RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8867
(355 letters)
>gnl|CDD|235968 PRK07209, PRK07209, ribonucleotide-diphosphate reductase subunit
beta; Validated.
Length = 369
Score = 677 bits (1749), Expect = 0.0
Identities = 250/340 (73%), Positives = 282/340 (82%)
Query: 16 SFERINKINKQIINGHTDVNQLVPFKYNWAWDRYLSSCANHWMPQEINMQRDIELWKNPI 75
R+N +K+IIN DVNQLVPFKY WAW++YL+ CANHWMPQE+NM RDI LWK+P
Sbjct: 30 GAARVNVDDKRIINCRADVNQLVPFKYKWAWEKYLAGCANHWMPQEVNMSRDIALWKSPN 89
Query: 76 GLTEEERRLVKRNLGFFSTADSLAANNIVLGTYRHITAPECRQYLLRQAFEEAIHTHAYQ 135
GLTE+ERR+VKRNLGFFSTADSL ANNIVL YRHIT PECRQYLLRQAFEEAIHTHAYQ
Sbjct: 90 GLTEDERRIVKRNLGFFSTADSLVANNIVLAIYRHITNPECRQYLLRQAFEEAIHTHAYQ 149
Query: 136 YIVESLGLDELEIFNAYHEIKSIRDKDEFLIPFIDVLTDLKFKTGNTKNDQKLLKSLIVF 195
YIVESLGLDE EIFN YHE+ SIR KDEFLIPF LTD FKTG +NDQKLL++LI F
Sbjct: 150 YIVESLGLDEGEIFNMYHEVPSIRAKDEFLIPFTRSLTDPNFKTGTPENDQKLLRNLIAF 209
Query: 196 ACIMEGLFFYVGFVQILALGRQNKMIGSSELYQYILRDESMHCNFGIDLINTIKMENPNL 255
CIMEG+FFYVGF QIL+LGRQNKM G +E YQYILRDESMH NFGIDLIN IK+ENP+L
Sbjct: 210 YCIMEGIFFYVGFTQILSLGRQNKMTGIAEQYQYILRDESMHLNFGIDLINQIKLENPHL 269
Query: 256 WTTEFCKEIEQLFLKAIELEYYYAEDTMPKGILGLNVKTFKSYLRFIANCRMKQIGIKQI 315
WT EF EI +L +A+ELEY YA DTMP+G+LGLN FK YLRFIAN R++QIG+K
Sbjct: 270 WTAEFQAEIRELIKEAVELEYRYARDTMPRGVLGLNASMFKDYLRFIANRRLQQIGLKPQ 329
Query: 316 FPYERNPFPWMSEMIHIKKESNFFETRVMEYQSGGTLDWE 355
+P NPFPWMSEMI +KKE NFFETRV+EYQ+GG L W+
Sbjct: 330 YPGTENPFPWMSEMIDLKKEKNFFETRVIEYQTGGALSWD 369
>gnl|CDD|223286 COG0208, NrdF, Ribonucleotide reductase, beta subunit [Nucleotide
transport and metabolism].
Length = 348
Score = 351 bits (903), Expect = e-120
Identities = 125/328 (38%), Positives = 181/328 (55%), Gaps = 7/328 (2%)
Query: 25 KQIINGH-TDVNQLVPFKYNWAWDRYLSSCANHWMPQEINMQRDIELWKNPIGLTEEERR 83
+I NG+ T+ P KY WA + Y AN W+P+EI++ DI+ WK L+++E+
Sbjct: 16 PKIFNGNPTNAINWNPIKYPWALELYKKLTANFWLPEEIDLSNDIKDWKK---LSDDEKD 72
Query: 84 LVKRNLGFFSTADSLAANNIVLGTYRHITAPECRQYLLRQAFEEAIHTHAYQYIVESLGL 143
L+ R L F + DS+ ANN V +T PE L QAF EAIH +Y YI ++LG
Sbjct: 73 LIIRVLAFLTLLDSIQANNGVPALSPLVTTPEEEAVLTNQAFMEAIHARSYSYIFDTLGP 132
Query: 144 DELEIFNAYHEIKSIRDKDEFLIPFIDVLTDLKFKTGNTKNDQKLLKSLIVFACIMEGLF 203
E E + + E + DL + ++ LLK L+V + I+EG+
Sbjct: 133 TEDEDEVFDDWVATNEILQEKAEIILRYYDDL-GDDPDDPLEEFLLK-LVVASVILEGIL 190
Query: 204 FYVGFVQILALGRQNKMIGSSELYQYILRDESMHCNFGIDLINTIKMENPNLWTTEFCKE 263
FY GF L L R+ KM G++E+ + I+RDE++H F LI + ENP LWT E E
Sbjct: 191 FYSGFAYPLYLARRGKMPGTAEIIRLIIRDEALHLYFIGYLIQRLVAENPELWTAELKDE 250
Query: 264 IEQLFLKAIELEYYYAEDTMPKGILGLNVKTFKSYLRFIANCRMKQIGIKQIFPYERNPF 323
I LF +A+ELE YAE P GILGL K Y+R+ AN R++ +G++ ++P E NP
Sbjct: 251 IYDLFKEAVELEKEYAEYLYP-GILGLTEDLVKQYIRYNANKRLQNLGLEPLYPAEENPI 309
