RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2295
(276 letters)
>1nb8_A Ubiquitin carboxyl-terminal hydrolase 7; UBP, deubiquitination,
hausp, P53 binding; 2.30A {Homo sapiens} SCOP: d.3.1.9
PDB: 1nbf_A
Length = 353
Score = 184 bits (468), Expect = 1e-56
Identities = 73/225 (32%), Positives = 109/225 (48%), Gaps = 25/225 (11%)
Query: 56 RDPNEFIGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPSLGFSGFYEP 115
+ ++GLKN GATCY+NSLLQ F RKAV D K+ P
Sbjct: 1 KKHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPL--------- 51
Query: 116 QTAIGHLQMLFALMQHSNKLLVDPTDFVLTLG---LDRSYQQDAQEFSKLFLSNFVEEKF 172
LQ +F +QHS+K V + G LD Q D QE ++ L N VE K
Sbjct: 52 -----ALQRVFYELQHSDK-PVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDN-VENKM 104
Query: 173 RVQSLPHIKNFIKDYFSGEYVYVTKCFACGNETDRSEIFYELVVNV--CKTLDESMREFL 230
+ + + I F G+ V +C +DR E +Y++ +++ K + ES +++
Sbjct: 105 KGTCV---EGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYV 161
Query: 231 KEELLEGDDQYFCNRCGKKQNAGRRIRLKYLPKVLNLQLMRFVFD 275
E L+GD++Y G Q A + ++ LP VL+LQLMRF++D
Sbjct: 162 AVEQLDGDNKYDAGEHG-LQEAEKGVKFLTLPPVLHLQLMRFMYD 205
>2f1z_A Ubiquitin carboxyl-terminal hydrolase 7; hausp, USP7, UBP,
deubiquitinating enzyme, substrate recognition; 3.20A
{Homo sapiens}
Length = 522
Score = 184 bits (468), Expect = 5e-55
Identities = 72/234 (30%), Positives = 110/234 (47%), Gaps = 25/234 (10%)
Query: 47 DDFDPDQELRDPNEFIGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPS 106
+ + ++GLKN GATCY+NSLLQ F RKAV D K+ P
Sbjct: 161 APHGVAWDSKKHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPL 220
Query: 107 LGFSGFYEPQTAIGHLQMLFALMQHSNKLLVDPTDFVLTLG---LDRSYQQDAQEFSKLF 163
LQ +F +QHS+K V + G LD Q D QE ++
Sbjct: 221 --------------ALQRVFYELQHSDK-PVGTKKLTKSFGWETLDSFMQHDVQELCRVL 265
Query: 164 LSNFVEEKFRVQSLPHIKNFIKDYFSGEYVYVTKCFACGNETDRSEIFYELVVNV--CKT 221
L + VE K + + + I F G+ V +C +DR E +Y++ +++ K
Sbjct: 266 L-DNVENKMKGTCV---EGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKN 321
Query: 222 LDESMREFLKEELLEGDDQYFCNRCGKKQNAGRRIRLKYLPKVLNLQLMRFVFD 275
+ ES +++ E L+GD++Y G Q A + ++ LP VL+LQLMRF++D
Sbjct: 322 IFESFVDYVAVEQLDGDNKYDAGEHG-LQEAEKGVKFLTLPPVLHLQLMRFMYD 374
>1vjv_A Ubiquitin carboxyl-terminal hydrolase 6; YFR010W, structural
genomics, JCSG, PSI, protein structure initiative; HET:
MSE; 1.74A {Saccharomyces cerevisiae} SCOP: d.3.1.9
Length = 415
Score = 136 bits (342), Expect = 1e-37
Identities = 49/247 (19%), Positives = 92/247 (37%), Gaps = 37/247 (14%)
Query: 48 DFDPDQELRDPNE-FIGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPS 106
P+Q+++ + +G KN+G TCY+N+ LQ + R +L++NP +
