RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4067
(1384 letters)
>4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B
2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B
Length = 1131
Score = 342 bits (878), Expect = 7e-99
Identities = 102/265 (38%), Positives = 160/265 (60%), Gaps = 2/265 (0%)
Query: 911 SPGLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTIRI 970
+ ++PYP HNQ+PRNTYQ AM KQA+G N Q R DT + L Y QRP+V+++ + I
Sbjct: 654 TASIIPYPEHNQSPRNTYQSAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQTRALDI 713
Query: 971 TNFHKLPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPNQTH 1030
+ PAG NA +AV+S++GY++ED++IMN++S++RG R +R +YP
Sbjct: 714 IGYTNRPAGNNAILAVISFTGYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEVKYPGGQE 773
Query: 1031 DRILGPLLEADTRKPVYRHRALDQDGIVAPGEQICERQVLVNKSMPTISVSAISMATPE- 1089
D+I+ P K +R L+ +G+V+P ++ VL+ K P + +PE
Sbjct: 774 DKIVMPEPGVRGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQ 833
Query: 1090 -YKEVPVSYKGSVPSYLEKVLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGL 1148
++ + + ++ VL++ +E L+K+ +R R P IGDKF+SRHGQKGVIG+
Sbjct: 834 AKRDTSIVTRHGEMGIVDLVLITETAEGNKLVKVRVRDLRIPSIGDKFASRHGQKGVIGM 893
Query: 1149 IVEQEDMPFNESGICPDIIMNPHGL 1173
++ Q DMP+ G+ PD+I+NPH L
Sbjct: 894 LIPQVDMPYTVKGVVPDVILNPHAL 918
Score = 322 bits (828), Expect = 3e-92
Identities = 87/203 (42%), Positives = 128/203 (63%), Gaps = 1/203 (0%)
Query: 1169 NPHGLKGCDRITEYKEVPVSYKGSVPSYLEKVLVSSNSEDAFLIKMLLRQTRRPEIGDKF 1228
K ++ + + ++ VL++ +E L+K+ +R R P IGDKF
Sbjct: 822 FLQEFKELSPEQAKRDTSIVTRHGEMGIVDLVLITETAEGNKLVKVRVRDLRIPSIGDKF 881
Query: 1229 SSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGYPSRMTVGKLIELLAGKAGLMEGN 1288
+SRHGQKGVIG+++ Q DMP+ G+ PD+I+NPH PSRMT+G+++E +AGK + GN
Sbjct: 882 ASRHGQKGVIGMLIPQVDMPYTVKGVVPDVILNPHALPSRMTLGQIMEGIAGKYAALSGN 941
Query: 1289 YKEGTAFGGTKLVDVQEELIRHGYNYQGKDIFYSGITGEALEAYIYSGPVYYQKLKHMVQ 1348
+ T F T + +Q E++++GY ++ Y G TG+ +++ IY G VYYQKL HMV
Sbjct: 942 IVDATPFYKTPIEQLQNEILKYGYLPDATEVTYDGRTGQKIKSRIYFGVVYYQKLHHMVA 1001
Query: 1349 DKIHARSRGPRVVLTRQPT-GRR 1370
DKIHAR+RGP +LTRQPT GR
Sbjct: 1002 DKIHARARGPVQILTRQPTEGRA 1024
Score = 167 bits (425), Expect = 4e-42
Identities = 53/178 (29%), Positives = 83/178 (46%), Gaps = 14/178 (7%)
Query: 173 IADKIIPKIKAAQFDIVNHMRQDTITNALTAAIQTGNWTIRRFKMERQGVTQVLSRLSYI 232
+K + + + + +R D +T + A+ TGNW R GV+Q+L R +++
Sbjct: 371 QLEKSKVRGR--KLALKALVRPDIVTERIRHALATGNWV-----GGRTGVSQLLDRTNWL 423
Query: 233 SGLGMMTRINSQFEKTRKVSGPRSLQGSQWGMLCPSDTPEGEACGLVKNLALMTHITTEN 292
S L + R+ S + + R L G+QWG +CP +TPEG GLVKNLALM I
Sbjct: 424 SMLSHLRRVISSLARGQPNFEARDLHGTQWGRMCPFETPEGPNSGLVKNLALMAQIAVGI 483
Query: 293 DEKNMLKIMYNIGIEHIAMFNGEEL-------SSPGVYLVFVNGILAGITCHHKEVCK 343
+EK + K +Y +G+ + V +NG L G +E+ K
Sbjct: 484 NEKIVEKTLYEMGVVPVEEVIRRVTEGGEDQNEYLKWSKVILNGRLVGYYRDGEELAK 541
Score = 138 bits (349), Expect = 5e-33
Identities = 57/135 (42%), Positives = 77/135 (57%), Gaps = 15/135 (11%)
Query: 688 GFKRFDDFLYEGKIEYLDVNEGNDSHIAVSESGIRPGVTTHLEIAPFTLLGVCAGIELLQ 747
G FDD + +GKIEYLD E ++++A+ S + P THLEI +LG+ A I
Sbjct: 603 GSITFDDLVRQGKIEYLDAEEEENAYVALEPSDLTP-EHTHLEIWSPAILGITASI---- 657
Query: 748 YNKRFHSPGLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVE 807
+PYP HNQ+PRNTYQ AM KQA+G N Q R DT + L Y QRP+V+
Sbjct: 658 ----------IPYPEHNQSPRNTYQSAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQ 707
Query: 808 SKTIRITNFHKLPAG 822
++ + I + PAG
Sbjct: 708 TRALDIIGYTNRPAG 722
Score = 108 bits (270), Expect = 1e-23
Identities = 28/112 (25%), Positives = 48/112 (42%), Gaps = 11/112 (9%)
Query: 301 MYNIGIEHIAMFNGE-ELSSPGVYLVFVNGILAGITCHHKEVCKPEIEESFNYTRQTTPH 359
++ I GE PG+ + + KP + ES R+ +P
Sbjct: 37 FVRNKLQEIIDEQGEIPTEIPGLKVRLGKI----------RIGKPRVRESDRGEREISPM 86
Query: 360 ECRLRDLTYSAPITVDIEYTRGSQRVVRSDLVIGRMPIMLQSSKCVLRNKTE 411
E RLR+LTY+AP+ + + + ++ IG +PIML+S+ + T
Sbjct: 87 EARLRNLTYAAPLWLTMIPVENNIEAEPEEVYIGDLPIMLKSAIDPISQYTL 138
Score = 98.4 bits (245), Expect = 1e-20
Identities = 25/90 (27%), Positives = 42/90 (46%)
Query: 444 RFQTYKKTPVDDARDFLSSTCIAHIPVINMRFKMKAMYLAVMIRRMVLALSDPDMLDDRD 503
++ ++ A+ + + H+ + KA YLA I +++ DD+D
Sbjct: 280 AIGQKRENRIEKAQQIIDKYFLPHLGTSADDRRKKAYYLAYAISKVIELYLGRREPDDKD 339
Query: 504 YYGNKRLELAGSLLSLMFEDVFKRFNSELK 533
+Y NKRL LAG L + +F FK F +L
Sbjct: 340 HYANKRLRLAGDLFASLFRVAFKAFVKDLT 369
Score = 89.1 bits (221), Expect = 7e-18
Identities = 17/69 (24%), Positives = 43/69 (62%), Gaps = 1/69 (1%)
Query: 104 SKLKDSPEIRDKWKLVLSFLKEKGLVKPHIDSFDYFINVEIKKLMQANANIYSDVDPLFY 163
++L + I ++WK++ ++ K KGLV+ H+DS++ F+ ++++++ I +++ P
Sbjct: 2 NELSSNLSIDERWKVIEAYFKSKGLVRQHLDSYNDFVRNKLQEIIDEQGEIPTEI-PGLK 60
Query: 164 LKYLDIHVG 172
++ I +G
Sbjct: 61 VRLGKIRIG 69
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1210
Score = 336 bits (862), Expect = 3e-96
Identities = 103/268 (38%), Positives = 157/268 (58%), Gaps = 3/268 (1%)
Query: 909 FHSPGLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTI 968
++P+P HNQ+PRNTYQ AMGKQAMG N Q R+DT+ L Y Q+P+ ++++
Sbjct: 739 GILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDTMANILYYPQKPLATTRSM 798
Query: 969 RITNFHKLPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPNQ 1028
F +LPAGQNA +A++ YSGY+ ED++IMN+AS+DRG R + YR K+
Sbjct: 799 EYLKFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFRSIFYRTYTDQEKKIGMT 858
Query: 1029 THDRILGPLLEADTRKPVYRHRALDQDGIVAPGEQICERQVLVNKSMPTI---SVSAISM 1085
+ P+ R + L+ DG++APG ++ +++ K+ P
Sbjct: 859 VMEEFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDIIIGKTAPIPLDHEELGQRT 918
Query: 1086 ATPEYKEVPVSYKGSVPSYLEKVLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGV 1145
++V + + +++V+V++N E +K+ +R TR P+IGDKF+SRHGQKG
Sbjct: 919 QLHAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRSTRIPQIGDKFASRHGQKGT 978
Query: 1146 IGLIVEQEDMPFNESGICPDIIMNPHGL 1173
IG+ EDMPF+ GI PDII+NPH +
Sbjct: 979 IGMTYRHEDMPFSAQGIVPDIIINPHAI 1006
Score = 313 bits (803), Expect = 1e-88
Identities = 86/190 (45%), Positives = 119/190 (62%), Gaps = 1/190 (0%)
Query: 1182 YKEVPVSYKGSVPSYLEKVLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGLI 1241
++V + + +++V+V++N E +K+ +R TR P+IGDKF+SRHGQKG IG+
Sbjct: 923 KRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRSTRIPQIGDKFASRHGQKGTIGMT 982
Query: 1242 VEQEDMPFNESGICPDIIMNPHGYPSRMTVGKLIELLAGKAGLMEGNYKEGTAFGGTKLV 1301
EDMPF+ GI PDII+NPH PSRMTV L+E K + G + T F +
Sbjct: 983 YRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKVSALSGFEGDATPFTDVTVE 1042
Query: 1302 DVQEELIRHGYNYQGKDIFYSGITGEALEAYIYSGPVYYQKLKHMVQDKIHARSRGPRVV 1361
V + L HG+ +G ++ Y G TG L A ++ GP YYQ+LKH+V DKIHAR+RGP +
Sbjct: 1043 AVSKLLRSHGFQSRGFEVMYHGHTGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQI 1102
Query: 1362 LTRQPT-GRR 1370
LTRQP GR
Sbjct: 1103 LTRQPVEGRS 1112
Score = 204 bits (521), Expect = 2e-53
Identities = 55/172 (31%), Positives = 98/172 (56%), Gaps = 5/172 (2%)
Query: 173 IADKIIPKIKAAQFDIVNHMRQDTITNALTAAIQTGNW-TIRRFKMERQGVTQVLSRLSY 231
K + + +F++ ++ + ITN L ++ TGNW +R + R GV+QVL+R ++
Sbjct: 417 YMQKCVETNR--EFNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTF 474
Query: 232 ISGLGMMTRINSQFEKTRKVSGPRSLQGSQWGMLCPSDTPEGEACGLVKNLALMTHITTE 291
S L + R N+ + K++ PR L + WGM+CP++TPEG+ACGLVKNL+LM++++
Sbjct: 475 ASTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVG 534
Query: 292 NDEKNMLKIMYNIGIEHIAMFNGEELSSPGVYLVFVNGILAGITCHHKEVCK 343
+ +++ + G+E + +N P VFVNG+ G+ + +
