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= psy10809
(136 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1KI1|B Chain B, Guanine Nucleotide Exchange Region Of Intersectin In
Complex With Cdc42
pdb|1KI1|D Chain D, Guanine Nucleotide Exchange Region Of Intersectin In
Complex With Cdc42
Length = 352
Score = 64.7 bits (156), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 51/81 (62%)
Query: 28 QQPEFVQLLKRLEMKPACQGRSLEMFLTFPMHQIPRYIVTLHELLAHTPHDHVERKSLQN 87
+ P+F + +KRLEM P C+G L F+ PM ++ RY + + +L +TP +H + L++
Sbjct: 121 EAPDFKEFVKRLEMDPRCKGMPLSSFILKPMQRVTRYPLIIKNILENTPENHPDHSHLKH 180
Query: 88 ARQQLEDLSRQMHDEVSETEN 108
A ++ E+L Q+++ V E EN
Sbjct: 181 ALEKAEELCSQVNEGVREKEN 201
>pdb|3JV3|A Chain A, Structure Of Sh3e-Dh Unit Of Murine Intersectin-1l
pdb|3JV3|B Chain B, Structure Of Sh3e-Dh Unit Of Murine Intersectin-1l
Length = 283
Score = 62.8 bits (151), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 50/81 (61%)
Query: 28 QQPEFVQLLKRLEMKPACQGRSLEMFLTFPMHQIPRYIVTLHELLAHTPHDHVERKSLQN 87
+ P+F + +KRL M P C+G L F+ PM ++ RY + + +L +TP +H + L++
Sbjct: 194 EAPDFKEFVKRLAMDPRCKGMPLSSFILKPMQRVTRYPLIIKNILENTPENHPDHSHLKH 253
Query: 88 ARQQLEDLSRQMHDEVSETEN 108
A ++ E+L Q+++ V E EN
Sbjct: 254 ALEKAEELCSQVNEGVREKEN 274
>pdb|3QBV|B Chain B, Structure Of Designed Orthogonal Interaction Between Cdc42
And Nucleotide Exchange Domains Of Intersectin
pdb|3QBV|D Chain D, Structure Of Designed Orthogonal Interaction Between Cdc42
And Nucleotide Exchange Domains Of Intersectin
Length = 351
Score = 62.0 bits (149), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 50/81 (61%)
Query: 28 QQPEFVQLLKRLEMKPACQGRSLEMFLTFPMHQIPRYIVTLHELLAHTPHDHVERKSLQN 87
+ P+F + +KRL M P C+G L F+ PM ++ RY + + +L +TP +H + L++
Sbjct: 121 EAPDFKEFVKRLAMDPRCKGMPLSEFILKPMQRVTRYPLIIKNILENTPENHPDHSHLKH 180
Query: 88 ARQQLEDLSRQMHDEVSETEN 108
A ++ E+L Q+++ V E EN
Sbjct: 181 ALEKAEELCSQVNEGVREKEN 201
>pdb|3GF9|A Chain A, Crystal Structure Of Human Intersectin 2 Rhogef Domain
Length = 295
Score = 59.7 bits (143), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 36/105 (34%), Positives = 56/105 (53%), Gaps = 8/105 (7%)
Query: 10 QEYVR------NHHYSLQVLTECKQQPEFVQLLKRLEMKPACQGRSLEMFLTFPMHQIPR 63
Q Y+R N LQ T+ + +F + LK+L P C+G L FL PM +I R
Sbjct: 188 QAYIRFCSCQLNGAALLQQKTD--EDTDFKEFLKKLASDPRCKGMPLSSFLLKPMQRITR 245
Query: 64 YIVTLHELLAHTPHDHVERKSLQNARQQLEDLSRQMHDEVSETEN 108
Y + + +L +TP H + SL+ A ++ E+L Q+++ V E EN