Sbjct: 10 HHHPEQQVQQFAQLPVGFKNMGNTCYLNATLQALYRVNDLRDMILNYNPSQGVSNSGAQD 69
Query: 107 LGFSGFYEPQTAIGHLQMLFALMQHSNKLLVDPTDFVLTLG------------LDRSYQQ 154
+ + ++ F +Q+ + V P + TL QQ
Sbjct: 70 EE-----IHKQIVIEMKRCFENLQNKSFKSVLPVVLLNTLRKCYPQFAERDSQGGFYKQQ 124
Query: 155 DAQEFSKLFLSNFVEEKFRVQSLPHIKNFIKDYFSGEYVYVTKCFACGNE--TDRSEIFY 212
DA+E + + + F ++ K A N+ +E
Sbjct: 125 DAEELFTQLFHSMSIV---------FGDKFSEDFRIQFKTTIKDTANDNDITVKENESDS 175
Query: 213 ELVVNVCKTLDESMREFLKEELLEGDDQYFCNRC---GKKQNAGRRIRLKYLPKVLNLQL 269
+L ++ T + F++ LLEG ++ R G ++ LPK L +Q
Sbjct: 176 KLQCHISGTTN-----FMRNGLLEGLNEKIEKRSDLTGANSIYSVEKKISRLPKFLTVQY 230
Query: 270 MRFVFDR 276
+RF + R
Sbjct: 231 VRFFWKR 237
>3mhs_A Ubiquitin carboxyl-terminal hydrolase 8; multi-protein complex,
hydrolase-transcription regulator-Pro binding complex,
acetylation, cytoplasm; 1.89A {Saccharomyces cerevisiae}
PDB: 3mhh_A 3m99_A
Length = 476
Score = 129 bits (325), Expect = 1e-34
Identities = 56/263 (21%), Positives = 91/263 (34%), Gaps = 28/263 (10%)
Query: 35 SRWFNEQKHDSSDDFDPDQELRDPNEFIGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWN 94
+ + P E RD GL N+G+TC+++S+LQ HN F +
Sbjct: 117 AILAKYWDDVCTKTMVPSMERRDG--LSGLINMGSTCFMSSILQCLIHNPYFIRH---SM 171
Query: 95 PREDSEEKNNPSLGFSGFYEPQTAIGHLQMLFALMQHSNKL-----LVDPTDFVLTLG-- 147
+ S S + L Q S+ +
Sbjct: 172 SQIHSNNCKVRSPDKCFSCALDKIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKI 231
Query: 148 ---LDRSYQQDAQEFSKLFLSNFVEEKFRVQ---------SLPHIKNFIKDYFSGEYVYV 195
L QQDA EF + ++ + + + + F G
Sbjct: 232 NQNLAGYSQQDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVFEGSLESS 291
Query: 196 TKCFACGNETDRS-EIFYELVVNV--CKTLDESMREFLKEELLEGDDQYFCNRCGKKQNA 252
C C N + + + F +L +++ K L E + F K+E L+ Y C C Q+A
Sbjct: 292 IVCPGCQNNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQLKDF-NYHCGECNSTQDA 350
Query: 253 GRRIRLKYLPKVLNLQLMRFVFD 275
+++ + LP VL LQL RF
Sbjct: 351 IKQLGIHKLPSVLVLQLKRFEHL 373
>2ayn_A Ubiquitin carboxyl-terminal hydrolase 14; deubiquitinating enzymes,
DUB, USP14, proteasome, enzyme mechanism; 3.20A {Homo
sapiens} SCOP: d.3.1.9 PDB: 2ayo_A
Length = 404
Score = 126 bits (318), Expect = 3e-34
Identities = 44/260 (16%), Positives = 80/260 (30%), Gaps = 46/260 (17%)
Query: 48 DFDPDQELRDPNEFIGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPSL 107
D +Q GL NLG TCY+N+ +Q + A+ + + + +
Sbjct: 1 DMTEEQLASAMELPCGLTNLGNTCYMNATVQCIRSVPELKDALKRYAGALRASGEMASA- 59
Query: 108 GFSGFYEPQTAIGHLQMLFALMQHSNKLLVDPTDFVLTLGLDRSY-----------QQDA 156
Q L+ LF M ++ + P + L + QQDA
Sbjct: 60 --------QYITAALRDLFDSMDKTSS-SIPPIILLQFLHMAFPQFAEKGEQGQYLQQDA 110
