RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 021839
(307 letters)
>2ihr_1 Peptide chain release factor 2; mixed alpha-beta, translation;
2.50A {Thermus thermophilus} PDB: 2b9m_Y* 3f1e_X 3f1g_X
2x9r_Y* 2x9t_Y* 2jl5_Y 2jl7_Y 2wh1_Y 2wh3_Y
Length = 365
Score = 213 bits (545), Expect = 2e-67
Identities = 68/163 (41%), Positives = 97/163 (59%), Gaps = 2/163 (1%)
Query: 144 QTSFSGAEVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTV 203
TSF+G EV+P + +E ++V + E+L I RA G GGQ VN ++AVR+ H+PTG+TV
Sbjct: 202 HTSFAGVEVIPEV-DEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITV 260
Query: 204 RCTEERSQLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQQIRNYVFHPYK 263
C RSQ+ NK AL LKA+L + ++R E+K +RG+ EWG QIR+YV
Sbjct: 261 TCQTTRSQIKNKELALKILKARLYELERKKREEELKALRGEVRPIEWGSQIRSYVLDK-N 319
Query: 264 LVKDVRTGHETSDIVSVMDGELEPFIKSYLKYKYSMSLSASDA 306
VKD RTG D +V+DG+L I + L++K +
Sbjct: 320 YVKDHRTGLMRHDPENVLDGDLMDLIWAGLEWKAGRRQGTEEV 362
Score = 113 bits (284), Expect = 5e-29
Identities = 31/135 (22%), Positives = 64/135 (47%), Gaps = 6/135 (4%)
Query: 10 DVEAASDRVEEIRASAGLQQLEKELAELEMKAADSSFWDNRAEAQETLQALTDVKDKINL 69
D+E + R+E + + Q E L ELE + D S W++ A++ Q ++ ++
Sbjct: 2 DLERLAQRLEGLGGIFDIPQKETRLKELERRLEDPSLWNDPEAARKVSQEAARLRRTVDT 61
Query: 70 LTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAASIIKELNKALDQFELTQLLSGPYDKEG 129
++ + + +++ + E ++E K LD+ LL+ P+ ++
Sbjct: 62 FRSLESDLQGLLELMEELPAEER------EALKPELEEAAKKLDELYHQTLLNFPHAEKN 115
Query: 130 AVISITAGAGGTDAQ 144
A+++I GAGGT+A
Sbjct: 116 AILTIQPGAGGTEAC 130
>1gqe_A Release factor 2, RF2; protein synthesis, ribosome, macromolecular
mimicry, translation; 1.81A {Escherichia coli} SCOP:
e.38.1.1 PDB: 1mi6_A 1ml5_Z*
Length = 365
Score = 202 bits (517), Expect = 3e-63
Identities = 65/151 (43%), Positives = 99/151 (65%), Gaps = 2/151 (1%)
Query: 144 QTSFSGAEVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTV 203
TSFS A V P + ++ +D++I DL I RA G GGQ+VN+ E+AVRITHIPTG+
Sbjct: 214 HTSFSSAFVYPEV-DDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVT 272
Query: 204 RCTEERSQLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQQIRNYVFHPYK 263
+C +RSQ NK +A+ ++KAKL + +++ +E + + + WG QIR+YV +
Sbjct: 273 QCQNDRSQHKNKDQAMKQMKAKLYEVEMQKKNAEKQAMEDNKSDIGWGSQIRSYVLDDSR 332
Query: 264 LVKDVRTGHETSDIVSVMDGELEPFIKSYLK 294
+KD+RTG ET + +V+DG L+ FI++ LK
Sbjct: 333 -IKDLRTGVETRNTQAVLDGSLDQFIEASLK 362
Score = 119 bits (300), Expect = 2e-31
Identities = 33/144 (22%), Positives = 65/144 (45%), Gaps = 2/144 (1%)
Query: 1 MQDFYNLRKDVEAASDRVEEIRASAGLQQLEKELAELEMKAADSSFWDNRAEAQETLQAL 60
M + + ++ ++R + +R ++ L E+ + W+ AQ +
Sbjct: 1 MFEINPVNNRIQDLTERSDVLRGYLDYDAKKERLEEVNAELEQPDVWNEPERAQALGKER 60
Query: 61 TDVKDKINLLTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAASIIKELNKALDQFELTQL 120
+ ++ ++ L K ++D +++L E D D EA + + L + L Q E ++
Sbjct: 61 SSLEAVVDTLDQMKQGLEDVSGLLELAVEAD--DEETFNEAVAELDALEEKLAQLEFRRM 118