Query: 324 PWMSEMIHIKKESNFFETRVMEYQSGGT 351
PW+ + ++++FFE RV YQ G
Sbjct: 310 PWIELSLSADEKTDFFEGRVSSYQKGSV 337
>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 = 292 bits (749), Expect = 4e-98
Identities = 114/298 (38%), Positives = 177/298 (59%), Gaps = 15/298 (5%)
Query: 35 NQLVPFKYNWAWDRYLSSCANHWMPQEINMQRDIELWKNPIGLTEEERRLVKRNLGFFST 94
L P KY WAW+ Y + AN W P+EI++ +D++ W+ LTE ER +KR L F +
Sbjct: 1 FNLNPIKYPWAWELYKKAEANFWTPEEIDLSKDLKDWEK---LTEAERHFIKRVLAFLAA 57
Query: 95 ADSLAANNIVLGTYRHITAPECRQYLLRQAFEEAIHTHAYQYIVESLGLDEL--EIFNAY 152
DS+ N+V RH+ PE R + QAF E IH+ +Y YI+++LG DE E+F A
Sbjct: 58 LDSIVGENLVELFSRHVQIPEARAFYGFQAFMENIHSESYSYILDTLGKDEERDELFEAI 117
Query: 153 HEIKSIRDKDEFLIPFIDVLTDLKFKTGNTKNDQKLLKSLIVFACIMEGLFFYVGFVQIL 212
+++ K ++++ + D L D + + L+ FA + EG+FFY GF I
Sbjct: 118 ETDPALKKKADWILRWYDNLDD--------NTKESFAERLVAFAIL-EGIFFYSGFAAIF 168
Query: 213 ALGRQNKMIGSSELYQYILRDESMHCNFGIDLINTIKMENPNLWTTEFCKEIEQLFLKAI 272
L R+ KM G +E+ + I RDES+H +F LI + ENP L+T EF +E+ +L +A+
Sbjct: 169 WLARRGKMPGLAEIIELISRDESLHGDFACLLIRELLNENPELFTEEFKEEVYELIKEAV 228
Query: 273 ELEYYYAEDTMPKGILGLNVKTFKSYLRFIANCRMKQIGIKQIFP-YERNPFPWMSEM 329
ELE +A D +P GILGLN + K Y+ ++AN R++ +G++++F ++NPF WM +
Sbjct: 229 ELEKEFARDLLPDGILGLNKEDMKQYIEYVANRRLENLGLEKLFNVEDKNPFDWMELI 286
>gnl|CDD|236591 PRK09614, nrdF, ribonucleotide-diphosphate reductase subunit beta;
Reviewed.
Length = 324
Score = 217 bits (554), Expect = 2e-68
Identities = 95/316 (30%), Positives = 149/316 (47%), Gaps = 24/316 (7%)
Query: 39 PFKYNWAWDRYLSSCANHWMPQEINMQRDIELWKNPIGLTEEERRLVKRNLGFFSTADSL 98
+ W ++ + AN W+P+E+ + D++ WK L++EE+ L R G + D+L
Sbjct: 16 KIEDPWDYEAWKRLTANFWLPEEVPLSNDLKDWKK---LSDEEKNLYTRVFGGLTLLDTL 72
Query: 99 AANNIVLGTYRHITAPECRQYLLRQAFEEAIHTHAYQYIVESLGLDELEIFNAYH---EI 155
NN + IT PE L AF EA+H +Y YI +L E EI A+ E
Sbjct: 73 QNNNGMPNLMPDITTPEEEAVLANIAFMEAVHAKSYSYIFSTLCSPE-EIDEAFEWAEEN 131
Query: 156 KSIRDKDEFLIPFIDVLTDLKFKTGNTKNDQKLLKSLIVFACIMEGLFFYVGFVQILALG 215
++ K + + F + L +K+L+ V + +EG FY GF L L
Sbjct: 132 PYLQKKADIIQDFYEPLK------------KKILRKAAVASVFLEGFLFYSGFYYPLYLA 179
Query: 216 RQNKMIGSSELYQYILRDESMHCNFGIDLINTIKMENPNLWTTEFCKEIEQLFLKAIELE 275
RQ KM G++++ + I+RDES+H + L E P L E EI L + E E
Sbjct: 180 RQGKMTGTAQIIRLIIRDESLHGYYIGYLFQEGLEELPELEQEELKDEIYDLLYELYENE 239
Query: 276 YYYAEDTMPKGILGLNVKTFKSYLRFIANCRMKQIGIKQIFP-YERNPFPWMSEMIHIKK 334
Y E I+GL + K Y+R+ AN R+ +G++ +FP E W++ + +
Sbjct: 240 EAYTELLY--DIVGL-AEDVKKYIRYNANKRLMNLGLEPLFPEEEEVNPIWLNGLSNNAD 296
Query: 335 E-SNFFETRVMEYQSG 349
E +FFE + Y G
Sbjct: 297 ENHDFFEGKGTSYVKG 312
>gnl|CDD|240315 PTZ00211, PTZ00211, ribonucleoside-diphosphate reductase small
subunit; Provisional.
