BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy6779
(144 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2I6D|A Chain A, The Structure Of A Putative Rna Methyltransferase Of The
Trmh Family From Porphyromonas Gingivalis
Length = 257
Score = 59.3 bits (142), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 41/145 (28%), Positives = 71/145 (48%), Gaps = 15/145 (10%)
Query: 4 MKSRKQREKKGWLMLEGKRILIDALKANLKLKMVFFSQWDILKELPLPED-----VPQHR 58
++ RK R ++ +EG +++ + L +V L+ + P D +P+
Sbjct: 16 LRERKYRLREQAFAVEGPKLVGEXLPFYRCRXLV--GTAAXLRAVSTPHDAEVVELPES- 72
Query: 59 VDYKNIQLWSDLVTPPGIIGIFELPAHPIASIDPASLPLNIVCDNIRDPGNMGSILRVCA 118
D+K I S TP + +F+LPA P +P L ++ D ++DPGN+G+ILR
Sbjct: 73 FDFKRI---STQTTPQPLXAVFDLPAEP----EPVVEGLTLLLDGVQDPGNVGTILRTAD 125
Query: 119 AVGARQVVCSRGCVDIYDNKVIRAA 143
G R V G D++ KV++A+
Sbjct: 126 WFGIRHVWLGTGSADVFSPKVVQAS 150
>pdb|1IPA|A Chain A, Crystal Structure Of Rna 2'-O Ribose Methyltransferase
Length = 274
Score = 52.4 bits (124), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 37/148 (25%), Positives = 67/148 (45%), Gaps = 8/148 (5%)
Query: 1 MVYMKSRKQREKKGWLMLEGKRILIDALKANLKLKMVFF-------SQWDILKELPLPED 53
+ + RK R+ + ++EG R + AL+A ++L+ + + L
Sbjct: 14 LARLLERKHRDSQRRFLIEGAREIERALQAGIELEQALVWEGGLNPEEQQVYAALGRVGR 73
Query: 54 VPQHRVDYKNIQLWSDLVTPPGIIGIFELPAHPIASIDPASLPLNIVCDNIRDPGNMGSI 113
+ V ++ S P G+I + +P + P+ L +V + PGN+G++
Sbjct: 74 LALLEVSEAVLKKLSVRDNPAGLIALARMPERTLEEYRPSPDALILVAVGLEKPGNLGAV 133
Query: 114 LRVCAAVGARQVVCSRGCVDIYDNKVIR 141
LR A GA V+ + G VD+Y +VIR
Sbjct: 134 LRSADAAGAEAVLVA-GGVDLYSPQVIR 160
>pdb|1X7P|A Chain A, Crystal Structure Of The Spou Methyltransferase Avirb From
Streptomyces Viridochromogenes In Complex With The
Cofactor Adomet
pdb|1X7P|B Chain B, Crystal Structure Of The Spou Methyltransferase Avirb From
Streptomyces Viridochromogenes In Complex With The
Cofactor Adomet
Length = 287
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 36/149 (24%), Positives = 70/149 (46%), Gaps = 11/149 (7%)
Query: 4 MKSRKQREKKGWLMLEGKRILIDALKANLKLKMVFFSQWDILKELPLPEDVPQHRVDYKN 63
+ +R +R + G ++ G R + A++ ++ + + D +EL V +
Sbjct: 29 LGNRNKRTRAGEFLVMGVRPISLAVEHGWPVRTLLY---DGQRELSKWARELLRTVRTEQ 85
Query: 64 IQLWSDLV--------TPPGIIGIFELPAHPIASIDPASLPLNIVCDNIRDPGNMGSILR 115
I + DL+ PP ++ + E+PA + I L ++ D PGN+GSI+R
Sbjct: 86 IAMAPDLLMELGEKNEAPPEVVAVVEMPADDLDRIPVREDFLGVLFDRPTSPGNIGSIIR 145
Query: 116 VCAAVGARQVVCSRGCVDIYDNKVIRAAA 144
A+GA ++ + D+YD K +R++
Sbjct: 146 SADALGAHGLIVAGHAADVYDPKSVRSST 174
>pdb|1X7O|A Chain A, Crystal Structure Of The Spou Methyltransferase Avirb From
Streptomyces Viridochromogenes
