RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3767
(246 letters)
>1ual_A TRNA (guanine-N(1)-)-methyltransferase; spout class, TRMD,
tRNA(M1G37)methyltrans tRNA modification; HET: SAH;
1.80A {Haemophilus influenzae} SCOP: c.116.1.4 PDB:
1uak_A* 1uaj_A* 1uam_A* 3axz_A* 1p9p_A*
Length = 274
Score = 376 bits (969), Expect = e-134
Identities = 110/247 (44%), Positives = 163/247 (65%), Gaps = 5/247 (2%)
Query: 1 MQFDVITLFPEMFSAITQSGITRRAFEKKQYSLNLWNPRNFSSNNYRKIDDYPYGGGVGM 60
M VI+LFPEMF AIT+ G+T RA + + WNPR+F+ + ++ +DD PYGGG GM
Sbjct: 21 MWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGM 80
Query: 61 IMLGKPIEDTITAIKKNIKKIPKIIYMSPQGKKLTHNIIIKLLKESNLILLCGRYQAIDQ 120
+M+ +P+ D I K + K+IY+SPQG+KL + +L + LIL+CGRY+ ID+
Sbjct: 81 LMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDE 140
Query: 121 RFLDNFIDEEISVGDFILSGGELPAMMLIDAIVRLLPKVLNNKLN-MQDSFINGLLDCSY 179
R + IDEE S+GD++L+GGELPAM LIDA+ R +P VL + + +DSF +GLLDC +
Sbjct: 141 RLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGKQASAEEDSFADGLLDCPH 200
Query: 180 YTKPRIYLNMEVPIVLLSGNHKKIKKWKRKNSLKITNKKRPDLIIKARKNKFLTCTDEEF 239
YT+P + + VP VL+SG+H++I+KW+ K SL+ T +RP+L+ LT +
Sbjct: 201 YTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLA----LTDEQRKL 256
Query: 240 LKKINKK 246
LK+ +
Sbjct: 257 LKEAQAE 263
>3ky7_A TRNA (guanine-N(1)-)-methyltransferase; putative tRNA
(guanine-7-)-methyltransferase, structural GEN
infectious diseases; 2.35A {Staphylococcus aureus subsp}
Length = 269
Score = 368 bits (947), Expect = e-130
Identities = 98/244 (40%), Positives = 152/244 (62%), Gaps = 7/244 (2%)
Query: 1 MQFDVITLFPEMFSAITQSGITRRAFEKKQYSLNLWNPRNFSSNNYRKIDDYPYGGGVGM 60
M+ D +TLFPEMF + I +RA E + +N N R+++ N + ++DDYPYGGG GM
Sbjct: 25 MKIDYLTLFPEMFDGVLNHSIMKRAQENNKLQINTVNFRDYAINKHNQVDDYPYGGGQGM 84
Query: 61 IMLGKPIEDTITAIKKNIKKIPKIIYMSPQGKKLTHNIIIKLLKESNLILLCGRYQAIDQ 120
++ +P+ + + + + ++I M PQG+ +H ++L K +++ +CG Y+ D+
Sbjct: 85 VLKPEPVFNAMEDLDVTEQ--ARVILMCPQGEPFSHQKAVELSKADHIVFICGHYEGYDE 142
Query: 121 RFLDNFIDEEISVGDFILSGGELPAMMLIDAIVRLLPKVLNNKLN-MQDSFINGLLDCSY 179
R + + +EIS+GD++L+GGELPAM + DAIVRL+P VL N+ + DSF +GLL+
Sbjct: 143 RIRTHLVTDEISMGDYVLTGGELPAMTMTDAIVRLIPGVLGNEQSHQDDSFSDGLLEFPQ 202
Query: 180 YTKPRIYLNMEVPIVLLSGNHKKIKKWKRKNSLKITNKKRPDLIIKARKNKFLTCTDEEF 239
YT+PR + + VP VLLSGNH I W+ + L T KRPDLI K LT D++
Sbjct: 203 YTRPREFKGLTVPDVLLSGNHANIDAWRHEQKLIRTYNKRPDLIEKYP----LTNADKQI 258
Query: 240 LKKI 243
L++
Sbjct: 259 LERY 262
>3ief_A TRNA (guanine-N(1)-)-methyltransferase; niaid, ssgcid, seattle
