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= 033470
(118 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1SE9|A Chain A, Structure Of At3g01050, A Ubiquitin-Fold Protein From
Arabidopsis Thaliana
Length = 126
Score = 108 bits (269), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 54/112 (48%), Positives = 75/112 (66%), Gaps = 2/112 (1%)
Query: 7 VELKFRLYDGSDIGPFRYSPTSTVAMLKERIFSDWPKDKKIVPKTANDIKLISAGKILEN 66
+E+KFRL DGSDIGP + +TV+ LKE + S+WP++K+ PKT ++KLISAGK+LEN
Sbjct: 17 LEIKFRLTDGSDIGPKAFPDATTVSALKETVISEWPREKENGPKTVKEVKLISAGKVLEN 76
Query: 67 NKTVGQCKVPFGELPKGTITMHVVVQPPLTKAKTEKKLDEPQKKNFCSCSIL 118
+KTV + P L TMHV++Q P+T+ EKK K N C CS++
Sbjct: 77 SKTVKDYRSPVSNLAGAVTTMHVIIQAPVTEK--EKKPKGDPKMNKCVCSVM 126
>pdb|2GOW|A Chain A, Solution Structure Of Bc059385 From Homo Sapiens
Length = 125
Score = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 29/115 (25%), Positives = 58/115 (50%), Gaps = 6/115 (5%)
Query: 5 ELVELKFRLYDGSDIGPFRYSPTSTVAMLKERIFSDWPKD-KKIVPKTANDIKLISAGKI 63
+++ L+ L G F +SP + + + + ++ +WP D ++ + N ++LI G+
Sbjct: 16 DMINLRLILVSGK-TKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRF 74
Query: 64 LENNKTVGQCKVPFGELPKGTITMHVVVQPPLTKAKTEKKLDEPQKKNFCSCSIL 118
L N T+G K+PFG+ T MH+V + L + ++ + + + C IL
Sbjct: 75 LHGNVTLGALKLPFGK----TTVMHLVARETLPEPNSQGQRNREKTGESNCCVIL 125
>pdb|1WGH|A Chain A, Solution Structure Of Mouse Ubiquitin-Like 3 Protein
Length = 116
Score = 48.5 bits (114), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 27/104 (25%), Positives = 54/104 (51%), Gaps = 6/104 (5%)
Query: 5 ELVELKFRLYDGSDIGPFRYSPTSTVAMLKERIFSDWPKD-KKIVPKTANDIKLISAGKI 63
+++ L+ L G F +SP + + + + ++ +WP D ++ + N ++LI G+
Sbjct: 15 DMINLRLILVSGK-TKEFLFSPNDSASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRF 73
Query: 64 LENNKTVGQCKVPFGELPKGTITMHVVVQPPLTKAKTEKKLDEP 107
L N T+G K+PFG+ T MH+V + L + ++ + P
Sbjct: 74 LHGNVTLGALKLPFGK----TTVMHLVARETLPEPNSQGQRSGP 113
>pdb|3M62|B Chain B, Crystal Structure Of Ufd2 In Complex With The
Ubiquitin-Like (Ubl) Domain Of Rad23
Length = 106
Score = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 45/94 (47%), Gaps = 13/94 (13%)
Query: 6 LVELKFRLYDGSDIGPFRYSPTSTVAMLKERIFSDWPKDKKIVPKTANDIKLISAGKILE 65
+V L F+ + + P P++T+ K ++ ++ + IKLI +GK+L+
Sbjct: 1 MVSLTFKNFKKEKV-PLDLEPSNTILETKTKLAQSISCEE-------SQIKLIYSGKVLQ 52
Query: 66 NNKTVGQCKVPFGELPKGTITMHVVVQPPLTKAK 99
++KTV +C L G + +V Q TK K
Sbjct: 53 DSKTVSECG-----LKDGDQVVFMVSQKKSTKTK 81
>pdb|1WX7|A Chain A, Solution Structure Of The N-Terminal Ubiquitin-Like
Domain In The Human Ubiquilin 3 (Ubqln3)
Length = 106
Score = 30.4 bits (67), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 13/71 (18%)
Query: 22 FRYSPTSTVAMLKERIFSDWPKDKKIVPKTANDIKLISAGKILENNKTVGQCKVPFGELP 81
