RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy505
(161 letters)
>3vu4_A KMHSV2; beta-propeller fold, protein transport; 2.60A
{Kluyveromyces marxianus} PDB: 4av9_A 4av8_A 4exv_A
Length = 355
Score = 76.2 bits (187), Expect = 3e-17
Identities = 10/83 (12%), Positives = 30/83 (36%), Gaps = 4/83 (4%)
Query: 66 SLSVGTKSGYRLFSLNSIDTLEQIYENSQEDVCIVERLFSSSLVAVVSLSSPRKLTVCHF 125
L + T + ++++ + I + V L ++ VA V+ + +
Sbjct: 33 CLILSTLKSFEIYNV---HPVAHIMSQEMRHLSKVRMLHRTNYVAFVT-GVKEVVHIWDD 88
Query: 126 KRGSEICNYSFSNTILAVKLNRK 148
+ ++ + + L+R+
Sbjct: 89 VKKQDVSRIKVDAPVKDLFLSRE 111
Score = 39.2 bits (91), Expect = 2e-04
Identities = 12/79 (15%), Positives = 21/79 (26%), Gaps = 20/79 (25%)
Query: 10 TPPNPNGICCLCVNSDNCYLAYPGSNSIGEVQI----------------FDADNLHAKTM 53
G+C N L Y ++G++ I L +
Sbjct: 135 DDIRFGGVCEFS----NGLLVYSNEFNLGQIHITKLQSSGSATTQDQGVQQKAILGKGVL 190
Query: 54 IPAHDSPLAALASLSVGTK 72
I AH +P+ +
Sbjct: 191 IKAHTNPIKMVRLNRKSDM 209
>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 = 40.0 bits (93), Expect = 1e-04
Identities = 14/94 (14%), Positives = 28/94 (29%), Gaps = 10/94 (10%)
Query: 43 FDADNLHAKTMIPAHDSPLAALASLSVGTKSGYRLF-----SLNSIDTLEQIYENSQEDV 97
A + + +S L ++ G +F + + + L +Y+
Sbjct: 127 ITARIMAKRPFDKKSNSAL--FRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHV-- 182
Query: 98 CIVERLFSSSLVAVVSLSSPRKLTVCHFKRGSEI 131
+V L S + L F +G I
Sbjct: 183 -LVGDLIKFSAETLSELIRTTLDAEKVFTQGLNI 215
>2mad_H Methylamine dehydrogenase (heavy subunit);
oxidoreductase(CHNH2(D)-deaminating); HET: TRQ; 2.25A
{Paracoccus versutus} SCOP: b.69.2.1 PDB: 1mae_H*
1maf_H*
Length = 373
Score = 30.6 bits (68), Expect = 0.21
Identities = 15/136 (11%), Positives = 39/136 (28%), Gaps = 18/136 (13%)
Query: 28 YLAYPGSNSI-GEVQIFDADNLHAKTMIPAHDSPLAALASLSVGTKSGYRLFSLNSIDTL 86
Y+ P +S + + DA + + P SG ++ +
Sbjct: 36 YINLPAHHSAIIQQWVLDAGSGSILGHVNGGFLPNPVA------AHSGSEFALAST--SF 87
Query: 87 EQIYENSQEDVCIVERLFSSSLVAVVSLSSPRKLTVCHFKRGSE---------ICNYSFS 137
+I + + D V + +A + L + V + + ++
Sbjct: 88 SRIAKGKRTDYVEVFDPVTFLPIADIELPDAPRFDVGPYSWMNANTPNNADLLFFQFAAG 147
Query: 138 NTILAVKLNRKKEEEE 153
+ V +++
Sbjct: 148 PAVGLVVQGGSSDDQL 163
>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 = 30.2 bits (67), Expect = 0.28
Identities = 22/126 (17%), Positives = 40/126 (31%), Gaps = 35/126 (27%)
Query: 44 DADNLHAKTMIPAHDSPLAALASLSVGTKSGYRLFSL-----N-SIDTLEQIYENSQEDV 97
+ D L T+I +S L L + + S+ + L I+ + +
Sbjct: 351 NCDKL--TTII---ESSLNVLEPAEY--RKMFDRLSVFPPSAHIPTILLSLIWFDVIKSD 403
Query: 98 C--IVERLFSSSLVAVVSLSSPRKLTVCHFKRGSEICNYSFSNTILAVKLNRKKEEEEDE 155
+V +L SLV K + S I ++ L K + E +
Sbjct: 404 VMVVVNKLHKYSLVE------------KQPKEST----IS----IPSIYLELKVKLENEY 443
Query: 156 EEEKKI 161
+ I