structural genomics center for infectious diseases;
2.50A {Bartonella henselae}
Length = 233
Score = 357 bits (919), Expect = e-126
Identities = 83/231 (35%), Positives = 137/231 (59%), Gaps = 5/231 (2%)
Query: 1 MQFDVITLFPEMFSAITQSGITRRAFEKKQYSLNLWNPRNFSSNNYRKIDDYPYGGGVGM 60
Q V+TL+PEMF + +A ++ +SL R+F+ + + +DD P GGG GM
Sbjct: 4 FQARVLTLYPEMFPGFLGCSLAGQALKQGIWSLETVQIRDFALDKHHSVDDTPAGGGAGM 63
Query: 61 IMLGKPIEDTITAIKKNIKKIPKIIYMSPQGKKLTHNIIIKLLKESNLILLCGRYQAIDQ 120
+M + + + + + MSP+G+ L L + S + L+CGR++ +D+
Sbjct: 64 VMRADVLAAALDSCPND----SPRLLMSPRGRLLNQAYARSLARSSGVTLVCGRFEGVDE 119
Query: 121 RFLDNFIDEEISVGDFILSGGELPAMMLIDAIVRLLPKVLNNKLN-MQDSFINGLLDCSY 179
R ++ EE+S+GD+ILSGGE A++L+DAIVRLLP V+ N+++ +SF NGLL+
Sbjct: 120 RIIEARELEEVSIGDYILSGGETAALVLLDAIVRLLPGVMGNEISAKCESFENGLLEHPQ 179
Query: 180 YTKPRIYLNMEVPIVLLSGNHKKIKKWKRKNSLKITNKKRPDLIIKARKNK 230
YT+P ++ +P VL SG+HK I W+++ + +T ++RPDL KN+
Sbjct: 180 YTRPAVFEGRGIPPVLTSGHHKAIANWRQQQAESLTRQRRPDLYALYNKNR 230
>1oy5_A TRNA (guanine-N(1)-)-methyltransferase; structural genomics, TRMD,
tRNA (M1G37) methyltransferase, B structure funded by
NIH; 2.60A {Aquifex aeolicus} SCOP: c.116.1.4
Length = 257
Score = 351 bits (904), Expect = e-124
Identities = 94/247 (38%), Positives = 151/247 (61%), Gaps = 10/247 (4%)
Query: 1 MQFDVITLFPEMFSAITQSGITRRAFEKKQYSLNLWNPRNFSSNNYRKIDDYPYGGGVGM 60
++F V+T+FP + S ++ GI ++A +K + + + R F+ ++DD PYGG GM
Sbjct: 6 LRFFVLTIFPHIISCYSEYGIVKQAIKKGKVEVYPIDLREFAPK--GQVDDVPYGGLPGM 63
Query: 61 IMLGKPIEDTITAIKKNIKKIPKIIYMSPQGKKLTHNIIIKLLKESNLILLCGRYQAIDQ 120
++ +PI + + +N K P ++ P G+KL ++ +L K+ ++++CGRY+ +D+
Sbjct: 64 VLKPEPIYEAYDYVVENYGK-PFVLITEPWGEKLNQKLVNELSKKERIMIICGRYEGVDE 122
Query: 121 RFLDNFIDEEISVGDFILSGGELPAMMLIDAIVRLLPKVLNNKLN-MQDSFINGLLDCSY 179
R + +D EIS+GDFILSGGE+ A+ +IDA+ R+LP VL+ + +DSF N L
Sbjct: 123 R-VKKIVDMEISLGDFILSGGEIVALAVIDAVSRVLPGVLSEPQSIQEDSFQNRWLGYPV 181
Query: 180 YTKPRIYLNMEVPIVLLSGNHKKIKKWKRKNSLKITNKKRPDLIIKARKNKFLTCTDEEF 239
YT+PR Y M+VP LLSG+HK I+ WK + ++ T KKRPDLI K LT +++
Sbjct: 182 YTRPREYRGMKVPEELLSGHHKLIELWKLWHRIENTVKKRPDLI-----PKDLTELEKDI 236
Query: 240 LKKINKK 246
L I
Sbjct: 237 LNSILSG 243
>3knu_A TRNA (guanine-N(1)-)-methyltransferase; niaid, ssgcid, seattle
structural genomics center for infect disease, tRNA
methyl transferase; 2.25A {Anaplasma phagocytophilum}
Length = 253
Score = 351 bits (903), Expect = e-124
Identities = 89/231 (38%), Positives = 141/231 (61%), Gaps = 3/231 (1%)
