RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12903
(267 letters)
>4ddg_A Ubiquitin-conjugating enzyme E2 D2, ubiquitin THI OTUB1;
inhibition, hydrolase-ligase complex; 3.30A {Homo
sapiens} PDB: 4ddi_A
Length = 399
Score = 294 bits (755), Expect = 3e-99
Identities = 120/240 (50%), Positives = 172/240 (71%), Gaps = 7/240 (2%)
Query: 32 QQSKNIEKEISDSIMLVGDKEDIMVLEQQY-IGDEVYKGKVKDLARKYSNLRRTRPDGNC 90
Q I++EI+ LV ++ ++ VL ++Y D +Y+ K+KDL +KYS +R+TRPDGN
Sbjct: 160 AQQDRIQQEIAVQNPLVSERLELSVLYKEYAEDDNIYQQKIKDLHKKYSYIRKTRPDGNS 219
Query: 91 FFRSFGFALLESLYH-----LDFRLIAEKSKDKLLELGFQKFTLEDFHDQFMEVVNLISK 145
F+R+FGF+ LE+L F+ ++ KSK+ L+ GF +FT+EDFH+ FM+++ + K
Sbjct: 220 FYRAFGFSHLEALLDDSKELQRFKAVSAKSKEDLVSQGFTEFTIEDFHNTFMDLIEQVEK 279
Query: 146 PETNEDTLVEVFNNKDYSDYVVVYLRLIASGQLQQDADFYQNFIEGNRTVFEFCRQEVEP 205
+T+ L+ FN++ SDY+VVYLRL+ SG LQ+++ F+++FIEG RTV EFC+QEVEP
Sbjct: 280 -QTSVADLLASFNDQSTSDYLVVYLRLLTSGYLQRESKFFEHFIEGGRTVKEFCQQEVEP 338
Query: 206 MFKESDHIHIIALSTALDVGVRVRYMDRGDSTEAIAHDFPEDKPPQIHLLYRPGHYDILY 265
M KESDHIHIIAL+ AL V ++V YMDRG+ H FPE P+++LLYRPGHYDILY
Sbjct: 339 MCKESDHIHIIALAQALSVSIQVEYMDRGEGGTTNPHIFPEGSEPKVYLLYRPGHYDILY 398
>4dhi_B Ubiquitin thioesterase otubain-like; ubiquitin E2 enzyme fold,
ubiquitination, hydrolase-ligase C; 1.80A
{Caenorhabditis elegans} PDB: 4dhj_A 4dhz_A
Length = 284
Score = 253 bits (646), Expect = 2e-84
Identities = 83/278 (29%), Positives = 137/278 (49%), Gaps = 17/278 (6%)
Query: 1 MADDNIEPDQASFDKGYSEDANQVNQDDLILQQSKN-IEKEISDSIMLVGDKEDIMVLEQ 59
MA++ + D V D+++LQ + ++ S+ LV +L
Sbjct: 1 MANEPQKSDDNG-----QAAEAVVTDDEIVLQDQQLKTIEDEQKSVPLVATLAPFSILCA 55
Query: 60 QY--IGDEVYKGKVKDLARKYSNLRRTRPDGNCFFRSFGFALLESLYH-----LDFRLIA 112
+Y + K +L+ Y +R R DGNCF+R+ L+E + F +
Sbjct: 56 EYDNETSAAFLSKATELSEVYGEIRYIRGDGNCFYRAILVGLIEIMLKDRARLEKFIASS 115
Query: 113 EKSKDKLLELGFQKFTLEDFHDQFMEVVNLISKPETNEDTLVEVFNNKDYSDYVVVYLRL 172
L+ELGF +T DF D F+E + I E+ + + N+ ++Y++++ RL
Sbjct: 116 RDWTRTLVELGFPDWTCTDFCDFFIEFLEKIHSGVHTEEAVYTILNDDGSANYILMFFRL 175
Query: 173 IASGQLQQDADFYQNFIEGNRTVFEFCRQEVEPMFKESDHIHIIALSTALDVGVRVRYMD 232
I S L+Q+++ Y FI+ TV ++C QE+EPM+K++DH+ I +L A VR+ YMD
Sbjct: 176 ITSAFLKQNSEEYAPFIDEGMTVAQYCEQEIEPMWKDADHLAINSLIKAAGTRVRIEYMD 235
Query: 233 RGDSTEAIAHDF----PEDKPPQIHLLYRPGHYDILYP 266
R + H + P+I LLYRPGHYD++Y
Sbjct: 236 RTAAPNGGWHYDIPSDDQQIAPEITLLYRPGHYDVIYK 273
>1tff_A Ubiquitin thiolesterase protein OTUB2; hydrolase; 2.10A {Homo
sapiens} SCOP: d.3.1.11
Length = 234
Score = 245 bits (626), Expect = 4e-82
Identities = 80/229 (34%), Positives = 142/229 (62%), Gaps = 7/229 (3%)
Query: 43 DSIMLVGDKEDIMVLEQQYIGDEVYKGKVKDLARKYSNLRRTRPDGNCFFRSFGFALLES 102
