMT- 160 V+I + DA LM+K +ISG+PVV+ GKL+G ++ D++ + + T Sbjct: 3 VVSIDSDERVLDAFKLMRKNNISGLPVVDEK-GKLIGNISASDLKGLLLSPDDLLLYRTI 61 Query: 161 -----------------RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVK 203 R LIT + L+ L +++ ++ VVD++G IG+IT+ Sbjct: 62 TFKELSEKFTDSDGVKSRPLITCTPSSTLKEVITKLVANKVHRVWVVDEEGKPIGVITLT 121 Query: 204 DI 205 DI Sbjct: 122 DI 123 Score = 28.3 bits (63), Expect = 5.1 Identities = 11/71 (15%), Positives = 28/71 (39%), Gaps = 1/71 (1%) Query: 75 IHRNFSPSEQVAQVHQVKKFESGMVVNPVTISPYATLADALALMKKYSISGIPVVESDVG 134 + + + +T +P +TL + + + + + VV+ + G Sbjct: 54 DLLLYRTITFKELSEKFTDSDGVKSRPLITCTPSSTLKEVITKLVANKVHRVWVVD-EEG 112 Query: 135 KLVGILTNRDV 145 K +G++T D+ Sbjct: 113 KPIGVITLTDI 123 >gnl|CDD|32420 COG2239, MgtE, Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]. Length = 451 Score = 58.7 bits (142), Expect = 3e-09 Identities = 57/229 (24%), Positives = 103/229 (44%), Gaps = 19/229 (8%) Query: 81 PSEQVAQVHQVKKFE-----SGMVVNPVTISPYATLADALALMKKY-----SISGIPVVE 130 E+ A+V Q+ + M VT+ T+ +AL +++ +I + VV+ Sbjct: 116 DPEERARVRQLLSYPEDTAGRIMTTEFVTLPEDVTVDEALDRIRERAEDAETIYYLYVVD 175 Query: 131 SDVGKLVGILTNRDVRFASNAQQAVGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVV 190 GKL+G+++ RD+ A + + +LM ++++V + E L ++ + + VV Sbjct: 176 EK-GKLLGVVSLRDLLTAEPDEL-LKDLMEDDVVSVLADDDQEEVARLFEKYDLLAVPVV 233 Query: 191 DDDGCCIGLITVKDIERSQLNPNATKDSK---GRLRVA-AAVSVAKDIADRVGPLFDVNV 246 D+D IG+IT+ DI + AT+D G L V SV K + R+ L + V Sbjct: 234 DEDNRLIGIITIDDI-IDVIEEEATEDILRMAGPLDVPDLFASVLKLVKKRIPWLLVLLV 292 Query: 247 DLVVVDTAHGHSQKVLDAVVQIKKNFPSLLVMAGNIATAEGALALIDAG 295 + + G + L+ +V + P + M GN T A +I Sbjct: 293 TATLTASVIGLFEDTLEQLVALAAFIPLVAGMGGNAGTQ--AATVIVRA 339 >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 = 58.6 bits (142), Expect = 4e-09 Identities = 35/111 (31%), Positives = 63/111 (56%), Gaps = 7/111 (6%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV--RFASNAQQA---- 154 N VTI AT+A+AL LMK++ +S + V + GI+T RD+ + + + Sbjct: 2 NVVTIDGLATVAEALQLMKEHGVSSLVVEKRRESDAYGIVTMRDILKKVVAEGRDPDRVN 61 Query: 155 VGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 V E+MT+ LI+V ++++ L+ + I + VV+++ IG+I++ DI Sbjct: 62 VYEIMTKPLISVSPDMDIKYCARLMERTNIRRAPVVENNE-LIGIISLTDI 111 Score = 29.7 bits (67), Expect = 1.8 Identities = 11/54 (20%), Positives = 26/54 (48%), Gaps = 1/54 (1%) Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVV-DDDGCCIGLITVKDIERSQLNPN 213 N++T+ + A L+ +H + L+V + G++T++DI + + Sbjct: 1 PNVVTIDGLATVAEALQLMKEHGVSSLVVEKRRESDAYGIVTMRDILKKVVAEG 54 >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 = 58.3 bits (141), Expect = 4e-09 Identities = 33/120 (27%), Positives = 61/120 (50%), Gaps = 16/120 (13%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASNAQQA------ 154 + VT++P +L +A AL++++ I +PVV+ D +LVGI+T RD+ + Sbjct: 3 DVVTVTPDTSLEEAWALLRRHRIKALPVVDGD-RRLVGIVTQRDLLRHARPDGRRPLRGR 61 Query: 155 ---------VGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 VG++M+ ++TV+ + LL + VVD+D +G++T D+ Sbjct: 62 LRGRDKPETVGDIMSPPVVTVRPDTPIAELVPLLADGGHHHVPVVDEDRRLVGIVTQTDL 121 Score = 47.1 bits (112), Expect = 9e-06 Identities = 34/109 (31%), Positives = 53/109 (48%), Gaps = 5/109 (4%) Query: 160 TRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERSQLNPNATKDSK 219 +R+++TV +LE A ALL +HRI+ L VVD D +G++T +D+ R P+ + + Sbjct: 1 SRDVVTVTPDTSLEEAWALLRRHRIKALPVVDGDRRLVGIVTQRDLLR-HARPDGRRPLR 59 Query: 220 GRLRVAAAVSVAKDIADRVGPLFDVN---VDLVVVDTAHGHSQ-KVLDA 264 GRLR DI + +LV + GH V+D Sbjct: 60 GRLRGRDKPETVGDIMSPPVVTVRPDTPIAELVPLLADGGHHHVPVVDE 108 >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 = 58.2 bits (141), Expect = 4e-09 Identities = 28/107 (26%), Positives = 59/107 (55%), Gaps = 7/107 (6%) Query: 104 TISPYATLADALALMKKYS-----ISGIPVVESDVGKLVGILTNRDVRFASNAQQAVGEL 158 + T+ +AL +++ + I I VV+ + G+L+G+++ RD+ ++ V ++ Sbjct: 1 AVREDWTVGEALEYLRRNADDPETIYYIYVVDEE-GRLLGVVSLRDL-LLADPDTPVSDI 58 Query: 159 MTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 M ++I+V + E L ++ + L VVD++G +G+ITV D+ Sbjct: 59 MDTDVISVSADDDQEEVARLFEKYDLLALPVVDEEGRLVGIITVDDV 105 Score = 40.9 bits (96), Expect = 8e-04 Identities = 16/48 (33%), Positives = 28/48 (58%), Gaps = 1/48 (2%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 M + +++S + L +KY + +PVV+ + G+LVGI+T DV Sbjct: 59 MDTDVISVSADDDQEEVARLFEKYDLLALPVVDEE-GRLVGIITVDDV 105 >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 = 58.2 bits (141), Expect = 4e-09 Identities = 33/112 (29%), Positives = 61/112 (54%), Gaps = 9/112 (8%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV-------RFASNAQQ 153 NPVT +P ++ +A+ + K ISG PVV+ + G LVG L+ +D + + Sbjct: 2 NPVTFTPDMSVTEAVEKLLKSKISGGPVVDDN-GNLVGFLSEQDCLKQLLESSYHCDGVA 60 Query: 154 AVGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 V ++MT ++TV ++ + L+ + + ++ VV DDG +G I+ +D+ Sbjct: 61 TVRDIMTTEVLTVSPDDSIVDLAQLMLKAKPKRYPVV-DDGKLVGQISRRDV 111 Score = 30.9 bits (70), Expect = 0.81 Identities = 14/51 (27%), Positives = 26/51 (50%) Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERSQLN 211 RN +T +++ A L + +I VVDD+G +G ++ +D + L Sbjct: 1 RNPVTFTPDMSVTEAVEKLLKSKISGGPVVDDNGNLVGFLSEQDCLKQLLE 51 >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 = 58.2 bits (141), Expect = 4e-09 Identities = 31/107 (28%), Positives = 57/107 (53%), Gaps = 2/107 (1%) Query: 99 VVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASNAQQAVGEL 158 + + ++ T+ D L K+ S PVV+ K+VGI+T++DV + ++ Sbjct: 1 LEDTGYLTTTDTVKDWHELNKETGHSRFPVVDEK-NKVVGIVTSKDVAGKDP-DTTIEKV 58 Query: 159 MTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 MT+N ITV ++ + ++ IE L VVDD+ +G+I+ +D+ Sbjct: 59 MTKNPITVNPKTSVASVAHMMIWEGIEMLPVVDDNKKLLGIISRQDV 105 Score = 36.7 bits (85), Expect = 0.013 Identities = 17/48 (35%), Positives = 30/48 (62%), Gaps = 1/48 (2%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 M NP+T++P ++A +M I +PVV+ + KL+GI++ +DV Sbjct: 59 MTKNPITVNPKTSVASVAHMMIWEGIEMLPVVDDN-KKLLGIISRQDV 105 >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 = 57.8 bits (140), Expect = 6e-09 Identities = 38/130 (29%), Positives = 64/130 (49%), Gaps = 29/130 (22%) Query: 103 VTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRD------------------ 144 VT+SP ++A+A LM ISG+PVV+ D G+LVGI++ D Sbjct: 5 VTVSPETSVAEAARLMLDNHISGLPVVDDD-GRLVGIVSEGDLLRRAELGTERRRARWLD 63 Query: 145 ---------VRFASNAQQAVGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGC 195 F + + V ++MTR ++TV + L L+ +HRI+++ VV G Sbjct: 64 LLAGAEELAAAFVRSHGRKVADVMTRPVVTVGEDTPLAEVAELMEEHRIKRVPVV-RGGR 122 Query: 196 CIGLITVKDI 205 +G+++ D+ Sbjct: 123 LVGIVSRADL 132 Score = 42.0 bits (99), Expect = 4e-04 Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 2/48 (4%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 M VT+ LA+ LM+++ I +PVV G+LVGI++ D+ Sbjct: 87 MTRPVVTVGEDTPLAEVAELMEEHRIKRVPVVRG--GRLVGIVSRADL 132 Score = 32.4 bits (74), Expect = 0.32 Identities = 28/144 (19%), Positives = 48/144 (33%), Gaps = 32/144 (22%) Query: 160 TRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERSQLNPNATKDSK 219 T +++TV ++ A L+ + I L VVDDDG +G+++ D+ R + Sbjct: 1 TTDVVTVSPETSVAEAARLMLDNHISGLPVVDDDGRLVGIVSEGDLLR-----------R 49 Query: 220 GRLRVAAAVSVAKDIADRVGPLFDVNVDLVVVDTAHGHSQKVLDAVVQIKKNFPSLLVMA 279 L + D+ L H +KV D VM Sbjct: 50 AELGTERRRARWLDLLAGAEEL--------AAAFVRSHGRKVAD-------------VMT 88 Query: 280 GNIATAEGALALIDAGADIIKVGI 303 + T L + + + I Sbjct: 89 RPVVTVGEDTPLAEVAELMEEHRI 112 >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 = 57.6 bits (139), Expect = 7e-09 Identities = 36/108 (33%), Positives = 65/108 (60%), Gaps = 3/108 (2%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASNAQQAVGELMT 160 + +T+SP T+ D + L+K+ G PVV D GK+VGI++ RD+ + V E+M+ Sbjct: 3 DVITVSPDNTVKDVIKLIKETGHDGFPVV--DNGKVVGIVSARDLLGKDPDET-VEEIMS 59 Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERS 208 ++L+ +++ +A ++ + I KL VVD++ +G+IT D+ RS Sbjct: 60 KDLVVAVPEMDIMDAARVMFRTGISKLPVVDENNNLVGIITNTDVIRS 107 >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 = 57.5 bits (139), Expect = 8e-09 Identities = 33/108 (30%), Positives = 56/108 (51%), Gaps = 9/108 (8%) Query: 103 VTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFA-----SNAQQAVGE 157 V+++P T++ A+ M++Y +S +PVV+ G++VG + D+ A + V E Sbjct: 4 VSVAPDDTVSQAIERMREYGVSQLPVVDD--GRVVGSIDESDLLDALIEGKAKFSLPVRE 61 Query: 158 LMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 +M L TV +E LL R +VVD+ G +G+IT D+ Sbjct: 62 VMGEPLPTVDPDAPIEELSELL--DRGNVAVVVDEGGKFVGIITRADL 107 Score = 33.2 bits (76), Expect = 0.18 Identities = 22/98 (22%), Positives = 38/98 (38%), Gaps = 11/98 (11%) Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERSQLNPNATKDSKG 220 ++++V + A + ++ + +L VVDD +G I E L+ +K Sbjct: 1 GDVVSVAPDDTVSQAIERMREYGVSQLPVVDDGR-VVGSID----ESDLLDALIEGKAKF 55 Query: 221 RLRVAAAVS-----VAKDIA-DRVGPLFDVNVDLVVVD 252 L V + V D + + L D VVVD Sbjct: 56 SLPVREVMGEPLPTVDPDAPIEELSELLDRGNVAVVVD 93 >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 = 57.5 bits (139), Expect = 8e-09 Identities = 35/111 (31%), Positives = 54/111 (48%), Gaps = 8/111 (7%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASNAQ------QA 154 P T+SP T+ +A LM++ +S + V+ D KLVGI T++D+ AQ Sbjct: 2 KPATVSPTTTVQEAAKLMREKRVSCVLVM--DGNKLVGIFTSKDIALRVVAQGLDPESTL 59 Query: 155 VGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 V +MT N + + A L+ Q + L VVD G +GL+ V + Sbjct: 60 VERVMTPNPVCATSDTPVLEALHLMVQGKFRHLPVVDKSGQVVGLLDVTKL 110 Score = 33.6 bits (77), Expect = 0.12 Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 1/44 (2%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILT 141 M NPV + + +AL LM + +PVV+ G++VG+L Sbjct: 64 MTPNPVCATSDTPVLEALHLMVQGKFRHLPVVDKS-GQVVGLLD 106 >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 = 55.7 bits (134), Expect = 2e-08 Identities = 34/111 (30%), Positives = 55/111 (49%), Gaps = 6/111 (5%) Query: 102 PVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV--RFASNAQ---QAVG 156 P + +A A+A M +PVV+ D +LVGI+T DV + + V Sbjct: 3 PSCVVLNTDIARAVAEMYTSGSRALPVVD-DKKRLVGIITRYDVLSYALESEELKDAKVR 61 Query: 157 ELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIER 207 E+M +IT+ ++ A+ L+ + I +L V+DD G G++T DI R Sbjct: 62 EVMNSPVITIDANDSIAKARWLMSNNNISRLPVLDDKGKVGGIVTEDDILR 112 Score = 38.4 bits (89), Expect = 0.005 Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 1/48 (2%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 M +TI ++A A LM +IS +PV++ GK+ GI+T D+ Sbjct: 64 MNSPVITIDANDSIAKARWLMSNNNISRLPVLDDK-GKVGGIVTEDDI 110 >gnl|CDD|73371 cd02809, alpha_hydroxyacid_oxid_FMN, Family of homologous FMN-dependent alpha-hydroxyacid oxidizing enzymes. