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= psy12788
(254 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MR6|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex With A
Cpd 2bp Upstream Of The Active Site (Tt4)
pdb|3TQ1|A Chain A, Human Dna Polymerase Eta In Binary Complex With Dna
pdb|4EEY|A Chain A, Crystal Structure Of Human Dna Polymerase Eta In Ternary
Complex With A Cisplatin Dna Adduct
Length = 435
Score = 30.8 bits (68), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 4/81 (4%)
Query: 18 GYILAAGSDRIVTIYESDGRVHRIFDYTAPHYKEREFTVAC-SSPSGQAVVVGSYDNIKL 76
G +A G DR+V + + D ++ PH + + V S G ++ SY+
Sbjct: 1 GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEA--- 57
Query: 77 FAWSPSKSVWEEQPNKTIPNL 97
A+ ++S+W + K P+L
Sbjct: 58 RAFGVTRSMWADDAKKLCPDL 78
>pdb|3MR2|A Chain A, Human Dna Polymerase Eta In Complex With Normal Dna And
Incoming Nucleotide (Nrm)
pdb|3MR3|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex With The
3't Of A Cpd In The Active Site (Tt1)
pdb|3MR5|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex With A
Cpd 1bp Upstream Of The Active Site (Tt3)
pdb|3SI8|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex With The
5't Of A Cpd In The Active Site (Tt2)
pdb|4DL2|A Chain A, Human Dna Polymerase Eta Inserting Dcmpnpp Opposite Cg
Template (Gg0a)
pdb|4DL3|A Chain A, Human Dna Polymerase Eta Inserting Dcmpnpp Opposite Gg
Template (Gg0b).
pdb|4DL4|A Chain A, Human Dna Polymerase Eta Inserting Dcmpnpp Opposite The
3'g Of Cisplatin Crosslinked Gs (Pt-Gg1).
pdb|4DL5|A Chain A, Human Dna Polymerase Eta Inserting Dcmpnpp Opposite The
5'g Of Cisplatin Crosslinked Gs (Pt-Gg2).
pdb|4DL6|A Chain A, Human Dna Polymerase Eta Extending Primer Immediately
After Cisplatin Crosslink (Pt-Gg3).
pdb|4DL7|A Chain A, Human Dna Polymerase Eta Fails To Extend Primer 2
Nucleotide After Cisplatin Crosslink (Pt-Gg4).
pdb|4ECQ|A Chain A, Human Dna Polymerase Eta- Dna Ternary Complex: At
Crystal At Ph6.8(K+ Mes) With 1 Ca2+ Ion
pdb|4ECR|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction
In The At Crystal At Ph 7.0 For 40 Sec
pdb|4ECS|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction
In The At Crystal At Ph 7.0 For 80 Sec
pdb|4ECT|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction
In The At Crystal At Ph 7.0 For 140 Sec
pdb|4ECU|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction
In The At Crystal At Ph 7.0 For 200 Sec
pdb|4ECV|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction
In The At Crystal At Ph 7.0 For 230 Sec
pdb|4ECW|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction
In The At Crystal At Ph 7.0 For 250 Sec
pdb|4ECX|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction
In The At Crystal At Ph 7.0 For 300 Sec
pdb|4ECY|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: At
Crystal At Ph 6.0 (Na+ Mes) With 1 Ca2+ Ion
pdb|4ECZ|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: At
Crystal At Ph 6.5 (Na+ Mes) With 1 Ca2+ Ion
pdb|4ED0|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: At
Crystal At Ph 6.8 (Na+ Mes) With 1 Ca2+ Ion
pdb|4ED1|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: At
Crystal At Ph 7.0 (Na+ Mes) With 1 Ca2+ Ion
pdb|4ED2|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: At
Crystal At Ph 7.2 (Na+ Hepes) With 1 Ca2+ Ion
pdb|4ED3|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: At
Crystal At Ph 7.5 (Na+ Hepes) With 1 Ca2+ Ion
pdb|4ED6|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction
In The At Crystal At Ph 6.7 For 15 Hr, Sideway
Translocation
pdb|4ED7|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Tg
Crystal At Ph 7.0 (K+ Mes) With 1 Ca2+ Ion
pdb|4ED8|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction
In The Tg Crystal At Ph 7.0, Normal Translocation
Length = 435
Score = 30.8 bits (68), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 4/81 (4%)
Query: 18 GYILAAGSDRIVTIYESDGRVHRIFDYTAPHYKEREFTVAC-SSPSGQAVVVGSYDNIKL 76
G +A G DR+V + + D ++ PH + + V S G ++ SY+
Sbjct: 1 GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEA--- 57
Query: 77 FAWSPSKSVWEEQPNKTIPNL 97
A+ ++S+W + K P+L
Sbjct: 58 RAFGVTRSMWADDAKKLCPDL 78
>pdb|3APO|A Chain A, Crystal Structure Of Full-Length Erdj5
Length = 780
