RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 040427
(329 letters)
>gnl|CDD|215272 PLN02492, PLN02492, ribonucleoside-diphosphate reductase.
Length = 324
Score = 710 bits (1834), Expect = 0.0
Identities = 279/324 (86%), Positives = 296/324 (91%), Gaps = 1/324 (0%)
Query: 7 EPLLAPNPDRFCMFPIQYPQIWEMYKKAEASFWTAEEVDLSQDLRHWEALTADEKHFVTH 66
EPLLA NPDRFCMFPI+YPQIWEMYKKAEASFWTAEEVDLS DL+ WE LT DE+HF++H
Sbjct: 1 EPLLAENPDRFCMFPIKYPQIWEMYKKAEASFWTAEEVDLSADLKDWEKLTDDERHFISH 60
Query: 67 VLAFFAASDGIVLENLAGRFMTEVQVAEARAFYGFQIAIENIHSEMYSLLLETYIKDSDE 126
VLAFFAASDGIVLENLA RFM EVQV EARAFYGFQIAIENIHSEMYSLLL+TYIKD E
Sbjct: 61 VLAFFAASDGIVLENLAARFMKEVQVPEARAFYGFQIAIENIHSEMYSLLLDTYIKDPKE 120
Query: 127 KNRLFHAIETVPCVAKKATWALNWIDGSETFAERLIAFACVEGIFFSGSFCAIFWLKKRG 186
K+RLF+AIET+PCVAKKA WAL WID S +FAERL+AFACVEGIFFSGSFCAIFWLKKRG
Sbjct: 121 KDRLFNAIETIPCVAKKADWALRWIDSSASFAERLVAFACVEGIFFSGSFCAIFWLKKRG 180
Query: 187 LMPGLTFSNELISRDEGLHCDFACLLYSLLRTKLSEERVKALVKEAVEIEREFVCDALPC 246
LMPGLTFSNELISRDEGLHCDFACLLYSLL+ KLSEERVK +V EAVEIE+EFVCDALPC
Sbjct: 181 LMPGLTFSNELISRDEGLHCDFACLLYSLLKNKLSEERVKEIVCEAVEIEKEFVCDALPC 240
Query: 247 ALVGMNGELMSQYIEFVADRLLGALGYGKLYGVANPFDWMELISLQGKTNFFEKRVGEYQ 306
ALVGMN +LMSQYIEFVADRLL ALGY K+Y V NPFDWMELISLQGKTNFFEKRVGEYQ
Sbjct: 241 ALVGMNADLMSQYIEFVADRLLVALGYEKVYNVVNPFDWMELISLQGKTNFFEKRVGEYQ 300
Query: 307 KASVMSSLNGN-GGNHVFKIDEDF 329
KA VMSSLNG NHVF +DEDF
Sbjct: 301 KAGVMSSLNGGGADNHVFSLDEDF 324
>gnl|CDD|240315 PTZ00211, PTZ00211, ribonucleoside-diphosphate reductase small
subunit; Provisional.
Length = 330
Score = 600 bits (1549), Expect = 0.0
Identities = 240/324 (74%), Positives = 269/324 (83%), Gaps = 4/324 (1%)
Query: 6 EEPLLAPNPDRFCMFPIQYPQIWEMYKKAEASFWTAEEVDLSQDLRHWEALTADEKHFVT 65
EEPLL NPDRF +FPI+YP IW MYKKAEASFWTAEE+DL DL+ WE L E+HF+
Sbjct: 11 EEPLLKENPDRFVLFPIKYPDIWRMYKKAEASFWTAEEIDLGNDLKDWEKLNDGERHFIK 70
Query: 66 HVLAFFAASDGIVLENLAGRFMTEVQVAEARAFYGFQIAIENIHSEMYSLLLETYIKDSD 125
HVLAFFAASDGIVLENLA RFM EVQV EAR FYGFQIA+ENIHSE YSLL++TYI D +
Sbjct: 71 HVLAFFAASDGIVLENLAQRFMREVQVPEARCFYGFQIAMENIHSETYSLLIDTYITDEE 130
Query: 126 EKNRLFHAIETVPCVAKKATWALNWIDGSETFAERLIAFACVEGIFFSGSFCAIFWLKKR 185
EK+RLFHAIET+P + KKA WA WI+ S +FAERL+AFA VEGIFFSGSFCAIFWLKKR
Sbjct: 131 EKDRLFHAIETIPAIKKKAEWAAKWINSSNSFAERLVAFAAVEGIFFSGSFCAIFWLKKR 190
Query: 186 GLMPGLTFSNELISRDEGLHCDFACLLYSLLRTKLSEERVKALVKEAVEIEREFVCDALP 245
GLMPGLTFSNELISRDEGLH DFACLLYS L+ KL ERV+ ++KEAVEIEREF+CDALP
Sbjct: 191 GLMPGLTFSNELISRDEGLHTDFACLLYSHLKNKLPRERVQEIIKEAVEIEREFICDALP 250
Query: 246 CALVGMNGELMSQYIEFVADRLLGALGYGKLYGVANPFDWMELISLQGKTNFFEKRVGEY 305
L+GMN LM+QYIEFVADRLL ALG K+Y NPFDWM++ISLQGKTNFFEKRVGEY
Sbjct: 251 VDLIGMNSRLMAQYIEFVADRLLVALGVPKIYNSKNPFDWMDMISLQGKTNFFEKRVGEY 310
Query: 306 QKASVMSSLNGNGGNHVFKIDEDF 329
QKA VM+ + VF +D DF
Sbjct: 311 QKAGVMA----ERTSKVFSLDADF 330
>gnl|CDD|144013 pfam00268, Ribonuc_red_sm, Ribonucleotide reductase, small chain.
