RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4259
(203 letters)
>1pve_A HHR23B, UV excision repair protein RAD23 homolog B; XPC binding
domain, solution structure, nucleotide excision repair,
chaps, DNA binding protein; NMR {Homo sapiens} SCOP:
a.189.1.1
Length = 72
Score = 91.5 bits (227), Expect = 7e-25
Identities = 41/64 (64%), Positives = 49/64 (76%)
Query: 131 SEDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEP 190
S PL FLR QPQFQQMR ++QQNP LLP +LQQIG+ NP LL+ IS +QE F++MLNEP
Sbjct: 2 SHMPLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEP 61
Query: 191 VAGD 194
V
Sbjct: 62 VQEA 65
>2f4m_B UV excision repair protein RAD23 homolog B; glycoproteins,
ubiquitin-dependent protein degradation, NUCL excision
repair, peptide:N-glycanase; 1.85A {Mus musculus} SCOP:
a.189.1.1 PDB: 2f4o_B*
Length = 61
Score = 89.5 bits (222), Expect = 3e-24
Identities = 40/58 (68%), Positives = 48/58 (82%)
Query: 134 PLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPV 191
PL FLR QPQFQQMR ++QQNP LLP +LQQIG+ NP LL+ IS +QE F++MLNEPV
Sbjct: 3 PLEFLRNQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPV 60
>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 = 87.8 bits (218), Expect = 4e-23
Identities = 42/80 (52%), Positives = 51/80 (63%), Gaps = 3/80 (3%)
Query: 17 QQTVSHLDVQEE--VKQLKEKIQSEKGSE-YLAEYQKLIYAGKILSDDQALSEYNIDESK 73
QQ +D+ E VK LKEKI+SEKG + + QKLIYAGKIL+DD AL EY IDE
Sbjct: 9 QQQTFKIDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKN 68
Query: 74 FIVVMLSKPKPTPAPYSGPS 93
F+VVM++KPK P
Sbjct: 69 FVVVMVTKPKAVSTPAPATL 88
>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 = 87.5 bits (217), Expect = 7e-23
Identities = 21/91 (23%), Positives = 41/91 (45%), Gaps = 4/91 (4%)
Query: 17 QQTVSHLDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKF 74
++ LD++ + + K K+ E KLIY+GK+L D + +SE + +
Sbjct: 10 KKEKVPLDLEPSNTILETKTKLAQSISCE--ESQIKLIYSGKVLQDSKTVSECGLKDGDQ 67
Query: 75 IVVMLSKPKPTPAPYSGPSDPTQPAGQESEA 105
+V M+S+ K T + + + + A
Sbjct: 68 VVFMVSQKKSTKTKVTERDPNSSSVDKLAAA 98
>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 = 83.1 bits (206), Expect = 2e-21
Identities = 35/70 (50%), Positives = 48/70 (68%), Gaps = 3/70 (4%)
Query: 17 QQTVSHLDVQEE--VKQLKEKIQSEKGSE-YLAEYQKLIYAGKILSDDQALSEYNIDESK 73
QQ + ++ + VK LKEKI++EKG + + QKLIYAGKILSDD + +Y IDE
Sbjct: 14 QQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKN 73
Query: 74 FIVVMLSKPK 83
F+VVM++K K
Sbjct: 74 FVVVMVTKTK 83
>2qsf_X RAD23, UV excision repair protein RAD23; alpha-beta structure, beta
hairpin, transglutaminase fold, DNA-damage recognition,
DNA repair; HET: DNA; 2.35A {Saccharomyces cerevisiae}
PDB: 2qsg_X* 2qsh_X* 1x3z_B* 1x3w_B* 3esw_B*
Length = 171
Score = 76.1 bits (186), Expect = 1e-17
Identities = 23/67 (34%), Positives = 29/67 (43%)
Query: 128 GGESEDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRML 187
+ P + T +R VV NPE L +L+ I P L E I N E FV ML
Sbjct: 19 AAQGGPPGSIGLTVEDLLSLRQVVSGNPEALAPLLENISARYPQLREHIMANPEVFVSML 78
Query: 188 NEPVAGD 194
E V +
Sbjct: 79 LEAVGDN 85
>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta,
structural genomics, protein structure initiative; NMR
{Arabidopsis thaliana}
Length = 94
Score = 72.8 bits (179), Expect = 2e-17
Identities = 21/67 (31%), Positives = 31/67 (46%), Gaps = 5/67 (7%)
Query: 22 HLDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDD-QALSEYNIDESKFIVVM 78
++V V LK+KI + + +L Y+G L+DD + L+EY I E IVV
Sbjct: 28 TVEVDRTETVSSLKDKIHIVEN--TPIKRMQLYYSGIELADDYRNLNEYGITEFSEIVVF 85
Query: 79 LSKPKPT 85
L
Sbjct: 86 LKSINRA 92
>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 = 71.9 bits (175), Expect = 3e-15
Identities = 40/67 (59%), Positives = 48/67 (71%)
Query: 128 GGESEDPLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRML 187
E+PL FLR QPQFQ MR V+QQNP LLP +LQQ+GQ NP LL+ IS +QE F++ML
Sbjct: 230 EAAGENPLEFLRDQPQFQNMRQVIQQNPALLPALLQQLGQENPQLLQQISRHQEQFIQML 289
Query: 188 NEPVAGD 194
NEP
Sbjct: 290 NEPPGEL 296
Score = 66.2 bits (160), Expect = 4e-13
Identities = 47/176 (26%), Positives = 74/176 (42%), Gaps = 3/176 (1%)
Query: 17 QQTVSHLDVQEE--VKQLKEKIQSEKGSE-YLAEYQKLIYAGKILSDDQALSEYNIDESK 73
QQ + ++ + VK LKEKI++EKG + + QKLIYAGKILSDD + +Y IDE
Sbjct: 16 QQQTFKIRMEPDETVKVLKEKIEAEKGRDAFPVAGQKLIYAGKILSDDVPIRDYRIDEKN 75
Query: 74 FIVVMLSKPKPTPAPYSGPSDPTQPAGQESEATRPATATSDSMLKVFFERVNPYGGESED 133
F+VVM++K K + P A + S + PA + S ES
Sbjct: 76 FVVVMVTKTKAGQGTSAPPEASPTAAPESSTSFPPAPTSGMSHPPPAAREDKSPSEESAP 135
Query: 134 PLAFLRTQPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNE 189
