RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9577
(354 letters)
>3rfa_A Ribosomal RNA large subunit methyltransferase N; radical SAM,
S-adenosylmethionine, iron sulfur cluster,
oxidoreductase; HET: SAM; 2.05A {Escherichia coli} PDB:
3rf9_A*
Length = 404
Score = 521 bits (1344), Expect = 0.0
Identities = 167/355 (47%), Positives = 236/355 (66%), Gaps = 11/355 (3%)
Query: 2 TNLLDLSPLKFVNYCKELGEMPFRAKQLQKWIHKFGVSDFNKMTDLSMSLRKKLKNSVYI 61
NLLDL+ + + K+LGE PFRA Q+ KW++ + +F++MTD++ LR KLK I
Sbjct: 18 INLLDLNRQQMREFFKDLGEKPFRADQVMKWMYHYCCDNFDEMTDINKVLRGKLKEVAEI 77
Query: 62 KAPHIMSDQISFDGTRKWIFHVKKNIIETVFIPEKNRNTLCISTQVGCAINCIFCSTGRQ 121
+AP ++ +Q S DGT KW V +ETV+IPE +R TLC+S+QVGCA+ C FCST +Q
Sbjct: 78 RAPEVVEEQRSSDGTIKWAIAVGDQRVETVYIPEDDRATLCVSSQVGCALECKFCSTAQQ 137
Query: 122 GFVRNLTVGEIIGQLWVTEFKLRREKNIKINSQGKRQITNIVMMGMGEPLLNYKSTIGAL 181
GF RNL V EIIGQ+W + K G+R ITN+VMMGMGEPLLN + + A+
Sbjct: 138 GFNRNLRVSEIIGQVWRAAKIVGAAK-----VTGQRPITNVVMMGMGEPLLNLNNVVPAM 192
Query: 182 KLILSDHAYGLSRRHVILSTSGIIPMIDKLAQECPVELAVSLHASNNNLRNKLVPISKKY 241
+++L D +GLS+R V LSTSG++P +DKL V LA+SLHA N+ +R+++VPI+KKY
Sbjct: 193 EIMLDDFGFGLSKRRVTLSTSGVVPALDKLGDMIDVALAISLHAPNDEIRDEIVPINKKY 252
Query: 242 PLKELILACHRYI--TYSPRHMITFEYCMLHGINDTDIHAIELISLMRKNKILTSCKINL 299
++ + A RY+ + + + +T EY ML +ND HA +L L++ T CKINL
Sbjct: 253 NIETFLAAVRRYLEKSNANQGRVTIEYVMLDHVNDGTEHAHQLAELLKD----TPCKINL 308
Query: 300 IPFNCFPNSNLICSKNSRIKIFAKILMNSGIFVTIRKIRGNDINAACGQLSGKIL 354
IP+N FP + S NSRI F+K+LM+ G +RK RG+DI+AACGQL+G ++
Sbjct: 309 IPWNPFPGAPYGRSSNSRIDRFSKVLMSYGFTTIVRKTRGDDIDAACGQLAGDVI 363
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 55.6 bits (133), Expect = 1e-08
Identities = 66/360 (18%), Positives = 128/360 (35%), Gaps = 84/360 (23%)
Query: 18 ELGEMPFRAKQ-LQKWIHKFGVSDFNKMTDLSMSLRKKLKNSVYIKAPHIMSDQISFDGT 76
E GE ++ K L + F V +F+ D+ + L HI+ + + GT
Sbjct: 10 ETGEHQYQYKDILSVFEDAF-VDNFD-CKDVQDMPKSILSKEEI---DHIIMSKDAVSGT 64
Query: 77 RK--WIFHVKKNIIETVFIPE---KNRNTLC--ISTQVGCAINCIFCSTGRQGFV----R 125
+ W K+ + F+ E N L I T+ S + ++ R
Sbjct: 65 LRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTE------QRQPSMMTRMYIEQRDR 118
Query: 126 NLTVGEIIGQLWVTEFKLRREKNIKINS--QGKRQITNIVMMGMG---------EPLLNY 174
++ + V+ R + +K+ R N+++ G+ + L+Y
Sbjct: 119 LYNDNQVFAKYNVS----RLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSY 174
Query: 175 KSTIGALKLILSDHAYGLSRRHVILSTSGIIPMIDKL-AQECPVELAVSLHASN-----N 228
K ++ + + L+ ++ S ++ M+ KL Q P + S H+SN +
Sbjct: 175 K-----VQCKMDFKIFWLNLKNCN-SPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIH 228
Query: 229 NLRNKLVPI--SKKYPLKELILACHRYITYSPRHMITFEY-C-ML---HGINDTDI---H 278
+++ +L + SK Y L+L + + + F C +L TD
Sbjct: 229 SIQAELRRLLKSKPYENCLLVL---LNV-QNAKAWNAFNLSCKILLTTRFKQVTDFLSAA 284
Query: 279 AIELISLMRKNKILT------------SCKINLIPFNCFPNSNLICSKNSR-IKIFAKIL 325
ISL + LT C+ +P + + N R + I A+ +
Sbjct: 285 TTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLP-------REVLTTNPRRLSIIAESI 337
Score = 43.7 bits (102), Expect = 9e-05
Identities = 66/430 (15%), Positives = 127/430 (29%), Gaps = 144/430 (33%)
Query: 10 LKFVNYCKELGEMPFRAKQLQKWIHKFGVSDFNKMTDLSMS-----------LRKKLKNS 58