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate dehydrogenase (MDH), and long chain hydroxyacid oxidase (LCHAO). In green plants, glycolate oxidase is one of the key enzymes in photorespiration where it oxidizes glycolate to glyoxylate. LMO catalyzes the oxidation of L-lactate to acetate and carbon dioxide. MDH oxidizes (S)-mandelate to phenylglyoxalate. It is an enzyme in the mandelate pathway that occurs in several strains of Pseudomonas which converts (R)-mandelate to benzoate.. Length = 299 Score = 55.8 bits (135), Expect = 3e-08 Identities = 38/123 (30%), Positives = 59/123 (47%), Gaps = 20/123 (16%) Query: 249 VVVDTAHGHSQKVLDAVVQIKKNFPSLLVMAGNIATAEGALALIDAGADIIKVGIGPGSI 308 + VDT + D + ++ + L++ G I T E AL +DAGAD I Sbjct: 148 LTVDTPVLGRRLTWDDLAWLRSQWKGPLILKG-ILTPEDALRAVDAGADGI--------- 197 Query: 309 CTTRVVTGVGCPQL----SAIMSVVEVAERAG--VAIVADGGIRFSGDIAKAIAAGSACV 362 VV+ G QL + I ++ E+ G + ++ DGGIR D+ KA+A G+ V Sbjct: 198 ----VVSNHGGRQLDGAPATIDALPEIVAAVGGRIEVLLDGGIRRGTDVLKALALGADAV 253 Query: 363 MIG 365 +IG Sbjct: 254 LIG 256 >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 = 55.6 bits (134), Expect = 3e-08 Identities = 39/113 (34%), Positives = 62/113 (54%), Gaps = 9/113 (7%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRD------VRFASNAQQA 154 N +T+ P T+ +A +M + +I + VV++ K VGI+T RD R + Sbjct: 2 NVITVDPDTTVYEAANIMTENNIGRLIVVDN--EKPVGIITERDLVKKVVSRNLKPREVP 59 Query: 155 VGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIER 207 VGE+M+ LIT+ +L A L+ +H I++L VVDDD +G++T DI Sbjct: 60 VGEVMSTPLITIDPNASLNEAAKLMAKHGIKRLPVVDDDE-LVGIVTTTDIVM 111 Score = 42.5 bits (100), Expect = 3e-04 Identities = 26/74 (35%), Positives = 36/74 (48%), Gaps = 10/74 (13%) Query: 72 LGVIHRNFSPSEQVAQVHQVKKFESGMVVNPVTISPYATLADALALMKKYSISGIPVVES 131 V+ RN P E M +TI P A+L +A LM K+ I +PVV+ Sbjct: 46 KKVVSRNLKPREVPV--------GEVMSTPLITIDPNASLNEAAKLMAKHGIKRLPVVDD 97 Query: 132 DVGKLVGILTNRDV 145 D +LVGI+T D+ Sbjct: 98 D--ELVGIVTTTDI 109 >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 = 54.6 bits (131), Expect = 6e-08 Identities = 30/125 (24%), Positives = 62/125 (49%), Gaps = 21/125 (16%) Query: 103 VTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV--RFASNAQQA------ 154 +T+ ++ A+ +++++ IS +PVV+ + GKL GI+T D+ + +A Sbjct: 4 ITVREDDSVGKAINVLREHGISRLPVVDDN-GKLTGIVTRHDIVDFVVRDRDKARTGDRS 62 Query: 155 ----------VGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVV--DDDGCCIGLITV 202 V + M+ +IT ++ +A + ++ ++VV DDD +G++T Sbjct: 63 GEKERMLDLPVYDAMSSPVITASPNDSVRDAVDRMLENDDSSVVVVTPDDDTKVVGILTK 122 Query: 203 KDIER 207 KD+ R Sbjct: 123 KDVLR 127 Score = 35.7 bits (82), Expect = 0.028 Identities = 17/45 (37%), Positives = 29/45 (64%) Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 ++ITV++ ++ A +L +H I +L VVDD+G G++T DI Sbjct: 1 EDVITVREDDSVGKAINVLREHGISRLPVVDDNGKLTGIVTRHDI 45 Score = 34.2 bits (78), Expect = 0.089 Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 1/54 (1%) Query: 93 KFESGMVVNPVTISPYATLADALALMKKYSISGIPVVE-SDVGKLVGILTNRDV 145 M +T SP ++ DA+ M + S + VV D K+VGILT +DV Sbjct: 72 PVYDAMSSPVITASPNDSVRDAVDRMLENDDSSVVVVTPDDDTKVVGILTKKDV 125 >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 = 53.7 bits (130), Expect = 1e-07 Identities = 19/51 (37%), Positives = 36/51 (70%) Query: 155 VGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 V ++MT +++TV +LE A L+ ++ I +L VVD+DG +G++T++D+ Sbjct: 1 VKDIMTPDVVTVPPDTSLEEALELMRENGISRLPVVDEDGKLVGIVTLRDL 51 Score = 51.8 bits (125), Expect = 5e-07 Identities = 25/51 (49%), Positives = 35/51 (68%), Gaps = 1/51 (1%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFA 148 M + VT+ P +L +AL LM++ IS +PVV+ D GKLVGI+T RD+ A Sbjct: 5 MTPDVVTVPPDTSLEEALELMRENGISRLPVVDED-GKLVGIVTLRDLLRA 54 >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 = 53.0 bits (127), Expect = 2e-07 Identities = 31/104 (29%), Positives = 52/104 (50%), Gaps = 3/104 (2%) Query: 102 PVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASNAQQAVGELMTR 161 P+T+ P L+DAL LM + + VV++D G+ +G +T R+ AS G+ Sbjct: 3 PITVRPDDPLSDALGLMDDSDLRALTVVDAD-GQPLGFVTRREAARAS--GGCCGDHAEP 59 Query: 162 NLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 +TV +L + + H + L VD+DG +G +T + I Sbjct: 60 FKVTVSVDDDLRIVLSRMFAHDMSWLPCVDEDGRYVGEVTQRSI 103 Score = 28.7 bits (64), Expect = 4.2 Identities = 15/45 (33%), Positives = 23/45 (51%) Query: 163 LITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIER 207 ITV+ L +A L+ + L VVD DG +G +T ++ R Sbjct: 3 PITVRPDDPLSDALGLMDDSDLRALTVVDADGQPLGFVTRREAAR 47 >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 = 52.6 bits (126), Expect = 3e-07 Identities = 36/132 (27%), Positives = 65/132 (49%), Gaps = 27/132 (20%) Query: 102 PVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASNAQQA------- 154 +T+ TL D + ++ ISG+PVV+++ G++VGI++ D+ + Sbjct: 3 VITVKKDDTLRDVVEILLTGKISGVPVVDNE-GRVVGIVSEGDLIRKIYKGKGLFYVTLL 61 Query: 155 ------------------VGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCC 196 V E+MT+ +ITV + +E+ ++ + I++L VV DDG Sbjct: 62 YSVIFLDESKIKKLLGKKVEEIMTKKVITVDEDTTIEDVARIMSKKNIKRLPVV-DDGKL 120 Query: 197 IGLITVKDIERS 208 +G+I+ DI RS Sbjct: 121 VGIISRGDIIRS 132 Score = 41.0 bits (96), Expect = 8e-04 Identities = 20/54 (37%), Positives = 30/54 (55%), Gaps = 2/54 (3%) Query: 92 KKFESGMVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 KK E M +T+ T+ D +M K +I +PVV+ GKLVGI++ D+ Sbjct: 78 KKVEEIMTKKVITVDEDTTIEDVARIMSKKNIKRLPVVDD--GKLVGIISRGDI 129 Score = 29.1 bits (65), Expect = 3.2 Identities = 15/48 (31%), Positives = 29/48 (60%) Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERS 208 +++ITVKK L + +L +I + VVD++G +G+++ D+ R Sbjct: 1 KDVITVKKDDTLRDVVEILLTGKISGVPVVDNEGRVVGIVSEGDLIRK 48 >gnl|CDD|144604 pfam01070, FMN_dh, FMN-dependent dehydrogenase. Length = 301 Score = 51.7 bits (125), Expect = 4e-07 Identities = 27/90 (30%), Positives = 43/90 (47%), Gaps = 19/90 (21%) Query: 282 IATAEGALALIDAGADIIKVGIGPGSICTTRVVTGVGCPQL----SAIMSVVEVAERAG- 336 I + E A ++AG D I VV+ G QL + I ++ E+ G Sbjct: 177 ILSPEDAKRAVEAGVDGI-------------VVSNHGGRQLDGAPATIDALPEIVAAVGG 223 Query: 337 -VAIVADGGIRFSGDIAKAIAAGSACVMIG 365 + ++ DGGIR D+ KA+A G+ V++G Sbjct: 224 RIPVLVDGGIRRGTDVLKALALGADAVLLG 253 >gnl|CDD|36975 KOG1764, KOG1764, KOG1764, 5'-AMP-activated protein kinase, gamma subunit [Energy production and conversion]. Length = 381 Score = 50.8 bits (121), Expect = 8e-07 Identities = 35/115 (30%), Positives = 56/115 (48%), Gaps = 14/115 (12%) Query: 104 TISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFA-----------SNAQ 152 +IS + +AL +M + IS +PVV+ + GK VG + DV S Sbjct: 241 SISEDTPVIEALKIMSERRISALPVVDEN-GKKVGNYSRFDVIHLAREGTYNNLDLSCLS 299 Query: 153 QAVGELMTRN--LITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 +A+ R ++T + T L L HR+ +L VVD+DG +G+I++ DI Sbjct: 300 EALSHRPIRFEGVVTCRPTSTLAEVIDKLVAHRVHRLWVVDEDGVLVGVISLSDI 354 Score = 43.1 bits (101), Expect = 2e-04 Identities = 31/126 (24%), Positives = 62/126 (49%), Gaps = 16/126 (12%) Query: 96 SGMVVNP--VTISPYATLADALALMKKYSISGIPVVESDVGKLVGILT-----------N 142 + P V+ISP ++L DA+ L+ K I +PV++ + G+++ ILT Sbjct: 156 LKETLKPPFVSISPESSLLDAVLLLIKSRIHRVPVIDPETGEVLYILTQRRILKFLWLNG 215 Query: 143 RDVRFASNAQQAVGEL---MTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGL 199 R + S +++ +L N+ ++ + + A ++ + RI L VVD++G +G Sbjct: 216 RLLPLPSLLSKSLSDLGIGTWSNIASISEDTPVIEALKIMSERRISALPVVDENGKKVGN 275 Query: 200 ITVKDI 205 + D+ Sbjct: 276 YSRFDV 281 Score = 28.1 bits (62), Expect = 5.4 Identities = 14/43 (32%), Positives = 26/43 (60%), Gaps = 1/43 (2%) Query: 103 VTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 VT P +TLA+ + + + + + VV+ D G LVG+++ D+ Sbjct: 313 VTCRPTSTLAEVIDKLVAHRVHRLWVVDED-GVLVGVISLSDI 354 >gnl|CDD|31445 COG1253, TlyC, Hemolysins and related proteins containing CBS domains [General function prediction only]. Length = 429 Score = 50.7 bits (121), Expect = 1e-06 Identities = 25/105 (23%), Positives = 51/105 (48%), Gaps = 2/105 (1%) Query: 103 VTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV--RFASNAQQAVGELMT 160 V + T+ + + L+ + S IPV + D+ ++GI+ +D+ ++ Sbjct: 219 VALDLTDTVEELIELILESGHSRIPVYDGDLDNIIGIVHVKDLLRALLDGQSDLDLRVLV 278 Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 R + V +T++L + + R +VVD+ G GL+T++DI Sbjct: 279 RPPLFVPETLSLSDLLEEFREERTHMAIVVDEYGGVEGLVTLEDI 323 Score = 31.1 bits (70), Expect = 0.82 Identities = 19/76 (25%), Positives = 38/76 (50%), Gaps = 3/76 (3%) Query: 151 AQQAVGELMT--RNLITVKKTVNLENAKALLHQHRIEKLLVVDDD-GCCIGLITVKDIER 207 + V E+MT +++ + T +E L+ + ++ V D D IG++ VKD+ R Sbjct: 204 DDRTVREIMTPRTDIVALDLTDTVEELIELILESGHSRIPVYDGDLDNIIGIVHVKDLLR 263 Query: 208 SQLNPNATKDSKGRLR 223 + L+ + D + +R Sbjct: 264 ALLDGQSDLDLRVLVR 279 >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 = 50.2 bits (120), Expect = 1e-06 Identities = 35/109 (32%), Positives = 55/109 (50%), Gaps = 5/109 (4%) Query: 104 TISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVR---FASNAQQAVGELMT 160 T+ + TL + + S VV + G+ VGI++ D+R + AQ V ++MT Sbjct: 5 TVPAHLTLREFVREYVLGSNQRRFVVVDNEGRYVGIISLADLRAIPTSQWAQTTVIQVMT 64 Query: 161 --RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIER 207 L+TV +L LL + +++L VV+D G IGLIT D+ R Sbjct: 65 PAAKLVTVLSEESLAEVLKLLEEQGLDELAVVEDSGQVIGLITEADLLR 113 >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 = 2e-06 Identities = 31/121 (25%), Positives = 60/121 (49%), Gaps = 15/121 (12%) Query: 102 PVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV--------------RF 147 PVT +P ++ LM + +G+PVV G+L+GI+T RD+ R Sbjct: 3 PVTCTPDDPVSKVWDLMLESGFTGLPVV-QKAGELIGIITRRDIIRAGSVRTSVEDQQRT 61 Query: 148 ASNAQQAVGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIER 207 + A V ++M+ + +V ++ A L+ +H I +L VV++ +G++ D+ + Sbjct: 62 QTKASPTVEKIMSTPVYSVTPDDSIATAVELMLEHDIGRLPVVNEKDQLVGIVDRHDVLK 121 Query: 208 S 208 + Sbjct: 122 A 122 Score = 38.0 bits (88), Expect = 0.006 Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 1/64 (1%) Query: 82 SEQVAQVHQVKKFESGMVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILT 141 +Q Q E M +++P ++A A+ LM ++ I +PVV + +LVGI+ Sbjct: 57 DQQRTQTKASPTVEKIMSTPVYSVTPDDSIATAVELMLEHDIGRLPVVN-EKDQLVGIVD 115 Query: 142 NRDV 145 DV Sbjct: 116 RHDV 119 >gnl|CDD|33419 COG3620, COG3620, Predicted