+ + ++ V ++ + + + +E V L
Sbjct: 136 TTSPESVSGSVPSSGSSGREEDAASTLVTGSEYETMLTEIMSMGYERERVVAALRA 191
>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 = 66.9 bits (164), Expect = 4e-15
Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 4/70 (5%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
V + VK+ KE I + +E Q+LIY G++L DD+ L EYN+ +V +
Sbjct: 20 FIVGAQMNVKEFKEHIAASVS--IPSEKQRLIYQGRVLQDDKKLQEYNVGGKVIHLVERA 77
Query: 81 KPKPTPAPYS 90
P+ +
Sbjct: 78 PPQTHLPSGA 87
>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana,
uncharacterized putative protein, NESG, structural
genomics; NMR {Arabidopsis thaliana}
Length = 84
Score = 65.7 bits (161), Expect = 9e-15
Identities = 15/67 (22%), Positives = 28/67 (41%), Gaps = 5/67 (7%)
Query: 17 QQTVSHLDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGK-ILSDDQALSEYNIDESK 73
+ L+V + +K+KI+ + Q LI G IL +D + + I +
Sbjct: 19 NGSSFELEVDYRDTLLVVKQKIERSQH--IPVSKQTLIVDGIVILREDLTVEQCQIVPTS 76
Query: 74 FIVVMLS 80
I + +S
Sbjct: 77 DIQLEVS 83
>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 = 65.5 bits (160), Expect = 2e-14
Identities = 16/68 (23%), Positives = 33/68 (48%), Gaps = 2/68 (2%)
Query: 29 VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPKPTPAP 88
++QLKE+I + + LI+AGKIL D +L++ + + + +++ +
Sbjct: 39 IQQLKEEISQRFKAH--PDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIKRQHRAMGN 96
Query: 89 YSGPSDPT 96
S P+
Sbjct: 97 ECPASGPS 104
>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 = 64.5 bits (158), Expect = 2e-14
Identities = 23/62 (37%), Positives = 34/62 (54%), Gaps = 4/62 (6%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
++V E V Q KE I G Q+LIY+GKIL DDQ + Y+I + + ++ S
Sbjct: 18 VNVAPESTVLQFKEAINKANGIP--VANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS 75
Query: 81 KP 82
+P
Sbjct: 76 QP 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 = 63.8 bits (155), Expect = 5e-14
Identities = 20/78 (25%), Positives = 32/78 (41%), Gaps = 2/78 (2%)
Query: 12 TQNQWQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEY-NID 70
Q +S D V LK + E Q+LIY+GK+L D Q L +
Sbjct: 16 NQRHRDLELS-GDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQ 74
Query: 71 ESKFIVVMLSKPKPTPAP 88
E + ++ ++ K P+
Sbjct: 75 EKRHVLHLVCNVKSGPSS 92
>3m63_B Ubiquitin domain-containing protein DSK2; armadillo-like repeats,
UBL conjugation pathway, nucleus, phosphoprotein; HET:
1PE; 2.40A {Saccharomyces cerevisiae}
Length = 101
Score = 62.3 bits (152), Expect = 3e-13
Identities = 23/62 (37%), Positives = 34/62 (54%), Gaps = 4/62 (6%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
++V E V Q KE I G Q+LIY+GKIL DDQ + Y+I + + ++ S
Sbjct: 42 VNVAPESTVLQFKEAINKANGIP--VANQRLIYSGKILKDDQTVESYHIQDGHSVHLVKS 99
Query: 81 KP 82
+P
Sbjct: 100 QP 101
>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural
genomics; NMR {Homo sapiens} SCOP: d.15.1.1
Length = 125
Score = 61.8 bits (150), Expect = 7e-13
Identities = 16/71 (22%), Positives = 31/71 (43%), Gaps = 2/71 (2%)
Query: 29 VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPKPTPAP 88
V+Q KE I S+ + LI+AGKIL D L ++ I + + +++ + + +
Sbjct: 54 VQQFKEAISKRFKSQ--TDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIKRDPNSSSV 111
Query: 89 YSGPSDPTQPA 99
+
Sbjct: 112 DKYAAALEHHH 122
>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 = 61.2 bits (149), Expect = 8e-13
Identities = 15/65 (23%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
V + ++QLKE+I + + LI+AGKIL D +L++ + + + +++
Sbjct: 36 FSVTDTCTIQQLKEEISQRFKAH--PDQLVLIFAGKILKDPDSLAQCGVRDGLTVHLVIK 93
Query: 81 KPKPT 85
+
Sbjct: 94 RQHRA 98
>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 = 59.0 bits (143), Expect = 6e-12
Identities = 14/60 (23%), Positives = 29/60 (48%), Gaps = 2/60 (3%)
Query: 29 VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPKPTPAP 88
V +K ++ + +G Q+ ++G+ L+D E I + + V++S+P P P
Sbjct: 46 VFHMKRRLHAAEG--VEPGSQRWFFSGRPLTDKMKFEELKIPKDYVVQVIVSQPVQNPTP 103
>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 = 59.1 bits (143), Expect = 1e-11
Identities = 5/59 (8%), Positives = 18/59 (30%), Gaps = 4/59 (6%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
V+E V + + ++ E + + + S + + + + +
Sbjct: 15 EVVEEFTPVVLATPIPEEVQQAQ--TEIKLFNKWSFEEVEVKDASLVDYVQVRQPIFVA 71
>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 = 56.5 bits (137), Expect = 2e-11
Identities = 15/60 (25%), Positives = 39/60 (65%), Gaps = 4/60 (6%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
+D++ V+++KE+++ ++G + Q+LIY+GK ++D++ ++Y I + ++L+