L N + + LQK +++ ++ +D S + LR+ LK+
Sbjct: 187 LNLKNCNSPETVL----EMLQKLLYQI-DPNWTSRSDHSSNIKLRIHSIQAELRRLLKSK 241
Query: 59 VYIKAPHIMSD----QI--SFDG-------TR-KWIFHVKKNIIETVFIPEKNRNTLCIS 104
Y ++ + + +F+ TR K + T + + TL
Sbjct: 242 PYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPD 301
Query: 105 TQVGCAINCIFCSTG---RQGFVRNLTVGEIIGQLWVTEFKLRRE--KNIKINSQGKRQI 159
+ + C R+ N II + + + + K++ + ++
Sbjct: 302 EVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAES-IRDGLATWDNWKHVNCD-----KL 355
Query: 160 TNIVMMGMGEPLLNYKSTIGALKLILSDHAYGLSRRHVILSTSGIIP------------- 206
T I+ +S++ L+ + R + S IP
Sbjct: 356 TTII-----------ESSLNVLEPAEYRKMF---DRLSVFPPSAHIPTILLSLIWFDVIK 401
Query: 207 -----MIDKLAQEC-----PVELAVSLH-------ASNNN---LRNKLV---PISKKYPL 243
+++KL + P E +S+ N L +V I K +
Sbjct: 402 SDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDS 461
Query: 244 KELILAC-----HRYITYSPRHMITFEY----------------------------CMLH 270
+LI + +I + H+ E+
Sbjct: 462 DDLIPPYLDQYFYSHIGH---HLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASG 518
Query: 271 GINDTDIHAIELISL------MRKNKILTSCKIN-LIPFNCFPNSNLICSKNSRIKIFAK 323
I +T L L + N +N ++ F NLICSK + + A
Sbjct: 519 SILNT------LQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIA- 571
Query: 324 ILM--NSGIF 331
LM + IF
Sbjct: 572 -LMAEDEAIF 580
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 48.5 bits (115), Expect = 3e-06
Identities = 42/199 (21%), Positives = 65/199 (32%), Gaps = 77/199 (38%)
Query: 183 LILSDHAYGLSRRHVIL-STS-------------GIIPM-IDKLAQE----CPVELAVSL 223
L LS +G S HV+L T+ I+P + A + P EL
Sbjct: 9 LTLS---HG-SLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKF 64
Query: 224 --HASNNNLRNKLVPISKKYPLKELILACHRYITYSPRHMITFEYCMLHGINDTDIHAI- 280
+ S+ LV SK +++ C FE C L G DIHA+
Sbjct: 65 LGYVSS------LVEPSKVGQFDQVLNLCLTE----------FENCYLEG---NDIHALA 105
Query: 281 ------ELISLMRKNKILTS----CKINLIPFNCFPNSNLI-CSKNSRIKIFAKILMNSG 329
+L++ +++ + + PF+ NS L ++ A
Sbjct: 106 AKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVA------- 158
Query: 330 IFVTIRKIRGNDINAACGQ 348
IF G GQ
Sbjct: 159 IF-------G-------GQ 163
Score = 34.3 bits (78), Expect = 0.074
Identities = 16/115 (13%), Positives = 30/115 (26%), Gaps = 51/115 (44%)
Query: 191 GLSRRHVILSTSGIIPMIDKLAQECPVELAVSLHASNNNLRNKLVPISKKYPLKELILAC 250
L++ V ++K P V + +L N
Sbjct: 343 NLTQEQVQ-------DYVNKTNSHLPAGKQVEI-----SLVN------------------ 372
Query: 251 HRYITYSPRHMITFEYCMLHGINDTDIHAIELISL---MRKNKILTSCKINLIPF 302
++++ + G L L +RK K + + IPF
Sbjct: 373 ------GAKNLV------VSG------PPQSLYGLNLTLRKAKAPSGLDQSRIPF 409
>2z2u_A UPF0026 protein MJ0257; metal binding protein; 2.40A
{Methanocaldococcus jannaschii}
Length = 311
Score = 35.6 bits (81), Expect = 0.020
Identities = 34/196 (17%), Positives = 68/196 (34%), Gaps = 29/196 (14%)
Query: 108 GCAINCIFCSTGRQGFVRN--------------LTVGEIIGQL--WVTEFKLRREKNIKI 151
C NCIFC + + +I+ + + ++ +
Sbjct: 61 WCQQNCIFCWRVLPRDIGIDISQIKEPKWEEPEVVYEKILAMHKRIIMGYAGVLDRVGEK 120
Query: 152 NSQGKRQITNIVMMGMGEPLLNYKSTIGALKLILSDHAYGLSRRHVILSTSGIIPMIDKL 211
+ + ++ + GEP L Y +K+ H G + ++GI+ D +
Sbjct: 121 KFKEALEPKHVAISLSGEPTL-YPYLDELIKIF---HKNGF---TTFVVSNGILT--DVI 171
