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= psy14943
(328 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1XBR|A Chain A, T Domain From Xenopus Laevis Bound To Dna
pdb|1XBR|B Chain B, T Domain From Xenopus Laevis Bound To Dna
Length = 184
Score = 271 bits (692), Expect = 5e-73, Method: Compositional matrix adjust.
Identities = 129/192 (67%), Positives = 153/192 (79%), Gaps = 11/192 (5%)
Query: 53 QVILEDLDLWLKFQSHTNEMIVTKNGRRMFPVVKVSIKGLEPDAMYTVLLEFLQIEQKRW 112
+V LE+ DLW +F+ TNEMIVTKNGRRMFPV+KVS+ GL+P+AMYTVLL+F+ + RW
Sbjct: 3 KVSLEERDLWTRFKELTNEMIVTKNGRRMFPVLKVSMSGLDPNAMYTVLLDFVAADNHRW 62
Query: 113 KYVNGEWVPAGKPEQPPMNAMYLHPESPNFGEHWMKDCVSFAKVKLTNHSNGSGQIMLNS 172
KYVNGEWVP GKPE + +Y+HP+SPNFG HWMKD VSF+KVKLTN NG GQIMLNS
Sbjct: 63 KYVNGEWVPGGKPEPQAPSCVYIHPDSPNFGAHWMKDPVSFSKVKLTNKMNGGGQIMLNS 122
Query: 173 LHKYEPRIHLVKVATEQQIIKTFPFPETQFIAVTAYQNEEFIAVTAYQNEEVTSLKIKFN 232
LHKYEPRIH+V+V Q++I + FPETQFIA VTAYQNEE+T+LKIK N
Sbjct: 123 LHKYEPRIHIVRVGGTQRMITSHSFPETQFIA-----------VTAYQNEEITALKIKHN 171
Query: 233 PFAKAFLDAKEK 244
PFAKAFLDAKE+
Sbjct: 172 PFAKAFLDAKER 183
Score = 93.6 bits (231), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 40/58 (68%), Positives = 46/58 (79%)
Query: 255 NEWKYVNGEWVPAGKPEQPPMNAMYLHPESPNFGEHWMKDCVSFAKVKLTNHSNGSGQ 312
+ WKYVNGEWVP GKPE + +Y+HP+SPNFG HWMKD VSF+KVKLTN NG GQ
Sbjct: 60 HRWKYVNGEWVPGGKPEPQAPSCVYIHPDSPNFGAHWMKDPVSFSKVKLTNKMNGGGQ 117
Score = 44.3 bits (103), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 18/28 (64%), Positives = 25/28 (89%)
Query: 1 MFPVVKVSIKGLEPDAMYTVLLEFLQIE 28
MFPV+KVS+ GL+P+AMYTVLL+F+ +
Sbjct: 31 MFPVLKVSMSGLDPNAMYTVLLDFVAAD 58
>pdb|1H6F|A Chain A, Human Tbx3, A Transcription Factor Responsible For Ulnar-
Mammary Syndrome, Bound To A Palindromic Dna Site
pdb|1H6F|B Chain B, Human Tbx3, A Transcription Factor Responsible For Ulnar-
Mammary Syndrome, Bound To A Palindromic Dna Site
Length = 193
Score = 166 bits (421), Expect = 1e-41, Method: Compositional matrix adjust.