Sbjct: 15 IDIEPTDKVERIKERVEEKEG--IPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLA 72
>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold,
GP78-binding, chaperone; 1.30A {Homo sapiens}
Length = 88
Score = 56.9 bits (138), Expect = 2e-11
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 4/52 (7%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDES 72
V + VK+ KE I + +E Q+LIY G++L DD+ L EYN+
Sbjct: 32 FIVGAQMNVKEFKEHIAASVS--IPSEKQRLIYQGRVLQDDKKLQEYNVGGK 81
>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 = 56.2 bits (136), Expect = 5e-11
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 29 VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI-DESKFIVVMLSKPKPTPA 87
V++ K++I A+ LI+ GKIL D LS+ I D S VV+ S P+
Sbjct: 39 VRRFKKQISKYLHCN--ADRLVLIFTGKILRDQDILSQRGILDGSTVHVVVRSHSGPSSG 96
>2dzi_A Ubiquitin-like protein 4A; GDX, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 81
Score = 55.0 bits (133), Expect = 9e-11
Identities = 16/59 (27%), Positives = 32/59 (54%), Gaps = 4/59 (6%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
L V E+ V LK+ + + Q+L++ GK L+D + LS+Y+I + + +++
Sbjct: 22 LQVPEDELVSTLKQLVSEKLN--VPVRQQRLLFKGKALADGKRLSDYSIGPNSKLNLVV 78
>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein
structur initiative, northeast structural genomics
consortium, NESG; NMR {Homo sapiens}
Length = 101
Score = 55.5 bits (134), Expect = 9e-11
Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 5/65 (7%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI-DESKFIVVML 79
V E V+Q KE+I S + LI+AGKIL D LS++ I D +V+
Sbjct: 39 FAVPENSSVQQFKEEISKRFKSH--TDQLVLIFAGKILKDQDTLSQHGIHDGLTVHLVIK 96
Query: 80 SKPKP 84
++ +P
Sbjct: 97 TQNRP 101
>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 = 53.5 bits (129), Expect = 4e-10
Identities = 15/60 (25%), Positives = 39/60 (65%), Gaps = 4/60 (6%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
+D++ V+++KE+++ ++G + Q+LIY+GK ++D++ ++Y I + ++L+
Sbjct: 15 IDIEPTDKVERIKERVEEKEG--IPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLA 72
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 57.4 bits (138), Expect = 5e-10
Identities = 45/267 (16%), Positives = 81/267 (30%), Gaps = 94/267 (35%)
Query: 1 MGMLAHDISDITQNQWQQTVSHLD----------VQEEVKQLKEKIQSEKGSEYLAEYQK 50
MGM + S Q+ W + +H V L EKG Y
Sbjct: 1631 MGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSA 1690
Query: 51 LIYAGKI---LSDDQALSEYNIDESKFIVVMLSKPKPTPAPYSGPSDP------TQPAGQ 101
+I+ + L ++ E N + + + TQPA
Sbjct: 1691 MIFETIVDGKLKTEKIFKEINEHSTSYT-------------FRSEKGLLSATQFTQPA-- 1735
Query: 102 ESEATRPATATSDSMLKVFFER-VNPYG--------GE-S-----------ED--PLAFL 138
T + + + + P GE + E + F
Sbjct: 1736 -------LTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFY 1788
Query: 139 R------TQPQFQQMRT---VVQQNP---------ELLPTVLQQIGQSNPALLELISHN- 179
R P+ + R+ ++ NP E L V++++G+ L+E++++N
Sbjct: 1789 RGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNV 1848
Query: 180 ---QEAFVRMLNEPVAGDRRNKNVLGT 203
Q +V AGD R + +
Sbjct: 1849 ENQQ--YV------AAGDLRALDTVTN 1867
>3n3k_B Ubiquitin; hydrolase, protease, thiol protease, DUB, zinc ribbon,
inhibitor, ubiqu acetylation, cytoplasm, isopeptide
bond, nucleus; 2.60A {Homo sapiens}
Length = 85
Score = 52.4 bits (126), Expect = 9e-10
Identities = 21/59 (35%), Positives = 36/59 (61%), Gaps = 4/59 (6%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
L+V+ ++ +K KIQ ++G + Q+LI+AGK L D + LS+YNI + ++L
Sbjct: 18 LEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIHNHSALYLLL 74
>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 = 51.5 bits (124), Expect = 2e-09
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 23 LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK 81
+ VK LK ++Q L QKLI+ GK+L + L + ++ +++M S+
Sbjct: 28 VSPDCTVKDLKSQLQPITN--VLPRGQKLIFKGKVLVETSTLKQSDVGSGAKLMLMASQ 84
>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 = 51.5 bits (123), Expect = 3e-09
Identities = 20/92 (21%), Positives = 41/92 (44%), Gaps = 6/92 (6%)
Query: 8 ISDITQNQWQQTVSHLDV--QEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDD-QAL 64
+ + ++ + T S L V E+ + + E G AE +++Y ++L+DD +L
Sbjct: 12 VYCVRRDLTEVTFS-LQVNPDFELSNFRVLCELESGVP--AEEAQIVYMEQLLTDDHCSL 68
Query: 65 SEYNIDESKFIVVMLSKPKPTPAPYSGPSDPT 96
Y + + +V++ P PS P+
Sbjct: 69 GSYGLKDGDMVVLLQKDNVGLRTPGRTPSGPS 100
>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 = 50.5 bits (121), Expect = 5e-09
Identities = 12/55 (21%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 19 TVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI-DES 72
