RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 018964
(348 letters)
>gnl|CDD|215272 PLN02492, PLN02492, ribonucleoside-diphosphate reductase.
Length = 324
Score = 684 bits (1768), Expect = 0.0
Identities = 256/324 (79%), Positives = 285/324 (87%), Gaps = 1/324 (0%)
Query: 26 EPILMEQNQRFCMFPIRYKQVWEMYKKAQASFWTAEEVDLSQDVQHWERLLDSEKHFISH 85
EP+L E RFCMFPI+Y Q+WEMYKKA+ASFWTAEEVDLS D++ WE+L D E+HFISH
Sbjct: 1 EPLLAENPDRFCMFPIKYPQIWEMYKKAEASFWTAEEVDLSADLKDWEKLTDDERHFISH 60
Query: 86 VLAFFAASDGIVLENLAARFLNDIQIPEARAFYGFQIAMENIHSEMYSLLLETYIKDSKE 145
VLAFFAASDGIVLENLAARF+ ++Q+PEARAFYGFQIA+ENIHSEMYSLLL+TYIKD KE
Sbjct: 61 VLAFFAASDGIVLENLAARFMKEVQVPEARAFYGFQIAIENIHSEMYSLLLDTYIKDPKE 120
Query: 146 KHRLFNAIENIPCVAQKAKWALDWIHSSDSFAERLVGFACVEGIFFSGSFCAIFWLKKRG 205
K RLFNAIE IPCVA+KA WAL WI SS SFAERLV FACVEGIFFSGSFCAIFWLKKRG
Sbjct: 121 KDRLFNAIETIPCVAKKADWALRWIDSSASFAERLVAFACVEGIFFSGSFCAIFWLKKRG 180
Query: 206 LMPGLTFSNELISRDEGLHCDFACLLYSLLRKRLHWQKVHHMVHEAVEIETQFVCEALPC 265
LMPGLTFSNELISRDEGLHCDFACLLYSLL+ +L ++V +V EAVEIE +FVC+ALPC
Sbjct: 181 LMPGLTFSNELISRDEGLHCDFACLLYSLLKNKLSEERVKEIVCEAVEIEKEFVCDALPC 240
Query: 266 ALIGMNSSLMSQYIKFVADRLLVALGCQRKYNVENPFDWMEFISLQGKANFFERRVGDYQ 325
AL+GMN+ LMSQYI+FVADRLLVALG ++ YNV NPFDWME ISLQGK NFFE+RVG+YQ
Sbjct: 241 ALVGMNADLMSQYIEFVADRLLVALGYEKVYNVVNPFDWMELISLQGKTNFFEKRVGEYQ 300
Query: 326 KASVMSSLQNGE-KNFVFKLDEDF 348
KA VMSSL G N VF LDEDF
Sbjct: 301 KAGVMSSLNGGGADNHVFSLDEDF 324
>gnl|CDD|240315 PTZ00211, PTZ00211, ribonucleoside-diphosphate reductase small
subunit; Provisional.
Length = 330
Score = 573 bits (1479), Expect = 0.0
Identities = 227/330 (68%), Positives = 271/330 (82%), Gaps = 4/330 (1%)
Query: 19 EQEQEDQEPILMEQNQRFCMFPIRYKQVWEMYKKAQASFWTAEEVDLSQDVQHWERLLDS 78
+E E++EP+L E RF +FPI+Y +W MYKKA+ASFWTAEE+DL D++ WE+L D
Sbjct: 5 MKENEEEEPLLKENPDRFVLFPIKYPDIWRMYKKAEASFWTAEEIDLGNDLKDWEKLNDG 64
Query: 79 EKHFISHVLAFFAASDGIVLENLAARFLNDIQIPEARAFYGFQIAMENIHSEMYSLLLET 138
E+HFI HVLAFFAASDGIVLENLA RF+ ++Q+PEAR FYGFQIAMENIHSE YSLL++T
Sbjct: 65 ERHFIKHVLAFFAASDGIVLENLAQRFMREVQVPEARCFYGFQIAMENIHSETYSLLIDT 124
Query: 139 YIKDSKEKHRLFNAIENIPCVAQKAKWALDWIHSSDSFAERLVGFACVEGIFFSGSFCAI 198
YI D +EK RLF+AIE IP + +KA+WA WI+SS+SFAERLV FA VEGIFFSGSFCAI
Sbjct: 125 YITDEEEKDRLFHAIETIPAIKKKAEWAAKWINSSNSFAERLVAFAAVEGIFFSGSFCAI 184
Query: 199 FWLKKRGLMPGLTFSNELISRDEGLHCDFACLLYSLLRKRLHWQKVHHMVHEAVEIETQF 258
FWLKKRGLMPGLTFSNELISRDEGLH DFACLLYS L+ +L ++V ++ EAVEIE +F
Sbjct: 185 FWLKKRGLMPGLTFSNELISRDEGLHTDFACLLYSHLKNKLPRERVQEIIKEAVEIEREF 244
Query: 259 VCEALPCALIGMNSSLMSQYIKFVADRLLVALGCQRKYNVENPFDWMEFISLQGKANFFE 318
+C+ALP LIGMNS LM+QYI+FVADRLLVALG + YN +NPFDWM+ ISLQGK NFFE
Sbjct: 245 ICDALPVDLIGMNSRLMAQYIEFVADRLLVALGVPKIYNSKNPFDWMDMISLQGKTNFFE 304
Query: 319 RRVGDYQKASVMSSLQNGEKNFVFKLDEDF 348
+RVG+YQKA VM+ + VF LD DF
Sbjct: 305 KRVGEYQKAGVMAE----RTSKVFSLDADF 330
>gnl|CDD|144013 pfam00268, Ribonuc_red_sm, Ribonucleotide reductase, small chain.