S L+ +K DI+ + + + + +Y+ K+++L+++++ +R+T+ D NCF+R+ G++ LES
Sbjct: 4 TSFNLISEKCDILSILRDHPENRIYRRKIEELSKRFTAIRKTKGDRNCFYRALGYSYLES 63
Query: 103 LYH-----LDFRLIAEKSKDKLLELGFQKFTLEDFHDQFMEVVNLISKPETNEDTLVEVF 157
L F+ ++ + LL GF++ +F + F VV L+ + + + +L++VF
Sbjct: 64 LLGKSREIFKFKERVLQTPNDLLAAGFEEHKFRNFFNAFYSVVELV-EKDGSVSSLLKVF 122
Query: 158 NNKDYSDYVVVYLRLIASGQLQQDADFYQNFIEGNRTVFEFCRQEVEPMFKESDHIHIIA 217
N++ SD++V +LRL+ S ++ ADF+++FI+ + +FC EVEPM E DHI I A
Sbjct: 123 NDQSASDHIVQFLRLLTSAFIRNRADFFRHFIDEEMDIKDFCTHEVEPMATECDHIQITA 182
Query: 218 LSTALDVGVRVRYMDRGDSTEAIAHDFPEDKPPQIHLLYRPGHYDILYP 266
LS AL + ++V Y+D D+ H FPE P ++LLY+ HY+ILY
Sbjct: 183 LSQALSIALQVEYVDEMDT-ALNHHVFPEAATPSVYLLYKTSHYNILYA 230
>2zfy_A Ubiquitin thioesterase OTUB1; otubain, structural genomics,
structural genomics consortium, SGC, alternative
splicing, hydrolase, immune response; 1.69A {Homo
sapiens} PDB: 4ddg_B 4ddi_A
Length = 234
Score = 240 bits (614), Expect = 4e-80
Identities = 118/232 (50%), Positives = 168/232 (72%), Gaps = 7/232 (3%)
Query: 40 EISDSIMLVGDKEDIMVLEQQY-IGDEVYKGKVKDLARKYSNLRRTRPDGNCFFRSFGFA 98
EI+ LV ++ ++ VL ++Y D +Y+ K+KDL +KYS +R+TRPDGNCF+R+FGF+
Sbjct: 3 EIAVQNPLVSERLELSVLYKEYAEDDNIYQQKIKDLHKKYSYIRKTRPDGNCFYRAFGFS 62
Query: 99 LLESLYHLD-----FRLIAEKSKDKLLELGFQKFTLEDFHDQFMEVVNLISKPETNEDTL 153
LE+L F+ ++ KSK+ L+ GF +FT+EDFH+ FM+++ + +T+ L
Sbjct: 63 HLEALLDDSKELQRFKAVSAKSKEDLVSQGFTEFTIEDFHNTFMDLIEQVE-KQTSVADL 121
Query: 154 VEVFNNKDYSDYVVVYLRLIASGQLQQDADFYQNFIEGNRTVFEFCRQEVEPMFKESDHI 213
+ FN++ SDY+VVYLRL+ SG LQ+++ F+++FIEG RTV EFC+QEVEPM KESDHI
Sbjct: 122 LASFNDQSTSDYLVVYLRLLTSGYLQRESKFFEHFIEGGRTVKEFCQQEVEPMCKESDHI 181
Query: 214 HIIALSTALDVGVRVRYMDRGDSTEAIAHDFPEDKPPQIHLLYRPGHYDILY 265
HIIAL+ AL V ++V YMDRG+ H FPE P+++LLYRPGHYDILY
Sbjct: 182 HIIALAQALSVSIQVEYMDRGEGGTTNPHIFPEGSEPKVYLLYRPGHYDILY 233
>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 = 58.1 bits (140), Expect = 1e-09
Identities = 55/344 (15%), Positives = 95/344 (27%), Gaps = 115/344 (33%)
Query: 2 ADDNIEPDQ-----ASFDKGY---SEDANQVNQDDLILQQS-KNIEKEISDSIMLVGDKE 52
A D+ EP F GY + ++V Q D +L E L G+
Sbjct: 49 AADD-EPTTPAELVGKF-LGYVSSLVEPSKVGQFDQVLNLCLTEFENCY-----LEGN-- 99
Query: 53 DIMVLEQQYIGD-EVYKGKVKDLARKY------SNLRRTRPDGNCFFRS----------- 94
DI L + + + + K K+L + Y + + + FR+
Sbjct: 100 DIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAI 159
Query: 95 FG--------FALLESLYHLDFRLIA---EKSKDKLLELGFQKFTLEDFHDQFMEVVNLI 143
FG F L LY L+ + S + L EL E Q + ++ +
Sbjct: 160 FGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWL 219
Query: 144 SKPETNEDTLVEVFNNKDYSDYVVVYLRLIASGQLQQ----------------------- 180
P D DY + + LI QL
