RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7629
(468 letters)
>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 = 61.4 bits (148), Expect = 3e-10
Identities = 75/530 (14%), Positives = 146/530 (27%), Gaps = 144/530 (27%)
Query: 3 NFEISENSSTDKVNKEFCELLQSAAKLSIPRGKTKRFNYFWNKKLSVLKSERN----AAR 58
+FE E K+ + + A + S+L E ++
Sbjct: 8 DFETGE---HQYQYKDILSVFEDAFV------DNFDCKDVQDMPKSILSKEEIDHIIMSK 58
Query: 59 KRAEKSNLLSDTVEWRKRAAILKKEINSSKRSSFNTFVEKMDYRKDGPKAYSFISSIKKG 118
+ L T+ K+ +++K FVE++ R + Y F+ S
Sbjct: 59 DAVSGTLRLFWTLL-SKQEEMVQK------------FVEEVL-RIN----YKFLMS--PI 98
Query: 119 QTSVNKPFSHNGRSISDSKKIASIFNTFYTSKYNIPKHEVLLTTSKTNKQKIEKVQNEAL 178
+T +P I ++ + F +KYN+ + + L +Q + +++
Sbjct: 99 KTEQRQPSMMTRMYIEQRDRLYNDNQVF--AKYNVSRLQPYLKL----RQALLELRPAKN 152
Query: 179 RLV---TGAVKTTPINAMYALTQNQSLSDIIEQQALTTYEKLTRLPNNNFWTT---YKED 232
L+ G+ KT + +Y+ ++ FW
Sbjct: 153 VLIDGVLGSGKTW-------VAL----------DVCLSYKVQCKMDFKIFWLNLKNCNSP 195
Query: 233 PTKLKTQTGYIQEVKKIKLLTEI-PDKKENLLHPPNPMDSFEITHS----LFLEETFRK- 286
T L+ KLL +I P+ H N + L + +
Sbjct: 196 ETVLEMLQ---------KLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC 246
Query: 287 ----QDVA-PLIAKTMALE---TINTRYPSD-DWL--HIYTDGSLINPEDGAGAGIFCEL 335
+V L + TR+ D+L T SL + L
Sbjct: 247 LLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSL 306
Query: 336 FSFYKRLGTFTTNFDGEIAAIKIALLQI----------LNRTNQFERAVILSDSKAAIQS 385
K L + E + ++ L + ++ V I+S
Sbjct: 307 LL--KYLDCRPQDLPRE--VLTTNPRRLSIIAESIRDGLATWDNWKH-VNCDKLTTIIES 361
Query: 386 ITNCSEDPSIKHN---------------KRLRNEGQGKKWQQIL--NTHDIIPNLPRKAA 428
N E + L W ++ + ++ L + +
Sbjct: 362 SLNVLEPAEYRKMFDRLSVFPPSAHIPTILL-----SLIWFDVIKSDVMVVVNKLHKYSL 416
Query: 429 VA-------------HFRLLTGHDCLAEHLHRFGLKTSPIGSRDLKTCFD 465
V + L + LHR S + ++ FD
Sbjct: 417 VEKQPKESTISIPSIYLELKVKLENEYA-LHR-----SIVDHYNIPKTFD 460
>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 = 43.9 bits (103), Expect = 1e-04
Identities = 62/379 (16%), Positives = 109/379 (28%), Gaps = 142/379 (37%)
Query: 202 LSDIIEQQALTTYEKLTRLPNNNFWTTY--------------KEDPTKLKTQTGYIQEVK 247
+S ++E + ++++ L F Y +E+ T L I+
Sbjct: 68 VSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYI 127
Query: 248 KIKLLTEIPDKK--ENLLHPPNPMDSFEITHSLF------------LEETFR--KQDVAP 291
+++ + P K + L + ++ ++F L + ++ V
Sbjct: 128 TARIMAKRPFDKKSNSALFRAVGEGNAQL-VAIFGGQGNTDDYFEELRDLYQTYHVLVGD 186
Query: 292 LIAKTMA--LETINTRYPSDDWLHIYTDGS-----LINPEDGAGAG-------------- 330
LI K A L + + D ++T G L NP +
Sbjct: 187 LI-KFSAETLSELIR--TTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGV 243
Query: 331 -------IFCELF-----SFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSD 378
