RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780964|ref|YP_003065377.1| ribonucleotide-diphosphate reductase subunit beta [Candidatus Liberibacter asiaticus str. psy62] (352 letters) >gnl|CDD|30557 COG0208, NrdF, Ribonucleotide reductase, beta subunit [Nucleotide transport and metabolism]. Length = 348 Score = 316 bits (810), Expect = 7e-87 Identities = 117/335 (34%), Positives = 172/335 (51%), Gaps = 7/335 (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 YIITSLGLDEGELFNMYREVPSITAKANWALQYTQTLSSPSFTTGTKDADQEFLQDLFVF 192 YI +LG E E V + A + D +EFL L V Sbjct: 125 YIFDTLGPTEDEDEVFDDWVATNEILQEKAEIILRYYDDLGDDP--DDPLEEFLLKLVVA 182 Query: 193 YVVFEGMWFYTGFAQILSLGRANKMVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHL 252 V+ EG+ FY+GFA L L R KM G AE + I+RDE+LHL F +I ++ ENP L Sbjct: 183 SVILEGILFYSGFAYPLYLARRGKMPGTAEIIRLIIRDEALHLYFIGYLIQRLVAENPEL 242 Query: 253 WTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPL 312 WT E + + + EA LE YA P GL +QY+++ AN+R +GLEPL Sbjct: 243 WTAELKDEIYDLFKEAVELEKEYAEYLYPGIL-GLTEDLVKQYIRYNANKRLQNLGLEPL 301 Query: 313 FKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 347 + ENP PW+ + ++ +FFE RV+ YQ+G+ Sbjct: 302 YPAEENPIPWIELSLSADEKTDFFEGRVSSYQKGS 336 >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 = 306 bits (787), Expect = 5e-84 Identities = 118/300 (39%), Positives = 172/300 (57%), Gaps = 15/300 (5%) 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 REVPSITAKANWALQYTQTLSSPSFTTGTKDADQEFLQDLFVFYVVFEGMWFYTGFAQIL 209 P++ KA+W L++ L + + F + L F ++ EG++FY+GFA I Sbjct: 118 ETDPALKKKADWILRWYDNLDDNT--------KESFAERLVAFAIL-EGIFFYSGFAAIF 168 Query: 210 SLGRANKMVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEAT 269 L R KM G+AE + I RDESLH +F +I ++ ENP L+T+EF+++ ++ EA Sbjct: 169 WLARRGKMPGLAEIIELISRDESLHGDFACLLIRELLNENPELFTEEFKEEVYELIKEAV 228 Query: 270 LLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFK-YTENPFPWMSEVID 328 LE +A + +P G +GLN +QY++++ANRR +GLE LF +NPF WM + D Sbjct: 229 ELEKEFARDLLPDGILGLNKEDMKQYIEYVANRRLENLGLEKLFNVEDKNPFDWMELISD 288 >gnl|CDD|36780 KOG1567, KOG1567, KOG1567, Ribonucleotide reductase, beta subunit [Nucleotide transport and metabolism]. Length = 344 Score = 157 bits (398), Expect = 4e-39 Identities = 103/328 (31%), Positives = 156/328 (47%), Gaps = 28/328 (8%) 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---LFNMYREVPSITAKANWALQYTQTLSSPSFTTGTKDADQEFLQDLFVFYVVFE 197 D E LFN +P + KA+WAL++ D D F + L F V E Sbjct: 141 DPKEREFLFNAIETIPEVKKKADWALRWIS------------DKDSLFAERLVAFAAV-E 187 Query: 198 GMWFYTGFAQILSLGRANKMVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEF 257 G++F FA I L + M G+ + I RDE LH +F + HL K Sbjct: 188 GIFFSGSFASIFWLKKRGLMPGLTFSNELISRDEGLHCDFAC-------LLFSHLKKKPN 240 Query: 258 QQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTE 317 +++ ++ EA +E + E +P +G+N QY++F+A+R ++G E + E Sbjct: 241 EERIEEIITEAVEIEQEFLTEALPVNLIGMNCDLMSQYIEFVADRLLVELGNEKYYN-AE 299 Query: 318 NPFPWMSEVIDLKKEKNFFETRVTEYQQ 345 NPF +M E I L + NFFE RV+EYQ+ Sbjct: 300 