T+ + + +++L+E++ + E Q+L Y GK L + L +Y++
Sbjct: 22 TIEDVSRKATIEELRERVWALFDVR--PECQRLFYRGKQLENGYTLFDYDVGLND 74
>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 = 50.5 bits (121), Expect = 6e-09
Identities = 15/59 (25%), Positives = 38/59 (64%), Gaps = 4/59 (6%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
+D++ V+++KE+++ ++G + Q+LIY+GK ++D++ ++Y I + ++L
Sbjct: 27 IDIEPTDKVERIKERVEEKEG--IPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVL 83
>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 = 50.0 bits (120), Expect = 7e-09
Identities = 11/60 (18%), Positives = 30/60 (50%), Gaps = 4/60 (6%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
++V + + QLKE + + A+ ++I+AGK L + + ++++ + ++
Sbjct: 15 VEVDSDTSILQLKEVVAKQ--QGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQR 72
>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 = 50.4 bits (120), Expect = 7e-09
Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 6/81 (7%)
Query: 17 QQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDD-QALSEYNIDESKFI 75
+ ++ ++ V LK K + S+ KLIY G++L D + LS NI + I
Sbjct: 18 TEELAVARPEDTVGTLKSKYFPGQESQ-----MKLIYQGRLLQDPARTLSSLNITNNCVI 72
Query: 76 VVMLSKPKPTPAPYSGPSDPT 96
S P + S S P+
Sbjct: 73 HCHRSPPGAAVSGPSASSGPS 93
>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident
ubiquitin-like domain member...; UBL domain, membrane,
polymorphism, transmembrane; NMR {Homo sapiens}
Length = 99
Score = 49.9 bits (119), Expect = 1e-08
Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 12 TQNQWQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEY 67
Q QT+S + V +LK + + S+ L + Q+L+Y+G++L D L +
Sbjct: 32 NQKYSDQTIS-CFLNWTVGKLKTHLSNVYPSKPLTKDQRLVYSGRLLPDHLQLKDI 86
>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 = 49.3 bits (118), Expect = 1e-08
Identities = 21/59 (35%), Positives = 37/59 (62%), Gaps = 4/59 (6%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
L+V+ ++ +K KIQ ++G + Q+LI+AGK L D + LS+YNI + + ++L
Sbjct: 18 LEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKWSTLFLLL 74
>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 = 49.4 bits (118), Expect = 1e-08
Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 10/83 (12%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML- 79
L+V+ ++ +K KIQ ++G + Q+LI+AGK L D + LS+YNI + + ++L
Sbjct: 16 LEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 73
Query: 80 -----SKPKPTPAPYSGPSDPTQ 97
+ P Q
Sbjct: 74 LRGYADLREDPDRQDHHPGSGAQ 96
>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 = 48.9 bits (117), Expect = 2e-08
Identities = 13/67 (19%), Positives = 29/67 (43%), Gaps = 4/67 (5%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
+ + LK++I+ + + Q+L + G++L D L Y I +S +++
Sbjct: 22 YAINPNSFILGLKQQIEDQ--QGLPKKQQQLEFQGQVLQDWLGLGIYGIQDSDTLILSKK 79
Query: 81 KPKPTPA 87
K +
Sbjct: 80 KGSGPSS 86
>1sif_A Ubiquitin; hydrophobic mutants, folding, stability, structural
protein; 2.18A {Homo sapiens} SCOP: d.15.1.1
Length = 88
Score = 48.9 bits (117), Expect = 2e-08
Identities = 20/59 (33%), Positives = 37/59 (62%), Gaps = 4/59 (6%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
++++ ++ LK KIQ ++G + Q+LI+AGK L D + LS+YNI + + ++L
Sbjct: 24 VEMEPSDTIENLKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL 80
>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 = 48.5 bits (116), Expect = 3e-08
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 19 TVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM 78
TV L +V++L+ KIQ E Q+L Y GK + D L +Y + + I ++
Sbjct: 17 TVDSLSRLTKVEELRRKIQELFHVE--PGLQRLFYRGKQMEDGHTLFDYEVRLNDTIQLL 74
Query: 79 L 79
+
Sbjct: 75 V 75
>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural
genomics, protein structure initiative, PSI; NMR {Homo
sapiens}
Length = 125
Score = 48.5 bits (115), Expect = 6e-08
Identities = 13/78 (16%), Positives = 25/78 (32%), Gaps = 6/78 (7%)
Query: 29 VKQLKEKIQSEKGSEY------LAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP 82
+ + + ++ +LIY G+ L + L + K V+ L
Sbjct: 40 ASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLVAR 99
Query: 83 KPTPAPYSGPSDPTQPAG 100
+ P P S + G
Sbjct: 100 ETLPEPNSQGQRNREKTG 117
>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 = 48.5 bits (115), Expect = 6e-08
Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 4/69 (5%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
L+V+ + +K KIQ ++G + Q+LI+AGK L D + LS+YNI + + ++L
Sbjct: 15 LEVESSDTIDNVKSKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72
Query: 81 KPKPTPAPY 89
P
Sbjct: 73 LRGGIIEPS 81