pdb|1X7O|B Chain B, Crystal Structure Of The Spou Methyltransferase Avirb From
Streptomyces Viridochromogenes
Length = 287
Score = 49.3 bits (116), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 36/149 (24%), Positives = 68/149 (45%), Gaps = 11/149 (7%)
Query: 4 MKSRKQREKKGWLMLEGKRILIDALKANLKLKMVFFSQWDILKELPLPEDVPQHRVDYKN 63
+ +R +R + G ++ G R + A++ ++ + + D +EL V +
Sbjct: 29 LGNRNKRTRAGEFLVXGVRPISLAVEHGWPVRTLLY---DGQRELSKWARELLRTVRTEQ 85
Query: 64 IQLWSDLV--------TPPGIIGIFELPAHPIASIDPASLPLNIVCDNIRDPGNMGSILR 115
I DL+ PP ++ + E PA + I L ++ D PGN+GSI+R
Sbjct: 86 IAXAPDLLXELGEKNEAPPEVVAVVEXPADDLDRIPVREDFLGVLFDRPTSPGNIGSIIR 145
Query: 116 VCAAVGARQVVCSRGCVDIYDNKVIRAAA 144
A+GA ++ + D+YD K +R++
Sbjct: 146 SADALGAHGLIVAGHAADVYDPKSVRSST 174
>pdb|1AIH|A Chain A, Catalytic Domain Of Bacteriophage Hp1 Integrase
pdb|1AIH|B Chain B, Catalytic Domain Of Bacteriophage Hp1 Integrase
pdb|1AIH|C Chain C, Catalytic Domain Of Bacteriophage Hp1 Integrase
pdb|1AIH|D Chain D, Catalytic Domain Of Bacteriophage Hp1 Integrase
Length = 170
Score = 32.0 bits (71), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 13/23 (56%), Positives = 18/23 (78%), Gaps = 1/23 (4%)
Query: 101 CDNIRDPGNMGSILRVCAAVGAR 123
CDN R+P ++G I+R+C A GAR
Sbjct: 19 CDNSRNP-DLGLIVRICLATGAR 40
>pdb|1V2X|A Chain A, Trmh
Length = 194
Score = 31.2 bits (69), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 97 LNIVCDNIRDPGNMGSILRVCAAVG 121
L ++ +N+ P N+ +ILR C AVG
Sbjct: 23 LTVLLENVHKPHNLSAILRTCDAVG 47
>pdb|1GZ0|A Chain A, 23s Ribosomal Rna G2251 2'o-Methyltransferase Rlmb
pdb|1GZ0|B Chain B, 23s Ribosomal Rna G2251 2'o-Methyltransferase Rlmb
pdb|1GZ0|C Chain C, 23s Ribosomal Rna G2251 2'o-Methyltransferase Rlmb
pdb|1GZ0|D Chain D, 23s Ribosomal Rna G2251 2'o-Methyltransferase Rlmb
pdb|1GZ0|E Chain E, 23s Ribosomal Rna G2251 2'o-Methyltransferase Rlmb
pdb|1GZ0|F Chain F, 23s Ribosomal Rna G2251 2'o-Methyltransferase Rlmb
pdb|1GZ0|G Chain G, 23s Ribosomal Rna G2251 2'o-Methyltransferase Rlmb
pdb|1GZ0|H Chain H, 23s Ribosomal Rna G2251 2'o-Methyltransferase Rlmb
Length = 253
Score = 30.0 bits (66), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 87 IASIDPASLPLNIVCDNIRDPGNMGSILRVCAAVGARQVV 126
IAS+D P ++ D + DP N+G+ LR A G V+
Sbjct: 99 IASLDQ---PFLLILDGVTDPHNLGACLRSADAAGVHAVI 135
>pdb|3NK6|A Chain A, Structure Of The Nosiheptide-Resistance Methyltransferase
pdb|3NK6|B Chain B, Structure Of The Nosiheptide-Resistance Methyltransferase
pdb|3NK7|A Chain A, Structure Of The Nosiheptide-Resistance Methyltransferase
S-Adenosyl- L-Methionine Complex
pdb|3NK7|B Chain B, Structure Of The Nosiheptide-Resistance Methyltransferase
S-Adenosyl- L-Methionine Complex
Length = 277