+ +L L T + G + A+ IA +D
Sbjct: 244 IQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIA----------------ETD 287
Query: 379 S-----KAAIQSIT--------------NCSEDPSIKHNKRLRNEGQ--------GKKWQ 411
S + ++IT N S PSI + NEG +
Sbjct: 288 SWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQE 347
Query: 412 QI------LNTHDIIPNLPRKAAVA--------HFRLLTGH----DCLAEHLHRF----G 449
Q+ N+H LP V + +++G L L + G
Sbjct: 348 QVQDYVNKTNSH-----LPAGKQVEISLVNGAKNL-VVSGPPQSLYGLNLTLRKAKAPSG 401
Query: 450 LKTS--PIGSRDLK--TCF 464
L S P R LK F
Sbjct: 402 LDQSRIPFSERKLKFSNRF 420
Score = 41.2 bits (96), Expect = 8e-04
Identities = 56/330 (16%), Positives = 88/330 (26%), Gaps = 130/330 (39%)
Query: 97 EKMD-YRKDGPKAYSF-ISSIKKGQTSVNKPFS---HNGRSISDSKKIASIFNTFYTSKY 151
+ D + KD Y F I I N P + H G K+I Y
Sbjct: 1647 NRADNHFKD---TYGFSILDIVI-----NNPVNLTIHFGGE--KGKRI--------RENY 1688
Query: 152 NIPKHEVLLTTSKTNKQKIEKVQNEALRLVTGAVKTTPINAMYALTQNQSLSDIIEQQAL 211
+ E T K K EK+ E T + + TQ Q AL
Sbjct: 1689 SAMIFE----TIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLS-ATQFT-------QPAL 1736
Query: 212 TTYEKLTRLPNNNFWTTYKEDPTKLKTQTGYIQEVKKIKLLTEIPDKKENLLHPPNPMDS 271
T + L K + L+ P D+
Sbjct: 1737 TL--------------------------MEKAA----FEDL-----KSKGLI----PADA 1757
Query: 272 FEITHSL--F--LEETFRKQDVAPLIAKTM----ALETINTRYPSDDWLHIYTDGSLIN- 322
HSL + L + +A M +E + R G +
Sbjct: 1758 TFAGHSLGEYAAL--------AS--LADVMSIESLVEVVFYR------------GMTMQV 1795
Query: 323 --PEDGAGAGIF--CELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQF-ERA---- 373
P D G + + G +F E A++ + ++ RT E
Sbjct: 1796 AVPRDELGRSNYGMIAI-----NPGRVAASFSQE--ALQYVVERVGKRTGWLVEIVNYNV 1848
Query: 374 ----VILSDSKAAIQSITNCSEDPSIKHNK 399
+ + A+ ++TN + K
Sbjct: 1849 ENQQYVAAGDLRALDTVTNV-----LNFIK 1873
>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO
enzyme, structural genomics, protein structure
initiative; NMR {Desulfitobacterium hafniense dcb-2}
PDB: 2kw4_A
Length = 147
Score = 40.0 bits (94), Expect = 4e-04
Identities = 19/115 (16%), Positives = 34/115 (29%), Gaps = 20/115 (17%)
Query: 312 LHIYTDGSLINPEDGAGAGIFC-----ELFSFYKRLGTFTT--NFDGEIAAIKIALLQIL 364
+YTDGS +N + + + T N GEIAA A+ +
Sbjct: 7 YDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKAS 66
Query: 365 NRTNQFERAVILSDSKAAIQSITNCSEDPSIKHNKRLRNEGQGKKWQQILNTHDI 419
+ IL D I + + + +++N +
Sbjct: 67 QLG---VKIRILHDY----AGIAF------WATGEWKAKNEFTQAYAKLMNQYRG 108
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 37.2 bits (87), Expect = 0.003
Identities = 23/85 (27%), Positives = 33/85 (38%), Gaps = 8/85 (9%)
Query: 310 DWLHIYTDGS-LINPEDGAGAGIFCEL-----FSFYKRLGTFTTNFDGEIAAIKIALLQI 363