Sbjct: 246 YPLLIRSILENTPESHADHSSLKLALERAEELCSQVNEGVREKEN 290
>pdb|3JZY|A Chain A, Crystal Structure Of Human Intersectin 2 C2 Domain
Length = 510
Score = 58.9 bits (141), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 46/78 (58%)
Query: 31 EFVQLLKRLEMKPACQGRSLEMFLTFPMHQIPRYIVTLHELLAHTPHDHVERKSLQNARQ 90
+F + LK+L P C+G L FL PM +I RY + + +L +TP H + SL+ A +
Sbjct: 142 DFKEFLKKLASDPRCKGMPLSSFLLKPMQRITRYPLLIRSILENTPESHADHSSLKLALE 201
Query: 91 QLEDLSRQMHDEVSETEN 108
+ E+L Q+++ V E EN
Sbjct: 202 RAEELCSQVNEGVREKEN 219
>pdb|3EO2|A Chain A, Crystal Structure Of The Rhogef Domain Of Human
Neuroepithelial Cell- Transforming Gene 1 Protein
Length = 231
Score = 47.4 bits (111), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 43/86 (50%)
Query: 3 LPMLGIYQEYVRNHHYSLQVLTECKQQPEFVQLLKRLEMKPACQGRSLEMFLTFPMHQIP 62
LP L Y+ Y N + +L + KQ P L+R P + L FL P ++
Sbjct: 115 LPRLNAYRGYCSNQLAAKALLDQKKQDPRVQDFLQRCLESPFSRKLDLWSFLDIPRSRLV 174
Query: 63 RYIVTLHELLAHTPHDHVERKSLQNA 88
+Y + L E+L HTP +H + + L++A
Sbjct: 175 KYPLLLKEILKHTPKEHPDVQLLEDA 200
>pdb|2Z0Q|A Chain A, Crystal Structure Of Dh-Ph Domain Of Rhogef3(Xpln)
Length = 352
Score = 45.4 bits (106), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 28/106 (26%), Positives = 51/106 (48%)
Query: 2 LLPMLGIYQEYVRNHHYSLQVLTECKQQPEFVQLLKRLEMKPACQGRSLEMFLTFPMHQI 61
LP L Y Y N + +L KQ L+R P + L FL P ++
Sbjct: 101 WLPCLSSYDSYCSNQVAAKALLDHKKQDHRVQDFLQRCLESPFSRKLDLWNFLDIPRSRL 160
Query: 62 PRYIVTLHELLAHTPHDHVERKSLQNARQQLEDLSRQMHDEVSETE 107
+Y + L E+L HTP+D+ +++ L+ A ++ + +++ + E+E
Sbjct: 161 VKYPLLLREILRHTPNDNPDQQHLEEAINIIQGIVAEINTKTGESE 206
>pdb|2DFK|A Chain A, Crystal Structure Of The Cdc42-Collybistin Ii Complex
pdb|2DFK|C Chain C, Crystal Structure Of The Cdc42-Collybistin Ii Complex
Length = 402
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/123 (24%), Positives = 57/123 (46%), Gaps = 2/123 (1%)
Query: 6 LGIYQEYVRNHHYSLQVLTECKQQPEFVQLLKRLEMKPACQGRSLEMFLTFPMHQIPRYI 65
IY EY NH + L++ + + + + +++ FL P+ +I +Y
Sbjct: 129 FWIYSEYCNNHLDACMELSKLMKDSRYQHFFEACRLLQQMIDIAIDGFLLTPVQKICKYP 188
Query: 66 VTLHELLAHTPHDHVERKSLQNARQQLEDLSRQMHDEVSETENLRK--NLAVERLIVEGC 123
+ L ELL +T DH + + + A + ++++Q+++ EN+ K L EG
Sbjct: 189 LQLAELLKYTAQDHSDYRYVAAALAVMRNVTQQINERKRRLENIDKIAQWQASVLDWEGD 248
Query: 124 DIL 126
DIL
Sbjct: 249 DIL 251
>pdb|2DX1|A Chain A, Crystal Structure Of Rhogef Protein Asef
Length = 482
Score = 41.2 bits (95), Expect = 2e-04, Method: Composition-based stats.