Query: 121 LSGPYDKEGAVISITAGAGGTDAQ 144
SG YD + I AG+GGT+AQ
Sbjct: 119 FSGEYDSADCYLDIQAGSGGTEAQ 142
>1zbt_A RF-1, peptide chain release factor 1; peptide chain release factor
1 (RF-1), structural joint center for structural
genomics, JCSG; 2.34A {Streptococcus mutans}
Length = 371
Score = 126 bits (318), Expect = 7e-34
Identities = 53/148 (35%), Positives = 78/148 (52%), Gaps = 12/148 (8%)
Query: 148 SGAEVMPLLPE-ESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCT 206
S A V+ ++PE E ++ +I +DL + A G GGQNVNKV TAVRI H+PT + V
Sbjct: 213 STATVL-VMPEVEEVEYEIDPKDLRVDIYHASGAGGQNVNKVATAVRIIHLPTNIKVEMQ 271
Query: 207 EERSQLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKAEWG-----QQIRNYVFHP 261
EER+Q N+ KA+ ++A++ + E R V G ++IR Y F P
Sbjct: 272 EERTQQKNRDKAMKIIRARVADHFAQIAQDEQDAERKSTV----GTGDRSERIRTYNF-P 326
Query: 262 YKLVKDVRTGHETSDIVSVMDGELEPFI 289
V D R G + S++ G+L+ I
Sbjct: 327 QNRVTDHRIGLTLQKLDSILSGKLDEVI 354
Score = 34.1 bits (79), Expect = 0.044
Identities = 26/121 (21%), Positives = 51/121 (42%), Gaps = 5/121 (4%)
Query: 27 LQQLEKELAELEMKAADSSFWDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKL 86
LQ +E EL +D + E + + ++ + + ++K + + ++
Sbjct: 19 LQAVEDRYEELGELLSDPDVVSDTKRFMELSREEANSRETVAVYREYKQVVQNIADAQEM 78
Query: 87 TEEMDSTDAGLLEEAASIIKELNKALDQFE--LTQLL--SGPYDKEGAVISITAGAGGTD 142
++ S D L E A +K A +++E L LL P D + ++ I AGG +
Sbjct: 79 IKD-ASGDPELEEMAKEELKNSKVAKEEYEEKLRFLLLPKDPNDDKNIILEIRGAAGGDE 137
Query: 143 A 143
A
Sbjct: 138 A 138
>3d5a_X RF1, peptide chain release factor 1; ribosome, ribonucleoprotein,
ribosomal protein, RNA-binding, binding, metal-binding,
zinc-finger; 3.21A {Thermus thermophilus} PDB: 2b64_Y
3d5c_X 3mr8_V 3ms0_V
Length = 354
Score = 124 bits (314), Expect = 2e-33
Identities = 53/144 (36%), Positives = 81/144 (56%), Gaps = 4/144 (2%)
Query: 148 SGAEVMPLLPE-ESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCT 206
S A V +LP+ E D + +++ I RA G GGQ VN ++AVR+ H+PTG+ V C
Sbjct: 195 STATVA-VLPKAEEEDFALNMDEIRIDVMRASGPGGQGVNTTDSAVRVVHLPTGIMVTCQ 253
Query: 207 EERSQLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKA-EWGQQIRNYVFHPYKLV 265
+ RSQ+ N+ KAL L+++LL + + A +++ R + E ++IR Y F P V
Sbjct: 254 DSRSQIKNREKALMILRSRLLEMKRAEEAERLRKTRLAQIGTGERSEKIRTYNF-PQSRV 312
Query: 266 KDVRTGHETSDIVSVMDGELEPFI 289
D R G T D+ V+ G L P +
Sbjct: 313 TDHRIGFTTHDLEGVLSGHLTPIL 336
Score = 35.6 bits (83), Expect = 0.013
Identities = 30/121 (24%), Positives = 56/121 (46%), Gaps = 9/121 (7%)
Query: 27 LQQLEKELAELEMKAADSSFWDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKL 86
L +LE+E ELE +D ++ Q + ++ + I L+ +++ ++D ++
Sbjct: 5 LDRLEEEYRELEALLSDPEVLKDKGRYQSLSRRYAEMGEVIGLIREYRKVLED----LEQ 60
Query: 87 TEEMDSTDAGLLEEAASIIKELNKALDQFE--LTQLL--SGPYDKEGAVISITAGAGGTD 142
E + D L E A + + L + E L + L P D+ A++ I AG GG +
Sbjct: 61 AESLLD-DPELKEMAKAEREALLARKEALEKELERHLLPKDPMDERDAIVEIRAGTGGEE 119
Query: 143 A 143
A
Sbjct: 120 A 120