Sbjct: 444 ALHRSI 449
Score = 29.1 bits (64), Expect = 0.76
Identities = 22/160 (13%), Positives = 45/160 (28%), Gaps = 37/160 (23%)
Query: 11 PPNPNGICCLCVNSDNCYLAYPGSNSIGEVQIFDADNLHAKTMIPAHDSPLAALASLSVG 70
P N CL V + + + ++A NL K ++ + +
Sbjct: 241 KPYEN---CLLVLLN-----------VQNAKAWNAFNLSCKILLTTRFKQVTD----FLS 282
Query: 71 TKSGYRLFSLNSIDTLEQIYENSQEDVCIVERLFSSSL-VAVVSLS------SPRKLTVC 123
+ + + TL + + L L L +PR+L++
Sbjct: 283 AATTTHISLDHHSMTLTP--DEVKS-------LLLKYLDCRPQDLPREVLTTNPRRLSII 333
Query: 124 HFKRGSEICNYSFSNTILAVKLNRKKE---EEEDEEEEKK 160
+ + + KL E + E +K
Sbjct: 334 AESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRK 373
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 29.4 bits (65), Expect = 0.35
Identities = 3/15 (20%), Positives = 7/15 (46%), Gaps = 1/15 (6%)
Query: 147 RKKE-EEEDEEEEKK 160
++K +E D +
Sbjct: 94 QRKRLQELDAASKVM 108
Score = 26.7 bits (58), Expect = 3.5
Identities = 2/17 (11%), Positives = 7/17 (41%), Gaps = 2/17 (11%)
Query: 144 KLNRKKEEE--EDEEEE 158
NR ++ + + +
Sbjct: 136 INNRIADKAFYQQPDAD 152
>1r8d_A Transcription activator MTAN; protein-DNA complex,
transcription/DNA complex; 2.70A {Bacillus subtilis}
SCOP: a.6.1.3 PDB: 1jbg_A
Length = 109
Score = 28.3 bits (64), Expect = 0.56
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 71 TKSGYRLFSLNSIDTLEQI 89
T +GYRL+S ++ L+QI
Sbjct: 34 TDAGYRLYSDADLERLQQI 52
>3gpv_A Transcriptional regulator, MERR family; protein structure
initiative II(PSI II), NYSGXRC, structural genomics;
1.90A {Bacillus thuringiensis serovarkonkukian}
Length = 148
Score = 28.1 bits (63), Expect = 0.79
Identities = 6/19 (31%), Positives = 11/19 (57%)
Query: 71 TKSGYRLFSLNSIDTLEQI 89
+ G R+F+ ++ LE I
Sbjct: 48 NEKGDRIFNEEALKYLEMI 66
>3qao_A LMO0526 protein, MERR-like transcriptional regulator; structural
genomics, the center for structural genomics of I
diseases, csgid; 1.87A {Listeria monocytogenes}
Length = 249
Score = 28.2 bits (63), Expect = 0.98
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 71 TKSGYRLFSLNSIDTLEQI 89
+GYR++S +D L+QI
Sbjct: 35 DWNGYRIYSEKDVDKLQQI 53
>3hh0_A Transcriptional regulator, MERR family; protein structure
initiative II(PSI II), NYSGXRC, 11183J, structural
genomics; 2.67A {Bacillus cereus atcc 14579}
Length = 146
Score = 27.7 bits (62), Expect = 1.1
Identities = 7/19 (36%), Positives = 14/19 (73%)
Query: 71 TKSGYRLFSLNSIDTLEQI 89
T+ G+RL++ + + L+QI
Sbjct: 36 TEGGHRLYTKDDLYVLQQI 54
>2vz4_A Tipal, HTH-type transcriptional activator TIPA; transcription,
resistance, antibiotic; 2.90A {Streptomyces lividans}
Length = 108
Score = 27.2 bits (61), Expect = 1.1
Identities = 7/19 (36%), Positives = 13/19 (68%)
Query: 71 TKSGYRLFSLNSIDTLEQI 89
+ +G+R +S +D L+QI
