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= 023877
(276 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3HL4|A Chain A, Crystal Structure Of A Mammalian Ctp:phosphocholine
Cytidylyltransferase With Cdp-Choline
pdb|3HL4|B Chain B, Crystal Structure Of A Mammalian Ctp:phosphocholine
Cytidylyltransferase With Cdp-Choline
Length = 236
Score = 226 bits (577), Expect = 8e-60, Method: Compositional matrix adjust.
Identities = 103/164 (62%), Positives = 131/164 (79%), Gaps = 2/164 (1%)
Query: 19 RPVRVYADGIYDLFHFGHARSLEQAKKSFPNTYLLVGCCNDETTHKFKGKTVMTEDERYE 78
RPVRVYADGI+DLFH GHAR+L QAK FPNTYL+VG C+DE TH FKG TVM E+ERY+
Sbjct: 75 RPVRVYADGIFDLFHSGHARALMQAKNLFPNTYLIVGVCSDELTHNFKGFTVMNENERYD 134
Query: 79 SLRHCKWVDEVIPDAPWVVTQEFLDKHQIDFVAHDSLPYADASGAGKDVYEFVKAAGKFK 138
+++HC++VDEV+ +APW +T EFL +H+IDFVAHD +PY +S DVY+ +K AG F
Sbjct: 135 AVQHCRYVDEVVRNAPWTLTPEFLAEHRIDFVAHDDIPY--SSAGSDDVYKHIKEAGMFA 192
Query: 139 ETKRTDGISTSDIIMRIVKDYNQYVMRNLDRGYSRKDLGVSYVK 182
T+RT+GISTSDII RIV+DY+ Y RNL RGY+ K+L VS++
Sbjct: 193 PTQRTEGISTSDIITRIVRDYDVYARRNLQRGYTAKELNVSFIN 236
>pdb|3ELB|A Chain A, Human Ctp: Phosphoethanolamine Cytidylyltransferase In
Complex With Cmp
Length = 341
Score = 124 bits (311), Expect = 6e-29, Method: Compositional matrix adjust.
Identities = 63/136 (46%), Positives = 86/136 (63%), Gaps = 4/136 (2%)
Query: 19 RPVRVYADGIYDLFHFGHARSLEQAKKSFPNTYLLVGCCNDETTHKFKGKTVMTEDERYE 78
R VRV+ DG YD H+GH+ L QA+ YL+VG DE K KG V T++ERY+
Sbjct: 6 RAVRVWCDGCYDXVHYGHSNQLRQARAX--GDYLIVGVHTDEEIAKHKGPPVFTQEERYK 63
Query: 79 SLRHCKWVDEVIPDAPWVVTQEFLDKHQIDFVAHDSLPYADASGAGKDVYEFVKAAGKFK 138
++ KWVDEV+P AP+V T E LDK+ DF H + + G+D YE VK AG+++
Sbjct: 64 XVQAIKWVDEVVPAAPYVTTLETLDKYNCDFCVHGND--ITLTVDGRDTYEEVKQAGRYR 121
Query: 139 ETKRTDGISTSDIIMR 154
E KRT G+ST+D++ R
Sbjct: 122 ECKRTQGVSTTDLVGR 137
Score = 74.7 bits (182), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 45/145 (31%), Positives = 73/145 (50%), Gaps = 9/145 (6%)
Query: 23 VYADGIYDLFHFGHARSLEQAKKSFPNTYLLVGCCNDETTHKFKGKT--VMTEDERYESL 80
+Y G +DLFH GH LE+ + Y++ G D+ + +KGK + ER S+
Sbjct: 201 IYVAGAFDLFHIGHVDFLEKVHRLAERPYIIAGLHFDQEVNHYKGKNYPIXNLHERTLSV 260
Query: 81 RHCKWVDEVIPDAPWVVTQEFLDKHQIDFVAH---DSLPYADASGAGKDVYEFVKAAGKF 137
C++V EV+ AP+ VT E L ++D V H + +P D G D Y+ K G F
Sbjct: 261 LACRYVSEVVIGAPYAVTAELLSHFKVDLVCHGKTEIIPDRD----GSDPYQEPKRRGIF 316
Query: 138 KETKRTDGISTSDIIMRIVKDYNQY 162
++ ++T I+ RI+ + +Y
Sbjct: 317 RQIDSGSNLTTDLIVQRIITNRLEY 341
>pdb|1COZ|A Chain A, Ctp:glycerol-3-Phosphate Cytidylyltransferase From
Bacillus Subtilis