Length = 281
Score = 399 bits (1027), Expect = e-141
Identities = 156/283 (55%), Positives = 192/283 (67%), Gaps = 4/283 (1%)
Query: 7 EPLLAPNPDRFCMFPIQYPQIWEMYKKAEASFWTAEEVDLSQDLRHWEALTADEKHFVTH 66
EPLL N RF +PIQ+P IWE+YKKAEA+ W AEEVDLS+D+ WE L E+ F +
Sbjct: 1 EPLLRENSKRF--YPIQHPDIWELYKKAEANRWLAEEVDLSKDIPDWEKLNEAEREFYSF 58
Query: 67 VLAFFAASDGIVLENLAGRFMTEVQVAEARAFYGFQIAIENIHSEMYSLLLETYIKDSDE 126
V AF AA+DGIV ENLA R E Q + +YG QIAIEN+HSE+YSL+ T D E
Sbjct: 59 VFAFLAAADGIVNENLAERLSAEFQQKDILHYYGEQIAIENVHSEVYSLIQLTLFNDEKE 118
Query: 127 KNRLFHAIETVPCVAKKATWALNWIDGSETFAERLIAFACVEGIFFSGSFCAIFWLKKRG 186
++ F+AIET P + +KA W L W+ +E+ AE+LIAFA VEGIFFS SF +I +L+KRG
Sbjct: 119 RDAYFNAIETDPAIQRKAQWLLRWVRDAESLAEKLIAFALVEGIFFSSSFASIAYLRKRG 178
Query: 187 LMPGLTFSNELISRDEGLHCDFACLLYS--LLRTKLSEERVKALVKEAVEIEREFVCDAL 244
LMPG SNELISRDE LH D ACLLY+ L K +R+ L +EAVEIE EF+ A
Sbjct: 179 LMPGTCQSNELISRDEALHTDAACLLYNNYLGLEKPEPKRIYKLFREAVEIEIEFIEAAA 238
Query: 245 PCALVGMNGELMSQYIEFVADRLLGALGYGKLYGVANPFDWME 287
P + GMN + QYIEF ADRLL A+GY L+ V NPF +
Sbjct: 239 PVDVHGMNVRAIKQYIEFSADRLLVAIGYKPLFNVPNPFFPLA 281
>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 = 388 bits (998), Expect = e-136
Identities = 165/289 (57%), Positives = 196/289 (67%), Gaps = 15/289 (5%)
Query: 17 FCMFPIQYPQIWEMYKKAEASFWTAEEVDLSQDLRHWEALTADEKHFVTHVLAFFAASDG 76
F + PI+YP WE+YKKAEA+FWT EE+DLS+DL+ WE LT E+HF+ VLAF AA D
Sbjct: 1 FNLNPIKYPWAWELYKKAEANFWTPEEIDLSKDLKDWEKLTEAERHFIKRVLAFLAALDS 60
Query: 77 IVLENLAGRFMTEVQVAEARAFYGFQIAIENIHSEMYSLLLETYIKDSDEKNRLFHAIET 136
IV ENL F VQ+ EARAFYGFQ +ENIHSE YS +L+T KD E++ LF AIET
Sbjct: 61 IVGENLVELFSRHVQIPEARAFYGFQAFMENIHSESYSYILDTLGKDE-ERDELFEAIET 119
Query: 137 VPCVAKKATWALNWIDGS-----ETFAERLIAFACVEGIFFSGSFCAIFWLKKRGLMPGL 191
P + KKA W L W D E+FAERL+AFA +EGIFF F AIFWL +RG MPGL
Sbjct: 120 DPALKKKADWILRWYDNLDDNTKESFAERLVAFAILEGIFFYSGFAAIFWLARRGKMPGL 179
Query: 192 TFSNELISRDEGLHCDFACLLYSLLR-------TKLSEERVKALVKEAVEIEREFVCDAL 244
ELISRDE LH DFACLL L T+ +E V L+KEAVE+E+EF D L
Sbjct: 180 AEIIELISRDESLHGDFACLLIRELLNENPELFTEEFKEEVYELIKEAVELEKEFARDLL 239
Query: 245 PCALVGMNGELMSQYIEFVADRLLGALGYGKLYGVA--NPFDWMELISL 291
P ++G+N E M QYIE+VA+R L LG KL+ V NPFDWMELIS
Sbjct: 240 PDGILGLNKEDMKQYIEYVANRRLENLGLEKLFNVEDKNPFDWMELISD 288
>gnl|CDD|223286 COG0208, NrdF, Ribonucleotide reductase, beta subunit [Nucleotide
transport and metabolism].