>1we6_A Splicing factor, putative; structural genomics, ubiquitin-like
domain, riken structural genomics/proteomics initiative,
RSGI; NMR {Arabidopsis thaliana} SCOP: d.15.1.1
Length = 111
Score = 47.9 bits (114), Expect = 7e-08
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 19 TVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVM 78
++ + E V LKEKI E A QKL L D+ +L+ YN+ + + +
Sbjct: 44 EITVQSLSENVGSLKEKIAGEIQ--IPANKQKLSGKAGFLKDNMSLAHYNVGAGEILTLS 101
Query: 79 L 79
L
Sbjct: 102 L 102
>2l7r_A Ubiquitin-like protein FUBI; structural genomics, PSI-biology,
protein structure initiati northeast structural
genomics consortium, NESG; NMR {Homo sapiens}
Length = 93
Score = 47.5 bits (113), Expect = 7e-08
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 23 LDV--QEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDE 71
+V QE V Q+K + S +G E Q ++ AG L D+ L + ++
Sbjct: 32 FEVTGQETVAQIKAHVASLEG--IAPEDQVVLLAGAPLEDEATLGQCGVEA 80
>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 = 46.9 bits (112), Expect = 7e-08
Identities = 21/59 (35%), Positives = 36/59 (61%), Gaps = 4/59 (6%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
L+V+ ++ +K KIQ ++G + Q+LI+AGK L D + LS+YNI + ++L
Sbjct: 15 LEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVL 71
>1x1m_A Ubiquitin-like protein SB132; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Mus musculus} SCOP: d.15.1.1
Length = 107
Score = 47.1 bits (111), Expect = 1e-07
Identities = 19/61 (31%), Positives = 26/61 (42%), Gaps = 2/61 (3%)
Query: 29 VKQLKEKIQSEKG-SEYLAEYQKLIYAGKILSDDQALSEYNIDESKFI-VVMLSKPKPTP 86
+ LK+ I + S E LIY G+ L DDQ L Y I + V+ S P+
Sbjct: 47 ISFLKQLIAGKLQESVPDPELIDLIYCGRKLKDDQTLDFYGIQPGSTVHVLRKSWSGPSS 106
Query: 87 A 87
Sbjct: 107 G 107
>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 = 46.7 bits (111), Expect = 1e-07
Identities = 16/66 (24%), Positives = 29/66 (43%), Gaps = 3/66 (4%)
Query: 22 HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSK 81
+ + +LK+KI S G QK++Y G + +D+ L E + I+V+ S
Sbjct: 32 KVPLDSTGSELKQKIHSITG--LPPAMQKVMYKGL-VPEDKTLREIKVTSGAKIMVVGST 88
Query: 82 PKPTPA 87
+
Sbjct: 89 ISGPSS 94
>1yx5_B Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo sapiens} SCOP:
d.15.1.1 PDB: 1yx6_B
Length = 98
Score = 46.7 bits (111), Expect = 2e-07
Identities = 21/59 (35%), Positives = 37/59 (62%), Gaps = 4/59 (6%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
L+V+ ++ +K KIQ ++G + Q+LI+AGK L D + LS+YNI + + ++L
Sbjct: 15 LEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL 71
>2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing, protein
binding; 2.60A {Homo sapiens}
Length = 111
Score = 46.8 bits (111), Expect = 2e-07
Identities = 21/59 (35%), Positives = 37/59 (62%), Gaps = 4/59 (6%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
L+V+ ++ +K KIQ ++G + Q+LI+AGK L D + LS+YNI + + ++L
Sbjct: 50 LEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL 106
>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion
protein; ubiquitin interacting motif, UIM, protein
domain interface; NMR {Saccharomyces cerevisiae}
Length = 114
Score = 46.7 bits (111), Expect = 3e-07
Identities = 21/59 (35%), Positives = 35/59 (59%), Gaps = 4/59 (6%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
L+V+ + +K KIQ ++G + Q+LI+AGK L D + LS+YNI + ++L
Sbjct: 24 LEVESSDTIDNVKSKIQDKEG--IPPDQQRLIWAGKQLEDGRTLSDYNIQRESTLHLVL 80
>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 = 46.0 bits (109), Expect = 3e-07
Identities = 15/74 (20%), Positives = 27/74 (36%), Gaps = 3/74 (4%)
Query: 23 LDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP 82
L+ E K ++ + G QK++ G L DD + +++M S
Sbjct: 24 LNTDEPPMVFKAQLFALTG--VQPARQKVMVKGGTLKDDD-WGNIKMKNGMTVLMMGSAD 80
Query: 83 KPTPAPYSGPSDPT 96
P + S P+
Sbjct: 81 ALPEEPSAKTSGPS 94
>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 = 46.3 bits (110), Expect = 4e-07
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 22 HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDE 71
L + ++V +K KI G A QKL Y G + D +L+ YN+
Sbjct: 51 TLPLTDQVSVIKVKIHEATG--MPAGKQKLQYEGIFIKDSNSLAYYNMAS 98
>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 = 44.7 bits (106), Expect = 8e-07
Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 4/59 (6%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
+V+ V LK+++ + + L + GK L D L EY + + + L
Sbjct: 19 YEVRLTQTVAHLKQQVSGLE--GVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNL 75
>3phx_B Ubiquitin-like protein ISG15; OTU domain, DE-ubiquitinase,
DE-isgylase, hydrolase-protein complex; 1.60A {Homo
sapiens}