F + T T+ LKE I + K P + + LI AGKIL++ ++ QC V G
Sbjct: 31 FSVTDTCTIQQLKEEISQRF----KAHP---DQLVLIFAGKILKDPDSLAQCGVRDG--- 80
Query: 82 KGTITMHVVVQ 92
+T+H+V++
Sbjct: 81 ---LTVHLVIK 88
>pdb|1YQB|A Chain A, Human Ubiquilin 3
Length = 100
Score = 30.0 bits (66), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 13/71 (18%)
Query: 22 FRYSPTSTVAMLKERIFSDWPKDKKIVPKTANDIKLISAGKILENNKTVGQCKVPFGELP 81
F + T T+ LKE I + K P + + LI AGKIL++ ++ QC V G
Sbjct: 36 FSVTDTCTIQQLKEEISQRF----KAHP---DQLVLIFAGKILKDPDSLAQCGVRDG--- 85
Query: 82 KGTITMHVVVQ 92
+T+H+V++
Sbjct: 86 ---LTVHLVIK 93
>pdb|1P1A|A Chain A, Nmr Structure Of Ubiquitin-Like Domain Of Hhr23b
Length = 85
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 26 PTSTVAMLKERIFSDWPKDKKIVPKTANDIKLISAGKILENNKTVGQCKV 75
P TV LKE+I S+ KD P KLI AGKIL ++ + + K+
Sbjct: 22 PEETVKALKEKIESEKGKDA--FPVAGQ--KLIYAGKILNDDTALKEYKI 67
>pdb|2BWE|S Chain S, The Crystal Structure Of The Complex Between The Uba And
Ubl Domains Of Dsk2
pdb|2BWE|T Chain T, The Crystal Structure Of The Complex Between The Uba And
Ubl Domains Of Dsk2
pdb|2BWE|U Chain U, The Crystal Structure Of The Complex Between The Uba And
Ubl Domains Of Dsk2
pdb|2BWF|A Chain A, Crystal Sturcture Of The Ubl Domain Of Dsk2 From S.
Cerevisiae
pdb|2BWF|B Chain B, Crystal Sturcture Of The Ubl Domain Of Dsk2 From S.
Cerevisiae
Length = 77
Score = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 39/88 (44%), Gaps = 13/88 (14%)
Query: 7 VELKFRLYDGSDIGPFRYSPTSTVAMLKERIFSDWPKDKKIVPKTANDIKLISAGKILEN 66
+ L + G D +P STV KE I +K AN +LI +GKIL++
Sbjct: 3 MSLNIHIKSGQDKWEVNVAPESTVLQFKEAI------NKANGIPVANQ-RLIYSGKILKD 55
Query: 67 NKTVGQCKVPFGELPKGTITMHVVVQPP 94
++TV + G ++H+V P
Sbjct: 56 DQTVESYHIQDGH------SVHLVKSQP 77
>pdb|1UEL|A Chain A, Solution Structure Of Ubiquitin-Like Domain Of Hhr23b
Complexed With Ubiquitin-Interacting Motif Of
Proteasome Subunit S5a
Length = 95
Score = 27.3 bits (59), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 26 PTSTVAMLKERIFSDWPKDKKIVPKTANDIKLISAGKILENNKTVGQCKV 75
P TV LKE+I S+ KD P KLI AGKIL ++ + + K+
Sbjct: 19 PEETVKALKEKIESEKGKDA--FPVAGQ--KLIYAGKILNDDTALKEYKI 64
>pdb|3M63|B Chain B, Crystal Structure Of Ufd2 In Complex With The
Ubiquitin-Like (Ubl) Domain Of Dsk2
Length = 101
Score = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 39/88 (44%), Gaps = 13/88 (14%)
Query: 7 VELKFRLYDGSDIGPFRYSPTSTVAMLKERIFSDWPKDKKIVPKTANDIKLISAGKILEN 66
+ L + G D +P STV KE I +K AN +LI +GKIL++
Sbjct: 27 MSLNIHIKSGQDKWEVNVAPESTVLQFKEAI------NKANGIPVANQ-RLIYSGKILKD 79
Query: 67 NKTVGQCKVPFGELPKGTITMHVVVQPP 94
++TV + G ++H+V P
Sbjct: 80 DQTVESYHIQDGH------SVHLVKSQP 101
>pdb|2LXC|A Chain A, Solution Structure Of The Complex Between The Sgt2
