RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11625
(314 letters)
>1a0a_A BHLH, protein (phosphate system positive regulatory protein PHO4);
transcription factor, basic helix loop helix; HET: DNA;
2.80A {Saccharomyces cerevisiae} SCOP: a.38.1.1
Length = 63
Score = 54.4 bits (131), Expect = 3e-10
Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 219 IMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQ 272
E+ RR R+ L+EL SLI K + KA +E ++++++Q+
Sbjct: 8 HAEQARRNRLAVALHELASLIPAEW-KQQNVSAAPSKATTVEAACRYIRHLQQN 60
>1an4_A Protein (upstream stimulatory factor); protein-DNA complex, double
helix, overhanging base, transcription/DNA complex; HET:
DNA; 2.90A {Homo sapiens} SCOP: a.38.1.1
Length = 65
Score = 52.7 bits (127), Expect = 1e-09
Identities = 14/55 (25%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 219 IMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQQ 273
+E+RRR +INN + +L +I ++ + S K IL ++Q +++
Sbjct: 11 EVERRRRDKINNWIVQLSKIIPDSSMESTK--SGQSKGGILSKASDYIQELRQSN 63
>1am9_A Srebp-1A, protein (sterol regulatory element binding protein 1A);
basic-helix-loop- helix-leucine zipper, transcription
factor; HET: DNA; 2.30A {Homo sapiens} SCOP: a.38.1.1
PDB: 1ukl_C
Length = 82
Score = 47.0 bits (112), Expect = 2e-07
Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 7/54 (12%)
Query: 219 IMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQ 272
+EKR R+ IN+ + ELK L+ +KL K+ +L + +++ +Q
Sbjct: 12 AIEKRYRSSINDKIIELKDLV-------VGTEAKLNKSAVLRKAIDYIRFLQHS 58
>1nkp_B MAX protein, MYC proto-oncogene protein; transcription, DNA, BHLHZ,
heterodimer, transcription/DNA complex; 1.80A {Homo
sapiens} SCOP: a.38.1.1 PDB: 1an2_A* 1r05_A 1nlw_B
Length = 83
Score = 45.8 bits (109), Expect = 5e-07
Identities = 12/56 (21%), Positives = 29/56 (51%), Gaps = 8/56 (14%)
Query: 219 IMEKRRRARINNCLNELKSLILEAMRKDPA-RHSKLEKADILEMTVKHLQNVQRQQ 273
+E++RR I + + L+ + P+ + K +A IL+ +++Q ++R+
Sbjct: 8 ALERKRRDHIKDSFHSLRDSV-------PSLQGEKASRAQILDKATEYIQYMRRKN 56
>1hlo_A Protein (transcription factor MAX); transcriptional regulation, DNA
binding, complex (transcription factor MAX/DNA),
transcription/DNA complex; HET: DNA; 2.80A {Homo
sapiens} SCOP: a.38.1.1
Length = 80
Score = 44.6 bits (106), Expect = 1e-06
Identities = 12/56 (21%), Positives = 29/56 (51%), Gaps = 8/56 (14%)
Query: 219 IMEKRRRARINNCLNELKSLILEAMRKDPA-RHSKLEKADILEMTVKHLQNVQRQQ 273
+E++RR I + + L+ + P+ + K +A IL+ +++Q ++R+
Sbjct: 18 ALERKRRDHIKDSFHSLRDSV-------PSLQGEKASRAQILDKATEYIQYMRRKN 66
>1nkp_A C-MYC, MYC proto-oncogene protein; transcription, DNA, BHLHZ,
heterodimer, transcription/DNA complex; 1.80A {Homo
sapiens} SCOP: a.38.1.1
Length = 88
Score = 42.3 bits (100), Expect = 9e-06
Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 5/55 (9%)
Query: 219 IMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQQ 273
++E++RR + L+ I E + K K IL+ ++ +VQ ++
Sbjct: 12 VLERQRRNELKRSFFALRDQIPE-----LENNEKAPKVVILKKATAYILSVQAEE 61
>1nlw_A MAD protein, MAX dimerizer; transcription factor, DNA, BHLHZ,
