RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5448
(322 letters)
>1hbx_A SRF, serum response factor; gene regulation, transcription complex;
3.15A {Homo sapiens} SCOP: d.88.1.1 PDB: 1srs_A*
Length = 92
Score = 131 bits (332), Expect = 7e-39
Identities = 84/92 (91%), Positives = 87/92 (94%)
Query: 127 SPPSNGKKTKGRVKIKMEYIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVMLLVASET 186
S GKKT+GRVKIKME+IDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQV+LLVASET
Sbjct: 1 SGAKPGKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASET 60
Query: 187 GHVYTFATRKLQPMITSEAGKALIQTCLNSPD 218
GHVYTFATRKLQPMITSE GKALIQTCLNSPD
Sbjct: 61 GHVYTFATRKLQPMITSETGKALIQTCLNSPD 92
>1k6o_B SRF, serum response factor; protein/DNA complex, transcription
factor, combinatorial gene regulation, ETS proteins,
MADS-box proteins; 3.19A {Homo sapiens} SCOP: d.88.1.1
Length = 103
Score = 129 bits (327), Expect = 4e-38
Identities = 87/102 (85%), Positives = 90/102 (88%), Gaps = 2/102 (1%)
Query: 129 PSNGKKTKGRVKIKMEYIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVMLLVASETGH 188
GKKT+GRVKIKME+IDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQV+LLVASETGH
Sbjct: 2 AKPGKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGH 61
Query: 189 VYTFATRKLQPMITSEAGKALIQTCLNSPDPCPSG--AGDQR 228
VYTFATRKLQPMITSE GKALIQTCLNSPD P DQR
Sbjct: 62 VYTFATRKLQPMITSETGKALIQTCLNSPDSPPRSDPTTDQR 103
>1mnm_A Protein (MCM1 transcriptional regulator); transcription regulation,
transcriptional repression, DNA- binding protein; HET:
DNA; 2.25A {Saccharomyces cerevisiae} SCOP: d.88.1.1
Length = 100
Score = 126 bits (319), Expect = 7e-37
Identities = 57/98 (58%), Positives = 75/98 (76%)
Query: 122 STQKGSPPSNGKKTKGRVKIKMEYIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVMLL 181
S + P+N + K R KI++++I+NK RR+ TFSKRK GIMKKA+ELS LTGTQV+LL
Sbjct: 2 SDIEEGTPTNNGQQKERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLL 61
Query: 182 VASETGHVYTFATRKLQPMITSEAGKALIQTCLNSPDP 219
V SETG VYTF+T K +P++T + G+ LIQ CLN+PD
Sbjct: 62 VVSETGLVYTFSTPKFEPIVTQQEGRNLIQACLNAPDD 99
>3p57_A Myocyte-specific enhancer factor 2A; protein-DNA complex,
transcription factor, transcriptional activation, zinc
finger; HET: DNA; 2.19A {Homo sapiens} PDB: 3kov_A*
1tqe_P 1n6j_A
Length = 90
Score = 74.8 bits (184), Expect = 3e-17
Identities = 23/65 (35%), Positives = 42/65 (64%)
Query: 137 GRVKIKMEYIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVMLLVASETGHVYTFATRK 196
GR KI++ I ++ R TF+KRK G+MKKAYELS L ++ L++ + + ++ +A+
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60
Query: 197 LQPMI 201
+ ++
Sbjct: 61 MDKVL 65
>1egw_A MADS box transcription enhancer factor 2, polypeptide A; MADS-box
transcription factor, DNA/protein complex,
transcription/DNA; HET: DNA; 1.50A {Homo sapiens} SCOP:
d.88.1.1 PDB: 1c7u_A 3mu6_A*
Length = 77
Score = 74.0 bits (182), Expect = 4e-17
Identities = 23/65 (35%), Positives = 42/65 (64%)
Query: 137 GRVKIKMEYIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVMLLVASETGHVYTFATRK 196
GR KI++ I ++ R TF+KRK G+MKKAYELS L ++ L++ + + ++ +A+
Sbjct: 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTD 60
Query: 197 LQPMI 201
+ ++
Sbjct: 61 MDKVL 65
>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus
interaction, metal-binding, nucleus, receptor,
transcription, transcription regulation, zinc-FIN
activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB:
3dzu_A* 3e00_A*
Length = 467
Score = 32.0 bits (72), Expect = 0.24
Identities = 8/63 (12%), Positives = 15/63 (23%)
Query: 259 PHLPSQPQSHPHQNYHPAGSPHQHHLYQSSPIIPCSSPGPMIGSYPSPIPHSAYPHMSHS 318
H+ + Q SP + + P PG + ++
Sbjct: 7 HHVDDDDKMFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSSPINGM 66
Query: 319 HPQ 321
P
Sbjct: 67 GPP 69
Score = 30.8 bits (69), Expect = 0.54
Identities = 7/56 (12%), Positives = 11/56 (19%)
Query: 267 SHPHQNYHPAGSPHQHHLYQSSPIIPCSSPGPMIGSYPSPIPHSAYPHMSHSHPQR 322
+H H ++ SS P S + P
Sbjct: 2 AHHHHHHVDDDDKMFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPIS 57
Score = 29.7 bits (66), Expect = 1.3
Identities = 20/71 (28%), Positives = 24/71 (33%), Gaps = 8/71 (11%)
Query: 258 SPHLPSQPQSHPHQNYHPAGSPHQHH---LYQSSPIIPCSSPGPMIGSYPSP----IPHS 310
+ P HP GSP Q H SSPI P +I S P +P +
Sbjct: 29 GRGSMAAPSLHPSLG-PGIGSPGQLHSPISTLSSPINGMGPPFSVISSPMGPHSMSVPTT 87
Query: 311 AYPHMSHSHPQ 321
S PQ
Sbjct: 88 PTLGFSTGSPQ 98
Score = 29.3 bits (65), Expect = 1.9
Identities = 18/68 (26%), Positives = 23/68 (33%), Gaps = 2/68 (2%)
Query: 255 YGGSPHLPSQPQSHPHQNYHPAGSP-HQHHLYQSSPIIPCSSPGPMIGSYPSPIPHSAYP 313
S P+ S + HP+ P SPI SSP +G P + S
Sbjct: 20 VNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSSPINGMGP-PFSVISSPMG 78
Query: 314 HMSHSHPQ 321
S S P
Sbjct: 79 PHSMSVPT 86
Score = 27.4 bits (60), Expect = 7.6
Identities = 15/102 (14%), Positives = 21/102 (20%), Gaps = 10/102 (9%)
Query: 212 TCLNSPDPCPSGAGD-------QRMSATGFEETELSYNIGDDEQKVRQLVYGGSPHLPSQ 264
T +NS P+G G + +L I + G P
Sbjct: 18 TQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSS---PINGMGPPFSVIS 74
Query: 265 PQSHPHQNYHPAGSPHQHHLYQSSPIIPCSSPGPMIGSYPSP 306
PH P P + P
Sbjct: 75 SPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPL 116
>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 = 31.6 bits (71), Expect = 0.42
Identities = 29/171 (16%), Positives = 45/171 (26%), Gaps = 65/171 (38%)
Query: 154 TTFSKRKTGIMKKAYELSTLTGTQVM------LLVASETGH--VYT-FATRKLQPMITSE 204
TT K K ++K + L A G+ + F
Sbjct: 114 TTLVKTKE-LIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIF------------ 160
Query: 205 AGKALIQTCLNSPDPCPSGAGDQRMSATGFEE-TELSYNIGDDEQKVRQLVYGGSPHLPS 263
G Q + FEE +L Y V L+ + L
Sbjct: 161 --------------------GGQGNTDDYFEELRDL-YQTYHVL--VGDLIKFSAETLSE 197
Query: 264 QPQSHPHQNYH-------------PAGSPHQHHLYQSSPIIPCSSPGPMIG 301
++ P+ +P + +L S PI S P+IG
Sbjct: 198 LIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYL-LSIPI---S--CPLIG 242
Score = 29.2 bits (65), Expect = 2.2
Identities = 30/157 (19%), Positives = 49/157 (31%), Gaps = 45/157 (28%)