Identities = 88/198 (44%), Positives = 123/198 (62%), Gaps = 20/198 (10%)
Query: 51 NPQVILEDLDLWLKFQSHTNEMIVTKNGRRMFPVVKVSIKGLEPDAMYTVLLEFLQIEQK 110
+P+V LE +LW +F EM++TK+GRRMFP KV GL+ A Y +L++ + +
Sbjct: 4 DPKVHLEAKELWDQFHKRGTEMVITKSGRRMFPPFKVRCSGLDKKAKYILLMDIIAADDC 63
Query: 111 RWKYVNGEWVPAGK--PEQPPMNAMYLHPESPNFGEHWMKDCVSFAKVKLTNH-SNGSGQ 167
R+K+ N W+ AGK PE P MY+HP+SP GE WM V+F K+KLTN+ S+ G
Sbjct: 64 RYKFHNSRWMVAGKADPEMP--KRMYIHPDSPATGEQWMSKVVTFHKLKLTNNISDKHGF 121
Query: 168 IMLNSLHKYEPRIHLVKVATEQQI----IKTFPFPETQFIAVTAYQNEEFIAVTAYQNEE 223
+LNS+HKY+PR H+V+ ++ +T+ FPET+FI AVTAYQN++
Sbjct: 122 TILNSMHKYQPRFHIVRANDILKLPYSTFRTYLFPETEFI-----------AVTAYQNDK 170
Query: 224 VTSLKIKFNPFAKAFLDA 241
+T LKI NPFAK F D
Sbjct: 171 ITQLKIDNNPFAKGFRDT 188
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/61 (47%), Positives = 37/61 (60%), Gaps = 6/61 (9%)
Query: 256 EWKYVNGEWVPAGK--PEQPPMNAMYLHPESPNFGEHWMKDCVSFAKVKLTNHSNGSGQS 313
+K+ N W+ AGK PE P MY+HP+SP GE WM V+F K+KLTN N S +
Sbjct: 64 RYKFHNSRWMVAGKADPEMP--KRMYIHPDSPATGEQWMSKVVTFHKLKLTN--NISDKH 119
Query: 314 G 314
G
Sbjct: 120 G 120
>pdb|2X6U|A Chain A, Crystal Structure Of Human Tbx5 In The Dna-Free Form
pdb|2X6V|A Chain A, Crystal Structure Of Human Tbx5 In The Dna-Bound And Dna-
Free Form
pdb|2X6V|B Chain B, Crystal Structure Of Human Tbx5 In The Dna-Bound And Dna-
Free Form
Length = 203
Score = 165 bits (418), Expect = 3e-41, Method: Compositional matrix adjust.
Identities = 85/198 (42%), Positives = 118/198 (59%), Gaps = 18/198 (9%)
Query: 53 QVILEDLDLWLKFQSHTNEMIVTKNGRRMFPVVKVSIKGLEPDAMYTVLLEFLQIEQKRW 112
+V L + +LWLKF EMI+TK GRRMFP KV + GL P Y +L++ + + R+
Sbjct: 7 KVFLHERELWLKFHEVGTEMIITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVPADDHRY 66
Query: 113 KYVNGEWVPAGKPEQPPMNAMYLHPESPNFGEHWMKDCVSFAKVKLT-NHSNGSGQIMLN 171
K+ + +W GK E +Y+HP+SP G HWM+ VSF K+KLT NH + G I+LN
Sbjct: 67 KFADNKWSVTGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILN 126
Query: 172 SLHKYEPRIHLVKV------ATEQQIIKTFPFPETQFIAVTAYQNEEFIAVTAYQNEEVT 225
S+HKY+PR+H+VK ++ T FPET F IAVT+YQN ++T
Sbjct: 127 SMHKYQPRLHIVKADENNGFGSKNTAFCTHVFPETAF-----------IAVTSYQNHKIT 175
Query: 226 SLKIKFNPFAKAFLDAKE 243
LKI+ NPFAK F + +
Sbjct: 176 QLKIENNPFAKGFRGSDD 193
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 32/51 (62%)
Query: 255 NEWKYVNGEWVPAGKPEQPPMNAMYLHPESPNFGEHWMKDCVSFAKVKLTN 305
+ +K+ + +W GK E +Y+HP+SP G HWM+ VSF K+KLTN
Sbjct: 64 HRYKFADNKWSVTGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTN 114
>pdb|4A04|A Chain A, Structure Of The Dna-Bound T-Box Domain Of Human Tbx1, A
Transcription Factor Associated With The Digeorge
Syndrome
pdb|4A04|B Chain B, Structure Of The Dna-Bound T-Box Domain Of Human Tbx1, A
Transcription Factor Associated With The Digeorge
Syndrome
Length = 203
Score = 154 bits (389), Expect = 7e-38, Method: Compositional matrix adjust.