pdb|1COZ|B Chain B, Ctp:glycerol-3-Phosphate Cytidylyltransferase From
Bacillus Subtilis
pdb|1N1D|A Chain A, Glycerol-3-phosphate Cytidylyltransferase Complexed With
Cdp-glycerol
pdb|1N1D|B Chain B, Glycerol-3-phosphate Cytidylyltransferase Complexed With
Cdp-glycerol
pdb|1N1D|C Chain C, Glycerol-3-phosphate Cytidylyltransferase Complexed With
Cdp-glycerol
pdb|1N1D|D Chain D, Glycerol-3-phosphate Cytidylyltransferase Complexed With
Cdp-glycerol
Length = 129
Score = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 43/131 (32%), Positives = 66/131 (50%), Gaps = 12/131 (9%)
Query: 22 RVYADGIYDLFHFGHARSLEQAKKSFPNTYLLVGCCNDETTHKFKGKTVMTEDERYESLR 81
+V G +DL H+GH + LE+AK+ YL+V DE + + K + + R L
Sbjct: 3 KVITYGTFDLLHWGHIKLLERAKQL--GDYLVVAISTDEFNLQKQKKAYHSYEHRKLILE 60
Query: 82 HCKWVDEVIPDAPWVVTQEFLDKHQID-FVAHDSLPYADASGAGKDVYEFVKAAGKFKET 140
++VDEVIP+ W ++ + H ID FV D D G ++F+K +
Sbjct: 61 TIRYVDEVIPEKNWEQKKQDIIDHNIDVFVMGD-----DWEGK----FDFLKDQCEVVYL 111
Query: 141 KRTDGISTSDI 151
RT+GIST+ I
Sbjct: 112 PRTEGISTTKI 122
>pdb|2B7L|A Chain A, Crystal Structure Of Ctp:glycerol-3-Phosphate
Cytidylyltransferase From Staphylococcus Aureus
pdb|2B7L|B Chain B, Crystal Structure Of Ctp:glycerol-3-Phosphate
Cytidylyltransferase From Staphylococcus Aureus
pdb|2B7L|C Chain C, Crystal Structure Of Ctp:glycerol-3-Phosphate
Cytidylyltransferase From Staphylococcus Aureus
pdb|2B7L|D Chain D, Crystal Structure Of Ctp:glycerol-3-Phosphate
Cytidylyltransferase From Staphylococcus Aureus
Length = 132
Score = 52.4 bits (124), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 39/132 (29%), Positives = 63/132 (47%), Gaps = 14/132 (10%)
Query: 22 RVYADGIYDLFHFGHARSLEQAKKSFPNTYLLVGCCNDETTHKFKGKTVMTEDERYESLR 81
RV G YDL H+GH L +A++ YL+V DE K+ ++R L
Sbjct: 3 RVITYGTYDLLHYGHIELLRRAREM--GDYLIVALSTDEFNQIKHKKSYYDYEQRKMMLE 60
Query: 82 HCKWVDEVIPDAPWVVTQEFLDKHQID--FVAHDSLPYADASGAGKDVYEFVKAAGKFKE 139
++VD VIP+ W ++ ++K +D + HD + ++F+K +
Sbjct: 61 SIRYVDLVIPEKGWGQKEDDVEKFDVDVFVMGHD----------WEGEFDFLKDKCEVIY 110
Query: 140 TKRTDGISTSDI 151
KRT+GIST+ I
Sbjct: 111 LKRTEGISTTKI 122
>pdb|3GLV|A Chain A, Crystal Structure Of The Lipopolysaccharide Core
Biosynthesis Protein From Thermoplasma Volcanium Gss1
pdb|3GLV|B Chain B, Crystal Structure Of The Lipopolysaccharide Core
Biosynthesis Protein From Thermoplasma Volcanium Gss1
Length = 143
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 2/70 (2%)
Query: 21 VRVYADGIYDLFHFGHARSLEQAKKSFPNTYLLVGCCNDETTHKFKGKTVMTEDERYESL 80
+RV A G++D+ H GH L+++KK L+V D T + E+ R +