Length = 348
Score = 305 bits (783), Expect = e-103
Identities = 110/335 (32%), Positives = 151/335 (45%), Gaps = 19/335 (5%)
Query: 1 MPSIPEEPLLAPNPDRFCMFPIQYPQIWEMYKKAEASFWTAEEVDLSQDLRHWEALTADE 60
+ + PI+YP E+YKK A+FW EE+DLS D++ W+ L+ DE
Sbjct: 11 DELEEPKIFNGNPTNAINWNPIKYPWALELYKKLTANFWLPEEIDLSNDIKDWKKLSDDE 70
Query: 61 KHFVTHVLAFFAASDGIVLENLAGRFMTEVQVAEARAFYGFQIAIENIHSEMYSLLLETY 120
K + VLAF D I N V E A Q +E IH+ YS + +T
Sbjct: 71 KDLIIRVLAFLTLLDSIQANNGVPALSPLVTTPEEEAVLTNQAFMEAIHARSYSYIFDTL 130
Query: 121 IKDSDEKNRLFHAIETVPCVAKKATWALN--------WIDGSETFAERLIAFAC-VEGIF 171
DE + T + +KA L D E F +L+ + +EGI
Sbjct: 131 GPTEDEDEVFDDWVATNEILQEKAEIILRYYDDLGDDPDDPLEEFLLKLVVASVILEGIL 190
Query: 172 FSGSFCAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLLYSLLRTKLSEER------- 224
F F +L +RG MPG LI RDE LH F L L + E
Sbjct: 191 FYSGFAYPLYLARRGKMPGTAEIIRLIIRDEALHLYFIGYLIQRLVAENPELWTAELKDE 250
Query: 225 VKALVKEAVEIEREFVCDALPCALVGMNGELMSQYIEFVADRLLGALGYGKLYGV-ANPF 283
+ L KEAVE+E+E+ P ++G+ +L+ QYI + A++ L LG LY NP
Sbjct: 251 IYDLFKEAVELEKEYAEYLYP-GILGLTEDLVKQYIRYNANKRLQNLGLEPLYPAEENPI 309
Query: 284 DWMEL-ISLQGKTNFFEKRVGEYQKASVMSSLNGN 317
W+EL +S KT+FFE RV YQK SV S +
Sbjct: 310 PWIELSLSADEKTDFFEGRVSSYQKGSVASETEDD 344
>gnl|CDD|235968 PRK07209, PRK07209, ribonucleotide-diphosphate reductase subunit
beta; Validated.
Length = 369
Score = 176 bits (448), Expect = 2e-52
Identities = 99/321 (30%), Positives = 152/321 (47%), Gaps = 35/321 (10%)
Query: 21 PIQYPQIWEMYKKAEASFWTAEEVDLSQDLRHWE---ALTADEKHFVTHVLAFFAASDGI 77
P +Y WE Y A+ W +EV++S+D+ W+ LT DE+ V L FF+ +D +
Sbjct: 53 PFKYKWAWEKYLAGCANHWMPQEVNMSRDIALWKSPNGLTEDERRIVKRNLGFFSTADSL 112
Query: 78 VLENLAGRFMTEVQVAEARAFYGFQIAIENIHSEMYSLLLETYIKDS---DEKNRLFHAI 134
V N+ + E R + Q E IH+ Y YI +S DE +F+
Sbjct: 113 VANNIVLAIYRHITNPECRQYLLRQAFEEAIHTHAYQ-----YIVESLGLDEG-EIFNMY 166
Query: 135 ETVPCVAKKATWALNWID-------------GSETFAERLIAFACV-EGIFFSGSFCAIF 180
VP + K + + + + LIAF C+ EGIFF F I
Sbjct: 167 HEVPSIRAKDEFLIPFTRSLTDPNFKTGTPENDQKLLRNLIAFYCIMEGIFFYVGFTQIL 226
Query: 181 WLKKRGLMPGLTFSNELISRDEGLHCDFACLLYSLLR-------TKLSEERVKALVKEAV 233
L ++ M G+ + I RDE +H +F L + ++ T + ++ L+KEAV
Sbjct: 227 SLGRQNKMTGIAEQYQYILRDESMHLNFGIDLINQIKLENPHLWTAEFQAEIRELIKEAV 286
Query: 234 EIEREFVCDALPCALVGMNGELMSQYIEFVADRLLGALGYGKLY-GVANPFDWM-ELISL 291
E+E + D +P ++G+N + Y+ F+A+R L +G Y G NPF WM E+I L
Sbjct: 287 ELEYRYARDTMPRGVLGLNASMFKDYLRFIANRRLQQIGLKPQYPGTENPFPWMSEMIDL 346
Query: 292 QGKTNFFEKRVGEYQKASVMS 312
+ + NFFE RV EYQ +S
Sbjct: 347 KKEKNFFETRVIEYQTGGALS 367
>gnl|CDD|236591 PRK09614, nrdF, ribonucleotide-diphosphate reductase subunit beta;
Reviewed.