Length = 281
Score = 379 bits (975), Expect = e-133
Identities = 144/283 (50%), Positives = 197/283 (69%), Gaps = 4/283 (1%)
Query: 26 EPILMEQNQRFCMFPIRYKQVWEMYKKAQASFWTAEEVDLSQDVQHWERLLDSEKHFISH 85
EP+L E ++RF +PI++ +WE+YKKA+A+ W AEEVDLS+D+ WE+L ++E+ F S
Sbjct: 1 EPLLRENSKRF--YPIQHPDIWELYKKAEANRWLAEEVDLSKDIPDWEKLNEAEREFYSF 58
Query: 86 VLAFFAASDGIVLENLAARFLNDIQIPEARAFYGFQIAMENIHSEMYSLLLETYIKDSKE 145
V AF AA+DGIV ENLA R + Q + +YG QIA+EN+HSE+YSL+ T D KE
Sbjct: 59 VFAFLAAADGIVNENLAERLSAEFQQKDILHYYGEQIAIENVHSEVYSLIQLTLFNDEKE 118
Query: 146 KHRLFNAIENIPCVAQKAKWALDWIHSSDSFAERLVGFACVEGIFFSGSFCAIFWLKKRG 205
+ FNAIE P + +KA+W L W+ ++S AE+L+ FA VEGIFFS SF +I +L+KRG
Sbjct: 119 RDAYFNAIETDPAIQRKAQWLLRWVRDAESLAEKLIAFALVEGIFFSSSFASIAYLRKRG 178
Query: 206 LMPGLTFSNELISRDEGLHCDFACLLYS--LLRKRLHWQKVHHMVHEAVEIETQFVCEAL 263
LMPG SNELISRDE LH D ACLLY+ L ++ ++++ + EAVEIE +F+ A
Sbjct: 179 LMPGTCQSNELISRDEALHTDAACLLYNNYLGLEKPEPKRIYKLFREAVEIEIEFIEAAA 238
Query: 264 PCALIGMNSSLMSQYIKFVADRLLVALGCQRKYNVENPFDWME 306
P + GMN + QYI+F ADRLLVA+G + +NV 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 = 368 bits (946), Expect = e-128
Identities = 152/289 (52%), Positives = 192/289 (66%), Gaps = 15/289 (5%)
Query: 36 FCMFPIRYKQVWEMYKKAQASFWTAEEVDLSQDVQHWERLLDSEKHFISHVLAFFAASDG 95
F + PI+Y WE+YKKA+A+FWT EE+DLS+D++ WE+L ++E+HFI VLAF AA D
Sbjct: 1 FNLNPIKYPWAWELYKKAEANFWTPEEIDLSKDLKDWEKLTEAERHFIKRVLAFLAALDS 60
Query: 96 IVLENLAARFLNDIQIPEARAFYGFQIAMENIHSEMYSLLLETYIKDSKEKHRLFNAIEN 155
IV ENL F +QIPEARAFYGFQ MENIHSE YS +L+T KD E+ LF AIE
Sbjct: 61 IVGENLVELFSRHVQIPEARAFYGFQAFMENIHSESYSYILDTLGKDE-ERDELFEAIET 119
Query: 156 IPCVAQKAKWALDWIHSSD-----SFAERLVGFACVEGIFFSGSFCAIFWLKKRGLMPGL 210
P + +KA W L W + D SFAERLV FA +EGIFF F AIFWL +RG MPGL
Sbjct: 120 DPALKKKADWILRWYDNLDDNTKESFAERLVAFAILEGIFFYSGFAAIFWLARRGKMPGL 179
Query: 211 TFSNELISRDEGLHCDFACLLYSLLRKRLH-------WQKVHHMVHEAVEIETQFVCEAL 263
ELISRDE LH DFACLL L ++V+ ++ EAVE+E +F + L
Sbjct: 180 AEIIELISRDESLHGDFACLLIRELLNENPELFTEEFKEEVYELIKEAVELEKEFARDLL 239
Query: 264 PCALIGMNSSLMSQYIKFVADRLLVALGCQRKYNV--ENPFDWMEFISL 310
P ++G+N M QYI++VA+R L LG ++ +NV +NPFDWME IS
Sbjct: 240 PDGILGLNKEDMKQYIEYVANRRLENLGLEKLFNVEDKNPFDWMELISD 288
>gnl|CDD|223286 COG0208, NrdF, Ribonucleotide reductase, beta subunit [Nucleotide
transport and metabolism].