Query: 1 MQFDVITLFPEMFSAITQSGITRRAFEKKQYSLNLWNPRNFSSNNYRKIDDYPYGGGVGM 60
M F+V+T+FP+MF A +K ++LN+++ R F++N + +DD PYGGG GM
Sbjct: 22 MIFNVLTIFPQMFPGPLGVSNLGSALKKGLWTLNVFDIRAFANNKHNTVDDTPYGGGPGM 81
Query: 61 IMLGKPIEDTITAIKKNIKKIPKIIYMSPQGKKLTHNIIIKLLKESNLILLCGRYQAIDQ 120
++ + I + K+++ SP+G T +I + + N+ LLCGR++ ID+
Sbjct: 82 LLRADVLGRCIDEVLSLHPN-TKLMFTSPRGVSFTQDIARQTMNFDNITLLCGRFEGIDE 140
Query: 121 RFLDNFIDEEISVGDFILSGGELPAMMLIDAIVRLLPKVLNNKLN-MQDSFINGLLDCSY 179
R +D + +E+S+GD++LSGGEL AM++ID VR++P V+ N + Q+S G L+
Sbjct: 141 RVVDFYKLQEVSIGDYVLSGGELAAMVIIDTCVRMVPGVIGNAESLKQESM-EGSLEYPQ 199
Query: 180 YTKPRIYLNMEVPIVLLSGNHKKIKKWKRKNSLKITNKKRPDLIIKARKNK 230
YT+P + MEVP VLL+GNH +I+KW+R SL IT +RPDL+
Sbjct: 200 YTRPASWKGMEVPEVLLTGNHGEIEKWRRNASLSITAARRPDLLKDRYGEN 250
>3quv_A TRNA (guanine-N(1)-)-methyltransferase; sssgcid, seattle structural
genomics center for infectious D ssgcid, tRNA
methyltransferase; 1.70A {Mycobacterium abscessus}
Length = 246
Score = 333 bits (856), Expect = e-117
Identities = 81/238 (34%), Positives = 132/238 (55%), Gaps = 12/238 (5%)
Query: 1 MQFDVITLFPEMFSAITQSGITRRAFEKKQYSLNLWNPRNFSSNNYRKIDDYPYGGGVGM 60
M+ DV+T+FPE + QS + +A + + + + R ++ + ++ +DD PYGGG GM
Sbjct: 5 MKIDVVTIFPEYLQPVRQS-LPGKAIDAGLVDVAVHDLRRWTHDVHKSVDDSPYGGGPGM 63
Query: 61 IMLGKPIEDTITAIKKNIKKIPKIIYMSPQGKKLTHNIIIKLLKESNLILLCGRYQAIDQ 120
+M D + I ++ +P G T + E +L++ CGRY+ IDQ
Sbjct: 64 VMKPTVWGDALDEICT---SETLLVVPTPAGYPFTQETAWQWSTEDHLVIACGRYEGIDQ 120
Query: 121 RFLDNFID----EEISVGDFILSGGELPAMMLIDAIVRLLPKVLNNKL-NMQDSFING-- 173
R D+ E+S+GD++L+GGE A+++I+A++RL+P VL N L +DS G
Sbjct: 121 RVADDAATRMRVREVSIGDYVLNGGEAAALVIIEAVLRLVPGVLGNALSAQEDSHSEGMA 180
Query: 174 -LLDCSYYTKPRIYLNMEVPIVLLSGNHKKIKKWKRKNSLKITNKKRPDLIIKARKNK 230
LL+ YT+P + M+VP VLLSG+H KI W+ + S + T ++RPDL+
Sbjct: 181 SLLEGPSYTRPPSWRGMDVPPVLLSGDHAKIAAWRAEQSRQRTIERRPDLLGFDSPTG 238
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 42.5 bits (99), Expect = 3e-05
Identities = 8/51 (15%), Positives = 23/51 (45%), Gaps = 12/51 (23%)
Query: 202 KIKKWKRKNSLKI------TNKKRPDLIIKARKNKFLTCTDEEFLKKINKK 246
I+KW+ + ++ + + KA+K+ EE+ ++ +++
Sbjct: 86 SIRKWREEQRKRLQELDAASKVMEQEWREKAKKDL------EEWNQRQSEQ 130
>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 = 43.5 bits (102), Expect = 4e-05
Identities = 23/136 (16%), Positives = 49/136 (36%), Gaps = 45/136 (33%)
Query: 34 NLWNPRNFSSNNYRKIDDY---PYGGGVGMIMLGKPIEDTITAIKKNIKKIPKIIYMSPQ 90
++WN + D++ YG + I++ P+ TI + +
Sbjct: 1644 DVWN----------RADNHFKDTYGFSILDIVINNPVNLTI-------------HFGGEK 1680