Identities = 26/104 (25%), Positives = 51/104 (49%)
Query: 8 IYQEYVRNHHYSLQVLTECKQQPEFVQLLKRLEMKPACQGRSLEMFLTFPMHQIPRYIVT 67
IY EY NH + L+ + ++V + + SL+ FL P+ +I +Y +
Sbjct: 245 IYSEYCNNHPNACVELSRLTKLSKYVYFFEACRLLQKXIDISLDGFLLTPVQKICKYPLQ 304
Query: 68 LHELLAHTPHDHVERKSLQNARQQLEDLSRQMHDEVSETENLRK 111
L ELL +T H + K ++ A +++++ +++ EN+ K
Sbjct: 305 LAELLKYTHPQHRDFKDVEAALHAXKNVAQLINERKRRLENIDK 348
>pdb|2PZ1|A Chain A, Crystal Structure Of Auto-Inhibited Asef
Length = 466
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 31/122 (25%), Positives = 60/122 (49%), Gaps = 2/122 (1%)
Query: 8 IYQEYVRNHHYSLQVLTECKQQPEFVQLLKRLEMKPACQGRSLEMFLTFPMHQIPRYIVT 67
IY EY NH + L+ + ++V + + SL+ FL P+ +I +Y +
Sbjct: 208 IYSEYCNNHPNACVELSRLTKLSKYVYFFEACRLLQKMIDISLDGFLLTPVQKICKYPLQ 267
Query: 68 LHELLAHTPHDHVERKSLQNARQQLEDLSRQMHDEVSETENLRKNLAVERLI--VEGCDI 125
L ELL +T H + K ++ A ++++++ +++ EN+ K + I EG D+
Sbjct: 268 LAELLKYTHPQHRDFKDVEAALHAMKNVAQLINERKRRLENIDKIAQWQSSIEDWEGEDL 327
Query: 126 LL 127
L+
Sbjct: 328 LV 329
>pdb|1KZG|A Chain A, Dbscdc42(Y889f)
pdb|1KZG|C Chain C, Dbscdc42(Y889f)
Length = 353
Score = 35.8 bits (81), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 38/70 (54%), Gaps = 5/70 (7%)
Query: 8 IYQEYVRNHHYSLQVLTECKQQPEFVQLLKRLEMKPACQGRSLEMFLTFPMHQIPRYIVT 67
IY++Y +N S + +C P F + K+L+ K SL+ +L P+ +I +Y +
Sbjct: 103 IYEKYCQNKPRSESLWRQCSDCPFFQECQKKLDHK-----LSLDSYLLKPVQRITKYQLL 157
Query: 68 LHELLAHTPH 77
L E+L ++ H
Sbjct: 158 LKEMLKYSKH 167
>pdb|1LB1|A Chain A, Crystal Structure Of The Dbl And Pleckstrin Homology
Domains Of Dbs In Complex With Rhoa
pdb|1LB1|C Chain C, Crystal Structure Of The Dbl And Pleckstrin Homology
Domains Of Dbs In Complex With Rhoa
pdb|1LB1|E Chain E, Crystal Structure Of The Dbl And Pleckstrin Homology
Domains Of Dbs In Complex With Rhoa
pdb|1LB1|G Chain G, Crystal Structure Of The Dbl And Pleckstrin Homology
Domains Of Dbs In Complex With Rhoa
Length = 353
Score = 35.8 bits (81), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 38/70 (54%), Gaps = 5/70 (7%)
Query: 8 IYQEYVRNHHYSLQVLTECKQQPEFVQLLKRLEMKPACQGRSLEMFLTFPMHQIPRYIVT 67
IY++Y +N S + +C P F + K+L+ K SL+ +L P+ +I +Y +
Sbjct: 103 IYEKYCQNKPRSESLWRQCSDCPFFQECQKKLDHK-----LSLDSYLLKPVQRITKYQLL 157
Query: 68 LHELLAHTPH 77
L E+L ++ H
Sbjct: 158 LKEMLKYSKH 167
>pdb|1RJ2|A Chain A, Crystal Structure Of The DhPH FRAGMENT OF DBS WITHOUT
Bound Gtpase
pdb|1RJ2|D Chain D, Crystal Structure Of The DhPH FRAGMENT OF DBS WITHOUT
Bound Gtpase
pdb|1RJ2|G Chain G, Crystal Structure Of The DhPH FRAGMENT OF DBS WITHOUT
