RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780818|ref|YP_003065231.1| DNA polymerase III subunit epsilon [Candidatus Liberibacter asiaticus str. psy62] (245 letters) >gnl|CDD|99835 cd06131, DNA_pol_III_epsilon_Ecoli_like, DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex. Length = 167 Score = 233 bits (596), Expect = 4e-62 Identities = 90/170 (52%), Positives = 116/170 (68%), Gaps = 6/170 (3%) Query: 9 KIVFDIETTGLDSK-NDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITD 67 +IV D ETTGLD + RIIEIG VEL++ T TF V++ P R EA K+HGITD Sbjct: 1 QIVLDTETTGLDPREGHRIIEIGCVELINRRLTGNTFHVYINPE-RDIPEEAFKVHGITD 59 Query: 68 EFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRI--NKDPLDPSRIID 125 EFL DKP F+ I EF DF AE + HNA FDVGF+NAEL + K +D R+ID Sbjct: 60 EFLADKPKFAEIADEFLDFIR--GAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVID 117 Query: 126 TLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMM 175 TL++AR+K P N L++LCKR+GI SHR+ HGALLD+ LL++VY+++ Sbjct: 118 TLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLDAELLAEVYLELT 167 >gnl|CDD|31188 COG0847, DnaQ, DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]. Length = 243 Score = 148 bits (373), Expect = 2e-36 Identities = 80/240 (33%), Positives = 115/240 (47%), Gaps = 13/240 (5%) Query: 6 KMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGI 65 R +V D+ETTGL+ K DRIIEIGAV L D R+F + P R PE K+HGI Sbjct: 12 PTRFVVIDLETTGLNPKKDRIIEIGAVTLEDGRIVERSFHTLVNPE-RPIPPEIFKIHGI 70 Query: 66 TDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIID 125 TDE L D P F+ + EF DF +AHNA FDVGF+ E +R+ + ++D Sbjct: 71 TDEMLADAPKFAEVLPEFLDFIGG-LRLLVAHNAAFDVGFLRVESERLGIEIPGD-PVLD 128 Query: 126 TLSIARRKHPSS-RNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMMVGGSQINFG 184 TL++ARR P R+ L++L +R GI + H AL D+ L+++++ + G + Sbjct: 129 TLALARRHFPGFDRSSLDALAERLGIDRNPFHPHRALFDALALAELFLL-LQTGLLLKAP 187 Query: 185 FKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKEELDEH----DKTIQTLGKNAIWDRY 240 D K + + EL H D + L + +W Y Sbjct: 188 LTAILDLDKLAHKALYD----TLKTAARLFCGIENELKAHGSWLDALAKELLEKKLWKEY 243 >gnl|CDD|176648 cd06127, DEDDh, DEDDh 3'-5' exonuclease domain family. DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others. Length = 159 Score = 143 bits (363), Expect = 4e-35 Identities = 71/165 (43%), Positives = 94/165 (56%), Gaps = 8/165 (4%) Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEF 69 +VFD ETTGLD K DRIIEIGAV++ + F+ + P GR PEA +HGITDE Sbjct: 1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEIVERFETLVNP-GRPIPPEATAIHGITDEM 59 Query: 70 LKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSI 129 L D P F + EF +F +AHNA FD+ F+N EL+R+ PL P+ IDTL + Sbjct: 60 LADAPPFEEVLPEFLEFLG--GRVLVAHNASFDLRFLNRELRRLGGPPL-PNPWIDTLRL 116 Query: 130 ARRKHP--SSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYI 172 ARR P S L +RYGI + H AL D+ +++ + Sbjct: 117 ARRLLPGLRSHRLGLLLAERYGIPLEGA--HRALADALATAELLL 159 >gnl|CDD|144506 pfam00929, Exonuc_X-T, Exonuclease. This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;. Length = 162 Score = 112 bits (283), Expect = 7e-26 Identities = 57/164 (34%), Positives = 87/164 (53%), Gaps = 5/164 (3%) Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEF 69 +V D ETTGLD + DRIIEI AV ++ F ++ P R + EA K HGIT E Sbjct: 2 VVIDCETTGLDPEKDRIIEIAAVSIVGGENIGPVFDTYVKPE-RLITDEATKFHGITPEM 60 Query: 70 LKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPL-DPSRIIDTLS 128 L++ PSF + F +F + + HNA FDVGF+ + R K P + +IDTL Sbjct: 61 LRNAPSFEEVLEAFLEFLKKLK-ILVGHNASFDVGFLLYDDLRFLKLPHPKLNDVIDTLI 119 Query: 129 IARRKHPSS-RNDLNSLCKRYGITISHRSKHGALLDSHLLSDVY 171 + + + R L++L ++ G+ R H AL D+ ++++ Sbjct: 120 LDKATYKGFKRRSLDALAEKLGLEKIQR-AHRALDDARATAELF 162 >gnl|CDD|32359 COG2176, PolC, DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]. Length = 1444 Score = 107 bits (269), Expect = 2e-24 Identities = 62/170 (36%), Positives = 93/170 (54%), Gaps = 14/170 (8%) Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNR---TFQVFLCPNGRKNSPEALKLHGIT 66 +VFDIETTGL D IIEI AV++ K R FQ F+ P GR S +L GIT Sbjct: 424 VVFDIETTGLSPVYDEIIEIAAVKI----KNGRIIDKFQFFIKP-GRPLSATITELTGIT 478 Query: 67 DEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDT 126 DE L++ P + +F +F ++ +AHNA FD+GF+N ++ +PL +IDT Sbjct: 479 DEMLENAPEIEEVLEKFREFI--GDSILVAHNASFDMGFLNTNYEKYGLEPLTNP-VIDT 535 Query: 127 LSIARRKHPSSRN-DLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMM 175 L +AR +P ++ L +LCK+ G+ + H A D+ + V+ + Sbjct: 536 LELARALNPEFKSHRLGTLCKKLGVELERH--HRADYDAEATAKVFFVFL 583 >gnl|CDD|99834 cd06130, DNA_pol_III_epsilon_like, an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex. Length = 156 Score = 76.0 bits (188), Expect = 1e-14 Identities = 36/110 (32%), Positives = 56/110 (50%), Gaps = 7/110 (6%) Query: 56 SPEALKLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINK 115 P + +HGIT E + D P+F ++ E F + +AHNA FD + A L+ Sbjct: 44 DPFNIAIHGITPEDVADAPTFPEVWPEIKPFL--GGSLVVAHNASFDRSVLRAALEAYGL 101 Query: 116 DPLDPSRIIDTLSIARRKHPSSRN-DLNSLCKRYGITISHRSKHGALLDS 164 P P + + T+ +ARR P N LN++ + GI ++H H AL D+ Sbjct: 102 PP-PPYQYLCTVRLARRVWPLLPNHKLNTVAEHLGIELNH---HDALEDA 147 >gnl|CDD|99837 cd06134, RNaseT, DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site. Length = 189 Score = 63.5 bits (155), Expect = 6e-11 Identities = 52/183 (28%), Positives = 86/183 (46%), Gaps = 21/183 (11%) Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTN-----RTFQVFLCP-NGRKNSPEALKLH 63 +V D+ET G + + D ++EI AV L+ + TF + P G P AL+ + Sbjct: 8 VVVDVETGGFNPQTDALLEIAAV-TLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFN 66 Query: 64 GITDEF------LKDKPSFSSIFSEFWDFFNEQN---AEWIAHNAKFDVGFINAELQR-- 112 GI D F + +K + IF Q A + HNA FD+GF+NA + R Sbjct: 67 GI-DPFHPFRFAVDEKEALKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCK 125 Query: 113 INKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYI 172 I ++P P DT ++A + + L C+ GI ++ H AL D+ ++++ Sbjct: 126 IKRNPFHPFSTFDTATLAGLAY--GQTVLAKACQAAGIEFDNKEAHSALYDTQKTAELFC 183 Query: 173 KMM 175 K++ Sbjct: 184 KIV 186 >gnl|CDD|99836 