Length = 348
Score = 292 bits (749), Expect = 2e-97
Identities = 107/338 (31%), Positives = 154/338 (45%), Gaps = 19/338 (5%)
Query: 21 EQEDQEPILMEQNQRFCMFPIRYKQVWEMYKKAQASFWTAEEVDLSQDVQHWERLLDSEK 80
E E+ + PI+Y E+YKK A+FW EE+DLS D++ W++L D EK
Sbjct: 12 ELEEPKIFNGNPTNAINWNPIKYPWALELYKKLTANFWLPEEIDLSNDIKDWKKLSDDEK 71
Query: 81 HFISHVLAFFAASDGIVLENLAARFLNDIQIPEARAFYGFQIAMENIHSEMYSLLLETYI 140
I VLAF D I N + PE A Q ME IH+ YS + +T
Sbjct: 72 DLIIRVLAFLTLLDSIQANNGVPALSPLVTTPEEEAVLTNQAFMEAIHARSYSYIFDTLG 131
Query: 141 KDSKEKHRLFNAIENIPCVAQKAKWAL--------DWIHSSDSFAERLVGFAC-VEGIFF 191
E + + + +KA+ L D + F +LV + +EGI F
Sbjct: 132 PTEDEDEVFDDWVATNEILQEKAEIILRYYDDLGDDPDDPLEEFLLKLVVASVILEGILF 191
Query: 192 SGSFCAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLLYSLLRKRLH--WQK-----V 244
F +L +RG MPG LI RDE LH F L L W +
Sbjct: 192 YSGFAYPLYLARRGKMPGTAEIIRLIIRDEALHLYFIGYLIQRLVAENPELWTAELKDEI 251
Query: 245 HHMVHEAVEIETQFVCEALPCALIGMNSSLMSQYIKFVADRLLVALGCQRKYNVE-NPFD 303
+ + EAVE+E ++ P ++G+ L+ QYI++ A++ L LG + Y E NP
Sbjct: 252 YDLFKEAVELEKEYAEYLYP-GILGLTEDLVKQYIRYNANKRLQNLGLEPLYPAEENPIP 310
Query: 304 WME-FISLQGKANFFERRVGDYQKASVMSSLQNGEKNF 340
W+E +S K +FFE RV YQK SV S ++ + +F
Sbjct: 311 WIELSLSADEKTDFFEGRVSSYQKGSVASETEDDDWDF 348
>gnl|CDD|235968 PRK07209, PRK07209, ribonucleotide-diphosphate reductase subunit
beta; Validated.