Bound Gtpase
pdb|1RJ2|J Chain J, Crystal Structure Of The DhPH FRAGMENT OF DBS WITHOUT
Bound Gtpase
Length = 353
Score = 35.8 bits (81), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 38/70 (54%), Gaps = 5/70 (7%)
Query: 8 IYQEYVRNHHYSLQVLTECKQQPEFVQLLKRLEMKPACQGRSLEMFLTFPMHQIPRYIVT 67
IY++Y +N S + +C P F + K+L+ K SL+ +L P+ +I +Y +
Sbjct: 103 IYEKYCQNKPRSESLWRQCSDCPFFQECQKKLDHK-----LSLDSYLLKPVQRITKYQLL 157
Query: 68 LHELLAHTPH 77
L E+L ++ H
Sbjct: 158 LKEMLKYSKH 167
>pdb|1KZ7|A Chain A, Crystal Structure Of The DhPH FRAGMENT OF MURINE DBS IN
Complex With The Placental Isoform Of Human Cdc42
pdb|1KZ7|C Chain C, Crystal Structure Of The DhPH FRAGMENT OF MURINE DBS IN
Complex With The Placental Isoform Of Human Cdc42
Length = 353
Score = 35.0 bits (79), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 5/70 (7%)
Query: 8 IYQEYVRNHHYSLQVLTECKQQPEFVQLLKRLEMKPACQGRSLEMFLTFPMHQIPRYIVT 67
IY++Y +N S + +C P F + K+L+ K SL+ +L P+ +I +Y +
Sbjct: 103 IYEKYCQNKPRSESLWRQCSDCPFFQECQKKLDHK-----LSLDSYLLKPVQRITKYQLL 157
Query: 68 LHELLAHTPH 77
L E L ++ H
Sbjct: 158 LKEXLKYSKH 167
>pdb|1XCG|A Chain A, Crystal Structure Of Human Rhoa In Complex With DhPH
Fragment Of Pdzrhogef
pdb|1XCG|E Chain E, Crystal Structure Of Human Rhoa In Complex With DhPH
Fragment Of Pdzrhogef
Length = 368
Score = 34.3 bits (77), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 20/87 (22%), Positives = 43/87 (49%)
Query: 22 VLTECKQQPEFVQLLKRLEMKPACQGRSLEMFLTFPMHQIPRYIVTLHELLAHTPHDHVE 81
+ T+ +++ F ++ E P C+ L + M ++ +Y + L ++ HT E
Sbjct: 130 IKTKQRKESRFQLFMQEAESHPQCRRLQLRDLIISEMQRLTKYPLLLESIIKHTEGGTSE 189
Query: 82 RKSLQNARQQLEDLSRQMHDEVSETEN 108
+ L AR Q ++ + +++ V +TEN
Sbjct: 190 HEKLCRARDQCREILKYVNEAVKQTEN 216
>pdb|3KZ1|A Chain A, Crystal Structure Of The Complex Of Pdz-Rhogef DhPH
DOMAINS WITH GTP- Gamma-S Activated Rhoa
pdb|3KZ1|B Chain B, Crystal Structure Of The Complex Of Pdz-Rhogef DhPH
DOMAINS WITH GTP- Gamma-S Activated Rhoa
Length = 383
Score = 33.9 bits (76), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 20/87 (22%), Positives = 43/87 (49%)
Query: 22 VLTECKQQPEFVQLLKRLEMKPACQGRSLEMFLTFPMHQIPRYIVTLHELLAHTPHDHVE 81
+ T+ +++ F ++ E P C+ L + M ++ +Y + L ++ HT E
Sbjct: 135 IKTKQRKESRFQLFMQEAESHPQCRRLQLRDLIISEMQRLTKYPLLLESIIKHTEGGTSE 194
Query: 82 RKSLQNARQQLEDLSRQMHDEVSETEN 108
+ L AR Q ++ + +++ V +TEN
Sbjct: 195 HEKLCRARDQCREILKYVNEAVKQTEN 221
>pdb|3T06|A Chain A, Crystal Structure Of The DhPH FRAGMENT OF PDZRHOGEF WITH
N-Terminal Regulatory Elements In Complex With Human