Length = 79
Score = 43.9 bits (104), Expect = 1e-06
Identities = 13/59 (22%), Positives = 23/59 (38%), Gaps = 4/59 (6%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVML 79
+V+ V LK+++ + L + GK L D L EY + + + L
Sbjct: 19 YEVRLTQTVAHLKQQVSGL--EGVQDDLFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNL 75
>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 = 45.4 bits (107), Expect = 1e-06
Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 4/86 (4%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
L+V+ ++ +K KIQ ++G + Q+LI+AGK L D + LS+YNI + + ++L
Sbjct: 15 LEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72
Query: 81 KPKPTPAPYSGPSDPTQPAGQESEAT 106
+ T E T
Sbjct: 73 LRGGMQIFVKTLTGKTITLEVEPSDT 98
Score = 40.8 bits (95), Expect = 5e-05
Identities = 19/70 (27%), Positives = 38/70 (54%), Gaps = 2/70 (2%)
Query: 10 DITQNQWQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI 69
+ + ++ + ++ +K KIQ ++G + Q+LI+AGK L D + LS+YNI
Sbjct: 80 FVKTLTGKTITLEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNI 137
Query: 70 DESKFIVVML 79
+ + ++L
Sbjct: 138 QKESTLHLVL 147
>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 = 44.6 bits (105), Expect = 3e-06
Identities = 14/78 (17%), Positives = 25/78 (32%), Gaps = 4/78 (5%)
Query: 1 MGMLAHDISDITQNQWQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSD 60
I T + + + V LK+++ + + L + GK L D
Sbjct: 77 KSDEPLSILVRNNKGRSSTY-EVRLTQTVAHLKQQVSGLE--GVQDDLFWLTFEGKPLED 133
Query: 61 DQALSEYNI-DESKFIVV 77
L EY + S +
Sbjct: 134 QLPLGEYGLKPLSTVFMN 151
Score = 43.4 bits (102), Expect = 7e-06
Identities = 18/111 (16%), Positives = 35/111 (31%), Gaps = 13/111 (11%)
Query: 1 MGMLAHDISDITQNQWQQTVSHLDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIY--AGK 56
MG D+T + + V +LK +I + G A Q+L +G
Sbjct: 1 MGW------DLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIG--VHAFQQRLAVHPSGV 52
Query: 57 ILSDDQALSEYNIDESKFIVVMLSKPKPTPAPY-SGPSDPTQPAGQESEAT 106
L D L+ + +++++ K + + T
Sbjct: 53 ALQDRVPLASQGLGPGSTVLLVVDKSDEPLSILVRNNKGRSSTYEVRLTQT 103
>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila}
PDB: 2xzn_9
Length = 189
Score = 44.7 bits (105), Expect = 4e-06
Identities = 7/49 (14%), Positives = 20/49 (40%), Gaps = 4/49 (8%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI 69
+++ V LK +I + + + L+ G I + + +++
Sbjct: 15 YTLEQGTSVLDLKSQISQDM--GFEIDMMTLVNNGFIAPNTELVTDDVT 61
>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}
Length = 172
Score = 44.3 bits (104), Expect = 5e-06
Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 4/86 (4%)
Query: 23 LDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLS 80
L+V+ ++ +K KIQ ++G + Q+LI+AGK L D + LS+YNI + + ++L
Sbjct: 35 LEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 92
Query: 81 KPKPTPAPYSGPSDPTQPAGQESEAT 106
+ T E T
Sbjct: 93 LRGGMQIFVKTLTGKTITLEVEPSDT 118
Score = 39.7 bits (92), Expect = 2e-04
Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 3/63 (4%)
Query: 11 ITQNQWQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI- 69
+ + ++ + ++ +K KIQ ++G + Q+LI+AGK L D + LS+YNI
Sbjct: 101 VKTLTGKTITLEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQ 158
Query: 70 DES 72
ES
Sbjct: 159 KES 161
>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 = 42.4 bits (99), Expect = 8e-06
Identities = 12/68 (17%), Positives = 23/68 (33%), Gaps = 6/68 (8%)
Query: 29 VKQLKEKIQSEKGSEY------LAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKP 82
+ + + ++ +LIY G+ L + L + K V+ L
Sbjct: 39 ASDIAKHVYDNWPMDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLVAR 98
Query: 83 KPTPAPYS 90
+ P P S
Sbjct: 99 ETLPEPNS 106
>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP,
oligomerization, ubiquitin insertion, hydrolase binding;
2.17A {Bacillus amyloliquefaciens}
Length = 189
Score = 43.8 bits (103), Expect = 8e-06
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 4/76 (5%)
Query: 6 HDISDITQNQWQQTVSHLDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQA 63
H I L+V+ ++ +K KIQ ++G + Q+LI+AGK L D +
Sbjct: 103 HYGGQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRT 160
Query: 64 LSEYNIDESKFIVVML 79
LS+YNI + + ++L
Sbjct: 161 LSDYNIQKESTLHLVL 176
Score = 26.9 bits (59), Expect = 3.8
Identities = 5/40 (12%), Positives = 13/40 (32%), Gaps = 2/40 (5%)
Query: 29 VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYN 68
+ K+ + G + + Y + D+ L +
Sbjct: 57 FSNREGKLPGKSGRTW--READINYTSGFRNSDRILYSSD 94
>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin,
fusion protein, fluore protein, transcription; HET: CR2;