Length = 369
Score = 171 bits (436), Expect = 2e-50
Identities = 94/318 (29%), Positives = 158/318 (49%), Gaps = 29/318 (9%)
Query: 40 PIRYKQVWEMYKKAQASFWTAEEVDLSQDVQHWE---RLLDSEKHFISHVLAFFAASDGI 96
P +YK WE Y A+ W +EV++S+D+ W+ L + E+ + L FF+ +D +
Sbjct: 53 PFKYKWAWEKYLAGCANHWMPQEVNMSRDIALWKSPNGLTEDERRIVKRNLGFFSTADSL 112
Query: 97 VLENLAARFLNDIQIPEARAFYGFQIAMENIHSEMYSLLLETYIKDSKEKHRLFNAIENI 156
V N+ I PE R + Q E IH+ Y ++E+ D E +FN +
Sbjct: 113 VANNIVLAIYRHITNPECRQYLLRQAFEEAIHTHAYQYIVESLGLDEGE---IFNMYHEV 169
Query: 157 PCVAQKAKWALDWIHSSD-------------SFAERLVGFACV-EGIFFSGSFCAIFWLK 202
P + K ++ + + S L+ F C+ EGIFF F I L
Sbjct: 170 PSIRAKDEFLIPFTRSLTDPNFKTGTPENDQKLLRNLIAFYCIMEGIFFYVGFTQILSLG 229
Query: 203 KRGLMPGLTFSNELISRDEGLHCDFACLLYSLLR-KRLH-W-----QKVHHMVHEAVEIE 255
++ M G+ + I RDE +H +F L + ++ + H W ++ ++ EAVE+E
Sbjct: 230 RQNKMTGIAEQYQYILRDESMHLNFGIDLINQIKLENPHLWTAEFQAEIRELIKEAVELE 289
Query: 256 TQFVCEALPCALIGMNSSLMSQYIKFVADRLLVALGCQRKY-NVENPFDWM-EFISLQGK 313
++ + +P ++G+N+S+ Y++F+A+R L +G + +Y ENPF WM E I L+ +
Sbjct: 290 YRYARDTMPRGVLGLNASMFKDYLRFIANRRLQQIGLKPQYPGTENPFPWMSEMIDLKKE 349
Query: 314 ANFFERRVGDYQKASVMS 331
NFFE RV +YQ +S
Sbjct: 350 KNFFETRVIEYQTGGALS 367
>gnl|CDD|236591 PRK09614, nrdF, ribonucleotide-diphosphate reductase subunit beta;
Reviewed.
Length = 324
Score = 162 bits (412), Expect = 3e-47
Identities = 74/306 (24%), Positives = 130/306 (42%), Gaps = 23/306 (7%)
Query: 40 PIRYKQVWEMYKKAQASFWTAEEVDLSQDVQHWERLLDSEKHFISHVLAFFAASDGIVLE 99
I +E +K+ A+FW EEV LS D++ W++L D EK+ + V D +
Sbjct: 16 KIEDPWDYEAWKRLTANFWLPEEVPLSNDLKDWKKLSDEEKNLYTRVFGGLTLLDTLQNN 75
Query: 100 NLAARFLNDIQIPEARAFYGFQIAMENIHSEMYSLLLETYIKDSKEKHRLFNAIENIPCV 159
N + DI PE A ME +H++ YS + T + +E F E P +
Sbjct: 76 NGMPNLMPDITTPEEEAVLANIAFMEAVHAKSYSYIFST-LCSPEEIDEAFEWAEENPYL 134
Query: 160 AQKAKWALDWIHS--SDSFAERLVGFACVEGIFFSGSFCAIFWLKKRGLMPGLTFSNELI 217
+KA D+ + V +EG F F +L ++G M G + ++I
Sbjct: 135 QKKADIIQDFYEPLKKKILRKAAVASVFLEGFLFYSGFYYPLYLARQGKMTG---TAQII 191
Query: 218 S---RDEGLHCDFACLLYSLLRKRL--HWQK-----VHHMVHEAVEIETQFVCEALPCAL 267
RDE LH + L+ + L Q+ ++ +++E E E + +
Sbjct: 192 RLIIRDESLHGYYIGYLFQEGLEELPELEQEELKDEIYDLLYELYENEEAYTELLYD--I 249
Query: 268 IGMNSSLMSQYIKFVADRLLVALGCQRKY--NVENPFDWMEFISLQG--KANFFERRVGD 323
+G + + +YI++ A++ L+ LG + + E W+ +S +FFE +
Sbjct: 250 VG-LAEDVKKYIRYNANKRLMNLGLEPLFPEEEEVNPIWLNGLSNNADENHDFFEGKGTS 308
Query: 324 YQKASV 329
Y K +
Sbjct: 309 YVKGAT 314
>gnl|CDD|139206 PRK12759, PRK12759, bifunctional
gluaredoxin/ribonucleoside-diphosphate reductase subunit
beta; Provisional.
