RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4181
(73 letters)
>3plu_A Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-1, SNU66,
peptide binding protein; 1.40A {Saccharomyces
cerevisiae} PDB: 3plv_A 1m94_A 1p0r_A
Length = 93
Score = 132 bits (333), Expect = 1e-42
Identities = 43/72 (59%), Positives = 56/72 (77%)
Query: 1 MIEITCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDY 60
MIE+ NDRLGKKVRVKC +D++GD KK+++ Q GT+ KIVL+K ++ KDHI + DY
Sbjct: 21 MIEVVVNDRLGKKVRVKCLGEDSVGDFKKVLSLQIGTQPNKIVLQKGGSVLKDHISLEDY 80
Query: 61 EIHDGMNLELYY 72
E+HD NLELYY
Sbjct: 81 EVHDQTNLELYY 92
>1uh6_A Ubiquitin-like 5; beta-grAsp fold, structural genomics, riken
structural genomics/proteomics initiative, RSGI, unknown
function; NMR {Mus musculus} SCOP: d.15.1.1
Length = 100
Score = 132 bits (333), Expect = 1e-42
Identities = 65/73 (89%), Positives = 68/73 (93%)
Query: 1 MIEITCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDY 60
MIE+ CNDRLGKKVRVKCN DDTIGDLKKLIAAQTGTRW KIVLKKWYTIFKDH+ + DY
Sbjct: 28 MIEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSLGDY 87
Query: 61 EIHDGMNLELYYQ 73
EIHDGMNLELYYQ
Sbjct: 88 EIHDGMNLELYYQ 100
>1ttn_A DC-UBP, dendritic cell-derived ubiquitin-like protein;
ubiquitin-like domain, solution structure, signaling
protein; NMR {Homo sapiens} SCOP: d.15.1.1
Length = 106
Score = 40.9 bits (96), Expect = 1e-06
Identities = 10/65 (15%), Positives = 24/65 (36%), Gaps = 10/65 (15%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIF-----KDHIRIMDYEIHDG 65
GK +++ DT+ +K+ + A G F D ++ + +I
Sbjct: 33 GKDLKLVVRSTDTVFHMKRRLHAAEGVEPGSQRW-----FFSGRPLTDKMKFEELKIPKD 87
Query: 66 MNLEL 70
+++
Sbjct: 88 YVVQV 92
>1yqb_A Ubiquilin 3; structural genomics consortium, ubiquitin,
ubiquitin-like domain, structural genomics, signaling
protein SGC; 2.00A {Homo sapiens} SCOP: d.15.1.1
Length = 100
Score = 40.8 bits (96), Expect = 2e-06
Identities = 17/75 (22%), Positives = 30/75 (40%), Gaps = 11/75 (14%)
Query: 1 MIEITCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIF-----KDHI 55
+I++T K TI LK+ I+ + +++VL IF KD
Sbjct: 22 LIKVTVKT-PKDKEDFSVTDTCTIQQLKEEISQRFKAHPDQLVL-----IFAGKILKDPD 75
Query: 56 RIMDYEIHDGMNLEL 70
+ + DG+ + L
Sbjct: 76 SLAQCGVRDGLTVHL 90
>3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL
conjugation pathway, DNA damage, nucleus,
phosphoprotein; HET: 1PE; 2.40A {Saccharomyces
cerevisiae}
Length = 106
Score = 39.3 bits (92), Expect = 7e-06
Identities = 15/70 (21%), Positives = 29/70 (41%), Gaps = 10/70 (14%)
Query: 1 MIEITCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIF-----KDHI 55
M+ +T + +KV + P +TI + K +A +I L I+ +D
Sbjct: 1 MVSLTFKNFKKEKVPLDLEPSNTILETKTKLAQSISCEESQIKL-----IYSGKVLQDSK 55
Query: 56 RIMDYEIHDG 65
+ + + DG
Sbjct: 56 TVSECGLKDG 65
>1wx8_A Riken cDNA 4931431F19; ubiquitin-like domain, ubiquilin 1-like,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus
musculus} SCOP: d.15.1.1
Length = 96
Score = 38.5 bits (90), Expect = 1e-05
Identities = 11/66 (16%), Positives = 21/66 (31%), Gaps = 10/66 (15%)
Query: 10 LGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIF-----KDHIRIMDYEIHD 64
+ + KK I+ +++VL IF +D + I D
Sbjct: 25 PQDCHEFFLAENSNVRRFKKQISKYLHCNADRLVL-----IFTGKILRDQDILSQRGILD 79
Query: 65 GMNLEL 70
G + +
Sbjct: 80 GSTVHV 85
>3dbh_I NEDD8; cell cycle, activating enzyme, apoptosis, membrane, UBL
conjugation pathway, ATP-binding, ligase, nucleotide-
binding, polymorphism; 2.85A {Homo sapiens} SCOP:
k.45.1.1 PDB: 3dbr_I 3dbl_I
Length = 88
Score = 38.1 bits (89), Expect = 1e-05
Identities = 14/60 (23%), Positives = 25/60 (41%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
GK++ + P D + +K+ + + G ++ L D DY+I G L L
Sbjct: 22 GKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHL 81
>1ndd_A NEDD8, protein (ubiquitin-like protein NEDD8); proteolysis,
signaling protei; 1.60A {Homo sapiens} SCOP: d.15.1.1
PDB: 1r4m_I 1r4n_I* 1xt9_B 2ko3_A 3gzn_I* 2bkr_B
2nvu_I* 3dqv_A 1bt0_A
Length = 76
Score = 38.0 bits (89), Expect = 1e-05
Identities = 15/65 (23%), Positives = 27/65 (41%), Gaps = 10/65 (15%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIF-----KDHIRIMDYEIHDG 65
GK++ + P D + +K+ + + G ++ L I+ D DY+I G
Sbjct: 10 GKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRL-----IYSGKQMNDEKTAADYKILGG 64
Query: 66 MNLEL 70
L L
Sbjct: 65 SVLHL 69
>1v86_A DNA segment, CHR 7, wayne state university 128, expressed;
ubiquitin fold, structural genomics, D7WSU128E protein;
HET: DNA; NMR {Mus musculus} SCOP: d.15.1.1
Length = 95
Score = 38.2 bits (89), Expect = 2e-05
Identities = 13/62 (20%), Positives = 26/62 (41%), Gaps = 5/62 (8%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWE--KIVLKKWYTIFKDHIRIMDYEIHDGMNL 68
K VK D T +LK+ I + TG K++ K + + + + ++ G +
Sbjct: 26 KTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMYKG---LVPEDKTLREIKVTSGAKI 82
Query: 69 EL 70
+
Sbjct: 83 MV 84
>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural
genomics; NMR {Homo sapiens} SCOP: d.15.1.1
Length = 125
Score = 38.3 bits (89), Expect = 2e-05
Identities = 14/66 (21%), Positives = 31/66 (46%), Gaps = 10/66 (15%)
Query: 10 LGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIF-----KDHIRIMDYEIHD 64