1.40A {Aequorea victoria} PDB: 3ako_B*
Length = 307
Score = 44.4 bits (104), Expect = 8e-06
Identities = 18/48 (37%), Positives = 31/48 (64%), Gaps = 2/48 (4%)
Query: 22 HLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI 69
++ + ++ +K KIQ ++G + Q+LI+AGK L D + LS+YNI
Sbjct: 249 EVEPSDTIENVKAKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNI 294
>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 = 40.3 bits (94), Expect = 9e-05
Identities = 21/51 (41%), Positives = 32/51 (62%), Gaps = 3/51 (5%)
Query: 29 VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI-DESKFIVVM 78
+ +K KIQ ++G + Q+LI+AGK L D + LS+YNI ES +V+
Sbjct: 23 IDNVKSKIQDKEG--IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL 71
>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold,
ubiquitination, ligase; 2.71A {Homo sapiens} PDB:
2lgy_A
Length = 105
Score = 35.8 bits (82), Expect = 0.002
Identities = 7/44 (15%), Positives = 19/44 (43%), Gaps = 2/44 (4%)
Query: 29 VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDES 72
V LK+ + + G Q+ + ++ D + L + + ++
Sbjct: 49 VASLKDMVFLDYGFP--PVLQQWVIGQRLARDQETLHSHGVRQN 90
>1se9_A Ubiquitin family; ubiquitin-like, cell-free, wheat GERM, structural
genomics, protein structure initiative, CESG; NMR
{Arabidopsis thaliana} SCOP: d.15.1.1
Length = 126
Score = 36.2 bits (83), Expect = 0.002
Identities = 21/104 (20%), Positives = 36/104 (34%), Gaps = 16/104 (15%)
Query: 6 HDISDITQNQWQQTVSHLDVQEEVKQLKEKIQSE--KGSEYL---AEYQKLIYAGKILSD 60
D SDI + + V LKE + SE + E + KLI AGK+L +
Sbjct: 24 TDGSDIGPKAFPDATT-------VSALKETVISEWPREKENGPKTVKEVKLISAGKVLEN 76
Query: 61 DQALSEYNI---DESKFIVVMLSKPKPT-PAPYSGPSDPTQPAG 100
+ + +Y + + + M + P +
Sbjct: 77 SKTVKDYRSPVSNLAGAVTTMHVIIQAPVTEKEKKPKGDPKMNK 120
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 36.4 bits (83), Expect = 0.005
Identities = 38/253 (15%), Positives = 73/253 (28%), Gaps = 68/253 (26%)
Query: 1 MGMLAHDISDITQNQWQQTVSHLDVQ------------EEVKQLKEKIQSEKGSEYL--- 45
G + DI V + D + EE+ + + G+ L
Sbjct: 11 TGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWT 70
Query: 46 -AEYQKLIYA---GKILSDDQALSEYNIDESKFIVVMLSK----PKPTPAPYSGPSDPTQ 97
Q+ + ++L + Y F++ + P Y D
Sbjct: 71 LLSKQEEMVQKFVEEVLRIN-----YK-----FLMSPIKTEQRQPSMMTRMYIEQRDRLY 120
Query: 98 PAGQ---ESEATRPATATSDSMLKVFFERVNP------YG----GESEDPLAF--LRTQP 142
Q + +R L+ + P G G++ +A +
Sbjct: 121 NDNQVFAKYNVSRLQPYLK---LRQALLELRPAKNVLIDGVLGSGKTW--VALDVCLSYK 175
Query: 143 QFQQMR------TVVQQN-PELLPTVLQQI-GQSNPALLELISHNQEAFVRMLNEPVAGD 194
+M + N PE + +LQ++ Q +P H+ +R ++ A
Sbjct: 176 VQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLR-IHSIQAEL 234
Query: 195 RR------NKNVL 201
RR +N L
Sbjct: 235 RRLLKSKPYENCL 247
>1wju_A NEDD8 ultimate buster-1; ubiquitin-like domain, structural
genomics, riken structural genomics/proteomics
initiative, RSGI, protein binding; NMR {Homo sapiens}
SCOP: d.15.1.1
Length = 100
Score = 31.9 bits (72), Expect = 0.037
Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 4/62 (6%)
Query: 30 KQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNIDESKFIVVMLSKPKPTPAPY 89
++L+ KI G + Y K++ K L + L E + + + M+ + K + P
Sbjct: 43 RELRSKIAETFGLQ--ENYIKIVINKKQLQLGKTLEEQGVAHN--VKAMVLELKQSSGPS 98
Query: 90 SG 91
SG
Sbjct: 99 SG 100
>1wxv_A BAG-family molecular chaperone regulator-1; structural genomics,
apoptosis, riken structural genomics/proteomics
initiative, RSGI, NPPSFA; NMR {Homo sapiens} SCOP:
d.15.1.1
Length = 92
Score = 30.9 bits (69), Expect = 0.069
Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 29 VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSD-DQALSEYNIDESKFIVVMLSK 81
V+ L + ++ G +QKLI+ GK L + + LS I + ++++ K
Sbjct: 34 VQDLAQVVEEVIGVP--QSFQKLIFKGKSLKEMETPLSALGIQDGCRVMLIGKK 85
>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast
structural genomics consortiu PSI-2, protein structure
initiative, hydrolase; NMR {Mus musculus}
Length = 86
Score = 29.4 bits (66), Expect = 0.19
Identities = 12/77 (15%), Positives = 31/77 (40%), Gaps = 7/77 (9%)
Query: 17 QQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLI--YAGKILS---DDQALSEYNIDE 71
+ L + +++L+ +I + + Q+++ Y + L D L + I
Sbjct: 11 THLLQGLSSRTRLRELQGQIAAI--TGIAPGSQRILVGYPPECLDLSDRDITLGDLPIQS 68
Query: 72 SKFIVVMLSKPKPTPAP 88
++V + +P +P
Sbjct: 69 GDMLIVEEDQTRPKASP 85
>2dzj_A Synaptic glycoprotein SC2; ubiquitin-like fold, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
Length = 88
Score = 29.2 bits (65), Expect = 0.25
Identities = 10/72 (13%), Positives = 24/72 (33%), Gaps = 4/72 (5%)
