RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11998
(245 letters)
>1khx_A SMAD2; TGF-beta signaling, phosphorylation, receptor kinase
signaling, cancer, transcription; HET: SEP; 1.80A {Homo
sapiens} SCOP: b.26.1.1 PDB: 1mk2_A 1u7v_A* 1dev_A
1u7f_A* 1mjs_A 1khu_A 3dit_A
Length = 227
Score = 137 bits (345), Expect = 3e-40
Identities = 62/233 (26%), Positives = 88/233 (37%), Gaps = 52/233 (22%)
Query: 19 SNVHLFFSPAGERRPGEWCKLAYWELSHRVGRLYPVVTPYIHV--FWAQPCGDGLCLETL 76
N L P P WC +AY+EL+ RVG + P + V F + CL L
Sbjct: 17 VNHSLDLQPVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDGFTDPSNSERFCLGLL 76
Query: 77 ATGNNSAPSGNGPHHVPDAVRRTRTKIGLVVESRRLNPSFGAVCPYTKASGCGYVPGRDR 136
+ N + V TR IG
Sbjct: 77 SNVNRN-----------ATVEMTRRHIG-------------------------------- 93
Query: 137 QGLTLSLEADGVWAYNRSEAPVFVNSPGLDDP-GPPTLLVYRIPPGHCLNIFD-----PA 190
+G+ L V+A S++ +FV SP + G V +IPPG L IF+
Sbjct: 94 RGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEFAAL 153
Query: 191 LPPRLRESFPAPPTGPVDPNSIRISFAKGWGPKYSRQEITACPAWLEVLLVPA 243
L + + F A +IR+SF KGWG +Y RQ +T+ P W+E+ L
Sbjct: 154 LAQSVNQGFEAV-YQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGP 205
>3gmj_D Protein mothers against DPP; MH2,SMAD,MAD, cytoplasm, developmental
protein, nucleus, phosphoprotein, transcription; 2.80A
{Drosophila melanogaster}
Length = 245
Score = 128 bits (323), Expect = 1e-36
Identities = 53/227 (23%), Positives = 82/227 (36%), Gaps = 51/227 (22%)
Query: 25 FSPAGERRPGEWCKLAYWELSHRVGRLYPVVTPYIHVFW---AQPCGDGLCLETLATGNN 81
+ P W +AY+EL+ RVG ++ + V D CL L+ N
Sbjct: 40 VAQVSYSEPAFWASIAYYELNCRVGEVFHCNNNSVIVDGFTNPSNNSDRCCLGQLSNVNR 99
Query: 82 SAPSGNGPHHVPDAVRRTRTKIGLVVESRRLNPSFGAVCPYTKASGCGYVPGRDRQGLTL 141
+ + TR IG +G+ L
Sbjct: 100 N-----------STIENTRRHIG--------------------------------KGVHL 116
Query: 142 SLEADGVWAYNRSEAPVFVNSPGLDDP-GPPTLLVYRIPPGHCLNIFDPALPPRL----R 196
V+A S++ +FV S + G V +IPPG L IF+ +L
Sbjct: 117 YYVTGEVYAECLSDSAIFVQSRNCNYQHGFHPSTVCKIPPGCSLKIFNNQEFAQLLSQSV 176
Query: 197 ESFPAPPTGPVDPNSIRISFAKGWGPKYSRQEITACPAWLEVLLVPA 243
+ +IR+SF KGWG +Y RQ++T+ P W+E+ L
Sbjct: 177 NNGFEAVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGP 223
>1ygs_A SMAD4; tumor suppressor C-terminal domain, TGF-beta signal
mediator, beta-sandwich scaffold with A three-helix
bundle, tumour suppressor; 2.10A {Homo sapiens} SCOP:
b.26.1.1 PDB: 1u7f_B* 1mr1_A 1u7v_B*
Length = 234
Score = 127 bits (319), Expect = 3e-36
Identities = 58/256 (22%), Positives = 86/256 (33%), Gaps = 88/256 (34%)
