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= 027704
(220 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2EBM|A Chain A, Solution Structure Of The Rwd Domain Of Human Rwd Domain
Containing Protein 1
Length = 128
Score = 79.3 bits (194), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 49/128 (38%), Positives = 76/128 (59%), Gaps = 11/128 (8%)
Query: 1 MTDHVQEQEMEIEALEAILMDEFKEIHSGESGLNTSNQCFQVTLSPQDDEADESTMPPVE 60
MTD+ +EQ E+EALE+I D F + L+ + F +T++ + E DE+ V+
Sbjct: 8 MTDYGEEQRNELEALESIYPDSF-------TVLSENPPSFTITVTSEAGENDET----VQ 56
Query: 61 LALIFSHTEKYPDEPPLLNVKSLRGIQAGDLKILKEKLEQEASENLGMAMIYTLVTSAKE 120
L F+++EKYPDE PL + S ++ D+ + + L +A ENLGM MI+TLVT+ +E
Sbjct: 57 TTLKFTYSEKYPDEAPLYEIFSQENLEDNDVSDILKLLALQAEENLGMVMIFTLVTAVQE 116
Query: 121 WLSERYSQ 128
L+E Q
Sbjct: 117 KLNEIVDQ 124
>pdb|1UKX|A Chain A, Solution Structure Of The Rwd Domain Of Mouse Gcn2
Length = 137
Score = 50.4 bits (119), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 34/119 (28%), Positives = 58/119 (48%), Gaps = 3/119 (2%)
Query: 6 QEQEMEIEALEAILMDEFKEIHSGESGLNTSNQCFQVTLSPQDDEADESTMPPVELALIF 65
Q Q+ E++ALEAI +F+++ G + L PQ +E V++ L
Sbjct: 13 QRQDHELQALEAIYGSDFQDLRPDARGRVREPPEINLVLYPQGLAGEEVY---VQVELRV 69
Query: 66 SHTEKYPDEPPLLNVKSLRGIQAGDLKILKEKLEQEASENLGMAMIYTLVTSAKEWLSE 124
YPD P +++K+ +G+ + +LK LE+ A + G MI+ L + +LSE
Sbjct: 70 KCPPTYPDVVPEIDLKNAKGLSNESVNLLKSHLEELAKKQCGEVMIFELAHHVQSFLSE 128
>pdb|2DAY|A Chain A, Solution Structure Of The Rwd Domain Of Human Ring Finger
Protein 25
Length = 128
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 35/113 (30%), Positives = 55/113 (48%), Gaps = 5/113 (4%)
Query: 11 EIEALEAILMDEFKEIHSGESGLNTSNQCFQVTLSPQDDEADESTMPPVELALIFSHTEK 70
E+E LE+I +DE + I + TS +TL P E +S V L+ +
Sbjct: 16 EVEVLESIYLDELQVI---KGNGRTSPWEIYITLHPATAEDQDSQY--VCFTLVLQVPAE 70
Query: 71 YPDEPPLLNVKSLRGIQAGDLKILKEKLEQEASENLGMAMIYTLVTSAKEWLS 123
YP E P +++++ RG+ + + + L A LG AM+Y L+ KE LS
Sbjct: 71 YPHEVPQISIRNPRGLSDEQIHTILQVLGHVAKAGLGTAMLYELIEKGKEILS 123
>pdb|2DMF|A Chain A, An Extended Conformation Of The Rwd Domain Of Human Ring
Finger Protein 25
Length = 137
Score = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 34/115 (29%), Positives = 56/115 (48%), Gaps = 5/115 (4%)
Query: 11 EIEALEAILMDEFKEIHSGESGLNTSNQCFQVTLSPQDDEADESTMPPVELALIFSHTEK 70
E+E LE+I +DE + I + TS +TL P E +S V L+ +
Sbjct: 16 EVEVLESIYLDELQVI---KGNGRTSPWEIYITLHPATAEDQDSQY--VCFTLVLQVPAE 70
Query: 71 YPDEPPLLNVKSLRGIQAGDLKILKEKLEQEASENLGMAMIYTLVTSAKEWLSER 125
YP E P +++++ RG+ + + + L A LG AM+Y L+ KE L++
Sbjct: 71 YPHEVPQISIRNPRGLSDEQIHTILQVLGHVAKAGLGTAMLYELIEKGKEILTDN 125
>pdb|2YZ0|A Chain A, Solution Structure Of RwdGI DOMAIN OF SACCHAROMYCES
Cerevisiae Gcn2
Length = 138
Score = 47.4 bits (111), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 31/115 (26%), Positives = 61/115 (53%), Gaps = 6/115 (5%)
Query: 11 EIEALEAILMDEFKEIHSGESGLNTSNQ-CFQVTLSPQDDEADESTMPPVELALIFSHTE 69
E+EA+ +I MD+F ++ +S + Q F++TL D E ES+ + L F+ T
Sbjct: 18 ELEAIRSIYMDDFTDLTKRKSSWDKQPQIIFEITLRSVDKEPVESS-----ITLHFAMTP 72
Query: 70 KYPDEPPLLNVKSLRGIQAGDLKILKEKLEQEASENLGMAMIYTLVTSAKEWLSE 124