Rhoa
pdb|3T06|E Chain E, Crystal Structure Of The DhPH FRAGMENT OF PDZRHOGEF WITH
N-Terminal Regulatory Elements In Complex With Human
Rhoa
Length = 418
Score = 33.9 bits (76), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 20/87 (22%), Positives = 43/87 (49%)
Query: 22 VLTECKQQPEFVQLLKRLEMKPACQGRSLEMFLTFPMHQIPRYIVTLHELLAHTPHDHVE 81
+ T+ +++ F ++ E P C+ L + M ++ +Y + L ++ HT E
Sbjct: 172 IKTKQRKESRFQLFMQEAESHPQCRRLQLRDLIISEMQRLTKYPLLLESIIKHTEGGTSE 231
Query: 82 RKSLQNARQQLEDLSRQMHDEVSETEN 108
+ L AR Q ++ + +++ V +TEN
Sbjct: 232 HEKLCRARDQCREILKYVNEAVKQTEN 258
>pdb|1BY1|A Chain A, Dbl Homology Domain From Beta-Pix
Length = 209
Score = 32.7 bits (73), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 29/103 (28%), Positives = 48/103 (46%), Gaps = 8/103 (7%)
Query: 2 LLP-MLGIYQEYVRNHHYSLQVLTECKQQPEFVQLLKRLEMKPACQGR--SLEMFLTFPM 58
L+P M +Y Y NH ++ VLTE + +L + +E K A L L+ P
Sbjct: 95 LMPQMKTLYLTYCANHPSAVNVLTEHSE-----ELGEFMETKGASSPGILVLTTGLSKPF 149
Query: 59 HQIPRYIVTLHELLAHTPHDHVERKSLQNARQQLEDLSRQMHD 101
++ +Y L EL H H +R+ +Q + ++LS Q +
Sbjct: 150 MRLDKYPTLLKELERHMEDYHTDRQDIQKSMAAFKNLSAQCQE 192
>pdb|2VRW|B Chain B, Critical Structural Role For The Ph And C1 Domains Of The
Vav1 Exchange Factor
Length = 406
Score = 32.0 bits (71), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 45/80 (56%), Gaps = 6/80 (7%)
Query: 44 ACQGR-SLEMFLTFPMHQIPRYIVTLHELLAHTPHDHVERKSLQNARQQLEDLSRQMHDE 102
A GR +L L PM ++ +Y + L EL+ HT D E+++L+ A + DL++ +++
Sbjct: 146 ANNGRFTLRDLLMVPMQRVLKYHLLLQELVKHT-QDATEKENLRLALDAMRDLAQCVNEV 204
Query: 103 VSETENLRK----NLAVERL 118
+ E LR+ L++E L
Sbjct: 205 KRDNETLRQITNFQLSIENL 224
>pdb|3TQ8|A Chain A, Structure Of The Dihydrofolate Reductase (Fola) From
Coxiella Burnetii In Complex With Trimethoprim
pdb|3TQ9|A Chain A, Structure Of The Dihydrofolate Reductase (Fola) From
Coxiella Burnetii In Complex With Methotrexate
pdb|3TQA|A Chain A, Structure Of The Dihydrofolate Reductase (Fola) From
Coxiella Burnetii In Complex With Nadph
pdb|3TQB|A Chain A, Structure Of The Dihydrofolate Reductase (Fola) From
Coxiella Burnetii In Complex With Folate
Length = 178
Score = 32.0 bits (71), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 63 RYIVTLHELLAHTPHDHVERKSLQNARQQLEDLSRQMHDEVSETENLRKNLAV---ERLI 119
R I +EL H P D KS+ + + + R+ D + + R+N+ + + LI
Sbjct: 13 RLIGRNNELPWHLPADLAHFKSITLGKPIV--MGRRTFDSIGKPLPHRRNIVITQQKNLI 70
Query: 120 VEGCDILLDVNQV 132
+EGCDI ++
Sbjct: 71 IEGCDIFYSLDDA 83
>pdb|3KY9|A Chain A, Autoinhibited Vav1
pdb|3KY9|B Chain B, Autoinhibited Vav1