transcriptional regulator with C-terminal CBS domains [Transcription]. Length = 187 Score = 49.5 bits (118), Expect = 2e-06 Identities = 36/116 (31%), Positives = 58/116 (50%), Gaps = 11/116 (9%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFA------SNA 151 M V++SP +++D + LM+ IS +PV+E D K+VG +T D+ A S Sbjct: 71 MHSPVVSVSPDDSISDVVNLMRDKGISQLPVIEED--KVVGSITENDIVRALLEGMESIR 128 Query: 152 QQAVGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIER 207 V E+M TV +L LL +H ++V ++G +G+IT DI + Sbjct: 129 SLRVREVMGEPFPTVSPDESLNVISQLLEEH---PAVLVVENGKVVGIITKADIMK 181 Score = 34.5 bits (79), Expect = 0.065 Identities = 23/105 (21%), Positives = 43/105 (40%), Gaps = 11/105 (10%) Query: 158 LMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERSQLNPNATKD 217 +M +++V ++ + L+ I +L V+++D +G IT DI R+ L + Sbjct: 70 IMHSPVVSVSPDDSISDVVNLMRDKGISQLPVIEEDK-VVGSITENDIVRALLE---GME 125 Query: 218 SKGRLRVAAAVSVAKDIADRVGPLFDVNVDLVVVDTAHGHSQKVL 262 S LRV +++ P + L V+ VL Sbjct: 126 SIRSLRV-------REVMGEPFPTVSPDESLNVISQLLEEHPAVL 163 >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 = 49.5 bits (118), Expect = 2e-06 Identities = 28/119 (23%), Positives = 52/119 (43%), Gaps = 14/119 (11%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV--------RFASNAQ 152 + + A+L A+ ++ I + V E + G+++GIL+ R + R Sbjct: 2 PFIPVPSTASLFQAIEILGSGGIHRVAVTEEESGEVIGILSQRRLVEFLWENARSFPGLD 61 Query: 153 QAVGELM------TRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 + T ++I++ L +A L+H I + VVD+ G IG I+V D+ Sbjct: 62 PLYPIPLRDLTIGTSDVISINGDQPLIDALHLMHNEGISSVAVVDNQGNLIGNISVTDV 120 >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 = 47.8 bits (114), Expect = 7e-06 Identities = 31/106 (29%), Positives = 50/106 (47%), Gaps = 13/106 (12%) Query: 110 TLADALALMKKYSISGIPVVESDVGKLVGILTNRDV----------RFASNAQQAVGELM 159 TL AL ++ K+ S IPV++ + GK VG ++ D+ V ++M Sbjct: 11 TLRHALLVLTKHGYSAIPVLDKE-GKYVGTISLTDILWKLKGLENLDLERLVDLKVIDVM 69 Query: 160 TRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 ++ + ++E LL L VVDDDG IG+IT ++I Sbjct: 70 NTDVPVIIDDADIEEILHLLIDQPF--LPVVDDDGIFIGIITRREI 113 Score = 34.7 bits (80), Expect = 0.056 Identities = 22/99 (22%), Positives = 36/99 (36%), Gaps = 9/99 (9%) Query: 162 NLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERSQLNPN-------- 213 + V+ T L +A +L +H + V+D +G +G I++ DI Sbjct: 2 EVAYVQDTNTLRHALLVLTKHGYSAIPVLDKEGKYVGTISLTDILWKLKGLENLDLERLV 61 Query: 214 ATKDSKGRLRVAAAVSVAKDIADRVGPLFDVNVDLVVVD 252 K + DI + + L D L VVD Sbjct: 62 DLKVIDVMNTDVPVIIDDADIEEILHLLIDQPF-LPVVD 99 >gnl|CDD|33866 COG4109, COG4109, Predicted transcriptional regulator containing CBS domains [Transcription]. Length = 432 Score = 47.6 bits (113), Expect = 8e-06 Identities = 33/107 (30%), Positives = 57/107 (53%), Gaps = 2/107 (1%) Query: 102 PVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASNAQQAVGELMTR 161 + T+ D L L++K S PVV K+VG++T RDV + + ++MT+ Sbjct: 200 TSYLRETDTVEDWLDLVEKTGHSRFPVVN-RSMKVVGVVTMRDVLDKKPSTT-IEKVMTK 257 Query: 162 NLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERS 208 N ITV+ ++ + ++ IE L VVD + +G+IT +D+ +S Sbjct: 258 NPITVRAKTSVASVAQMMIWEGIEMLPVVDSNNTLLGIITRQDVLKS 304 Score = 34.9 bits (80), Expect = 0.051 Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 1/53 (1%) Query: 93 KFESGMVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 E M NP+T+ ++A +M I +PVV+S+ L+GI+T +DV Sbjct: 250 TIEKVMTKNPITVRAKTSVASVAQMMIWEGIEMLPVVDSN-NTLLGIITRQDV 301 >gnl|CDD|33251 COG3448, COG3448, CBS-domain-containing membrane protein [Signal transduction mechanisms]. Length = 382 Score = 47.3 bits (112), Expect = 9e-06 Identities = 29/118 (24%), Positives = 55/118 (46%), Gaps = 11/118 (9%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV----------RF 147 M + VT+S ++ A L++++ I +PV++ + +LVGI+T RD+ R Sbjct: 251 MSRDVVTVSTDTSIDHARKLLQEHRIKALPVLD-EHRRLVGIVTQRDLLKHARPSPFQRL 309 Query: 148 ASNAQQAVGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 V +MT ++TV+ L + L V+D G +G+++ D+ Sbjct: 310 RFLRPPTVKGIMTTPVVTVRPDTPAVELVPRLADEGLHALPVLDAAGKLVGIVSQTDL 367 Score = 41.5 bits (97), Expect = 6e-04 Identities = 25/109 (22%), Positives = 50/109 (45%), Gaps = 8/109 (7%) Query: 157 ELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI-------ERSQ 209 ++M+R+++TV ++++A+ LL +HRI+ L V+D+ +G++T +D+ + Sbjct: 249 DIMSRDVVTVSTDTSIDHARKLLQEHRIKALPVLDEHRRLVGIVTQRDLLKHARPSPFQR 308 Query: 210 LNPNATKDSKGRLRVAAAVSVAKDIADRVGPLF-DVNVDLVVVDTAHGH 257 L KG + A + P D + + V A G Sbjct: 309 LRFLRPPTVKGIMTTPVVTVRPDTPAVELVPRLADEGLHALPVLDAAGK 357 Score = 30.0 bits (67), Expect = 1.4 Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 1/57 (1%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASNAQQA 154 M VT+ P + + + + +PV+++ GKLVGI++ D+ A + Sbjct: 321 MTTPVVTVRPDTPAVELVPRLADEGLHALPVLDAA-GKLVGIVSQTDLIAALYRNWS 376 >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 = 47.1 bits (112), Expect = 1e-05 Identities = 32/111 (28%), Positives = 55/111 (49%), Gaps = 7/111 (6%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVR-FASNAQQA----V 155 + VTI L + L ++ + PVV+ D G+LVGI++ D+R + Sbjct: 2 DVVTIPEDTPLNELLDVIAHSPENNFPVVDDD-GRLVGIVSLDDIREILFDPSLYDLVVA 60 Query: 156 GELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDD-GCCIGLITVKDI 205 ++MT+ + V +LE+A E+L VVDDD G +G+++ D+ Sbjct: 61 SDIMTKPPVVVYPEDSLEDALKKFEDSDYEQLPVVDDDPGKLLGILSRSDL 111 Score = 46.3 bits (110), Expect = 2e-05 Identities = 19/48 (39%), Positives = 27/48 (56%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 M PV + P +L DAL + +PVV+ D GKL+GIL+ D+ Sbjct: 64 MTKPPVVVYPEDSLEDALKKFEDSDYEQLPVVDDDPGKLLGILSRSDL 111 Score = 31.7 bits (72), Expect = 0.52 Identities = 12/45 (26%), Positives = 24/45 (53%) Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 R+++T+ + L ++ VVDDDG +G++++ DI Sbjct: 1 RDVVTIPEDTPLNELLDVIAHSPENNFPVVDDDGRLVGIVSLDDI 45 >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 = 46.8 bits (111), Expect = 1e-05 Identities = 34/105 (32%), Positives = 52/105 (49%), Gaps = 4/105 (3%) Query: 104 TISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFA---SNAQQAVGELMT 160 T+SP TL DA + + PVV+ D G LVG+LT D+ A V +M Sbjct: 5 TLSPADTLDDAADALLATTQHEFPVVDGD-GHLVGLLTRDDLIRALAEGGPDAPVRGVMR 63 Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 R+ TV + L+ L+ Q + VVD G +GL+T++++ Sbjct: 64 RDFPTVSPSATLDAVLRLMQQGGAPAVPVVDGSGRLVGLVTLENV 108 >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 = 46.9 bits (111), Expect = 1e-05 Identities = 36/136 (26%), Positives = 58/136 (42%), Gaps = 30/136 (22%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASNAQQ------- 153 + T+ P +L + M+K + + VV+ D GK VG++T RD+ FA Sbjct: 2 DIATVHPEHSLLHVVDEMEKNGVGRVIVVD-DNGKPVGVITYRDLAFAEFEDNERGLPKK 60 Query: 154 ---------------------AVGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDD 192 ++MT +ITV ++ +A L+ + I L VVD+ Sbjct: 61 SIKMKRKAGQKRYRYVKEVPLVAEDIMTEEIITVSPNDDVVDAAKLMLEANISGLPVVDN 120 Query: 193 DGCCIGLITVKDIERS 208 D +G+IT DI R Sbjct: 121 DN-IVGVITKTDICRE 135 Score = 43.8 bits (103), Expect = 1e-04 Identities = 19/48 (39%), Positives = 31/48 (64%), Gaps = 2/48 (4%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 M +T+SP + DA LM + +ISG+PVV++D +VG++T D+ Sbjct: 87 MTEEIITVSPNDDVVDAAKLMLEANISGLPVVDND--NIVGVITKTDI 132 Score = 34.5 bits (79), Expect = 0.066 Identities = 23/123 (18%), Positives = 58/123 (47%), Gaps = 6/123 (4%) Query: 162 NLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERSQLNPNATKDSKGR 221 ++ TV +L + + ++ + +++VVDD+G +G+IT +D+ ++ N K Sbjct: 2 DIATVHPEHSLLHVVDEMEKNGVGRVIVVDDNGKPVGVITYRDLAFAEFEDNERGLPKKS 61 Query: 222 LRVAAAVSVAKDIADRVGPLF--DVNVDLVVVDTAHGHSQKVLDAV-VQIKKNFPSLLVM 278 +++ + + PL D+ + ++ + + V+DA + ++ N L V+ Sbjct: 62 IKMKRKAGQKRYRYVKEVPLVAEDIMTEEIITVSP---NDDVVDAAKLMLEANISGLPVV 118 Query: 279 AGN 281 + Sbjct: 119 DND 121 >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 = 46.7 bits (111), Expect = 2e-05 Identities = 29/109 (26%), Positives = 52/109 (47%), Gaps = 8/109 (7%) Query: 102 PVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASNAQQ-----AVG 156 P+ + ++ DA LM+++ ++ D +GI+T D+ A VG Sbjct: 3 PLIVDASTSIRDAARLMREHGADA--LLVRDGDPRLGIVTRTDLLDAVLLDGLPSSTPVG 60 Query: 157 ELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 E+ T LITV L NA L+ +HRI +++V + +G++ D+ Sbjct: 61 EIATFPLITVDPDDFLFNALLLMTRHRIHRVVVREGGE-VVGVLEQTDL 108 Score = 31.6 bits (72), Expect = 0.47 Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 2/45 (4%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 +T+ P L +AL LM ++ I + V E G++VG+L D+ Sbjct: 66 PLITVDPDDFLFNALLLMTRHRIHRVVVREG--GEVVGVLEQTDL 108 >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 = 46.4 bits (110), Expect = 2e-05 Identities = 28/107 (26%), Positives = 58/107 (54%), Gaps = 6/107 (5%) Query: 103 VTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASNAQ----QAVGEL 158 TI A++ +AL M KY+ + +V+ + KL G++T D+ + + V + Sbjct: 4 PTIDEDASIREALHEMLKYN-TNEIIVKDNEEKLKGVVTFTDILDLDLFESFLEKKVFNI 62 Query: 159 MTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 +++++ V + ++ A ++ + +I +L VVDD+ IG++ KDI Sbjct: 63 VSQDVFYVNEEDTIDEALDIMREKQIGRLPVVDDNK-LIGVVRTKDI 108 Score = 36.0 bits (83), Expect = 0.025 Identities = 14/55 (25%), Positives = 32/55 (58%), Gaps = 2/55 (3%) Query: 92 KKFESGMVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVR 146 KK + + + ++ T+ +AL +M++ I +PVV+ + KL+G++ +D+ Sbjct: 57 KKVFNIVSQDVFYVNEEDTIDEALDIMREKQIGRLPVVDDN--KLIGVVRTKDIL 109 >gnl|CDD|73392 cd04730, NPD_like, 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase family that reduce a range of alternative electron acceptors. Most use FAD/FMN as a cofactor and NAD(P)H as electron donor. Some contain 4Fe-4S cluster to transfer electron from FAD to FMN.. Length = 236 Score = 45.9 bits (109), Expect = 2e-05 Identities = 25/100 (25%), Positives = 39/100 (39%), Gaps = 19/100 (19%) Query: 282 IATAEGALALIDAGADIIKVGIGPGSICTTRVVTGVGC-----PQLSAIMSVV-EVAERA 335 + + E A AGAD + V G ++V EV + Sbjct: 109 VTSVEEARKAEAAGADAL-------------VAQGAEAGGHRGTFDIGTFALVPEVRDAV 155 Query: 336 GVAIVADGGIRFSGDIAKAIAAGSACVMIGSLLAGTDESP 375 + ++A GGI IA A+A G+ V +G+ T+ES Sbjct: 156 DIPVIAAGGIADGRGIAAALALGADGVQMGTRFLATEESG 195 Score = 42.0 bits (99), Expect = 4e-04 Identities = 25/92 (27%), Positives = 40/92 (43%), Gaps = 5/92 (5%) Query: 45 LNLPIMSAAMDQVTDSRLAIAMAQAGGLGVIH-RNFSPSEQVAQVHQVKKFESGMV-VNP 102 + PI+ A M V+ LA A++ AGGLG I +P A++ +++ VN Sbjct: 1 IRYPIIQAPMAGVSTPELAAAVSNAGGLGFIGAGYLTPEALRAEIRKIRALTDKPFGVNL 