Sbjct: 220 ENPSNTPDK--------DYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGAT 271
Query: 181 -----------------DADFYQNFIEGNRTVFEF--CR-QEVEPMFKESDHIHIIALST 220
F+ + + +F F R E P + L
Sbjct: 272 GHSQGLVTAVAIAETDSWESFFVSVRKAITVLF-FIGVRCYEAYPNTS----LPPSILED 326
Query: 221 ALDVG-------VRVRYMDRGDSTEAIAHD---FPEDKPPQIHL 254
+L+ + + + + + + P K Q+ +
Sbjct: 327 SLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGK--QVEI 368
Score = 38.9 bits (90), Expect = 0.002
Identities = 32/197 (16%), Positives = 66/197 (33%), Gaps = 53/197 (26%)
Query: 106 LDF--RLIAEKSKDKLLELGFQKFTLEDFHDQFME-------VVNLISKPETNEDTLVEV 156
L + L+ + ++ L +F + ++E L+ + +T E+
Sbjct: 65 LGYVSSLVEPSKVGQFDQV--LNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKEL 122
Query: 157 FNNKDYSDYVVVYLRLIASGQ---LQQDADFYQNFIEGNRTVF-EFCRQ-EVEPMFKE-- 209
K+Y I + + + ++ ++ EGN + F Q + F+E
Sbjct: 123 I--KNY------ITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELR 174
Query: 210 ----------SDHIHIIA--LSTALDVGVRV-RYMDRG-DSTEAIAHDFPEDKPPQIHLL 255
D I A LS + + + +G + E + + P + P + +LL
Sbjct: 175 DLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLEN--PSNTPDKDYLL 232
Query: 256 YRP-----------GHY 261
P HY
Sbjct: 233 SIPISCPLIGVIQLAHY 249
Score = 35.8 bits (82), Expect = 0.016
Identities = 35/212 (16%), Positives = 66/212 (31%), Gaps = 70/212 (33%)
Query: 67 YKGKVKDLARKYSNLRR--TRPDGNCFFRSFGFALLESLYH----LDFRLIAEKSKDKLL 120
+G DL + + R D N F ++GF++L+ + + L EK K ++
Sbjct: 1628 EQGMGMDLYKTSKAAQDVWNRAD-NHFKDTYGFSILDIVINNPVNLTIHFGGEKGK-RIR 1685
Query: 121 ELGFQKFTLEDFHDQFMEVVNLISKPETNEDTLVEVFNNKD---------------YSDY 165
E + E D ++ + E NE + F ++
Sbjct: 1686 E-NYSAMIFETIVDGKLKTEKIF--KEINEHSTSYTFRSEKGLLSATQFTQPALTLME-- 1740
Query: 166 VVVYLRLIASGQLQQDADFYQNFIEGNRTVF------EF----CRQEVEPMFKESDHIHI 215
+ L + G + DA F E+ +V
Sbjct: 1741 KAAFEDLKSKGLIPADA------------TFAGHSLGEYAALASLADV------------ 1776
Query: 216 IALSTALDVGVRVRYMDRGDSTEAIAHDFPED 247
+++ + ++V V Y RG + P D
Sbjct: 1777 MSIESLVEV---VFY--RG---MTMQVAVPRD 1800
Score = 30.4 bits (68), Expect = 0.71
Identities = 23/108 (21%), Positives = 35/108 (32%), Gaps = 42/108 (38%)
Query: 93 RSF---GFALLESLYHLDFRLIAEK------------SKDKLLELGFQKFTLE------D 131
++ G +SLY L+ L K S+ KL KF+
Sbjct: 375 KNLVVSGPP--QSLYGLNLTLRKAKAPSGLDQSRIPFSERKL------KFSNRFLPVASP 426
Query: 132 FHDQFME-VVNLISKPETNEDTLVE-------VFNNKDYSDYVVVYLR 171
FH + +LI+K + V++ D SD LR
Sbjct: 427 FHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSD-----LR 469
>3phu_A RNA-directed RNA polymerase L; OTU domain, DE-ubiquitinase,
DE-isgylase, hydrolase; 2.20A {Crimean-congo hemorrhagic
fever VIRUSIBAR10200}
Length = 219