D++ +YTDG N AGI + RL TN EI A ++
Sbjct: 6 DFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAA-CKAIEQ 64
Query: 364 LNRTNQFERAVILSDSKAAIQSITN 388
N + V+ ++S I ITN
Sbjct: 65 AKTQN-INKLVLYTNSMFTINGITN 88
>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 = 36.9 bits (84), Expect = 0.004
Identities = 10/29 (34%), Positives = 16/29 (55%), Gaps = 6/29 (20%)
Query: 167 KQKIEKVQNEALRLVTGAVKTTP---INA 192
KQ ++K+Q +L+L A + P I A
Sbjct: 19 KQALKKLQA-SLKLY--ADDSAPALAIKA 44
Score = 30.3 bits (67), Expect = 0.67
Identities = 10/57 (17%), Positives = 15/57 (26%), Gaps = 29/57 (50%)
Query: 244 QEVKKIKLLTEIPDKKENLLHPPNPMDSFEITHSLFLEETFRKQDVAPLIAKTMALE 300
Q +KK+ + L DS AP +A +E
Sbjct: 20 QALKKL----------QASLKLYAD-DS------------------APALAIKATME 47
Score = 27.2 bits (59), Expect = 7.5
Identities = 9/33 (27%), Positives = 16/33 (48%), Gaps = 11/33 (33%)
Query: 114 SIKKGQTSVNKPFSHNGRSISDSK---KI-ASI 142
++KK Q S+ K ++ DS I A++
Sbjct: 21 ALKKLQASL-KLYA------DDSAPALAIKATM 46
>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV,
RNAse H, reverse transcriptase, transcription; 1.50A
{Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A
3v1r_A* 2hb5_A
Length = 165
Score = 35.2 bits (81), Expect = 0.019
Identities = 23/105 (21%), Positives = 42/105 (40%), Gaps = 17/105 (16%)
Query: 314 IYTDGS-LINP-EDGAGAGIFCEL-FSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQF 370
YTDGS + + AGA + E + + L T+ E+ A+ A L++
Sbjct: 26 WYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQA-LKMAEG---- 80
Query: 371 ERAVILSDSKAAIQSITNCSEDPSIKHNKRLRNEGQGKKWQQILN 415
++ + +DS+ A + SE IK+ + +L
Sbjct: 81 KKLNVYTDSRYAFATAHVHSEGREIKNK---------NEILALLK 116
>1zbf_A Ribonuclease H-related protein; RNAse H, RNA/DNA hybrid, DDE motif,
hydrolase; 1.50A {Bacillus halodurans} SCOP: c.55.3.1
PDB: 1zbi_A 2g8u_A 2g8i_A 2g8h_A 2g8k_A 2g8f_A 2g8v_A
2g8w_A 3ey1_A* 1zbl_A 3d0p_A* 3i8d_A* 2r7y_A*
Length = 142
Score = 34.4 bits (79), Expect = 0.026
Identities = 22/84 (26%), Positives = 32/84 (38%), Gaps = 10/84 (11%)
Query: 310 DWLHIYTDG-SLINPEDGAGAGIFC----ELFSFYKRLGTFTTNFDGEIAAIKIALLQIL 364
W + D S NP G+ LF + + TN GE AI L +
Sbjct: 10 IWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFER-EPIPI-GTNNMGEFLAIVHGLRYLK 67
Query: 365 NRTNQFERAVILSDSKAAIQSITN 388
R R I S+S+ AI+ + +
Sbjct: 68 ER---NSRKPIYSNSQTAIKWVKD 88
>1xdi_A RV3303C-LPDA; reductase, FAD, NAD, NADP, unkno function; HET: FAD;
2.81A {Mycobacterium tuberculosis} SCOP: c.3.1.5
d.87.1.1
Length = 499
Score = 30.6 bits (70), Expect = 1.2
Identities = 9/40 (22%), Positives = 11/40 (27%), Gaps = 11/40 (27%)