60 Query: 103 VTISPYATLADALALMKKYSISGIPVVESDVG 134 + S L + + G+PVV G Sbjct: 61 LVPSSNPDFEALLEVALEE---GVPVVSFSFG 89 >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 = 45.6 bits (108), Expect = 3e-05 Identities = 28/117 (23%), Positives = 52/117 (44%), Gaps = 13/117 (11%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV-------RFASNAQQ 153 N T P L D L ++ + +S +P+V+ + GK+V + + DV + + Sbjct: 2 NIATARPDTPLIDVLDMLVERRVSALPIVDEN-GKVVDVYSRFDVINLAKEGAYNNLDLT 60 Query: 154 AVGELMTR-----NLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 L R + T L L+ + R+ +L+VVD++ G+I++ DI Sbjct: 61 VGEALERRSQDFEGVRTCSPDDCLRTIFDLIVKARVHRLVVVDENKRVEGIISLSDI 117 >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 = 45.3 bits (107), Expect = 4e-05 Identities = 20/63 (31%), Positives = 32/63 (50%) Query: 146 RFASNAQQAVGELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 ++ V +++ R +T + L A L+H+H I L VVDDDG G+IT+ D+ Sbjct: 51 ILLADVHPRVRDVINRKPVTARPNDPLREALNLMHEHNIRTLPVVDDDGTPAGIITLLDL 110 Query: 206 ERS 208 Sbjct: 111 AEK 113 Score = 40.6 bits (95), Expect = 0.001 Identities = 19/45 (42%), Positives = 27/45 (60%), Gaps = 1/45 (2%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 PVT P L +AL LM +++I +PVV+ D G GI+T D+ Sbjct: 67 KPVTARPNDPLREALNLMHEHNIRTLPVVDDD-GTPAGIITLLDL 110 >gnl|CDD|73094 cd04594, CBS_pair_EriC_assoc_archaea, This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the EriC CIC-type chloride channels in 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 = 104 Score = 45.3 bits (107), Expect = 4e-05 Identities = 25/106 (23%), Positives = 51/106 (48%), Gaps = 5/106 (4%) Query: 100 VNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASNAQQAVGELM 159 + + + Y + +A +M + + +PVV D K +G + +D+ A+ V + + Sbjct: 1 IKDIKVKDYDKVYEAKRIMIENDLLSLPVV--DYNKFLGAVYLKDIENATYGD--VVDYI 56 Query: 160 TRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 R + V+ T E A ++ +++ VV DDG G++T+ I Sbjct: 57 VRGIPYVRLTSTAEEAWEVMMKNKTRWCPVV-DDGKFKGIVTLDSI 101 >gnl|CDD|32253 COG2070, COG2070, Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]. Length = 336 Score = 44.2 bits (104), Expect = 9e-05 Identities = 19/53 (35%), Positives = 28/53 (52%) Query: 35 ISTRIAKDFTLNLPIMSAAMDQVTDSRLAIAMAQAGGLGVIHRNFSPSEQVAQ 87 +STR + PI+ M V+ LA A++ AGGLG+I P+EQ+ Sbjct: 3 LSTRFILLLGIKYPIIQGGMAGVSTPELAAAVSNAGGLGIIASGGLPAEQLRA 55 Score = 41.5 bits (97), Expect = 5e-04 Identities = 29/99 (29%), Positives = 43/99 (43%), Gaps = 8/99 (8%) Query: 279 AGNIATAEGALALIDAGAD-IIKVGIGPGSICTTRVVTGVGCPQLSAIMSVVEVAE-RAG 336 ++ T AL AGAD +I G G G ++S V EV + G Sbjct: 131 IHSVITVREALKAERAGADAVIAQGAEAGGH------RGGVDLEVSTFALVPEVVDAVDG 184 Query: 337 VAIVADGGIRFSGDIAKAIAAGSACVMIGSLLAGTDESP 375 + ++A GGI IA A+A G+ V +G+ T E+ Sbjct: 185 IPVIAAGGIADGRGIAAALALGADGVQMGTRFLATKEAD 223 >gnl|CDD|73399 cd04737, LOX_like_FMN, L-Lactate oxidase (LOX) FMN-binding domain. LOX is a member of the family of FMN-containing alpha-hydroxyacid oxidases and catalyzes the oxidation of l-lactate using molecular oxygen to generate pyruvate and H2O2. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate dehydrogenase (MDH), and long chain hydroxyacid oxidase (LCHAO).. Length = 351 Score = 42.6 bits (100), Expect = 3e-04 Identities = 33/109 (30%), Positives = 51/109 (46%), Gaps = 11/109 (10%) Query: 259 QKVLDAVVQIKKNFPSLLVMAGNIATAEGALALIDAGADIIKVGIGPGSICTTRVVTGVG 318 QK+ A ++ L V+ I + E A I+AGAD I V G R + G Sbjct: 206 QKLSPADIEFIAKISGLPVIVKGIQSPEDADVAINAGADGIWVSNHGG-----RQLDGGP 260 Query: 319 CPQLSAIMSVVEVAERAG--VAIVADGGIRFSGDIAKAIAAGSACVMIG 365 ++ S+ E+AE V I+ D G+R + KA+A+G+ V +G Sbjct: 261 ----ASFDSLPEIAEAVNHRVPIIFDSGVRRGEHVFKALASGADAVAVG 305 >gnl|CDD|30418 COG0069, GltB, Glutamate synthase domain 2 [Amino acid transport and metabolism]. Length = 485 Score = 42.6 bits (100), Expect = 3e-04 Identities = 25/85 (29%), Positives = 38/85 (44%), Gaps = 6/85 (7%) Query: 288 ALALIDAGADIIKV-GIGPGSICTTRVVT-GVGCPQLSAIMSVVEVAE----RAGVAIVA 341 A + AGAD+I + G G+ + G P + + R V ++A Sbjct: 320 AAGVAKAGADVITIDGADGGTGASPLTSIDHAGIPWELGLAETHQTLVLNGLRDKVKLIA 379 Query: 342 DGGIRFSGDIAKAIAAGSACVMIGS 366 DGG+R D+AKA A G+ V G+ Sbjct: 380 DGGLRTGADVAKAAALGADAVGFGT 404 >gnl|CDD|73384 cd04722, TIM_phosphate_binding, TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN.. Length = 200 Score = 42.2 bits (98), Expect = 3e-04 Identities = 32/140 (22%), Positives = 58/140 (41%), Gaps = 9/140 (6%) Query: 229 SVAKDIADRVGPLFDVNVDLVVVDTAHGHSQKVLDAVV-QIKKNFPSLLVMAGNIATAEG 287 A + D V + A G+ + ++ ++++ P + V+ T E Sbjct: 68 DAAAAVDIAAAAARAAGADGVEIHGAVGYLAREDLELIRELREAVPDVKVVVKLSPTGEL 127 Query: 288 ALA-LIDAGADIIKVGIGPGSICTTRVVTGVGCPQLSAIMSVVEVAERAGVAIVADGGIR 346 A A +AG D + +G G G G A + ++ + V ++A GGI Sbjct: 128 AAAAAEEAGVDEVGLGNGGG-------GGGGRDAVPIADLLLILAKRGSKVPVIAGGGIN 180 Query: 347 FSGDIAKAIAAGSACVMIGS 366 D A+A+A G+ V++GS Sbjct: 181 DPEDAAEALALGADGVIVGS 200 >gnl|CDD|73370 cd02808, GltS_FMN, Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast and bacterial pathway for ammonia assimilation. It is a multifunctional enzyme that functions through three distinct active centers, carrying out L-glutamine hydrolysis, conversion of 2-oxoglutarate into L-glutamate, and electron uptake from an electron donor.. Length = 392 Score = 42.1 bits (99), Expect = 3e-04 Identities = 29/104 (27%), Positives = 42/104 (40%), Gaps = 22/104 (21%) Query: 276 LVMAGNIATAEGALALIDAGADIIKVGIGPGSICTTRVVTG---------VGCPQLSAIM 326 LV +A AGAD I + G TG VG P + Sbjct: 221 LVAGHGEGDIAAGVAA--AGADFITIDGAEGG-------TGAAPLTFIDHVGLPTELGLA 271 Query: 327 SVVEVAERAG----VAIVADGGIRFSGDIAKAIAAGSACVMIGS 366 + + G V+++A GG+R D+AKA+A G+ V IG+ Sbjct: 272 RAHQALVKNGLRDRVSLIASGGLRTGADVAKALALGADAVGIGT 315 >gnl|CDD|145943 pfam03060, NPD, 2-nitropropane dioxygenase. Members of this family catalyse the denitrification of a number of nitroalkanes using either FAD or FMN as a cofactor. Length = 330 Score = 42.0 bits (99), Expect = 4e-04 Identities = 28/96 (29%), Positives = 42/96 (43%), Gaps = 10/96 (10%) Query: 282 IATAEGALALIDAGADIIKV-GIGPGSICTTRVVTGVGCPQLSAIMSVVE-VAERAGVAI 339 +++A+ A AGAD + G G T V TG +V V + + + Sbjct: 144 VSSAKEARKAEAAGADAVVAQGPEAGGHRGTEVGTG--------TFLLVPTVVDAVDIPV 195 Query: 340 VADGGIRFSGDIAKAIAAGSACVMIGSLLAGTDESP 375 +A GGI IA A+A G+ V IG+ T E+ Sbjct: 196 IAAGGIADGRGIAAALALGAEGVQIGTRFLATKEAT 231 Score = 36.2 bits (84), Expect = 0.018 Identities = 14/40 (35%), Positives = 22/40 (55%) Query: 36 STRIAKDFTLNLPIMSAAMDQVTDSRLAIAMAQAGGLGVI 75 TR + PI+ M ++ LA A+++AGGLGV+ Sbjct: 1 RTRFTDLLKIKYPIVQPPMGGISTPELAAAVSEAGGLGVL 40 >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 = 41.7 bits (98), Expect = 5e-04 Identities = 27/114 (23%), Positives = 52/114 (45%), Gaps = 14/114 (12%) Query: 104 TISPYATLADALALMKKYS-ISGIPVVESDVGKLVGILTNRDV--RFASN------AQQA 154 T+SP T+ D L ++ +S + VV D G+ VG++ + ++ ++ Sbjct: 5 TVSPDTTVNDVLERFERDPDLSALAVV--DDGRPVGLIMREALMELLSTPYGRALYGKKP 62 Query: 155 VGELMTRNLITVKKTVNLENAKALL---HQHRIEKLLVVDDDGCCIGLITVKDI 205 V E+M + + V+ LE L + +V ++G +G+ TVKD+ Sbjct: 63 VSEVMDPDPLIVEADTPLEEVSRLATGRDSQNLYDGFIVTEEGRYLGIGTVKDL 116 >gnl|CDD|31495 COG1304, LldD, L-lactate dehydrogenase (FMN-dependent) and related alpha-hydroxy acid dehydrogenases [Energy production and conversion]. Length = 360 Score = 41.4 bits (97), Expect = 5e-04 Identities = 32/85 (37%), Positives = 41/85 (48%), Gaps = 13/85 (15%) Query: 287 GALALIDAGADIIKVGIGPGSICTTRVVTGVGCPQL----SAIMSVVEVAERAG--VAIV 340 G LA DA G G I V+ G QL S S+ E+ E G + ++ Sbjct: 225 GILAPEDAAG---AGGTGADGI----EVSNHGGRQLDWGISTADSLPEIVEAVGDRIEVI 277 Query: 341 ADGGIRFSGDIAKAIAAGSACVMIG 365 ADGGIR D+AKA+A G+ V IG Sbjct: 278 ADGGIRSGLDVAKALALGADAVGIG 302 >gnl|CDD|73391 cd04729, NanE, N-acetylmannosamine-6-phosphate epimerase (NanE) converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate. This reaction is part of the pathway that allows the usage of sialic acid as a carbohydrate source. Sialic acids are a family of related sugars that are found as a component of glycoproteins, gangliosides, and other sialoglycoconjugates.. Length = 219 Score = 41.3 bits (97), Expect = 7e-04 Identities = 31/135 (22%), Positives = 55/135 (40%), Gaps = 10/135 (7%) Query: 241 LFDVNVDLVVVDTAHGH--SQKVLDAVVQIKKNFPSLLVMAGNIATAEGALALIDAGADI 298 L D++ +D + L +++ + L+MA +I+T E AL G DI Sbjct: 88 LAAAGADIIALDATDRPRPDGETLAELIKRIHEEYNCLLMA-DISTLEEALNAAKLGFDI 146 Query: 299 IKVGIGPGSICTTRVVTGVGCPQLSAIMSVVEVAERAGVAIVADGGIRFSGDIAKAIAAG 358 I + G T L E+ + G+ ++A+G I AKA+ G Sbjct: 147 IGTTLS-GYTEETAKTEDPDFELLK------ELRKALGIPVIAEGRINSPEQAAKALELG 199 Query: 359 SACVMIGSLLAGTDE 373 + V++GS + + Sbjct: 200 ADAVVVGSAITRPEH 214 >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 = 40.4 bits (94), Expect = 0.001 Identities = 17/59 (28%), Positives = 26/59 (44%) Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERSQLNPNATKDSK 219 I V T L+ A L+ + +LVVD D G++T+ DI+R T+ Sbjct: 1 TKYIKVSPTTTLKEALNLMLDEKQSCVLVVDSDDFLEGILTLGDIQRFLFTNKTTRVQP 59 Score = 31.9 bits (72), Expect = 0.46 Identities = 19/44 (43%), Positives = 26/44 (59%), Gaps = 1/44 (2%) Query: 103 VTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVR 146 + +SP TL +AL LM S + VV+SD L GILT D++ Sbjct: 4 IKVSPTTTLKEALNLMLDEKQSCVLVVDSD-DFLEGILTLGDIQ 46 Score = 28.0 bits (62), Expect = 6.6 Identities = 10/33 (30%), Positives = 15/33 (45%) Query: 102 PVTISPYATLADALALMKKYSISGIPVVESDVG 134 T +P L A LM+ + +PVV+ V Sbjct: 88 LWTCTPDTDLTTAKKLMEAKGVKQLPVVKRGVD 120 >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 = 40.2 bits (94), Expect = 0.001 Identities = 26/107 (24%), Positives = 52/107 (48%), Gaps = 13/107 (12%) Query: 101 NPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASNAQQAVGELMT 160 N T+ L A+ +M+ ++ +PV++ D GKL GI+T RD+ S Sbjct: 2 NVPTVWEETPLPVAVRIMELANVKALPVLDDD-GKLSGIITERDLIAKSE---------- 50 Query: 161 RNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIER 207 ++T K + + ++RIE++ +++ + IGL+ D+ + Sbjct: 51 --VVTATKRTTVSECAQKMKRNRIEQIPIINGNDKLIGLLRDHDLLK 95 >gnl|CDD|110632 pfam01645, Glu_synthase, Conserved region in glutamate synthase. This family represents a region of the glutamate synthase protein. This region is expressed as a separate subunit in the glutamate synthase alpha subunit from archaebacteria, or part of a large multidomain enzyme in other organisms. The aligned region of these proteins contains a putative FMN binding site and Fe-S cluster. Length = 367 Score = 39.2 bits (92), Expect = 0.002 Identities = 31/90 (34%), Positives = 43/90 (47%), Gaps = 16/90 (17%) Query: 288 ALALIDAGADIIKV-------GIGPGSICTTRVVTGVGCPQLSAIMSV----VEVAERAG 336 A + AGADII + G P + + G P A+ V VE R Sbjct: 219 AAGVAKAGADIILIDGHDGGTGASPKTS-----IKHAGLPWELALAEVHQTLVENGLRDR 273 Query: 337 VAIVADGGIRFSGDIAKAIAAGSACVMIGS 366 V+++ADGG+R D+AKA A G+ V IG+ Sbjct: 274 VSLIADGGLRTGADVAKAAALGADAVYIGT 303 >gnl|CDD|73398 cd04736, MDH_FMN, Mandelate dehydrogenase (MDH)-like FMN-binding domain. MDH is part of a widespread family of homologous FMN-dependent a-hydroxy acid oxidizing enzymes that oxidizes (S)-mandelate to phenylglyoxalate. MDH is an enzyme in the mandelate pathway that occurs in several strains of Pseudomonas which converts (R)-mandelate to benzoate. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate dehydrogenase (MDH), and long chain hydroxyacid oxidase (LCHAO).. Length = 361 Score = 38.4 bits (89), Expect = 0.004 Identities = 28/107 (26%), Positives = 48/107 (44%), Gaps = 18/107 (16%) Query: 263 DAVVQIKKNFPSLLVMAGNIATAEGALALIDAGADIIKVGIGPGSICTTRVVTGVGCPQL 322 + ++ +P L++ G I TAE A I+ GAD + +++ G QL Sbjct: 226 QDLRWLRDLWPHKLLVKG-IVTAEDAKRCIELGADGV-------------ILSNHGGRQL 271 Query: 323 SAIMSVVEV----AERAGVAIVADGGIRFSGDIAKAIAAGSACVMIG 365 ++ +E ++ D GIR DI KA+A G+ V++G Sbjct: 272 DDAIAPIEALAEIVAATYKPVLIDSGIRRGSDIVKALALGANAVLLG 318 >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 = 38.3 bits (89), Expect = 0.005 Identities = 22/118 (18%), Positives = 51/118 (43%), Gaps = 15/118 (12%) Query: 102 PVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILT---------NRDVRFASNAQ 152 PVT+ P T A+A+ ++K+ +PVV+ GK++G++T + V+ + Sbjct: 4 PVTVLPTVTCAEAIEILKEKGFDQLPVVDES-GKILGMVTLGNLLSSLSSGKVQPSDPVS 62 Query: 153 QAVGELM-----TRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 +A+ + L + + + + + + + + IG++T D+ Sbjct: 63 KALYKQFKRVNKNDTLGKLSRILETDAFLLVFFEQISSAAIGKEKQEKPIGIVTKIDL 120 Score = 36.0 bits (83), Expect = 0.026 Identities = 14/56 (25%), Positives = 27/56 (48%) Query: 164 ITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERSQLNPNATKDSK 219 +TV TV A +L + ++L VVD+ G +G++T+ ++ S + Sbjct: 5 VTVLPTVTCAEAIEILKEKGFDQLPVVDESGKILGMVTLGNLLSSLSSGKVQPSDP 60 >gnl|CDD|73383 cd03332, LMO_FMN, L-Lactate 2-monooxygenase (LMO) FMN-binding domain. LMO is a FMN-containing enzyme that catalyzes the conversion of L-lactate and oxygen to acetate, carbon dioxide, and water. LMO is a member of the family of alpha-hydroxy acid oxidases. It is thought to be a homooctamer with two- and four- fold axes in the center of the octamer.. Length = 383 Score = 38.3 bits (89), Expect = 0.005 Identities = 27/84 (32%), Positives = 40/84 (47%), Gaps = 7/84 (8%) Query: 282 IATAEGALALIDAGADIIKVGIGPGSICTTRVVTGVGCPQLSAIMSVVEVAERAGVAIVA 341 I + A ++AG D + V G R V G L A+ +VE A + ++ Sbjct: 261 ILHPDDARRAVEAGVDGVVVSNHGG-----RQVDG-SIAALDALPEIVE-AVGDRLTVLF 313 Query: 342 DGGIRFSGDIAKAIAAGSACVMIG 365 D G+R DI KA+A G+ V+IG Sbjct: 314 DSGVRTGADIMKALALGAKAVLIG 337 >gnl|CDD|73124 cd04625, CBS_pair_12, 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 = 37.9 bits (88), Expect = 0.006 Identities = 28/111 (25%), Positives = 55/111 (49%), Gaps = 9/111 (8%) Query: 104 TISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV------RFASNAQQAVGE 157 T++P L++A+A M + + + V+E G+LVG+LT R+V A V Sbjct: 5 TVAPETLLSEAVATMAEQDLGSLVVMER--GELVGLLTFREVLQAMAQHGAGVLDTTVRA 62 Query: 158 LMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDIERS 208 +M I +++ + L+ + + L V+ D G +G+I+ D+ ++ Sbjct: 63 IMNPEPIVASPDDSIDEVRRLMVERHLRYLPVL-DGGTLLGVISFHDVAKA 112 Score = 30.6 bits (69), Expect = 1.1 Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 2/48 (4%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 M P+ SP ++ + LM + + +PV+ D G L+G+++ DV Sbjct: 64 MNPEPIVASPDDSIDEVRRLMVERHLRYLPVL--DGGTLLGVISFHDV 109 >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 = 37.6 bits (87), Expect = 0.008 Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 6/86 (6%) Query: 125 GIPVVESDVGKLVGILTNRD-VRFASNAQQ-----AVGELMTRNLITVKKTVNLENAKAL 178 + VV GKL G+LT D VR V +MTR +++ + L + + Sbjct: 25 DLVVVCDPHGKLAGVLTKTDVVRQMGRCGGPGCTAPVENVMTRAVVSCRPGDLLHDVWQV 84 Query: 179 LHQHRIEKLLVVDDDGCCIGLITVKD 204 + Q ++ + VVD++ +G++ +D Sbjct: 85 MKQRGLKNIPVVDENARPLGVLNARD 110 Score = 27.6 bits (61), Expect = 7.1 Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 1/51 (1%) Query: 95 ESGMVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 E+ M V+ P L D +MK+ + IPVV+ + + +G+L RD Sbjct: 62 ENVMTRAVVSCRPGDLLHDVWQVMKQRGLKNIPVVDEN-ARPLGVLNARDA 111 >gnl|CDD|32827 COG3010, NanE, Putative N-acetylmannosamine-6-phosphate epimerase [Carbohydrate transport and metabolism]. Length = 229 Score = 37.5 bits (87), Expect = 0.008 Identities = 34/132 (25%), Positives = 52/132 (39%), Gaps = 11/132 (8%) Query: 236 DRVGPLFDVNVDLVVVD-TAHGHSQKVLDAVVQIKKNFPSLLVMAGNIATAEGALALIDA 294 V L + D++ D T L+ ++ K +P L MA + +T E L Sbjct: 89 KEVDALAEAGADIIAFDATDRPRPDGDLEELIARIK-YPGQLAMA-DCSTFEEGLNAHKL 146 Query: 295 GADIIKVGIGPGSICTTRVVTGVGCPQLSAIMSVVEVAERAGVAIVADGGIRFSGDIAKA 354 G DII G+ T TG +V+ AG ++A+G KA Sbjct: 147 GFDII------GT--TLSGYTGYTEKPTEPDFQLVKQLSDAGCRVIAEGRYNTPEQAKKA 198 Query: 355 IAAGSACVMIGS 366 I G+ V++GS Sbjct: 199 IEIGADAVVVGS 210 >gnl|CDD|29938 cd00452, KDPG_aldolase, KDPG and KHG aldolase. This family belongs to the class I adolases whose reaction mechanism involves Schiff base formation between a substrate carbonyl and lysine residue in the active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, is best known for its role in the Entner-Doudoroff pathway of bacteria, where it catalyzes the reversible cleavage of KDPG to pyruvate and glyceraldehyde-3-phosphate. 2-keto-4-hydroxyglutarate (KHG) aldolase, which has enzymatic specificity toward glyoxylate, forming KHG in the presence of pyruvate, and is capable of regulating glyoxylate levels in the glyoxylate bypass, an alternate pathway when bacteria are grown on acetate carbon sources.. Length = 190 Score = 37.4 bits (87), Expect = 0.009 Identities = 30/107 (28%), Positives = 48/107 (44%), Gaps = 22/107 (20%) Query: 258 SQKVLDAVVQIKKNFPSLLVMAGNIATAEGALALIDAGADIIKVGIGPGSICTTRVVTGV 317 + L+A+ ++K FP L+ AG + T E A A I AGA I + PG Sbjct: 39 TPGALEAIRALRKEFPEALIGAGTVLTPEQADAAIAAGAQFI---VSPG---LDP----- 87 Query: 318 GCPQLSAIMSVVEVAERAGVAIVADGGIRFSGDIAKAIAAGSACVMI 364 VV+ A RAG+ ++ G+ +I +A+ G+ V + Sbjct: 88 ---------EVVKAANRAGIPLLP--GVATPTEIMQALELGADIVKL 123 >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 = 37.1 bits (86), Expect = 0.010 Identities = 34/126 (26%), Positives = 55/126 (43%), Gaps = 19/126 (15%) Query: 100 VNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRD------VRFASNAQQ 153 V P+ I ++ +AL LM K+ + + VV+SD +G++T D ++ Sbjct: 1 VKPIVIPADTSIDEALELMIKHGVRLLLVVDSD-DNFIGVITAVDLLGEEPIKRIQEGGI 59 Query: 154 AVGELMTRNLITVK------KTVNLENAK-----ALLHQHRIEKLLVVDDDGCCI-GLIT 201 + EL +++T K LENA L + LVVD + I G+I+ Sbjct: 60 SRSELTVADVMTPKEDLKALDLEELENASVGDVVETLKASGRQHALVVDREHHQIRGIIS 119 Query: 202 VKDIER 207 DI R Sbjct: 120 TSDIAR 125 >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 = 36.8 bits (85), Expect = 0.013 Identities = 30/106 (28%), Positives = 50/106 (47%), Gaps = 9/106 (8%) Query: 102 PVTISPYATLADALALMKKYSISGIPVVES--DVGKLVGILTNRDVRFASNAQQAVGELM 159 V + T+ D +L+ S +G PVV+S + +LVG + + A + + Sbjct: 4 VVLLPEGMTVEDLESLLSTTSHNGFPVVDSTEESPRLVGYILRSQLVVA------LKNYI 57 Query: 160 TRNLITVKKTVNLENAKALLHQHRIEKLLVVDDDGCCIGLITVKDI 205 + TV +LE L + + LLVVD+ G +G+IT KD+ Sbjct: 58 DPSPFTVSPRTSLEKVHQLFRKLGLRHLLVVDE-GRLVGIITRKDL 102 Score = 32.9 bits (75), Expect = 0.18 Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 2/51 (3%) Query: 98 MVVNPVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFA 148 + +P T+SP +L L +K + + VV D G+LVGI+T +D+ A Sbjct: 57 IDPSPFTVSPRTSLEKVHQLFRKLGLRHLLVV--DEGRLVGIITRKDLLKA 105 >gnl|CDD|31143 COG0800, Eda, 2-keto-3-deoxy-6-phosphogluconate aldolase [Carbohydrate transport and metabolism]. Length = 211 Score = 36.7 bits (85), Expect = 0.014 Identities = 34/140 (24%), Positives = 48/140 (34%), Gaps = 38/140 (27%) Query: 262 LDAVVQIKKNFPSLLVMAGNIATAEGALALIDAGADIIKVGIGPGSICTTRVVT---GVG 318 L+A+ + K FP L+ AG + E A I AGA I + PG V G Sbjct: 52 LEAIRALAKEFPEALIGAGTVLNPEQARQAIAAGAQFI---VSPG--LNPEVAKAANRYG 106 Query: 319 CPQLSAIMSVVEV--AERAG---------------------------VAIVADGGIRFSG 349 P + + + E+ A G V GG+ Sbjct: 107 IPYIPGVATPTEIMAALELGASALKFFPAEVVGGPAMLKALAGPFPQVRFCPTGGVSLD- 165 Query: 350 DIAKAIAAGSACVMIGSLLA 369 + A +AAG V +GS L Sbjct: 166 NAADYLAAGVVAVGLGSWLV 185 >gnl|CDD|73373 cd02811, IDI-2_FMN, Isopentenyl-diphosphate:dimethylallyl diphosphate isomerase type 2 (IDI-2) FMN-binding domain. Two types of IDIs have been characterized at present. The long known IDI-1 is only dependent on divalent metals for activity, whereas IDI-2 requires a metal, FMN and NADPH. IDI-2 catalyzes the interconversion of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) in the mevalonate pathway.. Length = 326 Score = 36.2 bits (84), Expect = 0.021 Identities = 36/135 (26%), Positives = 54/135 (40%), Gaps = 21/135 (15%) Query: 259 QKVLDAVVQIKK--NFPSLLVMAGNIATAEGALALIDAGADIIKVGIGPGSICTTRV--- 313 + L+ + ++ K + P ++ G + E A L DAG I V G G RV Sbjct: 164 RGWLERIEELVKALSVPVIVKEVGFGISRETAKRLADAGVKAIDVA-GAGGTSWARVENY 222 Query: 314 ------------VTGVGCPQLSAIMSVVEVAERAGVAIVADGGIRFSGDIAKAIAAGSAC 361 G P ++++ V + ++A GGIR DIAKA+A G+ Sbjct: 223 RAKDSDQRLAEYFADWGIPTAASLLEVRSALP--DLPLIASGGIRNGLDIAKALALGADL 280 Query: 362 V-MIGSLLAGTDESP 375 V M G L E Sbjct: 281 VGMAGPFLKAALEGE 295 >gnl|CDD|35758 KOG0538, KOG0538, KOG0538, Glycolate oxidase [Energy production and conversion]. Length = 363 Score = 35.6 bits (82), Expect = 0.029 Identities = 25/98 (25%), Positives = 41/98 (41%), Gaps = 19/98 (19%) Query: 274 SLLVMAGNIATAEGALALIDAGADIIKVGIGPGSICTTRVVTGVGCPQLSAIMSVVEV-- 331 L ++ + T E A ++AG I +V+ G QL + + +E Sbjct: 223 KLPIVVKGVLTGEDARKAVEAGVAGI-------------IVSNHGGRQLDYVPATIEALP 269 Query: 332 ----AERAGVAIVADGGIRFSGDIAKAIAAGSACVMIG 365 A + + DGG+R D+ KA+A G+ V IG Sbjct: 270 EVVKAVEGRIPVFLDGGVRRGTDVLKALALGAKGVFIG 307 >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 = 35.3 bits (81), Expect = 0.041 Identities = 32/114 (28%), Positives = 53/114 (46%), Gaps = 8/114 (7%) Query: 102 PVTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASNAQQA-----VG 