Length = 410
Score = 110 bits (276), Expect = 3e-27
Identities = 89/311 (28%), Positives = 147/311 (47%), Gaps = 27/311 (8%)
Query: 40 PIRYKQVWEMYKKAQASFWTAEEVDLSQDVQHWE--RLLDSEKHFISHVLAFFAASDGIV 97
P Y ++ K + + W +E+DLS+DV W+ ++ EK +I+++L F SD V
Sbjct: 102 PFNYPWAVDLTVKHEKAHWIEDEIDLSEDVTDWKNGKITKVEKEYITNILRLFTQSDVAV 161
Query: 98 LENLAARFLNDIQIPEARAFYGFQIAMENIHSEMYSLLLETYIKDSKEKHRLFNAIENIP 157
+N +F+ + E R G A E IH Y+LL +T E H A
Sbjct: 162 GQNYYDQFIPLFKNNEIRNMLGSFAAREGIHQRAYALLNDTLGLPDSEYH----AFLEYK 217
Query: 158 CVAQKAKWALDWIHSSDSFAERLVGFACVEGIFFSG-----SFCAIFWLKKRGLMPGLTF 212
+ K +D++ +D R +G + +F G SF + ++ G M G+
Sbjct: 218 AMTDK----IDFMMDADPTTRRGLGLCLAKTVFNEGVALFASFAMLLNFQRFGKMKGMGK 273
Query: 213 SNELISRDEGLHCDFACLLYSLLRKRLHW-------QKVHHMVHEAVEIETQFVCEALPC 265
E RDE +H + L+ + + + ++++ M +AVE+E +F+ A
Sbjct: 274 VVEWSIRDESMHVEGNAALFRIYCQENPYIVDNEFKKEIYLMASKAVELEDRFIELAYEL 333
Query: 266 ALI-GMNSSLMSQYIKFVADRLLVALGCQRKYNVE-NPFDWMEFISLQG--KANFFERRV 321
I G+ + + QYI+ + DR L LG + YN+E NP W+E+I L G NFFE RV
Sbjct: 334 GTIEGLKADEVKQYIRHITDRRLNQLGLKEIYNIEKNPLTWLEWI-LNGADHTNFFENRV 392
Query: 322 GDYQKASVMSS 332
+Y+ A + S
Sbjct: 393 TEYEVAGLTGS 403
>gnl|CDD|140023 PRK13967, nrdF1, ribonucleotide-diphosphate reductase subunit beta;
Provisional.
Length = 322
Score = 65.9 bits (160), Expect = 4e-12
Identities = 45/180 (25%), Positives = 78/180 (43%), Gaps = 5/180 (2%)
Query: 45 QVWEMYKKAQASFWTAEEVDLSQDVQHWERLLDSEKHFISHVLAFFAASDGIVLENLAAR 104
QVWE + +FW E++ LS D+ W+ L +E+ V D A
Sbjct: 24 QVWE---RLTGNFWLPEKIPLSNDLASWQTLSSTEQQTTIRVFTGLTLLDTAQATVGAVA 80
Query: 105 FLNDIQIPEARAFYGFQIAMENIHSEMYSLLLETYIKDSKEKHRLFNAIENIPCVAQKAK 164
++D P A ME++H++ YS + T + +K+ F+ E P + +KA+
Sbjct: 81 MIDDAVTPHEEAVLTNMAFMESVHAKSYSSIFST-LCSTKQIDDAFDWSEQNPYLQRKAQ 139
Query: 165 WALDWIHSSDSFAERLVGFACVEGIFFSGSFCAIFWLKKRGLMPGLTFSNELISRDEGLH 224
+D+ D+ + +F+SG + ++W RG + LI RDE +H
Sbjct: 140 IIVDYYRGDDALKRKASSVMLESFLFYSGFYLPMYW-SSRGKLTNTADLIRLIIRDEAVH 198
>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 = 65.3 bits (160), Expect = 6e-12
Identities = 46/199 (23%), Positives = 76/199 (38%), Gaps = 11/199 (5%)
Query: 44 KQVWEMYKKAQASFWTAEEVDLSQDVQHWERLLDSEKHFISHVLAFFAASDGIVLENLAA 103
+ WE + + FW EE+ LS D+ W L E+ V D +
Sbjct: 15 LEFWE---QNTSQFWLPEEIPLSNDLDSWRTLSPEEQDLYKKVFGGLTLLDTLQGTVGMP 71
Query: 104 RFLNDIQIPEARAFYGFQIAMENIHSEMYSLLLETYIKDSKEKHRLFNAIENIPCVAQKA 163
+ D +A ME++H++ YS + T ++E F +EN + +KA
Sbjct: 72 ALIPDADTLHEKAVLNNMGFMESVHAKSYSSIFSTLC-TTEEIDEAFRWVENNEYLQKKA 130
Query: 164 KWALDWIHSSDSFAERLVGFACVEGIFFSGSFCAIFWLKKRGLMPGLTFSNELIS---RD 220
K LD+ + D + V +E F F +L +G + S E+I RD
Sbjct: 131 KKILDYYQNDDPL-KAKVASVFLESFLFYSGFYLPLYLAGQGKLTN---SAEIIRLIIRD 186
Query: 221 EGLHCDFACLLYSLLRKRL 239
E +H + +L
Sbjct: 187 ESIHGVYIGYKAQEGYNKL 205
>gnl|CDD|140022 PRK13966, nrdF2, ribonucleotide-diphosphate reductase subunit beta;
Provisional.