YP P + K+++ + L++LK + ++ + + G +I+ + + +E L E
Sbjct: 73 MYPYTAPEIEFKNVQNVMDSQLQMLKSEFKKIHNTSRGQEIIFEITSFTQEKLDE 127
>pdb|1Z3D|A Chain A, Protein Crystal Growth Improvement Leading To The 2.5a
Crystallographic Structure Of Ubiquitin-Conjugating
Enzyme (Ubc-1) From Caenorhabditis Elegans
Length = 157
Score = 28.1 bits (61), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 29/108 (26%), Positives = 48/108 (44%), Gaps = 14/108 (12%)
Query: 19 LMDEFKEIH----SGESGLNTSNQCF---QVTLSPQDDEADESTMPPVELALIFSHTEKY 71
LM +FK++ +G SG T + + PQ+ ++ T +L+L F TE+Y
Sbjct: 12 LMRDFKKLQEDPPAGVSGAPTEDNILTWEAIIFGPQETPFEDGTF---KLSLEF--TEEY 66
Query: 72 PDEPPLLNV--KSLRGIQAGDLKILKEKLEQEASENLGMAMIYTLVTS 117
P++PP + K D I + L+ S +A I T + S
Sbjct: 67 PNKPPTVKFISKMFHPNVYADGSICLDILQNRWSPTYDVAAILTSIQS 114
>pdb|1Q34|A Chain A, Crystal Structures Of Two Ubc (E2) Enzymes Of The
Ubiquitin- Conjugating System In Caenorhabditis Elegans
pdb|1Q34|B Chain B, Crystal Structures Of Two Ubc (E2) Enzymes Of The
Ubiquitin- Conjugating System In Caenorhabditis Elegans
pdb|1Q34|C Chain C, Crystal Structures Of Two Ubc (E2) Enzymes Of The
Ubiquitin- Conjugating System In Caenorhabditis Elegans
Length = 163
Score = 27.7 bits (60), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 29/108 (26%), Positives = 48/108 (44%), Gaps = 14/108 (12%)
Query: 19 LMDEFKEIH----SGESGLNTSNQCF---QVTLSPQDDEADESTMPPVELALIFSHTEKY 71
LM +FK++ +G SG T + + PQ+ ++ T +L+L F TE+Y
Sbjct: 9 LMRDFKKLQEDPPAGVSGAPTEDNILTWEAIIFGPQETPFEDGTF---KLSLEF--TEEY 63
Query: 72 PDEPPLLNV--KSLRGIQAGDLKILKEKLEQEASENLGMAMIYTLVTS 117
P++PP + K D I + L+ S +A I T + S
Sbjct: 64 PNKPPTVKFISKMFHPNVYADGSICLDILQNRWSPTYDVAAILTSIQS 111
>pdb|4EFJ|A Chain A, Crystal Structure Of I-Gzemii Laglidadg Homing
Endonuclease In Complex With Dna Target Site
pdb|4EFJ|B Chain B, Crystal Structure Of I-Gzemii Laglidadg Homing
Endonuclease In Complex With Dna Target Site
Length = 300
Score = 26.9 bits (58), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 30/147 (20%), Positives = 68/147 (46%), Gaps = 30/147 (20%)
Query: 9 EMEIEALEAILMDEFKEIHSGESGLNTSNQ-CFQVTLSPQDDEADESTMPPVELALIFSH 67
+++++ + L++E K + +NTSN+ C S +D +++I SH
Sbjct: 40 QIKLDIRDKSLLEEIKNYFNNTGSINTSNKECVYKVRSLKD------------ISIIISH 87
Query: 68 TEKYPDEPPLLNVKSLRGIQAGDLKILKEKLEQ-EASENLGMAMIYTLVTSAKEWLSERY 126
+KY +L + D ++ K+ + + + E+L + T++ +E +S R
Sbjct: 88 FDKY----------NLITQKKADFELFKKIINKLNSQEHLSYEVGATVL---QEIISIRA 134
Query: 127 SQDAGIDNTGEEELEKDEVIVPHGEPV 153
S + G+ ++ +E+ I+P P+
Sbjct: 135 SMNLGLSSSVKEDFPH---IIPSNRPL 158
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
0.311 0.129 0.366
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,879,819
Number of Sequences: 62578
Number of extensions: 204352
Number of successful extensions: 491
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 483
Number of HSP's gapped (non-prelim): 14
length of query: 220
length of database: 14,973,337
effective HSP length: 95
effective length of query: 125
effective length of database: 9,028,427
effective search space: 1128553375
effective search space used: 1128553375
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 49 (23.5 bits)