RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= 537021.9.peg.74_1 (196 letters) >gnl|CDD|153108 cd01049, RNRR2, Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain. Ribonucleotide Reductase, R2/beta subunit (RNRR2) is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The RNR protein catalyzes the conversion of ribonucleotides to deoxyribonucleotides and is found in all eukaryotes, many prokaryotes, several viruses, and few archaea. The catalytically active form of RNR is a proposed alpha2-beta2 tetramer. The homodimeric alpha subunit (R1) contains the active site and redox active cysteines as well as the allosteric binding sites. The beta subunit (R2) contains a diiron cluster that, in its reduced state, reacts with dioxygen to form a stable tyrosyl radical and a diiron(III) cluster. This essential tyrosyl radical is proposed to generate a thiyl radical, located on a cysteine residue in the R1 active site that initiates ribonucleotide reduction. The beta subunit is composed of 10-13 helices, the 8 longest helices form an alpha-helical bundle; some have 2 addition beta strands. Yeast is unique in that it assembles both homodimers and heterodimers of RNRR2. The yeast heterodimer, Y2Y4, contains R2 (Y2) and a R2 homolog (Y4) that lacks the diiron center and is proposed to only assist in cofactor assembly, and perhaps stabilize R1 (Y1) in its active conformation. Length = 288 Score = 165 bits (420), Expect = 7e-42 Identities = 57/144 (39%), Positives = 79/144 (54%), Gaps = 5/144 (3%) Query: 32 NQLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKNGLTDDERLMIKRNLGFFAS 91 L P+KY WAWE Y A N W P E+ + DL W+ LT+ ER IKR L F A+ Sbjct: 1 FNLNPIKYPWAWELYKKAEANFWTPEEIDLSKDLKDWEK---LTEAERHFIKRVLAFLAA 57 Query: 92 SESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGLDE--GELFNMY 149 +S+V N+V RH+ PE R + QAF E +HS ++ YI+ +LG DE ELF Sbjct: 58 LDSIVGENLVELFSRHVQIPEARAFYGFQAFMENIHSESYSYILDTLGKDEERDELFEAI 117 Query: 150 REVPSITAKANWALQYTQTLSSPS 173 P++ KA+W L++ L + Sbjct: 118 ETDPALKKKADWILRWYDNLDDNT 141 >gnl|CDD|30557 COG0208, NrdF, Ribonucleotide reductase, beta subunit [Nucleotide transport and metabolism]. Length = 348 Score = 148 bits (376), Expect = 7e-37 Identities = 47/158 (29%), Positives = 74/158 (46%), Gaps = 4/158 (2%) Query: 14 EKRVNVDDKRMLNARS-DVNQLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKN 72 K +++ ++ N + P+KY WA E Y N W+P E+ + +D+ WK Sbjct: 8 TKNDELEEPKIFNGNPTNAINWNPIKYPWALELYKKLTANFWLPEEIDLSNDIKDWKK-- 65 Query: 73 GLTDDERLMIKRNLGFFASSESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQ 132 L+DDE+ +I R L F +S+ ANN V A+ ++ PE L QAF EA+H+ ++ Sbjct: 66 -LSDDEKDLIIRVLAFLTLLDSIQANNGVPALSPLVTTPEEEAVLTNQAFMEAIHARSYS 124 Query: 133 YIITSLGLDEGELFNMYREVPSITAKANWALQYTQTLS 170 YI +LG E E V + A + Sbjct: 125 YIFDTLGPTEDEDEVFDDWVATNEILQEKAEIILRYYD 162 >gnl|CDD|36780 KOG1567, KOG1567, KOG1567, Ribonucleotide reductase, beta subunit [Nucleotide transport and metabolism]. Length = 344 Score = 82.7 bits (204), Expect = 5e-17 Identities = 48/155 (30%), Positives = 72/155 (46%), Gaps = 6/155 (3%) Query: 21 DKRMLNARSDVNQLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKNGLTDDERL 80 D+ +L + P+KY W+ Y A + W EV + DL W+ L DDER Sbjct: 24 DEPLLMENPRRFVMFPIKYHDIWQMYKKAEASFWTAEEVDLSKDLDDWEK---LNDDERH 80 Query: 81 MIKRNLGFFASSESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGL 140 I L FFA+S+ +V N+V + + PE R + Q E +HS + +I + Sbjct: 81 FISHVLAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQIAIENIHSEMYSLLIDTYIR 140 Query: 141 DEGE---LFNMYREVPSITAKANWALQYTQTLSSP 172 D E LFN +P + KA+WAL++ S Sbjct: 141 DPKEREFLFNAIETIPEVKKKADWALRWISDKDSL 175 >gnl|CDD|144013 pfam00268, Ribonuc_red_sm, Ribonucleotide reductase, small chain. Length = 281 Score = 80.1 bits (198), Expect = 4e-16 Identities = 37/132 (28%), Positives = 56/132 (42%), Gaps = 6/132 (4%) Query: 36 PLKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKNGLTDDERLMIKRNLGFFASSESL 95 P+++ WE Y A N W+ EV + D+ W+ L + ER F A+++ + Sbjct: 13 PIQHPDIWELYKKAEANRWLAEEVDLSKDIPDWEK---LNEAEREFYSFVFAFLAAADGI 69 Query: 96 VANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGLDEGE---LFNMYREV 152 V N+ + + Y Q E VHS + I +L DE E FN Sbjct: 70 VNENLAERLSAEFQQKDILHYYGEQIAIENVHSEVYSLIQLTLFNDEKERDAYFNAIETD 129 Query: 153 PSITAKANWALQ 164 P+I KA W L+ Sbjct: 130 PAIQRKAQWLLR 141 >gnl|CDD|153120 cd07911, RNRR2_Rv0233_like, Ribonucleotide Reductase R2-like protein, Mn/Fe-binding domain. Rv0233 is a Mycobacterium tuberculosis ribonucleotide reductase R2 protein with a heterodinuclear manganese/iron-carboxylate cofactor located in its metal center. The Rv0233-like family may represent a structural/functional counterpart of the evolutionary ancestor of the RNRR2's (Ribonucleotide Reductase, R2/beta subunit) and the bacterial multicomponent monooxygenases. RNRR2s belong to a broad superfamily of ferritin-like diiron-carboxylate proteins. The RNR protein catalyzes the conversion of ribonucleotides to deoxyribonucleotides and is found in prokaryotes and archaea. The catalytically active form of RNR is a proposed alpha2-beta2 tetramer. The homodimeric alpha subunit (R1) contains the active site and redox active cysteines as well as the allosteric binding sites. Length = 280 Score = 33.9 bits (78), Expect = 0.034 Identities = 21/92 (22%), Positives = 40/92 (43%), Gaps = 5/92 (5%) Query: 54 WMPTEVPMQDDLALWKSKNGLTDDERLMIKRNLGFFASSESLVANNI--VLAIYRHLSNP 111 W P ++ D W L+++ER + R F + E V ++ ++ Sbjct: 22 WNPADIDFSQDREDW---EQLSEEERDLALRLCAGFIAGEEAVTLDLLPLMMAMAAEGRL 78 Query: 112 ECRQYLLRQAFEEAVHSHTFQYIITSLGLDEG 143 E YL + FEEA H+ F+ + ++G+ + Sbjct: 79 EEEMYLTQFLFEEAKHTDFFRRWLDAVGVSDD 110 >gnl|CDD|37956 KOG2745, KOG2745, KOG2745, Mitochondrial carrier protein [General function prediction only]. Length = 321 Score = 30.3 bits (68), Expect = 0.35 Identities = 19/92 (20%), Positives = 30/92 (32%), Gaps = 2/92 (2%) Query: 86 LGFFASSESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGLDEGEL 145 GFFA + ++++ L +Y+L F + H QY L Sbjct: 192 AGFFAGLVPRLLGDLLVLWGCSLLAHLINRYILDSEFGDTKDVH--QYNHAVTQFAVSSL 249 Query: 146 FNMYREVPSITAKANWALQYTQTLSSPSFHYW 177 V + A L SPS++ W Sbjct: 250 TYPLSVVSTCMAVNGSGLAAGLPPYSPSYNNW 281 >gnl|CDD|37643 KOG2432, KOG2432, KOG2432, Uncharacterized conserved protein [Function unknown]. Length = 565 Score = 29.6 bits (66), Expect = 0.57 Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 1/38 (2%) Query: 158 