Homodimerization Domain And The Get5 Ubl Domain
Length = 81
Score = 26.9 bits (58), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 11/72 (15%)
Query: 24 YSPTSTVAMLKERIFSDWPKDKKIVPKTANDIKLISAGKILENNKTVGQCKVPFGELPKG 83
+SP+ T+ +K+ + S+ ++IKL+ GK+L +N + KV P
Sbjct: 20 FSPSDTILQIKQHLISEEKASH------ISEIKLLLKGKVLHDNLFLSDLKVT----PAN 69
Query: 84 TITMHVVVQPPL 95
+ T+ V+++P L
Sbjct: 70 S-TITVMIKPNL 80
>pdb|2LXA|A Chain A, Solution Structure Of The Get5 Ubiquitin-like Domain
Length = 87
Score = 26.9 bits (58), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 11/72 (15%)
Query: 24 YSPTSTVAMLKERIFSDWPKDKKIVPKTANDIKLISAGKILENNKTVGQCKVPFGELPKG 83
+SP+ T+ +K+ + S+ ++IKL+ GK+L +N + KV P
Sbjct: 20 FSPSDTILQIKQHLISEEKASH------ISEIKLLLKGKVLHDNLFLSDLKVT----PAN 69
Query: 84 TITMHVVVQPPL 95
+ T+ V+++P L
Sbjct: 70 S-TITVMIKPNL 80
>pdb|4GOC|A Chain A, Crystal Structure Of The Get5 Ubiquitin-like Domain
pdb|4GOC|B Chain B, Crystal Structure Of The Get5 Ubiquitin-like Domain
pdb|4GOC|C Chain C, Crystal Structure Of The Get5 Ubiquitin-like Domain
Length = 76
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 27/52 (51%), Gaps = 6/52 (11%)
Query: 24 YSPTSTVAMLKERIFSDWPKDKKIVPKTANDIKLISAGKILENNKTVGQCKV 75
+SP+ T+ +K+ + S+ ++IKL+ GK+L +N + KV
Sbjct: 20 FSPSDTILQIKQHLISEEKASH------ISEIKLLLKGKVLHDNLFLSDLKV 65
>pdb|4A20|A Chain A, Crystal Structure Of The Ubl Domain Of Mdy2 (get5) At
1.78a
Length = 98
Score = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 27/52 (51%), Gaps = 6/52 (11%)
Query: 24 YSPTSTVAMLKERIFSDWPKDKKIVPKTANDIKLISAGKILENNKTVGQCKV 75
+SP+ T+ +K+ + S+ ++IKL+ GK+L +N + KV
Sbjct: 38 FSPSDTILQIKQHLISEEKASH------ISEIKLLLKGKVLHDNLFLSDLKV 83
>pdb|4ASW|C Chain C, Structure Of The Complex Between The N-terminal
Dimerisation Domain Of Sgt2 And The Ubl Domain Of Get5
Length = 83
Score = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 27/52 (51%), Gaps = 6/52 (11%)
Query: 24 YSPTSTVAMLKERIFSDWPKDKKIVPKTANDIKLISAGKILENNKTVGQCKV 75
+SP+ T+ +K+ + S+ ++IKL+ GK+L +N + KV
Sbjct: 23 FSPSDTILQIKQHLISEEKASH------ISEIKLLLKGKVLHDNLFLSDLKV 68
>pdb|1MYT|A Chain A, Crystal Structure To 1.74 Angstroms Resolution Of
Metmyoglobin From Yellowfin Tuna (Thunnus Albacares): An
Example Of A Myoglobin Lacking The D Helix
Length = 146
Score = 26.2 bits (56), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 5/87 (5%)
Query: 20 GPFRYSPTSTVAMLKERIFSDWPKDKKIVPKTANDIKLISAGK--ILENNKTVGQCKVPF 77
GP T+ ++ R+F + P+ +K+ PK A + AG I + TV +
Sbjct: 11 GPVEADYTTMGGLVLTRLFKEHPETQKLFPKFAGIAQADIAGNAAISAHGATVLK---KL 67
Query: 78 GELPKGTITMHVVVQPPLTKAKTEKKL 104
GEL K + +++P T+ K+
Sbjct: 68 GELLKAKGSHAAILKPLANSHATKHKI 94
>pdb|3QM5|A Chain A, Blackfin Tuna Oxy-Myoglobin, Atomic Resolution