Query: 157 QEF---------------SKLFLSNFVEEKFRVQSLPHIKNFIKDYFSGEYVYVTKCFAC 201
E + + K+ I +F E+ KC
Sbjct: 111 NECWIQMMRVLQQKLEAIEDDSVKETDSSSASAATPSKKKSLIDQFFGVEFETTMKCTES 170
Query: 202 GNETDRSEIFYELVVNV-----CKTLDESMREFLKEELLEGDDQYFCNRCGKKQNAGRRI 256
E +L ++ K L ++ L+EE+ + +
Sbjct: 171 EEEEVTKGKENQLQLSCFINQEVKYLFTGLKLRLQEEIT-----KQSPTLQRNALYIKSS 225
Query: 257 RLKYLPKVLNLQLMRFVFDR 276
++ LP L +Q++RF +
Sbjct: 226 KISRLPAYLTIQMVRFFYKE 245
>3nhe_A Ubiquitin carboxyl-terminal hydrolase 2; cysteine protease,
substrate ENZY complex, hydrolase-protein binding
complex; HET: CME; 1.26A {Homo sapiens} PDB: 2hd5_A
2ibi_A
Length = 348
Score = 117 bits (295), Expect = 3e-31
Identities = 62/251 (24%), Positives = 93/251 (37%), Gaps = 44/251 (17%)
Query: 62 IGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPSLGFSGFYEPQTAIGH 121
GL+NLG TC++NS+LQ + R L D +N
Sbjct: 10 AGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALV------EEFAK 63
Query: 122 LQMLFALMQHSNKLLVDPTDFVLTLG-----LDRSYQQDAQEFSKLFLSNFVEEKFRVQS 176
L + + S +V P++F + QQDAQEF + L E RV
Sbjct: 64 L--IQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTL 121
Query: 177 LPHIKN-------------------------FIKDYFSGEYVYVTKCFACGNETDRSEIF 211
P I D F G+ C CG + + F
Sbjct: 122 RPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPF 181
Query: 212 YEL------VVNVCKTLDESMREFLKEELLEGDDQYFCNRCGKKQNAGRRIRLKYLPKVL 265
++L TL + MR F KE++L+GD++ C RC ++ ++ ++ PK+L
Sbjct: 182 WDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKIL 241
Query: 266 NLQLMRFVFDR 276
L L RF R
Sbjct: 242 VLHLKRFSESR 252
>2gfo_A Ubiquitin carboxyl-terminal hydrolase 8; protease, thiol protease,
UBL conjugation pathway deubiquitinating enzyme, DUB,
zinc ribbon; 2.00A {Homo sapiens} SCOP: d.3.1.9 PDB:
3n3k_A
Length = 396
Score = 117 bits (294), Expect = 1e-30
Identities = 57/248 (22%), Positives = 97/248 (39%), Gaps = 41/248 (16%)
Query: 63 GLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPSLGFSGFYEPQTAIGHL 122
GL+NLG TCY+NS+LQ + N +D ++N LG G
Sbjct: 64 GLRNLGNTCYMNSILQCLCNAPHLADYFN-RNCYQDDINRSNL-LGHKG-----EVAEEF 116
Query: 123 QMLFALMQHSNKLLVDPTDFVLTLG-----LDRSYQQDAQEFSKLFLSNFVEEKFRVQSL 177
++ + + P DF +T+G QQD+QE + E+ + +
Sbjct: 117 GIIMKALWTGQYRYISPKDFKITIGKINDQFAGYSQQDSQELLLFLMDGLHEDLNKADNR 176
Query: 178 PHIKN-------------------------FIKDYFSGEYVYVTKCFACGNETDRSEIFY 212
K I F G++ +C C ++ E F
Sbjct: 177 KRYKEENNDHLDDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFM 236
Query: 213 ----ELVVNVCKTLDESMREFLKEELLEGDDQYFCNRCGKKQNAGRRIRLKYLPKVLNLQ 268
L TL + +R F KEE L +++++C+ C ++++ ++I + LP VL +