NPFDFM-ENISLAGKTNFFEKRVSEYQK 326 >gnl|CDD|144013 pfam00268, Ribonuc_red_sm, Ribonucleotide reductase, small chain. Length = 281 Score = 140 bits (355), Expect = 5e-34 Identities = 77/292 (26%), Positives = 123/292 (42%), Gaps = 26/292 (8%) 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 PSITAKANWALQYTQTLSSPSFTTGTKDADQEFLQDLFVFYVVFEGMWFYTGFAQILSLG 212 P+I KA W L+ D E L + + + + EG++F + FA I L Sbjct: 130 PAIQRKAQWLLR--------------WVRDAESLAEKLIAFALVEGIFFSSSFASIAYLR 175 Query: 213 RANKMVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLE 272 + M G + + I RDE+LH + + N K ++ + EA +E Sbjct: 176 KRGLMPGTCQSNELISRDEALHTDAACLLYNNYLGLE-----KPEPKRIYKLFREAVEIE 230 Query: 273 IAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMS 324 I + P G+N + +QY++F A+R IG +PLF NPF ++ Sbjct: 231 IEFIEAAAPVDVHGMNVRAIKQYIEFSADRLLVAIGYKPLFN-VPNPFFPLA 281 >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 = 48.1 bits (115), Expect = 3e-06 Identities = 51/272 (18%), Positives = 96/272 (35%), Gaps = 41/272 (15%) Query: 54 WMPTEVPMQDDLALWKSKNGLTDDERLMIKRNLGFFASSESLVANNI--VLAIYRHLSNP 111 W P ++ D W L+++ER + R F + E V ++ ++ Sbjct: 22 WNPADIDFSQDREDW---EQLSEEERDLALRLCAGFIAGEEAVTLDLLPLMMAMAAEGRL 78 Query: 112 ECRQYLLRQAFEEAVHSHTFQYIITSLGLDEG----------ELFNMYREVPSITAKANW 161 E YL + FEEA H+ F+ + ++G+ + E F Y +P Sbjct: 79 EEEMYLTQFLFEEAKHTDFFRRWLDAVGVSDDLSDLHTAVYREPF--YEALPY------- 129 Query: 162 ALQYTQTLSSPSFTTGTKDADQEFLQDLFVFYVVFEGMWFYTG---FAQILSLGRANKMV 218 L + ++ + ++ EG+ TG + I + + Sbjct: 130 ---AELRLY-------LDASPAAQVRASVTYNMIVEGVLAETGYYAWRTICE--KRGILP 177 Query: 219 GIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHE 278 G+ E + + DES H+ +G ++ + W F+++ ++ A L I E Sbjct: 178 GMQEGIRRLGDDESRHIAWGTFTCRRLVAADDANWDV-FEERMNELVPHALGL-IDEIFE 235 Query: 279 TMPKGFVGLNAPSCEQYMQFIANRRCHQIGLE 310 + GL+ QY RR I Sbjct: 236 LYDEMPFGLDPDELMQYAVDQFQRRLGYIERA 267 >gnl|CDD|176707 cd08359, Glo_EDI_BRP_like_22, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The structures of this family demonstrate domain swapping, which is shared by glyoxalase I and antibiotic resistance proteins. Length = 119 Score = 31.8 bits (73), Expect = 0.28 Identities = 13/51 (25%), Positives = 19/51 (37%), Gaps = 7/51 (13%) Query: 171 SPSFTTGTKDADQEFLQDLFVFYVVFEGMWFYTGFAQILSLGRANKMVGIA 221 P T +F F F VVF+ W+ +SL + V +A Sbjct: 4 YPVIVTDDLAETADFYVRHFGFTVVFDSDWY-------VSLRSPDGGVELA 47 >gnl|CDD|176781 cd08803, Death_ank3, Death domain of Ankyrin-3. Death Domain (DD) of the human protein ankyrin-3 (ANK-3) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-3, also called anykyrin-G (for general or giant), is found in neurons and at least one splice variant has been shown to be essential for propagation of action potentials as a binding partner to neurofascin and voltage-gated sodium channels. It is required for maintaining axo-dendritic polarity, and may be a genetic risk factor associated with bipolar disorder. ANK-3 may also play roles in other cell types. Mutations affecting ANK-3 pathways for Na channel localization are associated with Brugada syndrome, a potentially fata arrythmia. 