RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 045358
(200 letters)
>2p02_A S-adenosylmethionine synthetase isoform type-2; structural
genomics, structural genomics consortium, SGC,
transferase; HET: SAM; 1.21A {Homo sapiens} SCOP:
d.130.1.1 d.130.1.1 d.130.1.1 PDB: 1qm4_A 1o92_A*
1o93_A* 1o90_A* 1o9t_A 2obv_A*
Length = 396
Score = 403 bits (1038), Expect = e-143
Identities = 131/199 (65%), Positives = 158/199 (79%), Gaps = 2/199 (1%)
Query: 1 METFLFTSESVNEGHPDKLCDQVSDAVLDACLAQDPDSKVACETCTKTNMVMVFGEITTK 60
TFLFTSESV EGHPDK+CDQ+SDAVLDA L QDPD+KVACET KT M+++ GEIT++
Sbjct: 16 EGTFLFTSESVGEGHPDKICDQISDAVLDAHLQQDPDAKVACETVAKTGMILLAGEITSR 75
Query: 61 ANVDYEKIVRDTCRSIGFTSADVGLDADHCKVLVNIEQQSPDIAQGVHGHLTKRPEEIGA 120
A VDY+K+VR+ + IG+ + G D C VLV +EQQSPDIAQGV HL + E+IGA
Sbjct: 76 AAVDYQKVVREAVKHIGYDDSSKGFDYKTCNVLVALEQQSPDIAQGV--HLDRNEEDIGA 133
Query: 121 GDQGHMFGYATDETPELMPLSHVLATKLGAKLTEVRKNGTCPWLRPDGKTQVTVEYYNEN 180
GDQG MFGYATDET E MPL+ VLA KL AKL E+R+NGT PWLRPD KTQVTV+Y +
Sbjct: 134 GDQGLMFGYATDETEECMPLTIVLAHKLNAKLAELRRNGTLPWLRPDSKTQVTVQYMQDR 193
Query: 181 GAMVPVRVHTVLISTQHDE 199
GA++P+RVHT++IS QHDE
Sbjct: 194 GAVLPIRVHTIVISVQHDE 212
>3so4_A Methionine-adenosyltransferase; structural genomics, medical
structural genomics of pathogen protozoa, MSGPP; 3.18A
{Entamoeba histolytica}
Length = 415
Score = 403 bits (1037), Expect = e-143
Identities = 120/199 (60%), Positives = 148/199 (74%), Gaps = 2/199 (1%)
Query: 1 METFLFTSESVNEGHPDKLCDQVSDAVLDACLAQDPDSKVACETCTKTNMVMVFGEITTK 60
F FTSESV+ GHPDK+CDQ+SDA+LDACLAQDP S VACET TKT +++V GEITT
Sbjct: 20 GSRFFFTSESVSGGHPDKMCDQISDAILDACLAQDPKSHVACETATKTGLILVLGEITTN 79
Query: 61 ANVDYEKIVRDTCRSIGFTSADVGLDADHCKVLVNIEQQSPDIAQGVHGHLTKRPEEIGA 120
A +D KIVR +SIG+ + G D C VL +EQQS DIA+GVH K+ E+IGA
Sbjct: 80 AVIDIPKIVRGVVKSIGYDDTNKGFDYQTCSVLSCVEQQSQDIAKGVHVE--KKEEDIGA 137
Query: 121 GDQGHMFGYATDETPELMPLSHVLATKLGAKLTEVRKNGTCPWLRPDGKTQVTVEYYNEN 180
GDQG MFGYATDE+ E+MPL+HVL+TKL +L E R+ G PWLRPD K+QVT+EY
Sbjct: 138 GDQGIMFGYATDESKEMMPLTHVLSTKLILRLQECREKGILPWLRPDSKSQVTLEYEEVE 197
Query: 181 GAMVPVRVHTVLISTQHDE 199
G + P+RVHT++ISTQH +
Sbjct: 198 GHLKPIRVHTIVISTQHAD 216
>3iml_A S-adenosylmethionine synthetase; structural genomics, ATP-BI
cobalt, magnesium, metal-binding, nucleotide-binding,
one-C metabolism; 2.35A {Burkholderia pseudomallei}
Length = 399
Score = 384 bits (990), Expect = e-136
Identities = 107/199 (53%), Positives = 136/199 (68%), Gaps = 5/199 (2%)
Query: 1 METFLFTSESVNEGHPDKLCDQVSDAVLDACLAQDPDSKVACETCTKTNMVMVFGEITTK 60
+LFTSESV+EGHPDK+ DQ+SDA+LDA LAQD S+VA ET T +V++ GEITT
Sbjct: 6 ANDYLFTSESVSEGHPDKVADQISDAILDAILAQDKYSRVAAETLCNTGLVVLAGEITTT 65
Query: 61 ANVDYEKIVRDTCRSIGFTSADVGLDADHCKVLVNIEQQSPDIAQGVHGHLTKRPEEIGA 120