+K + ++ K+ I+ + ++ +++VL IF KD ++ + IHD
Sbjct: 40 PKEKEEFAVPENSSVQQFKEAISKRFKSQTDQLVL-----IFAGKILKDQDTLIQHGIHD 94
Query: 65 GMNLEL 70
G+ + L
Sbjct: 95 GLTVHL 100
>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein
structur initiative, northeast structural genomics
consortium, NESG; NMR {Homo sapiens}
Length = 101
Score = 37.7 bits (88), Expect = 2e-05
Identities = 14/66 (21%), Positives = 29/66 (43%), Gaps = 10/66 (15%)
Query: 10 LGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIF-----KDHIRIMDYEIHD 64
+K + ++ K+ I+ + + +++VL IF KD + + IHD
Sbjct: 33 PKEKEEFAVPENSSVQQFKEEISKRFKSHTDQLVL-----IFAGKILKDQDTLSQHGIHD 87
Query: 65 GMNLEL 70
G+ + L
Sbjct: 88 GLTVHL 93
>1wx7_A Ubiquilin 3; ubiquitin-like domain, structural genomics, riken
structural genomics/proteomics initiative, RSGI,
unknown function; NMR {Homo sapiens} SCOP: d.15.1.1
Length = 106
Score = 38.1 bits (89), Expect = 2e-05
Identities = 15/66 (22%), Positives = 25/66 (37%), Gaps = 10/66 (15%)
Query: 10 LGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIF-----KDHIRIMDYEIHD 64
K TI LK+ I+ + +++VL IF KD + + D
Sbjct: 25 PKDKEDFSVTDTCTIQQLKEEISQRFKAHPDQLVL-----IFAGKILKDPDSLAQCGVRD 79
Query: 65 GMNLEL 70
G+ + L
Sbjct: 80 GLTVHL 85
>2l7r_A Ubiquitin-like protein FUBI; structural genomics, PSI-biology,
protein structure initiati northeast structural
genomics consortium, NESG; NMR {Homo sapiens}
Length = 93
Score = 37.4 bits (87), Expect = 3e-05
Identities = 9/60 (15%), Positives = 21/60 (35%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
+ + +T+ +K +A+ G E V+ +D + + LE+
Sbjct: 27 QELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAGAPLEDEATLGQCGVEALTTLEV 86
>1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair,
proteasome-mediated degradation, protein- protein
interaction, replication; NMR {Homo sapiens} SCOP:
a.5.2.1 a.5.2.1 a.189.1.1 d.15.1.1 PDB: 1qze_A 1tp4_A
Length = 368
Score = 38.8 bits (89), Expect = 3e-05
Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 7/75 (9%)
Query: 2 IEITCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIF-----KDHIR 56
+ IT + +++ PD+T+ LK+ I A+ G + + I+ D +
Sbjct: 8 VTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKG--RDAFPVAGQKLIYAGKILSDDVP 65
Query: 57 IMDYEIHDGMNLELY 71
I DY I + + +
Sbjct: 66 IRDYRIDEKNFVVVM 80
>4fbj_B NEDD8; effector-HOST target complex, glutamine deamidase,
deamidati bacterial effector, cell cycle-protein
binding complex; 1.60A {Homo sapiens} PDB: 4f8c_B
Length = 88
Score = 36.2 bits (84), Expect = 7e-05
Identities = 14/60 (23%), Positives = 25/60 (41%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
GK++ + P D + +K+ + + G ++ L D DY+I G L L
Sbjct: 10 GKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHL 69
>1we7_A SF3A1 protein; structural genomics, ubiquitin-like domain, riken
structural genomics/proteomics initiative, RSGI, gene
regulation; NMR {Mus musculus} SCOP: d.15.1.1 PDB:
1zkh_A
Length = 115
Score = 36.7 bits (85), Expect = 9e-05
Identities = 15/74 (20%), Positives = 23/74 (31%), Gaps = 13/74 (17%)
Query: 2 IEITCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIF-----KDHIR 56
E N G+ + D + +K I TG K L + KD
Sbjct: 39 TEWKLN---GQGLVFTLPLTDQVSVIKVKIHEATGMPAGKQKL-----QYEGIFIKDSNS 90
Query: 57 IMDYEIHDGMNLEL 70
+ Y + G + L
Sbjct: 91 LAYYNMASGAVIHL 104
>1wh3_A 59 kDa 2'-5'-oligoadenylate synthetase like protein; P59 OASL,
ubiquitin family, structural genomics; NMR {Homo
sapiens} SCOP: d.15.1.1
Length = 87
Score = 35.8 bits (83), Expect = 1e-04
Identities = 16/60 (26%), Positives = 25/60 (41%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
G NP+ I LK+ I Q G ++ L+ + +D + + Y I D L L
Sbjct: 17 GGSYAYAINPNSFILGLKQQIEDQQGLPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLIL 76
>3n3k_B Ubiquitin; hydrolase, protease, thiol protease, DUB, zinc ribbon,
inhibitor, ubiqu acetylation, cytoplasm, isopeptide
bond, nucleus; 2.60A {Homo sapiens}
Length = 85
Score = 35.8 bits (83), Expect = 1e-04
Identities = 16/60 (26%), Positives = 28/60 (46%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
G+ + ++ P DTI ++K I + G ++ L +D + DY IH+ L L
Sbjct: 13 GRTIILEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIHNHSALYL 72
>2dzi_A Ubiquitin-like protein 4A; GDX, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 81
Score = 35.7 bits (83), Expect = 1e-04
Identities = 14/65 (21%), Positives = 27/65 (41%), Gaps = 10/65 (15%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIF-----KDHIRIMDYEIHDG 65
G++ ++ D+ + LK+L++ + + L +F D R+ DY I
Sbjct: 17 GRECSLQVPEDELVSTLKQLVSEKLNVPVRQQRL-----LFKGKALADGKRLSDYSIGPN 71
Query: 66 MNLEL 70
L L
Sbjct: 72 SKLNL 76
>3mtn_B UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquitin-specific
protease activity, hydrolase, ubiquitin B structural
genomics consortium, SGC; 2.70A {Homo sapiens}
Length = 85
Score = 35.4 bits (82), Expect = 2e-04
Identities = 16/60 (26%), Positives = 26/60 (43%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
GK + ++ P DTI ++K I + G ++ L +D + DY I L L
Sbjct: 13 GKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKWSTLFL 72
>3k9o_B Ubiquitin, UBB+1; E2-25K, complex structure, ATP-binding,