Length = 330
Score = 153 bits (387), Expect = 2e-43
Identities = 95/341 (27%), Positives = 171/341 (50%), Gaps = 35/341 (10%)
Query: 18 ERINKINKQIINGHTDVNQLVPFKYNWAWDRYLSSCANHWMPQEINMQRDIELWKNPIGL 77
+ N+ + ++ + D L P KY W Y + A+ W +EI++ D++ W+ L
Sbjct: 5 MKENEEEEPLLKENPDRFVLFPIKYPDIWRMYKKAEASFWTAEEIDLGNDLKDWEK---L 61
Query: 78 TEEERRLVKRNLGFFSTADSLAANNIVLGTYRHITAPECRQYLLRQAFEEAIHTHAYQYI 137
+ ER +K L FF+ +D + N+ R + PE R + Q E IH+ Y +
Sbjct: 62 NDGERHFIKHVLAFFAASDGIVLENLAQRFMREVQVPEARCFYGFQIAMENIHSETYSLL 121
Query: 138 VESLGLDELE---IFNAYHEIKSIRDKDEFLIPFIDVLTDLKFKTGNTKNDQKLLKSLIV 194
+++ DE E +F+A I +I+ K E+ +I+ + + L+
Sbjct: 122 IDTYITDEEEKDRLFHAIETIPAIKKKAEWAAKWIN-------------SSNSFAERLVA 168
Query: 195 FACIMEGLFFYVGFVQILALGRQNKMIG---SSELYQYILRDESMHCNFGIDLINTIKME 251
FA + EG+FF F I L ++ M G S+EL I RDE +H +F L + +K +
Sbjct: 169 FAAV-EGIFFSGSFCAIFWLKKRGLMPGLTFSNEL---ISRDEGLHTDFACLLYSHLKNK 224
Query: 252 NPNLWTTEFCKEIEQLFLKAIELEYYYAEDTMPKGILGLNVKTFKSYLRFIANCRMKQIG 311
P + ++++ +A+E+E + D +P ++G+N + Y+ F+A+ + +G
Sbjct: 225 LPR-------ERVQEIIKEAVEIEREFICDALPVDLIGMNSRLMAQYIEFVADRLLVALG 277
Query: 312 IKQIFPYERNPFPWMSEMIHIKKESNFFETRVMEYQSGGTL 352
+ +I+ +NPF WM +MI ++ ++NFFE RV EYQ G +
Sbjct: 278 VPKIY-NSKNPFDWM-DMISLQGKTNFFEKRVGEYQKAGVM 316
>gnl|CDD|139206 PRK12759, PRK12759, bifunctional
gluaredoxin/ribonucleoside-diphosphate reductase subunit
beta; Provisional.
Length = 410
Score = 142 bits (359), Expect = 7e-39
Identities = 100/319 (31%), Positives = 152/319 (47%), Gaps = 17/319 (5%)
Query: 39 PFKYNWAWDRYLSSCANHWMPQEINMQRDIELWKNPIGLTEEERRLVKRNLGFFSTADSL 98
PF Y WA D + HW+ EI++ D+ WKN +T+ E+ + L F+ +D
Sbjct: 102 PFNYPWAVDLTVKHEKAHWIEDEIDLSEDVTDWKNG-KITKVEKEYITNILRLFTQSDVA 160
Query: 99 AANNIVLGTYRHITAPECRQYLLRQAFEEAIHTHAYQYIVESLGLDELEIFNAYHEIKSI 158
N E R L A E IH AY + ++LGL + E ++A+ E K++
Sbjct: 161 VGQNYYDQFIPLFKNNEIRNMLGSFAAREGIHQRAYALLNDTLGLPDSE-YHAFLEYKAM 219
Query: 159 RDKDEFLIPFIDVLTDLKFKTGNTKNDQKLLKSLIVFACIMEGLFFYVGFVQILALGRQN 218
DK +F++ T+ L + VF EG+ + F +L R
Sbjct: 220 TDKIDFMMD----------ADPTTRRGLGLCLAKTVFN---EGVALFASFAMLLNFQRFG 266
Query: 219 KMIGSSELYQYILRDESMHCNFGIDLINTIKMENPNLWTTEFCKEIEQLFLKAIELEYYY 278
KM G ++ ++ +RDESMH L ENP + EF KEI + KA+ELE +
Sbjct: 267 KMKGMGKVVEWSIRDESMHVEGNAALFRIYCQENPYIVDNEFKKEIYLMASKAVELEDRF 326
Query: 279 AEDTMPKG-ILGLNVKTFKSYLRFIANCRMKQIGIKQIFPYERNPFPWMSEMIHIKKESN 337
E G I GL K Y+R I + R+ Q+G+K+I+ E+NP W+ +++ +N
Sbjct: 327 IELAYELGTIEGLKADEVKQYIRHITDRRLNQLGLKEIYNIEKNPLTWLEWILNGADHTN 386
Query: 338 FFETRVMEYQSGG-TLDWE 355
FFE RV EY+ G T W+
Sbjct: 387 FFENRVTEYEVAGLTGSWD 405
>gnl|CDD|144013 pfam00268, Ribonuc_red_sm, Ribonucleotide reductase, small chain.
Length = 281
Score = 137 bits (348), Expect = 2e-38
Identities = 80/293 (27%), Positives = 134/293 (45%), Gaps = 28/293 (9%)
Query: 39 PFKYNWAWDRYLSSCANHWMPQEINMQRDIELWKNPIGLTEEERRLVKRNLGFFSTADSL 98
P ++ W+ Y + AN W+ +E+++ +DI W+ L E ER F + AD +
Sbjct: 13 PIQHPDIWELYKKAEANRWLAEEVDLSKDIPDWEK---LNEAEREFYSFVFAFLAAADGI 69
Query: 99 AANNIVLGTYRHITAPECRQYLLRQAFEEAIHTHAYQYIVESLGLDELE---IFNAYHEI 155
N+ + Y Q E +H+ Y I +L DE E FNA
Sbjct: 70 VNENLAERLSAEFQQKDILHYYGEQIAIENVHSEVYSLIQLTLFNDEKERDAYFNAIETD 129
Query: 156 KSIRDKDEFLIPFIDVLTDLKFKTGNTKNDQKLLKSLIVFACIMEGLFFYVGFVQILALG 215
+I+ K ++L+ ++ + + L + LI FA + EG+FF F I L
Sbjct: 130 PAIQRKAQWLLRWVR-------------DAESLAEKLIAFALV-EGIFFSSSFASIAYLR 175
Query: 216 RQNKMIGSSELYQYILRDESMHCNFGIDLINT-IKMENPNLWTTEFCKEIEQLFLKAIEL 274
++ M G+ + + I RDE++H + L N + +E P K I +LF +A+E+
Sbjct: 176 KRGLMPGTCQSNELISRDEALHTDAACLLYNNYLGLEKPEP------KRIYKLFREAVEI 229
Query: 275 EYYYAEDTMPKGILGLNVKTFKSYLRFIANCRMKQIGIKQIFPYERNPFPWMS 327
E + E P + G+NV+ K Y+ F A+ + IG K +F NPF ++
Sbjct: 230 EIEFIEAAAPVDVHGMNVRAIKQYIEFSADRLLVAIGYKPLFNVP-NPFFPLA 281
>gnl|CDD|215272 PLN02492, PLN02492, ribonucleoside-diphosphate reductase.