Query: 91 GKKLTHNIIIKLLKESNLILLCGRYQAIDQRFLDNFIDEEISVGDFILSG--GEL----- 143
GK++ N ++ E+ + G+ + + I+E + + G L
Sbjct: 1681 GKRIREN-YSAMIFETIVD---GKLKT---EKIFKEINEHST--SYTFRSEKGLLSATQF 1731
Query: 144 --PAMMLID-AIVRLL 156
PA+ L++ A L
Sbjct: 1732 TQPALTLMEKAAFEDL 1747
>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 = 40.2 bits (93), Expect = 4e-04
Identities = 34/226 (15%), Positives = 78/226 (34%), Gaps = 56/226 (24%)
Query: 23 RRAFEKKQY--SL----NLWNPR-----NFSS-----NNYRKIDDYPYGGGVGMIMLGKP 66
RR + K Y L N+ N + N S ++++ D+ I L
Sbjct: 235 RRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISL-DH 293
Query: 67 IEDTIT----------AIKKNIKKIPK-IIYMSPQGKKLTHNIIIKLLKESNLILLCGRY 115
T+T + + +P+ ++ +P +II + +++ +
Sbjct: 294 HSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNP----RRLSIIAESIRDGLATW--DNW 347
Query: 116 QAIDQRFLDNFIDEEISVGDFILSGGELPAMMLIDAI----VRLLPKVL---------NN 162
+ ++ L I+ ++V L E M ++ + +L ++
Sbjct: 348 KHVNCDKLTTIIESSLNV----LEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSD 403
Query: 163 KLNMQDSFIN-GLLDC----SYYTKPRIYLNMEVPIVLLSGNHKKI 203
+ + + L++ S + P IYL ++V + H+ I
Sbjct: 404 VMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSI 449
Score = 37.5 bits (86), Expect = 0.004
Identities = 26/130 (20%), Positives = 52/130 (40%), Gaps = 19/130 (14%)
Query: 114 RYQAIDQRFLDNFI-DEEIS-VGDF---ILSGGELPAMML----IDAIVRLLPKVLNNKL 164
+Y+ I F D F+ + + V D ILS E+ +++ + +RL +L+ +
Sbjct: 17 QYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQE 76
Query: 165 NMQDSFINGLLDCSY-YTKPRIYLNMEVPIVLLSGNHKKIKKWKRK--NSLKITNK---K 218
M F+ +L +Y + I P S + + + + N ++ K
Sbjct: 77 EMVQKFVEEVLRINYKFLMSPIKTEQRQP----SMMTRMYIEQRDRLYNDNQVFAKYNVS 132
Query: 219 RPDLIIKARK 228
R +K R+
Sbjct: 133 RLQPYLKLRQ 142
>3oii_A Essential for mitotic growth 1; EMG1, scnep1, spout, ribosome
biogenesis, methyltransferase, processing, ribosomal
protein; HET: SAH; 1.85A {Saccharomyces cerevisiae} PDB:
3oij_A* 3oin_A* 2v3j_A 2v3k_A*
Length = 253
Score = 36.1 bits (83), Expect = 0.005
Identities = 11/68 (16%), Positives = 29/68 (42%), Gaps = 1/68 (1%)
Query: 74 IKKNIKKIPKIIYMSPQGKKLTHNIIIKLLKES-NLILLCGRYQAIDQRFLDNFIDEEIS 132
I ++ + + +S + I+ L + ++ + G F D ++DE++
Sbjct: 168 ITDHLPTKCRKVTLSFDAPVIRVQDYIEKLDDDESICVFVGAMARGKDNFADEYVDEKVG 227
Query: 133 VGDFILSG 140
+ ++ LS
Sbjct: 228 LSNYPLSA 235
>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 = 33.0 bits (74), Expect = 0.034
Identities = 10/27 (37%), Positives = 15/27 (55%), Gaps = 3/27 (11%)