isopeptide BO ligase, nucleotide-binding, UBL
conjugation pathway; 1.80A {Homo sapiens} PDB: 2k25_A
2kx0_A
Length = 96
Score = 35.5 bits (82), Expect = 2e-04
Identities = 16/60 (26%), Positives = 26/60 (43%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
GK + ++ P DTI ++K I + G ++ L +D + DY I L L
Sbjct: 11 GKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHL 70
>3u5c_F RP14, S2, YS8, 40S ribosomal protein S5; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_F 3o30_D 3o2z_D 3u5g_F 3jyv_G*
2noq_F 1s1h_G 3iz6_F
Length = 225
Score = 35.9 bits (83), Expect = 2e-04
Identities = 1/65 (1%), Positives = 9/65 (13%), Gaps = 10/65 (15%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIF-----KDHIRIMDYEIHDG 65
++ + + + E + + +
Sbjct: 10 VQEDFEVVEEFTPVVLATPIPEEVQQAQTEIKLF-----NKWSFEEVEVKDASLVDYVQV 64
Query: 66 MNLEL 70
Sbjct: 65 RQPIF 69
>2kd0_A LRR repeats and ubiquitin-like domain-containing protein
AT2G30105; ubiquitin-like protein, NESG, leucine-rich
repeat, structural genomics; NMR {Arabidopsis thaliana}
Length = 85
Score = 35.0 bits (81), Expect = 3e-04
Identities = 14/62 (22%), Positives = 26/62 (41%), Gaps = 4/62 (6%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWE--KIVLKKWYTIFKDHIRIMDYEIHDGMNL 68
GK + + +PD T+ DLK + T K++ K + + + ++ G L
Sbjct: 21 GKSIPLSVSPDCTVKDLKSQLQPITNVLPRGQKLIFKG--KVLVETSTLKQSDVGSGAKL 78
Query: 69 EL 70
L
Sbjct: 79 ML 80
>1yx5_B Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo sapiens} SCOP:
d.15.1.1 PDB: 1yx6_B
Length = 98
Score = 34.8 bits (80), Expect = 3e-04
Identities = 16/60 (26%), Positives = 26/60 (43%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
GK + ++ P DTI ++K I + G ++ L +D + DY I L L
Sbjct: 10 GKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHL 69
>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15,
structure, northeast structural genomics consortium,
protein structure initiative, NESG; NMR {Homo sapiens}
Length = 88
Score = 34.3 bits (79), Expect = 4e-04
Identities = 8/60 (13%), Positives = 23/60 (38%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
G+ + T+ LK+ ++ G + + L +D + + +Y + + +
Sbjct: 14 GRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFM 73
>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion
protein; ubiquitin interacting motif, UIM, protein
domain interface; NMR {Saccharomyces cerevisiae}
Length = 114
Score = 34.8 bits (80), Expect = 5e-04
Identities = 15/60 (25%), Positives = 25/60 (41%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
GK + ++ DTI ++K I + G ++ L +D + DY I L L
Sbjct: 19 GKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLEDGRTLSDYNIQRESTLHL 78
>3phx_B Ubiquitin-like protein ISG15; OTU domain, DE-ubiquitinase,
DE-isgylase, hydrolase-protein complex; 1.60A {Homo
sapiens}
Length = 79
Score = 33.9 bits (78), Expect = 5e-04
Identities = 8/60 (13%), Positives = 23/60 (38%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
G+ + T+ LK+ ++ G + + L +D + + +Y + + +
Sbjct: 14 GRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFM 73
>1sif_A Ubiquitin; hydrophobic mutants, folding, stability, structural
protein; 2.18A {Homo sapiens} SCOP: d.15.1.1
Length = 88
Score = 33.9 bits (78), Expect = 6e-04
Identities = 18/60 (30%), Positives = 25/60 (41%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
GK V+ P DTI +LK I + G ++ L +D + DY I L L
Sbjct: 19 GKTFTVEMEPSDTIENLKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHL 78
>3a9j_A Ubiquitin; protein complex, cytoplasm, isopeptide bond,
metal-binding, zinc; 1.18A {Mus musculus} PDB: 3a1q_B
2znv_B 3a9k_A 3h7p_A 3jsv_A 3dvg_Y 3dvn_Y 3nob_A
2o6v_D* 3jw0_X 3jvz_X 3nhe_B* 1aar_A 1d3z_A 1f9j_A
1fxt_B 1g6j_A 1nbf_C 1cmx_B 1q5w_B ...
Length = 76
Score = 33.4 bits (77), Expect = 7e-04
Identities = 16/60 (26%), Positives = 26/60 (43%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
GK + ++ P DTI ++K I + G ++ L +D + DY I L L
Sbjct: 10 GKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHL 69
>2dzm_A FAS-associated factor 1; ubiquitin-like domain, HFAF1, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 100
Score = 33.9 bits (77), Expect = 8e-04
Identities = 14/71 (19%), Positives = 31/71 (43%), Gaps = 2/71 (2%)
Query: 1 MIEITCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYT-IFKDHIRIMD 59
M++ R + V V T+G++K+++ + K++LK W T +D +
Sbjct: 9 MLDFRVEYR-DRNVDVVLEDTCTVGEIKQILENELQIPVSKMLLKGWKTGDVEDSTVLKS 67
Query: 60 YEIHDGMNLEL 70
+ +L +
Sbjct: 68 LHLPKNNSLYV 78
>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold,
GP78-binding, chaperone; 1.30A {Homo sapiens}
Length = 88
Score = 33.4 bits (77), Expect = 9e-04
Identities = 10/59 (16%), Positives = 20/59 (33%), Gaps = 10/59 (16%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIF-----KDHIRIMDYEIHD 64
+ + + K+ IAA EK L I+ +D ++ +Y +
Sbjct: 27 SQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRL-----IYQGRVLQDDKKLQEYNVGG 80
>2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing, protein
binding; 2.60A {Homo sapiens}
Length = 111
Score = 33.7 bits (77), Expect = 0.001
Identities = 16/60 (26%), Positives = 26/60 (43%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