Sbjct: 3 IRVMATGVFDILHLGHIHYLKESKK--LGDELVVVVARDSTARNNGKIPIFDENSRLALI 60
Query: 81 RHCKWVDEVI 90
K VD I
Sbjct: 61 SELKVVDRAI 70
>pdb|1UYW|H Chain H, Crystal Structure Of The Antiflavivirus Fab4g2
pdb|1UYW|M Chain M, Crystal Structure Of The Antiflavivirus Fab4g2
Length = 218
Score = 32.0 bits (71), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 21 VRVYA-DGIYDLFHFGHARSLEQAKKSFPNTYLLVGCCNDET 61
R+Y DG +D++ G A ++ AK + P+ Y L C D T
Sbjct: 96 ARIYHYDGYFDVWGAGTAVTVSSAKTTAPSVYPLAPVCGDTT 137
>pdb|3AVR|A Chain A, Catalytic Fragment Of UtxKDM6A BOUND WITH HISTONE H3K27ME3
PEPTIDE, N-Oxyalylglycine, And Ni(Ii)
pdb|3AVS|A Chain A, Catalytic Fragment Of UtxKDM6A BOUND WITH
N-Oxyalylglycine, And Ni(Ii)
Length = 531
Score = 31.2 bits (69), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 83 CKWVDEVIPDAPWVVTQEFLDKHQIDFVAHDSLP-YADASGAGKDVYEFVKAAG 135
C+W V+P+ W V +F +K+ ++F+ P D A VY F++ G
Sbjct: 294 CEWF--VVPEGYWGVLNDFCEKNNLNFLMGSWWPNLEDLYEANVPVYRFIQRPG 345
>pdb|3ZLI|A Chain A, Crystal Structure Of Jmjc Domain Of Human Histone
Demethylase Uty
pdb|3ZLI|B Chain B, Crystal Structure Of Jmjc Domain Of Human Histone
Demethylase Uty
Length = 478
Score = 30.8 bits (68), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 83 CKWVDEVIPDAPWVVTQEFLDKHQIDFVAHDSLP-YADASGAGKDVYEFVKAAG 135
C+W V+P+ W V +F +K+ ++F+ P D A VY F++ G
Sbjct: 235 CEWF--VVPEDYWGVLNDFCEKNNLNFLMSSWWPNLEDLYEANVPVYRFIQRPG 286
>pdb|1MPA|H Chain H, Bactericidal Antibody Against Neisseria Meningitidis
pdb|1MNU|H Chain H, Unliganded Bactericidal Antibody Against Neisseria
Meningitidis
pdb|2MPA|H Chain H, Bactericidal Antibody Against Neisseria Meningitidis
Length = 225
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 19/38 (50%)
Query: 24 YADGIYDLFHFGHARSLEQAKKSFPNTYLLVGCCNDET 61
YAD I D + G ++ AK + P+ Y L C D T
Sbjct: 103 YADFIMDYWGQGTTVTVSSAKTTAPSVYPLAPVCGDTT 140
>pdb|4BCF|A Chain A, Structure Of Cdk9 In Complex With Cyclin T And A
2-amino-4- Heteroaryl-pyrimidine Inhibitor
Length = 331
Score = 29.3 bits (64), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 17/31 (54%)
Query: 21 VRVYADGIYDLFHFGHARSLEQAKKSFPNTY 51
V + DG+ L FG AR+ AK S PN Y
Sbjct: 156 VLITRDGVLKLADFGLARAFSLAKNSQPNRY 186
>pdb|3BLH|A Chain A, Crystal Structure Of Human Cdk9CYCLINT1
pdb|3BLQ|A Chain A, Crystal Structure Of Human Cdk9CYCLINT1 IN COMPLEX WITH
ATP
pdb|3BLR|A Chain A, Crystal Structure Of Human Cdk9CYCLINT1 IN COMPLEX WITH
Flavopiridol
pdb|3MY1|A Chain A, Structure Of Cdk9CYCLINT1 IN COMPLEX WITH DRB
pdb|3LQ5|A Chain A, Structure Of Cdk9CYCLINT IN COMPLEX WITH S-Cr8