Length = 324
Score = 134 bits (338), Expect = 2e-36
Identities = 89/320 (27%), Positives = 160/320 (50%), Gaps = 35/320 (10%)
Query: 37 LVPFKYNWAWDRYLSSCANHWMPQEINMQRDIELWKNPIGLTEEERRLVKRNLGFFSTAD 96
+ P KY W+ Y + A+ W +E+++ D++ W+ LT++ER + L FF+ +D
Sbjct: 13 MFPIKYPQIWEMYKKAEASFWTAEEVDLSADLKDWEK---LTDDERHFISHVLAFFAASD 69
Query: 97 SLAANNIVLGTYRHITAPECRQYLLRQAFEEAIHTHAYQYIVESLGLDELE---IFNAYH 153
+ N+ + + PE R + Q E IH+ Y ++++ D E +FNA
Sbjct: 70 GIVLENLAARFMKEVQVPEARAFYGFQIAIENIHSEMYSLLLDTYIKDPKEKDRLFNAIE 129
Query: 154 EIKSIRDKDEFLIPFIDVLTDLKFKTGNTKNDQKLLKSLIVFACIMEGLFFYVGFVQILA 213
I + K ++ + +ID + + L+ FAC+ EG+FF F I
Sbjct: 130 TIPCVAKKADWALRWID-------------SSASFAERLVAFACV-EGIFFSGSFCAIFW 175
Query: 214 LGRQNKMIG---SSELYQYILRDESMHCNFGIDLINTIKMENPNLWTTEFCKEIEQLFLK 270
L ++ M G S+EL I RDE +HC+F L + ++N ++++ +
Sbjct: 176 LKKRGLMPGLTFSNEL---ISRDEGLHCDFACLLYS--LLKNKLSEE-----RVKEIVCE 225
Query: 271 AIELEYYYAEDTMPKGILGLNVKTFKSYLRFIANCRMKQIGIKQIFPYERNPFPWMSEMI 330
A+E+E + D +P ++G+N Y+ F+A+ + +G ++++ NPF WM E+I
Sbjct: 226 AVEIEKEFVCDALPCALVGMNADLMSQYIEFVADRLLVALGYEKVYNVV-NPFDWM-ELI 283
Query: 331 HIKKESNFFETRVMEYQSGG 350
++ ++NFFE RV EYQ G
Sbjct: 284 SLQGKTNFFEKRVGEYQKAG 303
>gnl|CDD|181647 PRK09101, nrdB, ribonucleotide-diphosphate reductase subunit beta;
Reviewed.
Length = 376
Score = 86.6 bits (215), Expect = 5e-19
Identities = 72/295 (24%), Positives = 135/295 (45%), Gaps = 32/295 (10%)
Query: 57 WMPQEINMQRDIELWKNPIGLTEEERRLVKRNLGFFSTADSLAAN--NIVLGTYRHITAP 114
W P+E+++ RD ++ L E E+ + NL + + DS+ N+ L ++ P
Sbjct: 49 WRPEEVDVSRDRIDYQA---LPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPL--VSIP 103
Query: 115 ECRQYLLRQAFEEAIHTHAYQYIVESLGLDELEIFNAYHEIKSIRDKDEFLIPFIDVLTD 174
E ++ +F E IH+ +Y +I+ ++ D +F+ + I + + + + D L +
Sbjct: 104 ELETWIETWSFSETIHSRSYTHIIRNIVNDPSVVFDDIVTNEEILKRAKDISSYYDDLIE 163
Query: 175 LK-----FKTGNTKNDQK--------LLKSLIVFACIM-----EGLFFYVGFVQILALGR 216
+ G + K L K L + C+M E + FYV F A
Sbjct: 164 MTSYYHLLGEGTHTVNGKTVTVSLRELKKKL--YLCLMSVNALEAIRFYVSFACSFAFAE 221
Query: 217 QNKMIGSSELYQYILRDESMHCNFGIDLINTIKMENPNLWTTEFCKEIEQ----LFLKAI 272
+ M G++++ + I RDE++H ++N ++ + E +E +Q LF++A
Sbjct: 222 RELMEGNAKIIRLIARDEALHLTGTQHMLNLMRSGKDDPEMAEIAEECKQECYDLFVQAA 281
Query: 273 ELEYYYAEDTMPKG-ILGLNVKTFKSYLRFIANCRMKQIGIKQIFPYERNPFPWM 326
E E +A+ G ++GLN Y+ +I N RM+ +G+ F NP PW+
Sbjct: 282 EQEKEWADYLFKDGSMIGLNKDILCQYVEYITNIRMQAVGLDLPFQTRSNPIPWI 336
>gnl|CDD|213892 TIGR04171, RNR_1b_NrdF, ribonucleoside-diphosphate reductase, class
1b, beta subunit. Members of this family are NrdF, the
beta subunit of class 1b ribonucleotide reductase. This
form uses a dimanganese moiety associated with a
tyrosine radical to reduce the cellular requirement for
iron [Purines, pyrimidines, nucleosides, and
nucleotides, 2'-Deoxyribonucleotide metabolism].