cd06133, ERI-1_3'hExo_like, DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins. This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional homolog of either ERI-1 or 3'hExo. Length = 176 Score = 53.4 bits (129), Expect = 6e-08 Identities = 37/177 (20%), Positives = 72/177 (40%), Gaps = 13/177 (7%) Query: 10 IVFDIETTGLDSKNDR-----IIEIGAVEL-LDYSKTNRTFQVFLCP-NGRKNSPEALKL 62 +V D E T + + IIEIGAV + + + TF ++ P K S +L Sbjct: 2 LVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTEL 61 Query: 63 HGITDEFLKDKPSFSSIFSEFWDFFNE-QNAEWIAHNAKFDVGFINAELQRINKDPLDP- 120 GIT E + + PSF + EF ++ + ++ +D+ + + L P Sbjct: 62 TGITQEDVDNAPSFPEVLKEFLEWLGKNGKYAFVT-WGDWDLKDLLQNQCKYKIINLPPF 120 Query: 121 -SRIIDTLSIARRKHPSSRN-DLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMM 175 + ID + + + L+ + G+ R H L D+ ++ + +++ Sbjct: 121 FRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFEGR-HHRGLDDARNIARILKRLL 176 >gnl|CDD|99839 cd06136, TREX1_2, DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TREX2 that point to different biological roles for these proteins. The main difference is the presence of about 70 amino acids at the C-terminus of TREX1. In addition, TREX1 has a nonrepetitive proline-rich region that is not present in the TREX2 protein. Furthermore, TREX2 contains a conserved DNA binding loop positioned adjacent to the active site that has a sequence distinct from the corresponding loop in TREX1. Truncations in the C-terminus of human TREX1 cause autosomal dominant retinal vasculopathy with cerebral leukodystrophy (RVCL), a neurovascular syndrome featuring a progressive loss of visual acuity combined with a variable neurological picture. Length = 177 Score = 42.3 bits (100), Expect = 1e-04 Identities = 49/184 (26%), Positives = 77/184 (41%), Gaps = 27/184 (14%) Query: 10 IVFDIETTGL-DSKNDRIIEIGAV-----ELLDYSKTNRTF-----QVFLCPNGRKN-SP 57 + D+ETTGL I E+ V LL+ S+ ++ LC N + SP Sbjct: 2 VFLDLETTGLPKHNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGRAISP 61 Query: 58 EALKLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWI---AHNA-KFDVGFINAELQRI 113 A ++ G++++ L+ K F S + F + + I AHN +FD + +EL+R+ Sbjct: 62 GASEITGLSNDLLEHKAPFDSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERL 121 Query: 114 NKDPLDPSRI--IDTLSIARRKHPSSRNDLNSLCKR-YGITISHRSKHGALLDSHLLSDV 170 P I +D+L R S L SL KR +G + H A D L Sbjct: 122 GTK--LPDDILCVDSLPAFRELDQS----LGSLYKRLFGQEPKN--SHTAEGDVLALLKC 173 Query: 171 YIKM 174 + Sbjct: 174 ALHK 177 >gnl|CDD|176647 cd06125, DnaQ_like_exo, DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer. Length = 96 Score = 40.5 bits (95), Expect = 4e-04 Identities = 30/124 (24%), Positives = 40/124 (32%), Gaps = 39/124 (31%) Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEF 69 I D E TGLD IIEI ++ T + L Sbjct: 1 IAIDTEATGLDGAVHEIIEIALADVNP----EDTAVIDLKD------------------I 38 Query: 70 LKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRIN-KDPLDPSRIIDTLS 128 L+DKP + HN FD+ F+N + K PL IDT+ Sbjct: 39 LRDKPLAILV----------------GHNGSFDLPFLNNRCAELGLKYPLLAGSWIDTIK 82 Query: 129 IARR 132 +A Sbjct: 83 LAAD 86 >gnl|CDD|99841 