GK + ++ P DTI ++K I + G ++ L +D + DY I L L
Sbjct: 45 GKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHL 104
>1v5o_A 1700011N24RIK protein; hypothetical protein, ubiquitin-like fold,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus
musculus} SCOP: d.15.1.1
Length = 102
Score = 33.8 bits (77), Expect = 0.001
Identities = 14/72 (19%), Positives = 28/72 (38%), Gaps = 13/72 (18%)
Query: 2 IEITC--NDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFK------D 53
I + C D ++ NPD + + + L ++G E+ + ++ D
Sbjct: 10 ITVYCVRRDLTEVTFSLQVNPDFELSNFRVLCELESGVPAEEAQI-----VYMEQLLTDD 64
Query: 54 HIRIMDYEIHDG 65
H + Y + DG
Sbjct: 65 HCSLGSYGLKDG 76
>1v5t_A 8430435I17RIK protein; hypothetical protein, ubiquitin-like fold,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus
musculus} SCOP: d.15.1.1 PDB: 2kx3_A
Length = 90
Score = 33.3 bits (76), Expect = 0.001
Identities = 11/56 (19%), Positives = 25/56 (44%), Gaps = 3/56 (5%)
Query: 16 VKCNPDDTIGDLKKLIAAQTGTRWEK---IVLKKWYTIFKDHIRIMDYEIHDGMNL 68
+ DDT+ DLK+ + TG E+ + LK ++ +++ ++ +
Sbjct: 22 TTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKLKPNTKI 77
>1wgd_A Homocysteine-responsive endoplasmic reticulum- resident
ubiquitin-like domain member...; ENDPLASMIC reticulum
stress, UBL domain; NMR {Homo sapiens} SCOP: d.15.1.1
Length = 93
Score = 33.4 bits (76), Expect = 0.001
Identities = 8/61 (13%), Positives = 24/61 (39%), Gaps = 2/61 (3%)
Query: 2 IEITCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYT--IFKDHIRIMD 59
+ + ++ + + + + ++G LK ++ R + Y+ + DH + D
Sbjct: 10 LLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRD 69
Query: 60 Y 60
Sbjct: 70 L 70
>3b1l_X E3 ubiquitin-protein ligase parkin; proteasome,
ALFA-beta-protein; 1.85A {Mus musculus} PDB: 1mg8_A
2zeq_A 2knb_A 1iyf_A
Length = 76
Score = 33.0 bits (76), Expect = 0.001
Identities = 11/65 (16%), Positives = 29/65 (44%), Gaps = 10/65 (15%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIF-----KDHIRIMDYEIHDG 65
V+ + D +I LK+++A Q G +++ + IF +H+ + + ++
Sbjct: 10 SYGFPVEVDSDTSILQLKEVVAKQQGVPADQLRV-----IFAGKELPNHLTVQNCDLEQQ 64
Query: 66 MNLEL 70
+ +
Sbjct: 65 SIVHI 69
>1wy8_A NP95-like ring finger protein, isoform A; ubiquitin-like domain,
NP95/ICBP90-like ring finger (NIRF), ubiquitin ligase,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.15.1.1
Length = 89
Score = 32.8 bits (75), Expect = 0.002
Identities = 10/53 (18%), Positives = 22/53 (41%)
Query: 18 CNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
+ TI +L++ + A R E L ++ + DY++ ++L
Sbjct: 26 VSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQL 78
>3rt3_B Ubiquitin-like protein ISG15; ubiquitin-like domain, isgylation,
antiviral protein-viral P complex; 2.01A {Homo sapiens}
PDB: 3sdl_C 3r66_C 3pse_B 1z2m_A
Length = 159
Score = 33.8 bits (77), Expect = 0.002
Identities = 9/60 (15%), Positives = 22/60 (36%), Gaps = 2/60 (3%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWY--TIFKDHIRIMDYEIHDGMNL 68
G + +V + ++ +LK I + G + L +D + + + G +
Sbjct: 12 GNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPLASQGLGPGSTV 71
Score = 29.2 bits (65), Expect = 0.065
Identities = 9/70 (12%), Positives = 26/70 (37%)
Query: 1 MIEITCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDY 60
+ I + G+ + T+ LK+ ++ G + + L +D + + +Y
Sbjct: 81 PLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLGEY 140
Query: 61 EIHDGMNLEL 70
+ + +
Sbjct: 141 GLKPLSTVFM 150
>4dwf_A HLA-B-associated transcript 3; ubiquitin-like domain, BAT3
protein, PF00240, structural GEN joint center for
structural genomics, JCSG; 1.80A {Homo sapiens} PDB:
1wx9_A
Length = 90
Score = 32.6 bits (75), Expect = 0.002
Identities = 10/59 (16%), Positives = 20/59 (33%), Gaps = 10/59 (16%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIF-----KDHIRIMDYEIHD 64
+ + + K+ IAA EK L I+ +D ++ +Y +
Sbjct: 15 SQTRTFIVGAQMNVKEFKEHIAASVSIPSEKQRL-----IYQGRVLQDDKKLQEYNVGG 68
>3m63_B Ubiquitin domain-containing protein DSK2; armadillo-like repeats,
UBL conjugation pathway, nucleus, phosphoprotein; HET:
1PE; 2.40A {Saccharomyces cerevisiae}
Length = 101
Score = 31.9 bits (73), Expect = 0.005
Identities = 16/66 (24%), Positives = 23/66 (34%), Gaps = 10/66 (15%)
Query: 10 LGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIF-----KDHIRIMDYEIHD 64
K V P+ T+ K+ I G L I+ KD + Y I D
Sbjct: 36 GQDKWEVNVAPESTVLQFKEAINKANGIPVANQRL-----IYSGKILKDDQTVESYHIQD 90
Query: 65 GMNLEL 70
G ++ L
Sbjct: 91 GHSVHL 96
>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}
Length = 172
Score = 31.9 bits (72), Expect = 0.007
Identities = 17/70 (24%), Positives = 29/70 (41%)
Query: 1 MIEITCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDY 60
++I GK + ++ P DTI ++K I + G ++ L +D + DY
Sbjct: 96 GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY 155
Query: 61 EIHDGMNLEL 70
I L L
Sbjct: 156 NIQKESTLHL 165
Score = 30.8 bits (69), Expect = 0.021
Identities = 16/63 (25%), Positives = 27/63 (42%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
GK + ++ P DTI ++K I + G ++ L +D + DY I L L
Sbjct: 30 GKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHL 89
Query: 71 YYQ 73
+
Sbjct: 90 VLR 92
>3b08_A Polyubiquitin-C, ubiquitin; protein complex, signaling
