RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11118
(137 letters)
>2ql2_B Neurod1, neurogenic differentiation factor 1;
basic-helix-loop-helix; HET: DNA; 2.50A {Mus musculus}
Length = 60
Score = 92.7 bits (231), Expect = 3e-26
Identities = 32/56 (57%), Positives = 43/56 (76%)
Query: 38 RRLESNERERMRMHSLNDAFQSLREVIPHVKKERRLSKIETLTLAKNYIMALTNVI 93
RR+++N RER RMH LN A +LR+V+P K ++LSKIETL LAKNYI AL+ ++
Sbjct: 2 RRMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEIL 57
>1mdy_A Protein (MYOD BHLH domain); protein-DNA complex,
transcription/DNA complex; HET: DNA; 2.80A {Mus
musculus} SCOP: a.38.1.1 PDB: 1mdy_B*
Length = 68
Score = 74.3 bits (183), Expect = 4e-19
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 38 RRLESNERERMRMHSLNDAFQSLREVIPHVKKERRLSKIETLTLAKNYIMALTNVI 93
RR + RER R+ +N+AF++L+ +RL K+E L A YI L ++
Sbjct: 12 RRKAATMRERRRLSKVNEAFETLKRSTSS-NPNQRLPKVEILRNAIRYIEGLQALL 66
>3u5v_A Protein MAX, transcription factor E2-alpha chimer; basic
helix-loop-helix (BHLH); 1.70A {Mus musculus} PDB:
2ql2_A*
Length = 76
Score = 66.1 bits (161), Expect = 1e-15
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 38 RRLESNERERMRMHSLNDAFQSL-REVIPHVKKERRLSKIETLTLAKNYIMAL 89
+R N ER R +N+AF+ L R H+K ++ +K+ L A I+ L
Sbjct: 5 KRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGL 57
>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 = 55.0 bits (133), Expect = 2e-11
Identities = 18/66 (27%), Positives = 32/66 (48%)
Query: 34 EKNMRRLESNERERMRMHSLNDAFQSLREVIPHVKKERRLSKIETLTLAKNYIMALTNVI 93
N++R N ER R + L +F +LR+ IP ++ + K+ L A YI+++
Sbjct: 2 HMNVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEE 61
Query: 94 CDMRGE 99
+ E
Sbjct: 62 QKLISE 67
>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 = 43.1 bits (102), Expect = 7e-07
Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 1/67 (1%)
Query: 33 REKNMRRLESNERERMRMHSLNDAFQSLREVIPHVKKERRLSKIETLTLAKNYIMALTNV 92
+R N ER R + D+F SLR+ +P ++ E + S+ + L A YI +
Sbjct: 7 ESDADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGE-KASRAQILDKATEYIQYMRRK 65
Query: 93 ICDMRGE 99
+ +
Sbjct: 66 NHTHQQD 72
>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 = 42.9 bits (101), Expect = 9e-07
Identities = 14/57 (24%), Positives = 25/57 (43%)
Query: 43 NERERMRMHSLNDAFQSLREVIPHVKKERRLSKIETLTLAKNYIMALTNVICDMRGE 99
NE E+ R L + + L+ ++P R + + LT AK +I L + +
Sbjct: 6 NEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQ 62
>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 = 42.4 bits (100), Expect = 1e-06
Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 38 RRLESNERERMRMHSLNDAFQSLREVIPHVKKERRLSKIETLTLAKNYIMALTNVICDMR 97
+R N ER R + D+F SLR+ +P ++ E+ S+ + L A YI + +
Sbjct: 2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKA-SRAQILDKATEYIQYMRRKNHTHQ 60
Query: 98 GE 99
+
Sbjct: 61 QD 62
>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 = 42.4 bits (100), Expect = 2e-06
Identities = 15/67 (22%), Positives = 31/67 (46%), Gaps = 2/67 (2%)
Query: 33 REKNMRRLESNERERMRMHSLNDAFQSLREVIPHVKKERRLSKIETLTLAKNYIMALTNV 92
+ + +R N E+ S+ND L++++ + +L+K L A +YI L +
Sbjct: 1 QSRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEA--KLNKSAVLRKAIDYIRFLQHS 58
Query: 93 ICDMRGE 99
++ E
Sbjct: 59 NQKLKQE 65
>2lfh_A DNA-binding protein inhibitor ID-3; structural genomics,
northeast structural genomics consortiu PSI-biology,
protein structure initiative; NMR {Homo sapiens}
Length = 68
Score = 35.9 bits (82), Expect = 4e-04
Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 38 RRLESNERERMRM-HSLNDAFQSLREVIPHVKKERRLSKIETLTLAKNYIMAL 89
E + + +N + LRE++P V + +LS++E L +YI+ L
Sbjct: 13 GGKGPAAEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDL 65
>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 = 34.6 bits (80), Expect = 0.001
Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 38 RRLESNERERMRMHSLNDAFQSLREVIPHVKKE---RRLSKIETLTLAKNYIMAL 89
RR + NE ER R +N+ L ++IP E SK L+ A +YI L
Sbjct: 5 RRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQEL 59
>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 = 36.1 bits (82), Expect = 0.001
Identities = 11/50 (22%), Positives = 16/50 (32%), Gaps = 23/50 (46%)
Query: 68 KKERRLSKIETLTLAKNYIMALTNVICDMRGEDSPYVAPDSSTGLITSGT 117
K+ L K++ +L K Y A DS+ L T
Sbjct: 19 KQA--LKKLQA-SL-KLY-------------------ADDSAPALAIKAT 45
>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 = 31.3 bits (71), Expect = 0.018
Identities = 17/57 (29%), Positives = 23/57 (40%), Gaps = 4/57 (7%)
Query: 37 MRRLESNERERMRMHSLNDAFQSLREVIPHVKKE----RRLSKIETLTLAKNYIMAL 89
M+R E+ R + L A L +IP K+ SK T+ A YI L
Sbjct: 1 MKRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHL 57
>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 = 31.9 bits (72), Expect = 0.062
Identities = 15/62 (24%), Positives = 21/62 (33%), Gaps = 10/62 (16%)
Query: 76 IETLTLAKNYIMALTNVICDMRGEDSPYVAPDSSTGLITSGTQG--DTALTAHAHTEESF 133
I + LA +Y+ V + G +P G QG A + ESF
Sbjct: 241 IGVIQLA-HYV-----VTAKLLGF-TPGELRSYLKGATGHS-QGLVTAVAIAETDSWESF 292
Query: 134 FD 135
F
Sbjct: 293 FV 294
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 30.1 bits (67), Expect = 0.15
Identities = 10/56 (17%), Positives = 18/56 (32%), Gaps = 9/56 (16%)
Query: 33 REKNMRRLESNERERMRMHS---------LNDAFQSLREVIPHVKKERRLSKIETL 79
RE+ +RL+ + M L + Q E + K R++
Sbjct: 91 REEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKAFY 146
>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 = 27.9 bits (61), Expect = 1.2
Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 15/62 (24%)
Query: 37 MRRLESNER-ERMRMHSLNDAFQSLREVIPHVKKERRLSKIETLTLAKNYIMALTNVICD 95
++ +E ER RM L+ F L KI + A N ++ N +
Sbjct: 481 LKNIEHPERMTLFRMVFLDFRF--LE------------QKIRHDSTAWNASGSILNTLQQ 526
Query: 96 MR 97
++
Sbjct: 527 LK 528
>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins,
transcription-activato; 2.27A {Mus musculus}
Length = 387
Score = 27.3 bits (60), Expect = 1.9
Identities = 17/92 (18%), Positives = 33/92 (35%), Gaps = 8/92 (8%)
Query: 35 KNMRRLESNERERMRMHSLNDAFQSLREVIPHVKK-ERRLSKIETLTLAKNYIMALTNVI 93
R ++ E+ R +N L ++P R+L K+ L +A ++
Sbjct: 10 IKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKT----- 64
Query: 94 CDMRGEDSPYVAPDSSTGLITSGTQGDTALTA 125
+RG +PY + ++ L A
Sbjct: 65 --LRGATNPYTEANYKPTFLSDDELKHLILRA 94
>2gki_A Nuclease; anti-DNA antibody, catalytic antibody, immune system;
2.88A {Mus musculus}
Length = 291
Score = 26.1 bits (58), Expect = 4.6
Identities = 9/15 (60%), Positives = 9/15 (60%)
Query: 9 SGGGAGGGRGGSSSG 23
S GG G G GGS G
Sbjct: 142 SRGGGGSGGGGSGGG 156
Score = 25.8 bits (57), Expect = 4.7
Identities = 9/19 (47%), Positives = 9/19 (47%)
Query: 5 TCSISGGGAGGGRGGSSSG 23
T S GGG GG G G
Sbjct: 139 TVSSRGGGGSGGGGSGGGG 157
>2ell_A Acidic leucine-rich nuclear phosphoprotein 32 FAM B; phapi2
protein, silver-stainable protein SSP29, acidic prote
in leucines, structural genomics; NMR {Homo sapiens}
PDB: 2rr6_A 2jqd_A