Length = 324
Score = 170 bits (434), Expect = 9e-51
Identities = 76/306 (24%), Positives = 131/306 (42%), Gaps = 23/306 (7%)
Query: 21 PIQYPQIWEMYKKAEASFWTAEEVDLSQDLRHWEALTADEKHFVTHVLAFFAASDGIVLE 80
I+ P +E +K+ A+FW EEV LS DL+ W+ L+ +EK+ T V D +
Sbjct: 16 KIEDPWDYEAWKRLTANFWLPEEVPLSNDLKDWKKLSDEEKNLYTRVFGGLTLLDTLQNN 75
Query: 81 NLAGRFMTEVQVAEARAFYGFQIAIENIHSEMYSLLLETYIKDSDEKNRLFHAIETVPCV 140
N M ++ E A +E +H++ YS + T + +E + F E P +
Sbjct: 76 NGMPNLMPDITTPEEEAVLANIAFMEAVHAKSYSYIFST-LCSPEEIDEAFEWAEENPYL 134
Query: 141 AKKATWALNWIDG--SETFAERLIAFACVEGIFFSGSFCAIFWLKKRGLMPGLTFSNELI 198
KKA ++ + + + +A +EG F F +L ++G M G + ++I
Sbjct: 135 QKKADIIQDFYEPLKKKILRKAAVASVFLEGFLFYSGFYYPLYLARQGKMTG---TAQII 191
Query: 199 S---RDEGLHCDFACLLYSLLRTKLSE-------ERVKALVKEAVEIEREFVCDALPCAL 248
RDE LH + L+ +L E + + L+ E E E + +
Sbjct: 192 RLIIRDESLHGYYIGYLFQEGLEELPELEQEELKDEIYDLLYELYENEEAYTELLYD--I 249
Query: 249 VGMNGELMSQYIEFVADRLLGALGYGKLYGVANPFD--WMELISLQG--KTNFFEKRVGE 304
VG E + +YI + A++ L LG L+ + W+ +S +FFE +
Sbjct: 250 VG-LAEDVKKYIRYNANKRLMNLGLEPLFPEEEEVNPIWLNGLSNNADENHDFFEGKGTS 308
Query: 305 YQKASV 310
Y K +
Sbjct: 309 YVKGAT 314
>gnl|CDD|139206 PRK12759, PRK12759, bifunctional
gluaredoxin/ribonucleoside-diphosphate reductase subunit
beta; Provisional.
Length = 410
Score = 108 bits (272), Expect = 9e-27
Identities = 87/312 (27%), Positives = 145/312 (46%), Gaps = 29/312 (9%)
Query: 21 PIQYPQIWEMYKKAEASFWTAEEVDLSQDLRHWE--ALTADEKHFVTHVLAFFAASDGIV 78
P YP ++ K E + W +E+DLS+D+ W+ +T EK ++T++L F SD V
Sbjct: 102 PFNYPWAVDLTVKHEKAHWIEDEIDLSEDVTDWKNGKITKVEKEYITNILRLFTQSDVAV 161
Query: 79 LENLAGRFMTEVQVAEARAFYGFQIAIENIHSEMYSLLLETY-IKDSDEKNRLFHAIETV 137
+N +F+ + E R G A E IH Y+LL +T + DS+ +HA
Sbjct: 162 GQNYYDQFIPLFKNNEIRNMLGSFAAREGIHQRAYALLNDTLGLPDSE-----YHAFLEY 216
Query: 138 PCVAKKATWALNWIDGSETFAERLIAFACVEGIFFSG-----SFCAIFWLKKRGLMPGLT 192
+ K + ++ ++ R + + +F G SF + ++ G M G+
Sbjct: 217 KAMTDKIDFMMD----ADPTTRRGLGLCLAKTVFNEGVALFASFAMLLNFQRFGKMKGMG 272
Query: 193 FSNELISRDEGLHCDFACLLYSL-------LRTKLSEERVKALVKEAVEIEREFVCDALP 245
E RDE +H + L+ + + ++ + + +AVE+E F+ A
Sbjct: 273 KVVEWSIRDESMHVEGNAALFRIYCQENPYIVDNEFKKEIYLMASKAVELEDRFIELAYE 332
Query: 246 CALV-GMNGELMSQYIEFVADRLLGALGYGKLYGV-ANPFDWMELISLQG--KTNFFEKR 301
+ G+ + + QYI + DR L LG ++Y + NP W+E I L G TNFFE R
Sbjct: 333 LGTIEGLKADEVKQYIRHITDRRLNQLGLKEIYNIEKNPLTWLEWI-LNGADHTNFFENR 391
Query: 302 VGEYQKASVMSS 313
V EY+ A + S
Sbjct: 392 VTEYEVAGLTGS 403
>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 = 63.7 bits (156), Expect = 2e-11
Identities = 46/210 (21%), Positives = 84/210 (40%), Gaps = 8/210 (3%)
Query: 29 EMYKKAEASFWTAEEVDLSQDLRHWEALTADEKHFVTHVLAFFAASDGIVLENLAGRFMT 88
E +++ + FW EE+ LS DL W L+ +E+ V D + +
Sbjct: 16 EFWEQNTSQFWLPEEIPLSNDLDSWRTLSPEEQDLYKKVFGGLTLLDTLQGTVGMPALIP 75
Query: 89 EVQVAEARAFYGFQIAIENIHSEMYSLLLETYIKDSDEKNRLFHAIETVPCVAKKATWAL 148
+ +A +E++H++ YS + T ++E + F +E + KKA L
Sbjct: 76 DADTLHEKAVLNNMGFMESVHAKSYSSIFSTLC-TTEEIDEAFRWVENNEYLQKKAKKIL 134
Query: 149 NWIDGSETFAERLIAFACVEGIFFSGSFCAIFWLKKRGLMPGLTFSNELIS---RDEGLH 205
++ + + +A +E F F +L +G + S E+I RDE +H
Sbjct: 135 DYYQNDDPL-KAKVASVFLESFLFYSGFYLPLYLAGQGKLTN---SAEIIRLIIRDESIH 190
Query: 206 CDFACLLYSLLRTKLSEERVKALVKEAVEI 235
+ KLSEE + L ++
Sbjct: 191 GVYIGYKAQEGYNKLSEEEQEELKDWMYDL 220
>gnl|CDD|140022 PRK13966, nrdF2, ribonucleotide-diphosphate reductase subunit beta;
Provisional.