Sbjct: 237 YLSLPLASTSKCTLQDCLRLFSKEEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVH 296
Query: 269 LMRFVFDR 276
L RF +D
Sbjct: 297 LKRFSYDG 304
>3i3t_A Ubiquitin carboxyl-terminal hydrolase 21; hydrolase, structural
genomics consortium, SGC, activator, alternative
splicing, chromatin regulator, nucleus, polymorphism,
protease; 2.59A {Homo sapiens} PDB: 2y5b_A 3mtn_A
Length = 355
Score = 114 bits (287), Expect = 6e-30
Identities = 62/268 (23%), Positives = 96/268 (35%), Gaps = 62/268 (23%)
Query: 62 IGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPSLGFSGFYEPQTAIGH 121
+GL+NLG TC++N++LQ P R L + P G + +
Sbjct: 4 VGLRNLGNTCFLNAVLQCLSSTRPLRDFCLR-----RDFRQEVPGGGRAQ----ELTEAF 54
Query: 122 LQMLFALMQHSNKLLVDPTDFVLTLG-----LDRSYQQDAQEFSKLFLSNFVEEKFRVQS 176
++ AL + V+PT F QQDAQEF KL + E R
Sbjct: 55 ADVIGALWHPDSCEAVNPTRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGR 114
Query: 177 LPHIKN----------------------------------------FIKDYFSGEYVYVT 196
I D F G+
Sbjct: 115 RAPPILANGPVPSPPRRGGALLEEPELSDDDRANLMWKRYLEREDSKIVDLFVGQLKSCL 174
Query: 197 KCFACGNETDRSEIFYELVVNV--------CKTLDESMREFLKEELLEGDDQYFCNRCGK 248
KC ACG + E+F +L + + +L + F KEE LE ++ C+RC +
Sbjct: 175 KCQACGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCFNLFTKEEELESENAPVCDRCRQ 234
Query: 249 KQNAGRRIRLKYLPKVLNLQLMRFVFDR 276
K + +++ ++ P++L L L RF R
Sbjct: 235 KTRSTKKLTVQRFPRILVLHLNRFSASR 262
>2y6e_A Ubiquitin carboxyl-terminal hydrolase 4; HET: CME; 2.40A {Homo
sapiens}
Length = 367
Score = 106 bits (265), Expect = 8e-27
Identities = 60/266 (22%), Positives = 88/266 (33%), Gaps = 58/266 (21%)
Query: 62 IGLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPSLGFSGFYEPQTAIGH 121
GL NLG TC++NS LQ + P L ++E + LG G
Sbjct: 9 CGLGNLGNTCFMNSALQCLSNTAPLTDYFL--KDEYEAEINRDNPLGMKGE-----IAEA 61
Query: 122 LQMLFALMQHSNKLLVDPTDFVLTLG-----LDRSYQQDAQEFSKLFLSNFVEEKFRVQS 176
L M V P F +G QQD+QE L E+ RV+
Sbjct: 62 YAELIKQMWSGRDAHVAPRMFKTQVGRFAPQFSGYQQQDSQELLAFLLDGLHEDLNRVKK 121
Query: 177 LPHIKN-------------------------FIKDYFSGEYVYVTKCFACGNETDRSEIF 211
P+++ I D F G + C C + + F
Sbjct: 122 KPYLELKDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPF 181
Query: 212 YELVVNV---------------------CKTLDESMREFLKEELLEGDDQYFCNRCGKKQ 250
L + + L + + F E L D ++C C K Q
Sbjct: 182 CYLTLPLPLKKDRVMEGPMLQPQKKKKTTVALRDCIELFTTMETLGEHDPWYCPNCKKHQ 241
Query: 251 NAGRRIRLKYLPKVLNLQLMRFVFDR 276
A ++ L LPK+L + L RF ++R
Sbjct: 242 QATKKFDLWSLPKILVVHLKRFSYNR 267
>3ihp_A Ubiquitin carboxyl-terminal hydrolase 5; hydrolase, protease, thiol
protease, UBL conjugation pathway, metal-binding,
zinc-finger,structural genomics; 2.80A {Homo sapiens}
Length = 854