Query: 8 ISDITQNQWQQTVSHLDVQEEVKQLKEKIQSEKGSEYLAEYQ--KLIYAGKILSDDQALS 65
I D + + ++ + ++K ++ Q +L GK L D+ L
Sbjct: 15 ILDAKTREKLCFLDKVEPHATIAEIKNLFTKTH-PQWYPARQSLRLDPKGKSLKDEDVLQ 73
Query: 66 EYNI-DESKFIV 76
+ + +
Sbjct: 74 KLPVGTTATLYF 85
>3q5w_A Protein CUT8; proteasome, tether, chromosome, cell cycle, dimer,
NOVE; 2.75A {Schizosaccharomyces pombe} PDB: 3q5x_A
Length = 245
Score = 30.5 bits (68), Expect = 0.34
Identities = 15/81 (18%), Positives = 27/81 (33%), Gaps = 4/81 (4%)
Query: 102 ESEATRPATATSDSMLKVFFERVN---PYGGESEDPLAFLRTQPQFQQ-MRTVVQQNPEL 157
P+ T L+ +N PYGG+ AF R + ++ + + P
Sbjct: 86 RGILPAPSMDTCVETLRKLLINLNDSFPYGGDKRGDYAFNRIREKYMAVLHALNDMVPCY 145
Query: 158 LPTVLQQIGQSNPALLELISH 178
LP ++ L +
Sbjct: 146 LPPYSTCFEKNITFLDAATNV 166
>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 = 27.7 bits (61), Expect = 1.5
Identities = 13/57 (22%), Positives = 23/57 (40%), Gaps = 4/57 (7%)
Query: 15 QWQQTVSHLDVQEE--VKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNI 69
+ +T D +E V +LK ++ E Q+L ++L D + L E
Sbjct: 8 RRHKTTIFTDAKESSTVFELKRIVEGILKRP--PEEQRLYKDDQLLDDGKTLGECGF 62
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 27.4 bits (60), Expect = 2.6
Identities = 10/65 (15%), Positives = 28/65 (43%), Gaps = 11/65 (16%)
Query: 15 QWQQT----VSHLDVQEEVKQLKEKIQSEKGSEYLAEYQKLIYAGKILSDDQALSEYNID 70
+W++ + LD +V +++ + EK + L E+ + + ++ ++ I
Sbjct: 89 KWREEQRKRLQELDAASKVM--EQEWR-EKAKKDLEEWNQR-QSEQV---EKNKINNRIA 141
Query: 71 ESKFI 75
+ F
Sbjct: 142 DKAFY 146
>1xee_A Chemotaxis-inhibiting protein chips; chemotaxis inhibitory protein,
superantigen, C5A, immune system; NMR {Staphylococcus
aureus} PDB: 2k3u_A*
Length = 91
Score = 26.2 bits (57), Expect = 2.8
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 13/58 (22%)
Query: 158 LPTVLQQI----------GQSNPALLE---LISHNQEAFVRMLNEPVAGDRRNKNVLG 202
LPT L ++ G N A E +++ N+ + LN P+A DR+N +LG
Sbjct: 4 LPTTLGKLDERLRNYLKKGTKNSAQFEKMVILTENKGYYTVYLNTPLAEDRKNVELLG 61
>2j01_J 50S ribosomal protein L10; ribosome, tRNA, paromomycin, mRNA,
translation; 2.8A {Thermus thermophilus} PDB: 2j03_J
3d5b_J 3d5d_J 3i8i_Y 3kir_J 3kit_J 3kiw_J 3kiy_J 3mrz_I
3ms1_I 3pyt_I 3pyr_I 3pyo_I 3pyv_I
Length = 173
Score = 26.9 bits (60), Expect = 3.7
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 26 QEEVKQLKEKIQSEKGSEYLAEYQKL 51
E + LKE ++ +GS +L YQ L
Sbjct: 7 VELLATLKENLERAQGSFFLVNYQGL 32
>3p8c_B NCK-associated protein 1; actin polymerization, protein binding;
2.29A {Homo sapiens}
Length = 1128
Score = 27.0 bits (59), Expect = 4.9
Identities = 9/52 (17%), Positives = 21/52 (40%)
Query: 107 RPATATSDSMLKVFFERVNPYGGESEDPLAFLRTQPQFQQMRTVVQQNPELL 158
+ S ++ E + PYG + Q +++ +V +N ++L
Sbjct: 826 NAEEYSDISEMRSLSELLGPYGMKFLSESLMWHISSQVAELKKLVVENVDVL 877
>2j5u_A MREC protein; bacterial cell shape determining protein MREC, cell
shape regulation; 2.5A {Listeria monocytogenes}
Length = 255
Score = 26.2 bits (58), Expect = 7.8
Identities = 9/71 (12%), Positives = 24/71 (33%), Gaps = 8/71 (11%)
Query: 4 LAHDISDITQNQWQQTVSHLDVQEEVKQLKEKI-----QSEKGSEYLAEYQKLIYAGKIL 58
+ + V + E + LKE++ + ++ E + L + L
Sbjct: 3 IVAKPTSFISGAVDGVVDLKNTYTENQHLKERLEELAQLESEVADLKKENKDL---KESL 59
Query: 59 SDDQALSEYNI 69
++ +Y+
Sbjct: 60 DITDSIRDYDP 70
>3hun_A Penicillin-binding protein 4; ampicillin, beta-lactamase, serine
type D-Ala, D-Ala-carboxypeptidase, antibiotics; HET:
ZZ7; 2.00A {Staphylococcus aureus} PDB: 3hum_A*
Length = 453
Score = 26.0 bits (57), Expect = 9.2
Identities = 6/19 (31%), Positives = 10/19 (52%)
Query: 171 ALLELISHNQEAFVRMLNE 189
L + +S N FV ++N
Sbjct: 168 ILAKKVSKNTSDFVDLMNN 186
>4dj2_A Period circadian protein homolog 1; PAS domains, circadian clock
protein, protein binding; 2.75A {Mus musculus}
Length = 320
Score = 26.1 bits (57), Expect = 9.2
Identities = 12/51 (23%), Positives = 17/51 (33%)
Query: 141 QPQFQQMRTVVQQNPELLPTVLQQIGQSNPALLELISHNQEAFVRMLNEPV 191
+ F R V+ P P+L I E R+L +PV
Sbjct: 269 KVAFVLGRHKVRTAPLNEDVFTPPAPSPAPSLDSDIQELSEQIHRLLLQPV 319
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
0.311 0.128 0.356
Gapped
Lambda K H
0.267 0.0716 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,859,860
Number of extensions: 155160
Number of successful extensions: 473
Number of sequences better than 10.0: 1
Number of HSP's gapped: 428
Number of HSP's successfully gapped: 104
Length of query: 203
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 114
Effective length of database: 4,216,824
Effective search space: 480717936
Effective search space used: 480717936
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 55 (25.0 bits)