Score = 29.3 bits (64), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 31/144 (21%), Positives = 62/144 (43%), Gaps = 7/144 (4%)
Query: 6 SRKQREKKGWLMLEGKRILIDALKANLKLKMVFFSQWD----ILKELPLPEDVPQHRVDY 61
++ R ++E L++ ++A ++ V+ S L +L ++P +D
Sbjct: 25 TKHSRASIKTTLIEDTEPLMECIRAGVQFIEVYGSSGTPLDPALLDLCRQREIPVRLIDV 84
Query: 62 KNIQLWSDLVTPPGIIGIFELPAHPIASIDPASLPLNIVC-DNIRDPGNMGSILRVCAAV 120
+ + GI +P P D A ++V D ++ GN+G+I+R A+
Sbjct: 85 SIVNQLFKAERKAKVFGIARVP-RPARLADIAERGGDVVVLDGVKIVGNIGAIVRTSLAL 143
Query: 121 GARQVV-CSRGCVDIYDNKVIRAA 143
GA +V I D +++RA+
Sbjct: 144 GAAGIVLVDSDLATIADRRLLRAS 167
>pdb|1ZJR|A Chain A, Crystal Structure Of A. Aeolicus TrmhSPOU TRNA MODIFYING
ENZYME
Length = 211
Score = 28.9 bits (63), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 97 LNIVCDNIRDPGNMGSILRVCAAVG 121
L + DN+++ N +I+R C AVG
Sbjct: 26 LIVFADNVKNEHNFSAIVRTCDAVG 50
>pdb|3E9A|A Chain A, Crystal Structure Of 2-dehydro-3-deoxyphosphooctonate
Aldolase From Vibrio Cholerae O1 Biovar Eltor Str.
N16961
Length = 286
Score = 28.9 bits (63), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 97 LNIVCDNIRDPGNMGSILRVCAAVGARQVV-CSRGCVDIYDNKVI 140
+N+ PG +G+I+ A G +V+ C RG YDN V+
Sbjct: 138 INVKKPQFMSPGQVGNIVEKFAECGNDKVILCERGSCHGYDNLVV 182
>pdb|3GYQ|A Chain A, Structure Of The Thiostrepton-Resistance Methyltransferase
S-Adenosyl-L-Methionine Complex
pdb|3GYQ|B Chain B, Structure Of The Thiostrepton-Resistance Methyltransferase
S-Adenosyl-L-Methionine Complex
Length = 272
Score = 28.1 bits (61), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 99 IVCDNIRDPGNMGSILRVCAAVGARQVV-CSRGCVDIYDNKVIRAA 143
+V D ++ GN+G+I+R A+GA ++ I D ++ RA+
Sbjct: 122 VVLDGVKIVGNIGAIVRTSLALGASGIILVDSDITSIADRRLQRAS 167
>pdb|3E5Y|A Chain A, Crystal Structure Of Trmh Family Rna Methyltransferase
From Burkholderia Pseudomallei
pdb|3E5Y|B Chain B, Crystal Structure Of Trmh Family Rna Methyltransferase
From Burkholderia Pseudomallei
Length = 160
Score = 27.7 bits (60), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 92 PASLPLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGCVDIYDNKVIRAA 143
P S+ N+V P N G+++R+CA GAR + + D K+ RA
Sbjct: 2 PGSM-FNVVLVEPEIPPNTGNVIRLCANTGARLHLIEPLGFPLDDAKMRRAG 52
>pdb|3D5W|A Chain A, Crystal Structure Of A Phosphorylated Polo-Like Kinase 1
(Plk1) Catalytic Domain In Complex With Adp
Length = 317
Score = 27.3 bits (59), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 84 AHPIASIDPASLPLNIVCDNIRDPGNMGSILR 115
A P A +DP S PL + D + DP M +R
Sbjct: 15 AKPSAHVDPKSAPLKEIPDVLVDPRTMKRYMR 46
>pdb|3D5V|A Chain A, Crystal Structure Of An Activated (Thr->asp) Polo-Like
Kinase 1 (Plk1) Catalytic Domain.