Score = 88.4 bits (218), Expect = 6e-20
Identities = 52/300 (17%), Positives = 89/300 (29%), Gaps = 65/300 (21%)
Query: 31 SLGESRWFNEQKHDSSDDFDPDQELRDPNE---FIGLKNLGATCYVNSLLQLWFHNLPFR 87
++ E Q+ + P + G++NLG +CY+NS++Q+ F F+
Sbjct: 311 TMTELEIDMNQRIGEWELIQESGVPLKPLFGPGYTGIRNLGNSCYLNSVVQVLFSIPDFQ 370
Query: 88 KAVLDWNPREDSEEKNNPSLGF------------SGFYEPQTAIGHLQMLFALMQHSNKL 135
+ +D + +P+ F SG Y +
Sbjct: 371 RKYVDKLEKIFQNAPTDPTQDFSTQVAKLGHGLLSGEYSKPVPESGDGERVPEQKEVQD- 429
Query: 136 LVDPTDFVLTLGLD----RSY-QQDAQEFSKLFLSNFVEEKFRVQSLPHIKNFIKDYFSG 190
+ P F +G + QQDAQEF L L N VE R P+ + F
Sbjct: 430 GIAPRMFKALIGKGHPEFSTNRQQDAQEFF-LHLINMVERNCRSSENPN------EVFRF 482
Query: 191 EYVYVTKCFACGNETDRSEIFYELVVNVCK------------------------------ 220
KC A + Y + + V
Sbjct: 483 LVEEKIKCLATEKVKYTQRVDYIMQLPVPMDAALNKEELLEYEEKKRQAEEEKMALPELV 542
Query: 221 ----TLDESMREFLKEELLEGDDQYFCNRCGKKQNAGRRIRLKYLPKVLNLQLMRFVFDR 276
+ + E ++ ++ K A + R P L +Q+ +F F
Sbjct: 543 RAQVPFSSCLEAYGAPEQVDD---FWSTALQAKSVAVKTTRFASFPDYLVIQIKKFTFGL 599
>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 = 50.2 bits (119), Expect = 3e-07
Identities = 42/246 (17%), Positives = 71/246 (28%), Gaps = 71/246 (28%)
Query: 22 CKGNPFCLASLGES------RWFNEQKHDSSDDFDPDQELR----DPNEFIGLKNLGATC 71
NP L+ + ES W + KH + D E +P E+
Sbjct: 323 LTTNPRRLSIIAESIRDGLATW-DNWKHVNCDKLTTIIESSLNVLEPAEY---------- 371
Query: 72 YVNSLLQLWFHNLP-FRK------AVLD--WN--PREDSE----EKNNPSLGFSGFYEPQ 116
+ F L F +L W + D + + SL E
Sbjct: 372 ------RKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKEST 425
Query: 117 TAIGHLQMLFALMQ------H--------------SNKLLVDPTD--FVLTLG--LDRSY 152
+I + + + H S+ L+ D F +G L
Sbjct: 426 ISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIE 485
Query: 153 Q-QDAQEFSKLFLS-NFVEEKFRVQSLP-HIKNFIKDYFSGEYVYVTKCFACGNETDRSE 209
+ F +FL F+E+K R S + I + Y K + C N+
Sbjct: 486 HPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFY--KPYICDNDPKYER 543
Query: 210 IFYELV 215
+ ++
Sbjct: 544 LVNAIL 549
Score = 48.7 bits (115), Expect = 1e-06
Identities = 46/352 (13%), Positives = 89/352 (25%), Gaps = 117/352 (33%)
Query: 28 CLASLGESRWFNEQK---HDSSDDFDPD---------------QELRDPNEFI---GLKN 66
+R + EQ+ ++ + F ELR P + + G+
Sbjct: 102 QRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELR-PAKNVLIDGVLG 160
Query: 67 LGATCYVNSLLQ------------LW--FHNLPFRKAVLD--WN--PREDSEEKNNPSLG 108
G T + W N + VL+ + D +
Sbjct: 161 SGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHS 220
Query: 109 FSGFYEPQTAIGHLQMLFALMQHSNKLLV-----DPT-----DF-----VLT-------- 145
+ + L+ L + N LLV + + + T
Sbjct: 221 SNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDF 280