Length = 587
Score = 30.0 bits (66), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 46/80 (57%), Gaps = 6/80 (7%)
Query: 44 ACQGR-SLEMFLTFPMHQIPRYIVTLHELLAHTPHDHVERKSLQNARQQLEDLSRQMHDE 102
A GR +L L PM ++ +Y + L EL+ HT + +E+++L+ A + DL++ +++
Sbjct: 318 ANNGRFTLRDLLMVPMQRVLKYHLLLQELVKHT-QEAMEKENLRLALDAMRDLAQCVNEV 376
Query: 103 VSETENLRK----NLAVERL 118
+ E LR+ L++E L
Sbjct: 377 KRDNETLRQITNFQLSIENL 396
>pdb|3BJI|A Chain A, Structural Basis Of Promiscuous Guanine Nucleotide
Exchange By The T-Cell Essential Vav1
pdb|3BJI|B Chain B, Structural Basis Of Promiscuous Guanine Nucleotide
Exchange By The T-Cell Essential Vav1
Length = 378
Score = 30.0 bits (66), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 46/80 (57%), Gaps = 6/80 (7%)
Query: 44 ACQGR-SLEMFLTFPMHQIPRYIVTLHELLAHTPHDHVERKSLQNARQQLEDLSRQMHDE 102
A GR +L L PM ++ +Y + L EL+ HT + +E+++L+ A + DL++ +++
Sbjct: 127 ANNGRFTLRDLLMVPMQRVLKYHLLLQELVKHT-QEAMEKENLRLALDAMRDLAQCVNEV 185
Query: 103 VSETENLRK----NLAVERL 118
+ E LR+ L++E L
Sbjct: 186 KRDNETLRQITNFQLSIENL 205
>pdb|1F5X|A Chain A, Nmr Structure Of The Y174 Autoinhibited Dbl Homology
Domain
Length = 208
Score = 28.9 bits (63), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 32/55 (58%), Gaps = 2/55 (3%)
Query: 44 ACQGR-SLEMFLTFPMHQIPRYIVTLHELLAHTPHDHVERKSLQNARQQLEDLSR 97
A GR +L L PM ++ +Y + L EL+ HT D E+++L+ A + DL++
Sbjct: 148 ANNGRFTLRDLLMVPMQRVLKYHLLLQELVKHT-QDATEKENLRLALDAMRDLAQ 201
>pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|M Chain M, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 1752
Score = 28.5 bits (62), Expect = 1.1, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 33/75 (44%), Gaps = 3/75 (4%)
Query: 48 RSLEMFLTFPMHQIPRYIVTLHELLAHTPHDHVERKSLQNARQQLEDLSRQMHDEVSETE 107
RS+ LT+P P I L EL+ + P +H K + R E + + H +
Sbjct: 374 RSIAKTLTYPETVTPYNIYQLQELVRNGPDEHPGAKYI--IRDTGERIDLRYHKRAGDIP 431
Query: 108 NLRKNLAVERLIVEG 122
LR VER I +G
Sbjct: 432 -LRYGWRVERHIRDG 445
>pdb|3QKT|A Chain A, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
Complex With Amp- Pnp
pdb|3QKT|B Chain B, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
Complex With Amp- Pnp
pdb|3QKT|C Chain C, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
Complex With Amp- Pnp
pdb|3QKT|D Chain D, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
Complex With Amp- Pnp
Length = 339
Score = 26.6 bits (57), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 58 MHQIPRYIVTLHELLAHTPHDHVERKSLQNARQQLEDLS 96
+ +IP+ I+ H+ DHV R SL+N ++E +S