156 P +S L +A + + VV+ D G +VGI+T D+ A A +A V Sbjct: 3 PPVLSATTPLREAAEQLIESKHGSALVVDRD-GGVVGIITLPDLLRALEADEAGEPSAVD 61 Query: 157 ELMTRNLITVKKTVNLENAKALLHQHRIEKLLVVDDD--GCCIGLITVKDIERS 208 E+ T L+TV L +A + + +L VVD G +GL+T +++ + Sbjct: 62 EVATPPLLTVHPDEPLAHALDRMASRGLRQLPVVDRGNPGQVLGLLTRENVLLA 115 >gnl|CDD|144709 pfam01212, Beta_elim_lyase, Beta-eliminating lyase. Length = 288 Score = 34.9 bits (81), Expect = 0.045 Identities = 27/114 (23%), Positives = 38/114 (33%), Gaps = 24/114 (21%) Query: 279 AGNIATAEGALALIDAGADIIKVGIGPGSIC---TTRVVTGVGCPQLSAIMSVVEVAERA 335 AG + E A I DI G I T G L + + +A Sbjct: 106 AGKL-DLEDLEAAIRPVGDIHFPPTG--LISLENTHNSAGGQ-VVSLEELREIRAIAREH 161 Query: 336 GVAIVADGGIRF------SGDIAKAIAAG----------SACVMIGSLLAGTDE 373 G+ + DG R G I K I + +GS+LAG+D+ Sbjct: 162 GIPLHLDGA-RLANAAVALGVIVKEITSYADSVSMSLSKGLGAPVGSVLAGSDD 214 >gnl|CDD|73117 cd04618, CBS_pair_5, 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 = 98 Score = 34.8 bits (80), Expect = 0.052 Identities = 16/43 (37%), Positives = 25/43 (58%) Query: 103 VTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRDV 145 V+I P +L DA L+ K I +PV++ G + ILT+R + Sbjct: 53 VSIHPERSLFDAALLLLKNKIHRLPVIDPSTGTGLYILTSRRI 95 Score = 31.3 bits (71), Expect = 0.55 Identities = 21/94 (22%), Positives = 43/94 (45%), Gaps = 13/94 (13%) Query: 114 ALALMKKYSISGIPVVESDVGKLVGILTNRDVRFASNAQQAVGELMTRNLITVKKTVNLE 173 A + + I P+ +S + VG+LT D ++ L+++ +L Sbjct: 15 AFNALVENGIRSAPLWDSRKQQFVGMLTITDF------------ILILRLVSIHPERSLF 62 Query: 174 NAKALLHQHRIEKLLVVD-DDGCCIGLITVKDIE 206 +A LL +++I +L V+D G + ++T + I Sbjct: 63 DAALLLLKNKIHRLPVIDPSTGTGLYILTSRRIL 96 >gnl|CDD|29940 cd00945, Aldolase_Class_I, Class I aldolases. The class I aldolases use an active-site lysine which stablilzes a reaction intermediates via Schiff base formation, and have TIM beta/alpha barrel fold. The members of this family include 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-4-hydroxyglutarate (KHG) aldolases, transaldolase, dihydrodipicolinate synthase sub-family, Type I 3-dehydroquinate dehydratase, DeoC and DhnA proteins, and metal-independent fructose-1,6-bisphosphate aldolase. Although structurally similar, the class II aldolases use a different mechanism and are believed to have an independent evolutionary origin.. Length = 201 Score = 34.6 bits (79), Expect = 0.060 Identities = 26/93 (27%), Positives = 34/93 (36%), Gaps = 13/93 (13%) Query: 273 PSLLVMAGNIATAEGALALIDAGADIIKVGIGPGSICTTRVVTGVGCPQLSAIMSVVEVA 332 L A IA A A +AGAD IK G G T + + + E Sbjct: 122 TRGLKTADEIAKA--ARIAAEAGADFIKTSTGFGGGGAT----------VEDVKLMKEAV 169 Query: 333 ERAGVAIVADGGIRFSGDIAKAIAAGSACVMIG 365 V + A GGI+ D AI AG+ + Sbjct: 170 -GGRVGVKAAGGIKTLEDALAAIEAGADGIGTS 201 >gnl|CDD|34182 COG4535, CorC, Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]. Length = 293 Score = 34.1 bits (78), Expect = 0.090 Identities = 43/176 (24%), Positives = 79/176 (44%), Gaps = 27/176 (15%) Query: 103 VTISPYATLADALALMKKYSISGIPVVESDVGKLVGILTNRD-VRF-ASNAQQAVGELMT 160 +T+ TL + L ++ + + S PV+ D + GIL +D + F S+A+ + + Sbjct: 80 ITLKRNQTLDECLDVIIESAHSRFPVISEDKDHVEGILLAKDLLPFMRSDAEPFDIKELL 139 Query: 161 RNLITVKKTVNLENAKALLHQHRIEK---LLVVDDDGCCIGLITVKDI------------ 205 R + V ++ ++ LL + R ++ +V+D+ G GL+T++DI Sbjct: 140 RPAVVVPESKRVD---RLLKEFRSQRNHMAIVIDEFGGVSGLVTIEDILEQIVGDIEDEY 196 Query: 206 -ERSQLNPNATKDSKGRLRVAAAVSVAKDIADRVGPLF-DVNVDLV--VVDTAHGH 257 E + S+ RV A + +D + G F D VD + +V A GH Sbjct: 197 DEEEDADIRQL--SRHTWRVRALTEI-EDFNEAFGTHFSDEEVDTIGGLVMQAFGH 249 >gnl|CDD|146945 pfam04551, GcpE, GcpE protein. In a variety of organisms, including plants and several eubacteria, isoprenoids are synthesized by the mevalonate-independent 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. Although different enzymes of this pathway have been described, the terminal biosynthetic steps of the MEP pathway have not been fully elucidated. GcpE gene of Escherichia coli is involved in this pathway. Length = 345 Score = 34.0 bits (79), Expect = 0.10 Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 19/83 (22%) Query: 283 ATAEGALALIDAGADIIKVGIGPGSICTTRVVTGVGCPQLSAIMSVVEVAERAGVAIVAD 342 AT L +AG DI++ V P + A ++ E+ +++ + +VAD Sbjct: 32 ATVAQIKRLEEAGCDIVR----------------VAVPDMEAAEALKEIKKQSPIPLVAD 75 Query: 343 GGIRFSGDIA-KAIAAGSACVMI 364 I F +A +AI AG + I Sbjct: 76 --IHFDYRLALEAIEAGVDKIRI 96 >gnl|CDD|145121 pfam01791, DeoC, DeoC/LacD family aldolase. This family includes diverse aldolase enzymes. This family includes the enzyme deoxyribose-phosphate aldolase EC:4.1.2.4, which is involved in nucleotide metabolism. The family also includes a group of related bacterial proteins of unknown function. The family also includes tagatose 1,6-diphosphate aldolase (EC:4.1.2.40) is part of the tagatose-6-phosphate pathway of galactose-6-phosphate degradation. Length = 231 Score = 32.7 bits (75), Expect = 0.25 Identities = 20/77 (25%), Positives = 27/77 (35%), Gaps = 13/77 (16%) Query: 283 ATAEGALALIDAGADIIKVGIGPGSICTTRVVTGVGCPQLSAIMSVVEVAERAGVAIVAD 342 A+ +AGAD +K G G T + EV A + A Sbjct: 145 LVAKATRVGAEAGADFVKTSTGFGERGAT----------EEDVQIFKEVVGGAPPGVKAS 194 Query: 343 GGIR---FSGDIAKAIA 356 GGI+ F + AIA Sbjct: 195 GGIKEKDFLRTVEDAIA 211 >gnl|CDD|73394 cd04732, HisA, HisA. Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1'-ribulosylformimino)-5-amino-1-(5''- phospho-ribosyl)-4-imidazolecarboxamide). In bacteria and archaea, ProFAR isomerase is encoded by the HisA gene.. Length = 234 Score = 32.4 bits (74), Expect = 0.32 Identities = 33/145 (22%), Positives = 60/145 (41%), Gaps = 20/145 (13%) Query: 236 DRVGPLFDVNVDLVVVDTAHGHSQKVLDAVVQIKKNFPSLLVMA------GNIAT----A 285 + + L D+ V V++ TA + K + V ++ K + ++ G +AT Sbjct: 86 EDIERLLDLGVSRVIIGTA---AVKNPELVKELLKEYGGERIVVGLDAKDGKVATKGWLE 142 Query: 286 EGALALIDAGADIIKVGIGPGSICT--TRVVTGVGCPQLSAIMSVVEVAERAGVAIVADG 343 ++L + ++G+ I T +R T G P E+A G+ ++A G Sbjct: 143 TSEVSLEELAKRFEELGVK-AIIYTDISRDGTLSG-PNFELY---KELAAATGIPVIASG 197 Query: 344 GIRFSGDIAKAIAAGSACVMIGSLL 368 G+ DI G A V++G L Sbjct: 198 GVSSLDDIKALKELGVAGVIVGKAL 222 Score = 27.4 bits (61), Expect = 8.5 Identities = 12/38 (31%), Positives = 21/38 (55%) Query: 330 EVAERAGVAIVADGGIRFSGDIAKAIAAGSACVMIGSL 367 E+ + G+ + GGIR DI + + G + V+IG+ Sbjct: 67 EIVKAVGIPVQVGGGIRSLEDIERLLDLGVSRVIIGTA 104 >gnl|CDD|110106 pfam01081, Aldolase, KDPG and KHG aldolase. This family includes the following members: 4-hydroxy-2-oxoglutarate aldolase (KHG-aldolase) Phospho-2-dehydro-3-deoxygluconate aldolase (KDPG-aldolase). Length = 196 Score = 31.7 bits (72), Expect = 0.50 Identities = 26/92 (28%), Positives = 41/92 (44%), Gaps = 7/92 (7%) Query: 217 DSKGRLRVAAAVSVAKDIADRVGPLFDVNVD--LVVVDTAHGHSQKVLDAVVQIKKNFPS 274 +S R V V KD D + PL + + V++ + LDA+ ++KN P Sbjct: 2 ESILREAKIVPVIVIKDKEDAL-PLAEALAAGGIRVLEVTL-RTPCALDAIRLLRKNRPD 59 Query: 275 LLVMAGNIATAEGALALIDAGADIIKVGIGPG 306 LV AG + A+ +AGA + + PG Sbjct: 60 ALVGAGTVLNAQQLAEAAEAGAQFV---VSPG 88 >gnl|CDD|31001 COG0656, ARA1, Aldo/keto reductases, related to diketogulonate reductase [General function prediction only]. Length = 280 Score = 31.0 bits (70), Expect = 0.78 Identities = 28/129 (21%), Positives = 50/129 (38%), Gaps = 21/129 (16%) Query: 65 AMAQAGGLGVIHR----NFSPSEQVAQVHQVKKFESGMVVNPVTISPYATLADALALMKK 120 A+ + G+I NF E + ++ + K + VN + PY + L ++ Sbjct: 125 ALEELVDEGLIRAIGVSNFGV-EHLEELLSLAKVK--PAVNQIEYHPYLRQPELLPFCQR 181 Query: 121 YSISGIPVVE-SDVGKLVGILTNRDVRF------ASNAQQAVGELMTRNLITVKKTVN-- 171 + GI V S + K +L N + + AQ A+ + R +I + K+ Sbjct: 182 H---GIAVEAYSPLAKGGKLLDNPVLAEIAKKYGKTPAQVALRWHIQRGVIVIPKSTTPE 238 Query: 172 --LENAKAL 178 EN A Sbjct: 239 RIRENLAAF 247 >gnl|CDD|73376 cd02922, FCB2_FMN, Flavocytochrome b2 (FCB2) FMN-binding domain. FCB2 (AKA L-lactate:cytochrome c oxidoreductase) is a respiratory enzyme located in the intermembrane space of fungal mitochondria which catalyzes the oxidation of L-lactate to pyruvate. FCB2 also participates in a short electron-transport chain involving cytochrome c and cytochrome oxidase which ultimately directs the reducing equivalents gained from L-lactate oxidation to oxygen, yielding one molecule of ATP for every L-lactate molecule consumed. FCB2 is composed of 2 domains: a C-terminal flavin-binding domain, which includes the active site for lacate oxidation, and an N-terminal b2-cytochrome domain, required for efficient cytochrome c reduction. FCB2 is a homotetramer and contains two noncovalently bound cofactors, FMN and heme per subunit.. Length = 344 Score = 30.9 bits (70), Expect = 0.88 Identities = 22/93 (23%), Positives = 39/93 (41%), Gaps = 22/93 (23%) Query: 282 IATAEGALALIDAGADIIKVGIGPGSICTTRVVTGVGCPQL----SAIMSVVEVAERA-- 335 + T E A+ + G D I V++ G QL + I ++E+ + Sbjct: 221 VQTVEDAVLAAEYGVDGI-------------VLSNHGGRQLDTAPAPIEVLLEIRKHCPE 267 Query: 336 ---GVAIVADGGIRFSGDIAKAIAAGSACVMIG 365 + + DGG+R D+ KA+ G+ V +G Sbjct: 268 VFDKIEVYVDGGVRRGTDVLKALCLGAKAVGLG 300 >gnl|CDD|30516 COG0167, PyrD, Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]. Length = 310 Score = 30.6 bits (69), Expect = 0.93 Identities = 35/124 (28%), Positives = 54/124 (43%), Gaps = 16/124 (12%) Query: 260 KVLDAVVQIKKNFPSLLVMAGNIAT-AEGALALIDAGAD----------IIKVGIGPGSI 308 K+L+AV P + +A NI E A A +AGAD +K+ + Sbjct: 151 KLLEAVKA-ATKVPVFVKLAPNITDIDEIAKAAEEAGADGLIAINTTKSGMKIDLETKKP 209 Query: 309 CTTRVVTGVGCPQLS--AIMSVVEVAERAG--VAIVADGGIRFSGDIAKAIAAGSACVMI 364 G+ P L A+ V E+ +R G + I+ GGI D + I AG++ V + Sbjct: 210 VLANETGGLSGPPLKPIALRVVAELYKRLGGDIPIIGVGGIETGEDALEFILAGASAVQV 269 Query: 365 GSLL 368 G+ L Sbjct: 270 GTAL 273 >gnl|CDD|35696 KOG0475, KOG0475, KOG0475, Cl- channel CLC-3 and related proteins (CLC superfamily) [Inorganic ion transport and metabolism]. Length = 696 Score = 30.3 bits (68), Expect = 1.1 Identities = 43/203 (21%), Positives = 68/203 (33%), Gaps = 52/203 (25%) Query: 47 LPIMSAAM--DQVTD--SRLAIAMAQAGGLGVIHRNFSPSEQV---------AQVHQVKK 93 LP+M A M + D + I A I N P V + + Sbjct: 500 LPLMLAVMISKWIGDGLGKTGIYDAH------IELNGYPFLDSKSEFSSTLAIPVMEPCR 553 Query: 94 FESGMVVNPVTISPYATLADALALMKKYSISGIPVV-ESDVGKLVGILTNRDVRFASNAQ 152 ES ++V TL D +LM+ SG PVV D +LVG + R++ A Sbjct: 554 SESCLIVITQD---SMTLEDLESLMEDTDFSGFPVVLSEDSQRLVGFVLRRNLFLAILNA 610 Query: 153 QAVGE----------------------------LMTRNLITVKKTVNLENAKALLHQHRI 184 + + ++ TV +E L + Sbjct: 611 RKIQSFIVTTSIYFNDPSPSAVAGIPSRLDLKDILDMTPFTVTDLTPMETV-VDLFRKLG 669 