transcription/DNA complex; 2.00A {Homo sapiens} SCOP:
a.38.1.1
Length = 80
Score = 41.7 bits (98), Expect = 1e-05
Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 5/54 (9%)
Query: 220 MEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQQ 273
MEK RRA + L +LK L+ S+ +L H++ ++
Sbjct: 8 MEKNRRAHLRLSLEKLKGLVPLG-----PDSSRHTTLSLLTKAKLHIKKLEDSD 56
>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS,
circadian rhythm proteins, transcription-activato; 2.27A
{Mus musculus}
Length = 361
Score = 43.8 bits (103), Expect = 3e-05
Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 10/88 (11%)
Query: 221 EKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQNVQRQQLSVAVAS 280
EK+RR + N + EL S++ P K++K+ +L+ ++ L+ + A +
Sbjct: 20 EKKRRDQFNVLIKELGSML-------PGNARKMDKSTVLQKSIDFLRKHKETT---AQSD 69
Query: 281 DPTVLQKFKSGFGDCAVEINRYISRLDG 308
+ Q +K F + LDG
Sbjct: 70 ASEIRQDWKPTFLSNEEFTQLMLEALDG 97
>2db7_A Hairy/enhancer-OF-split related with YRPW motif 1; structural
genomics, unknown function, DNA binding protein, NPPSFA;
1.90A {Homo sapiens} SCOP: a.273.1.1
Length = 64
Score = 38.9 bits (90), Expect = 1e-04
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 291 GFGDCAVEINRYISRLDGLDTE 312
GF +C E+ RY+S ++GLD
Sbjct: 23 GFRECLAEVARYLSIIEGLDAS 44
Score = 27.7 bits (61), Expect = 0.96
Identities = 6/14 (42%), Positives = 11/14 (78%)
Query: 7 VKSRLLNHLNSCVS 20
++ RL++HLN+ S
Sbjct: 47 LRVRLVSHLNNYAS 60
>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 = 41.8 bits (97), Expect = 2e-04
Identities = 26/165 (15%), Positives = 46/165 (27%), Gaps = 72/165 (43%)
Query: 150 TTQD-NVF-KVPSLQTKAFSSKPSYFSPYTNES-SLLMKV--------PPYHQAEPCSSS 198
TT+ V + + T S + +E SLL+K P E +++
Sbjct: 271 TTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPR----EVLTTN 326
Query: 199 ILIITALNTVLIWIFQSNKPIMEKRRRARINNCLNELKSLILEAMRKDPAR-----HSKL 253
+ S+I E++R A H
Sbjct: 327 PRRL----------------------------------SIIAESIRDGLATWDNWKHVNC 352
Query: 254 EK-ADILEMTVKHLQNVQRQQLSVAVASDPTVLQKFKSGFGDCAV 297
+K I+E ++ L +P +K F +V
Sbjct: 353 DKLTTIIESSLNVL--------------EPAEYRKM---FDRLSV 380
>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins,
transcription-activato; 2.27A {Mus musculus}
Length = 387
Score = 40.4 bits (94), Expect = 5e-04
Identities = 18/51 (35%), Positives = 31/51 (60%), Gaps = 6/51 (11%)
Query: 221 EKRRRARINNCLNELKSLI-LEAMRKDPARHSKLEKADILEMTVKHLQNVQ 270
EKRRR ++N+ ++EL SL+ A KL+K +L M V+H++ ++
Sbjct: 21 EKRRRDKMNSFIDELASLVPTCN-----AMSRKLDKLTVLRMAVQHMKTLR 66
>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 = 37.0 bits (85), Expect = 0.009
Identities = 42/264 (15%), Positives = 80/264 (30%), Gaps = 79/264 (29%)
Query: 56 NEASARLQMISSG-IQV-IPSRLPTGELALLLSGSSGL---FSS----PPEVSSSE---S 103
+ S R +S G ++ + +PT +S L F+ P E +++ +
Sbjct: 2 DAYSTRPLTLSHGSLEHVLL--VPTA----SFFIASQLQEQFNKILPEPTEGFAADDEPT 55
Query: 104 SSSDRVSAF-SVVEHKKPKSPPPSPTSSTDGDVV----------YLSPHNAEVTSTSTTQ 152
+ ++ V F V PS D V+ YL ++ +
Sbjct: 56 TPAELVGKFLGYVSSLVE----PSKVGQFD-QVLNLCLTEFENCYL--EGNDIHAL---- 104