cd06138, ExoI_N, N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site. Length = 183 Score = 39.6 bits (93), Expect = 9e-04 Identities = 35/134 (26%), Positives = 54/134 (40%), Gaps = 20/134 (14%) Query: 12 FDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQV-----FLC--PNGRKNSPEALKLHG 64 +D ET GL+ D+I++ A+ T+ F C P SPEAL + G Sbjct: 3 YDYETFGLNPSFDQILQFAAIR------TDENFNEIEPFNIFCRLPPDVLPSPEALIVTG 56 Query: 65 IT-DEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNA-KFDVGFINAELQRINKDP----- 117 IT + LK+ S ++ FN + +N +FD F+ R DP Sbjct: 57 ITPQQLLKEGLSEYEFIAKIHRLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEW 116 Query: 118 LDPSRIIDTLSIAR 131 + + D L + R Sbjct: 117 KNGNSRWDLLDVVR 130 >gnl|CDD|99838 cd06135, Orn, DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling. Length = 173 Score = 37.5 bits (88), Expect = 0.004 Identities = 11/20 (55%), Positives = 15/20 (75%) Query: 13 DIETTGLDSKNDRIIEIGAV 32 D+E TGLD + DRI+EI + Sbjct: 5 DLEMTGLDPEKDRILEIACI 24 >gnl|CDD|176651 cd06139, DNA_polA_I_Ecoli_like_exo, DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases. Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair. Length = 193 Score = 35.6 bits (83), Expect = 0.014 Identities = 34/150 (22%), Positives = 54/150 (36%), Gaps = 35/150 (23%) Query: 3 RKNKMRKIVFDIETTGLDSKNDRIIEIG-AVELLDYSKTNRTFQVFLCPNGRKNSPEALK 61 K + FD ETT LD ++ I AVE + + P G E L Sbjct: 1 ELEKAKVFAFDTETTSLDPMQAELVGISFAVEP------GEAYYI---PLGHDYGGEQLP 51 Query: 62 LHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFI-NA--ELQRINKDPL 118 + KP + + + + N KFD+ + N EL+ D + Sbjct: 52 REEVLAAL---KP-----------LLEDPSIKKVGQNLKFDLHVLANHGIELRGPAFDTM 97 Query: 119 DPSRIIDTLSIARRKHPSSRNDLNSLCKRY 148 S +++ RR+H L+ L +RY Sbjct: 98 LASYLLNP---GRRRH-----GLDDLAERY 119 >gnl|CDD|35762 KOG0542, KOG0542, KOG0542, Predicted exonuclease [Replication, recombination and repair]. Length = 280 Score = 34.9 bits (80), Expect = 0.023 Identities = 42/208 (20%), Positives = 80/208 (38%), Gaps = 21/208 (10%) Query: 10 IVFDIETTGLD----SKNDRIIEIGAVELL--DYSKTNRTFQVFLCPN-GRKNSPEALKL 62 ++ D E T + IIE AV L + S F ++ P + S L Sbjct: 59 LILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSL 118 Query: 63 HGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKF------DVG-FINAELQRIN- 114 GI E + + P+F + SEF + + + F D+ F+ + + N Sbjct: 119 TGIQQETVDEAPTFPQVLSEFDSWLRKDSLGDKNGKFAFVTDGDWDLWVFLQYQCKLKNI 178 Query: 115 KDPLDPSRIIDTLSIARR--KHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYI 172 + P ++ I+ I + P+ N + + + YG+ R H + D+ ++ + Sbjct: 179 RIPAFFNQWINIRKIYKNFYNRPAPTN-ITGMLEHYGLQFEGR-AHSGIDDARNIARIAQ 236 Query: 173 KMMVGGS--QINFGFKTNEDRFFKEEKK 198 KM+ G+ +IN E + + Sbjct: 237 KMIRDGAEFRINELCDLWERQPLVPNRS 264 >gnl|CDD|176654 cd06142, RNaseD_exo, DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins. Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein. Length = 178 Score = 34.8 bits (81), Expect = 0.023 Identities = 21/111 (18%), Positives = 36/111 (32%), Gaps = 21/111 (18%) Query: 80 FSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRN 139 S + + N + H A+ D+ + + + P + DT AR Sbjct: 53 LSPLKELLADPNIVKVFHAAREDLELLKRDFGIL------PQNLFDTQIAARLLGLGDSV 106 Query: 140 DLNSLCKRY-GITI---------SHRS-----KHGALLDSHLLSDVYIKMM 175 L +L + G+ + S R A LD L +Y K+ Sbjct: 107 GLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLK 157 >gnl|CDD|32132 COG1949, Orn, Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]. Length = 184 Score = 34.5 bits (79), Expect = 0.025 Identities = 15/29 (51%), Positives = 18/29 (62%) Query: 4 KNKMRKIVFDIETTGLDSKNDRIIEIGAV 32 NK I D+E TGLD + DRIIEI + Sbjct: 3 ANKNNLIWIDLEMTGLDPERDRIIEIATI 31 >gnl|CDD|28891 cd00007, 35EXOc, 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).. Length = 155 Score = 33.1 bits (75), Expect = 0.074 Identities = 27/141 (19%), Positives = 49/141 (34%), Gaps = 37/141 (26%) Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEF 69 + FD ETTGL+ +++ I Q+ + EA + Sbjct: 3 VAFDTETTGLNYHRGKLVGI---------------QIA-------TAGEAA--------Y 32 Query: 70 LKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSI 129 + D+ + +++ + H+AKFD+ + P I DT+ Sbjct: 33 IPDELELEEDLEALKELLEDEDITKVGHDAKFDLVVLA------RDGIELPGNIFDTMLA 86 Query: 130 ARRKHPS-SRNDLNSLCKRYG 149 A +P + L+ L K Y Sbjct: 87 AYLLNPGEGSHSLDDLAKEYL 107 >gnl|CDD|144991 pfam01612, 3_5_exonuc, 3'-5' exonuclease. This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D). Werner syndrome is a human genetic disorder causing premature aging; the WRN protein has helicase activity in the 3'-5' direction. The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homologue of the WRN protein. RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome. Length = 172 Score = 32.3 bits (74), Expect = 0.12 Identities = 15/63 (23%), Positives = 25/63 (39%), Gaps = 6/63 (9%) Query: 86 FFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLC 145 + N + HNAKFD+ L R + + DT+ A + L+ L Sbjct: 70 LLEDPNITKVGHNAKFDLEV----LARDFG--IKLENLFDTMLAAYLLGYPRSHSLDDLA 123 Query: 146 KRY 148 ++Y Sbjct: 124 EKY 126 >gnl|CDD|38452 KOG3242, KOG3242, KOG3242, Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]. Length = 208 Score = 31.5 bits (71), Expect = 0.21 Identities = 33/144 (22%), Positives = 57/144 (39%), Gaps = 16/144 (11%) Query: 6 KMRKIVFDIETTGLDSKNDRIIEIGAV---ELLDYSKTNRTFQVFLCPNGRKNSPEALKL 62 K + D E TGLD + DRIIEI + L+ + E Sbjct: 25 KQPLVWIDCEMTGLDVEKDRIIEIACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIE 84 Query: 63 H----GITDEFLKDKPSFSSIFSEFWDFFNEQ---NAEWIAHNAKF-DVGFINAELQRIN 114 H G+T++ L K + + +E ++ + +A N+ + D F+ + ++ Sbjct: 85 HHGNSGLTEKVLASKITLADAENEVLEYIKKHIPKGKCPLAGNSVYMDRLFLKKYMPKL- 143 Query: 115 KDPLDPSRIIDTLSI---ARRKHP 135 RI+D +I ARR +P Sbjct: 144 -IKHLHYRIVDVSTIKELARRWYP 166 >gnl|CDD|33167 COG3359, COG3359, Predicted exonuclease [DNA replication, recombination, and repair]. Length = 278 Score = 30.7 bits (69), Expect = 0.33 Identities = 39/151 (25%), Positives = 55/151 (36%), Gaps = 34/151 (22%) Query: 5 NKMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHG 64 FDIETTGLD + I +G +D + R Q FL A + Sbjct: 