Identities = 86/201 (42%), Positives = 118/201 (58%), Gaps = 21/201 (10%)
Query: 50 GNPQVILEDLDLWLKFQSHTNEMIVTKNGRRMFPVVKVSIKGLEPDAMYTVLLEFLQIEQ 109
G V LE LW +F EMIVTK GRRMFP +V + G++P A Y +L++F+ ++
Sbjct: 14 GGVSVQLEMKALWDEFNQLGTEMIVTKAGRRMFPTFQVKLFGMDPMADYMLLMDFVPVDD 73
Query: 110 KRWKYV--NGEWVPAGKPEQPPMNAMYLHPESPNFGEHWMKDCVSFAKVKLTNH-SNGSG 166
KR++Y + W+ AGK + ++ HP+SP G WMK VSF K+KLTN+ + +G
Sbjct: 74 KRYRYAFHSSSWLVAGKADPATPGRVHYHPDSPAKGAQWMKQIVSFDKLKLTNNLLDDNG 133
Query: 167 QIMLNSLHKYEPRIHLVKVATE-------QQIIKTFPFPETQFIAVTAYQNEEFIAVTAY 219
I+LNS+H+Y+PR H+V V ++ KTF F ET+ F AVTAY
Sbjct: 134 HIILNSMHRYQPRFHVVYVDPRKDSEKYAEENFKTFVFEETR-----------FTAVTAY 182
Query: 220 QNEEVTSLKIKFNPFAKAFLD 240
QN +T LKI NPFAK F D
Sbjct: 183 QNHRITQLKIASNPFAKGFRD 203
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 30/51 (58%)
Query: 256 EWKYVNGEWVPAGKPEQPPMNAMYLHPESPNFGEHWMKDCVSFAKVKLTNH 306
+ + + W+ AGK + ++ HP+SP G WMK VSF K+KLTN+
Sbjct: 77 RYAFHSSSWLVAGKADPATPGRVHYHPDSPAKGAQWMKQIVSFDKLKLTNN 127
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 21/30 (70%)
Query: 1 MFPVVKVSIKGLEPDAMYTVLLEFLQIEQK 30
MFP +V + G++P A Y +L++F+ ++ K
Sbjct: 45 MFPTFQVKLFGMDPMADYMLLMDFVPVDDK 74
>pdb|2HAK|A Chain A, Catalytic And Ubiqutin-Associated Domains Of Mark1PAR-1
pdb|2HAK|B Chain B, Catalytic And Ubiqutin-Associated Domains Of Mark1PAR-1
pdb|2HAK|C Chain C, Catalytic And Ubiqutin-Associated Domains Of Mark1PAR-1
pdb|2HAK|D Chain D, Catalytic And Ubiqutin-Associated Domains Of Mark1PAR-1
pdb|2HAK|E Chain E, Catalytic And Ubiqutin-Associated Domains Of Mark1PAR-1
pdb|2HAK|F Chain F, Catalytic And Ubiqutin-Associated Domains Of Mark1PAR-1
pdb|2HAK|G Chain G, Catalytic And Ubiqutin-Associated Domains Of Mark1PAR-1
pdb|2HAK|H Chain H, Catalytic And Ubiqutin-Associated Domains Of Mark1PAR-1
Length = 328
Score = 27.7 bits (60), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 26/117 (22%), Positives = 46/117 (39%), Gaps = 17/117 (14%)
Query: 138 ESPNFGEHWMKDCV---SFAKVKLTNHSNGSGQIML----------NSLHKYEPRIHLVK 184
E P+ G + ++ + +FAKVKL H ++ + SL K + ++K
Sbjct: 10 EQPHIGNYRLQKTIGKGNFAKVKLARHVLTGREVAVKIIDKTQLNPTSLQKLFREVRIMK 69
Query: 185 VATEQQIIKTFPFPETQ----FIAVTAYQNEEFIAVTAYQNEEVTSLKIKFNPFAKA 237
+ I+K F ET+ + A E F + A+ + + KF A
Sbjct: 70 ILNHPNIVKLFEVIETEKTLYLVMEYASGGEVFDYLVAHGRMKEKEARAKFRQIVSA 126
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
0.316 0.132 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,502,627
Number of Sequences: 62578
Number of extensions: 449484
Number of successful extensions: 940
Number of sequences better than 100.0: 35
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 893
Number of HSP's gapped (non-prelim): 51
length of query: 328
length of database: 14,973,337
effective HSP length: 99
effective length of query: 229
effective length of database: 8,778,115
effective search space: 2010188335
effective search space used: 2010188335
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)