Query: 212 AQECPVELAVSLHASNNNLRNKLVPISKKYPLKELILACHRYITYSPRHMITFEYCMLHG 271
+ P +L +SL A + + ++ K+Y E IL + R ++ G
Sbjct: 172 EKIEPTQLYISLDAYDLDSYRRICGGKKEY--WESILNTLDILKEKKR--TCIRTTLIRG 227
Query: 272 INDTDIHAIELISLMR 287
ND + +EL
Sbjct: 228 YNDDILKFVELYERAD 243
>2yx0_A Radical SAM enzyme; predicted tRNA modification enzyme, metal
binding protein, structural genomics, NPPSFA; 2.21A
{Pyrococcus horikoshii}
Length = 342
Score = 31.0 bits (69), Expect = 0.57
Identities = 42/236 (17%), Positives = 81/236 (34%), Gaps = 27/236 (11%)
Query: 108 GCAINCIFCSTGRQGFVRNLTVGEIIGQLWVTEFKLRREKNIKINSQGK----------- 156
C NCIFC + F+ ++ E ++ ++ + I +G
Sbjct: 80 WCTHNCIFCWRPMENFLGTELPQPWDDPAFIVEESIKAQRKLLIGYKGNPKVDKKKFEEA 139
Query: 157 RQITNIVMMGMGEPLLNYKSTIGALKLILSDHAYGLSRRHVILSTSGIIP-MIDKLAQEC 215
T+ + GEP+L Y ++ H G + T+G IP ++++ +E
Sbjct: 140 WNPTHAAISLSGEPML-YPYMGDLVEEF---HKRGF---TTFIVTNGTIPERLEEMIKED 192
Query: 216 --PVELAVSLHASNNNLRNKLVPISKKYPLKELILACHRYI-TYSPRHMITFEYCMLHGI 272
P +L VS+ A + N + E IL + R ++ G
Sbjct: 193 KLPTQLYVSITAPDIETYNSVNIP-MIPDGWERILRFLELMRDLPTR--TVVRLTLVKGE 249
Query: 273 NDTDIHAI-ELISLMRKNKILTSCKINLIPFNCFPNSNLICSKNSRIKIFAKILMN 327
N +LI R + + ++ + + I+ FA+ L+
Sbjct: 250 NMHSPEKYAKLILKARPMFVEAK-AYMFVGYSRNRLTINNMPSHQDIREFAEALVK 304
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 29.5 bits (65), Expect = 1.0
Identities = 6/15 (40%), Positives = 10/15 (66%), Gaps = 1/15 (6%)
Query: 50 SLRKKLKNSVYIKAP 64
+L KKL+ S+ + A
Sbjct: 21 AL-KKLQASLKLYAD 34
>3mdu_A N-formimino-L-glutamate iminohydrolase; amonohydralase family,
N-formimino-L-glutamate iminohydrolas
guanidino-L-glutamate; HET: NGQ; 1.40A {Pseudomonas
aeruginosa} PDB: 3mdw_A*
Length = 453
Score = 28.8 bits (65), Expect = 3.0
Identities = 9/29 (31%), Positives = 13/29 (44%)
Query: 202 SGIIPMIDKLAQECPVELAVSLHASNNNL 230
GI P D LAQ + + H S + +
Sbjct: 300 DGIFPATDFLAQGGRLGIGSDSHVSLSVV 328
>3c8f_A Pyruvate formate-lyase 1-activating enzyme; adoMet radical, SAM
radical, activase, glycyl radical, 4Fe- 4S, carbohydrate
metabolism, cytoplasm; HET: MT2 PGE; 2.25A {Escherichia
coli} PDB: 3cb8_A*
Length = 245
Score = 27.6 bits (62), Expect = 5.2
Identities = 20/112 (17%), Positives = 40/112 (35%), Gaps = 26/112 (23%)
Query: 108 GCAINCIFCST-----GRQGFVRNLTVGEIIGQLWVTEFKLRREKNIKINSQGKRQITNI 162
GC + C++C G + +TV +++ + + ++ S G +
Sbjct: 28 GCLMRCLYCHNRDTWDTHGG--KEVTVEDLMKE-------VVTYRHFMNASGG-----GV 73
Query: 163 VMMGMGEPLLNYKSTIGALKLILSDHAYGLSRRHVILSTSGIIPMIDKLAQE 214
G GE +L + + G+ H L T+G + D + E
Sbjct: 74 TASG-GEAILQAEFVRDWFRAC---KKEGI---HTCLDTNGFVRRYDPVIDE 118
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.325 0.139 0.416
Gapped
Lambda K H
0.267 0.0500 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,280,824
Number of extensions: 307993
Number of successful extensions: 759
Number of sequences better than 10.0: 1
Number of HSP's gapped: 754
Number of HSP's successfully gapped: 13
Length of query: 354
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 259
Effective length of database: 4,049,298
Effective search space: 1048768182
Effective search space used: 1048768182
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: 58 (26.7 bits)