Length = 313
Score = 67.6 bits (166), Expect = 1e-12
Identities = 69/282 (24%), Positives = 118/282 (41%), Gaps = 38/282 (13%)
Query: 46 WDRYLSSCANHWMPQEINMQRDIELWKNPIGLTEEERRLVKRNLGFFSTADSLAANNIVL 105
W++ S W+P+EI + D++ W+ L+ EE+ L K+ G + D+L +
Sbjct: 18 WEQNTS---QFWLPEEIPLSNDLDSWRT---LSPEEQDLYKKVFGGLTLLDTLQGTVGMP 71
Query: 106 GTYRHITAPECRQYLLRQAFEEAIHTHAYQYIVESLGLDELEIFNAYHEIKSIRDKDEFL 165
+ L F E++H +Y I +L EI A+ + + +E+
Sbjct: 72 ALIPDADTLHEKAVLNNMGFMESVHAKSYSSIFSTL-CTTEEIDEAFRWV----ENNEY- 125
Query: 166 IPFIDVLTDLKFKTG---NTKNDQKLLKSLI--VFACIMEGLFFYVGFVQILALGRQNKM 220
L+ K + + LK+ + VF +E FY GF L L Q K+
Sbjct: 126 ---------LQKKAKKILDYYQNDDPLKAKVASVF---LESFLFYSGFYLPLYLAGQGKL 173
Query: 221 IGSSELYQYILRDESMHCNFGIDLINTIKMEN-PNLWTTEFCKEIEQLFLKAIELEYYYA 279
S+E+ + I+RDES+H + I E + L + E E Y
Sbjct: 174 TNSAEIIRLIIRDESIHGVY-IGYKAQEGYNKLSEEEQEELKDWMYDLLYELYENEEKYT 232
Query: 280 EDTMPKGILGL--NVKTFKSYLRFIANCRMKQIGIKQIFPYE 319
E+ + +GL +VK F +R+ AN + +G + +FP E
Sbjct: 233 EELYDE--VGLTEDVKKF---VRYNANKALMNLGFEPLFPEE 269
>gnl|CDD|140022 PRK13966, nrdF2, ribonucleotide-diphosphate reductase subunit beta;
Provisional.
Length = 324
Score = 61.7 bits (149), Expect = 1e-10
Identities = 74/334 (22%), Positives = 135/334 (40%), Gaps = 45/334 (13%)
Query: 35 NQLVPFKYNWAWDRYLSSCANHWMPQEINMQRDIELWKNPIGLTEEERRLVKRNLGFFST 94
N+L K WDR N W+P+++ + DI W LT E++L R +
Sbjct: 17 NRLQDEKDAEVWDRL---TGNFWLPEKVPVSNDIPSWGT---LTAGEKQLTMRVFTGLTM 70
Query: 95 ADSLAANNIVLGTYRHITAPECRQYLLRQAFEEAIHTHAYQYIVESLGLDELEIFNAY-- 152
D++ + P L AF E++H +Y I +L EI +A+
Sbjct: 71 LDTIQGTVGAVSLIPDALTPHEEAVLTNIAFMESVHAKSYSQIFSTL-CSTAEIDDAFRW 129
Query: 153 -HEIKSIRDKDEFLIPFIDVLTDLKFKTGNTKNDQKLLKSLIVFACIMEGLFFYVGFVQI 211
E ++++ K E ++ + LK K +T ++E FY GF
Sbjct: 130 SEENRNLQRKAEIVLQYYRGDEPLKRKVAST---------------LLESFLFYSGFYLP 174
Query: 212 LALGRQNKMIGSSELYQYILRDESMHCNF-------GIDLINTIKMENPNLWTTEFCKEI 264
+ + K+ ++++ + I+RDE++H + G+ L++ + +T E
Sbjct: 175 MYWSSRAKLTNTADMIRLIIRDEAVHGYYIGYKFQRGLALVDDVTRAELKDYTYE----- 229
Query: 265 EQLFLKAIELEYYYAEDTMPKGILGLNVKTFKSYLRFIANCRMKQIGIKQIFPYER---N 321
L + + E Y +D + L +VK F LR+ AN + +G + +FP + N
Sbjct: 230 --LLFELYDNEVEYTQDLYDEVGLTEDVKKF---LRYNANKALMNLGYEALFPRDETDVN 284
Query: 322 PFPWMSEMIHIKKESNFFETRVMEYQSGGTLDWE 355
P + + + +FF Y G + E
Sbjct: 285 PAILSALSPNADENHDFFSGSGSSYVIGKAVVTE 318
>gnl|CDD|184425 PRK13965, PRK13965, ribonucleotide-diphosphate reductase subunit
beta; Provisional.