Query: 101 SSM---TNLTGDCGSDIVDE--GYSPSTQK---------------GSPPS-NGKKTKGRV 139
S M +NLT + D V++ + P+ ++ G P S G R
Sbjct: 336 SPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLR- 394
Query: 140 KIKMEYIDNKLRRYTTFSKRK---------------TGIMKKAYEL--STLTGTQVMLLV 182
K K ++ R FS+RK + ++ A +L L V
Sbjct: 395 KAKAPSGLDQSR--IPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNA 452
Query: 183 ASETGHVYTFAT----RKLQPMITSEAGKALIQTCLN 215
VY R L I+ +I+ +
Sbjct: 453 KDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVK 489
>2zjr_1 50S ribosomal protein L33; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: g.41.8.6 PDB: 1nwx_1* 1xbp_1* 2zjp_1*
2zjq_1 1nwy_1 3cf5_1* 3dll_1* 3pio_1* 3pip_1* 1pnu_1
1pny_1 1vor_3 1vou_3 1vow_3 1voy_3 1vp0_3
Length = 55
Score = 26.4 bits (59), Expect = 2.3
Identities = 10/32 (31%), Positives = 13/32 (40%)
Query: 134 KTKGRVKIKMEYIDNKLRRYTTFSKRKTGIMK 165
K R+ +KME YTT R+ K
Sbjct: 3 KDGPRIIVKMESSAGTGFYYTTTKNRRNTQAK 34
>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 = 27.6 bits (60), Expect = 3.3
Identities = 11/40 (27%), Positives = 16/40 (40%), Gaps = 15/40 (37%)
Query: 193 ATRKLQPMITSEAGKALIQTCLNSPDPCPSGAGDQRMSAT 232
A +KLQ + K L + D P+ A + AT
Sbjct: 21 ALKKLQASL-----K------LYADDSAPALA----IKAT 45
>1nkw_1 50S ribosomal protein L33; ribosome, large subunit, X- RAY
structure, peptidyl-transferase, peptide bond formation;
3.10A {Deinococcus radiodurans} SCOP: i.1.1.2 PDB:
1sm1_1* 1yl3_6 2b66_6 2b9n_6 2b9p_6
Length = 82
Score = 26.3 bits (58), Expect = 3.9
Identities = 9/28 (32%), Positives = 12/28 (42%)
Query: 134 KTKGRVKIKMEYIDNKLRRYTTFSKRKT 161
K R+ +KME YTT R+
Sbjct: 30 KDGPRIIVKMESSAGTGFYYTTTKNRRN 57
>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor,
microtubles, motor protein; HET: ADP SPM; 2.81A
{Dictyostelium discoideum} PDB: 3vkh_A* 3vkh_C*
Length = 3245
Score = 27.9 bits (62), Expect = 5.6
Identities = 7/40 (17%), Positives = 14/40 (35%), Gaps = 8/40 (20%)
Query: 20 MDTPTGGGR---DSR----FSMGYNMSILNNETSPEIYSS 52
+ PT GR R + + + + +IY +
Sbjct: 1429 CNPPTDAGRVQLTHRFLRHAPI-LLVDFPSTSSLTQIYGT 1467
>3u5c_E RP5, S7, YS6, 40S ribosomal protein S4-A; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_D 3u5g_E
Length = 261
Score = 25.4 bits (55), Expect = 7.7
Identities = 2/40 (5%), Positives = 4/40 (10%)
Query: 123 TQKGSPPSNGKKTKGRVKIKMEYIDNKLRRYTTFSKRKTG 162
K+ + K
Sbjct: 18 WLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALN 57
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 0.128 0.378
Gapped
Lambda K H
0.267 0.0600 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,762,379
Number of extensions: 266016
Number of successful extensions: 480
Number of sequences better than 10.0: 1
Number of HSP's gapped: 462
Number of HSP's successfully gapped: 33
Length of query: 322
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 228
Effective length of database: 4,077,219
Effective search space: 929605932
Effective search space used: 929605932
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 (21.8 bits)
S2: 57 (26.0 bits)