Length = 324
Score = 61.7 bits (149), Expect = 1e-10
Identities = 41/177 (23%), Positives = 70/177 (39%), Gaps = 2/177 (1%)
Query: 48 EMYKKAQASFWTAEEVDLSQDVQHWERLLDSEKHFISHVLAFFAASDGIVLENLAARFLN 107
E++ + +FW E+V +S D+ W L EK V D I A +
Sbjct: 26 EVWDRLTGNFWLPEKVPVSNDIPSWGTLTAGEKQLTMRVFTGLTMLDTIQGTVGAVSLIP 85
Query: 108 DIQIPEARAFYGFQIAMENIHSEMYSLLLETYIKDSKEKHRLFNAIENIPCVAQKAKWAL 167
D P A ME++H++ YS + T + + E F E + +KA+ L
Sbjct: 86 DALTPHEEAVLTNIAFMESVHAKSYSQIFST-LCSTAEIDDAFRWSEENRNLQRKAEIVL 144
Query: 168 DWIHSSDSFAERLVGFACVEGIFFSGSFCAIFWLKKRGLMPGLTFSNELISRDEGLH 224
+ + ++ +F+SG + ++W R + LI RDE +H
Sbjct: 145 QYYRGDEPLKRKVASTLLESFLFYSGFYLPMYW-SSRAKLTNTADMIRLIIRDEAVH 200
>gnl|CDD|236242 PRK08326, PRK08326, ribonucleotide-diphosphate reductase subunit
beta; Validated.
Length = 311
Score = 57.7 bits (140), Expect = 2e-09
Identities = 46/211 (21%), Positives = 79/211 (37%), Gaps = 49/211 (23%)
Query: 39 FPIRYKQVWEMYKKAQASFWTAEEVDLSQDVQHWERLLDSEKHFISHVLAFFAASDGIVL 98
FP++ ++ K A FW ++D S+D + WE+L D E+ + + + A F A + V
Sbjct: 26 FPMK------LFAKGNAKFWNPADIDFSRDAEDWEKLSDEERDYATRLCAQFIAGEEAVT 79
Query: 99 ENL-----AAR---------FLNDIQIPEARAFYGFQIAMENIHSEMYSLLLET------ 138
++ A +L EA+ H+E + +
Sbjct: 80 LDIQPLISAMAAEGRLEDEMYLTQFAFEEAK------------HTEAFRRWFDAVGVTED 127
Query: 139 ---YIKDSKEKHRLFNAIENIPCVAQKAKWALDWIHSSDSFAERLVGF-ACVEGIFFSGS 194
Y D+ ++F E +P A L S ++ V + VEG+
Sbjct: 128 LSVYTDDNPSYRQIF--YEELP----AALNRLSTDPSPENQVRASVTYNHVVEGVLAETG 181
Query: 195 FCAIFWL-KKRGLMPGLTFSNELISRDEGLH 224
+ A + RG++PGL I DE H
Sbjct: 182 YYAWRKICVTRGILPGLQELVRRIGDDERRH 212
>gnl|CDD|184425 PRK13965, PRK13965, ribonucleotide-diphosphate reductase subunit
beta; Provisional.