Sbjct: 33 SHAGHRRYSDADLDRLQQI 51
>1r8e_A Multidrug-efflux transporter regulator; protein-DNA complex,
MERR-family transcription activator, MU binding
protein; HET: P4P; 2.40A {Bacillus subtilis} SCOP:
a.6.1.3 d.60.1.1 PDB: 1exi_A* 1exj_A* 3iao_A 3q5p_A*
3d71_A* 3q3d_A* 3q1m_A* 3q2y_A* 3q5r_A* 3q5s_A* 3d70_A
3d6z_A* 3d6y_A* 1bow_A 2bow_A*
Length = 278
Score = 27.4 bits (61), Expect = 2.3
Identities = 5/21 (23%), Positives = 11/21 (52%)
Query: 69 VGTKSGYRLFSLNSIDTLEQI 89
V + YR ++ + + L+ I
Sbjct: 36 VDPDTSYRYYTDSQLIHLDLI 56
>2e85_A Hydrogenase 3 maturation protease; structural genomics, NPPSFA,
national project on protein structural and functional
analyses; 1.70A {Escherichia coli} PDB: 2i8l_A
Length = 159
Score = 26.3 bits (58), Expect = 3.3
Identities = 11/38 (28%), Positives = 18/38 (47%)
Query: 30 AYPGSNSIGEVQIFDADNLHAKTMIPAHDSPLAALASL 67
A + GE++I D D++ M+ H+ PL L
Sbjct: 66 ATDMGLNPGEIRIIDPDDIAEMFMMTTHNMPLNYLIDQ 103
>3rmg_A Octaprenyl-diphosphate synthase; structural genomics, protein
structure initiative, isoprene biosynthesis,
transferase; 2.30A {Bacteroides thetaiotaomicron}
Length = 334
Score = 26.1 bits (58), Expect = 5.9
Identities = 7/33 (21%), Positives = 16/33 (48%)
Query: 82 SIDTLEQIYENSQEDVCIVERLFSSSLVAVVSL 114
S+D++ I + ++ + LF + L +L
Sbjct: 2 SLDSISLIKTPIEAELEDFKALFDTPLSDSNAL 34
>3gp4_A Transcriptional regulator, MERR family; structural genomics,
DNA-BI transcription regulator, PSI-2; 1.85A {Listeria
monocytogenes str}
Length = 142
Score = 25.3 bits (56), Expect = 6.4
Identities = 4/19 (21%), Positives = 7/19 (36%)
Query: 71 TKSGYRLFSLNSIDTLEQI 89
+SG R F + +
Sbjct: 34 NESGVRKFGAEDLRWILFT 52
>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase
activation, cytochrome C, procaspase-9, A nucleotide,
cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A*
3iyt_A* 3iza_A*
Length = 1249
Score = 25.9 bits (57), Expect = 8.6
Identities = 10/51 (19%), Positives = 19/51 (37%), Gaps = 2/51 (3%)
Query: 15 NGICCLCVNSDNCYLAYPGSNSIGEVQIFDADNLHAKTMIPAHDSPLAALA 65
+ + C + D +A +Q+F A+ I AH+ + A
Sbjct: 616 DAVYHACFSQDGQRIAS-CGAD-KTLQVFKAETGEKLLDIKAHEDEVLCCA 664
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
0.316 0.131 0.378
Gapped
Lambda K H
0.267 0.0550 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,306,149
Number of extensions: 120473
Number of successful extensions: 304
Number of sequences better than 10.0: 1
Number of HSP's gapped: 299
Number of HSP's successfully gapped: 20
Length of query: 161
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 75
Effective length of database: 4,300,587
Effective search space: 322544025
Effective search space used: 322544025
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: 53 (24.6 bits)