Length = 335
Score = 61.3 bits (149), Expect = 2e-10
Identities = 59/284 (20%), Positives = 109/284 (38%), Gaps = 42/284 (14%)
Query: 46 WDRYLSSCANHWMPQEINMQRDIELWKNPIGLTEEERRLVKRNLGFFSTADSLAANNIVL 105
W+R N W+P+++ + D+ W+ L E+ ++L+ R + D++ A +
Sbjct: 39 WNRVTQ---NFWLPEKVPVSNDLNSWR---SLGEDWQQLITRTFTGLTLLDTVQATVGDV 92
Query: 106 GTYRHITAPECRQYLLRQAFEEAIHTHAYQYIVESLGLDELEIFNAYH---EIKSIRDKD 162
H + AF AIH +Y I +L E +I A+ +S++ +
Sbjct: 93 AQIPHSQTDHEQVIYTNFAFMVAIHARSYGTIFSTLCSSE-QIEEAHEWVVSTESLQRRA 151
Query: 163 EFLIPFIDVLTDLKFKTGNTKNDQKLLKSLIVFACIMEGLFFYVGFVQILALGRQNKMIG 222
LIP+ LK K V A +M G Y GF L + K+
Sbjct: 152 RVLIPYYTGDDPLKSK---------------VAAAMMPGFLLYGGFYLPFYLSARGKLPN 196
Query: 223 SSELYQYILRDESMHCNF-------GIDLINTIKMENPNLWTTEFCKEIEQLFLKAIELE 275
+S++ + ILRD+ +H + + ++ K + + E+ I+LE
Sbjct: 197 TSDIIRLILRDKVIHNYYSGYKYQQKVARLSPEKQAEMKAFVFDLLYEL-------IDLE 249
Query: 276 YYYAEDTMPKGILGLNVKTFKSYLRFIANCRMKQIGIKQIFPYE 319
Y + L + F + A ++ +G + F E
Sbjct: 250 KAYLRELYAGFDLAEDAIRF---SLYNAGKFLQNLGYESPFTEE 290
>gnl|CDD|236242 PRK08326, PRK08326, ribonucleotide-diphosphate reductase subunit
beta; Validated.
Length = 311
Score = 59.6 bits (145), Expect = 4e-10
Identities = 66/302 (21%), Positives = 115/302 (38%), Gaps = 45/302 (14%)
Query: 30 GHTDVNQLVPFKYNWAWDRY---LSSCANH--WMPQEINMQRDIELWKNPIGLTEEERRL 84
HTD L NW + + L + N W P +I+ RD E W+ L++EER
Sbjct: 9 VHTDFKSLRSGGLNW--NSFPMKLFAKGNAKFWNPADIDFSRDAEDWE---KLSDEERDY 63
Query: 85 VKRNLGFFSTADSLAANNIVLGTYRHITAPECR----QYLLRQAFEEAIHTHAYQYIVES 140
R F + +I A E R YL + AFEEA HT A++ ++
Sbjct: 64 ATRLCAQFIAGEEAVTLDIQ--PLISAMAAEGRLEDEMYLTQFAFEEAKHTEAFRRWFDA 121
Query: 141 LGLDE-LEIF----NAYHEIKSIRDKDEFLIPFIDVLTDLKFKTGNTKNDQKLLKSLIVF 195
+G+ E L ++ +Y +I F + L + + + +++ + +
Sbjct: 122 VGVTEDLSVYTDDNPSYRQI------------FYEELPAALNRLSTDPSPENQVRASVTY 169
Query: 196 ACIMEG---LFFYVGFVQILALGRQNKMIGSSELYQYILRDESMHCNFGIDLINTIKMEN 252
++EG Y + +I + + G EL + I DE H +G + +
Sbjct: 170 NHVVEGVLAETGYYAWRKI--CVTRGILPGLQELVRRIGDDERRHIAWGTYTCRRLVAAD 227
Query: 253 PNLWTTEFCKEIEQLFLKA---IELEYYYAEDTMPKGILGLNVKTFKSYLRFIANCRMKQ 309
+ W F + + +L A I+ + D +P L+ F Y R+
Sbjct: 228 DSNW-DVFEERMNELLPLALGLIDEIFALYGDQIP---FELSNDEFVDYAADRGQRRLGA 283
Query: 310 IG 311
I
Sbjct: 284 IE 285
>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 = 54.7 bits (132), Expect = 2e-08
Identities = 58/265 (21%), Positives = 99/265 (37%), Gaps = 31/265 (11%)
Query: 57 WMPQEINMQRDIELWKNPIGLTEEERRLVKRNLGFFSTADSLAANNIVLGTYRHITAPEC 116
W P +I+ +D E W+ L+EEER L R F + A + L A E
Sbjct: 22 WNPADIDFSQDREDWE---QLSEEERDLALRLCAGFIAGEE--AVTLDLLPLMMAMAAEG 76
Query: 117 R----QYLLRQAFEEAIHTHAYQYIVESLGL-DELEIFNAYHEIKSIRDKDEFLIPFIDV 171
R YL + FEEA HT ++ ++++G+ D+L + ++ F
Sbjct: 77 RLEEEMYLTQFLFEEAKHTDFFRRWLDAVGVSDDLSDLHTAV------YREPFYEALPYA 130
Query: 172 LTDLKFKTGNTKNDQKLLKSLIVFACIMEG---LFFYVGFVQILALGRQNKMIGSSELYQ 228
L + +++ + + I+EG Y + I ++ + G E +
Sbjct: 131 ELRLY----LDASPAAQVRASVTYNMIVEGVLAETGYYAWRTICE--KRGILPGMQEGIR 184
Query: 229 YILRDESMHCNFGIDLINTIKMENPNLWTTEFCKEIEQLFLKAIELEYYYAE--DTMPKG 286
+ DES H +G + + W F + + +L A+ L E D MP
Sbjct: 185 RLGDDESRHIAWGTFTCRRLVAADDANWDV-FEERMNELVPHALGLIDEIFELYDEMPF- 242
Query: 287 ILGLNVKTFKSYLRFIANCRMKQIG 311
GL+ Y R+ I
Sbjct: 243 --GLDPDELMQYAVDQFQRRLGYIE 265
>gnl|CDD|140023 PRK13967, nrdF1, ribonucleotide-diphosphate reductase subunit beta;
Provisional.