Sbjct: 301 LKKIPQVILVSHDEELKDAADHVIRISLENGSSKVEVVS 339
>pdb|3QKU|A Chain A, Mre11 Rad50 Binding Domain In Complex With Rad50 And
Amp-Pnp
pdb|3QKU|B Chain B, Mre11 Rad50 Binding Domain In Complex With Rad50 And
Amp-Pnp
Length = 359
Score = 26.6 bits (57), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 58 MHQIPRYIVTLHELLAHTPHDHVERKSLQNARQQLEDLS 96
+ +IP+ I+ H+ DHV R SL+N ++E +S
Sbjct: 321 LKKIPQVILVSHDEELKDAADHVIRISLENGSSKVEVVS 359
>pdb|1F2T|B Chain B, Crystal Structure Of Atp-free Rad50 Abc-atpase
pdb|1F2U|B Chain B, Crystal Structure Of Rad50 Abc-Atpase
pdb|1F2U|D Chain D, Crystal Structure Of Rad50 Abc-Atpase
Length = 148
Score = 26.6 bits (57), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 58 MHQIPRYIVTLHELLAHTPHDHVERKSLQNARQQLEDLS 96
+ +IP+ I+ H+ DHV R SL+N ++E +S
Sbjct: 110 LKKIPQVILVSHDEELKDAADHVIRISLENGSSKVEVVS 148
>pdb|1US8|B Chain B, The Rad50 Signature Motif: Essential To Atp Binding And
Biological Function
Length = 144
Score = 26.6 bits (57), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 58 MHQIPRYIVTLHELLAHTPHDHVERKSLQNARQQLEDLS 96
+ +IP+ I+ H+ DHV R SL+N ++E +S
Sbjct: 106 LKKIPQVILVSHDEELKDAADHVIRISLENGSSKVEVVS 144
>pdb|1II8|B Chain B, Crystal Structure Of The P. Furiosus Rad50 Atpase Domain
Length = 174
Score = 26.6 bits (57), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 58 MHQIPRYIVTLHELLAHTPHDHVERKSLQNARQQLEDLS 96
+ +IP+ I+ H+ DHV R SL+N ++E +S
Sbjct: 136 LKKIPQVILVSHDEELKDAADHVIRISLENGSSKVEVVS 174
>pdb|3QKR|B Chain B, Mre11 Rad50 Binding Domain Bound To Rad50
pdb|3QKS|B Chain B, Mre11 Rad50 Binding Domain Bound To Rad50
Length = 179
Score = 26.6 bits (57), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 58 MHQIPRYIVTLHELLAHTPHDHVERKSLQNARQQLEDLS 96
+ +IP+ I+ H+ DHV R SL+N ++E +S
Sbjct: 141 LKKIPQVILVSHDEELKDAADHVIRISLENGSSKVEVVS 179
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 0.137 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,678,963
Number of Sequences: 62578
Number of extensions: 125125
Number of successful extensions: 502
Number of sequences better than 100.0: 47
Number of HSP's better than 100.0 without gapping: 31
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 471
Number of HSP's gapped (non-prelim): 47
length of query: 136
length of database: 14,973,337
effective HSP length: 88
effective length of query: 48
effective length of database: 9,466,473
effective search space: 454390704
effective search space used: 454390704
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: 46 (22.3 bits)