Length = 168
Score = 25.1 bits (55), Expect = 6.9
Identities = 17/92 (18%), Positives = 34/92 (36%), Gaps = 9/92 (9%)
Query: 13 AGGGRGGSSSGRRRKPVLNAREKN---MRRLESNERERMRMHSLNDAFQSLREV------ 63
G G RR L R L++ + ++ L F +L +
Sbjct: 1 GSSGSSGMDMKRRIHLELRNRTPAAVRELVLDNCKSNDGKIEGLTAEFVNLEFLSLINVG 60
Query: 64 IPHVKKERRLSKIETLTLAKNYIMALTNVICD 95
+ V +L K++ L L++N I +++ +
Sbjct: 61 LISVSNLPKLPKLKKLELSENRIFGGLDMLAE 92
>2gzx_A Putative TATD related DNAse; deoxyribonuclease, NESG, ZR237,
structural GENO PSI, protein structure initiative; 2.20A
{Staphylococcus aureus subsp}
Length = 265
Score = 25.2 bits (56), Expect = 7.3
Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 23/49 (46%)
Query: 58 QSLREVIPHVKKERRLSKIETLTLAKNYIMALTNVICDMRGEDSPYVAP 106
+ +EV HV ER L +ET D+PY++P
Sbjct: 185 KQPKEVAKHVSMERLL--VET---------------------DAPYLSP 210
>2jis_A Cysteine sulfinic acid decarboxylase; pyridoxal phosphate,
alternative splicing, pyridoxal phosphate (PLP),
structural genomics consortium (SGC); HET: PLP; 1.6A
{Homo sapiens}
Length = 515
Score = 25.4 bits (56), Expect = 8.3
Identities = 5/29 (17%), Positives = 12/29 (41%)
Query: 34 EKNMRRLESNERERMRMHSLNDAFQSLRE 62
++R ++++ER +M L
Sbjct: 227 TDSVRVVKADERGKMVPEDLERQIGMAEA 255
>1j6o_A TATD-related deoxyribonuclease; structural genomics, TM0667, JCSG,
PSI, protein structure initiative, joint center for
structural genomics; 1.80A {Thermotoga maritima} SCOP:
c.1.9.12
Length = 268
Score = 25.2 bits (56), Expect = 8.3
Identities = 11/49 (22%), Positives = 18/49 (36%), Gaps = 23/49 (46%)
Query: 58 QSLREVIPHVKKERRLSKIETLTLAKNYIMALTNVICDMRGEDSPYVAP 106
++LREV+ V E + +ET D P++ P
Sbjct: 195 EALREVVKRVGLEYIV--LET---------------------DCPFLPP 220
>2ghw_B Anti-SARS SCFV antibody, 80R; S protein, neutralizing antibody,
virus/viral protein/antibiotic complex; 2.30A {Homo
sapiens} SCOP: b.1.1.1 b.1.1.1
Length = 247
Score = 24.9 bits (55), Expect = 9.2
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 8 ISGGGAGGGRGGSSSG 23
+S GG G G GGS G
Sbjct: 117 VSSGGGGSGGGGSGGG 132
>3ami_A Zinc peptidase; alpha/beta, zinc binding, hydrolase; 2.40A
{Sphingomonas} PDB: 3amj_C
Length = 445
Score = 25.0 bits (55), Expect = 9.8
Identities = 12/61 (19%), Positives = 20/61 (32%), Gaps = 27/61 (44%)
Query: 44 ERERMRMHSLNDA-FQSLREVIPHVKKERRLSKIETLTLAKNYIMALTNVICDMRGEDSP 102
E +RM ++D F+ +V + +ERR R +D P
Sbjct: 107 EADRMANLVVDDELFKKEIQV---IAEERR-----------------------WRTDDKP 140
Query: 103 Y 103
Sbjct: 141 R 141
>2qma_A Diaminobutyrate-pyruvate transaminase and L-2,4- diaminobutyrate
decarboxylase; structural genomics, APC91511.1,
glutamate decarboxylase; HET: MSE; 1.81A {Vibrio
parahaemolyticus}
Length = 497
Score = 25.0 bits (55), Expect = 9.9
Identities = 5/29 (17%), Positives = 13/29 (44%)
Query: 34 EKNMRRLESNERERMRMHSLNDAFQSLRE 62
EK + +++N M + L++ +
Sbjct: 226 EKAVMTVDANADGTMDITKLDEVIAQAKA 254
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
0.314 0.130 0.365
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: 2,028,784
Number of extensions: 110085
Number of successful extensions: 403
Number of sequences better than 10.0: 1
Number of HSP's gapped: 386
Number of HSP's successfully gapped: 45
Length of query: 137
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 53
Effective length of database: 4,356,429
Effective search space: 230890737
Effective search space used: 230890737
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 (22.0 bits)
S2: 52 (24.2 bits)