Length = 322
Score = 53.6 bits (128), Expect = 5e-08
Identities = 61/314 (19%), Positives = 122/314 (38%), Gaps = 61/314 (19%)
Query: 18 ERINKINKQIINGHTDVNQLVPFKYNWAWDRYLSSCANHWMPQEINMQRDIELWKNPIGL 77
ER++ IN N+L+ K W+R N W+P++I + D+ W+ L
Sbjct: 7 ERVHAIN---------WNRLLDAKDLQVWERL---TGNFWLPEKIPLSNDLASWQT---L 51
Query: 78 TEEERRLVKRNLGFFSTADSLAANNIVLGTYRHITAPECRQYLLRQAFEEAIHTHAYQYI 137
+ E++ R + D+ A + P L AF E++H +Y I
Sbjct: 52 SSTEQQTTIRVFTGLTLLDTAQATVGAVAMIDDAVTPHEEAVLTNMAFMESVHAKSYSSI 111
Query: 138 VESLGLDEL--EIFNAYHEIKSIRDKDEFLIPFIDVLTDLKFKTGNTKNDQKLLKSLIVF 195
+L + + F+ + ++ K + ++ + LK K +
Sbjct: 112 FSTLCSTKQIDDAFDWSEQNPYLQRKAQIIVDYYRGDDALKRKASSV------------- 158
Query: 196 ACIMEGLFFYVGFVQILALGRQNKMIGSSELYQYILRDESMH-------CNFGIDLINTI 248
++E FY GF + + K+ +++L + I+RDE++H C G+ +
Sbjct: 159 --MLESFLFYSGFYLPMYWSSRGKLTNTADLIRLIIRDEAVHGYYIGYKCQRGLADLTDA 216
Query: 249 KMENPNLWTTEFCKEIEQLFLKAIEL------EYYYAEDTMPKGILGLNVKTFKSYLRFI 302
+ + +T C+ + L+ I+ E + +D +P Y+R+
Sbjct: 217 ERADHREYT---CELLHTLYANEIDYAHDLYDELGWTDDVLP-------------YMRYN 260
Query: 303 ANCRMKQIGIKQIF 316
AN + +G + F
Sbjct: 261 ANKALANLGYQPAF 274
>gnl|CDD|165536 PHA03279, PHA03279, envelope glycoprotein K; Provisional.
Length = 361
Score = 30.4 bits (68), Expect = 1.4
Identities = 24/118 (20%), Positives = 37/118 (31%), Gaps = 26/118 (22%)
Query: 197 CIMEGLFFYVGFVQILALGRQNKMIGSSELYQYILRDESMHCNFGIDLINTIKMENPNLW 256
C + + F LA Q + G LR ++ H N+ + ++ P L
Sbjct: 151 CASAAILHMLAF---LADNCQRRGFGPWLCRANALRADAYHLNYWTAFAARLFLKVPYLK 207
Query: 257 TTEFCKEIEQ-----------------------LFLKAIELEYYYAEDTMPKGILGLN 291
F +E E L LKAIE+ Y+A L +
Sbjct: 208 LQRFLREFEHRRDCKSLNFSADPLGFCICHPGALLLKAIEIGLYFASLIASAMTLRIC 265
>gnl|CDD|232945 TIGR00376, TIGR00376, DNA helicase, putative. The gene product may
represent a DNA helicase. Eukaryotic members of this
family have been characterized as binding certain
single-stranded G-rich DNA sequences (GGGGT and GGGCT).
A number of related proteins are characterized as
helicases [DNA metabolism, DNA replication,
recombination, and repair].
Length = 637
Score = 30.2 bits (68), Expect = 1.7
Identities = 32/137 (23%), Positives = 55/137 (40%), Gaps = 25/137 (18%)
Query: 65 QRDIELWKNPIG------LTEEERRLVKRNLGFFSTADS-LAANNIVLGTYRHITAPECR 117
+D+ L P G L E R+LVKR L TA S +A +N++ C
Sbjct: 172 SKDLFLIHGPPGTGKTRTLVELIRQLVKRGLRVLVTAPSNIAVDNLLERL------ALCD 225
Query: 118 QYLLR----QAFEEAIHTHAYQYIVESLGLDELEIFNAYHEIKSIRDKDEFLIPFIDVLT 173
Q ++R ++ H+ Y++E+ Y + IR+K + LI +
Sbjct: 226 QKIVRLGHPARLLKSNKQHSLDYLIEN--------HPKYQIVADIREKIDELIEERNKKL 277
Query: 174 DLKFKTGNTKNDQKLLK 190
+ +D K+L+
Sbjct: 278 KPSPQKRRGLSDIKILR 294
>gnl|CDD|206775 cd11370, RNase_PH_RRP41, RRP41 subunit of eukaryotic exosome. The
RRP41 subunit of eukaryotic exosome is a member of the
RNase_PH family, named after the bacterial Ribonuclease
PH, a 3'-5' exoribonuclease. Structurally all members of
this family form hexameric rings (trimers of
Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The
eukaryotic exosome core is composed of six individually
encoded RNase PH-like subunits and three additional
proteins (Rrp4, Csl4 and Rrp40) that form a stable cap
and contain RNA-binding domains. The RNase PH-like
subunits are no longer phosphorolytic enzymes, the
exosome directly associates with Rrp44 and Rrp6,
hydrolytic exoribonucleases related to bacterial RNase
II/R and RNase D. The exosome plays an important role in
RNA turnover. It plays a crucial role in the maturation
of stable RNA species such as rRNA, snRNA and snoRNA,
quality control of mRNA, and the degradation of RNA
processing by-products and non-coding transcripts.