Score = 45.5 bits (107), Expect = 5e-06
Identities = 23/188 (12%), Positives = 48/188 (25%), Gaps = 61/188 (32%)
Query: 81 LRRTRPDGNCFFRSFGFALLESLYHLDFRLIAEKSKDKLLELGFQKFTLEDFHDQFMEVV 140
+ R DGNCF+ S + + + I E ++ +
Sbjct: 33 IVRQPGDGNCFYHSIAELTMPNKTDHSYHYIKR--------------LTESAARKYYQ-- 76
Query: 141 NLISKPETNEDTLVEVFNNKDYSDYVVVYLRLIASGQLQQDADFYQNFIEGNRTVFEFCR 200
+ DY+ ++ D ++
Sbjct: 77 ----------EEPEARLVGLSLEDYLK---------RMLSDNEW---------------- 101
Query: 201 QEVEPMFKESDHIHIIALSTALDVGVRVRYMDRGDSTEAIAHDFPEDKPPQIHLLY-RPG 259
+ L+ + + + + + D EA D ++LL+
Sbjct: 102 ---------GSTLEASMLAKEMGITIIIWTVAASDEVEAGIKFGDGDVFTAVNLLHSGQT 152
Query: 260 HYDILYPL 267
H+D L L
Sbjct: 153 HFDALRIL 160
>3pfy_A OTU domain-containing protein 5; structural genomics, structural
genomics consortium, SGC, PE C65 otubain, hydrolase;
HET: MSE PG4; 1.70A {Homo sapiens} PDB: 3tmp_A* 3tmo_A*
Length = 185
Score = 44.0 bits (103), Expect = 1e-05
Identities = 17/99 (17%), Positives = 39/99 (39%), Gaps = 6/99 (6%)
Query: 170 LRLIASGQLQQDADFYQNFIEGNRTVFEFCRQEVEPMFKESDHIHIIALSTALDVGVRVR 229
+R L ++AD++ N++ + + ++ + +HI + A++ + V V
Sbjct: 89 VRKHCMDYLMKNADYFSNYVTED--FTTYINRKRKNNC-HGNHIEMQAMAEMYNRPVEV- 144
Query: 230 YMDRGDSTEAIAHDFPEDKPPQIHLLY-RPGHYDILYPL 267
Y + + P I + Y R HY+ +
Sbjct: 145 YQYSTEPINTFHGIHQNEDEP-IRVSYHRNIHYNSVVNP 182
Score = 26.6 bits (58), Expect = 7.0
Identities = 5/27 (18%), Positives = 12/27 (44%)
Query: 81 LRRTRPDGNCFFRSFGFALLESLYHLD 107
+++ + DG C FR+ + +
Sbjct: 61 IKQMKEDGACLFRAVADQVYGDQDMHE 87
>3phx_A RNA-directed RNA polymerase L; OTU domain, DE-ubiquitinase,
DE-isgylase, hydrolase-protein complex; 1.60A
{Crimean-congo hemorrhagic fever virus} PDB: 3phw_A
3pt2_A 3pse_A 3prp_A 3prm_A
Length = 185
Score = 42.3 bits (99), Expect = 4e-05
Identities = 23/188 (12%), Positives = 49/188 (26%), Gaps = 61/188 (32%)
Query: 81 LRRTRPDGNCFFRSFGFALLESLYHLDFRLIAEKSKDKLLELGFQKFTLEDFHDQFMEVV 140
+ R DGNCF+ S + + + I ++ ++ + E
Sbjct: 33 IVRQPGDGNCFYHSIAELTMPNKTDHSYHYIKRLTESAA----------RKYYQEEPE-- 80
Query: 141 NLISKPETNEDTLVEVFNNKDYSDYVVVYLRLIASGQLQQDADFYQNFIEGNRTVFEFCR 200
DY+ ++ D ++
Sbjct: 81 --------------ARLVGLSLEDYLK---------RMLSDNEW---------------- 101
Query: 201 QEVEPMFKESDHIHIIALSTALDVGVRVRYMDRGDSTEAIAHDFPEDKPPQIHLLY-RPG 259
+ L+ + + + + + D EA D ++LL+
Sbjct: 102 ---------GSTLEASMLAKEMGITIIIWTVAASDEVEAGIKFGDGDVFTAVNLLHSGQT 152
Query: 260 HYDILYPL 267
H+D L L
Sbjct: 153 HFDALRIL 160
>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 = 41.0 bits (95), Expect = 3e-04
Identities = 36/214 (16%), Positives = 65/214 (30%), Gaps = 57/214 (26%)
Query: 19 EDANQVNQDDLILQQSKNIEKEISD-SIMLVGDKEDIMVLEQQYIGDEVYKGKVKDLARK 77