>2rsm_A Probable peptide chain release factor C12ORF65 HO mitochondrial;
GGQ domain, translation; NMR {Mus musculus}
Length = 115
Score = 115 bits (290), Expect = 2e-32
Identities = 26/97 (26%), Positives = 43/97 (44%), Gaps = 2/97 (2%)
Query: 141 TDAQ-TSFSGAEVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPT 199
+ S +V + + + E +LE F + G GGQ NK V + H+P+
Sbjct: 19 LLFPGMAASTVQVAGR-KDYPALLPLNESELEEQFVKGHGPGGQATNKTSNCVVLKHVPS 77
Query: 200 GVTVRCTEERSQLANKIKALSRLKAKLLVIAEEQRAS 236
G+ V+C + RS N+ A L+ K+ V +S
Sbjct: 78 GIVVKCHQTRSVDQNRKIARKVLQEKVDVFYNSGPSS 114
>1rq0_A RF-1, peptide chain release factor 1; X-RAY, crystal, peptide
release factor 1, ribosome, structural genomics, BSGC
structure funded by NIH; 2.65A {Thermotoga maritima}
SCOP: e.38.1.1 PDB: 2fvo_A
Length = 342
Score = 121 bits (307), Expect = 2e-32
Identities = 61/136 (44%), Positives = 82/136 (60%), Gaps = 3/136 (2%)
Query: 156 LPE-ESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERSQLAN 214
LPE E D++I EDL+I RA G GGQ VNK E+AVRITH+PTG+ V C ERSQ N
Sbjct: 183 LPEIEEKDIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQN 242
Query: 215 KIKALSRLKAKLLVIAEEQRASEIKQIRGDAV-KAEWGQQIRNYVFHPYKLVKDVRTGHE 273
K AL L+A+L + +EQ+ EI Q R + E ++IR Y F P V D R +
Sbjct: 243 KQTALRILRARLYQLQKEQKEREISQKRKSQIGTGERSEKIRTYNF-PQNRVTDHRINYT 301
Query: 274 TSDIVSVMDGELEPFI 289
+ + ++DG+L+ I
Sbjct: 302 SYRLQEILDGDLDEII 317
>2b3t_B RF-1, peptide chain release factor 1; translation termination,
methylation, conformational changes; HET: SAH; 3.10A
{Escherichia coli} SCOP: e.38.1.1
Length = 360
Score = 118 bits (299), Expect = 3e-31
Identities = 50/143 (34%), Positives = 71/143 (49%), Gaps = 11/143 (7%)
Query: 152 VMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVTVRCTEERSQ 211
VMP ++ + DL I R+ G GGQ+VN ++A+RITH+PTG+ V C +ERSQ
Sbjct: 205 VMPE-LPDAELPDVNPADLRIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQ 263
Query: 212 LANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKAEWG-----QQIRNYVFHPYKLVK 266
NK KALS L A++ +R R + + G + R Y F P V
Sbjct: 264 HKNKAKALSVLGARIHAAEMAKRQQAEASTRRNLL----GSGDRSDRNRTYNF-PQGRVT 318
Query: 267 DVRTGHETSDIVSVMDGELEPFI 289
D R + VM+G+L+ I
Sbjct: 319 DHRINLTLYRLDEVMEGKLDMLI 341
Score = 33.3 bits (77), Expect = 0.095
Identities = 26/121 (21%), Positives = 51/121 (42%), Gaps = 9/121 (7%)
Query: 27 LQQLEKELAELEMKAADSSFWDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKL 86
L+ L + E++ D+ ++ + + + D TD++ +D ++
Sbjct: 9 LEALHERHEEVQALLGDAQTIADQERFRALSREYAQLSDVSRCFTDWQQVQED----IET 64
Query: 87 TEEMDSTDAGLLEEAASIIKELNKALDQFE--LTQLL--SGPYDKEGAVISITAGAGGTD 142
+ M D + E A ++E + +Q E L LL P D+ A + + AG GG +
Sbjct: 65 AQMMLD-DPEMREMAQDELREAKEKSEQLEQQLQVLLLPKDPDDERNAFLEVRAGTGGDE 123
Query: 143 A 143
A
Sbjct: 124 A 124
>4dh9_Y YAEJ; ribosome, YAEJ, ribosome stalling, ribosome rescue, rescue F
alternative rescue factor, ARFB, release factor, rescue