Query: 146 LGLDRSYQQDAQEFSKLF--------LSNFVEEKFRVQSLPH------------IKNFIK 185
L + S L +++ + Q LP I I+
Sbjct: 281 LSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCR--PQDLPREVLTTNPRRLSIIAESIR 338
Query: 186 DYFS--GEYVYVT---------KCFACGNETDRSEIFYELVV---NV---CKTLDESMRE 228
D + + +V + ++F L V + L
Sbjct: 339 DGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILL-----S 393
Query: 229 FLKEELLEGDDQYFCNRCGK-----KQNAGRRIR-----LKYLPKVLNLQLM 270
+ ++++ D N+ K KQ I L+ K+ N +
Sbjct: 394 LIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYAL 445
Score = 32.1 bits (72), Expect = 0.20
Identities = 22/151 (14%), Positives = 48/151 (31%), Gaps = 37/151 (24%)
Query: 121 HLQMLFAL--MQHSNKLLVDPTDFVLTLGLDRSYQQDAQEFSKLFLSNFVEEKFRVQSLP 178
H M F Q+ K ++ +F FV+ F +
Sbjct: 4 HHHMDFETGEHQYQYKDIL-----------------------SVFEDAFVDN-FDCK--- 36
Query: 179 HIKNFIKDYFSG-EYVYVTKCFACGNETDRSEIFYELVVNVCKTLDESMREFLKEELLEG 237
+++ K S E ++ D L + +E +++F+ EE+L
Sbjct: 37 DVQDMPKSILSKEEIDHII------MSKDAVSGTLRLFWTLLSKQEEMVQKFV-EEVLRI 89
Query: 238 DDQYFCNRCGKKQNAGRRIRLKYLPKVLNLQ 268
+ ++ + +Q + Y+ + L
Sbjct: 90 NYKFLMSPIKTEQRQPSMMTRMYIEQRDRLY 120
>2vhf_A Ubiquitin carboxyl-terminal hydrolase CYLD; cytokine signalling,
linkage specificity, deubiquitinating enzyme, Lys63-
linked, anti-oncogene; 2.8A {Homo sapiens}
Length = 374
Score = 34.7 bits (79), Expect = 0.024
Identities = 34/220 (15%), Positives = 70/220 (31%), Gaps = 63/220 (28%)
Query: 63 GLKNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNPSLGF----------SGF 112
G++ +CY++S L F VL ++ E + +
Sbjct: 11 GIQGHYNSCYLDSTLFCLFAFSSVLDTVLLRPKEKNDVEYYSETQELLRTEIVNPLRIYG 70
Query: 113 YEPQTAIGHLQMLFALMQHSNKLLVDPTDFVLTLGLDRSYQQDAQEFSKLFLSNFVEEKF 172
Y T I L+ + ++ ++ + ++D +EF L+
Sbjct: 71 YVCATKIMKLRKILEKVEAASGFTSE--------------EKDPEEF----LNILFHHIL 112
Query: 173 RVQSLPHIKNFIKDYFSGEYVYVTKCFACGNETDRSEIFYELVVNVCKTLDESMREFLKE 232
RV+ L I++ + + FY++ + +E + +
Sbjct: 113 RVEPLLKIRS-------------------AGQKVQDCYFYQIFMEK----NEKVGVPTIQ 149
Query: 233 ELLEGDDQYFCNRCGKKQNAGRRIRLKYLPKVLNLQLMRF 272
+LLE F N ++ P L +Q+ RF
Sbjct: 150 QLLE---WSFINS---------NLKFAEAPSCLIIQMPRF 177
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 33.5 bits (76), Expect = 0.045
Identities = 9/37 (24%), Positives = 14/37 (37%), Gaps = 10/37 (27%)
Query: 179 HIKNFIKDYFSGEYVYVTKCFACG-----NETD-RSE 209
+ ++ + G+ V C CG D RSE
Sbjct: 30 YPPKIVERFSEGDVV----CALCGLVLSDKLVDTRSE 62
>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 = 34.3 bits (78), Expect = 0.047
Identities = 44/272 (16%), Positives = 78/272 (28%), Gaps = 88/272 (32%)