N++++ L+ +Q K I + L E+ L + + + Y + +
Sbjct: 406 VVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIV--DHYN-----IPKT 458
Query: 78 YSNLRRTRP-DGNCFFRSFGFALLESLYHLDFRLIAEKSKDKLLELGFQKFTLEDFHDQF 136
+ + P F+ G +HL E+ F+ L DF F
Sbjct: 459 FDSDDLIPPYLDQYFYSHIG-------HHLKNIEHPERMT------LFRMVFL-DFR--F 502
Query: 137 MEVVNLISKPETNEDTLVEVFNNKDYSDYVVVYLRLIASGQLQQDADFYQNFIEGNRTVF 196
+E I T + + N Q FY+ +I N +
Sbjct: 503 LE--QKIRHDSTAWNASGSILN-------------------TLQQLKFYKPYICDNDPKY 541
Query: 197 E--------FCRQEVEPMFKESDHIHI--IALST 220
E F + +E S + + IAL
Sbjct: 542 ERLVNAILDFLPK-IEENLICSKYTDLLRIALMA 574
Score = 34.4 bits (78), Expect = 0.037
Identities = 33/279 (11%), Positives = 78/279 (27%), Gaps = 56/279 (20%)
Query: 5 NIEPDQASFDKGYSEDANQVNQDDLILQQSKNIE-KEISDSIMLVGDKEDIMVLEQQYIG 63
+++ + Y +D V +D + N + K++ D + KE+I
Sbjct: 6 HMDFETGEHQYQY-KDILSVFEDAFV----DNFDCKDVQDMPKSILSKEEI--------- 51
Query: 64 DEVYKGKVKDLARKYSNLRRTRPDGNCFFRSFGFALLESLYHLDFRLIAEKSKDKLLELG 123
D + K ++ + F +E + ++++ + K + +
Sbjct: 52 DHIIMSK-DAVSGTLRLFWTLLSKQEEMVQKF----VEEVLRINYKFLMSPIKTEQRQPS 106
Query: 124 FQKFTLEDFHDQFMEVVNLISKPETNEDTLVEVFNNKDYS----DYVVVY---------- 169
+ D+ + +K + V++
Sbjct: 107 MMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWV 166
Query: 170 -LRLIASGQLQQDAD---FYQNFIEGNRTVFEFCRQEVEPMFKESDHIHIIALSTALDVG 225
L + S ++Q D F+ N N C ++ + L
Sbjct: 167 ALDVCLSYKVQCKMDFKIFWLNL--KN------CNSPET----------VLEMLQKLLYQ 208
Query: 226 VRVRYMDRGDSTEAIAHDFPEDKPPQIHLLYRPGHYDIL 264
+ + R D + I + LL + + L
Sbjct: 209 IDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL 247
>3by4_A OTU1, ubiquitin thioesterase OTU1; ubiquitin hydrolase,
deubiquitinase, cell cycle, hydrolase; 1.55A
{Saccharomyces cerevisiae} PDB: 3c0r_A
Length = 212
Score = 37.2 bits (86), Expect = 0.003
Identities = 23/106 (21%), Positives = 40/106 (37%), Gaps = 8/106 (7%)
Query: 162 YSDYVVVYLRLIASGQLQQDADFYQNFIEGNRTVFEFCRQEVEPMFKESDHIHIIALSTA 221
+ V LR + S ++ + + + I + ++ + ++ I I +S A
Sbjct: 41 FKQDSVRDLREMVSKEVLNNPVKFNDAILD-KPNKDYAQWILKMESWG-GAIEIGIISDA 98
Query: 222 LDVGVRVRYMDRGDSTEAIAHDFPEDKPPQ-IHLLYRPGHYDILYP 266
L V + V D F EDK I +L+ HYD L
Sbjct: 99 LAVAIYVV-----DIDAVKIEKFNEDKFDNYILILFNGIHYDSLTM 139
>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP,
translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A
Length = 504
Score = 30.3 bits (69), Expect = 0.65
Identities = 9/31 (29%), Positives = 16/31 (51%), Gaps = 3/31 (9%)
Query: 112 AEKSKDKLLELGFQKFTLEDFHDQFMEVVNL 142
E +KL +FTL D ++QF ++ +
Sbjct: 315 NEALIEKLKH---GQFTLRDMYEQFQNIMKM 342
>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition
particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A
{Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A
Length = 433
Score = 29.4 bits (67), Expect = 1.3
Identities = 8/31 (25%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 112 AEKSKDKLLELGFQKFTLEDFHDQFMEVVNL 142
+K + ++E G K TL D + Q + + +
Sbjct: 314 IQKKMEDVME-GKGKLTLRDVYAQIIALRKM 343
>1mfq_C SRP54, signal recognition particle 54KDA protein; RNA-protein
complex, A-minor motif, 3-helix junction, signaling
protein/RNA complex; HET: CCC; 3.10A {Homo sapiens}
SCOP: a.36.1.1
Length = 129
Score = 28.0 bits (63), Expect = 1.5
Identities = 6/31 (19%), Positives = 12/31 (38%), Gaps = 3/31 (9%)
Query: 112 AEKSKDKLLELGFQKFTLEDFHDQFMEVVNL 142
+FTL D ++QF ++ +
Sbjct: 3 GSHHHHHHKH---GQFTLRDMYEQFQNIMKM 30
>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal
recognition particle, SRP-GTPase, protein targeting,
cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus
furiosus}
Length = 443
Score = 29.1 bits (66), Expect = 1.7
Identities = 8/31 (25%), Positives = 15/31 (48%), Gaps = 3/31 (9%)
Query: 112 AEKSKDKLLELGFQKFTLEDFHDQFMEVVNL 142
E+ ++ L KFTL+D + Q + +
Sbjct: 316 KEEDIERFLR---GKFTLKDMYAQLEAMRKM 343
>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding,
signal recognition particle, GTP-binding, RNA-binding;
2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B
Length = 432
Score = 28.7 bits (65), Expect = 2.2
Identities = 9/31 (29%), Positives = 15/31 (48%), Gaps = 3/31 (9%)
Query: 112 AEKSKDKLLELGFQKFTLEDFHDQFMEVVNL 142
E+S D ++ KFTL + Q + N+
Sbjct: 313 TEESIDAIMR---GKFTLNELMTQLEAIENM 340
>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA
binding protein, hydrolase, gtpas; HET: GCP; 3.94A
{Escherichia coli} PDB: 2j28_9
Length = 433
Score = 27.9 bits (63), Expect = 3.6
Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 112 AEKSKDKLLELGFQKFTLEDFHDQFMEVVNL 142
AEK KL + F L DF +Q ++ N+
Sbjct: 316 AEKLASKLKKG--DGFDLNDFLEQLRQMKNM 344
>1m1h_A Transcription antitermination protein NUSG; transcription
termination, RNP motif, immunoglobulin fold, nucleic
acid interaction; 1.95A {Aquifex aeolicus} SCOP:
b.114.1.1 d.58.42.1 PDB: 1m1g_A 1npp_A 1npr_A
Length = 248
Score = 27.7 bits (62), Expect = 3.7
Identities = 6/44 (13%), Positives = 12/44 (27%), Gaps = 6/44 (13%)
Query: 35 KNIEKEISDSIMLVGDKEDIMVLEQQYIGDEVYKGKVKDLARKY 78
+++E + + I Q+ E L K
Sbjct: 97 ESVEGDTCVNAP------PISKPGQKITCKENKTEAKIVLDNKI 134
>4ecd_A Chorismate synthase; 4-layer sandwich, lyase; 2.50A
{Bifidobacterium longum subsp}
Length = 398
Score = 27.5 bits (62), Expect = 4.5
Identities = 17/77 (22%), Positives = 24/77 (31%), Gaps = 24/77 (31%)