Length = 324
Score = 62.8 bits (152), Expect = 3e-11
Identities = 56/256 (21%), Positives = 102/256 (39%), Gaps = 12/256 (4%)
Query: 29 EMYKKAEASFWTAEEVDLSQDLRHWEALTADEKHFVTHVLAFFAASDGIVLENLAGRFMT 88
E++ + +FW E+V +S D+ W LTA EK V D I A +
Sbjct: 26 EVWDRLTGNFWLPEKVPVSNDIPSWGTLTAGEKQLTMRVFTGLTMLDTIQGTVGAVSLIP 85
Query: 89 EVQVAEARAFYGFQIAIENIHSEMYSLLLETYIKDSDEKNRLFHAIETVPCVAKKATWAL 148
+ A +E++H++ YS + T + + E + F E + +KA L
Sbjct: 86 DALTPHEEAVLTNIAFMESVHAKSYSQIFST-LCSTAEIDDAFRWSEENRNLQRKAEIVL 144
Query: 149 NWIDGSETFAERLIAFACVEGIFFSGSFCAIFWLKKRGLMPGLTFSNELISRDEGLHCDF 208
+ G E ++ + +F+SG + ++W R + LI RDE +H +
Sbjct: 145 QYYRGDEPLKRKVASTLLESFLFYSGFYLPMYW-SSRAKLTNTADMIRLIIRDEAVHGYY 203
Query: 209 ACLLYSLLRTKLSEERVKALVKEAVEI-------EREFVCDALPCALVGMNGELMSQYIE 261
+ + + L E+ E E+ D VG+ E + +++
Sbjct: 204 IGYKFQRGLALVDDVTRAELKDYTYELLFELYDNEVEYTQDLYDE--VGLT-EDVKKFLR 260
Query: 262 FVADRLLGALGYGKLY 277
+ A++ L LGY L+
Sbjct: 261 YNANKALMNLGYEALF 276
>gnl|CDD|184425 PRK13965, PRK13965, ribonucleotide-diphosphate reductase subunit
beta; Provisional.
Length = 335
Score = 62.1 bits (151), Expect = 6e-11
Identities = 57/288 (19%), Positives = 120/288 (41%), Gaps = 29/288 (10%)
Query: 3 SIPEEPLLAPNPDRFCMFPIQYPQIWEMYKKAEASFWTAEEVDLSQDLRHWEALTADEKH 62
S ++PL + N + + + E++ + +FW E+V +S DL W +L D +
Sbjct: 16 SETQKPLRSINWNY-----LNDDKDLEVWNRVTQNFWLPEKVPVSNDLNSWRSLGEDWQQ 70
Query: 63 FVTHVLAFFAASDGIVLENLAGRFMTEV-QVAEAR-----AFYGFQIAIENIHSEMYSLL 116
+T G+ L + + +V Q+ ++ Y + IH+ Y +
Sbjct: 71 LITRTFT------GLTLLDTVQATVGDVAQIPHSQTDHEQVIYTNFAFMVAIHARSYGTI 124
Query: 117 LETYIKDSDEKNRLFHAIETVPCVAKKATWALNWIDGSETFAERLIAFACVEGIFFSGSF 176
T + S++ + + + ++A + + G + + +A A + G G F
Sbjct: 125 FST-LCSSEQIEEAHEWVVSTESLQRRARVLIPYYTGDDP-LKSKVAAAMMPGFLLYGGF 182
Query: 177 CAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLLYSLLRTKLSEER-------VKALV 229
F+L RG +P + LI RD+ +H ++ Y +LS E+ V L+
Sbjct: 183 YLPFYLSARGKLPNTSDIIRLILRDKVIHNYYSGYKYQQKVARLSPEKQAEMKAFVFDLL 242
Query: 230 KEAVEIEREFVCDALPCALVGMNGELMSQYIEFVADRLLGALGYGKLY 277
E +++E+ ++ + A + + + + + A + L LGY +
Sbjct: 243 YELIDLEKAYLRELY--AGFDLAEDAIR-FSLYNAGKFLQNLGYESPF 287
>gnl|CDD|236242 PRK08326, PRK08326, ribonucleotide-diphosphate reductase subunit
beta; Validated.
Length = 311
Score = 61.6 bits (150), Expect = 9e-11
Identities = 44/199 (22%), Positives = 75/199 (37%), Gaps = 39/199 (19%)
Query: 30 MYKKAEASFWTAEEVDLSQDLRHWEALTADEKHFVTHVLAFFAASDGIVLENLA------ 83
++ K A FW ++D S+D WE L+ +E+ + T + A F A + V ++
Sbjct: 30 LFAKGNAKFWNPADIDFSRDAEDWEKLSDEERDYATRLCAQFIAGEEAVTLDIQPLISAM 89
Query: 84 ---GR-----FMTEVQVAEARAFYGFQIAIENIHSEMYSLLLETYIKDSD-----EKNRL 130
GR ++T+ EA+ H+E + + D + N
Sbjct: 90 AAEGRLEDEMYLTQFAFEEAK------------HTEAFRRWFDAVGVTEDLSVYTDDNPS 137
Query: 131 FHAI--ETVPCVAKKATWALNWIDGSETFAERLIAF-ACVEGIFFSGSFCAIFWL-KKRG 186
+ I E +P A L+ E + + VEG+ + A + RG
Sbjct: 138 YRQIFYEELP----AALNRLSTDPSPENQVRASVTYNHVVEGVLAETGYYAWRKICVTRG 193
Query: 187 LMPGLTFSNELISRDEGLH 205
++PGL I DE H
Sbjct: 194 ILPGLQELVRRIGDDERRH 212
>gnl|CDD|140023 PRK13967, nrdF1, ribonucleotide-diphosphate reductase subunit beta;
Provisional.