AN+DY +I RDT + IG+ + D G+D C VLV ++QSPDIAQGV + GA
Sbjct: 66 ANIDYIQIARDTIKRIGYDNTDYGIDYRGCAVLVAYDKQSPDIAQGVD-RAHDNNLDQGA 124
Query: 121 GDQGHMFGYATDETPELMPLSHVLATKLGAKLTEVRKNGTCPWLRPDGKTQVTVEYYNEN 180
GDQG MFGYA DETPELMPL L+ +L + +R++G PWLRPD K+QVTV Y +
Sbjct: 125 GDQGLMFGYACDETPELMPLPIHLSHRLVERQANLRRDGRLPWLRPDAKSQVTVRY--VD 182
Query: 181 GAMVPVRVHTVLISTQHDE 199
G P + TV++STQH
Sbjct: 183 G--KPHSIDTVVLSTQHAP 199
>3s82_A S-adenosylmethionine synthase; seattle structural genomics center
for infectious disease, S adenosylmethionine synthetase,
transferase; 1.73A {Mycobacterium avium} PDB: 3tde_A
3rv2_A
Length = 407
Score = 376 bits (967), Expect = e-132
Identities = 112/209 (53%), Positives = 133/209 (63%), Gaps = 14/209 (6%)
Query: 1 METFLFTSESVNEGHPDKLCDQVSDAVLDACLAQDPDSKVACETCTKTNMVMVFGEITTK 60
+ LFTSESV EGHPDK+CD +SD+VLDA LAQDP S+VA ET T V V GE+TT
Sbjct: 7 EKGRLFTSESVTEGHPDKICDAISDSVLDALLAQDPRSRVAVETLVTTGQVHVVGEVTTT 66
Query: 61 AN---VDYEKIVRDTCRSIGFTSADVGLDADHCKVLVNIEQQSPDIAQGVH-------GH 110
A D VR+ IG+ S+D G D C V + I QSPDIAQGV
Sbjct: 67 AKEAFADITNTVRERILDIGYDSSDKGFDGASCGVNIGIGAQSPDIAQGVDTAHETRVEG 126
Query: 111 LTKRPEEIGAGDQGHMFGYATDETPELMPLSHVLATKLGAKLTEVRKNGTCPWLRPDGKT 170
+ GAGDQG MFGYA ++TPE MPL LA +L +LTEVRKNG P+LRPDGKT
Sbjct: 127 AADPLDAQGAGDQGLMFGYAINDTPERMPLPIALAHRLSRRLTEVRKNGVLPYLRPDGKT 186
Query: 171 QVTVEYYNENGAMVPVRVHTVLISTQHDE 199
QVT+E+ E+ VPVR+ TV+ISTQH
Sbjct: 187 QVTIEF--EDD--VPVRLDTVVISTQHAA 211
>1p7l_A S-adenosylmethionine synthetase; AMPPNP, SAM, transferase; HET: SAM
ANP PPK; 2.50A {Escherichia coli} SCOP: d.130.1.1
d.130.1.1 d.130.1.1 PDB: 1fug_A 1mxb_A* 1mxc_A* 1mxa_A*
1rg9_A* 1xra_A 1xrb_A 1xrc_A
Length = 383
Score = 370 bits (952), Expect = e-130
Identities = 114/196 (58%), Positives = 137/196 (69%), Gaps = 7/196 (3%)
Query: 4 FLFTSESVNEGHPDKLCDQVSDAVLDACLAQDPDSKVACETCTKTNMVMVFGEITTKANV 63
LFTSESV+EGHPDK+ DQ+SDAVLDA L QDP ++VACET KT MV+V GEITT A V
Sbjct: 3 HLFTSESVSEGHPDKIADQISDAVLDAILEQDPKARVACETYVKTGMVLVGGEITTSAWV 62
Query: 64 DYEKIVRDTCRSIGFTSADVGLDADHCKVLVNIEQQSPDIAQGVHGHLTKRPEEIGAGDQ 123
D E+I R+T R IG+ +D+G DA+ C VL I +QSPDI QGV P E GAGDQ
Sbjct: 63 DIEEITRNTVREIGYVHSDMGFDANSCAVLSAIGKQSPDINQGVD---RADPLEQGAGDQ 119
Query: 124 GHMFGYATDETPELMPLSHVLATKLGAKLTEVRKNGTCPWLRPDGKTQVTVEYYNENGAM 183
G MFGYAT+ET LMP A +L + EVRKNGT PWLRPD K+QVT +Y ++G
Sbjct: 120 GLMFGYATNETDVLMPAPITYAHRLVQRQAEVRKNGTLPWLRPDAKSQVTFQY--DDG-- 175
Query: 184 VPVRVHTVLISTQHDE 199
V + V++STQH E
Sbjct: 176 KIVGIDAVVLSTQHSE 191
>2ee0_A Protocadherin-9; Ca domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 114
Score = 34.0 bits (79), Expect = 0.009
Identities = 8/42 (19%), Positives = 17/42 (40%), Gaps = 3/42 (7%)
Query: 55 GEITTKANVDYEKIVRDTCRSIGFTSADVGLDADHCKVLVNI 96