protein-metal binding protein COM; HET: TRE; 1.70A
{Homo sapiens} PDB: 2w9n_A* 3b0a_A* 3axc_A 2zvn_A
2zvo_A 2y5b_B
Length = 152
Score = 31.1 bits (70), Expect = 0.014
Identities = 16/63 (25%), Positives = 27/63 (42%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
GK + ++ P DTI ++K I + G ++ L +D + DY I L L
Sbjct: 10 GKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHL 69
Query: 71 YYQ 73
+
Sbjct: 70 VLR 72
Score = 30.8 bits (69), Expect = 0.021
Identities = 17/70 (24%), Positives = 29/70 (41%)
Query: 1 MIEITCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDY 60
++I GK + ++ P DTI ++K I + G ++ L +D + DY
Sbjct: 76 GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY 135
Query: 61 EIHDGMNLEL 70
I L L
Sbjct: 136 NIQKESTLHL 145
>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana,
uncharacterized putative protein, NESG, structural
genomics; NMR {Arabidopsis thaliana}
Length = 84
Score = 30.3 bits (69), Expect = 0.015
Identities = 10/66 (15%), Positives = 24/66 (36%), Gaps = 11/66 (16%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIF------KDHIRIMDYEIHD 64
G ++ + DT+ +K+ I K L I ++ + + +I
Sbjct: 20 GSSFELEVDYRDTLLVVKQKIERSQHIPVSKQTL-----IVDGIVILREDLTVEQCQIVP 74
Query: 65 GMNLEL 70
+++L
Sbjct: 75 TSDIQL 80
>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta,
structural genomics, protein structure initiative; NMR
{Arabidopsis thaliana}
Length = 94
Score = 30.4 bits (69), Expect = 0.016
Identities = 11/67 (16%), Positives = 26/67 (38%), Gaps = 11/67 (16%)
Query: 10 LGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFK------DHIRIMDYEIH 63
K+ V+ + +T+ LK I T +++ L + D+ + +Y I
Sbjct: 23 PSKQFTVEVDRTETVSSLKDKIHIVENTPIKRMQL-----YYSGIELADDYRNLNEYGIT 77
Query: 64 DGMNLEL 70
+ + +
Sbjct: 78 EFSEIVV 84
>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling
proteins; 1.15A {Saccharomyces cerevisiae} SCOP:
d.15.1.1 PDB: 2bwe_S
Length = 77
Score = 29.5 bits (67), Expect = 0.023
Identities = 16/65 (24%), Positives = 23/65 (35%), Gaps = 10/65 (15%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIF-----KDHIRIMDYEIHDG 65
K V P+ T+ K+ I G L I+ KD + Y I DG
Sbjct: 13 QDKWEVNVAPESTVLQFKEAINKANGIPVANQRL-----IYSGKILKDDQTVESYHIQDG 67
Query: 66 MNLEL 70
++ L
Sbjct: 68 HSVHL 72
>2faz_A Ubiquitin-like containing PHD and ring finger DOM protein 1; cell
cycle, DNA damage, DNA repair, DNA-binding, ligase, Met
binding, nuclear protein; 2.00A {Homo sapiens} SCOP:
d.15.1.1
Length = 78
Score = 29.2 bits (66), Expect = 0.028
Identities = 8/53 (15%), Positives = 18/53 (33%)
Query: 18 CNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
+ + +L++ I L +D + DYE+ ++L
Sbjct: 21 LSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQL 73
>2kj6_A Tubulin folding cofactor B; methods development, NESG, solution
PSI-2, structural genomics, protein structure
initiative; NMR {Arabidopsis thaliana}
Length = 97
Score = 29.5 bits (66), Expect = 0.035
Identities = 12/75 (16%), Positives = 26/75 (34%), Gaps = 7/75 (9%)
Query: 2 IEITCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVL-------KKWYTIFKDH 54
+ IT + + +P ++ +K+ + + GT + L K + D
Sbjct: 17 LHITHANLKSFSADARFSPQMSVEAVKEKLWKKCGTSVNSMALELYDDSGSKVAVLSDDS 76
Query: 55 IRIMDYEIHDGMNLE 69
+ + DG L
Sbjct: 77 RPLGFFSPFDGFRLH 91
>1wgh_A Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fold, structural
genomics, riken structural genomics/proteomics
initiative, RSGI, unknown function; NMR {Mus musculus}
SCOP: d.15.1.1
Length = 116
Score = 29.6 bits (66), Expect = 0.037
Identities = 10/42 (23%), Positives = 17/42 (40%)
Query: 1 MIEITCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKI 42
MI + GK +P+D+ D+ K + WE+
Sbjct: 16 MINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEE 57
>2wyq_A HHR23A, UV excision repair protein RAD23 homolog A; DNA binding
protein, DNA excision repair, proteasomal degrad
polyubiquitin; 1.65A {Homo sapiens} PDB: 1p98_A 1p9d_U
1p1a_A
Length = 85
Score = 29.1 bits (66), Expect = 0.037
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 1 MIEITCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTG 36
+ IT + +++ PD+T+ LK+ I A+ G
Sbjct: 5 AVTITLKTLQQQTFKIRMEPDETVKVLKEKIEAEKG 40
>1wf9_A NPL4 family protein; beta-grAsp fold like domain, hypothetical
protein, structural genomics, NPPSFA; NMR {Arabidopsis
thaliana} SCOP: d.15.1.1
Length = 107
Score = 29.4 bits (65), Expect = 0.038
Identities = 10/31 (32%), Positives = 11/31 (35%), Gaps = 1/31 (3%)
Query: 15 RVKC-NPDDTIGDLKKLIAAQTGTRWEKIVL 44
RV P T+ LK LI Q L
Sbjct: 20 RVSVDGPHITVSQLKTLIQDQLQIPIHNQTL 50
>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP,
oligomerization, ubiquitin insertion, hydrolase binding;
2.17A {Bacillus amyloliquefaciens}
Length = 189
Score = 30.0 bits (67), Expect = 0.039
Identities = 14/55 (25%), Positives = 23/55 (41%)
Query: 16 VKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
++ P DTI ++K I + G ++ L +D + DY I L L
Sbjct: 120 LEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHL 174
>1wgg_A Ubiquitin carboxyl-terminal hydrolase 14; ubiquitin specific
protease 14, USP14, ubiquitin-like fold, structural
genomics; NMR {Mus musculus} SCOP: d.15.1.1