of ribosomes; 3.20A {Escherichia coli} PDB: 2jy9_A
Length = 140
Score = 98.3 bits (245), Expect = 1e-25
Identities = 34/141 (24%), Positives = 57/141 (40%), Gaps = 30/141 (21%)
Query: 160 SMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRI------THIPTGV------------ 201
S V IP+ +LEI+ RA G GGQ+VNK TA+ + + +P
Sbjct: 5 SRHVAIPDGELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEYYKERLLAASHHLI 64
Query: 202 ------TVRCTEERSQLANKIKALSRLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQQIR 255
++ E RSQ N+ AL+RL A + + E++A + + + + +
Sbjct: 65 SSDGVIVIKAQEYRSQELNREAALARLVAMIKELTTEKKARRPTRPTRASKERRLASKAQ 124
Query: 256 NYVFHPYKLVKDVRTGHETSD 276
VK +R +
Sbjct: 125 KS------SVKAMRGKVRSGR 139
>2jva_A Peptidyl-tRNA hydrolase domain protein; GFT hydrolase, structural
genomics, PSI-2, protein STRU initiative; NMR
{Pseudomonas syringae PV}
Length = 108
Score = 83.0 bits (205), Expect = 3e-20
Identities = 24/99 (24%), Positives = 44/99 (44%), Gaps = 24/99 (24%)
Query: 160 SMDVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTG------------------- 200
S +V +P+ ++E++ RA G GGQNVNKV +A+ +
Sbjct: 5 SNNVHLPDAEIELTAIRAQGAGGQNVNKVSSAMHLRFDINASSLPPFYKERLLALNDSRI 64
Query: 201 -----VTVRCTEERSQLANKIKALSRLKAKLLVIAEEQR 234
+ ++ + R+Q N+ AL RL ++ A+ +
Sbjct: 65 TSDGVIVLKAQQYRTQEQNRADALLRLSELIVNAAKLEH 103
>1j26_A Immature colon carcinoma transcript 1; peptide chain release
factors, RF-1, the GGQ motif, immature carcinoma
transcript 1; NMR {Mus musculus} SCOP: d.50.4.1
Length = 112
Score = 68.2 bits (166), Expect = 1e-14
Identities = 19/90 (21%), Positives = 31/90 (34%), Gaps = 25/90 (27%)
Query: 162 DVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTG--------------------- 200
IP + L IS+ R+ G GGQNVNKV + +
Sbjct: 14 SSYIPLDRLSISYCRSSGPGGQNVNKVNSKAEVRFHLASADWIEEPVRQKIALTHKNKIN 73
Query: 201 ----VTVRCTEERSQLANKIKALSRLKAKL 226
+ + R Q N + L +++ +
Sbjct: 74 KAGELVLTSESSRYQFRNLAECLQKIRDMI 103
>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 = 48.5 bits (115), Expect = 2e-06
Identities = 54/306 (17%), Positives = 98/306 (32%), Gaps = 125/306 (40%)
Query: 26 GLQQLE--KELAELEMKAADSSFWDNRAEA--QETL-QALTD-VKDKINLLT-------- 71
G Q+ +L + A D W+ RA+ ++T ++ D V + LT
Sbjct: 1625 GSQEQGMGMDLYKTSKAAQD--VWN-RADNHFKDTYGFSILDIVINNPVNLTIHFGGEKG 1681
Query: 72 ----------DFKTKMDDAVTIVKLTEEMDSTDAGLLEEAASII----KELNKALDQFEL 117
F+T +D + K+ +E++ E + S K L L +
Sbjct: 1682 KRIRENYSAMIFETIVDGKLKTEKIFKEIN-------EHSTSYTFRSEKGL---LSATQF 1731
Query: 118 TQ----LLSGPYDKEGAVISITAGAGGTDAQTSFSG------------AEVMPLLPEESM 161
TQ L+ A G A +F+G A+VM +
Sbjct: 1732 TQPALTLME--K----AAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSI------ 1779
Query: 162 DVQIPEED-LEISFSRAGGKGGQN-VNKVET--------AVRITHIPTGVTVRCTEERS- 210
E +E+ F R G Q V + E A+ P V ++E
Sbjct: 1780 ------ESLVEVVFYR--GMTMQVAVPRDELGRSNYGMIAIN----PGRVAASFSQEALQ 1827
Query: 211 --------------QLAN------------KIKA-------LSRLKAKLLVIAEEQRASE 237