G IT + ++D E+ + ++D V +N+
Sbjct: 72 GLITVQRSLDREET---AIHKVTVLASDGSSTPARATVTINV 110
>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 = 34.8 bits (79), Expect = 0.017
Identities = 17/172 (9%), Positives = 45/172 (26%), Gaps = 61/172 (35%)
Query: 64 DYEK---IVRDTCRSIGFTSADVGLDA-D-HCKVLVNIEQQSPDIAQGVHGHLTKRPEEI 118
YE ++ + +A +A + CK+L+ + + + T
Sbjct: 242 PYENCLLVLLNVQ------NAKA-WNAFNLSCKILLTTRFKQ--VTDFLSAATTTHISLD 292
Query: 119 GAGDQGHMFGYATDET---------------PELMPLSHVLATKL-GAKLTEVRKNGTC- 161
H DE P + ++ + + ++G
Sbjct: 293 -----HHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESI----RDGLAT 343
Query: 162 --PWLRPDGKTQVTV--------------EYYNE-----NGAMVPVRVHTVL 192
W + T+ + ++ A +P + +++
Sbjct: 344 WDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLI 395
>2yst_A Protocadherin-7; BH-PCDH, beta-sandwich, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 119
Score = 30.9 bits (71), Expect = 0.088
Identities = 9/44 (20%), Positives = 17/44 (38%), Gaps = 5/44 (11%)
Query: 55 GEITTKANVDYEKIVRDTCRSIGFTSADVGLD--ADHCKVLVNI 96
G ++ +D E++ + D G D V++NI
Sbjct: 71 GWLSVLHRIDREEV---NQLRFTVMARDRGQPPKTDKATVVLNI 111
>2v05_A Choline binding protein F; CBPF, lipid-binding-protein; 1.67A
{Streptococcus pneumoniae} PDB: 2v04_A 2x8m_A* 2x8o_A*
2x8p_A* 2vyu_A
Length = 311
Score = 27.8 bits (62), Expect = 2.3
Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 6/30 (20%)
Query: 157 KNGTCP--WLRPDGKTQVTVEYYNENGAMV 184
K+ W + DGKT Y+ + G MV
Sbjct: 18 KDDHKAIYWHKIDGKTY----YFGDIGEMV 43
>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 = 27.2 bits (59), Expect = 2.5
Identities = 7/18 (38%), Positives = 8/18 (44%), Gaps = 4/18 (22%)
Query: 129 YATDETPELMPLSHVLAT 146
YA D P L + AT
Sbjct: 32 YADDSAPALA----IKAT 45
>2fiq_A Putative tagatose 6-phosphate kinase 1; structural genomics, PSI,
protein structure initiative, NEW research center for
structural genomics; 2.25A {Escherichia coli} SCOP:
c.1.10.7
Length = 420
Score = 27.7 bits (61), Expect = 3.0
Identities = 19/69 (27%), Positives = 27/69 (39%), Gaps = 4/69 (5%)
Query: 24 SDAVLDACL--AQDPDSKVACETCTKTNMVMVFGEITTKANVDYEKIVRDTCRSIGFTSA 81
V++A L ++ KV E T N V FG T D+ + V +GF
Sbjct: 23 HPLVIEAALAFDRNSTRKVLIE-ATS-NQVNQFGGYTGMTPADFREFVFAIADKVGFARE 80
Query: 82 DVGLDADHC 90
+ L DH
Sbjct: 81 RIILGGDHL 89
>3txv_A Probable tagatose 6-phosphate kinase; structural genomics,
PSI-biology, NEW YORK structural genomi research
consortium, nysgrc; 2.80A {Sinorhizobium meliloti}
Length = 450
Score = 27.3 bits (60), Expect = 3.5
Identities = 17/69 (24%), Positives = 24/69 (34%), Gaps = 4/69 (5%)
Query: 24 SDAVLDACL--AQDPDSKVACETCTKTNMVMVFGEITTKANVDYEKIVRDTCRSIGFTSA 81
V++A + A + V E T N V G T D+ + V I F