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 34/143 (23%), Positives = 53/143 (37%), Gaps = 40/143 (27%)
Query: 14 SWPAGYILAAGSDRIVTIYES---DGRVHRIFDYTAP-------------------HYKE 51
SW G++ A D + G+ H + D+ AP K
Sbjct: 649 SWGLGFLPQASIDLTPQTFNEKVLQGKTHWVVDFYAPWSGPSQNFAPEFELLARMIKGKV 708
Query: 52 REFTVACSS--PSGQAVVVGSYDNIKLFAWS-PSKSVWEEQPNKTIPNLYTISALSWKRD 108
R V C + + Q + +Y ++KL+ + KS+WEEQ N RD
Sbjct: 709 RAGKVDCQAYPQTCQKAGIKAYPSVKLYQYERAKKSIWEEQIN--------------SRD 754
Query: 109 GSRIACGGLCGSVELFESVLKRT 131
IA + G +E +S +KR
Sbjct: 755 AKTIA-ALIYGKLETLQSQVKRN 776
>pdb|3KOW|A Chain A, Crystal Structure Of Ornithine 4,5 Aminomutase Backsoaked
Complex
pdb|3KOW|B Chain B, Crystal Structure Of Ornithine 4,5 Aminomutase Backsoaked
Complex
pdb|3KOW|C Chain C, Crystal Structure Of Ornithine 4,5 Aminomutase Backsoaked
Complex
pdb|3KOW|D Chain D, Crystal Structure Of Ornithine 4,5 Aminomutase Backsoaked
Complex
pdb|3KOX|A Chain A, Crystal Structure Of Ornithine 4,5 Aminomutase In Complex
With 2,4- Diaminobutyrate (Anaerobic)
pdb|3KOX|B Chain B, Crystal Structure Of Ornithine 4,5 Aminomutase In Complex
With 2,4- Diaminobutyrate (Anaerobic)
pdb|3KOX|C Chain C, Crystal Structure Of Ornithine 4,5 Aminomutase In Complex
With 2,4- Diaminobutyrate (Anaerobic)
pdb|3KOX|D Chain D, Crystal Structure Of Ornithine 4,5 Aminomutase In Complex
With 2,4- Diaminobutyrate (Anaerobic)
pdb|3KOY|A Chain A, Crystal Structure Of Ornithine 4,5 Aminomutase In Complex
With Ornithine (Aerobic)
pdb|3KOY|B Chain B, Crystal Structure Of Ornithine 4,5 Aminomutase In Complex
With Ornithine (Aerobic)
pdb|3KOY|C Chain C, Crystal Structure Of Ornithine 4,5 Aminomutase In Complex
With Ornithine (Aerobic)
pdb|3KOY|D Chain D, Crystal Structure Of Ornithine 4,5 Aminomutase In Complex
With Ornithine (Aerobic)
pdb|3KOZ|A Chain A, Crystal Structure Of Ornithine 4,5 Aminomutase In Complex
With Ornithine (Anaerobic)
pdb|3KOZ|B Chain B, Crystal Structure Of Ornithine 4,5 Aminomutase In Complex
With Ornithine (Anaerobic)
pdb|3KOZ|C Chain C, Crystal Structure Of Ornithine 4,5 Aminomutase In Complex
With Ornithine (Anaerobic)
pdb|3KOZ|D Chain D, Crystal Structure Of Ornithine 4,5 Aminomutase In Complex
With Ornithine (Anaerobic)
pdb|3KP0|A Chain A, Crystal Structure Of Ornithine 4,5 Aminomutase In Complex
With 2,4- Diaminobutyrate (Dab) (Aerobic)
pdb|3KP0|B Chain B, Crystal Structure Of Ornithine 4,5 Aminomutase In Complex
With 2,4- Diaminobutyrate (Dab) (Aerobic)
pdb|3KP0|C Chain C, Crystal Structure Of Ornithine 4,5 Aminomutase In Complex
With 2,4- Diaminobutyrate (Dab) (Aerobic)
pdb|3KP0|D Chain D, Crystal Structure Of Ornithine 4,5 Aminomutase In Complex
With 2,4- Diaminobutyrate (Dab) (Aerobic)
pdb|3KP1|A Chain A, Crystal Structure Of Ornithine 4,5 Aminomutase (Resting
State)
pdb|3KP1|B Chain B, Crystal Structure Of Ornithine 4,5 Aminomutase (Resting
State)
pdb|3KP1|D Chain D, Crystal Structure Of Ornithine 4,5 Aminomutase (Resting
State)
pdb|3KP1|C Chain C, Crystal Structure Of Ornithine 4,5 Aminomutase (Resting
State)
Length = 763
Score = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 7/52 (13%)
Query: 179 NDRYLVARTPD-------TLLLGDLHRNLLSEVLWPDSGRNEKFYFDNVTVC 223
N +Y+ A T + LL+ L R + + PD GRN ++ N+ C
Sbjct: 298 NTKYMEASTREATVTHVLNLLISKLTRADIQSTITPDEGRNVPWHIYNIEAC 349
>pdb|2ZEZ|A Chain A, Family 16 Carbohydrate Binding Module-2
pdb|2ZEZ|B Chain B, Family 16 Carbohydrate Binding Module-2
pdb|2ZEZ|C Chain C, Family 16 Carbohydrate Binding Module-2
pdb|2ZEZ|D Chain D, Family 16 Carbohydrate Binding Module-2
Length = 144
Score = 27.3 bits (59), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 204 VLWPDSGRNEKFYFDNVTVCLV 225
VLW D N FY DN+T+ V
Sbjct: 123 VLWKDDASNADFYADNITLVEV 144
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
0.319 0.137 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,192,016
Number of Sequences: 62578
Number of extensions: 342115
Number of successful extensions: 797
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 795
Number of HSP's gapped (non-prelim): 15
length of query: 254
length of database: 14,973,337
effective HSP length: 97
effective length of query: 157
effective length of database: 8,903,271
effective search space: 1397813547
effective search space used: 1397813547
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)