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 = 84 Score = 29.6 bits (66), Expect = 1.3 Identities = 13/41 (31%), Positives = 23/41 (56%) Query: 216 KMVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPHLWTKE 256 +M +A+ + + LNF +D INQI++ENP+ + Sbjct: 6 RMAIVADHLGLSWTELARELNFSVDEINQIRVENPNSLIAQ 46 >gnl|CDD|39857 KOG4658, KOG4658, KOG4658, Apoptotic ATPase [Signal transduction mechanisms]. Length = 889 Score = 29.1 bits (65), Expect = 2.1 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|33462 COG3664, XynB, Beta-xylosidase [Carbohydrate transport and metabolism]. Length = 428 Score = 28.8 bits (64), Expect = 2.3 Identities = 11/56 (19%), Positives = 26/56 (46%) Query: 125 AVHSHTFQYIITSLGLDEGELFNMYREVPSITAKANWALQYTQTLSSPSFTTGTKD 180 + + ++ S+ L G+L+N++ E+ + +L Y Q + P+ T+ Sbjct: 347 PLKTGRYKDGSFSIDLTNGDLYNVWAEMGARYGPDKSSLDYLQEATQPAPTSEKIT 402 >gnl|CDD|176783 cd08805, Death_ank1, Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. 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 = 84 Score = 28.4 bits (63), Expect = 3.3 Identities = 12/36 (33%), Positives = 20/36 (55%) Query: 216 KMVGIAEQYQYIMRDESLHLNFGIDVINQIKIENPH 251 KM I E + + L F ++ IN+I++ENP+ Sbjct: 6 KMAVIREHLGLSWAELARELQFSVEDINRIRVENPN 41 >gnl|CDD|176732 cd08317, Death_ank, Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. 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 = 84 Score = 28.0 bits (63), Expect = 3.6 Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 4/33 (12%) Query: 234 HLNFGIDVINQIKIENPHLWTKEFQQKSRTMLH 266 L I+ IK ENP+ Q+++ ML Sbjct: 24 ELGVSETDIDLIKAENPN----SLAQQAQAMLK 52 >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 = 4.0 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|40030 KOG4833, KOG4833, KOG4833, Uncharacterized conserved protein [Function unknown]. Length = 573 Score = 27.8 bits (61), Expect = 5.3 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 = 27.3 bits (60), Expect = 5.7 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|34330 COG4714, COG4714, Uncharacterized membrane-anchored protein conserved in bacteria [Function unknown]. Length = 303 Score = 26.9 bits (59), Expect = 9.6 Identities = 8/23 (34%), Positives = 12/23 (52%) Query: 280 MPKGFVGLNAPSCEQYMQFIANR 302 +P G + + A QYM+ I N Sbjct: 67 LPAGMIFIPAEEANQYMELIGNN 89 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 0.320 0.134 0.412 Gapped Lambda K H 0.267 0.0780 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 4,353,728 Number of extensions: 226991 Number of successful extensions: 487 Number of sequences better than 10.0: 1 Number of HSP's gapped: 470 Number of HSP's successfully gapped: 22 Length of query: 352 Length of database: 6,263,737 Length adjustment: 95 Effective length of query: 257 Effective length of database: 4,210,882 Effective search space: 1082196674 Effective search space used: 1082196674 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: 58 (26.0 bits)