++ N ++A L+ +K + + I E Q++
Sbjct: 1828 YVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKLQKIDIIELQKSLS 1887
Query: 238 IKQIRG 243
++++ G
Sbjct: 1888 LEEVEG 1893
Score = 34.6 bits (79), Expect = 0.047
Identities = 54/308 (17%), Positives = 89/308 (28%), Gaps = 101/308 (32%)
Query: 45 SFWDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAASI 104
F E E A + L+ F + ++ ++ + G ++
Sbjct: 36 QFNKILPEPTEGFAADDEPTTPAELVGKF---------LGYVSSLVEPSKVGQFDQV--- 83
Query: 105 IKELNKALDQFELTQLLSGPYDKEGAVISITAGAGGTDAQT-----SFSGAEVMPLLPEE 159
LN L +FE L G D + T +T ++ A +M P +
Sbjct: 84 ---LNLCLTEFE-NCYLEGN-DIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFD 138
Query: 160 SMDVQIPEEDLEISFSRAG-GK-------GGQNVNKVETAVRITHIPTGVTVRCTEERSQ 211
L F G G GGQ G T EE
Sbjct: 139 KK----SNSAL---FRAVGEGNAQLVAIFGGQ----------------GNTDDYFEELRD 175
Query: 212 L----ANKIKALSRLKAKLL--VIAEEQRASEIKQIRG-DAVKAEWGQ------------ 252
L + L + A+ L +I A ++ +G + + EW +
Sbjct: 176 LYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFT-QGLNIL--EWLENPSNTPDKDYLL 232
Query: 253 ------------QIRNYV-------FHPYKLVKDVR--TGHETSDIVSV----MDGELEP 287
Q+ +YV F P +L ++ TGH + +V+ E
Sbjct: 233 SIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGH-SQGLVTAVAIAETDSWES 291
Query: 288 FIKSYLKY 295
F S K
Sbjct: 292 FFVSVRKA 299
Score = 33.1 bits (75), Expect = 0.13
Identities = 35/191 (18%), Positives = 62/191 (32%), Gaps = 62/191 (32%)
Query: 9 KDVEAASDRVEEIRASAGLQQLEKELAELEMKAA-DSSFWDNRAEAQETL--------QA 59
+ + + + + +A +GL Q + E K + F L
Sbjct: 384 QSLYGLNLTLRKAKAPSGLDQSRIPFS--ERKLKFSNRF----------LPVASPFHSHL 431
Query: 60 LTDVKDKINLLTDFKTKMDDAVTI--------VKLTEEMDSTDAGLLEEAASIIKELNKA 111
L D I D + + V+ V T D +D L + SI + +
Sbjct: 432 LVPASDLI--NKDL---VKNNVSFNAKDIQIPVYDTF--DGSD--LRVLSGSISERIVDC 482
Query: 112 L----------DQFELTQLLS-GPYDKEGAVISITAGAGG-TDAQTSFSGAEVMPLLPEE 159
+ QF+ T +L GP G +G G T +G V +
Sbjct: 483 IIRLPVKWETTTQFKATHILDFGP----GGA----SGLGVLTHRNKDGTGVRV---IVAG 531
Query: 160 SMDVQIPEEDL 170
++D+ P++D
Sbjct: 532 TLDIN-PDDDY 541
>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 = 45.6 bits (107), Expect = 1e-05
Identities = 54/350 (15%), Positives = 103/350 (29%), Gaps = 102/350 (29%)
Query: 1 MQDFY-NLRKDVEAASDRVEEIRASAGLQQLEKELAEL--EMKAADS-----SFWDNRAE 52
+Q + + + SD I+ + ++ EL L + + +
Sbjct: 202 LQKLLYQIDPNWTSRSDHSSNIKLR--IHSIQAELRRLLKSKPYENCLLVLLNVQNA--- 256
Query: 53 AQETLQALTDVKDKINLLTDFKTKMDDAVTIVKLTEEMDSTDAGLLE-EAASIIKELNKA 111
+ A ++ KI L T FK D +D L E S+ L K
Sbjct: 257 --KAWNAF-NLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSL---LLKY 310
Query: 112 LDQ--FEL-TQLLSG-PYDKEGAVISITAGAG--------------GTDAQTSFSGAEVM 153
LD +L ++L+ P +SI D T+ + +
Sbjct: 311 LDCRPQDLPREVLTTNPR-----RLSI-IAESIRDGLATWDNWKHVNCDKLTTIIESSLN 364
Query: 154 PLLPEE--------SM---DVQIPEEDLEISFSRAGGKGGQNVNKVETAVRITHIPTGVT 202
L P E S+ IP L + + + +++ V + V
Sbjct: 365 VLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWF----------DVIKSDVMV------VV 408