Query: 153 DNVFKVPSLQTKAFSSKPSYFSPYTNESSLLMKVPPYHQAEPCSSSILIITAL--NTVLI 210
K+ Y + ++ K P + S+S L N L+
Sbjct: 105 --AAKLLQENDTTLVKTKELIKNYI-TARIMAKRPF----DKKSNSALFRAVGEGNAQLV 157
Query: 211 WIF--QSNKPIMEKRRRARINNCLNELKSLILEAMRKDPARHSKLEKADILEMTVKHLQN 268
IF Q N ++ EL+ L + + D+++ + + L
Sbjct: 158 AIFGGQGN-----------TDDYFEELRDL---------YQTYHVLVGDLIKFSAETLSE 197
Query: 269 VQRQQLSVAVASDPTVLQKFKSGF 292
+ R D + F G
Sbjct: 198 LIRT------TLDAEKV--FTQGL 213
Score = 32.3 bits (73), Expect = 0.23
Identities = 59/377 (15%), Positives = 110/377 (29%), Gaps = 136/377 (36%)
Query: 40 PVTLPPAPSLLEDVNNNEASARLQMISSGIQVIPSRLPTG-------EL----------- 81
P +L V A+L I G Q G EL
Sbjct: 136 PFDKKSNSALFRAVGEGN--AQLVAIFGG-Q--------GNTDDYFEELRDLYQTYHVLV 184
Query: 82 ALLLSGSSGLFSSPPEVSSSESSSSDRVSAFSVVE-HKKPKSPPP------SPTS----- 129
L+ S+ S + ++ + +++E + P + P P S
Sbjct: 185 GDLIKFSAETLS--ELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIG 242
Query: 130 -------STDGDVVYLSPHN--AEVTSTSTTQDNVFKVPSLQTKAFSSKPSYFSPYTNES 180
++ +P + + + + V ++ A + S+ S + +
Sbjct: 243 VIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGL--VTAV---AIAETDSWESFFVS-V 296
Query: 181 SLLMKVPPY-----HQAEPCS------------------SSILIITALN--TVLIWIFQS 215
+ V + ++A P + S +L I+ L V ++ ++
Sbjct: 297 RKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKT 356
Query: 216 NK--PIMEKRRRARINNCLN--------ELKSLILEAMRK-------DPAR--------- 249
N P ++ + +N N L L L +RK D +R
Sbjct: 357 NSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNL-TLRKAKAPSGLDQSRIPFSERKLK 415
Query: 250 ------------HSK-LEKA--DILEMTVKHLQNVQRQQLSVAV-----ASDPTVLQKFK 289
HS L A I + VK+ + + + + V SD L+
Sbjct: 416 FSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSD---LRVLS 472
Query: 290 SGFGDCAVEINRYISRL 306
G + I I RL
Sbjct: 473 ---GSISERIVDCIIRL 486
Score = 28.1 bits (62), Expect = 5.2
Identities = 10/36 (27%), Positives = 14/36 (38%), Gaps = 14/36 (38%)
Query: 49 LLEDVNNNEASARLQMISSGIQVIPSRLPTGEL-AL 83
L+E VN N Q + + G+L AL
Sbjct: 1840 LVEIVNYN---------VENQQYVAA----GDLRAL 1862
>3hjl_A Flagellar motor switch protein FLIG; armadillo repeat motif,
superhelix, conformational plasticit repeat, torque
generation; 2.40A {Aquifex aeolicus}
Length = 329
Score = 28.3 bits (62), Expect = 3.0
Identities = 11/52 (21%), Positives = 22/52 (42%), Gaps = 9/52 (17%)
Query: 242 AMRKDPARHSKLEKADILEMTV---------KHLQNVQRQQLSVAVASDPTV 284
M ++ + SK +KA +L +++ K L + Q+L +V
Sbjct: 1 GMAQEKSALSKAQKAAVLLLSLPEEVSMNIVKELSEEELQKLFALAKDLESV 52
>3bma_A D-alanyl-lipoteichoic acid synthetase; structural genomics,
D-alanyl-lipoteichoic acid biosynthesis structure
initiative, PSI-2; 2.24A {Streptococcus pneumoniae}
Length = 407
Score = 28.4 bits (63), Expect = 3.2
Identities = 15/51 (29%), Positives = 21/51 (41%), Gaps = 1/51 (1%)
Query: 142 NAEVTSTSTTQDNVFKVPSLQTKAFSSKPSYFSPYTNESSLLMKVPPYHQA 192
AE S T + FK S + +A S F P+ SS ++ H A
Sbjct: 12 GAEKRSAVATTIDSFKERSQKVRALSDPNVRFVPFFG-SSEWLRFDGAHPA 61
>2yg9_A DNA-3-methyladenine glycosidase II, putative; hydrolase, DNA
repair; 1.95A {Deinococcus radiodurans} PDB: 2yg8_A