Query: 326 GAGAGIFCELFSFYKRLGTFTT----------NFDGEIAA 355
G+G E Y LG T D + A
Sbjct: 189 GSGV-TGAEFVDAYTELGVPVTVVASQDHVLPYEDADAAL 227
>1mo9_A ORF3; nucleotide binding motifs, nucleotide binding domain, oxidor;
HET: FAD KPC; 1.65A {Xanthobacter autotrophicus} SCOP:
c.3.1.5 c.3.1.5 d.87.1.1 PDB: 1mok_A* 2c3c_A* 2c3d_A*
3q6j_A*
Length = 523
Score = 30.3 bits (69), Expect = 1.5
Identities = 8/40 (20%), Positives = 9/40 (22%), Gaps = 11/40 (27%)
Query: 326 GAGAGIFCELFSFYKRLGTFTT----------NFDGEIAA 355
G E F+ G T D E A
Sbjct: 221 GGSK-TAVEYGCFFNATGRRTVMLVRTEPLKLIKDNETRA 259
>2a8x_A Dihydrolipoyl dehydrogenase, E3 component of alpha; lipoamide
dehydrogenase, pyruvate dehydrogenase, alpha keto acid
dehydrogenase; HET: FAD; 2.40A {Mycobacterium
tuberculosis} PDB: 3ii4_A*
Length = 464
Score = 30.2 bits (69), Expect = 1.6
Identities = 11/40 (27%), Positives = 14/40 (35%), Gaps = 11/40 (27%)
Query: 326 GAGAGIFCELFSFYKRLGTFTT----------NFDGEIAA 355
GAGA I E K G T N D +++
Sbjct: 178 GAGA-IGMEFGYVLKNYGVDVTIVEFLPRALPNEDADVSK 216
>1ci6_A Transcription factor ATF-4; BZIP; 2.60A {Homo sapiens} SCOP:
h.1.3.1
Length = 63
Score = 26.5 bits (59), Expect = 3.1
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 45 KKLSVLKSERNAA-----RKRAEKSNLLSDTVEWRKRAAILKKEINSSKR 89
KKL ++ + AA +KRAE+ L + E K+ LK+ +S +
Sbjct: 2 KKLKKMEQNKTAATRYRQKKRAEQEALTGECKELEKKNEALKERADSLAK 51
>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase,
hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} PDB:
3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A
Length = 150
Score = 27.9 bits (63), Expect = 4.2
Identities = 27/118 (22%), Positives = 41/118 (34%), Gaps = 24/118 (20%)
Query: 314 IYTDGS-LINPEDGAGAGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFER 372
Y DG+ + G AG T TTN E+ AI +AL +
Sbjct: 15 FYVDGAANRETKLG-KAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQ------DSGLE 67
Query: 373 AVILSDSKAAIQSITNCSEDPSIKHNKRLRNEGQGKK-------WQQIL----NTHDI 419
I++DS+ A+ IT I + K+ + KK QI+ +
Sbjct: 68 VNIVTDSQYALGIITQW-----IHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKV 120
>1onf_A GR, grase, glutathione reductase; oxidoreductase; HET: FAD; 2.60A
{Plasmodium falciparum} SCOP: c.3.1.5 c.3.1.5 d.87.1.1
Length = 500
Score = 28.7 bits (65), Expect = 4.6
Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 11/38 (28%)
Query: 328 GAG-IFCELFSFYKRLGTFTT----------NFDGEIA 354
G+G I EL + KRLG + FD +
Sbjct: 183 GSGYIAVELINVIKRLGIDSYIFARGNRILRKFDESVI 220
>3ic9_A Dihydrolipoamide dehydrogenase; APC62701, colwellia psychrer 34H,
structural genomics, PSI-2; HET: FAD; 2.15A {Colwellia
psychrerythraea}
Length = 492