96 EAEDVAFFDIETTGLDRAGNTITLVGGARGVDDTMHVR--QHFL---------PAPEEEV 144 Query: 65 ITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLD---PS 121 E P F+ + S FN FD+ FI +R+ +D L+ Sbjct: 145 AVLENFLHDPDFNMLVS-----FN---------GKAFDIPFI----KRMVRDRLELSLEF 186 Query: 122 RIIDTLSIARR--KHPSSRNDLNSLCKRYGI 150 D +RR KH R L ++ + GI Sbjct: 187 GHFDLYHPSRRLWKHLLPRCGLKTVERILGI 217 >gnl|CDD|99825 cd05782, DNA_polB_like1_exo, Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair. Length = 208 Score = 30.7 bits (70), Expect = 0.36 Identities = 34/197 (17%), Positives = 58/197 (29%), Gaps = 86/197 (43%) Query: 10 IVFDIET----------------------------TGLDSKND-------RIIEIGAVEL 34 +VFDIET S +D +++ I A+ Sbjct: 2 LVFDIETVPDVDLGRRLYLLLELDDLEVLEKRFAQRLEKSGSDFLPLPFHKVVSISALYR 61 Query: 35 LDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEW 94 D +V + E E L+D F+ ++N Sbjct: 62 DDDGGF---LKVR----TLDGADEK--------ELLED----------FFQLIEKKNPRL 96 Query: 95 IAHNAK-FDVGFIN-----------AELQRINKDPLDPSR----IIDTLSI-----ARRK 133 ++ N + FD+ ++ A NKD +R +D + + AR + Sbjct: 97 VSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAFYGARAR 156 Query: 134 HPSSRNDLNSLCKRYGI 150 L+ L K GI Sbjct: 157 AS-----LDLLAKLLGI 168 >gnl|CDD|36229 KOG1011, KOG1011, KOG1011, Neurotransmitter release regulator, UNC-13 [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport]. Length = 1283 Score = 30.0 bits (67), Expect = 0.56 Identities = 16/65 (24%), Positives = 32/65 (49%), Gaps = 4/65 (6%) Query: 56 SPEALKLH----GITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQ 111 S + + LH + +E++ D P++ S E+ +F +W+ N + + F+ L+ Sbjct: 707 SADYMNLHFKVKWLYNEYVADLPTYKSSVPEYPAWFEPFVMQWLDENEEVSMDFLRGALE 766 Query: 112 RINKD 116 R KD Sbjct: 767 RDKKD 771 >gnl|CDD|33213 COG3407, MVD1, Mevalonate pyrophosphate decarboxylase [Lipid metabolism]. Length = 329 Score = 28.3 bits (63), Expect = 2.1 Identities = 20/68 (29%), Positives = 27/68 (39%), Gaps = 3/68 (4%) Query: 60 LKLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLD 119 +K G DE L P SSI DF AE + N + D +N EL + Sbjct: 17 IKYWGKRDEALN-IPLNSSISVTLEDFSTTTTAEELTENDEEDTFILNGELSEDENEKA- 74 Query: 120 PSRIIDTL 127 R++D Sbjct: 75 -RRVLDRF 81 >gnl|CDD|176237 cd08276, MDR7, Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family. This group is a member of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, but lacks the zinc-binding sites of the zinc-dependent alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P)-binding Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Length = 336 Score = 27.9 bits (63), Expect = 2.8 Identities = 9/27 (33%), Positives = 15/27 (55%) Query: 14 IETTGLDSKNDRIIEIGAVELLDYSKT 40 I T+ D K +R +GA +++Y T Sbjct: 188 IATSSSDEKLERAKALGADHVINYRTT 214 >gnl|CDD|32342 COG2159, COG2159, Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]. Length = 293 Score = 27.3 bits (60), Expect = 4.2 Identities = 12/67 (17%), Positives = 19/67 (28%) Query: 46 VFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGF 105 F+ R+ + GI L + I N+ A A VGF Sbjct: 44 