Length = 322
Score = 56.3 bits (135), Expect = 5e-09
Identities = 40/180 (22%), Positives = 76/180 (42%), Gaps = 5/180 (2%)
Query: 26 QIWEMYKKAEASFWTAEEVDLSQDLRHWEALTADEKHFVTHVLAFFAASDGIVLENLAGR 85
Q+WE + +FW E++ LS DL W+ L++ E+ V D A
Sbjct: 24 QVWE---RLTGNFWLPEKIPLSNDLASWQTLSSTEQQTTIRVFTGLTLLDTAQATVGAVA 80
Query: 86 FMTEVQVAEARAFYGFQIAIENIHSEMYSLLLETYIKDSDEKNRLFHAIETVPCVAKKAT 145
+ + A +E++H++ YS + T + + + + F E P + +KA
Sbjct: 81 MIDDAVTPHEEAVLTNMAFMESVHAKSYSSIFST-LCSTKQIDDAFDWSEQNPYLQRKAQ 139
Query: 146 WALNWIDGSETFAERLIAFACVEGIFFSGSFCAIFWLKKRGLMPGLTFSNELISRDEGLH 205
+++ G + + + +F+SG + ++W RG + LI RDE +H
Sbjct: 140 IIVDYYRGDDALKRKASSVMLESFLFYSGFYLPMYW-SSRGKLTNTADLIRLIIRDEAVH 198
>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 = 49.6 bits (119), Expect = 7e-07
Identities = 41/206 (19%), Positives = 75/206 (36%), Gaps = 52/206 (25%)
Query: 29 EMYKKAEA-SFWTAEEVDLSQDLRHWEALTADEKHFVTHVLAFFAASDGIVLENLA---- 83
++++K + FW ++D SQD WE L+ +E+ + A F A + V +L
Sbjct: 11 KLFEKGKRKGFWNPADIDFSQDREDWEQLSEEERDLALRLCAGFIAGEEAVTLDLLPLMM 70
Query: 84 -----GR-----FMTEVQVAEARAFYGFQIAIENIHSEMYSL---------LLETYIKDS 124
GR ++T+ EA+ H++ + L
Sbjct: 71 AMAAEGRLEEEMYLTQFLFEEAK------------HTDFFRRWLDAVGVSDDLSDLHTAV 118
Query: 125 DEKNRLFHAIETVPCVAKKATWALNWIDGSETFAERLIAFAC----VEGIFFSGSFCAIF 180
F+ E +P +A + + A ++ A VEG+ + A
Sbjct: 119 Y--REPFY--EALP-------YAELRLYLDASPAAQVRASVTYNMIVEGVLAETGYYAWR 167
Query: 181 -WLKKRGLMPGLTFSNELISRDEGLH 205
+KRG++PG+ + DE H
Sbjct: 168 TICEKRGILPGMQEGIRRLGDDESRH 193
>gnl|CDD|181647 PRK09101, nrdB, ribonucleotide-diphosphate reductase subunit beta;
Reviewed.
Length = 376
Score = 46.5 bits (111), Expect = 8e-06
Identities = 36/133 (27%), Positives = 64/133 (48%), Gaps = 15/133 (11%)
Query: 168 EGIFFSGSFCAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLLYSLLRT--------- 218
E I F SF F +R LM G LI+RDE LH + +L+R+
Sbjct: 205 EAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLMRSGKDDPEMAE 264
Query: 219 --KLSEERVKALVKEAVEIEREFVCDAL--PCALVGMNGELMSQYIEFVADRLLGALGYG 274
+ ++ L +A E E+E+ D L +++G+N +++ QY+E++ + + A+G
Sbjct: 265 IAEECKQECYDLFVQAAEQEKEWA-DYLFKDGSMIGLNKDILCQYVEYITNIRMQAVGLD 323
Query: 275 KLYGV-ANPFDWM 286
+ +NP W+
Sbjct: 324 LPFQTRSNPIPWI 336
Score = 34.6 bits (80), Expect = 0.058
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 38 FWTAEEVDLSQDLRHWEALTADEKH 62
FW EEVD+S+D ++AL EKH
Sbjct: 48 FWRPEEVDVSRDRIDYQALPEHEKH 72
>gnl|CDD|234883 PRK00979, PRK00979, tetrahydromethanopterin S-methyltransferase
subunit H; Provisional.