Length = 226
Score = 29.4 bits (67), Expect = 2.3
Identities = 8/15 (53%), Positives = 9/15 (60%)
Query: 120 LLRQAFEEAIHTHAY 134
+RQ FE I TH Y
Sbjct: 91 AIRQTFEAVILTHLY 105
>gnl|CDD|153097 cd00657, Ferritin_like, Ferritin-like superfamily of
diiron-containing four-helix-bundle proteins.
Ferritin-like, diiron-carboxylate proteins participate
in a range of functions including iron regulation,
mono-oxygenation, and reactive radical production. These
proteins are characterized by the fact that they
catalyze dioxygen-dependent oxidation-hydroxylation
reactions within diiron centers; one exception is
manganese catalase, which catalyzes peroxide-dependent
oxidation-reduction within a dimanganese center.
Diiron-carboxylate proteins are further characterized by
the presence of duplicate metal ligands, glutamates and
histidines (ExxH) and two additional glutamates within a
four-helix bundle. Outside of these conserved residues
there is little obvious homology. Members include
bacterioferritin, ferritin, rubrerythrin, aromatic and
alkene monooxygenase hydroxylases (AAMH), ribonucleotide
reductase R2 (RNRR2), acyl-ACP-desaturases
(Acyl_ACP_Desat), manganese (Mn) catalases,
demethoxyubiquinone hydroxylases (DMQH), DNA protecting
proteins (DPS), and ubiquinol oxidases (AOX), and the
aerobic cyclase system, Fe-containing subunit (ACSF).
Length = 130
Score = 28.2 bits (63), Expect = 3.1
Identities = 10/34 (29%), Positives = 13/34 (38%)
Query: 109 RHITAPECRQYLLRQAFEEAIHTHAYQYIVESLG 142
P+ + LL A EE H A + LG
Sbjct: 22 ARAPDPDLKDELLEIADEERRHADALAERLRELG 55
>gnl|CDD|149395 pfam08321, PPP5, PPP5 TPR repeat region. This region is specific
to the PPP5 subfamily of serine/threonine phosphatases
and contains TPR repeats.
Length = 95
Score = 27.7 bits (62), Expect = 3.2
Identities = 11/39 (28%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 115 ECRQYLLRQAFEEAIHT-HAYQYIVESLGLDELEIFNAY 152
EC + + + AFEEAI + + +S+ ++ + I + Y
Sbjct: 4 ECEKLVKQIAFEEAIAVPEQKRSVADSIDIENMTIEDDY 42
>gnl|CDD|130737 TIGR01676, GLDHase, galactonolactone dehydrogenase. This model
represents L-Galactono-gamma-lactone dehydrogenase (EC
1.3.2.3). This enzyme catalyzes the final step in
ascorbic acid biosynthesis in higher plants. This
protein is homologous to ascorbic acid biosynthesis
enzymes of other species: L-gulono-gamma-lactone oxidase
in rat and L-galactono-gamma-lactone oxidase in yeast.
All three covalently bind the cofactor FAD.
Length = 541
Score = 29.3 bits (65), Expect = 3.4
Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 7/86 (8%)
Query: 81 ERRLVKRNLGFFSTADSLAANNIV--LGTYRHITAPECRQYLLRQAFEEAIHTHAYQYIV 138
E+R + S A S A ++I +G ++ + RQ ++ EE H Y+++
Sbjct: 422 EQRWTACSKSPMSPASSSADDDIFSWVGIIMYLPTMDARQR--KEITEEFFH---YRHLT 476
Query: 139 ESLGLDELEIFNAYHEIKSIRDKDEF 164
++L D F + +I+ +DKDE
Sbjct: 477 QALLWDHFSAFEHWAKIEVPKDKDEL 502
>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 = 27.3 bits (60), Expect = 4.0
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 239 NFGIDLINTIKMENPNLWTTE 259
NF +D IN I++ENPN +
Sbjct: 26 NFSVDEINQIRVENPNSLIAQ 46
>gnl|CDD|236084 PRK07739, flgK, flagellar hook-associated protein FlgK; Validated.
Length = 507
Score = 28.1 bits (63), Expect = 9.6
Identities = 8/21 (38%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 10 KTLKINS-FERINKINKQIIN 29
+INS +I+ +NKQI
Sbjct: 176 TVKEINSLASQISDLNKQIAK 196
>gnl|CDD|227696 COG5409, COG5409, EXS domain-containing protein [Signal
transduction mechanisms].
Length = 384
Score = 27.8 bits (62), Expect = 9.8
Identities = 16/55 (29%), Positives = 21/55 (38%), Gaps = 8/55 (14%)
Query: 168 FIDVLTDLKFKTGNTKNDQKLLK--------SLIVFACIMEGLFFYVGFVQILAL 214
FI + L N D + SL +F +EGL F + FV L L
Sbjct: 69 FIFLFEQLSSTARNFNLDFHRIIIPFHFFTTSLFIFLNAVEGLKFILLFVYFLPL 123
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.323 0.139 0.421
Gapped
Lambda K H
0.267 0.0758 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,452,194
Number of extensions: 1811254
Number of successful extensions: 1690
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1647
Number of HSP's successfully gapped: 41
Length of query: 355
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 257
Effective length of database: 6,590,910
Effective search space: 1693863870
Effective search space used: 1693863870
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 60 (26.8 bits)