Sbjct: 535 SPSAPIIEFLEEWGLETLEDYNPSAS--PNATKVFVNGVWLGVHRDPAHLTE 584
Score = 119 bits (299), Expect = 4e-27
Identities = 29/96 (30%), Positives = 48/96 (50%), Gaps = 2/96 (2%)
Query: 438 KKLRQKRFQTYKKTPVDDARDFLSSTCIAHIPVINMRFKMKAMYLAVMIRRMVLALSDPD 497
K+ ++ + A D L + HI + KA +L MI RM+L +
Sbjct: 322 KRGSTTGVT--REKRLRYAHDILQKELLPHITTMEGFETRKAFFLGYMIHRMLLCALERR 379
Query: 498 MLDDRDYYGNKRLELAGSLLSLMFEDVFKRFNSELK 533
DDRD++G KRL+LAG LL+ +F +F++ ++
Sbjct: 380 EPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVY 415
Score = 103 bits (258), Expect = 3e-22
Identities = 52/159 (32%), Positives = 70/159 (44%), Gaps = 42/159 (26%)
Query: 692 FDDFLYEGKIEYLDVNEGNDSHIAVSESGIRPG--------------------------- 724
+ + G IEYLD E IA+S +
Sbjct: 665 WTALVSSGLIEYLDAEEEETVMIAMSPEDLEASRQMQAGYEVKEELDPAQRVKPAPNPHV 724
Query: 725 -VTTHLEIAPFTLLGVCAGIELLQYNKRFHSPGLVPYPHHNQAPRNTYQCAMGKQAMGCI 783
TH EI P +LG+ A I +P+P HNQ+PRNTYQ AMGKQAMG
Sbjct: 725 HAWTHCEIHPAMILGILASI--------------IPFPDHNQSPRNTYQSAMGKQAMGVY 770
Query: 784 GYNQQNRIDTLMYNLVYAQRPMVESKTIRITNFHKLPAG 822
N Q R+DT+ L Y Q+P+ ++++ F +LPAG
Sbjct: 771 LTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRELPAG 809
Score = 102 bits (256), Expect = 6e-22
Identities = 31/139 (22%), Positives = 58/139 (41%), Gaps = 28/139 (20%)
Query: 291 ENDEKNMLKIMYNIGIEHIAMFNGEELSS-PGVYLVFVNGILAGITCHHKEVCKPEIEES 349
+N + ++ + ++ A G + + F I + +P + E+
Sbjct: 43 QNTMQEIVDDDSTLTLDQYAQHTGAQGDVTRRYEINFGQ-----I-----YLSRPTMTEA 92
Query: 350 FNYTRQTTPHECRLRDLTYSAPITVDI-----------------EYTRGSQRVVRSDLVI 392
T P E RLR+LTYS+P+ VD+ E+ + S + I
Sbjct: 93 DGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAADSNVPIGEEEWLVEEEDEEPSKVFI 152
Query: 393 GRMPIMLQSSKCVLRNKTE 411
G++PIML+S+ C+L ++
Sbjct: 153 GKIPIMLRSTFCILNGVSD 171
Score = 89.2 bits (221), Expect = 7e-18
Identities = 14/85 (16%), Positives = 38/85 (44%), Gaps = 11/85 (12%)
Query: 99 VTDETSKLKDSPEIRDKWKLVLSFLKEKGLVKPHIDSFDYFINVEIKKLMQANANI---- 154
++ E + ++ D W ++ SF +E L + + SFD F+ +++++ ++ +
Sbjct: 1 MSYEDYQYNETLTQEDCWTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQ 60
Query: 155 -------YSDVDPLFYLKYLDIHVG 172
DV + + + I++
Sbjct: 61 YAQHTGAQGDVTRRYEINFGQIYLS 85
>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B
1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B*
1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B*
1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ...
Length = 1224
Score = 333 bits (856), Expect = 3e-95
Identities = 102/268 (38%), Positives = 156/268 (58%), Gaps = 3/268 (1%)
Query: 909 FHSPGLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESKTI 968
+ ++P+P HNQ+PRNTYQ AMGKQAMG N R+DT+ L Y Q+P+ ++ +
Sbjct: 750 GVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAM 809
Query: 969 RITNFHKLPAGQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPNQ 1028
F +LPAGQNA +A+ YSGY+ ED++IMN++S+DRG R L +R+ K+Y
Sbjct: 810 EYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMS 869
Query: 1029 THDRILGPLLEADTRKPVYRHRALDQDGIVAPGEQICERQVLVNKSMPTI---SVSAISM 1085
+ P R + LD DG++APG ++ V++ K+ P
Sbjct: 870 ITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRT 929
Query: 1086 ATPEYKEVPVSYKGSVPSYLEKVLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGV 1145
A ++ + + +++VLV++N + +K+ +R T+ P+IGDKF+SRHGQKG
Sbjct: 930 AYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGT 989
Query: 1146 IGLIVEQEDMPFNESGICPDIIMNPHGL 1173
IG+ +EDMPF GI PD+I+NPH +
Sbjct: 990 IGITYRREDMPFTAEGIVPDLIINPHAI 1017
Score = 316 bits (811), Expect = 2e-89
Identities = 94/226 (41%), Positives = 132/226 (58%), Gaps = 4/226 (1%)
Query: 1146 IGLIVEQEDMPFNESGICPDIIMNPHGLKGCDRITEYKEVPVSYKGSVPSYLEKVLVSSN 1205
G+ V ED+ G I + L ++ + + +++VLV++N
Sbjct: 901 PGVRVSGEDVII---GKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTN 957
Query: 1206 SEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGY 1265
+ +K+ +R T+ P+IGDKF+SRHGQKG IG+ +EDMPF GI PD+I+NPH
Sbjct: 958 QDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAI 1017
Query: 1266 PSRMTVGKLIELLAGKAGLMEGNYKEGTAFGGTKLVDVQEELIRHGYNYQGKDIFYSGIT 1325
PSRMTV LIE L K + GN + + F + + + L HGY +G ++ Y+G T
Sbjct: 1018 PSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHT 1077
Query: 1326 GEALEAYIYSGPVYYQKLKHMVQDKIHARSRGPRVVLTRQPT-GRR 1370
G+ L A I+ GP YYQ+L+HMV DKIHAR+RGP VLTRQP GR
Sbjct: 1078 GKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRS 1123
Score = 201 bits (513), Expect = 2e-52
Identities = 57/172 (33%), Positives = 96/172 (55%), Gaps = 5/172 (2%)
Query: 173 IADKIIPKIKAAQFDIVNHMRQDTITNALTAAIQTGNWTIRRFKME-RQGVTQVLSRLSY 231
+ + + F++ + TIT+ L A+ TGNW ++ M R GV+QVL+R +Y
Sbjct: 431 YMQRTVEEAH--DFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTY 488
Query: 232 ISGLGMMTRINSQFEKTRKVSGPRSLQGSQWGMLCPSDTPEGEACGLVKNLALMTHITTE 291
S L + R N+ + K++ PR L + WG++CP++TPEG+ACGLVKNL+LM+ I+
Sbjct: 489 SSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVG 548
Query: 292 NDEKNMLKIMYNIGIEHIAMFNGEELSSPGVYLVFVNGILAGITCHHKEVCK 343
D ++ + G+E + + + SP VFVNG+ G+ + + +
Sbjct: 549 TDPMPIITFLSEWGMEPLEDYVPHQ--SPDATRVFVNGVWHGVHRNPARLME 598
Score = 121 bits (304), Expect = 1e-27
Identities = 31/93 (33%), Positives = 49/93 (52%)
Query: 441 RQKRFQTYKKTPVDDARDFLSSTCIAHIPVINMRFKMKAMYLAVMIRRMVLALSDPDMLD 500
R K+ + A+D L + HI + KA +L MI R++L D D
Sbjct: 337 RGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQD 396
Query: 501 DRDYYGNKRLELAGSLLSLMFEDVFKRFNSELK 533
DRD++G KRL+LAG LL+ +F+ +FK+ ++
Sbjct: 397 DRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIF 429
Score = 104 bits (260), Expect = 2e-22
Identities = 52/155 (33%), Positives = 69/155 (44%), Gaps = 37/155 (23%)
Query: 691 RFDDFLYEGKIEYLDVNEGNDSHIAVSESGIRPGVT-----------------------T 727
+ L EG +EY+D E IA+ + P T
Sbjct: 680 TWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFT 739
Query: 728 HLEIAPFTLLGVCAGIELLQYNKRFHSPGLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQ 787
H EI P +LGV A I +P+P HNQ+PRNTYQ AMGKQAMG N
Sbjct: 740 HCEIHPSMILGVAASI--------------IPFPDHNQSPRNTYQSAMGKQAMGVFLTNY 785
Query: 788 QNRIDTLMYNLVYAQRPMVESKTIRITNFHKLPAG 822
R+DT+ L Y Q+P+ ++ + F +LPAG
Sbjct: 786 NVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAG 820
Score = 101 bits (252), Expect = 1e-21
Identities = 36/141 (25%), Positives = 55/141 (39%), Gaps = 30/141 (21%)
Query: 291 ENDEKNMLKIMYNIGIEHIAMFNGEELS-SPGVYLVFVNGILAGITCHHKEVCKPEIEES 349
+ ++++ + +E +A E + S + F I V KP + ES
Sbjct: 56 DYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGK-----IY-----VTKPMVNES 105
Query: 350 FNYTRQTTPHECRLRDLTYSAPITVDIEYTRGSQRVVRS-------------------DL 390
T P E RLR+LTYS+ + VD++ V +
Sbjct: 106 DGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKV 165
Query: 391 VIGRMPIMLQSSKCVLRNKTE 411
IGR+PIML+S C L TE
Sbjct: 166 FIGRLPIMLRSKNCYLSEATE 186
Score = 88.0 bits (218), Expect = 1e-17
Identities = 17/85 (20%), Positives = 39/85 (45%), Gaps = 13/85 (15%)
Query: 101 DETSKLKDSPEI--RDKWKLVLSFLKEKGLVKPHIDSFDYFINVEIKKLMQANANI---- 154
D +S I D W ++ +F +EKGLV +DSF+ F++ ++ ++ ++ +
Sbjct: 14 DPYGFEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQ 73
Query: 155 -------YSDVDPLFYLKYLDIHVG 172
++ + + + I+V
Sbjct: 74 LAQHTTESDNISRKYEISFGKIYVT 98
>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1
PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C*
2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C*
3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ...