Length = 335
Score = 57.1 bits (138), Expect = 4e-09
Identities = 54/265 (20%), Positives = 108/265 (40%), Gaps = 24/265 (9%)
Query: 48 EMYKKAQASFWTAEEVDLSQDVQHWERLLDSEKHFISHVLAFFAASDGIVLENLAARFLN 107
E++ + +FW E+V +S D+ W L + + I+ G+ L + +
Sbjct: 37 EVWNRVTQNFWLPEKVPVSNDLNSWRSLGEDWQQLITRTFT------GLTLLDTVQATVG 90
Query: 108 DI-QIPEAR-----AFYGFQIAMENIHSEMYSLLLETYIKDSKEKHRLFNAIENIPCVAQ 161
D+ QIP ++ Y M IH+ Y + T + S++ + + + +
Sbjct: 91 DVAQIPHSQTDHEQVIYTNFAFMVAIHARSYGTIFST-LCSSEQIEEAHEWVVSTESLQR 149
Query: 162 KAKWALDWIHSSDSFAERLVGFACVEGIFFSGSFCAIFWLKKRGLMPGLTFSNELISRDE 221
+A+ + + D + V A + G G F F+L RG +P + LI RD+
Sbjct: 150 RARVLIPYYTGDDP-LKSKVAAAMMPGFLLYGGFYLPFYLSARGKLPNTSDIIRLILRDK 208
Query: 222 GLHCDFACLLYSLLRKRLHWQK-------VHHMVHEAVEIETQFVCEALPCALIGMNSSL 274
+H ++ Y RL +K V +++E +++E ++ E A +
Sbjct: 209 VIHNYYSGYKYQQKVARLSPEKQAEMKAFVFDLLYELIDLEKAYLRELY--AGFDLAEDA 266
Query: 275 MSQYIKFVADRLLVALGCQRKYNVE 299
+ + + A + L LG + + E
Sbjct: 267 IR-FSLYNAGKFLQNLGYESPFTEE 290
>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 = 47.3 bits (113), Expect = 4e-06
Identities = 54/278 (19%), Positives = 95/278 (34%), Gaps = 41/278 (14%)
Query: 48 EMYKKAQA-SFWTAEEVDLSQDVQHWERLLDSEKHFISHVLAFFAASDGIVLENLA---- 102
++++K + FW ++D SQD + WE+L + E+ + A F A + V +L
Sbjct: 11 KLFEKGKRKGFWNPADIDFSQDREDWEQLSEEERDLALRLCAGFIAGEEAVTLDLLPLMM 70
Query: 103 --AR--------FLNDIQIPEARAFYGFQIAMENIHSEMYSLLLETYIKDSKEKHRLFNA 152
A +L EA+ H++ + L+ + S + L A
Sbjct: 71 AMAAEGRLEEEMYLTQFLFEEAK------------HTDFFRRWLDA-VGVSDDLSDLHTA 117
Query: 153 IENIPCVAQKAKWALDWIHSSDSFAERLVGFAC-----VEGIFFSGSFCAIF-WLKKRGL 206
+ P L + A V + VEG+ + A +KRG+
Sbjct: 118 VYREPFYEALPYAELRLYLDASPAA--QVRASVTYNMIVEGVLAETGYYAWRTICEKRGI 175
Query: 207 MPGLTFSNELISRDEGLHCDFACLLYSLL--RKRLHWQKVHHMVHEAVEIETQFVCEALP 264
+PG+ + DE H + L +W ++E V + E
Sbjct: 176 LPGMQEGIRRLGDDESRHIAWGTFTCRRLVAADDANWDVFEERMNELVPHALGLIDEIFE 235
Query: 265 CAL---IGMNSSLMSQYIKFVADRLLVALGCQRKYNVE 299
G++ + QY R L + R VE
Sbjct: 236 LYDEMPFGLDPDELMQYAVDQFQRRLGYIERARGQPVE 273
>gnl|CDD|181647 PRK09101, nrdB, ribonucleotide-diphosphate reductase subunit beta;
Reviewed.