Sbjct: 30 HPLVIEAAMLRAHREKAPVLIE-ATC-NQVNQDGGYTGMTPEDFTRFVGAIADRIEFPRE 87
Query: 82 DVGLDADHC 90
+ L DH
Sbjct: 88 KILLGGDHL 96
>2qj6_A Toxin A; clostridial repetitive oligo peptides; 2.50A {Clostridium
difficile}
Length = 332
Score = 27.1 bits (60), Expect = 4.0
Identities = 6/22 (27%), Positives = 10/22 (45%), Gaps = 4/22 (18%)
Query: 163 WLRPDGKTQVTVEYYNENGAMV 184
+ +GK Y+N +G M
Sbjct: 17 YTSINGKHF----YFNTDGIMQ 34
>3ubh_A Neural-cadherin; cell adhesion; 2.70A {Drosophila melanogaster}
Length = 419
Score = 26.5 bits (59), Expect = 6.4
Identities = 5/51 (9%), Positives = 12/51 (23%), Gaps = 13/51 (25%)
Query: 55 GEITTKANVDYEKI--------VRDTCRSIGFTSADVGLDADHCKVLVNIE 97
G + T+ ++ D D + ++I
Sbjct: 166 GVVRTRGTDLFQLDMEYVLYVKAED-----QNGKVDDRRFQSTPEERLSIV 211
>2qae_A Lipoamide, dihydrolipoyl dehydrogenase; FAD-cystine-oxidoreductase,
homodimer; HET: FAD; 1.90A {Trypanosoma cruzi}
Length = 468
Score = 26.3 bits (59), Expect = 7.5
Identities = 10/49 (20%), Positives = 16/49 (32%), Gaps = 10/49 (20%)
Query: 147 KLGAKLTEVRKNGTCPWLRPDGKTQVTVEYYNENGAMVPVRVHTVLIST 195
K+ NG V++E +NG V +L+S
Sbjct: 234 MTSTKVVGGTNNGD----------SVSLEVEGKNGKRETVTCEALLVSV 272
>1a1d_A RNA polymerase; RPB8, OB fold, eukaryotic, yeast,
nucleotidyltransferase; NMR {Saccharomyces cerevisiae}
SCOP: b.40.4.8 PDB: 1i3q_H 1i50_H 1i6h_H 1k83_H* 1nik_H
1nt9_H 1pqv_H 1r5u_H 1r9s_H* 1r9t_H* 1sfo_H* 1twa_H*
1twc_H* 1twf_H* 1twg_H* 1twh_H* 1wcm_H 1y1v_H 1y1w_H
1y1y_H ...
Length = 146
Score = 25.7 bits (56), Expect = 9.4
Identities = 12/75 (16%), Positives = 21/75 (28%), Gaps = 10/75 (13%)
Query: 53 VFGEITTKANVD---YEKIVRDTCRSIGFTSADVGLDADHCKVLVNIEQQSPDIAQGVHG 109
+F +I + VD Y K+ R S + LD +N+E +
Sbjct: 5 LFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLD-------INVELFPVAAQDSLTV 57
Query: 110 HLTKRPEEIGAGDQG 124
+
Sbjct: 58 TIASSLNLEDTPAND 72
>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 = 25.8 bits (56), Expect = 9.5
Identities = 8/55 (14%), Positives = 17/55 (30%), Gaps = 14/55 (25%)
Query: 34 QDPDSKVACETCTKTNMVMVFGEITTKANVDYEK--IVRDTCRSIGFTSADVGLD 86
+ + + C C +V + + +V C G +D +D
Sbjct: 16 PNLNIVLTCPECKVYPPKIVE---------RFSEGDVV---CALCGLVLSDKLVD 58
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 0.132 0.395
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,045,371
Number of extensions: 178693
Number of successful extensions: 464
Number of sequences better than 10.0: 1
Number of HSP's gapped: 454
Number of HSP's successfully gapped: 27
Length of query: 200
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 111
Effective length of database: 4,216,824
Effective search space: 468067464
Effective search space used: 468067464
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: 55 (25.0 bits)