pdb|3TN8|A Chain A, Cdk9CYCLIN T IN COMPLEX WITH CAN508
pdb|3TNH|A Chain A, Cdk9CYCLIN T IN COMPLEX WITH CAN508
pdb|3TNI|A Chain A, Structure Of Cdk9CYCLIN T F241L
pdb|4BCH|A Chain A, Structure Of Cdk9 In Complex With Cyclin T And A
2-amino-4- Heteroaryl-pyrimidine Inhibitor
pdb|4BCI|A Chain A, Structure Of Cdk9 In Complex With Cyclin T And A
2-amino-4- Heteroaryl-pyrimidine Inhibitor
pdb|4BCJ|A Chain A, Structure Of Cdk9 In Complex With Cyclin T And A
2-amino-4- Heteroaryl-pyrimidine Inhibitor
Length = 331
Score = 29.3 bits (64), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 17/31 (54%)
Query: 21 VRVYADGIYDLFHFGHARSLEQAKKSFPNTY 51
V + DG+ L FG AR+ AK S PN Y
Sbjct: 156 VLITRDGVLKLADFGLARAFSLAKNSQPNRY 186
>pdb|3MI9|A Chain A, Crystal Structure Of Hiv-1 Tat Complexed With Human P-Tefb
pdb|3MIA|A Chain A, Crystal Structure Of Hiv-1 Tat Complexed With Atp-Bound
Human P-Tefb
Length = 351
Score = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 17/31 (54%)
Query: 21 VRVYADGIYDLFHFGHARSLEQAKKSFPNTY 51
V + DG+ L FG AR+ AK S PN Y
Sbjct: 155 VLITRDGVLKLADFGLARAFSLAKNSQPNRY 185
>pdb|4EC8|A Chain A, Structure Of Full Length Cdk9 In Complex With Cyclint And
Drb
pdb|4EC9|A Chain A, Crystal Structure Of Full-Length Cdk9 In Complex With
Cyclin T
Length = 373
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 17/31 (54%)
Query: 21 VRVYADGIYDLFHFGHARSLEQAKKSFPNTY 51
V + DG+ L FG AR+ AK S PN Y
Sbjct: 156 VLITRDGVLKLADFGLARAFSLAKNSQPNRY 186
>pdb|1QO8|A Chain A, The Structure Of The Open Conformation Of A
Flavocytochrome C3 Fumarate Reductase
pdb|1QO8|D Chain D, The Structure Of The Open Conformation Of A
Flavocytochrome C3 Fumarate Reductase
Length = 566
Score = 27.3 bits (59), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 124 GKDVYEFVKAAGKFKETKRTDGISTSDIIMRIVKDYNQYVMRNLDRGYSRKDL 176
G D E + ++ ++ G+ +D+ + V DYN YV D + R D+
Sbjct: 429 GYDHLEMLYKGDTVEQLAKSTGMKVADL-AKTVSDYNGYVASGKDTAFGRADM 480
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
0.325 0.139 0.425
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,688,451
Number of Sequences: 62578
Number of extensions: 247920
Number of successful extensions: 729
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 705
Number of HSP's gapped (non-prelim): 21
length of query: 276
length of database: 14,973,337
effective HSP length: 97
effective length of query: 179
effective length of database: 8,903,271
effective search space: 1593685509
effective search space used: 1593685509
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 bits)