YFINGKLRRVDLAFMDAAGIDLFVLSGMGEVAIIPDLRRALANDDLAALAAEYPDRFVGF 103 Query: 106 INAELQR 112 + + Sbjct: 104 ARVDPRD 110 >gnl|CDD|99848 cd06145, REX1_like, DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T. Length = 150 Score = 26.7 bits (60), Expect = 6.3 Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 3/33 (9%) Query: 118 LDPSRIIDTLSI--ARRKHPSSRNDLNSLCKRY 148 L R+IDT +I + P + L +L K+Y Sbjct: 93 LIHPRVIDT-AILFPHPRGPPYKPSLKNLAKKY 124 >gnl|CDD|153225 cd03131, GATase1_HTS, Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS). Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS). HTS, the first enzyme in methionine biosynthesis in Escherichia coli, transfers a succinyl group from succinyl-CoA to homoserine forming succinyl homoserine. It has been suggested that the succinyl group of succinyl-CoA is initially transferred to an enzyme nucleophile before subsequent transfer to homoserine. The catalytic triad typical of GATase1 domains is not conserved in this GATase1-like domain. However, in common with GATase1 domains a reactive cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. It has been proposed that this cys is in the active site of the molecule. However, as succinyl has been found bound to a conserved lysine residue, this conserved cys may play a role in dimer formation. HTS activity is tightly regulated by several mechanisms including feedback inhibition and proteolysis. It represents a critical control point for cell growth and viability. Length = 175 Score = 26.5 bits (59), Expect = 6.9 Identities = 8/18 (44%), Positives = 13/18 (72%) Query: 32 VELLDYSKTNRTFQVFLC 49 E+LD++KT+ T +F C Sbjct: 88 TEILDWAKTHVTSTLFSC 105 >gnl|CDD|35403 KOG0182, KOG0182, KOG0182, 20S proteasome, regulatory subunit alpha type PSMA6/SCL1 [Posttranslational modification, protein turnover, chaperones]. Length = 246 Score = 26.5 bits (58), Expect = 7.0 Identities = 8/28 (28%), Positives = 16/28 (57%) Query: 197 KKTVPNISLLKRDKPLFTRITKEELDEH 224 K + + ++ D P F ++ EE++EH Sbjct: 211 KSSELEVGVVTVDNPEFRILSAEEIEEH 238 >gnl|CDD|32749 COG2925, SbcB, Exonuclease I [DNA replication, recombination, and repair]. Length = 475 Score = 26.0 bits (57), Expect = 8.8 Identities = 20/87 (22%), Positives = 37/87 (42%), Gaps = 19/87 (21%) Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTF------QVFLC--PNGRKNSPEALK 61 + +D ET G+ DR + + +T+ F VF C + P A+ Sbjct: 12 LFYDYETFGVHPALDRPAQFAGI------RTDIEFNIIGEPIVFYCKPADDYLPQPGAVL 65 Query: 62 LHGITDEFLKDK----PSFSS-IFSEF 83 + GIT + ++K +F++ I +E Sbjct: 66 ITGITPQEAREKGINEAAFAARIHAEL 92 >gnl|CDD|36671 KOG1458, KOG1458, KOG1458, Fructose-1,6-bisphosphatase [Carbohydrate transport and metabolism]. Length = 343 Score = 26.0 bits (57), Expect = 9.1 Identities = 11/36 (30%), Positives = 12/36 (33%), Gaps = 7/36 (19%) Query: 116 DPLDPSRIIDTL-------SIARRKHPSSRNDLNSL 144 DPLD S ID L I R + L Sbjct: 129 DPLDGSSNIDALVSVGTIFGIYRLLSDDEPTIKDVL 164 >gnl|CDD|34109 COG4403, LcnDR2, Lantibiotic modifying enzyme [Defense mechanisms]. Length = 963 Score = 26.1 bits (57), Expect = 9.3 Identities = 15/71 (21%), Positives = 19/71 (26%), Gaps = 9/71 (12%) Query: 1 MIRKNKMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTN----RTFQVFLCPNGRKNS 56 I N + KN ELLDY K R + LC + Sbjct: 382 NINLNTDEMKIVKEPYMFESEKNLPTFNGKDKELLDYIKEITEGFRNMYLLLCSGISE-- 439 Query: 57 PEALKLHGITD 67 +K I Sbjct: 440 ---IKEKNILA 447 >gnl|CDD|176650 cd06129, RNaseD_like, DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins. The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Egl is a component of an mRNA-binding complex which is required for oocyte specification. The Egl subfamily does not possess a completely conserved YX(3)D pattern at the ExoIII motif. Length = 161 Score = 25.9 bits (57), Expect = 9.4 Identities = 24/115 (20%), Positives = 37/115 (32%), Gaps = 25/115 (21%) Query: 81 SEFWDFFNE--QNAE--WIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPS 136 S W +N H + D+ +L R + R+ DT A K Sbjct: 53 SVDWQGLKMLLENPSIVKALHGIEGDL----WKLLRDFGEK--LQRLFDTTIAANLKGLP 106 Query: 137 SRNDLNSLCKRY-GIT--------------ISHRSKHGALLDSHLLSDVYIKMMV 176 R L SL + + G T ++ K A D + L +Y K+ Sbjct: 107 ERWSLASLVEHFLGKTLDKSISCADWSYRPLTEDQKLYAAADVYALLIIYTKLRN 161 >gnl|CDD|58113 cd03782, MATH_Meprin_Beta, Meprin family, Beta subunit, MATH domain; Meprins are multidomain extracellular metalloproteases capable of cleaving growth factors, cytokines, extracellular matrix proteins, and biologically active peptides. They are composed of two related subunits, alpha and beta, which form homo- or hetro-complexes where the basic unit is a disulfide-linked dimer. The beta subunit is a type I membrane protein, which forms homodimers or heterotetramers (alpha2beta2 or alpha3beta). Meprin beta shows preference for acidic residues at the P1 and P1' sites of its substrate. Among its best substrates are growth factors and chemokines such as gastrin and osteopontin. Both alpha and beta subunits contain a catalytic astacin (M12 family) protease domain followed by the adhesion or interaction domains MAM, MATH and AM. The MATH and MAM domains provide symmetrical intersubunit disulfide bonds necessary for the dimerization of meprin subunits. The MATH domain may also be required for folding of an activable zymogen.. Length = 167 Score = 26.1 bits (57), Expect = 9.4 Identities = 10/27 (37%), Positives = 14/27 (51%) Query: 37 YSKTNRTFQVFLCPNGRKNSPEALKLH 63 S T +FQV L NG + P L ++ Sbjct: 30 LSSTGYSFQVGLYLNGTDDYPGNLAIY 56 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 0.319 0.136 0.398 Gapped Lambda K H 0.267 0.0761 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,010,136 Number of extensions: 155648 Number of successful extensions: 457 Number of sequences better than 10.0: 1 Number of HSP's gapped: 431 Number of HSP's successfully gapped: 42 Length of query: 245 Length of database: 6,263,737 Length adjustment: 91 Effective length of query: 154 Effective length of database: 4,297,318 Effective search space: 661786972 Effective search space used: 661786972 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 56 (25.3 bits)