KANWALQYTQTLSSPSFHYWNKRRRSRILTRSLRFLCR 195 K +W Y + L SP+F W RR R L ++L+ L Sbjct: 459 KGDWKGLYRRFLRSPNFRGWFGARR-RELQQTLQDLQL 495 >gnl|CDD|39857 KOG4658, KOG4658, KOG4658, Apoptotic ATPase [Signal transduction mechanisms]. Length = 889 Score = 28.4 bits (63), Expect = 1.4 Identities = 17/85 (20%), Positives = 31/85 (36%), Gaps = 12/85 (14%) Query: 47 LSACNNHWMPTEVPMQD---DLALWKSKNGLTDDERLMIKRNLGFFASSESL-------- 95 L + V M D ++ALW + + +E ++ +G + Sbjct: 469 LIEERDEGRKETVKMHDVVREMALWIASDFGKQEENQIVSDGVGLSEIPQVKSWNSVRRM 528 Query: 96 -VANNIVLAIYRHLSNPECRQYLLR 119 + NN + I NP+ R LL+ Sbjct: 529 SLMNNKIEHIAGSSENPKLRTLLLQ 553 >gnl|CDD|36427 KOG1213, KOG1213, KOG1213, Sister chromatid cohesion complex Cohesin, subunit RAD21/SCC1 [Cell cycle control, cell division, chromosome partitioning]. Length = 614 Score = 28.1 bits (62), Expect = 1.4 Identities = 16/94 (17%), Positives = 28/94 (29%), Gaps = 4/94 (4%) Query: 8 SPIQAGEKRVNVDDKRMLNARSDVNQLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLAL 67 I +++++VD +L+ QL MP E + L Sbjct: 305 DSILRRKRKLSVDGVTLLSEEEFKEQLADFSDILTSLDLAPPTRVLMMPKETGRVEKLFS 364 Query: 68 WKSKNGLTDDERLMIKRNLGFFASSESLVANNIV 101 + + + F S ESL + V Sbjct: 365 SPEPDLFANRLLFTGR----LFLSLESLKPEDSV 394 >gnl|CDD|36726 KOG1513, KOG1513, KOG1513, Nuclear helicase MOP-3/SNO (DEAD-box superfamily) [Transcription, Signal transduction mechanisms]. Length = 1300 Score = 27.7 bits (61), Expect = 2.4 Identities = 15/39 (38%), Positives = 19/39 (48%) Query: 144 ELFNMYREVPSITAKANWALQYTQTLSSPSFHYWNKRRR 182 L Y +V S AK +W QY +L+ S YWN R Sbjct: 1179 SLSKKYHKVSSEEAKEHWEQQYDLSLNMCSHAYWNGNCR 1217 >gnl|CDD|40030 KOG4833, KOG4833, KOG4833, Uncharacterized conserved protein [Function unknown]. Length = 573 Score = 27.4 bits (60), Expect = 2.4 Identities = 10/36 (27%), Positives = 17/36 (47%) Query: 103 AIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSL 138 A RH E ++ +AFE A+ + F+ + L Sbjct: 256 AEERHFLMDEDHSSVVHKAFEAAILLNFFEILQRLL 291 >gnl|CDD|36693 KOG1480, KOG1480, KOG1480, Netrin transmembrane receptor unc-5 [Signal transduction mechanisms]. Length = 909 Score = 27.0 bits (59), Expect = 3.3 Identities = 13/65 (20%), Positives = 25/65 (38%), Gaps = 2/65 (3%) Query: 78 ERLMIKRNLGFFASSESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITS 137 ++L + R L +FA+ S A ++L ++ P+ L A EE + + Sbjct: 842 QKLHLDRYLSYFATKPSPTA--VILDLWEARHQPDGDLSSLAAALEEMGRPDAVLSLASE 899 Query: 138 LGLDE 142 Sbjct: 900 GQCFP 904 >gnl|CDD|33462 COG3664, XynB, Beta-xylosidase [Carbohydrate transport and metabolism]. Length = 428 Score = 26.8 bits (59), Expect = 3.6 Identities = 10/48 (20%), Positives = 23/48 (47%) Query: 125 AVHSHTFQYIITSLGLDEGELFNMYREVPSITAKANWALQYTQTLSSP 172 + + ++ S+ L G+L+N++ E+ + +L Y Q + P Sbjct: 347 PLKTGRYKDGSFSIDLTNGDLYNVWAEMGARYGPDKSSLDYLQEATQP 394 >gnl|CDD|145853 pfam02915, Rubrerythrin, Rubrerythrin. This domain has a ferritin-like fold. Length = 137 Score = 26.2 bits (58), Expect = 6.3 Identities = 10/64 (15%), Positives = 19/64 (29%), Gaps = 3/64 (4%) Query: 85 NLGFFASSESLVANNIVLAIYRHL--SNPECRQYLLRQAFEEAVHSHTFQYIITSLGLDE 142 L + + ES A + P+ + A EE H+ ++ L Sbjct: 2 ILEYAIAGESS-ARRRYKELAEKAKGEGPQIAELFEEMAEEERRHAGFLNKLLKDLFPGL 60 Query: 143 GELF 146 + Sbjct: 61 EPVI 64 >gnl|CDD|176779 cd08801, Death_UNC5D, Death domain found in Uncoordinated-5D. Death Domain (DD) found in Uncoordinated-5D (UNC5D). UNC5D is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. Length = 98 Score = 25.8 bits (56), Expect = 7.7 Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 7/76 (9%) Query: 78 ERLMIKRNLGFFA--SSESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYII 135 ++ I RNL +FA SS S V ++ A ++H + + L A EE +H+ Q I Sbjct: 28 QKNSIDRNLSYFATQSSPSAVILSLWEARHQHDGDLDS----LACALEEIGRTHSKQSTI 83 Query: 136 TSLGLDEGELFNMYRE 151 E + FN R+ Sbjct: 84 AETLDRESD-FNYSRQ 98 >gnl|CDD|35429 KOG0208, KOG0208, KOG0208, Cation transport ATPase [Inorganic ion transport and metabolism]. Length = 1140 Score = 25.7 bits (56), Expect = 9.0 Identities = 16/71 (22%), Positives = 26/71 (36%), Gaps = 11/71 (15%) Query: 130 TFQYIITSLGLDEGE--LFNMYREVPSITAKA-----NWALQYTQTLSSPSFHYWNKRRR 182 +FQYI +L L +G +++ V L + L F W + Sbjct: 1035 SFQYIFIALVLSKGSPFRRPLWKNVLFKVFITVIILSTIYLLFVNYL----FIEWKLLQL 1090 Query: 183 SRILTRSLRFL 193 + I T RF+ Sbjct: 1091 TYIPTTFDRFI 1101 >gnl|CDD|107363 cd06368, PBP1_iGluR_non_NMDA_like, N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the non-NMDA (N-methyl-d-asparate) subtypes of ionotropic glutamate receptors. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the non-NMDA (N-methyl-d-asparate) subtypes of ionotropic glutamate receptors. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Glutamate mediates the majority of excitatory synaptic transmission in the central nervous system via two broad classes of ionotropic receptors, characterized by their response to glutamate agonists: N-methyl-d -aspartate (NMDA) and non-NMDA receptors. NMDA receptors have intrinsically slow kinetics, are highly permeable to Ca2+, and are blocked by extracellular Mg2+ in a voltage-dependent manner. Non-NMDA receptors have faster kinetics, are most often only weakly permeable to Ca2+, and are not blocked by extracellular Mg2+. While non-NMDA receptors typically mediate excitatory synaptic responses at resting membrane potentials, NMDA receptors contribute several forms of synaptic plasticity and are thought to play an important role in the development of synaptic pathways. Non-NMDA receptors include alpha-amino-3-hydroxy-5-methyl-4-isoxazole proprionate (AMPA) and kainate receptors. Length = 324 Score = 25.7 bits (57), Expect = 9.4 Identities = 10/30 (33%), Positives = 15/30 (50%) Query: 117 LLRQAFEEAVHSHTFQYIITSLGLDEGELF 146 L QA E + S + YI+T+L +L Sbjct: 196 FLEQAVEVGMMSEYYHYILTNLDFHTLDLE 225 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 0.321 0.133 0.411 Gapped Lambda K H 0.267 0.0691 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,429,135 Number of extensions: 119331 Number of successful extensions: 273 Number of sequences better than 10.0: 1 Number of HSP's gapped: 266 Number of HSP's successfully gapped: 20 Length of query: 196 Length of database: 6,263,737 Length adjustment: 89 Effective length of query: 107 Effective length of database: 4,340,536 Effective search space: 464437352 Effective search space used: 464437352 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 55 (25.0 bits)