Length = 96
Score = 29.4 bits (66), Expect = 0.042
Identities = 8/25 (32%), Positives = 11/25 (44%)
Query: 12 KKVRVKCNPDDTIGDLKKLIAAQTG 36
K V+ N D+ K + A TG
Sbjct: 18 KFEGVELNTDEPPMVFKAQLFALTG 42
>1t0y_A Tubulin folding cofactor B; ubiquitin-like, cytoskeleton,
microtubule, CESG, structural genomics, protein
structure initiative, PSI; NMR {Caenorhabditis elegans}
SCOP: d.15.1.1
Length = 122
Score = 29.5 bits (66), Expect = 0.043
Identities = 9/59 (15%), Positives = 20/59 (33%), Gaps = 7/59 (11%)
Query: 19 NPDDTIGDLKKLIAAQTGTRWEKIVL-------KKWYTIFKDHIRIMDYEIHDGMNLEL 70
++ DLKK + GT + + + + + + D + DG +
Sbjct: 25 PAGMSLNDLKKKLELVVGTTVDSMRIQLFDGDDQLKGELTDGAKSLKDLGVRDGYRIHA 83
>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila}
PDB: 2xzn_9
Length = 189
Score = 29.7 bits (66), Expect = 0.050
Identities = 7/34 (20%), Positives = 13/34 (38%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVL 44
G+ ++ DLK I+ G + + L
Sbjct: 10 GETKIYTLEQGTSVLDLKSQISQDMGFEIDMMTL 43
>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural
genomics, protein structure initiative, PSI; NMR {Homo
sapiens}
Length = 125
Score = 29.2 bits (65), Expect = 0.057
Identities = 10/42 (23%), Positives = 17/42 (40%)
Query: 1 MIEITCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKI 42
MI + GK +P+D+ D+ K + WE+
Sbjct: 17 MINLRLILVSGKTKEFLFSPNDSASDIAKHVYDNWPMDWEEE 58
>3fmw_A Oxygenase; mithramycin, baeyer-villiger, flavin binding protein,
oxidoreductase; HET: FAD; 2.89A {Streptomyces
argillaceus}
Length = 570
Score = 29.7 bits (67), Expect = 0.060
Identities = 10/40 (25%), Positives = 13/40 (32%)
Query: 20 PDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMD 59
T+ DL +A GT W + F D R
Sbjct: 278 GPVTLEDLGAAVARVRGTPLTLTEPVSWLSRFGDASRQAK 317
>1uel_A HHR23B, UV excision repair protein RAD23 homolog B; UBL, UIM,
riken structural genomics/proteomics initiative, RSGI,
structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1
Length = 95
Score = 28.4 bits (64), Expect = 0.076
Identities = 7/35 (20%), Positives = 20/35 (57%)
Query: 2 IEITCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTG 36
+++T + ++ +P++T+ LK+ I ++ G
Sbjct: 1 MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKG 35
>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold,
ubiquitination, ligase; 2.71A {Homo sapiens} PDB:
2lgy_A
Length = 105
Score = 28.8 bits (64), Expect = 0.080
Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 9/76 (11%)
Query: 2 IEITCNDRL--GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWY---TIFKDHIR 56
+ ++ D + + PD T+ LK ++ G VL++W + +D
Sbjct: 25 LWVSVEDAQMHTVTIWLTVRPDMTVASLKDMVFLDYGF---PPVLQQWVIGQRLARDQET 81
Query: 57 IMDYEI-HDGMNLELY 71
+ + + +G + LY
Sbjct: 82 LHSHGVRQNGDSAYLY 97
>2fnj_B Transcription elongation factor B polypeptide 2; beta-sandwich,
lectin-like, SPRY, protein transport/signaling protein
complex; 1.80A {Mus musculus} SCOP: d.15.1.1 PDB:
1lm8_B 1lqb_A 1vcb_A 2c9w_B 2izv_B 2jz3_B 2xai_C 3dcg_A
3zrc_A* 3zrf_A
Length = 118
Score = 28.1 bits (62), Expect = 0.14
Identities = 7/46 (15%), Positives = 16/46 (34%)
Query: 18 CNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIH 63
T+ +LK+++ E+ L K + D + +
Sbjct: 18 AKESSTVFELKRIVEGILKRPPEEQRLYKDDQLLDDGKTLGECGFT 63
>3l0w_B Monoubiquitinated proliferating cell nuclear antigen,
proliferating cell nuclear antigen; replication, DNA
damage, DNA repair; 2.80A {Saccharomyces cerevisiae}
PDB: 3l10_B
Length = 169
Score = 28.4 bits (63), Expect = 0.15
Identities = 17/65 (26%), Positives = 26/65 (40%), Gaps = 10/65 (15%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFK-----DHIRIMDYEIHDG 65
GK + ++ DTI ++K I + G ++ L IF D + DY I
Sbjct: 10 GKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRL-----IFAGKQLEDGRTLSDYNIQKE 64
Query: 66 MNLEL 70
L L
Sbjct: 65 STLHL 69
>3u5e_m 60S ribosomal protein L40; translation, ribosome, ribosomal R
ribosomal protein, STM1, eukaryotic ribosome; 3.00A
{Saccharomyces cerevisiae} PDB: 3u5i_m 4a18_K 4a19_K
4a1b_K 4a1d_K 4adx_5 3izc_p 3izs_p 3iz5_p 3izr_p
Length = 128
Score = 27.7 bits (61), Expect = 0.19
Identities = 9/34 (26%), Positives = 17/34 (50%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVL 44
GK + ++ DTI ++K I + G ++ L
Sbjct: 10 GKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRL 43
>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast
structural genomics consortiu PSI-2, protein structure
initiative, hydrolase; NMR {Mus musculus}
Length = 86
Score = 27.5 bits (61), Expect = 0.20
Identities = 14/68 (20%), Positives = 22/68 (32%), Gaps = 15/68 (22%)
Query: 13 KVRVKC----------NPDDTIGDLKKLIAAQTGTRWEKIVLKKWY-----TIFKDHIRI 57
+VR K + + +L+ IAA TG + Y + I +
Sbjct: 2 RVRCKAKGGTHLLQGLSSRTRLRELQGQIAAITGIAPGSQRILVGYPPECLDLSDRDITL 61
Query: 58 MDYEIHDG 65
D I G
Sbjct: 62 GDLPIQSG 69
>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster}
Length = 320
Score = 27.9 bits (61), Expect = 0.26
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTR 38
GK+ V DT+ L+ I +T R
Sbjct: 14 GKEYPVDLTDQDTVEVLRHEIFRKTQVR 41
>1wia_A Hypothetical ubiquitin-like protein (riken cDNA 2010008E23);
'structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus
musculus} SCOP: d.15.1.1
Length = 95
Score = 26.9 bits (59), Expect = 0.38
Identities = 10/70 (14%), Positives = 20/70 (28%), Gaps = 14/70 (20%)
Query: 2 IEITCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFK------DHI 55
I + + P+DT+G LK ++ L I++
Sbjct: 8 INVRLKFLNDTEELAVARPEDTVGTLKSKYFPGQE---SQMKL-----IYQGRLLQDPAR 59
Query: 56 RIMDYEIHDG 65
+ I +
Sbjct: 60 TLSSLNITNN 69
>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident
ubiquitin-like domain member...; UBL domain, membrane,
polymorphism, transmembrane; NMR {Homo sapiens}
Length = 99
Score = 26.1 bits (57), Expect = 0.63
Identities = 6/37 (16%), Positives = 16/37 (43%)
Query: 2 IEITCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTR 38
+ I ++ + C + T+G LK ++ ++
Sbjct: 26 LIIKAPNQKYSDQTISCFLNWTVGKLKTHLSNVYPSK 62
>3tql_A Arginine-binding protein; transport and binding proteins, transport
protein; HET: MSE ARG; 1.59A {Coxiella burnetii}
Length = 227
Score = 26.0 bits (58), Expect = 0.84
Identities = 11/58 (18%), Positives = 21/58 (36%), Gaps = 5/58 (8%)
Query: 14 VRVKCNPDDTIGDLK-KLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
+ LK K+I Q GT ++ + + + I I Y + ++L
Sbjct: 94 ADKNTPLTLSKQGLKGKIIGVQGGTTFDSYLQDSF----GNSITIQRYPSEEDALMDL 147
>2kjr_A CG11242; UBL, ubiquitin, ubiquitin-like, structural genomics,
PSI-2, protein structure initiative; NMR {Drosophila
melanogaster}
Length = 95
Score = 25.6 bits (56), Expect = 0.94
Identities = 15/74 (20%), Positives = 28/74 (37%), Gaps = 6/74 (8%)
Query: 2 IEITCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGTRWE--KIVLKKWYT----IFKDHI 55
+ ++ + VK D T+ LK + TG K+ + K T + +
Sbjct: 18 VNVSNSHNDAVAFEVKLAKDLTVAQLKTKLEILTGGCAGTMKVQVFKGDTCVSTMDNNDA 77
Query: 56 RIMDYEIHDGMNLE 69
++ Y DG+ L
Sbjct: 78 QLGYYANSDGLRLH 91
>2qa2_A CABE, polyketide oxygenase CABE; FAD, angucycline, aromatic
hydroxylase, oxidored; HET: FAD; 2.70A {Streptomyces}
Length = 499
Score = 26.1 bits (58), Expect = 0.98
Identities = 6/39 (15%), Positives = 10/39 (25%), Gaps = 1/39 (2%)
Query: 21 DDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMD 59
++ TG W + F D R +
Sbjct: 236 PPPYQEVAAAWQRLTGQDISHGEPV-WVSAFGDPARQVS 273
>2qa1_A PGAE, polyketide oxygenase PGAE; FAD, angucycline, aromatic
hydroxylase, oxidored; HET: FAD; 1.80A {Streptomyces}
Length = 500
Score = 26.1 bits (58), Expect = 1.1
Identities = 5/40 (12%), Positives = 11/40 (27%), Gaps = 1/40 (2%)
Query: 20 PDDTIGDLKKLIAAQTGTRWEKIVLKKWYTIFKDHIRIMD 59
+ ++ TG W + F + R +
Sbjct: 234 TPPSWHEVADAWKRLTGDDIAHAEPV-WVSAFGNATRQVT 272
>2pjh_A Protein NPL4, nuclear protein localization protein 4 homolog;
UFD1, NPL4, AAA, protein binding, transport protein;
NMR {Mus musculus}
Length = 80
Score = 25.2 bits (55), Expect = 1.2
Identities = 5/22 (22%), Positives = 9/22 (40%)
Query: 15 RVKCNPDDTIGDLKKLIAAQTG 36
R+ +T K +A + G
Sbjct: 17 RITATKRETAATFLKKVAKEFG 38
>4efo_A Serine/threonine-protein kinase TBK1; ubiquitin like domain,
transferase; 1.77A {Homo sapiens}
Length = 94
Score = 25.3 bits (55), Expect = 1.3
Identities = 4/23 (17%), Positives = 10/23 (43%)
Query: 14 VRVKCNPDDTIGDLKKLIAAQTG 36
++ + +T +L+ QT
Sbjct: 26 HKIYIHSYNTATIFHELVYKQTK 48
>1v6e_A Cytoskeleton-associated protein 1; tubulin-specific chaperone B,
tubulin folding cofactor B, microtubule, ubiquitin-like
fold, structural genomics; NMR {Mus musculus} SCOP:
d.15.1.1
Length = 95
Score = 25.2 bits (55), Expect = 1.3
Identities = 9/58 (15%), Positives = 20/58 (34%), Gaps = 7/58 (12%)
Query: 19 NPDDTIGDLKKLIAAQTGTRWE--KIVLKKWYTIF-----KDHIRIMDYEIHDGMNLE 69
+ TI + K + G+ ++ L F ++ + Y + DG +
Sbjct: 26 SRSLTIAEFKCKLELVVGSPASCMELELYGADDKFYSKLDQEDALLGSYPVDDGCRIH 83
>1lst_A Lysine, arginine, ornithine-binding protein; amino-acid binding
protein; HET: LYS; 1.80A {Salmonella typhimurium} SCOP:
c.94.1.1 PDB: 2lao_A 1lag_E* 1lah_E 1laf_E 1hsl_A*
1hpb_P*
Length = 239
Score = 24.9 bits (55), Expect = 2.7
Identities = 10/58 (17%), Positives = 18/58 (31%), Gaps = 4/58 (6%)
Query: 14 VRVKCNPDDTIGDLK-KLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
T+ LK K + G+ E W + ++ Y D + +L
Sbjct: 96 AAKGSPIQPTLESLKGKHVGVLQGSTQEAYANDNW---RTKGVDVVAYANQDLIYSDL 150
>2q88_A EHUB, putative ABC transporter amino acid-binding prote;
substrate-binding protein, compatible solues,
ABC-transporte osmoprotection; HET: 4CS; 1.90A
{Sinorhizobium meliloti} PDB: 2q89_A*
Length = 257
Score = 24.2 bits (53), Expect = 3.8
Identities = 10/50 (20%), Positives = 14/50 (28%), Gaps = 5/50 (10%)
Query: 22 DTIGDLK-KLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
I D I A G EK+ L+ R++ L
Sbjct: 117 KDIADNPDAKIGAPGGGTEEKLALEAGV----PRDRVIVVPDGQSGLKML 162
>3d2f_A Heat shock protein homolog SSE1; nucleotide exchange factor,
protein folding, ATP-binding, Ca binding, chaperone,
nucleotide-binding, phosphoprotein; HET: ATP; 2.30A
{Saccharomyces cerevisiae} PDB: 3d2e_A* 3c7n_A* 2qxl_A*
Length = 675
Score = 24.6 bits (54), Expect = 4.0
Identities = 5/13 (38%), Positives = 10/13 (76%)
Query: 19 NPDDTIGDLKKLI 31
N +T+ +LK++I
Sbjct: 60 NIKNTVANLKRII 72
>1uuj_A Platelet-activating factor acetylhydrolase IB ALP subunit;
mitosis, neuroge cytoskeleton, cell division,
microtubule; 1.75A {Mus musculus} SCOP: a.221.1.1