Query: 203 VRCTEERSQLANK--------IKALS-RLKAKLLVIAEEQRASEIKQIRGDAVKAEWGQ- 252
+ + L K I ++ LK KL E + A + + +
Sbjct: 409 NKL--HKYSLVEKQPKESTISIPSIYLELKVKL----ENEYALHRSIVDHYNIPKTFDSD 462
Query: 253 -----QIRNYVFHPYKLVKDVRTGHETSDIVSVMDGELEPFIKSYLKYKY 297
+ Y + + GH +I + F +L +++
Sbjct: 463 DLIPPYLDQYFYS-H-------IGHHLKNI--EHPERMTLFRMVFLDFRF 502
Score = 31.4 bits (70), Expect = 0.51
Identities = 32/209 (15%), Positives = 64/209 (30%), Gaps = 61/209 (29%)
Query: 147 FSGAEVMPLLPEESMDVQIPEEDLEISFSRAGGKGGQNVNK-VETAVRI----------- 194
S E+ ++ + F K + V K VE +RI
Sbjct: 46 LSKEEIDHIIMSKD-----AVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKT 100
Query: 195 -THIPTGVTVRCTEERSQLAN-----------------KIK-ALSRLK-AKLLVI----- 229
P+ +T E+R +L N K++ AL L+ AK ++I
Sbjct: 101 EQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLG 160
Query: 230 -------AEEQRASEIKQIRGDAVKAEW---GQQIR-NYVFHP-----YKLVKDVRTGHE 273
+ + +++ + W V Y++ + + +
Sbjct: 161 SGKTWVALDVCLSYKVQCKMDFKI--FWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSD 218
Query: 274 TSDIVSVMDGELEPFIKSYLKYK-YSMSL 301
S + + ++ ++ LK K Y L
Sbjct: 219 HSSNIKLRIHSIQAELRRLLKSKPYENCL 247
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 31.7 bits (71), Expect = 0.17
Identities = 15/78 (19%), Positives = 30/78 (38%), Gaps = 12/78 (15%)
Query: 6 NLRKDVEAASDRVEEIRASAGLQQLEKELAELEMKAADS--SFWDNRAEAQETLQALTDV 63
++RK E R++E+ A++ + E KA + ++E E + +
Sbjct: 86 SIRKWREEQRKRLQELDAAS-----KVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRI 140
Query: 64 KDKINLLTDFKTKMDDAV 81
DK F + D +
Sbjct: 141 ADK-----AFYQQPDADI 153
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 30.7 bits (68), Expect = 0.31
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 28 QQLEKELAELEMKAADSS 45
Q L+K A L++ A DS+
Sbjct: 20 QALKKLQASLKLYADDSA 37
Score = 28.0 bits (61), Expect = 3.0
Identities = 7/36 (19%), Positives = 16/36 (44%), Gaps = 11/36 (30%)
Query: 183 QNVNKVETAVRITHIPTGVTVRCTEERSQLANKIKA 218
Q + K++ ++++ + + LA IKA
Sbjct: 20 QALKKLQASLKL-YAD--------DSAPALA--IKA 44
>3cmm_A Ubiquitin-activating enzyme E1 1; UBA1, protein turnover, ligase,
conformationa thioester, adenylation,
transthioesterification, ATP-bindin nucleotide-binding;
2.70A {Saccharomyces cerevisiae}
Length = 1015
Score = 30.6 bits (68), Expect = 0.69
Identities = 19/85 (22%), Positives = 38/85 (44%)
Query: 28 QQLEKELAELEMKAADSSFWDNRAEAQETLQALTDVKDKINLLTDFKTKMDDAVTIVKLT 87
+ L+++L+ E +D + +D A+ QAL + N +DA ++KL
Sbjct: 258 KSLKQQLSNPEFVFSDFAKFDRAAQLHLGFQALHQFAVRHNGELPRTMNDEDANELIKLV 317
Query: 88 EEMDSTDAGLLEEAASIIKELNKAL 112
++ +L E + ++L K L
Sbjct: 318 TDLSVQQPEVLGEGVDVNEDLIKEL 342
>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A
{Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20
c.37.1.20
Length = 854
Score = 30.6 bits (70), Expect = 0.77
Identities = 18/116 (15%), Positives = 44/116 (37%), Gaps = 33/116 (28%)