Query: 185 EKLLVVDDDGCCIGLITVKDIER 207 + ++V +G +G+IT KD R Sbjct: 670 LRQILVTKNGILLGIITKKDCLR 692 >gnl|CDD|31163 COG0821, GcpE, Enzyme involved in the deoxyxylulose pathway of isoprenoid biosynthesis [Lipid metabolism]. Length = 361 Score = 30.5 bits (69), Expect = 1.1 Identities = 24/83 (28%), Positives = 34/83 (40%), Gaps = 19/83 (22%) Query: 283 ATAEGALALIDAGADIIKVGIGPGSICTTRVVTGVGCPQLSAIMSVVEVAERAGVAIVAD 342 AT AL AG DI++V P + A ++ E+ +R V +VAD Sbjct: 37 ATVAQIKALERAGCDIVRVT----------------VPDMEAAEALKEIKQRLNVPLVAD 80 Query: 343 GGIRFSGDIA-KAIAAGSACVMI 364 I F +A +A G V I Sbjct: 81 --IHFDYRLALEAAECGVDKVRI 101 >gnl|CDD|31139 COG0796, MurI, Glutamate racemase [Cell envelope biogenesis, outer membrane]. Length = 269 Score = 30.5 bits (69), Expect = 1.2 Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 1/48 (2%) Query: 259 QKVLDAVVQIKKNFPSLLVMAGNIATAEGALALIDAGADIIKVGIGPG 306 ++ L+ V + + LV+A N A+A AL + DI VG+ P Sbjct: 54 ERTLEIVDFLLERGIKALVIACNTASAV-ALEDLREKFDIPVVGVIPA 100 >gnl|CDD|33977 COG4254, COG4254, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 339 Score = 30.0 bits (67), Expect = 1.4 Identities = 20/94 (21%), Positives = 32/94 (34%), Gaps = 1/94 (1%) Query: 333 ERAGVAIVADGGIRFSGDIAKAIAAGSACVMIGSLLAGTDESPGDIFLYQGRSFKSYRGM 392 AG +A G+R + K A SA ++ + R+ R + Sbjct: 219 LDAGRRTLATLGVRPALPPVKGDARLSASILSMQGSQTISAAVEIKPTAPERAAPPERAL 278 Query: 393 GSVA-AMERGSSARYSQDGVTDVLKLVPEGIEGR 425 + R S R S+ G+ K G +GR Sbjct: 279 PASDPRPLRTFSNRPSKRGLDKGKKAKDTGYKGR 312 >gnl|CDD|143497 cd06824, PLPDE_III_Yggs_like, Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins. This subfamily contains mainly uncharacterized proteobacterial proteins with similarity to the hypothetical Escherichia coli protein YggS, a homolog of yeast YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. Like yeast YBL036c, Yggs is a single domain monomeric protein with a typical TIM-barrel fold. Its structure, which shows a covalently-bound PLP cofactor, is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. YggS has not been characterized extensively and its biological function is still unkonwn. Length = 224 Score = 29.9 bits (68), Expect = 1.5 Identities = 12/19 (63%), Positives = 14/19 (73%) Query: 348 SGDIAKAIAAGSACVMIGS 366 SGD+ AIAAGS V IG+ Sbjct: 201 SGDLEAAIAAGSTMVRIGT 219 >gnl|CDD|73374 cd02812, PcrB_like, PcrB_like proteins. One member of this family, a protein from Archaeoglobus fulgidus, has been characterized as a (S)-3-O-geranylgeranylglyceryl phosphate synthase (AfGGGPS). AfGGGPS catalyzes the formation of an ether linkage between sn-glycerol-1-phosphate (G1P) and geranylgeranyl diphosphate (GGPP), the committed step in archaeal lipid biosynthesis. Therefore, it has been proposed that PcrB-like proteins are either prenyltransferases or are involved in lipoteichoic acid biosynthesis although the exact function is still unknown.. Length = 219 Score = 29.4 bits (66), Expect = 2.0 Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 1/41 (2%) Query: 263 DAVVQIKKNF-PSLLVMAGNIATAEGALALIDAGADIIKVG 302 + V +KK + L++ G I + E A + +AGAD I VG Sbjct: 164 EVVRAVKKVLGDTPLIVGGGIRSGEQAKEMAEAGADTIVVG 204 >gnl|CDD|73402 cd04740, DHOD_1B_like, Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively.. Length = 296 Score = 29.7 bits (67), Expect = 2.1 Identities = 22/90 (24%), Positives = 38/90 (42%), Gaps = 11/90 (12%) Query: 288 ALALIDAGADII---------KVGIGPGSICTTRVVTGVGCPQLS--AIMSVVEVAERAG 336 A A +AGAD + + I V G+ P + A+ V +V + Sbjct: 172 ARAAEEAGADGLTLINTLKGMAIDIETRKPILGNVTGGLSGPAIKPIALRMVYQVYKAVE 231 Query: 337 VAIVADGGIRFSGDIAKAIAAGSACVMIGS 366 + I+ GGI D + + AG++ V +G+ Sbjct: 232 IPIIGVGGIASGEDALEFLMAGASAVQVGT 261 >gnl|CDD|35999 KOG0780, KOG0780, KOG0780, Signal recognition particle, subunit Srp54 [Intracellular trafficking, secretion, and vesicular transport]. Length = 483 Score = 29.5 bits (66), Expect = 2.1 Identities = 27/100 (27%), Positives = 45/100 (45%), Gaps = 9/100 (9%) Query: 209 QLNPNATKDS---KGRLRVAAAVSVAKDIADRVGPLFDVNVDLVVVDTAHGHSQK--VLD 263 QL NATK G A V +A + DR N D+++VDT+ H Q+ + + Sbjct: 147 QLKQNATKARVPFYGSYTEADPVKIASEGVDRFK---KENFDVIIVDTSGRHKQEASLFE 203 Query: 264 AVVQIKKNF-PSLLVMAGNIATAEGALALIDAGADIIKVG 302 + Q+ K P ++ + + + A A A + + VG Sbjct: 204 EMKQVSKAIKPDEIIFVMDASIGQAAEAQARAFKETVDVG 243 >gnl|CDD|73401 cd04739, DHOD_like, Dihydroorotate dehydrogenase (DHOD) like proteins. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. This subgroup has the conserved FMN binding site, but lacks some catalytic residues and may therefore be inactive.. Length = 325 Score = 29.4 bits (66), Expect = 2.7 Identities = 12/35 (34%), Positives = 19/35 (54%) Query: 334 RAGVAIVADGGIRFSGDIAKAIAAGSACVMIGSLL 368 R ++ A GG+ + D+ K + AG+ VM S L Sbjct: 235 RVKASLAASGGVHDAEDVVKYLLAGADVVMTTSAL 269 >gnl|CDD|34183 COG4536, CorB, Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]. Length = 423 Score = 29.0 bits (65), Expect = 2.9 Identities = 22/87 (25%), Positives = 37/87 (42%), Gaps = 10/87 (11%) Query: 126 IPVVESDVGKLVGILTNRDVRFASNAQQAVGELMTRNLIT----VKKTVNLENAKALLHQ 181 IP+ D+ ++G+L RD+ N + + V + L + L Sbjct: 236 IPLYRDDLDNIIGVLHVRDLLRLLNEKNEFTKEDILRAADEPYFVPEGTPLSDQ---LVA 292 Query: 182 HRIEKL---LVVDDDGCCIGLITVKDI 205 + K LVVD+ G GL+T++DI Sbjct: 293 FQRNKKHIALVVDEYGDIQGLVTLEDI 319 >gnl|CDD|176259 cd08299, alcohol_DH_class_I_II_IV, class I, II, IV alcohol dehydrogenases. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes or ketones. This group includes alcohol dehydrogenases corresponding to mammalian classes I, II, IV. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine (His-51), the ribose of NAD, a serine (Ser-48) , then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. Length = 373 Score = 28.8 bits (65), Expect = 3.0 Identities = 23/59 (38%), Positives = 26/59 (44%), Gaps = 21/59 (35%) Query: 286 EGALALIDAGADIIKV---------GIG---------PGSICTTRVVTGVGCPQLSAIM 326 E A+A IDA A + KV G G PGS C V G+G LSAIM Sbjct: 153 EIAVAKIDAAAPLEKVCLIGCGFSTGYGAAVNTAKVTPGSTC---AVFGLGGVGLSAIM 208 >gnl|CDD|73385 cd04723, HisA_HisF, Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase (HisA) and the cyclase subunit of imidazoleglycerol phosphate synthase (HisF). The ProFAR isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1'-ribulosylformimino)-5-amino-1-(5''- phospho-ribosyl)-4-imidazolecarboxamide). In bacteria and archaea, ProFAR isomerase is encoded by the HisA gene. The Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4- carboxamide ribonucleotide (PRFAR) to imidazole glycerol phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR). This conversion involves two tightly coupled reactions in distinct active sites of IGPS. The two catalytic domains can be fused, like in fungi and plants, or peformed by a heterodimer (HisH-glutaminase and HisF-cyclase), like in bacteria.. Length = 233 Score = 28.7 bits (64), Expect = 3.6 Identities = 11/39 (28%), Positives = 21/39 (53%) Query: 330 EVAERAGVAIVADGGIRFSGDIAKAIAAGSACVMIGSLL 368 +A RA + ++A GG+R D+ G++ ++ S L Sbjct: 183 RLAARADIPVIAAGGVRSVEDLELLKKLGASGALVASAL 221 >gnl|CDD|30673 COG0325, COG0325, Predicted enzyme with a TIM-barrel fold [General function prediction only]. Length = 228 Score = 28.7 bits (64), Expect = 3.7 Identities = 10/23 (43%), Positives = 13/23 (56%) Query: 348 SGDIAKAIAAGSACVMIGSLLAG 370 S D AIA G+ V IG+ + G Sbjct: 202 SNDYEIAIAEGATMVRIGTAIFG 224 >gnl|CDD|173951 cd08192, Fe-ADH7, Iron-containing alcohol dehydrogenases-like, involved in the linear alkylbenzenesulfonate (LAS) degradation pathway. NAD-dependent iron-containing alcohol dehydrogenase-like. Proteins in this family are NAD-dependent alcohol dehydrogenases which are involved in the linear alkylbenzenesulfonate (LAS) degradation pathway. They catalyze the oxidation of beta-hydroxy CoA ester to beta-oxo CoA ester, which then be subject to CoA-dependent thiolysis to yield acetyl-CoA and 6-C8-SPC-CoA. The major laundry surfactant in worldwide use is commercial linear alkylbenzenesulfonate (LAS) which contains 20 congeners of linear alkanes (C10 to C13). LAS is fully biodegradable in oxic environments. Degradation involves microbial communities. Parvibaculum lavamentivorans DS-1T is a representative member of many heterotrophic, LAS-degrading communities, in which it catalyzes the first steps of LAS degradation. Strain DS-1T is a small heterotrophic bacterium able to omega-oxygenate the commercial surfactant linear alkylbenzenesulfonate (LAS) and shorten the side chain by beta-oxidation to yield sulfophenylcarboxylates (SPC). Parvibaculum lavamentivorans utilizes 3-C12-LAS as the sole carbon and energy source, and excretes largely 4-C6-SPC. Length = 370 Score = 28.7 bits (65), Expect = 3.8 Identities = 16/68 (23%), Positives = 26/68 (38%), Gaps = 8/68 (11%) Query: 311 TRVVTGVGCPQLSAIMSVVEVAERAGVA---IVADGGIRFSGDIAKAIAAGSACVMIGSL 367 TR+ G G AI + G+ IV D G+ G +A+ +A + +L Sbjct: 3 TRIRFGAG-----AIKELPAECAELGIKRPLIVTDPGLAALGLVARVLALLEDAGLAAAL 57 Query: 368 LAGTDESP 375 +P Sbjct: 58 FDEVPPNP 65 >gnl|CDD|145185 pfam01884, PcrB, PcrB family. This family contains proteins that are related to PcrB. The function of these proteins is unknown. Length = 231 Score = 28.6 bits (64), Expect = 3.9 Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 1/59 (1%) Query: 245 NVDLVVVDTAHGHSQKVLDAVVQIKKNFP-SLLVMAGNIATAEGALALIDAGADIIKVG 302 + + ++ G V + V+ +KK + L++ G I + E A + AGAD+I G Sbjct: 153 GMRIFYLEAGSGAPGPVPEEVIAVKKVLDDARLIVGGGIKSGEKAKEMARAGADVIVTG 211 >gnl|CDD|30455 COG0106, HisA, Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase [Amino acid transport and metabolism]. Length = 241 Score = 28.6 bits (64), Expect = 4.3 Identities = 20/84 (23%), Positives = 33/84 (39%), Gaps = 10/84 (11%) Query: 284 TAEGALALIDAGADIIKVGIGPGSICTTRVVTGVGCPQLSAIMSVVEVAERAGVAIVADG 343 E A D GA+ + + + G + ++ E+ E V + G Sbjct: 33 PLEVAKKWSDQGAEWLHL----------VDLDGAKAGGPRNLEAIKEILEATDVPVQVGG 82 Query: 344 GIRFSGDIAKAIAAGSACVMIGSL 367 GIR D+ + AG A V+IG+ Sbjct: 83 GIRSLEDVEALLDAGVARVIIGTA 106 Score = 28.2 bits (63), Expect = 5.8 Identities = 16/55 (29%), Positives = 28/55 (50%) Query: 248 LVVVDTAHGHSQKVLDAVVQIKKNFPSLLVMAGNIATAEGALALIDAGADIIKVG 302 LV +D A + L+A+ +I + + + G I + E AL+DAG + +G Sbjct: 50 LVDLDGAKAGGPRNLEAIKEILEATDVPVQVGGGIRSLEDVEALLDAGVARVIIG 104 >gnl|CDD|73400 cd04738, DHOD_2_like, Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences, their