Length = 88
Score = 24.0 bits (52), Expect = 4.2
Identities = 7/49 (14%), Positives = 21/49 (42%), Gaps = 4/49 (8%)
Query: 17 KCNPDDTIGDLKKL----IAAQTGTRWEKIVLKKWYTIFKDHIRIMDYE 61
++ KK + + ++ ++ KKW ++ + ++M+ E
Sbjct: 23 SNGYEEAYSVFKKEAELDMNEELDKKYAGLLEKKWTSVIRLQKKVMELE 71
>2pyy_A Ionotropic glutamate receptor bacterial homologue; GLUR0 ligand
binding domain, transport protein; HET: GLU; 2.10A
{Nostoc punctiforme}
Length = 228
Score = 24.1 bits (53), Expect = 4.8
Identities = 8/41 (19%), Positives = 16/41 (39%), Gaps = 4/41 (9%)
Query: 14 VRVKCNPDDTI---GDLK-KLIAAQTGTRWEKIVLKKWYTI 50
VR + I DL K++A G+ + + ++
Sbjct: 94 VRNLESGTGDIRSIDDLPGKVVATTAGSTAATYLREHHISV 134
>3v76_A Flavoprotein; structural genomics, PSI-biology, NEW YORK
structural genomi research consortium, nysgrc; HET:
FDA; 2.51A {Sinorhizobium meliloti}
Length = 417
Score = 24.0 bits (53), Expect = 5.1
Identities = 5/17 (29%), Positives = 9/17 (52%), Gaps = 4/17 (23%)
Query: 7 NDRLGKKVRV----KCN 19
G+K+R+ +CN
Sbjct: 59 ARAPGEKIRISGGGRCN 75
>7odc_A Protein (ornithine decarboxylase); pyridoxal-5'-phosphate, PLP,
group IV decarboxylase, polyami parasitical,
chemotherapy target, putrescine; HET: PLP; 1.60A {Mus
musculus} SCOP: b.49.2.3 c.1.6.1 PDB: 2on3_A 1d7k_A*
Length = 424
Score = 23.8 bits (52), Expect = 6.0
Identities = 9/21 (42%), Positives = 10/21 (47%), Gaps = 2/21 (9%)
Query: 16 VKCNPDDTIGDLKKLIAAQTG 36
VKCN I + L A TG
Sbjct: 68 VKCNDSRAI--VSTLAAIGTG 86
>2gqf_A Hypothetical protein HI0933; structural genomics, FAD-utilizing
protein, flavoprotein, PS protein structure initiative;
HET: FAD; 2.70A {Haemophilus influenzae} SCOP: c.3.1.8
e.74.1.1
Length = 401
Score = 24.0 bits (53), Expect = 6.0
Identities = 4/17 (23%), Positives = 9/17 (52%), Gaps = 4/17 (23%)
Query: 7 NDRLGKKVRV----KCN 19
++G+K+ + CN
Sbjct: 36 GKKIGRKILMSGGGFCN 52
>3h7m_A Sensor protein; histidine kinase sensor domain, kinase,
phosphoprotein, transferase; 2.40A {Geobacter
sulfurreducens}
Length = 234
Score = 23.7 bits (52), Expect = 6.1
Identities = 4/27 (14%), Positives = 12/27 (44%), Gaps = 1/27 (3%)
Query: 23 TIGDLK-KLIAAQTGTRWEKIVLKKWY 48
+ DL+ + +A + + ++ Y
Sbjct: 111 GLEDLRGRKVALHRDGIMHEYLAERGY 137
>2nva_A Arginine decarboxylase, A207R protein; PLP, TIM barrel,
eukaryotic ODC- like, lyase; HET: PL2; 1.80A
{Paramecium bursaria chlorella virus 1} PDB: 2nv9_A*
Length = 372
Score = 23.7 bits (52), Expect = 7.0
Identities = 7/21 (33%), Positives = 10/21 (47%), Gaps = 2/21 (9%)
Query: 16 VKCNPDDTIGDLKKLIAAQTG 36
VKCN D+ + LK +
Sbjct: 47 VKCNNDEVL--LKTMCDKNVN 65
>2oo0_A ODC, ornithine decarboxylase; beta-alpha barrel, sheet, lyase;
HET: PLP; 1.90A {Homo sapiens}
Length = 471
Score = 23.9 bits (52), Expect = 7.0
Identities = 10/21 (47%), Positives = 11/21 (52%), Gaps = 2/21 (9%)
Query: 16 VKCNPDDTIGDLKKLIAAQTG 36
VKCN I +K L A TG
Sbjct: 78 VKCNDSKAI--VKTLAATGTG 96
>4dz1_A DALS D-alanine transporter; D-alanine binding, periplasmic,
transport protein; 1.90A {Salmonella enterica} PDB:
3r39_A 4f3s_A
Length = 259
Score = 23.5 bits (51), Expect = 7.7
Identities = 5/51 (9%), Positives = 17/51 (33%), Gaps = 2/51 (3%)
Query: 22 DTIGDLK-KLIAAQTGTRWEKIVLKKWYTI-FKDHIRIMDYEIHDGMNLEL 70
+ + +L I G + ++ + ++ Y ++ +L
Sbjct: 130 NNLNELNKYSIGYPRGMAYSDLIKNDLEPKGYYSLSKVKLYPTYNETMADL 180
>3kzg_A Arginine 3RD transport system periplasmic binding protein; arginine
transport system, protein structure initiative II(PSI
II); 2.06A {Legionella pneumophila subsp}
Length = 237
Score = 23.4 bits (51), Expect = 7.7
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 6/49 (12%)
Query: 23 TIGDLK-KLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
T DL K I + GT + + VL + +++ YE+ M L L
Sbjct: 104 TFDDLHGKKIGVRKGTPYARQVLSENRN-----NQVIFYELIQDMLLGL 147
>2i0z_A NAD(FAD)-utilizing dehydrogenases; structural genomics, PSI-2,
protein structure initiative, midwest center for
structural genomics, MCSG; HET: FAD; 1.84A {Bacillus
cereus} SCOP: c.3.1.8 e.74.1.1
Length = 447
Score = 23.6 bits (52), Expect = 8.2
Identities = 5/17 (29%), Positives = 11/17 (64%), Gaps = 4/17 (23%)
Query: 7 NDRLGKKVRV----KCN 19
++LG+K+ + +CN
Sbjct: 58 GNKLGRKLAISGGGRCN 74
>2y7i_A STM4351; arginine-binding protein; HET: ARG; 1.90A {Salmonella
enterica subsp}
Length = 229
Score = 23.3 bits (51), Expect = 9.2
Identities = 11/49 (22%), Positives = 20/49 (40%), Gaps = 6/49 (12%)
Query: 23 TIGDLK-KLIAAQTGTRWEKIVLKKWYTIFKDHIRIMDYEIHDGMNLEL 70
T DLK K + + GT ++ + K I + Y+ + +L
Sbjct: 106 TFADLKGKKVGLENGTTHQRYLQDKQ-----QAITPVAYDSYLNAFTDL 149
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.324 0.141 0.446
Gapped
Lambda K H
0.267 0.0739 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,272,810
Number of extensions: 63906
Number of successful extensions: 275
Number of sequences better than 10.0: 1
Number of HSP's gapped: 270
Number of HSP's successfully gapped: 106
Length of query: 73
Length of database: 6,701,793
Length adjustment: 43
Effective length of query: 30
Effective length of database: 5,501,190
Effective search space: 165035700
Effective search space used: 165035700
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (23.4 bits)