Score = 28.3 bits (64), Expect = 5.7
Identities = 10/40 (25%), Positives = 11/40 (27%), Gaps = 11/40 (27%)
Query: 326 GAGAGIFCELFSFYKRLGTFTT----------NFDGEIAA 355
G G I EL RLG D E+
Sbjct: 181 GPGV-IGLELGQALSRLGVIVKVFGRSGSVANLQDEEMKR 219
>2yqu_A 2-oxoglutarate dehydrogenase E3 component; lipoamide dehydrogenase,
2-oxoglutarate dehydrogenase comple pyruvate
dehydrogenase complex; HET: FAD; 1.70A {Thermus
thermophilus} PDB: 2eq7_A*
Length = 455
Score = 28.2 bits (64), Expect = 5.9
Identities = 10/39 (25%), Positives = 13/39 (33%), Gaps = 11/39 (28%)
Query: 326 GAGAGIFCELFSFYKRLGT----------FTTNFDGEIA 354
G G I EL + RLG D E++
Sbjct: 174 GGGV-IGLELGVVWHRLGAEVIVLEYMDRILPTMDLEVS 211
>3p42_A Predicted protein; beta-grAsp, unknown function; HET: MSE; 1.91A
{Escherichia coli O127}
Length = 236
Score = 28.0 bits (62), Expect = 6.1
Identities = 2/33 (6%), Positives = 11/33 (33%)
Query: 182 TGAVKTTPINAMYALTQNQSLSDIIEQQALTTY 214
+ ++ ++++ ++ Q L
Sbjct: 5 MVTIYLPGEQQTLSVGPVENVAQLVTQPQLRDR 37
>1dxl_A Dihydrolipoamide dehydrogenase; oxidoreductase, multienzyme complex
protein, pyruvate dehydrogenase complex, glycine
decarboxylase complex; HET: FAD; 3.15A {Pisum sativum}
SCOP: c.3.1.5 c.3.1.5 d.87.1.1
Length = 470
Score = 27.9 bits (63), Expect = 8.1
Identities = 11/39 (28%), Positives = 15/39 (38%), Gaps = 11/39 (28%)
Query: 326 GAGAGIFCELFSFYKRLGT----------FTTNFDGEIA 354
GAG I E+ S + R+G+ D EI
Sbjct: 184 GAGY-IGLEMGSVWGRIGSEVTVVEFASEIVPTMDAEIR 221
>2xu0_A Erythrocyte membrane protein 1; adhesion, virulence,
duffy-binding-like-DO; 2.06A {Plasmodium falciparum palo
alto}
Length = 487
Score = 27.8 bits (62), Expect = 9.2
Identities = 19/84 (22%), Positives = 33/84 (39%), Gaps = 11/84 (13%)
Query: 72 EWRKRAAILKKEINSSKRSSFNTFVEKMDYRKDGPKAYS----FISSIKKGQTSVNKPFS 127
E+ K+ EI K++ N + ++ Y K+YS F++ + G+
Sbjct: 390 EFYKQNLKYSMEIQKWKKTKNNYYDKEF-YENLDKKSYSTIDKFLNLLNNGKHC--HDNK 446
Query: 128 HNGRSISDSKKIASIFNTFYTSKY 151
I +K I TF S+Y
Sbjct: 447 DEKNKIDFNKPI----KTFSISEY 466
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
0.315 0.130 0.371
Gapped
Lambda K H
0.267 0.0811 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,809,461
Number of extensions: 400231
Number of successful extensions: 686
Number of sequences better than 10.0: 1
Number of HSP's gapped: 679
Number of HSP's successfully gapped: 31
Length of query: 468
Length of database: 6,701,793
Length adjustment: 97
Effective length of query: 371
Effective length of database: 3,993,456
Effective search space: 1481572176
Effective search space used: 1481572176
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 59 (26.4 bits)