Length = 308
Score = 33.0 bits (76), Expect = 0.17
Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 5/47 (10%)
Query: 222 EERVKALVKEAVEIEREFVCDALPCAL--VGMNGELMSQYIEFVADR 266
+E+ +AL+ E+ + P L VG + E M +YI+FV++
Sbjct: 51 KEKAEALINRQEELSDKT---GNPALLDVVGESPEAMEKYIDFVSEI 94
>gnl|CDD|223441 COG0364, Zwf, Glucose-6-phosphate 1-dehydrogenase [Carbohydrate
transport and metabolism].
Length = 483
Score = 30.3 bits (69), Expect = 1.5
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 6/56 (10%)
Query: 182 LKKRGLMPGLTFSNELISRDEGLHCDFACLLYSLLRTKLSEERVKALVKEAVEIER 237
L +R L P L + ++ L DF + + R+K S E +ALV+EA+E +
Sbjct: 19 LARRKLFPALYR----LYKEGLLPEDFRIIGVA--RSKWSNEEFRALVREAIEFAK 68
>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and
CTD-associated factor 4 (SCAF4), SR-related and
CTD-associated factor 8 (SCAF8) and similar proteins.
This subfamily corresponds to the RRM in a new class of
SCAFs (SR-like CTD-associated factors), including SCAF4,
SCAF8 and similar proteins. The biological role of SCAF4
remains unclear, but it shows high sequence similarity
to SCAF8 (also termed CDC5L complex-associated protein
7, or RNA-binding motif protein 16, or CTD-binding
SR-like protein RA8). SCAF8 is a nuclear matrix protein
that interacts specifically with a highly
serine-phosphorylated form of the carboxy-terminal
domain (CTD) of the largest subunit of RNA polymerase II
(pol II). The pol II CTD plays a role in coupling
transcription and pre-mRNA processing. In addition,
SCAF8 co-localizes primarily with transcription sites
that are enriched in nuclear matrix fraction, which is
known to contain proteins involved in pre-mRNA
processing. Thus, SCAF8 may play a direct role in
coupling with both, transcription and pre-mRNA
processing, processes. SCAF8 and SCAF4 both contain a
conserved N-terminal CTD-interacting domain (CID), an
atypical RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNPs (ribonucleoprotein domain),
and serine/arginine-rich motifs.
Length = 77
Score = 27.3 bits (61), Expect = 3.2
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 6/40 (15%)
Query: 216 LRTKLSEERVKALVKEAVEIEREFVCDALP---CALVGMN 252
L K++EE +K L +E EI+ D +P CA V M
Sbjct: 10 LSKKVTEEDLKNLFEEYGEIQS---IDMIPPRGCAYVCME 46
>gnl|CDD|240133 cd04863, MtLigD_Pol_like, MtLigD_Pol_like: Polymerase (Pol) domain
of bacterial LigD proteins similar to Mycobacterium
tuberculosis (Mt)LigD. The LigD Pol domain belongs to
the archaeal/eukaryal primase (AEP) superfamily. In
prokaryotes, LigD along with Ku is required for
non-homologous end joining (NHEJ)-mediated repair of DNA
double-strand breaks (DSB). NHEJ-mediated DNA DSB repair
is error-prone. MtLigD is monomeric and contains an
N-terminal Pol domain, a central phosphoesterase module,
and a C-terminal ligase domain. It has been suggested
that LigD Pol contributes to NHEJ-mediated DNA DSB
repair in vivo, by filling in short 5'-overhangs with
ribonucleotides; the filled in termini would then be
sealed by the associated LigD ligase domain, resulting
in short stretches of RNA incorporated into the genomic
DNA. The MtLigD Pol domain is stimulated by manganese,
is error-prone, and prefers adding rNTPs to dNTPs in
vitro. The MtLigD Pol domain has been shown to prefer
DNA gapped substrates containing a 5'-phosphate group at
the gap.
Length = 231
Score = 28.5 bits (64), Expect = 3.7
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 7/37 (18%)
Query: 203 GLHCDFACLLYSLLRTKLSEERVKALVKE-AVEIERE 238
GLH LY L +S ++ K K A E+ERE
Sbjct: 147 GLH------LYVPLDGPVSSDQTKEFAKALARELERE 177
>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed.
Length = 1068
Score = 28.9 bits (65), Expect = 4.5
Identities = 13/25 (52%), Positives = 15/25 (60%), Gaps = 5/25 (20%)
Query: 32 KKAEASFWTAEEVDLSQDLRHWEAL 56
K AEA W DLS L+HWEA+
Sbjct: 175 KSAEALQW-----DLSFRLKHWEAI 194
>gnl|CDD|235578 PRK05720, mtnA, methylthioribose-1-phosphate isomerase; Reviewed.
Length = 344
Score = 28.2 bits (64), Expect = 5.7
Identities = 13/38 (34%), Positives = 17/38 (44%), Gaps = 3/38 (7%)
Query: 216 LRTKLSEERVKALVKEAVEIEREFVCDALPCALVGMNG 253
L ER AL +EA+EI E D +G +G
Sbjct: 106 LAPLPGAERKAALEEEAIEIHEE---DVEINRAIGEHG 140
>gnl|CDD|234130 TIGR03161, ribazole_CobZ, alpha-ribazole phosphatase CobZ.
Sequences in the seed alignment were the experimentally
characterized CobZ of the methanogenic archaeon
Methanosarcina mazei, and other archaeal proteins found
similarly next to or very near to other cobalamin
biosynthesis genes. CobZ replaces the
alpha-ribazole-phosphate phosphatase (EC 3.1.3.73)
called CobC in analogous bacterial pathways for
cobalamin biosynthesis under anaerobic conditions
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Heme, porphyrin, and cobalamin].