Length = 1119
Score = 128 bits (323), Expect = 7e-30
Identities = 65/203 (32%), Positives = 97/203 (47%), Gaps = 43/203 (21%)
Query: 1211 LIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGYPSRMT 1270
++++ + Q R+ ++GDK ++RHG KGV+ I+ EDMP G D+I+NP G PSRM
Sbjct: 822 VVRVYVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMN 881
Query: 1271 VGKLIELLAGKAGLMEGNYKEGTAFGGTKLVDVQEELIR--------------------- 1309
+G+++E G AG G F G K +++E L +
Sbjct: 882 LGQILETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREV 941
Query: 1310 ----------------------HGYNYQGKDIFYSGITGEALEAYIYSGPVYYQKLKHMV 1347
QGK + Y G TGE +E I G ++ KL HMV
Sbjct: 942 EVLRRAEKLGLVTPGKTPEEQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMV 1001
Query: 1348 QDKIHARSRGPRVVLTRQPTGRR 1370
+DK+HARS GP ++T+QP G +
Sbjct: 1002 EDKMHARSTGPYSLITQQPLGGK 1024
Score = 84.7 bits (210), Expect = 1e-16
Identities = 62/228 (27%), Positives = 100/228 (43%), Gaps = 55/228 (24%)
Query: 979 GQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVL-----KQYPNQTHDRI 1033
GQN +A+M + GY+ EDA+++++ L+ R+ ++Y + D
Sbjct: 669 GQNVLVAIMPFDGYNFEDAIVISE---------ELLKRD---FYTSIHIERYEIEARDTK 716
Query: 1034 LGPLLEADTRK-P-VYRH--RALDQDGIVAPGEQICERQVLVNKSMPTISVSAISMATPE 1089
LGP E TR P + R LD++G+V G ++ +LV + S S TPE
Sbjct: 717 LGP--ERITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGR----TSFKGESEPTPE 770
Query: 1090 YK------------------EVPVSYKGSVPSYLEKVLVSSNSEDAFL-------IKMLL 1124
+ VP G V + V + L +++ +
Sbjct: 771 ERLLRSIFGEKARDVKDTSLRVPPGEGGIV---VRTVRLRRGDPGVELKPGVREVVRVYV 827
Query: 1125 RQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHG 1172
Q R+ ++GDK ++RHG KGV+ I+ EDMP G D+I+NP G
Sbjct: 828 AQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLG 875
Score = 40.7 bits (96), Expect = 0.004
Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 357 TPHECRLRDLTYSAPITVDIEYTRGSQRVVRSDLV-IGRMPIM 398
ECR +DLTY AP+ ++ +++ D V +G +P+M
Sbjct: 79 PQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHIPLM 121
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase,
nucleotidyltransferase, transcription, transferase;
11.20A {Escherichia coli} PDB: 3iyd_C*
Length = 1342
Score = 110 bits (277), Expect = 2e-24
Identities = 106/489 (21%), Positives = 179/489 (36%), Gaps = 124/489 (25%)
Query: 979 GQNATIAVMSYSGYDIEDALIMNKASLDRGFGRCLVYRN--SKCVLKQYPNQTHDRILGP 1036
GQN +A M ++GY+ ED++++++ +V + + +++ + D LGP
Sbjct: 797 GQNMRVAFMPWNGYNFEDSILVSER---------VVQEDRFTTIHIQELACVSRDTKLGP 847
Query: 1037 LLEADTR------KPVYRHRALDQDGIVAPGEQICERQVLVNKSMPTISVSAISMATPEY 1090
E T + LD+ GIV G ++ +LV K P + TPE
Sbjct: 848 --EEITADIPNVGEAALSK--LDESGIVYIGAEVTGGDILVGKVTP----KGETQLTPEE 899
Query: 1091 K------------------EVPVSYKGSV----------PSYLEKVLVSSNSEDAFLIKM 1122
K VP G+V ++ L + K
Sbjct: 900 KLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKD 959
Query: 1123 LLRQTRRPEIGDKFSSRHGQKGVIGLIVEQEDMPFNESGICPDIIMNPHGLKGCDRITEY 1182
L + + I + + ++ VE E + ++ + ++ +
Sbjct: 960 LSEELQ---ILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDE-----EKQNQL 1011
Query: 1183 KEVPVSYKGSVPS----YLEKVLVSSNSEDA-----FLIKMLLRQTRRPEIGDKFSSRHG 1233
+++ Y K + +D ++K+ L RR + GDK + RHG
Sbjct: 1012 EQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHG 1071
Query: 1234 QKGVIGLIVEQEDMPFNESGICPDIIMNPHGYPSRMTVGKLIELLAGKAGLMEGNYKEGT 1293
KGVI I EDMP++E+G DI++NP G PSRM +G+++E G A G+
Sbjct: 1072 NKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAM 1131
Query: 1294 AFGGTKLVDVQEEL--IRHGYNYQGKDIFYSGITGE----------------------AL 1329
++ ++E + + + S + E A
Sbjct: 1132 LKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAK 1191
Query: 1330 EAYI-----------------YSG--------PV-----YYQKLKHMVQDKIHARSRGPR 1359
EA I Y G PV Y KL H+V DK+HARS G
Sbjct: 1192 EAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSY 1251
Query: 1360 VVLTRQPTG 1368
++T+QP G
Sbjct: 1252 SLVTQQPLG 1260
Score = 38.9 bits (91), Expect = 0.014
Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 8/50 (16%)
Query: 357 TPHECRLRDLTYSAPITV-------DIEYTRGSQRVVRSDLV-IGRMPIM 398
EC++R +TYSAP+ V + E G+ + ++ V +G +P+M
Sbjct: 81 DVQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQEVYMGEIPLM 130
Score = 34.7 bits (80), Expect = 0.31
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 228 RLSYISGLGMMTRINSQFEKTRKVSGPRSLQGSQWGMLCPSDTPEGEACGLVKNLALMTH 287
R+S + G G +TR + FE R + + +G +CP +TPEG GL+ +L++
Sbjct: 529 RISAL-GPGGLTRERAGFEV-------RDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ 580
Query: 288 I 288
Sbjct: 581 T 581
>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 = 65.8 bits (160), Expect = 1e-10
Identities = 119/662 (17%), Positives = 204/662 (30%), Gaps = 202/662 (30%)
Query: 60 VSLREL-LSHVTYQKRLYRLTVQPNWLGTVKAVHGTYL-----TMVTDETSKLKDSPEIR 113
S R L LSH + + + L V P T + L ++ + T E
Sbjct: 4 YSTRPLTLSHGSLE---HVLLV-P----TASFFIASQLQEQFNKILPEPTEGFAADDEPT 55
Query: 114 DKWKLVLSFLKEKGLVKPHIDSFDYFINVEIKKLMQANANIYSDVDPL----F---YLKY 166
+LV FL +++ ++ + + V L F YL+
Sbjct: 56 TPAELVGKFLG--------------YVSSLVE---PSKVGQFDQVLNLCLTEFENCYLEG 98
Query: 167 LDIH------VGIADKIIPKIK-------AAQFDIVNHMRQDTITNALTAAIQTGN---W 210
DIH + D + K K A+ + +AL A+ GN
Sbjct: 99 NDIHALAAKLLQENDTTLVKTKELIKNYITARI-MAKRPFDKKSNSALFRAVGEGNAQLV 157
Query: 211 TIRRF--KMERQGVTQVLSRLSYISGLGMMTRINSQFEKTRKVSGPRSLQGSQWGMLCPS 268
I F QG T Y L R L
Sbjct: 158 AI--FGG----QGNTDD-----YFEEL-------------------RDLY---------- 177
Query: 269 DTPEGEACGLVKNLA--LMTHITTENDEKNMLKIMYNIGIEHIAMFNGEELSSPGV-YL- 324
T L+K A L I T D + + + G+ + ++P YL
Sbjct: 178 QTYHVLVGDLIKFSAETLSELIRTTLDAEKV----FTQGLNILEWLENPS-NTPDKDYLL 232
Query: 325 -VFVNGILAGIT--CHHKEVCK-----PEIEESFNYTRQTTPHECRLRDLTYSAPI---- 372
+ ++ L G+ H+ K P E +Y + T H + L + I