Query: 17 ISSRNCKGNPFCLASLGE---------SRWFN-EQKHDS--------SDDFDPDQELRDP 58
S+R P L S G + +F Q + ++ F D E P
Sbjct: 4 YSTR-----PLTL-SHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTP 57
Query: 59 NE----FIGL-------KNLGATCYVNSLLQLWFHNLPFRKAVLDWNPREDSEEKNNP-- 105
E F+G +G + +L L F L + N
Sbjct: 58 AELVGKFLGYVSSLVEPSKVGQF---DQVLNLCLTE--FENCYL----------EGNDIH 102
Query: 106 SLGFSGFYEPQTAIGHLQML----FALMQHSNKLLVDPTDFVLTLGLDRSYQQDAQEFSK 161
+L E T + + L + + ++ L + +AQ +
Sbjct: 103 ALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSAL---FRAVGEGNAQLVA- 158
Query: 162 LF-----LSNFVEEKFRVQSL-----PHIKNFIKDYFSGEYVYVTKCFACGNETDRSEIF 211
+F ++ EE ++ L + + IK FS E T +E
Sbjct: 159 IFGGQGNTDDYFEE---LRDLYQTYHVLVGDLIK--FSAE-----TLSELIRTTLDAEKV 208
Query: 212 YELVVNVCKTLDESMREFLKEELLEGDDQYFC 243
+ +N+ E+L+ D Y
Sbjct: 209 FTQGLNI--------LEWLENPSNTPDKDYLL 232
Score = 33.9 bits (77), Expect = 0.065
Identities = 39/244 (15%), Positives = 72/244 (29%), Gaps = 91/244 (37%)
Query: 102 KNNP---SLGFSGFYEPQTAIGHLQMLFALM----QHSNKLL--VDPTDFVLTLG----- 147
NNP ++ F G + + M+F + + K+ ++ T
Sbjct: 1666 INNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGL 1725
Query: 148 LDR-SYQQDAQEFSKLFLSNF-----VEEKFRVQSLPHIKNFIKDYF---S-GEY----- 192
L + Q A L L ++ K + + F S GEY
Sbjct: 1726 LSATQFTQPA-----LTLMEKAAFEDLKSKGLIPA--------DATFAGHSLGEYAALAS 1772
Query: 193 ----------VYVTK-------CFACGNETDRSEIFYELV-VN---VCKTLD-ESMREFL 230
V V +E RS Y ++ +N V + E+++ +
Sbjct: 1773 LADVMSIESLVEVVFYRGMTMQVAVPRDELGRSN--YGMIAINPGRVAASFSQEALQYVV 1830
Query: 231 KE------ELLE------GDDQYFCNRCGK-----------KQNAGRRIRLKYLPKVLNL 267
+ L+E + QY G ++I + L K L+L
Sbjct: 1831 ERVGKRTGWLVEIVNYNVENQQYVA--AGDLRALDTVTNVLNFIKLQKIDIIELQKSLSL 1888
Query: 268 QLMR 271
+ +
Sbjct: 1889 EEVE 1892
>1m1c_A GAG protein, major coat protein; dsRNA virus structure, RNA-protein
interaction, mRNA decapping, L-A virus,
QUAI-equivalence; 3.50A {Saccharomyces cerevisiae virus
l-a} SCOP: e.42.1.1
Length = 680
Score = 28.8 bits (63), Expect = 2.6
Identities = 18/155 (11%), Positives = 45/155 (29%), Gaps = 16/155 (10%)
Query: 55 LRDPNEFIGLKNLGATCYVNSLLQL-WFHNLPFRKAVLDWNPREDSEEKNNPSLGFSGFY 113
L+ E Y + +++ + + D + P
Sbjct: 133 LQVLTEQGQYSAGDIPMYHDGHVKIKLPVTIDDTAGPTQFAWPSDRSTDSYPDWAQFSES 192
Query: 114 EPQTAIGH--------------LQMLFALMQHSNKLLVDPTDFVLTLGLDRSYQQDAQEF 159
P + + L M+ + +N L +D L + Q+
Sbjct: 193 FPSIDVPYLDVRPLTVTEVNFVLMMMSKWHRRTN-LAIDYEAPQLADKFAYRHALTVQDA 251
Query: 160 SKLFLSNFVEEKFRVQSLPHIKNFIKDYFSGEYVY 194
+ + +++FR S + + ++ Y + +Y
Sbjct: 252 DEWIEGDRTDDQFRPPSSKVMLSALRKYVNHNRLY 286
>2jm4_A Relaxin receptor 1; LDL-A module, RXFP1 receptor, LGR7, signaling