pdb|3QM6|A Chain A, Blackfin Tuna Deoxy-Myoglobin, Atomic Resolution
pdb|3QM7|A Chain A, Blackfin Tuna Carbonmonoxy-Myoglobin, Atomic Resolution
pdb|3QM8|A Chain A, Blackfin Tuna Cyanomet-Myoglobin, Atomic Resolution
pdb|3QM9|A Chain A, Blackfin Tuna Azido-Myoglobin, Atomic Resolution
pdb|3QMA|A Chain A, Blackfin Tuna Myoglobin Imidazole Complex, Atomic
Resolution
Length = 146
Score = 26.2 bits (56), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 1/85 (1%)
Query: 20 GPFRYSPTSTVAMLKERIFSDWPKDKKIVPKTANDIKLISAGKILENNKTVGQCKVPFGE 79
GP T+ ++ R+F + P+ +K+ PK A + AG + K GE
Sbjct: 12 GPVEADYTTIGGLVLTRLFKEHPETQKLFPKFAGIAQADIAGNAAVSAHGATVLK-KLGE 70
Query: 80 LPKGTITMHVVVQPPLTKAKTEKKL 104
L K + +++P T+ K+
Sbjct: 71 LLKAKGSHAAILKPLANSHATKHKI 95
>pdb|2NRL|A Chain A, Blackfin Tuna Myoglobin
pdb|2NX0|A Chain A, Ferrous Nitrosyl Blackfin Tuna Myoglobin
Length = 147
Score = 26.2 bits (56), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 1/85 (1%)
Query: 20 GPFRYSPTSTVAMLKERIFSDWPKDKKIVPKTANDIKLISAGKILENNKTVGQCKVPFGE 79
GP T+ ++ R+F + P+ +K+ PK A + AG + K GE
Sbjct: 12 GPVEADYTTIGGLVLTRLFKEHPETQKLFPKFAGIAQADIAGNAAVSAHGATVLK-KLGE 70
Query: 80 LPKGTITMHVVVQPPLTKAKTEKKL 104
L K + +++P T+ K+
Sbjct: 71 LLKAKGSHAAILKPLANSHATKHKI 95
>pdb|2KNB|A Chain A, Solution Nmr Structure Of The Parkin Ubl Domain In
Complex With The Endophilin-A1 Sh3 Domain
Length = 81
Score = 25.8 bits (55), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 27/42 (64%), Gaps = 6/42 (14%)
Query: 52 ANDIKLISAGKILENNKTVGQCKVPFGELPKGTITMHVVVQP 93
A+ +++I AGK L+N+ TV C +L + +I +H+V +P
Sbjct: 43 ADQLRVIFAGKELQNHLTVQNC-----DLEQQSI-VHIVQRP 78
>pdb|2NRM|A Chain A, S-Nitrosylated Blackfin Tuna Myoglobin
Length = 147
Score = 25.8 bits (55), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 1/85 (1%)
Query: 20 GPFRYSPTSTVAMLKERIFSDWPKDKKIVPKTANDIKLISAGKILENNKTVGQCKVPFGE 79
GP T+ ++ R+F + P+ +K+ PK A + AG + K GE
Sbjct: 12 GPVEADYTTIGGLVLTRLFKEHPETQKLFPKFAGIAQADIAGNAAVSAHGATVLK-KLGE 70
Query: 80 LPKGTITMHVVVQPPLTKAKTEKKL 104
L K + +++P T+ K+
Sbjct: 71 LLKAKGSHAAILKPLANSHATKHKI 95
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 0.135 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,553,230
Number of Sequences: 62578
Number of extensions: 133803
Number of successful extensions: 274
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 266
Number of HSP's gapped (non-prelim): 24
length of query: 118
length of database: 14,973,337
effective HSP length: 81
effective length of query: 37
effective length of database: 9,904,519
effective search space: 366467203
effective search space used: 366467203
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: 45 (21.9 bits)