Sbjct: 233 SIPISCPLIGVIQLAHYVVTAKLLGFTPG--ELRSYLKGATGH---SQGLVTAVAIAETD 287
Query: 373 TVDIEYTRGSQRVVRSDLVIGRMPIMLQSSKCVLRNKTEYTSSSRRAST--SSVTMHSQR 430
+ + + ++ + IG +R Y ++S S S+ +
Sbjct: 288 SWE-SFFVSVRKAITVLFFIG------------VRCYEAYPNTSLPPSILEDSLENNEGV 334
Query: 431 TSPLLSCKKLRQKRFQTYKKTPVDDARDFLSSTCIAHIPVINMRFKM------KAMY-LA 483
SP+LS L Q++ Q Y V+ L + I ++N + +++Y L
Sbjct: 335 PSPMLSISNLTQEQVQDY----VNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLN 390
Query: 484 VMIRRMVLALSDPDMLD-DRDYYGNKRLELAGSLLSLMFEDVFKRFNSELKETNLSGVVN 542
+ +R+ P LD R + ++L+ S F V F+S L L +
Sbjct: 391 LTLRK----AKAPSGLDQSRIPFSERKLK-----FSNRFLPVASPFHSHL----LVPASD 437
Query: 543 LVSGWWFELKYGNKIYIRSPSRKLLAAGFSGPHSGRVRLMPEGPTILLNSCLRSGGKAQH 602
L++ +L N + ++ + + G LR +
Sbjct: 438 LINK---DLVKNN---VSFNAKDIQIPVYD-TFDGSD--------------LRVLSGSIS 476
Query: 603 EALYNAVQRH------ATKCCTLNFLFFLGGGGILPSIQRQTTCLLTLILFSLNGDGKRG 656
E + + + R T+ + L F G G + L N DG G
Sbjct: 477 ERIVDCIIRLPVKWETTTQFKATHILDF--GPGGASGLGV---------LTHRNKDG-TG 524
Query: 657 AR 658
R
Sbjct: 525 VR 526
Score = 62.0 bits (150), Expect = 2e-09
Identities = 90/591 (15%), Positives = 166/591 (28%), Gaps = 192/591 (32%)
Query: 315 EELSSP----GVYLVFVNGIL-AGITCHHKEVCKPEIEESF--NYTRQTTPHECRLRDLT 367
+E ++P G +L +V+ ++ +V + E F Y H L
Sbjct: 52 DEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTE-FENCYLEGNDIH-----ALA 105
Query: 368 YSAPITVDIEYTRGSQRVVRSDLVIGRMPIMLQSSKCVLRNKTEYTSSS--RRASTSSVT 425
D + ++ ++++ + + R + ++S+ R +
Sbjct: 106 AKLLQENDTTLVK-TKELIKN---------YITARIMAKRPFDKKSNSALFRAVGEGNAQ 155
Query: 426 MHSQ------RTSPLLSCKKLRQKRFQTYKKTPVDDARDFLSSTCIAHIPVINMRFKMKA 479
+ + ++LR +QTY V D F + T +I +
Sbjct: 156 LVAIFGGQGNTDDYF---EELR-DLYQTYH-VLVGDLIKFSAETLS---ELIRTTLDAEK 207
Query: 480 MYLAVM-IRRMVLALSDPDMLDDRDYYGNKRLELAGSLLSLMFEDVFKRFNSELKETNLS 538
++ + I L +P D+DY L +S L
Sbjct: 208 VFTQGLNILE---WLENPSNTPDKDY-------LLSIPISC----------------PLI 241
Query: 539 GVVNLVSGWWFELKYGNKIYIRSPSRKLLAAGFSGPHSGRVRLMPEGPT-----ILLNSC 593
GV+ L Y+ + KLL G G +R +G T ++
Sbjct: 242 GVIQLAH------------YVVT--AKLL-----GFTPGELRSYLKGATGHSQGLVTAVA 282
Query: 594 LRSGGKAQHEALYNAVQRHATKCCTLNFLFFLGGGGILPSIQRQTTCLLTLILFSLNGDG 653
+ E+ + +V++ + LFF+G C SL
Sbjct: 283 IAETDSW--ESFFVSVRK------AITVLFFIG-----------VRCYEAYPNTSLP--- 320
Query: 654 KRGARNSQQYCDCPDGYSSGCQPRPTFLNMHQFLGFKRFDDFLYEGKIEYLDVNEGNDSH 713
+ + +G P P M L + + + +
Sbjct: 321 ---PSILEDSLENNEG-----VPSP----M---LSISNLTQEQVQDYVNKTNSHLPAGKQ 365
Query: 714 IAVSE---------SGIRP-----GVTTHLEIAPFTLLGVCAGIELLQ----YNKR---- 751
+ +S SG P G+ L A L Q +++R
Sbjct: 366 VEISLVNGAKNLVVSG--PPQSLYGLNLTLR-------KAKAPSGLDQSRIPFSERKLKF 416
Query: 752 ----------FHSPGLVPYPHHNQAPRNTYQCAMGKQAMGC------IGYNQQNRIDTLM 795
FHS LVP + + + G + + ++
Sbjct: 417 SNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSIS 476
Query: 796 YNLVYAQRPMVESKTI---RITNF---HKLPAGKCQISPGGA---EELTAR 837
+V + + T F H L G PGGA LT R
Sbjct: 477 ERIV----DCIIRLPVKWETTTQFKATHILDFG-----PGGASGLGVLTHR 518
Score = 61.2 bits (148), Expect = 2e-09
Identities = 96/535 (17%), Positives = 158/535 (29%), Gaps = 207/535 (38%)
Query: 47 PLFKQVDFGDSKVVS--------------LRELLSHVTYQKRLYRLTVQPNWLGTVKAVH 92
LF+ V G++++V+ LR+L YQ Y + V +K
Sbjct: 144 ALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDL-----YQ--TYHVLVGD----LIKFSA 192
Query: 93 GTYLTMVTDETSKLKDSPEIRDKWKLVLSFLKEKGLVKPHIDSFDYFINVEIK----KLM 148
T ++ K + + +L +L+ P DY +++ I ++
Sbjct: 193 ETLSELIRTTLDAEKVFTQGLN----ILEWLENPS-NTP---DKDYLLSIPISCPLIGVI 244
Query: 149 QANANIYSDVDPLFYLKYLDIHVGIADKIIPKIKAAQFDIVNHMRQDTITNALTAAIQTG 208
Q A+ Y + K L G ++ +K A H Q +T A T
Sbjct: 245 QL-AH-Y-----VVTAKLLGFTPG---ELRSYLKGA----TGHS-QGLVTAVAIAE--TD 287
Query: 209 NWTIRRFKMERQGVTQVLSRLSYISGLGMMTRINSQFEKTRKVSGPRSLQGSQWGMLCPS 268
+W F V + ++ L +I G R + L PS
Sbjct: 288 SW--ESF---FVSVRKAITVLFFI--------------------GVRCYEAYPNTSLPPS 322
Query: 269 DTPEGEACGLVKNLALMTHITTENDEKN---MLKIMYNIGI------EHIAMFNGEELSS 319
+ + EN+E ML I + +++ N +
Sbjct: 323 ----------------ILEDSLENNEGVPSPMLSI---SNLTQEQVQDYVNKTNSHLPAG 363
Query: 320 PGVYLVFVNG----ILAGITCHHKEVCKPEIEESFNYTRQTTPHECRLRDLTYSAPITVD 375
V + VNG +++G P+ N LR AP +D
Sbjct: 364 KQVEISLVNGAKNLVVSG---------PPQSLYGLN---------LTLRKA--KAPSGLD 403
Query: 376 IEYTRGSQRVVRSDLVIGR-MPIMLQSSKCVLRNKTEYTSSSRRASTSSVTMHSQRTSPL 434
S+R ++ R +P+ + H S L
Sbjct: 404 QSRIPFSERKLK---FSNRFLPV-------------------------ASPFH----SHL 431
Query: 435 L-SCKKLRQKRFQTYK--------KTPV---DDARDF--LSST-------CIAHIPV--- 470
L L K + PV D D LS + CI +PV
Sbjct: 432 LVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWE 491
Query: 471 INMRFKM---------KAMYLAVMIR--------RMVLALSDPDMLDDRDYYGNK 508
+FK A L V+ R+++A D+ D D YG K
Sbjct: 492 TTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVRVIVA-GTLDINPDDD-YGFK 544
Score = 61.2 bits (148), Expect = 3e-09
Identities = 99/557 (17%), Positives = 159/557 (28%), Gaps = 200/557 (35%)
Query: 685 QFLGF----------KRFDDFL------YEGKIEYLDVNEGNDSHIAVSESGIRPGVTTH 728
+FLG+ +FD L +E YL EGND H +
Sbjct: 63 KFLGYVSSLVEPSKVGQFDQVLNLCLTEFE--NCYL---EGNDIHALAA----------K 107
Query: 729 LEIAPFTLLGVCAGIELLQYNKRFHSPGLVPYPHHNQAPRNTYQCAMGKQA-----MGCI 783
L T L + + Y + + P ++ ++ A G
Sbjct: 108 LLQENDTTLVKTKEL-IKNY---ITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFG-- 161
Query: 784 GYNQQNRIDTL-----MYNLVYAQRPMVESKTIRITNFHKLPAGKCQISPGGAEELTARE 838
G Q N D +Y Y +V +S L A +
Sbjct: 162 G--QGNTDDYFEELRDLYQ-TY--HVLVGDLIKFSAE---------TLSELIRTTLDAEK 207
Query: 839 SCHEVLKIISFSISVAVFDSVWLGDVKQ-----------------GVHQLSEEKEPRLLR 881
+ L I+ WL + GV QL+
Sbjct: 208 VFTQGLNILE-----------WLENPSNTPDKDYLLSIPISCPLIGVIQLA--------- 247
Query: 882 KFQYFDVR-----TPYRLRRLLC--------------------WECVLYNKR------FH 910
Y TP LR L WE + R F