Query: 201 KKIKKWKRKNSLKI-TNKKRPDLIIKA 226
+ +KK + SLK+ + P L IKA
Sbjct: 20 QALKKLQ--ASLKLYADDSAPALAIKA 44
Score = 27.6 bits (60), Expect = 2.5
Identities = 12/57 (21%), Positives = 18/57 (31%), Gaps = 28/57 (49%)
Query: 23 RRAFEKKQYSLNLWNPRNFSSNNYRKIDDYPYGGGVGMIMLGKPIEDTITAIKKNIK 79
++A +K Q SL L+ D P L AIK ++
Sbjct: 19 KQALKKLQASLKLYAD-----------DSAP--------AL---------AIKATME 47
>3lvh_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 9.00A {Bos
taurus}
Length = 205
Score = 32.2 bits (72), Expect = 0.11
Identities = 8/51 (15%), Positives = 23/51 (45%), Gaps = 12/51 (23%)
Query: 202 KIKKWKRKNSLKI------TNKKRPDLIIKARKNKFLTCTDEEFLKKINKK 246
I+KW+ + ++ + + KA+K+ EE+ ++ +++
Sbjct: 101 SIRKWREEQRKRLQELDAASKVMEQEWREKAKKDL------EEWNQRQSEQ 145
>1p9o_A Phosphopantothenoylcysteine synthetase; ligase; 2.30A {Homo
sapiens} SCOP: c.72.3.1
Length = 313
Score = 27.4 bits (60), Expect = 4.8
Identities = 11/61 (18%), Positives = 17/61 (27%), Gaps = 13/61 (21%)
Query: 199 NHKKIKKWKRKNSLKITNKKRPDLIIKARKNKFLTC--------TDEEFL-----KKINK 245
+ K L+IT K P L+ K+ TD + K +
Sbjct: 192 EMPEHKIESSGGPLQITMKMVPKLLSPLVKDWAPKAFIISFKLETDPAIVINRARKALEI 251
Query: 246 K 246
Sbjct: 252 Y 252
>2q8u_A Exonuclease, putative; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI-2, hydrolase; HET: MSE; 2.20A {Thermotoga maritima
MSB8} PDB: 3thn_A
Length = 336
Score = 26.6 bits (59), Expect = 7.3
Identities = 6/14 (42%), Positives = 9/14 (64%)
Query: 187 LNMEVPIVLLSGNH 200
+ P+V+L GNH
Sbjct: 93 MMRTAPVVVLPGNH 106
>3tho_B Exonuclease, putative; adenosine triphosphate, bacterial proteins,
DNA breaks, DOUB stranded, DNA repair, DNA repair
enzymes; HET: ADP; 2.61A {Thermotoga maritima} PDB:
3qg5_C
Length = 379
Score = 26.6 bits (59), Expect = 8.9
Identities = 5/14 (35%), Positives = 8/14 (57%)
Query: 187 LNMEVPIVLLSGNH 200
+ P+V+L GN
Sbjct: 75 MMRTAPVVVLPGNQ 88
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
0.322 0.140 0.407
Gapped
Lambda K H
0.267 0.0668 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,906,257
Number of extensions: 242146
Number of successful extensions: 524
Number of sequences better than 10.0: 1
Number of HSP's gapped: 506
Number of HSP's successfully gapped: 28
Length of query: 246
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 155
Effective length of database: 4,160,982
Effective search space: 644952210
Effective search space used: 644952210
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 (21.9 bits)
S2: 56 (25.5 bits)