protein; NMR {Homo sapiens}
Length = 43
Score = 25.0 bits (55), Expect = 4.8
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 6 YFFCPNLILCIISSRNCKGNPFC 28
YF C N+ C+ +C G C
Sbjct: 11 YFPCGNITKCLPQLLHCNGVDDC 33
>2kzf_A RBFA, ribosome-binding factor A; JCSG, joint center structural
genomics, PSI-biology, protein structure initiative; NMR
{Thermotoga maritima}
Length = 106
Score = 26.0 bits (58), Expect = 6.7
Identities = 6/24 (25%), Positives = 11/24 (45%), Gaps = 6/24 (25%)
Query: 253 GRRIRLKYLPKVLNLQLMRFVFDR 276
+ +RL P++ RF D+
Sbjct: 82 AKNLRLYVAPEI------RFYEDK 99
>3db7_A Putative calcium-regulated periplasmic protein; structural
genomics, joint center for structural genomics; HET:
MSE; 1.40A {Bacteroides thetaiotaomicron} PDB: 3due_A*
Length = 127
Score = 26.0 bits (57), Expect = 7.6
Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 6/46 (13%)
Query: 169 EEKFRVQSLPH-IKNFIKDYFSGEYVYVTKCFACGNETDRSEIFYE 213
++ +V +P + FIK +FS V + K E+D YE
Sbjct: 5 DKPIQVTQMPQLAQQFIKQHFSDSKVALAK-----MESDFLYKSYE 45
>2eap_A Lymphocyte cytosolic protein 2; cell-free protein synthesis,
protein regulation, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 90
Score = 25.4 bits (55), Expect = 8.1
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 81 FHNLPFRKAVLDWNPRE 97
N+PFR VL W+P
Sbjct: 10 LRNVPFRSEVLGWDPDS 26
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1210
Score = 27.1 bits (60), Expect = 8.9
Identities = 9/35 (25%), Positives = 13/35 (37%), Gaps = 3/35 (8%)
Query: 229 FLKEELLEGDDQYF---CNRCGKKQNAGRRIRLKY 260
L+E L + D Y C+ CG A +
Sbjct: 1135 VLRERLFDCSDAYRVIVCDICGLIAIASYKKDSYE 1169
>1we9_A PHD finger family protein; structural genomics, PHD domain, riken
structural genomics/proteomics initiative, RSGI, DNA
binding protein; NMR {Arabidopsis thaliana} SCOP:
g.50.1.2
Length = 64
Score = 24.8 bits (54), Expect = 9.2
Identities = 6/22 (27%), Positives = 7/22 (31%)
Query: 230 LKEELLEGDDQYFCNRCGKKQN 251
+ E QY C C K
Sbjct: 39 ITPARAEHIKQYKCPSCSNKSG 60
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 0.439
Gapped
Lambda K H
0.267 0.0476 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,250,884
Number of extensions: 241256
Number of successful extensions: 740
Number of sequences better than 10.0: 1
Number of HSP's gapped: 703
Number of HSP's successfully gapped: 32
Length of query: 276
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 184
Effective length of database: 4,133,061
Effective search space: 760483224
Effective search space used: 760483224
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: 57 (26.3 bits)