Sbjct: 248 --HYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFF 305
Query: 911 SPGLV---PYPHHNQAPRNTYQC-AMGKQAMGCIGYNQQNRIDTLMYNLVYAQRPMVESK 966
G+ YP+ + P + + M ++ + V+
Sbjct: 306 I-GVRCYEAYPNTSLPPSILEDSLENNEGVP------------SPMLSISNLTQEQVQ-D 351
Query: 967 TIRITNFHKLPAGQNATIAVMSYSGYDIEDALIM--NKASLDRGFGRCLVYRNSKCVLKQ 1024
+ TN H LPAG+ I++ +G L++ SL G L R +K
Sbjct: 352 YVNKTNSH-LPAGKQVEISL--VNGAK---NLVVSGPPQSL-YGL--NLTLRKAKAPSGL 402
Query: 1025 YPNQTHDRILGPLLEADTRKPVYRHRALDQDGIVAP---------GEQICERQVLVNKSM 1075
+Q+ RI P E RK + +R L + +P + I + LV
Sbjct: 403 --DQS--RI--PFSE---RKLKFSNRFLP---VASPFHSHLLVPASDLINKD--LVKN-- 446
Query: 1076 PTISVSAISMATPEYKEVPVSYKGSVPSYLEKVLVSSNSEDAFLIKMLLRQTRRPEIGDK 1135
+S +A + P Y ++ GS L + ++ ++R + E +
Sbjct: 447 -NVSFNAKDIQIPVYD----TFDGSDLRVLSGSISER------IVDCIIRLPVKWETTTQ 495
Query: 1136 FSSRH----GQKGVIGL 1148
F + H G G GL
Sbjct: 496 FKATHILDFGPGGASGL 512
Score = 59.3 bits (143), Expect = 1e-08
Identities = 100/608 (16%), Positives = 164/608 (26%), Gaps = 238/608 (39%)
Query: 510 LELAGSLLSLMFEDVFKRFNSELKETNLSGVVNLVSGWWFELKY--GNKIYIRSPSRKLL 567
EL G L + V K V+NL FE Y GN I
Sbjct: 58 AELVGKFLGYVSSLV-----EPSKVGQFDQVLNLCL-TEFENCYLEGNDI---------- 101
Query: 568 AAGFSGPHSGRVRLMPEGPTILLNS-------------CLRSGGKAQHEALYNAVQRHAT 614
H+ +L+ E T L+ + R K + AL+ AV
Sbjct: 102 -------HALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNA 154
Query: 615 KCCTLNFLFFLGGGG-------------------ILPSIQRQTTCLLTLILFSLNGDGKR 655
+ + F GG G + I+ L L
Sbjct: 155 QLVAI----F-GGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSEL----------- 198
Query: 656 GARNSQQYCDCPDGYSSGCQPRPTFLNMHQFLGFKRFDDFLYEGKIEYLDVNEGNDSHIA 715
+ D ++ G LN+ ++L ++ +YL I
Sbjct: 199 ----IRTTLDAEKVFTQG-------LNILEWL-----ENPSNTPDKDYL-------LSIP 235
Query: 716 VS-----------------ESGIRP--------GVTTHLE-------IAP------FTLL 737
+S G P G T H + IA F +
Sbjct: 236 ISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVS 295
Query: 738 GVCAGIELLQYNKRFHSPGLV---PYPHHNQAPRNTYQC-AMGKQAMGCIGYNQQNRIDT 793
A I +L F G+ YP+ + P + +
Sbjct: 296 VRKA-ITVL-----FFI-GVRCYEAYPNTSLPPSILEDSLENNEGVP------------S 336
Query: 794 LMYNLVYAQRPMVESKTIRITNFHKLPAGKCQISPGGAEELTARESCHEVLKIISFSISV 853
M ++ + V+ + TN H LPAGK + +
Sbjct: 337 PMLSISNLTQEQVQ-DYVNKTNSH-LPAGK--------------------------QVEI 368
Query: 854 AVFDS----VWLGDVK--QG-VHQLSEEKEPRLLRKFQYFDVRTPYRLRRLLCWECVLYN 906
++ + V G + G L + K P L Q R P+ R+L N
Sbjct: 369 SLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLD--QS---RIPFSERKL-----KFSN 418
Query: 907 K------RFHSPGLVPYPHHNQAPRNTYQCAMGKQAMGC------IGYNQQNRIDTLMYN 954
+ FHS LVP + + + G + + ++
Sbjct: 419 RFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISER 478
Query: 955 LVYAQRPMVESKTI---RITNF---HKL---PAGQNATIAVMSY-----SGYDIEDALIM 1000
+V + + T F H L P G + + V+++ +G + A
Sbjct: 479 IV----DCIIRLPVKWETTTQFKATHILDFGP-GGASGLGVLTHRNKDGTGVRVIVA--- 530
Query: 1001 NKASLDRG 1008
+LD
Sbjct: 531 --GTLDIN 536
Score = 48.9 bits (116), Expect = 2e-05
Identities = 50/259 (19%), Positives = 76/259 (29%), Gaps = 104/259 (40%)
Query: 23 HPIGTPGPAYIFFLLEGL-----QAIL-----FLPLFKQVDF----GDSKVVSLRELLSH 68
+ G P P + L Q + LP KQV+ G +V
Sbjct: 330 NNEGVPSPM---LSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLV-------- 378
Query: 69 VT-YQKRLYRLTVQPNWLGTVKAVHGTYLTMVTDETSKLKDSPEIRDKWKLVLSFLKEKG 127
V+ + LY L + L KA G + S++ S K K FL
Sbjct: 379 VSGPPQSLYGLNLT---LRKAKAPSGL-------DQSRIPFSER---KLKFSNRFL---- 421
Query: 128 LVKP-----HIDSFDYFINVEIKKLMQANANIYSDVDP---LFYLKYLDIHVGIADKIIP 179
P H S L+ A+ I D+ F K + I V
Sbjct: 422 ---PVASPFH--S-HL--------LVPASDLINKDLVKNNVSFNAKDIQIPV-------- 459
Query: 180 KIKAAQFDIVN--HMRQ--DTITNALTAAIQTG--NWTIRRFKMERQGVTQVLSRLSYI- 232
+D + +R +I+ + I W T + ++I
Sbjct: 460 ------YDTFDGSDLRVLSGSISERIVDCIIRLPVKWE-----------TTTQFKATHIL 502
Query: 233 -------SGLGMMTRINSQ 244
SGLG++T N
Sbjct: 503 DFGPGGASGLGVLTHRNKD 521
Score = 40.4 bits (94), Expect = 0.005
Identities = 82/508 (16%), Positives = 142/508 (27%), Gaps = 197/508 (38%)
Query: 957 YAQRPMVESK-TIRIT----------------NFHK-LP------AGQNATIA----VMS 988
Y+ RP+ S ++ F+K LP A + V
Sbjct: 4 YSTRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGK 63
Query: 989 YSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQY------PNQTHDRILGPLLEADT 1042
+ GY + + +K F + L L ++ N H L +
Sbjct: 64 FLGY-VSSLVEPSKVGQ---FDQVL-----NLCLTEFENCYLEGNDIHALAAK--LLQEN 112
Query: 1043 RKPVYRHRALDQDGIVAPGEQICERQVLVNKSMPTISVSAISMATPEYKEVPVSY----- 1097
+ + + L ++ I A +++ + S SA+ A E +
Sbjct: 113 DTTLVKTKELIKNYITA--------RIMAKRPFDKKSNSALFRAVGE-GNAQL-VAIFGG 162
Query: 1098 KGSVPSYLEKVLVSSNSEDAFLIKMLLR---QTRRPEIGDKFSSRHGQKGVIGLIVEQED 1154
+G+ Y E E LR QT +GD + + LI D
Sbjct: 163 QGNTDDYFE--------E--------LRDLYQTYHVLVGD-LIKFSAET-LSELIRTTLD 204
Query: 1155 M-PFNESGICPDI---IMNPHGLKGCDRITEY-KEVPVSYK-----------------GS 1192
G+ +I + NP D Y +P+S G
Sbjct: 205 AEKVFTQGL--NILEWLENPSNTPDKD----YLLSIPISCPLIGVIQLAHYVVTAKLLGF 258
Query: 1193 VPSYL-----------EKVLV-----SSNSEDAFL------IKMLLRQTRRPEIGDKFSS 1230
P L + ++ ++S ++F I +L F
Sbjct: 259 TPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVL------------FF- 305
Query: 1231 RHGQKGVIGLIVEQEDMPFNESGICPDIIM----NPHGYPSRMTVGKLIELLAGKAGLME 1286
IG+ E P + + P I+ N G PS M L+
Sbjct: 306 -------IGVRC-YEAYP--NTSLPPSILEDSLENNEGVPSPM--------LSIS----- 342
Query: 1287 GNYKEGTAFGGTKLVDVQEELIRH--GYNYQGKDIFYSGITGEALEAYIYSGP------- 1337
VQ+ + + GK + S + G + + SGP
Sbjct: 343 ----------NLTQEQVQD-YVNKTNSHLPAGKQVEISLVNGA--KNLVVSGPPQSLYGL 389
Query: 1338 -VYYQKLK---HMVQDKIHARSRGPRVV 1361
+ +K K + Q +I R +
Sbjct: 390 NLTLRKAKAPSGLDQSRIPFSERKLKFS 417
Score = 34.6 bits (79), Expect = 0.32
Identities = 45/325 (13%), Positives = 88/325 (27%), Gaps = 127/325 (39%)
Query: 258 QGSQW-GMLCPSDTPEG----EACGLVKNL-ALMTHITTENDEKNMLKIMYNIGIEHIAM 311