Length = 225
Score = 27.3 bits (61), Expect = 5.6
Identities = 7/23 (30%), Positives = 10/23 (43%), Gaps = 2/23 (8%)
Query: 272 QQLSVAVASDPTVLQKFKSGFGD 294
QQLSV A + + + G
Sbjct: 72 QQLSVKAAQ--AIYGRLEGLPGG 92
>3u4g_A NAMN:DMB phosphoribosyltransferase; structural genomics,
PSI-biology, midwest center for structu genomics, MCSG;
1.90A {Pyrococcus horikoshii}
Length = 337
Score = 27.5 bits (61), Expect = 5.7
Identities = 10/68 (14%), Positives = 26/68 (38%), Gaps = 1/68 (1%)
Query: 31 PSSTTAPPPPVTLPPAPSLLEDVNNNEASARLQMISSGIQVIPSRLPTGELALLLSGSSG 90
P + P P P+++ ++ + ++ G + P +P ++ ++
Sbjct: 51 PLTIDTIPVTPEGHPTPAIITKAARELSNFPILVVRGGTYLAPL-IPHVHISNVVGRDFR 109
Query: 91 LFSSPPEV 98
+ PEV
Sbjct: 110 REPALPEV 117
>2h56_A DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, struc
genomics, PSI-2, protein structure initiative, joint
center structural genomics; 2.55A {Bacillus halodurans}
Length = 233
Score = 27.3 bits (61), Expect = 6.1
Identities = 7/23 (30%), Positives = 11/23 (47%), Gaps = 2/23 (8%)
Query: 272 QQLSVAVASDPTVLQKFKSGFGD 294
QQLS+ AS + + + G
Sbjct: 62 QQLSIKAAS--AIYGRVEQLVGG 82
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 27.3 bits (60), Expect = 7.5
Identities = 45/184 (24%), Positives = 63/184 (34%), Gaps = 19/184 (10%)
Query: 20 SGLQQLTPFSLPSSTTAPPPPVTLPPAPSLLEDVNNNEASARLQMISSGIQ-VIPSRLPT 78
G +P PSS P +P +P + + S S PS PT
Sbjct: 1549 PGYGLTSPSYSPSSPGYSTSPAYMPSSP------SYSPTSPSYSPTSPSYSPTSPSYSPT 1602
Query: 79 GELALLLSGSSGLFS--SP--PEVSSSESSSSDRVSAFSVVEHKKPKSPPPSPTSST-DG 133
+ S +S +S SP S S S +S S S P SP SPTS +
Sbjct: 1603 ---SPSYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTS--PSYSPTSPSYSPTSPSYSP 1657
Query: 134 DVVYLSPHNAEVTSTSTTQDNVFKVPSLQTKAFSSKPSYFSPYTNESSLLMKVPPYHQAE 193
SP + + TS + S + ++S +SP + S P Y
Sbjct: 1658 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS--PSYSPTS 1715
Query: 194 PCSS 197
P S
Sbjct: 1716 PSYS 1719
>1zy8_K Pyruvate dehydrogenase protein X component, mitochondrial; human,
dihydrolipoamide dehydrogenase, dihydrolipoyl
dehydrogenase; HET: FAD; 2.59A {Homo sapiens}
Length = 229
Score = 26.7 bits (59), Expect = 8.8
Identities = 8/64 (12%), Positives = 12/64 (18%)
Query: 77 PTGELALLLSGSSGLFSSPPEVSSSESSSSDRVSAFSVVEHKKPKSPPPSPTSSTDGDVV 136
G L L+ + + + S P
Sbjct: 70 RLGSLIGLIVEEGEDWKHVEIPKDVGPPPPVSKPSEPRPSPEPQISIPVKKEHIPGTLRF 129
Query: 137 YLSP 140
LSP
Sbjct: 130 RLSP 133
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
0.312 0.127 0.359
Gapped
Lambda K H
0.267 0.0557 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,392,041
Number of extensions: 239019
Number of successful extensions: 506
Number of sequences better than 10.0: 1
Number of HSP's gapped: 496
Number of HSP's successfully gapped: 35
Length of query: 314
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 221
Effective length of database: 4,105,140
Effective search space: 907235940
Effective search space used: 907235940
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 (21.9 bits)
S2: 57 (26.1 bits)