pdb|3DB8|A Chain A, Crystal Structure Of An Activated (Thr->asp) Polo-Like
Kinase 1 (Plk1) Catalytic Domain In Complex With
Compound 041
pdb|3DBC|A Chain A, Crystal Structure Of An Activated (Thr->asp) Polo-Like
Kinase 1 (Plk1) Catalytic Domain In Complex With
Compound 257
pdb|3DBD|A Chain A, Crystal Structure Of An Activated (Thr->asp) Polo-Like
Kinase 1 (Plk1) Catalytic Domain In Complex With
Compound 094
Length = 317
Score = 27.3 bits (59), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 84 AHPIASIDPASLPLNIVCDNIRDPGNMGSILR 115
A P A +DP S PL + D + DP M +R
Sbjct: 15 AKPSAHVDPKSAPLKEIPDVLVDPRTMKRYMR 46
>pdb|3D5U|A Chain A, Crystal Structure Of A Wildtype Polo-Like Kinase 1 (Plk1)
Catalytic Domain
Length = 317
Score = 27.3 bits (59), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 84 AHPIASIDPASLPLNIVCDNIRDPGNMGSILR 115
A P A +DP S PL + D + DP M +R
Sbjct: 15 AKPSAHVDPKSAPLKEIPDVLVDPRTMKRYMR 46
>pdb|3GNU|P Chain P, Toxin Fold As Basis For Microbial Attack And Plant Defense
Length = 213
Score = 27.3 bits (59), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 12/47 (25%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 37 VFFSQWDILKELPLPEDVPQ----HRVDYKNIQLWSDLVTPPGIIGI 79
+ +DI+ +P+D P HR D++N+ +W D I+ +
Sbjct: 77 TYNGYYDIMYSWYMPKDSPSIGIGHRHDWENVVVWLDNAASANIVAL 123
>pdb|1K77|A Chain A, Crystal Structure Of Ec1530, A Putative Oxygenase From
Escherichia Coli
Length = 260
Score = 26.6 bits (57), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 19 EGKRILIDALKANLKLKMVFFSQWDIL 45
GKRIL++AL +K +F SQ+ L
Sbjct: 136 HGKRILVEALSPGVKPHYLFSSQYQAL 162
>pdb|3N4J|A Chain A, Putative Rna Methyltransferase From Yersinia Pestis
pdb|3N4K|A Chain A, Putative Rna Methyltransferase From Yersinia Pestis In
Complex With S- Adenosyl-L-Homocysteine.
pdb|3N4K|B Chain B, Putative Rna Methyltransferase From Yersinia Pestis In
Complex With S- Adenosyl-L-Homocysteine
Length = 165
Score = 26.6 bits (57), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 97 LNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGCVDIYDNKVIRAAA 144
LNIV P N G+I+R+CA G Q+ + +D+K +R A
Sbjct: 5 LNIVLFEPEIPPNTGNIIRLCANTGC-QLHLIKPLGFTWDDKRLRRAG 51
>pdb|4ACO|A Chain A, Structure Of The Budding Yeast Ndc10 N-Terminal Domain
Length = 956
Score = 25.8 bits (55), Expect = 9.1, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 5/53 (9%)
Query: 24 LIDALKA----NLKLKMVFFSQWDILKEL-PLPEDVPQHRVDYKNIQLWSDLV 71
L+D+LK K + QW L ++ P PED + V YK++ + ++L+
Sbjct: 33 LVDSLKPRTAHQYKTYYTKYIQWCQLNQIIPTPEDNSVNSVPYKDLPISAELI 85
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.324 0.141 0.438
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,508,095
Number of Sequences: 62578
Number of extensions: 189745
Number of successful extensions: 399
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 383
Number of HSP's gapped (non-prelim): 19
length of query: 144
length of database: 14,973,337
effective HSP length: 89
effective length of query: 55
effective length of database: 9,403,895
effective search space: 517214225
effective search space used: 517214225
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 46 (22.3 bits)