QGSQ GM G + +++ + + ++L I+ N +
Sbjct: 1624 QGSQEQGM--------GMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIH 1675
Query: 312 FNGEELSSPGVYLVFVNGILAGITCHHKEVCKPEIEESFNYTRQTTPHECRLRDLTYSAP 371
F GE+ G + N + + K + E+ F + T+ +
Sbjct: 1676 FGGEK----GKRIR-EN--YSAMIFETIVDGKLKTEKIFKEINE------HSTSYTFRSE 1722
Query: 372 -----ITVDIEYTRGSQRVVRSDLVIGRMPIMLQSSKC---VLRNKT------------- 410
T ++T Q P + K L++K
Sbjct: 1723 KGLLSAT---QFT---Q------------PALTLMEKAAFEDLKSKGLIPADATFAGHSL 1764
Query: 411 -EYTSSSRRASTSSVTMHSQRTSPLLSCKKLRQKRFQTYKKTPVDDA------RDFLSST 463
EY + AS + V +S ++ R
Sbjct: 1765 GEYAA---LASLADV----------MS----------------IESLVEVVFYRGMTMQV 1795
Query: 464 CIAHIPVINMRFKMKAMYLAVMIRRMVLALSDPDMLDDRDYYGNKRLELAGSLLSLMFED 523
+ + + M +A+ R+ + S + Y + + G L+ +
Sbjct: 1796 AVPRDELGRSNYGM----IAINPGRVAASFSQ----EALQYVVERVGKRTGWLVEI---- 1843
Query: 524 VFKRFNSELKETNLSG--VVNLVSG 546
V N N+ V +G
Sbjct: 1844 V----NY-----NVENQQYV--AAG 1857
Score = 31.9 bits (72), Expect = 2.1
Identities = 21/113 (18%), Positives = 32/113 (28%), Gaps = 51/113 (45%)
Query: 1284 LMEGNYKEGTA-FGGTKLVDVQEELIRHGY-----------NYQGKDIFYSGITGEALEA 1331
++ N T FGG K + IR Y + + IF E +
Sbjct: 1664 IVINNPVNLTIHFGGEK-----GKRIRENYSAMIFETIVDGKLKTEKIF--KEINEHSTS 1716
Query: 1332 YIYSGPVYYQKLKHMVQDKIHARSRGPRVVLTRQPTGRRWKLT-FT-PALCTI 1382
Y + R + +L+ T FT PAL +
Sbjct: 1717 YTF---------------------RSEKGLLS---------ATQFTQPALTLM 1739
Score = 30.8 bits (69), Expect = 4.0
Identities = 35/250 (14%), Positives = 75/250 (30%), Gaps = 52/250 (20%)
Query: 107 KDSPEIRDKWKLVLSFLKEK-GLVKPHIDSFDYFINVEIKKLMQANANIYSDVDPLFYLK 165
K S +D W + K+ G I + +N+ I + I + + +
Sbjct: 1637 KTSKAAQDVWNRADNHFKDTYGFSILDI-VINNPVNLTIHFGGEKGKRIRENYSAMIFET 1695
Query: 166 YLDIHVGIADKIIPKIKAAQFDIVNHMRQDTITNALTA----AIQTGNWTIRRFK-MERQ 220
+D + +KI +I + ++ T A+ F+ ++ +
Sbjct: 1696 IVDGKL-KTEKIFKEINEHSTSYTFRSEKGLLS--ATQFTQPALTL--MEKAAFEDLKSK 1750
Query: 221 GVTQVLSRL---S---YISGL----GMMTRINSQFEKTRKVSGPRSLQGSQWGMLCPSDT 270
G+ + S Y + L +M+ E +V R G + P D
Sbjct: 1751 GLIPADATFAGHSLGEY-AALASLADVMS-----IESLVEVVFYR---GMTMQVAVPRDE 1801
Query: 271 PEGEACGLVK-NLALMTHITTENDEKNMLKIMYNIGIEHIAMFNGEELS-----SPG-VY 323
G++ N + ++ + + +E + G + Y
Sbjct: 1802 LGRSNYGMIAINPGRVAASFSQEALQYV--------VERVGKRTGWLVEIVNYNVENQQY 1853
Query: 324 LVFVNGILAG 333
+ AG
Sbjct: 1854 ------VAAG 1857
>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 = 62.2 bits (150), Expect = 1e-09
Identities = 76/516 (14%), Positives = 159/516 (30%), Gaps = 127/516 (24%)
Query: 284 LMTHITTENDEKNMLKIMYNIGIEHIAMFNGEELSSPG-VY------------------- 323
LM+ I TE + +M+ MY + ++N ++ + V
Sbjct: 94 LMSPIKTEQRQPSMMTRMYI--EQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAK 151
Query: 324 LVFVNGIL-AGITCHHKEVCK-PEIEESFNY-------TRQTTPHEC--RLRDLTYSAPI 372
V ++G+L +G T +VC +++ ++ +P L+ L Y
Sbjct: 152 NVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLY---- 207
Query: 373 TVDIEYTRGSQRV----VRSDLVIGRMPIMLQSS---KC--VLRN--------------K 409
+D +T S +R + + +L+S C VL N K
Sbjct: 208 QIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCK 267
Query: 410 TEYTSSSRRASTSSVTMHSQRTSPLLSCKKLRQKRFQTYKKTPVDDARDFLSSTCIAHIP 469
T +R + + T L TP D+ + L
Sbjct: 268 ILLT--TRFKQVTDFLSAATTTHISL---DHHSMTL-----TP-DEVKSLLLK------- 309
Query: 470 VINMRFKMKAMYL---AVMIRRMVLAL------SDPDMLDDRDYYGNKRLE--LAGSLLS 518
++ R + L + L++ D+ + +L + SL
Sbjct: 310 YLDCRPQD----LPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNV 365
Query: 519 LMFEDVFKRFNSEL----KETNLSGVVNLVSGWWFELKYGNKIYIRSPSRKLLAAGFSGP 574
L + K F+ L ++ ++ L W+ +K + + + L P
Sbjct: 366 LEPAEYRKMFD-RLSVFPPSAHIPTIL-LSLIWFDVIKSDVMVVVNKLHKYSLVEK--QP 421
Query: 575 HSGRVRLMPEGPTILLNSCLRSGGKAQ-HEAL---YNAVQRHATKCCTLN-----FLFFL 625
+ + P+I L ++ + H ++ YN + + F +
Sbjct: 422 KESTISI----PSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHI 477
Query: 626 GGGGILPSIQR-QTTCLLTLILFSLN-GDGKRGARNSQQYCDCPDGYSSGCQPRPTFLNM 683
G L +I+ + L ++ + K R+ + T +
Sbjct: 478 GHH--LKNIEHPERMTLFRMVFLDFRFLEQK--IRHDSTAWNASGSIL------NTLQQL 527
Query: 684 HQFLGFKRFDDFLYEGKI-EYLDVNEGNDSHIAVSE 718
+ + +D YE + LD + ++ S+
Sbjct: 528 KFYKPYICDNDPKYERLVNAILDFLPKIEENLICSK 563
Score = 52.9 bits (126), Expect = 7e-07
Identities = 84/620 (13%), Positives = 164/620 (26%), Gaps = 207/620 (33%)
Query: 155 YSDVDPLF---YLKYLDIHVGIADKIIPKIKAAQFD-IVNHMRQDTIT------------ 198
Y D+ +F ++ D + D + + D I+ + T
Sbjct: 18 YKDILSVFEDAFVDNFDCK-DVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQE 76
Query: 199 NALTAAIQTG-----NWTIRRFKMERQGVTQVLSRLSYISGLGMMTRINSQFEKTRKVSG 253
+ ++ + + K E++ + + YI + N F K VS
Sbjct: 77 EMVQKFVEEVLRINYKFLMSPIKTEQRQPS--MMTRMYIEQRDRLYNDNQVFAK-YNVSR 133
Query: 254 PR----------SLQGSQW----GMLCPSDTPEGEACGLVKN-LALMT------------ 286
+ L+ ++ G+L G G K +AL
Sbjct: 134 LQPYLKLRQALLELRPAKNVLIDGVL-------G--SG--KTWVALDVCLSYKVQCKMDF 182
Query: 287 -----HITTENDEKNMLKIMYNIGIEHIAMFNGEELSSPGVYLVF--VNGILAGITCHHK 339
++ N + +L+++ + + + S + L + L +
Sbjct: 183 KIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKP 242
Query: 340 ---------EVCKPEIEESFNYTRQTTPHECRLRDLTYSAPITVDIEYTRGSQRVVRSDL 390
V + +FN C++ T +T + + L
Sbjct: 243 YENCLLVLLNVQNAKAWNAFN-------LSCKILLTTRFKQVTDFL----SAATTTHISL 291
Query: 391 VIGRMPIMLQSSKCVLRN--KTEYTSSSRRASTSSVTMHSQRTSPLL------------- 435
M + K +L R T T+P
Sbjct: 292 DHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLT---------TNPRRLSIIAESIRDGLA 342
Query: 436 --------SCKKLR---------------QKRFQT------------------YKKTPVD 454
+C KL +K F +
Sbjct: 343 TWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKS 402
Query: 455 DARDFL----SSTCIA--------HIPVINMRFKMKAMYLAVMIRRMVLALSDPDMLDDR 502
D + + + IP I + K+K + R +V + P D
Sbjct: 403 DVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSD 462