Query: 206 MFKESDHIHIIALSTALDVGVR-----------------VRYMDRGDSTEAIAHDFPEDK 248
M E D + + L+ GVR S +A+ HD P +
Sbjct: 53 MKFEQDKVRL--LT-----GVRHGLTLGSPVAIEIANTEWPKWTEVMSADALDHDLPREG 105
Query: 249 PPQIHLLYRPGHYDILY 265
RPGH D+
Sbjct: 106 RNAPLSRPRPGHADLTG 122
>1qxo_A Chorismate synthase; beta-alpha-beta, flavoprotein, shikimate,
anti-infective, lyase; HET: FMN EPS; 2.00A
{Streptococcus pneumoniae} SCOP: d.258.1.1
Length = 388
Score = 27.5 bits (62), Expect = 4.5
Identities = 12/67 (17%), Positives = 23/67 (34%), Gaps = 7/67 (10%)
Query: 206 MFKESDHIHIIA-----LSTALDVGVRVRYMDRGDSTE--AIAHDFPEDKPPQIHLLYRP 258
M E+D + + +T + + V D + + K + RP
Sbjct: 49 MKIENDQVVFTSGVRHGKTTGAPITMDVINKDHQKWLDIMSAEDIEDRLKSKRKITHPRP 108
Query: 259 GHYDILY 265
GH D++
Sbjct: 109 GHADLVG 115
>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M
domain, RNA-binding, signal sequence-binding,
helix-turn-helix, protein targeting; 3.20A {Thermus
aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB:
2iy3_A
Length = 425
Score = 27.1 bits (61), Expect = 6.1
Identities = 6/18 (33%), Positives = 10/18 (55%)
Query: 125 QKFTLEDFHDQFMEVVNL 142
++ +LEDF Q + L
Sbjct: 318 KELSLEDFLKQMQNLKRL 335
>1qb2_A SRP54, human signal recognition particle 54 KD protein;
alpha-helix, helix-turn-helix, signaling protein; 2.10A
{Homo sapiens} SCOP: a.36.1.1 PDB: 1ry1_W* 2go5_W
Length = 109
Score = 25.7 bits (57), Expect = 7.3
Identities = 6/17 (35%), Positives = 12/17 (70%)
Query: 126 KFTLEDFHDQFMEVVNL 142
+FTL D ++QF ++ +
Sbjct: 1 QFTLRDMYEQFQNIMKM 17
>3fhr_A MAP kinase-activated protein kinase 3; kinase-inhibitor complex,
ATP-binding, cytoplasm, nucleotide-binding, nucleus,
phosphoprotein, polymorphism; HET: P4O; 1.90A {Homo
sapiens} PDB: 3fxw_A* 3r1n_A* 3she_A* 2oza_A 3fyk_X*
3fyj_X* 2p3g_X* 3ka0_A* 3fpm_A* 2pzy_A* 3a2c_A* 3kc3_A*
3gok_A* 2jbo_A* 2jbp_A* 3r2y_A* 3r30_A* 3r2b_A*
Length = 336
Score = 26.9 bits (60), Expect = 8.0
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 199 CRQEVEPMFKESDHIHIIAL 218
RQEV+ ++ S HI+ +
Sbjct: 68 ARQEVDHHWQASGGPHIVCI 87
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
0.320 0.139 0.399
Gapped
Lambda K H
0.267 0.0816 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,168,072
Number of extensions: 252350
Number of successful extensions: 585
Number of sequences better than 10.0: 1
Number of HSP's gapped: 562
Number of HSP's successfully gapped: 45
Length of query: 267
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 175
Effective length of database: 4,133,061
Effective search space: 723285675
Effective search space used: 723285675
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.2 bits)