Query: 7 LRKDVEAAS-DRVEEIRASAGLQQLEKELAELEMKAAD-SSFWDNRAEAQETLQALTDVK 64
L+K+ + S +R L+ +E E+A+L + A + W+ +
Sbjct: 420 LKKEKDPDSQER---------LKAIEAEIAKLTEEIAKLRAEWERE-------------R 457
Query: 65 DKINLLTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAASI----IKELNKALDQFE 116
+ + L + + ++D+ + E + L AA + + +L ++
Sbjct: 458 EILRKLREAQHRLDEV----RREIE-LAERQYDLNRAAELRYGELPKLEAEVEALS 508
>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp
contractIle protein-transport protein complex; 24.00A
{Gallus gallus}
Length = 1080
Score = 30.5 bits (69), Expect = 0.85
Identities = 17/118 (14%), Positives = 38/118 (32%), Gaps = 12/118 (10%)
Query: 7 LRKDVEAASDRVEEIRASAGLQQLEKELAELEMKAADSSFWDNRAEAQETLQALTDVKDK 66
+K +++ +++ + + KE L K + + L ++
Sbjct: 919 YKKLHIGLENKIMQLQRK--IDEQNKEYKSLLEKMNNL-----EITYSTETEKLRSDVER 971
Query: 67 INLLTDFKTKMDDAVTIVKLTEEMDSTDAGL--LEEAASIIKELNKALDQFELTQLLS 122
+ + + + V L EE+ L + I+E E QL+S
Sbjct: 972 LRMSEEEAKNATNRVL--SLQEEIAKLRKELHQTQTEKKTIEEWADKYKH-ETEQLVS 1026
>3t6o_A Sulfate transporter/antisigma-factor antagonist S; structural
genomics, PSI-biology, midwest center for structu
genomics, MCSG; 2.10A {Planctomyces limnophilus}
Length = 121
Score = 28.9 bits (65), Expect = 0.99
Identities = 7/41 (17%), Positives = 14/41 (34%)
Query: 68 NLLTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAASIIKEL 108
N + D + + VT++ +E+ AS
Sbjct: 2 NAMADIRVTHEAQVTVISFPAVFQRLRETEVEQIASTFLAA 42
>2ka5_A Putative anti-sigma factor antagonist TM_1081; termotoga marithima,
phosphoprotein, structural GENO PSI-2, protein structure
initiative; NMR {Thermotoga maritima} PDB: 3f43_A*
Length = 125
Score = 28.4 bits (64), Expect = 1.3
Identities = 8/31 (25%), Positives = 16/31 (51%)
Query: 71 TDFKTKMDDAVTIVKLTEEMDSTDAGLLEEA 101
F K+ D V I+ +E++ +A L ++
Sbjct: 12 HMFPYKIVDDVVILMPNKELNIENAHLFKKW 42
>2asb_A Transcription elongation protein NUSA; protein-RNA complex,
transcription/RNA complex; 1.50A {Mycobacterium
tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB:
2atw_A
Length = 251
Score = 28.3 bits (64), Expect = 3.1
Identities = 10/28 (35%), Positives = 13/28 (46%), Gaps = 4/28 (14%)
Query: 158 EESMDVQIPEEDLEISFSRAGGKGGQNV 185
+ V +P+ L S A GK GQN
Sbjct: 183 ARAARVVVPDFQL----SLAIGKEGQNA 206
>1hh2_P NUSA, N utilization substance protein A; transcription regulation,
termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5
d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A
Length = 344
Score = 28.2 bits (64), Expect = 3.2
Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 4/28 (14%)
Query: 158 EESMDVQIPEEDLEISFSRAGGKGGQNV 185
++ V +P L S A GKGGQN
Sbjct: 302 NKAARVLVPPTQL----SLAIGKGGQNA 325
>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment
2, heavy meromyosin, essential light chain, motor
protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1
PDB: 3j04_A 3dtp_B 3dtp_A
Length = 1184
Score = 27.9 bits (62), Expect = 5.9