Query: 503 D--------YYGN------KRLELAG--SLLSLMFEDVFKRF------NSELKETNLSGV 540
D Y+ + K +E +L ++F D F RF + +
Sbjct: 463 DLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLD-F-RFLEQKIRHDSTAWNASGSI 520
Query: 541 VNLVSGWWFELK-YGNKIYIRSPSRKLLAAGFSGPHSGRVRLMPEGPTILLNS----CLR 595
+N + +LK Y I P + L + +P+ L+ S LR
Sbjct: 521 LNTLQ----QLKFYKPYICDNDPKYERLVNAI-------LDFLPKIEENLICSKYTDLLR 569
Query: 596 SGGKAQHEALYNAVQRHATK 615
A+ EA++ + +
Sbjct: 570 IALMAEDEAIFEEAHKQVQR 589
Score = 52.9 bits (126), Expect = 8e-07
Identities = 104/705 (14%), Positives = 195/705 (27%), Gaps = 230/705 (32%)
Query: 472 NMRFKMKAMYLAVMIRRMVLALSDPDMLDDRDYYGNKRLELAGSLLSLMFEDVFKRFNSE 531
+M F+ + +L++ + +D+ D ++ S+LS E
Sbjct: 6 HMDFETGEHQYQY---KDILSVFEDAFVDNFDCK--DVQDMPKSILS----------KEE 50
Query: 532 LKE-----TNLSGVVNLVSGWWFELKYGNKIYIR------SPSRKLLAAGFSGPHSGRVR 580
+ +SG + L W L ++ + + K L +
Sbjct: 51 IDHIIMSKDAVSGTLRLF---WTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQ--- 104
Query: 581 LMPEGPTILLNSCLRSGGKAQHEALYNAVQ----RHATKCCTLNFLFFLGGGGILPSIQR 636
P T + Q + LYN Q + ++ L +
Sbjct: 105 --PSMMTRMYIE--------QRDRLYNDNQVFAKYNVSR---------------LQPYLK 139
Query: 637 QTTCLLTL------ILFSLNGDGK-----RGARNSQQYCDCPDG-Y--SSGCQPRP-TFL 681
LL L ++ + G GK + + C + + P T L
Sbjct: 140 LRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVL 199
Query: 682 NMHQFLGFKRFDDFLYEGKIEYLDVNEGNDSHIAVSESGIRPGVTTHLEIAPF--TLL-- 737
M Q LY+ + ++ + + S I+ + L+ P+ LL
Sbjct: 200 EMLQ--------KLLYQIDPNWTSRSDHSSNIKLRIHS-IQAELRRLLKSKPYENCLLVL 250
Query: 738 -GVCAGIELLQYNKR------FHSPGLVPYPHHNQAPRNTYQCAMGKQAMGCIGYNQQNR 790
V N + L+ R KQ +
Sbjct: 251 LNVQ--------NAKAWNAFNLSCKILL-------TTRF-------KQVTDFLSAATTTH 288
Query: 791 IDTLMYNLVYAQRPMVESKTIRI------TNFHKLPAGKCQISPG-----GAE--ELTAR 837
I L + + + + LP +P + A
Sbjct: 289 IS-----LDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLAT 343
Query: 838 ------ESCHEVLKIISFSISV-------------AVF-DSV----------WLGDVKQG 867
+C ++ II S++V +VF S W +K
Sbjct: 344 WDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSD 403
Query: 868 VHQLSEEKEPRLLRKFQ-----------YFDVRTP----YRL-RRLLCWECVLYNKRFHS 911
V + + L + Q Y +++ Y L R ++ + K F S
Sbjct: 404 VMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIV--DHYNIPKTFDS 461
Query: 912 PGLVPYPHHNQAPRNTYQCAMGKQAMGCIGY---NQQNRIDTLMYNLVYAQRPMVESKTI 968
L+P Y + IG+ N ++ ++ +V+ +E K
Sbjct: 462 DDLIPPYLDQ------YFYSH-------IGHHLKNIEHPERMTLFRMVFLDFRFLEQKIR 508
Query: 969 RITNFHKLPAGQNATIAVMS-YSGYDIEDALIMNKASLDRGFGRCLVYRNSKCVLKQYPN 1027
+ T+ + Y Y I D N +R LV
Sbjct: 509 HDSTAWNASGSILNTLQQLKFYKPY-ICD----NDPKYER-----LV------------- 545
Query: 1028 QTHDRILGPLLEADTRKPVYRHRALDQDGIVAPGEQICE---RQV 1069
+ IL L + + ++ L + ++A E I E +QV
Sbjct: 546 ---NAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQV 587
Score = 44.8 bits (105), Expect = 2e-04
Identities = 42/218 (19%), Positives = 74/218 (33%), Gaps = 61/218 (27%)
Query: 36 LLEGLQAILFL---PLFKQVDFGDSKVVS-------LRELLSHVTYQKRLYRL-TVQPNW 84
+LE LQ +L+ + D + + LR LL Y+ L L VQ
Sbjct: 198 VLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAK 257
Query: 85 -----------LGT---------VKAVHGTYLTMV-------TDETSKL---------KD 108
L T + A T++++ DE L +D
Sbjct: 258 AWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQD 317
Query: 109 SP-EIRDKWKLVLSFLKEKGLVKPHIDSFDYFINVEIKKLMQANANIYSDVDPLFYLK-Y 166
P E+ LS + E ++ + ++D + +V KL + + ++P Y K +
Sbjct: 318 LPREVLTTNPRRLSIIAE--SIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMF 375
Query: 167 LDIHVGIADKIIP----------KIKAAQFDIVNHMRQ 194
+ V IP IK+ +VN + +
Sbjct: 376 DRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHK 413
Score = 37.9 bits (87), Expect = 0.027
Identities = 58/353 (16%), Positives = 95/353 (26%), Gaps = 99/353 (28%)
Query: 1101 VPSYLEKVLVSSNSEDAFLIKMLLRQTRRPEIGDKFSSRHGQKGVIGLIVE---QEDMPF 1157
V + +L + + K + T R + S+ Q+ ++ VE + + F
Sbjct: 38 VQDMPKSILSKEEIDHIIMSKDAVSGTLR--LFWTLLSK--QEEMVQKFVEEVLRINYKF 93
Query: 1158 NESGI---CPDIIMNPHGLKGC-DRITEYKEVPVSYKGSVPSYLEKVLVSSNSEDAFLIK 1213
S I M DR+ Y + V K +V L+ L L +
Sbjct: 94 LMSPIKTEQRQPSMMTRMYIEQRDRL--YNDNQVFAKYNVSR-LQPYLK--------LRQ 142
Query: 1214 MLLRQTRRPEIGDKFSSRHGQKGVIG---LIVE-------QEDMPFN----ESGIC--PD 1257
LL RP K G G G + ++ Q M F C P+
Sbjct: 143 ALLEL--RPA---KNVLIDGVLG-SGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPE 196
Query: 1258 IIMNP-----------------HGYPSRMTVGKLIELLAGKAGLMEGNYKEG-------- 1292
++ H ++ + + L + L Y+
Sbjct: 197 TVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAEL--RRLLKSKPYENCLLVLLNVQ 254
Query: 1293 -----TAFGG-------TKLVDVQEELIRHGYNYQGKDIFYSGIT-GEALEAYIYSGPVY 1339
AF T+ V + L + D +T E +
Sbjct: 255 NAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKS-------LL 307
Query: 1340 YQKLKHMVQD-KIHARSRGPRVV-----LTRQPTGR--RWKLTFTPALCTIRS 1384
+ L QD + PR + R WK L TI
Sbjct: 308 LKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIE 360
Score = 35.6 bits (81), Expect = 0.15
Identities = 52/449 (11%), Positives = 114/449 (25%), Gaps = 163/449 (36%)
Query: 860 WLGDVKQGVHQLSEE-KEPRLLRKFQYFDVR----------TPYRLRRLLCWECV----- 903
+L + + E ++P ++ + Y + R Y + RL +
Sbjct: 93 FL------MSPIKTEQRQPSMMTR-MYIEQRDRLYNDNQVFAKYNVSRL---QPYLKLRQ 142
Query: 904 -LYNKRFHSPGLVPYPHHNQAPRNTYQCAM---GKQ---AMGCIGYNQQNRIDTLMYNLV 956
L R + ++ + GK C ++ M +
Sbjct: 143 ALLELR-PAKNVLID-------------GVLGSGKTWVALDVC----LSYKVQCKMDFKI 184
Query: 957 Y----AQRPMVESKTIRITNF-HKLPAGQNATIAVMSYSGYDIEDALIMNKASL-----D 1006
+ E+ + +++ + S I +A L
Sbjct: 185 FWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSI----QAELRRLLKS 240
Query: 1007 RGFGRCL-VYRN--SKCVLKQYPNQ------THDRILGPLLEADTRKPVY---RHRALDQ 1054
+ + CL V N + + T + + L A T + L
Sbjct: 241 KPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTP 300