cellular location and their natural electron acceptor used to reoxidize the flavin group. Members of class 1 are cytosolic enzymes and multimers, while class 2 enzymes are membrane associated, monomeric and use respiratory quinones as their physiological electron acceptors.. Length = 327 Score = 28.5 bits (64), Expect = 4.6 Identities = 8/27 (29%), Positives = 16/27 (59%) Query: 275 LLVMAGNIATAEGALALIDAGADIIKV 301 ++ G I++ E A I AGA ++++ Sbjct: 282 PIIGVGGISSGEDAYEKIRAGASLVQL 308 >gnl|CDD|31306 COG1109, {ManB}, Phosphomannomutase [Carbohydrate transport and metabolism]. Length = 464 Score = 28.4 bits (63), Expect = 4.7 Identities = 17/83 (20%), Positives = 27/83 (32%), Gaps = 6/83 (7%) Query: 189 VVDDDGCCIGLITVKDIERSQLNPNATKDSKGRL--RVAAAVSVAKDIADRVGPLFDVNV 246 DG I ++IE R+ + + L DV++ Sbjct: 115 FFGSDGGKISDDIEEEIEAILAEEVDLPRPSWGELGRLKRIPDALDRYIEFIKSLVDVDL 174 Query: 247 DL----VVVDTAHGHSQKVLDAV 265 L VVVD A+G + V + Sbjct: 175 KLRGLKVVVDCANGAAGLVAPRL 197 >gnl|CDD|34006 COG4284, COG4284, UDP-glucose pyrophosphorylase [Carbohydrate transport and metabolism]. Length = 472 Score = 28.4 bits (63), Expect = 5.0 Identities = 9/56 (16%), Positives = 21/56 (37%), Gaps = 2/56 (3%) Query: 420 EGIEGRVPYKGPIASVLHQMSGGLKSSMGYVGASNIEEFQKKANFIRVSVAGLRES 475 EG G +A + ++GG + +G G + E + + + ++ Sbjct: 94 EGWGLLKIKLGKLAVLK--LAGGQGTRLGCDGPKGLFEVKDGKSLFDLQAEQIKYL 147 >gnl|CDD|144535 pfam00977, His_biosynth, Histidine biosynthesis protein. Proteins involved in steps 4 and 6 of the histidine biosynthesis pathway are contained in this family. Histidine is formed by several complex and distinct biochemical reactions catalysed by eight enzymes. The enzymes in this Pfam entry are called His6 and His7 in eukaryotes and HisA and HisF in prokaryotes. The structure of HisA is known to be a TIM barrel fold. In some archaeal HisA proteins the TIM barrel is composed of two tandem repeats of a half barrel. This family belong to the common phosphate binding site TIM barrel family. Length = 229 Score = 28.2 bits (64), Expect = 5.2 Identities = 12/39 (30%), Positives = 21/39 (53%) Query: 330 EVAERAGVAIVADGGIRFSGDIAKAIAAGSACVMIGSLL 368 E+AE + ++A GG+ D+ + + G V+ GS L Sbjct: 185 ELAEAVNIPVIASGGVGSLEDLKELFSEGVDGVIAGSAL 223 >gnl|CDD|107348 cd06353, PBP1_BmpA_Med_like, Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea. Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea. Med, a cell-surface localized protein, which regulates the competence transcription factor gene comK in Bacillus subtilis, lacks the DNA binding domain when compared with structures of transcription regulators from the LacI family. Nevertheless, Med has significant overall sequence homology to various periplasmic substrate-binding proteins. Moreover, the structure of Med shows a striking similarity to PnrA, a periplasmic nucleoside binding protein of an ATP-binding cassette transport system. Members of this group contain the type I periplasmic sugar-binding protein-like fold. Length = 258 Score = 28.3 bits (64), Expect = 5.4 Identities = 11/15 (73%), Positives = 12/15 (80%) Query: 285 AEGALALIDAGADII 299 E ALALID GAD+I Sbjct: 169 KEAALALIDQGADVI 183 >gnl|CDD|31832 COG1646, COG1646, Predicted phosphate-binding enzymes, TIM-barrel fold [General function prediction only]. Length = 240 Score = 28.3 bits (63), Expect = 5.5 Identities = 11/29 (37%), Positives = 17/29 (58%) Query: 274 SLLVMAGNIATAEGALALIDAGADIIKVG 302 + L++ G I + E A + +AGAD I G Sbjct: 192 TPLIVGGGIRSPEQAREMAEAGADTIVTG 220 >gnl|CDD|73397 cd04735, OYE_like_4_FMN, Old yellow enzyme (OYE)-related FMN binding domain, group 4. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.. Length = 353 Score = 28.2 bits (63), Expect = 5.5 Identities = 10/27 (37%), Positives = 18/27 (66%) Query: 276 LVMAGNIATAEGALALIDAGADIIKVG 302 L+ G+I T + AL ++ GAD++ +G Sbjct: 287 LIAVGSINTPDDALEALETGADLVAIG 313 >gnl|CDD|144181 pfam00490, ALAD, Delta-aminolevulinic acid dehydratase. Length = 322 Score = 27.8 bits (63), Expect = 6.4 Identities = 18/61 (29%), Positives = 26/61 (42%), Gaps = 25/61 (40%) Query: 264 AVVQIKKNFPSLLVMA----------G-----------NIAT----AEGALALIDAGADI 298 A+ IK+ FP L+V+ G N T A+ AL+ +AGADI Sbjct: 102 AIRAIKEAFPDLVVITDVCLCEYTSHGHCGILEDGEVDNDETLELLAKQALSHAEAGADI 161 Query: 299 I 299 + Sbjct: 162 V 162 >gnl|CDD|73388 cd04726, KGPDC_HPS, 3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC) and D-arabino-3-hexulose-6-phosphate synthase (HPS). KGPDC catalyzes the formation of L-xylulose 5-phosphate and carbon dioxide from 3-keto-L-gulonate 6-phosphate as part of the anaerobic pathway for L-ascorbate utilization in some eubacteria. HPS catalyzes the formation of D-arabino-3-hexulose-6-phosphate from D-ribulose 5-phosphate and formaldehyde in microorganisms that can use formaldehyde as a carbon source. Both catalyze reactions that involve the Mg2+-assisted formation and stabilization of 1,2-enediolate reaction intermediates.. Length = 202 Score = 27.8 bits (62), Expect = 6.8 Identities = 23/84 (27%), Positives = 36/84 (42%), Gaps = 18/84 (21%) Query: 262 LDAVVQIKKNFPSLLVMAGNIATAEGAL---ALIDAGADIIKVGIGPGSICTTRVVTGVG 318 ++AV +++ FP +++A GAL AGADI VT +G Sbjct: 41 MEAVRALREAFPDKIIVADLKTADAGALEAEMAFKAGADI---------------VTVLG 85 Query: 319 CPQLSAIMSVVEVAERAGVAIVAD 342 LS I V+ A++ G + D Sbjct: 86 AAPLSTIKKAVKAAKKYGKEVQVD 109 >gnl|CDD|30848 COG0502, BioB, Biotin synthase and related enzymes [Coenzyme metabolism]. Length = 335 Score = 27.9 bits (62), Expect = 6.9 Identities = 22/92 (23%), Positives = 38/92 (41%), Gaps = 14/92 (15%) Query: 259 QKVLDAVVQIKKNFPSLLVMAGNIATAEGALALIDAGADIIKVGIGP-----GSICTTRV 313 ++V++A+ +K+ + + + T E A L DAG D + +I TTR Sbjct: 118 EEVVEAIKAVKEELGLEVCASLGMLTEEQAEKLADAGVDRYNHNLETSPEFYENIITTR- 176 Query: 314 VTGVGCPQLSAIMSVVEVAERAGVAIVADGGI 345 ++ +E AG+ V GGI Sbjct: 177 -------TYEDRLNTLENVREAGIE-VCSGGI 200 >gnl|CDD|37546 KOG2335, KOG2335, KOG2335, tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]. Length = 358 Score = 27.9 bits (62), Expect = 7.0 Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 2/45 (4%) Query: 262 LDAVVQIKKNFPSLLVMA-GNIATA-EGALALIDAGADIIKVGIG 304 +A+ +++N P + V+A GNI + + L GAD + G Sbjct: 191 WEAIKAVRENVPDIPVIANGNILSLEDVERCLKYTGADGVMSARG 235 >gnl|CDD|144163 pfam00465, Fe-ADH, Iron-containing alcohol dehydrogenase. Length = 312 Score = 27.6 bits (62), Expect = 7.7 Identities = 15/46 (32%), Positives = 17/46 (36%), Gaps = 8/46 (17%) Query: 320 PQLSAIMSVVEVAERAGV-AIVADGGIRFSG---DIAKAIAAGSAC 361 P L + A G I+A GG G D AKAIA Sbjct: 63 PTLEEVDEAAAAAREEGADVIIAVGG----GSVIDTAKAIALLLTN 104 >gnl|CDD|163675 cd07937, DRE_TIM_PC_TC_5S, Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain. This family includes the carboxyltransferase domains of pyruvate carboxylase (PC) and the transcarboxylase (TC) 5S subunit. Transcarboxylase 5S is a cobalt-dependent metalloenzyme subunit of the biotin-dependent transcarboxylase multienzyme complex. Transcarboxylase 5S transfers carbon dioxide from the 1.3S biotin to pyruvate in the second of two carboxylation reactions catalyzed by TC. The first reaction involves the transfer of carbon dioxide from methylmalonyl-CoA to the 1.3S biotin, and is catalyzed by the 12S subunit. These two steps allow a carboxylate group to be transferred from oxaloacetate to propionyl-CoA to yield pyruvate and methylmalonyl-CoA. The catalytic domain of transcarboxylase 5S has a canonical TIM-barrel fold with a large C-terminal extension that forms a funnel leading to the active site. Transcarboxylase 5S forms a homodimer and there are six dimers per complex. In addition to the catalytic domain, transcarboxylase 5S has several other domains including a carbamoyl-phosphate synthase domain, a biotin carboxylase domain, a carboxyltransferase domain, and an ATP-grasp domain. Pyruvate carboxylase, like TC, is a biotin-dependent enzyme that catalyzes the carboxylation of pyruvate to produce oxaloacetate. In mammals, PC has critical roles in gluconeogenesis, lipogenesis, glyceroneogenesis, and insulin secretion. Inherited PC deficiencies are linked to serious diseases in humans such as lactic acidemia, hypoglycemia, psychomotor retardation, and death. PC is a single-chain enzyme and is active only in its homotetrameric form. PC has three domains, an N-terminal biotin carboxylase domain, a carboxyltransferase domain (this alignment model), and a C-terminal biotin-carboxyl carrier protein domain. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name "DRE-TIM". Length = 275 Score = 27.8 bits (63), Expect = 7.8 Identities = 10/22 (45%), Positives = 12/22 (54%) Query: 289 LALIDAGADIIKVGIGPGSICT 310 LA +AG DI+ I P S T Sbjct: 211 LAAAEAGVDIVDTAISPLSGGT 232 >gnl|CDD|173946 cd08187, BDH, Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process. The butanol dehydrogenase (BDH) is involved in the final step of the butanol formation pathway in anaerobic micro-organism. Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process. Activity in the reverse direction was 50-fold lower than that in the forward direction. The NADH-BDH had higher activity with longer chained aldehydes and was inhibited by metabolites containing an adenine moiety. This protein family belongs to the so-called iron-containing alcohol dehydrogenase superfamily. Since members of this superfamily use different divalent ions, preferentially iron or zinc, it has been suggested to be renamed to family III metal-dependent polyol dehydrogenases. Length = 382 Score = 27.4 bits (62), Expect = 8.2 Identities = 17/46 (36%), Positives = 24/46 (52%), Gaps = 8/46 (17%) Query: 320 PQLSAIMSVVEVAERAGV-AIVADGGIRFSG---DIAKAIAAGSAC 361 P+L + +E+ + V I+A GG G D AKAIAAG+ Sbjct: 70 PRLETVREGIELCKEEKVDFILAVGG----GSVIDSAKAIAAGAPY 111 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 0.318 0.134 0.371 Gapped Lambda K H 0.267 0.0826 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 5,481,612 Number of extensions: 292520 Number of successful extensions: 1379 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1188 Number of HSP's successfully gapped: 282 Length of query: 493 Length of database: 6,263,737 Length adjustment: 98 Effective length of query: 395 Effective length of database: 4,146,055 Effective search space: 1637691725 Effective search space used: 1637691725 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 59 (26.3 bits)