Identities = 23/124 (18%), Positives = 47/124 (37%), Gaps = 15/124 (12%)
Query: 6 NLRKDVEAASDRVEEIRA-----SAGLQQLEKELAELEMKAADSSFWDNRAEAQETLQAL 60
+ D+ D+ ++ + L LAE E KA + + N+ E+ +
Sbjct: 987 KMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESM-----I 1041
Query: 61 TDVKDKINLLTDFKTKMDDAVTIVKLTEEMDSTDAGLLEEAASIIKELNKALD--QFELT 118
++++ ++ K++ + KL E + E + I EL L + EL
Sbjct: 1042 SELEVRLKKEE--KSRQELEKIKRKLEGESSDLHE-QIAELQAQIAELKAQLAKKEEELQ 1098
Query: 119 QLLS 122
L+
Sbjct: 1099 AALA 1102
>1sbo_A Putative anti-sigma factor antagonist TM1442; open sandwich, JCSG,
structural genomics, joint center for structural
genomics, PSI; NMR {Thermotoga maritima} SCOP: c.13.2.1
PDB: 1t6r_A* 1vc1_A
Length = 110
Score = 26.4 bits (59), Expect = 6.3
Identities = 6/30 (20%), Positives = 14/30 (46%)
Query: 72 DFKTKMDDAVTIVKLTEEMDSTDAGLLEEA 101
D IV++ ++D+ ++ L+E
Sbjct: 5 KLDIVEQDDKAIVRVQGDIDAYNSSELKEQ 34
>1th8_B Anti-sigma F factor antagonist; SPOIIAB, SPOIIAA, anti-ANTI-sigma,
sporulation, serine kinase, transcription; HET: ADP;
2.40A {Geobacillus stearothermophilus} SCOP: c.13.2.1
PDB: 1thn_B* 1tid_B* 1til_B* 1auz_A 1buz_A
Length = 116
Score = 26.4 bits (59), Expect = 6.4
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 72 DFKTKMDDAVTIVKLTEEMDSTDAGLLEEA 101
++ V IV+L+ E+D A L E
Sbjct: 4 AIDLEVKQDVLIVRLSGELDHHTAEELREQ 33
>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology
domains., structural genomics, PSI, protein structure
initiative; 1.70A {Mycobacterium tuberculosis} SCOP:
b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1
Length = 366
Score = 27.2 bits (61), Expect = 8.5
Identities = 10/28 (35%), Positives = 13/28 (46%), Gaps = 4/28 (14%)
Query: 158 EESMDVQIPEEDLEISFSRAGGKGGQNV 185
+ V +P+ L S A GK GQN
Sbjct: 306 ARAARVVVPDFQL----SLAIGKEGQNA 329
>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding,
nucleotide-binding, phosphorylation, acetylation,
alternative splicing, coiled coil; HET: GDP GTP; 4.00A
{Homo sapiens}
Length = 427
Score = 27.0 bits (59), Expect = 9.4
Identities = 10/62 (16%), Positives = 25/62 (40%), Gaps = 5/62 (8%)
Query: 7 LRKDVEAASDRVEEIRASAGLQQLEKELAELEMKAADSSFWDNRAEAQETLQALTDVKDK 66
L+K + ++E+ + + L+ E+ + + + ++ Q L K+K
Sbjct: 371 LKKLHQDEKKKLEDKK-----KSLDDEVNAFKQRKTAAELLQSQGSQAGGSQTLKRDKEK 425
Query: 67 IN 68
N
Sbjct: 426 KN 427
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 0.341
Gapped
Lambda K H
0.267 0.0661 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,511,368
Number of extensions: 275384
Number of successful extensions: 715
Number of sequences better than 10.0: 1
Number of HSP's gapped: 695
Number of HSP's successfully gapped: 92
Length of query: 307
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 214
Effective length of database: 4,105,140
Effective search space: 878499960
Effective search space used: 878499960
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: 57 (25.9 bits)