Query: 1055 D---GIVA----------PGEQICE-----------------------RQVLVNKSMPTI 1078
D ++ P ++ + V +K I
Sbjct: 301 DEVKSLLLKYLDCRPQDLP-REVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTII 359
Query: 1079 SVSAISMATPEYKEV-------PVSYKGSVPSYLEKVLV----SSNSEDAFLI------- 1120
S + EY+++ P S +P +L D ++
Sbjct: 360 ESSLNVLEPAEYRKMFDRLSVFPPSAH--IP---TILLSLIWFDVIKSDVMVVVNKLHKY 414
Query: 1121 KMLLRQTRRPEIG------------DKFSSRHGQKGVIGLIVEQEDMP--FNESGICPDI 1166
++ +Q + I + + H IV+ ++P F+ + P
Sbjct: 415 SLVEKQPKESTISIPSIYLELKVKLENEYALHRS------IVDHYNIPKTFDSDDLIPPY 468
Query: 1167 IMN------PHGLKGCDRITEYKEVPVSY 1189
+ H LK + + +
Sbjct: 469 LDQYFYSHIGHHLKNIEHPERMTLFRMVF 497
Score = 32.1 bits (72), Expect = 1.5
Identities = 54/367 (14%), Positives = 103/367 (28%), Gaps = 116/367 (31%)
Query: 8 NSVGPHFSCSMTLKHHPIG-TPGPAYIFFLL------EGL--QAILFLPL---------- 48
+ + + ++L HH + TP L + L + + P
Sbjct: 279 DFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIR 338
Query: 49 --------FKQVDFGDSKVVSLREL----LSHVTYQKRLYRLTVQPNWLGTVKAVHGTYL 96
+K V+ K+ ++ E L Y+K RL+V P + H +
Sbjct: 339 DGLATWDNWKHVNC--DKLTTIIESSLNVLEPAEYRKMFDRLSVFP------PSAHIPTI 390
Query: 97 TMVTDETSKLKDSPEIRDKWKLVLSFLKEKGLVKPHIDSFDYFIN-------VEIKKLMQ 149
+ +K +V++ L + LV+ I V+++
Sbjct: 391 LLSLIWFDVIKSDVM------VVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYA 444
Query: 150 ANANIYSDVDPLFYLKYLDIHVGIADKIIPKIKA--AQFDIVNHMRQDTITNALTAAIQT 207
+ +I VD K D D I P + I +H++
Sbjct: 445 LHRSI---VDHYNIPKTFDSD----DLIPPYLDQYFYSH-IGHHLKN---------IEHP 487
Query: 208 GNWTIRRFKMERQGVTQVLSRLSYISGLGMMTRINSQFEKTRKVSGPRSLQGSQWGML-- 265
T+ R V ++ K R S + GS L
Sbjct: 488 ERMTLFR---------MVFLDFRFLEQ------------KIRHDSTAWNASGSILNTLQQ 526
Query: 266 --------CPSD-TPEGEACGLVKNLALMTHITTENDEKNMLKIMYNIGIEHIAMFNGEE 316
C +D E ++ L + + ++L IA+ +E
Sbjct: 527 LKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLL---------RIALMAEDE 577
Query: 317 LSSPGVY 323
++
Sbjct: 578 ----AIF 580
>3mlq_A DNA-directed RNA polymerase subunit beta; tudor,
transferase-transcription complex; 2.91A {Thermus
aquaticus}
Length = 188
Score = 36.8 bits (86), Expect = 0.025
Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 357 TPHECRLRDLTYSAPITVDIEYTRGSQRVVRSDLV-IGRMPIM 398
+ ECR +DLTY AP+ ++ +++ D V +G +P+M
Sbjct: 64 SQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHLPLM 106
>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 = 32.2 bits (72), Expect = 0.50
Identities = 9/24 (37%), Positives = 14/24 (58%), Gaps = 2/24 (8%)
Query: 143 EIKKLMQANANIYS-DVDPLFYLK 165
+KKL QA+ +Y+ D P +K
Sbjct: 21 ALKKL-QASLKLYADDSAPALAIK 43
>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 = 30.8 bits (69), Expect = 1.9
Identities = 16/57 (28%), Positives = 20/57 (35%), Gaps = 20/57 (35%)
Query: 237 MMTRINSQFEKTRKVSGPRSLQGSQWGMLCPS----------DTPEGE----ACGLV 279
MMTR E K +G R + + CP EG+ CGLV
Sbjct: 1 MMTR-----ESIDKRAGRRGPNLNI-VLTCPECKVYPPKIVERFSEGDVVCALCGLV 51
>3bf4_A Ethyl TERT-butyl ether degradation ETHD protein; ferredoxin-like
fold, structural genomics, joint center for structural
genomics, JCSG; 2.10A {Ralstonia eutropha JMP134}
Length = 127
Score = 29.9 bits (67), Expect = 2.6
Identities = 9/48 (18%), Positives = 19/48 (39%)
Query: 471 INMRFKMKAMYLAVMIRRMVLALSDPDMLDDRDYYGNKRLELAGSLLS 518
I+ + +Y MI+ V+ D YY ++ + + + L
Sbjct: 6 IHHHHHHENLYFQGMIKVNVMYPYTEGARFDHAYYCDRHMPMVKARLG 53
>3t4n_C Nuclear protein SNF4; CBS domain, nucleotide binding, cytosol,
protein binding; HET: ADP; 2.30A {Saccharomyces
cerevisiae} PDB: 3tdh_C* 3te5_C* 2qlv_C
Length = 323
Score = 30.7 bits (69), Expect = 3.8
Identities = 24/178 (13%), Positives = 57/178 (32%), Gaps = 7/178 (3%)
Query: 298 LKIMYNIGIEHIAMFNGEELSSPGVYLVFVNGILAGITCHHKEVCKPEIEESFNYTRQTT 357
L ++ I +++ + G+ + + I + K E+ +
Sbjct: 55 LNVLLQNSIVSAPLWDSKTSRFAGL--LTTTDFINVIQYYFSNPDKFELVDKLQLDGLKD 112
Query: 358 PHECRLRDLTYSAPITVDIEYTRGSQRVVRSDLVIGRMPIMLQSSKCVLRNKTEYTSSSR 417
D +A I +++ S GR+P++ Q + + R
Sbjct: 113 IERALGVDQLDTASIHPSRPLFEACLKMLESR--SGRIPLIDQDEETHREIVVSVLTQYR 170
Query: 418 --RASTSSVTMHSQRTSPLLSCKKLRQKRFQT-YKKTPVDDARDFLSSTCIAHIPVIN 472
+ + P+ + Q ++ TPV D L+ ++ +P+I+
Sbjct: 171 ILKFVALNCRETHFLKIPIGDLNIITQDNMKSCQMTTPVIDVIQMLTQGRVSSVPIID 228
>1urj_A Major DNA-binding protein; SSB, ICP8, HSV-1, DNA replication,
zinc-finger, nuclear protein.; 3.0A {Human herpesvirus
1} SCOP: e.58.1.1
Length = 1136
Score = 30.8 bits (69), Expect = 4.5
Identities = 10/36 (27%), Positives = 16/36 (44%)
Query: 75 LYRLTVQPNWLGTVKAVHGTYLTMVTDETSKLKDSP 110
+ LTV+ + V V G+ T + LK +P
Sbjct: 52 VVGLTVESGFEANVAVVVGSRTTGLGGTAVSLKLTP 87
>1iru_G 20S proteasome; cell cycle, immune response, proteolysis,
ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4
PDB: 3unb_F* 3une_F 3unf_F* 3unh_F
Length = 254
Score = 29.6 bits (67), Expect = 5.8
Identities = 14/62 (22%), Positives = 28/62 (45%), Gaps = 15/62 (24%)
Query: 832 EELTARESCHEVLKII----------SFSISVAVFDSVWLGDVKQGVHQLSEEKEPRLLR 881
+E+T R+ EV KII +F + ++ W+G++ G H++ +
Sbjct: 182 KEMTCRDIVKEVAKIIYIVHDEVKDKAFELELS-----WVGELTNGRHEIVPKDIREEAE 236
Query: 882 KF 883
K+
Sbjct: 237 KY 238
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
0.321 0.137 0.411
Gapped
Lambda K H
0.267 0.0620 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 21,364,918
Number of extensions: 1331229
Number of successful extensions: 2316
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2276
Number of HSP's successfully gapped: 61
Length of query: 1384
Length of database: 6,701,793
Length adjustment: 105
Effective length of query: 1279
Effective length of database: 3,770,088
Effective search space: 4821942552
Effective search space used: 4821942552
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 (21.9 bits)
S2: 63 (28.3 bits)