Length = 376
Score = 47.6 bits (114), Expect = 5e-06
Identities = 79/320 (24%), Positives = 134/320 (41%), Gaps = 67/320 (20%)
Query: 42 RYKQ----VWEMYKKAQASF-WTAEEVDLSQDVQHWERLLDSEKH-FISHVLAFFAASDG 95
RY Q ++E + Q SF W EEVD+S+D ++ L + EKH FIS+ L + D
Sbjct: 28 RYDQQKYEIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISN-LKYQTLLDS 86
Query: 96 IVLENLAARFLNDIQIPEARAF---YGFQIAMENIHSEMYSLLLETYIKDSKEKHRLFNA 152
I + L + IPE + + F E IHS Y+ ++ + D +F+
Sbjct: 87 IQGRSPNVALLPLVSIPELETWIETWSFS---ETIHSRSYTHIIRNIVNDPSV---VFDD 140
Query: 153 I---ENIPCVAQK-AKWALDWIHSSDSFAERLVG----------------------FACV 186
I E I A+ + + D I + + L+G + C+
Sbjct: 141 IVTNEEILKRAKDISSYYDDLIEMTSYY--HLLGEGTHTVNGKTVTVSLRELKKKLYLCL 198
Query: 187 ------EGIFFSGSFCAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLLYSLLR---- 236
E I F SF F +R LM G LI+RDE LH + +L+R
Sbjct: 199 MSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLMRSGKD 258
Query: 237 --------KRLHWQKVHHMVHEAVEIETQFVCEAL--PCALIGMNSSLMSQYIKFVADRL 286
+ Q+ + + +A E E ++ + L ++IG+N ++ QY++++ +
Sbjct: 259 DPEMAEIAEECK-QECYDLFVQAAEQEKEWA-DYLFKDGSMIGLNKDILCQYVEYITNIR 316
Query: 287 LVALGCQRKYNVE-NPFDWM 305
+ A+G + NP W+
Sbjct: 317 MQAVGLDLPFQTRSNPIPWI 336
>gnl|CDD|221378 pfam12013, DUF3505, Protein of unknown function (DUF3505). This
family of proteins is functionally uncharacterized. This
protein is found in eukaryotes. Proteins in this family
are typically between 247 to 1018 amino acids in length.
This region contains two segments that are likely to be
C2H2 zinc binding domains.
Length = 108
Score = 28.9 bits (65), Expect = 1.6
Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 2/38 (5%)
Query: 208 PGLTFSNELISRDEGLHCDFACLLYSLLRKRLHWQKVH 245
PGL + + + C + SL R HW++ H
Sbjct: 72 PGLPVYDGYRCQRDPPGCPYITR--SLKTMRKHWREHH 107
>gnl|CDD|184887 PRK14893, PRK14893, V-type ATP synthase subunit K; Provisional.
Length = 161
Score = 29.4 bits (66), Expect = 1.7
Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 91 AASDGIVLEN--LAARFLNDIQIPEARAFYGFQIAM 124
A S G V E+ + AR + +PE +A YGF IA+
Sbjct: 35 AGSVGAVAEDSDMFARGIIFSALPETQAIYGFLIAI 70
Score = 28.7 bits (64), Expect = 3.4
Identities = 15/36 (41%), Positives = 23/36 (63%), Gaps = 2/36 (5%)
Query: 91 AASDGIVLEN--LAARFLNDIQIPEARAFYGFQIAM 124
A+S G V+E+ + AR + +PE +A YGF IA+
Sbjct: 116 ASSVGAVVEDPDMFARGIIFSALPETQAIYGFLIAI 151
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 29.3 bits (66), Expect = 3.3
Identities = 13/75 (17%), Positives = 25/75 (33%), Gaps = 8/75 (10%)
Query: 1 MGSLKNETENEVNQREQGEQEQEDQEPILMEQNQRFCMFPIRYKQVWEMYKKAQASFWTA 60
+ +LK + R + EQ + +L EQ + + + +
Sbjct: 163 IDALKATLKQLAAVRAEIAAEQAELTTLLSEQRAQ--------QAKLAQLLEERKKTLAQ 214
Query: 61 EEVDLSQDVQHWERL 75
+LS D + E L
Sbjct: 215 LNSELSADQKKLEEL 229
>gnl|CDD|236121 PRK07868, PRK07868, acyl-CoA synthetase; Validated.
Length = 994
Score = 29.3 bits (66), Expect = 3.7
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 3/33 (9%)
Query: 72 WERLLDSEKHFISHVLAFFAASDG-IVLENLAA 103
WER+ E +HV+ FFA +DG VL N++
Sbjct: 735 WERV--VEAFAPAHVVEFFATTDGQAVLANVSG 765
>gnl|CDD|202496 pfam02981, FokI_N, Restriction endonuclease FokI, recognition
domain.
Length = 145
Score = 27.2 bits (60), Expect = 8.3
Identities = 7/39 (17%), Positives = 15/39 (38%), Gaps = 2/39 (5%)
Query: 121 QIAMEN--IHSEMYSLLLETYIKDSKEKHRLFNAIENIP 157
I + IH E+ + + + ++ L + I P
Sbjct: 29 SIFDPDSKIHKELIDTRIPELVTELNLRYELKSVINQTP 67
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
0.324 0.136 0.418
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,777,676
Number of extensions: 1714407
Number of successful extensions: 1817
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1782
Number of HSP's successfully gapped: 30
Length of query: 348
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 250
Effective length of database: 6,590,910
Effective search space: 1647727500
Effective search space used: 1647727500
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 59 (26.5 bits)