Query: 33 PGEWCKLAYWELSHRVGRLYPVVTPYIHV----FWAQPCGDGLCLETLATGNNSAPSGNG 88
P WC +AY+E+ +VG + V + V + GD CL L+ + +
Sbjct: 2 PEYWCSIAYFEMDVQVGETFKVPSSCPIVTVDGYVDPSGGDRFCLGQLSNVHRT------ 55
Query: 89 PHHVPDAVRRTRTKIGLVVESRRLNPSFGAVCPYTKASGCGYVPGRDRQGLTLSLEADG- 147
+A+ R R IG +G+ L + +G
Sbjct: 56 -----EAIERARLHIG--------------------------------KGVQLECKGEGD 78
Query: 148 VWAYNRSEAPVFVNSPGLDDPG--PPTLLVYRIPPGHCLNIFDPA-----LPPRLRESFP 200
VW S+ VFV S LD P V++I P + +FD + + +
Sbjct: 79 VWVRCLSDHAVFVQSYYLDREAGRAPGDAVHKIYPSAYIKVFDLRQCHRQMQQQAATAQA 138
Query: 201 AP----------PTGPVDPNS-----------------------IRISFAKGWGPKYSRQ 227
A GP +R+SF KGWGP Y RQ
Sbjct: 139 AAAAQAAAVAGNIPGPGSVGGIAPAISLSAAAGIGVDDLRRLCILRMSFVKGWGPDYPRQ 198
Query: 228 EITACPAWLEVLLVPA 243
I P W+E+ L A
Sbjct: 199 SIKETPCWIEIHLHRA 214
>1dd1_A SMAD4; B-sheet sandwich helix-turn-helix, signaling protein; 2.62A
{Homo sapiens} SCOP: b.26.1.1 PDB: 1g88_A
Length = 268
Score = 124 bits (311), Expect = 9e-35
Identities = 61/276 (22%), Positives = 90/276 (32%), Gaps = 92/276 (33%)
Query: 17 HLSNVHLFFSPAG----ERRPGEWCKLAYWELSHRVGRLYPVVTPYIHV----FWAQPCG 68
H VH + P WC +AY+E+ +VG + V + V + G
Sbjct: 16 HYWPVHNELAFQPPISNHPAPEYWCSIAYFEMDVQVGETFKVPSSCPIVTVDGYVDPSGG 75
Query: 69 DGLCLETLATGNNSAPSGNGPHHVPDAVRRTRTKIGLVVESRRLNPSFGAVCPYTKASGC 128
D CL L+ + + +A+ R R IG
Sbjct: 76 DRFCLGQLSNVHRT-----------EAIERARLHIG------------------------ 100
Query: 129 GYVPGRDRQGLTLSLEADG-VWAYNRSEAPVFVNSPGLDDPGP--PTLLVYRIPPGHCLN 185
+G+ L + +G VW S+ VFV S LD P V++I P +
Sbjct: 101 --------KGVQLECKGEGDVWVRCLSDHAVFVQSYYLDREAGRAPGDAVHKIYPSAYIK 152
Query: 186 IFDPA-----LPPRLRESFPAP----------PTGPVDPNS------------------- 211
+FD + + + A GP
Sbjct: 153 VFDLRQCHRQMQQQAATAQAAAAAQAAAVAGNIPGPGSVGGIAPAISLSAAAGIGVDDLR 212
Query: 212 ----IRISFAKGWGPKYSRQEITACPAWLEVLLVPA 243
+R+SF KGWGP Y RQ I P W+E+ L A
Sbjct: 213 RLCILRMSFVKGWGPDYPRQSIKETPCWIEIHLHRA 248
>3dsh_A IRF-5, interferon regulatory factor 5; phosphoactivation induced
dimerization, DNA-binding, nucleus transcription,
transcription regulation; 2.00A {Homo sapiens}
Length = 246
Score = 36.6 bits (84), Expect = 0.004
Identities = 22/107 (20%), Positives = 34/107 (31%), Gaps = 7/107 (6%)
Query: 138 GLTLSLEADGVWAYNRSEAPVFVNSPGLDDPGPPTLLVYRIPPGHCLNIFDPALPPRLRE 197
GL L L+ ++A + VF + P + R +F
Sbjct: 93 GLILQLQGQDLYAIRLCQCKVFWSGPCASAHDSCPNPIQR---EVKTKLFSLEHFLNELI 149
Query: 198 SFPAPPTGPVDPNSIRISFAKGWGPKYSRQE--ITA--CPAWLEVLL 240
F T P I F + W + R++ IT P +LL
Sbjct: 150 LFQKGQTNTPPPFEIFFCFGEEWPDRKPREKKLITVQVVPVAARLLL 196