Length = 140
Score = 27.4 bits (61), Expect = 5.8
Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 4/60 (6%)
Query: 211 LLYSLLRTKLSEERVKALVKEAVEIEREFVCDALPCALVGMNGELMSQYIEFVADRLLGA 270
L L L + V AL+ A+ +ER +P G+ ++ VAD LLGA
Sbjct: 35 RLLRELERYLEDPNVAALLIAALLLERHGKAGGIPGLSDEYEGDPVN----IVADELLGA 90
>gnl|CDD|116097 pfam07476, MAAL_C, Methylaspartate ammonia-lyase C-terminus.
Methylaspartate ammonia-lyase EC:4.3.1.2 catalyzes the
second step of fermentation of glutamate. It is a
homodimer. This family represents the C-terminal region
of Methylaspartate ammonia-lyase and contains a TIM
barrel fold similar to the pfam01188. This family
represents the catalytic domain and contains a metal
binding site.
Length = 249
Score = 28.1 bits (63), Expect = 6.1
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 17/56 (30%)
Query: 226 KALVKEAVEIEREFVCDALPCAL------VGMNGELMSQYIEFVADRL--LGALGY 273
K ++K A D LP AL +G GE + Y++++ R+ LG+ Y
Sbjct: 23 KMIIKGA---------DVLPHALINNVEKLGEKGEKLLDYVKWLKQRIRKLGSEDY 69
>gnl|CDD|239430 cd03314, MAL, Methylaspartate ammonia lyase (3-methylaspartase,
MAL) is a homodimeric enzyme, catalyzing the
magnesium-dependent reversible alpha,beta-elimination of
ammonia from L-threo-(2S,3S)-3-methylaspartic acid to
mesaconic acid. This reaction is part of the main
catabolic pathway for glutamate. MAL belongs to the
enolase superfamily of enzymes, characterized by the
presence of an enolate anion intermediate which is
generated by abstraction of the alpha-proton of the
carboxylate substrate by an active site residue and is
stabilized by coordination to the essential Mg2+ ion.
Length = 369
Score = 28.1 bits (63), Expect = 6.4
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 17/56 (30%)
Query: 226 KALVKEAVEIEREFVCDALPCAL------VGMNGELMSQYIEFVADRL--LGALGY 273
K ++K A D LP AL G GE + +Y+++++DR+ LG GY
Sbjct: 145 KMILKGA---------DVLPHALINNVEEKGPKGEKLLEYVKWLSDRIRKLGRPGY 191
>gnl|CDD|239285 cd02987, Phd_like_Phd, Phosducin (Phd)-like family, Phd subfamily;
Phd is a cytosolic regulator of G protein functions. It
specifically binds G protein betagamma (Gbg)-subunits
with high affinity, resulting in the solubilization of
Gbg from the plasma membrane. This impedes the formation
of a functional G protein trimer (G protein
alphabetagamma), thereby inhibiting G protein-mediated
signal transduction. Phd also inhibits the GTPase
activity of G protein alpha. Phd can be phosphorylated
by protein kinase A and G protein-coupled receptor
kinase 2, leading to its inactivation. Phd was
originally isolated from the retina, where it is highly
expressed and has been implicated to play an important
role in light adaptation. It is also found in the pineal
gland, liver, spleen, striated muscle and the brain. The
C-terminal domain of Phd adopts a thioredoxin fold, but
it does not contain a CXXC motif. Phd interacts with G
protein beta mostly through the N-terminal helical
domain.
Length = 175
Score = 27.3 bits (61), Expect = 8.6
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 3/42 (7%)
Query: 224 RVKALVKEAVEIEREFVCDALPCALVGMNGELMSQYIEFVAD 265
+++A A EF DALP LV GEL+ ++ D
Sbjct: 119 KIRA---SATGASDEFDTDALPALLVYKGGELIGNFVRVTED 157
>gnl|CDD|236121 PRK07868, PRK07868, acyl-CoA synthetase; Validated.
Length = 994
Score = 28.1 bits (63), Expect = 9.0
Identities = 11/20 (55%), Positives = 15/20 (75%), Gaps = 1/20 (5%)
Query: 66 HVLAFFAASDG-IVLENLAG 84
HV+ FFA +DG VL N++G
Sbjct: 746 HVVEFFATTDGQAVLANVSG 765
>gnl|CDD|240347 PTZ00290, PTZ00290, galactokinase; Provisional.
Length = 468
Score = 27.9 bits (62), Expect = 9.3
Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 10/52 (19%)
Query: 213 YSLLRTKLSEERVKALVKEAVEIEREFVCDALPCALVGMNGELMSQYIEFVA 264
YS+L EE ++ L K+A IE EF C G+N +M Q+I A
Sbjct: 182 YSILPPMSKEELIE-LAKQARRIETEF-C--------GVNVGIMDQFISAFA 223
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 0.138 0.425
Gapped
Lambda K H
0.267 0.0592 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,240,459
Number of extensions: 1684618
Number of successful extensions: 1554
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1517
Number of HSP's successfully gapped: 41
Length of query: 329
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 232
Effective length of database: 6,635,264
Effective search space: 1539381248
Effective search space used: 1539381248
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 (22.0 bits)
S2: 59 (26.8 bits)