>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 = 37.3 bits (86), Expect = 0.004
Identities = 65/354 (18%), Positives = 105/354 (29%), Gaps = 148/354 (41%)
Query: 4 KIREILKFYYWVAHLSNVH--------LFFS-PAGERR-----PGEWCKLAYW-ELSHRV 48
K +E++K Y ++ LF + G + G+ Y+ EL
Sbjct: 118 KTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRD-- 175
Query: 49 GRLY----PVVTPYIHVFWAQPCGDGLCLETLATGNNSA----PSG-------NGPHHVP 93
LY +V I L L A G P + P
Sbjct: 176 --LYQTYHVLVGDLIKFS-------AETLSELIRTTLDAEKVFTQGLNILEWLENPSNTP 226
Query: 94 D-------AVRRTRTKIGLV------VESRRLNPSFGAVCPYTK-ASGCGYVPGRDRQGL 139
D + + IG++ V ++ L + G + Y K A+G QGL
Sbjct: 227 DKDYLLSIPI--SCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHS-------QGL 277
Query: 140 TLSL---EADGVWA--YN--------------RS--EAPVFVNSPG-LDDP-----GPPT 172
++ E D W + R P P L+D G P+
Sbjct: 278 VTAVAIAETDS-WESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPS 336
Query: 173 --LLV----------------YRIPPGHCLNIFDPAL-----------PPR--------L 195
L + +P G + I +L PP+ L
Sbjct: 337 PMLSISNLTQEQVQDYVNKTNSHLPAGKQVEI---SLVNGAKNLVVSGPPQSLYGLNLTL 393
Query: 196 RESFPAPPTGPVDPNSIRISFAKGWGPKYSRQ--EITA---CPAWLEVLLVPAA 244
R++ AP + RI F++ K+S + + + LLVPA+
Sbjct: 394 RKAK-APS----GLDQSRIPFSER-KLKFSNRFLPVASPFHSH-----LLVPAS 436
>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 = 34.4 bits (78), Expect = 0.032
Identities = 27/167 (16%), Positives = 44/167 (26%), Gaps = 48/167 (28%)
Query: 60 HVFW---AQPCGDGLCLETLAT---------GNNSAPSGNGPHHVPDAVRRTRTKIG--- 104
+FW LE L + S S N + R +
Sbjct: 183 KIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKP 242
Query: 105 -----LV---VESRRLNPSFGAVCPY---TKASGCGYVPGRDRQGLTLSLEADGVWAYNR 153
LV V++ + +F C T R +Q D + A
Sbjct: 243 YENCLLVLLNVQNAKAWNAFNLSCKILLTT----------RFKQ------VTDFLSAATT 286
Query: 154 SEAPVFVNSPGLDDPGPPTLLVYRIPPGHCLNIFDPALPPRLRESFP 200
+ + +S L +LL L+ LP + + P
Sbjct: 287 THISLDHHSMTLTPDEVKSLL------LKYLDCRPQDLPREVLTTNP 327
>3a77_A IRF-3, interferon regulatory factor 3; phosphorylated protein,
activator, antiviral defense, DNA-BI HOST-virus
interaction, nucleus, phosphoprotein; HET: SEP; 1.80A
{Homo sapiens} PDB: 1j2f_A 1qwt_A 1zoq_A
Length = 242
Score = 30.8 bits (69), Expect = 0.35
Identities = 12/83 (14%), Positives = 21/83 (25%), Gaps = 1/83 (1%)
Query: 138 GLTLSLEADGVWAYNRSEAPVFVNSPGLDDPGPPTLLVYRIPPGHCLNIFDPALPPRLRE 197
GL L +WA + P +P +FD
Sbjct: 86 GLALWRAGQWLWAQRLGHCHTYWAVSEELLPNSGHGPDGEVPKDKEGGVFDLGPFIVDLI 145
Query: 198 SFPAPPTGPVDPNSIRISFAKGW 220
+F +G ++ + W
Sbjct: 146 TFTE-GSGRSPRYALWFCVGESW 167
>3oqv_A ALBC; rossman fold, cyclodipeptide synthase, aminoacyl-tRNA, prote
binding; 1.90A {Streptomyces noursei}
Length = 247
Score = 30.5 bits (68), Expect = 0.40
Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 4/69 (5%)
Query: 133 GRDRQGLTLSLEADGVWAYNRSEAPVFVNSPGLDDPGPPTLLVYRIPPGHCLNIFDP--A 190
D G++ G+ Y +EAP+F +SPG+ P ++L Y I +
Sbjct: 161 PGDGVGISAEHLRAGL-NYVLAEAPLFADSPGVFSV-PSSVLCYHIDTPITAFLSRRETG 218
Query: 191 LPPRLRESF 199
+++
Sbjct: 219 FRAAEGQAY 227
>3oqi_A YVMC, putative uncharacterized protein YVMC; tRNA, rossmann fold,
ligase; HET: NHE; 1.70A {Bacillus licheniformis} PDB:
3oqh_A* 3oqj_A* 3s7t_A* 3oqi_B*
Length = 257
Score = 29.4 bits (65), Expect = 0.93
Identities = 17/93 (18%), Positives = 26/93 (27%), Gaps = 5/93 (5%)
Query: 111 RLNPSFGAVCPYTKASGCGYVPGRDRQGLTLSLEADGVWA--YNRSEAPVFVNSPGLDDP 168
F C + R + A Y +E P F+ +P +
Sbjct: 138 FDQTHFRNACLEMSHAAILGRARGTRMDVVEVSADMLELAVEYVIAELPFFIAAPDILGV 197
Query: 169 GPPTLLVYRIPPGHCLNIFDP--ALPPRLRESF 199
TLL Y P I A+ R + +
Sbjct: 198 -EETLLAYHRPWKLGEQISRNEFAVKMRPNQGY 229
>2x9q_A Cyclodipeptide synthetase; ligase; 2.02A {Mycobacterium
tuberculosis}
Length = 289
Score = 29.4 bits (65), Expect = 1.0
Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 4/68 (5%)
Query: 134 RDRQGLTLSLEADGVWAYNRSEAPVFVNSPGLDDPGPPTLLVYRIPPGHCLNIFDP--AL 191
RQG T + E + Y +EAP+F+++P + P +L Y ++ L
Sbjct: 213 GPRQGATATQEQVCM-DYICAEAPLFLDTPAILGV-PSSLNCYHQSLPLAEMLYARGSGL 270
Query: 192 PPRLRESF 199
+
Sbjct: 271 RASRNQGH 278
>3pfe_A Succinyl-diaminopimelate desuccinylase; metal binding, merops M20
familiy, phosphorylase/hydrolase-L structural genomics;
HET: MSE; 1.50A {Legionella pneumophila subsp}
Length = 472
Score = 28.1 bits (63), Expect = 3.1
Identities = 9/42 (21%), Positives = 14/42 (33%), Gaps = 10/42 (23%)
Query: 165 LDDPGPPTLLVYRIPPGHCLNIFD--PALPPRLRESFPAPPT 204
+ T+L+Y GH D P + + P P
Sbjct: 84 IPGQIDDTVLLY----GH----LDKQPEMSGWSDDLHPWKPV 117
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
0.322 0.141 0.480
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,110,295
Number of extensions: 244756
Number of successful extensions: 455
Number of sequences better than 10.0: 1
Number of HSP's gapped: 448
Number of HSP's successfully gapped: 34
Length of query: 245
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 154
Effective length of database: 4,160,982
Effective search space: 640791228
Effective search space used: 640791228
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (25.4 bits)