RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14029
(277 letters)
>3flp_A SAP-like pentraxin; physiological doubly-stacked heptamer,
pentraxin fold, cyclic heptamer, invertebrate lectin,
sugar binding protein; 2.30A {Limulus polyphemus} PDB:
3flr_A 3flt_A
Length = 217
Score = 49.3 bits (117), Expect = 3e-07
Identities = 28/190 (14%), Positives = 62/190 (32%), Gaps = 20/190 (10%)
Query: 80 FSFPGK-KGSAMVLPPLAKWPHENGFTFTTWFRLDPINSVNIEREKPYLYSFKTSKGVGY 138
SFPG L + P T + N+ Y++S TS
Sbjct: 9 ISFPGTQNPKFPHLRFMQTLPAVRQLTVCQRIKPFHRNT-------GYIFSCATSNQDNQ 61
Query: 139 TAHFV---GNCLVLTSMKIKGKGFQHCV-KYEFQPRKWYMIAIVYIYNRWTKSEIKCFVN 194
+ + + +++ ++ E + +WY + V+ + + N
Sbjct: 62 FITSMYVKSDGTLNLGLQVNASSNKYISCPIEIELGQWYHVCHVW---SGVDGRMAVYAN 118
Query: 195 GQLASSTEMAWFVSTNEPFDKCYIGATP-----ELDEERVFCGQMAAIYLFNESLSTHQI 249
G + E IG +E+ + G+++ + +++E+L+THQ+
Sbjct: 119 GSPCGTMENVGKGHQISAGGTVVIGQEQDKIGGGFEEQESWSGELSDLQVWDEALTTHQV 178
Query: 250 CAMHRLGPGY 259
+
Sbjct: 179 STVASCNGIR 188
>4dqa_A Uncharacterized protein; two domains structure, DUF 1735,
laminin_G_3 concanavalin A- lectin/glucanases
superfamily domain; HET: MSE; 1.50A {Bacteroides ovatus}
Length = 355
Score = 49.7 bits (118), Expect = 3e-07
Identities = 26/161 (16%), Positives = 55/161 (34%), Gaps = 17/161 (10%)
Query: 102 NGFTFTTWFRLDPINSVN--IEREKPYLYSFKTSKGVGYTAHFVGNCLVLTSMKIKGKGF 159
+ FT+ +D N + E + + G ++ G
Sbjct: 161 SSFTYEALINVDYFLDNNTIMGTEGVMILRIGDAGGGITPKDYLEV----------AGGQ 210
Query: 160 QHCVKYEFQPRKWYMIAIVYIYNRWTKSEIKCFVNGQLASSTEMAWFVSTNEPFDKCYIG 219
+ V +WY +A+ Y + +VNG+ + ++ YIG
Sbjct: 211 NYRVTKPLLTNRWYHVALTYDQ---PTGKTGIYVNGEKWAGSDWGIDGFDPNSDMGFYIG 267
Query: 220 ATPELDE-ERVFCGQMAAIYLFNESLSTHQICA-MHRLGPG 258
ER F G+M+ + +++ + + +Q+ M + P
Sbjct: 268 RIYGFKWGERPFHGKMSEVRVWSVARTENQLKQNMLGVDPA 308
>2vxr_A Botulinum neurotoxin type G; hydrolase, ganglioside, protease,
recepto secreted, binding domain, metalloprotease; 1.90A
{Clostridium botulinum} PDB: 3mpp_G
Length = 482
Score = 39.9 bits (92), Expect = 6e-04
Identities = 30/184 (16%), Positives = 61/184 (33%), Gaps = 22/184 (11%)
Query: 102 NGFTFTTWFRLDPINSVNIEREKPYLYSFKTSKG--VGYTAHFVGNCLVLTSMKIKGKGF 159
+ F+ W R N+ +I+ Y+ + G+ GN ++ T + + K
Sbjct: 114 DNFSINFWVRTPKYNNNDIQTYLQNEYTIISCIKNDSGWKVSIKGNRIIWTLIDVNAKSK 173
Query: 160 QHCVKYEF------QPRKWYMIAIVYIYNRWTKSEIKCFVNGQLASSTEMAWFVSTNEPF 213
+Y KW+ I I +R + I ++NG L S ++ N
Sbjct: 174 SIFFEYSIKDNISDYINKWFSITIT--NDRLGNANI--YINGSLKKSEKILNLDRINSSN 229
Query: 214 DKCYIGATPELDEERVFCGQMAAIYLFNESLSTHQICAMHRLGPGYKVKTGWVEELNSSW 273
D + + + +F L+ ++ +++ + L W
Sbjct: 230 DIDFKLIN---CTDTTKFVWIKDFNIFGRELNATEVSSLYWIQSSTNT-------LKDFW 279
Query: 274 GEEL 277
G L
Sbjct: 280 GNPL 283
>2vu9_A Botulinum neurotoxin A heavy chain; hydrolase, metalloprotease,
ganglioside, metal-B toxin, protease, membrane,
receptor, secreted; HET: BGC GAL SIA NGA; 1.6A
{Clostridium botulinum} PDB: 2vua_A 3fuo_A
Length = 444
Score = 39.9 bits (92), Expect = 6e-04
Identities = 25/182 (13%), Positives = 60/182 (32%), Gaps = 21/182 (11%)
Query: 102 NGFTFTTWFRLDPINSVNIEREKPYLYSFKTSKGVGYTAHFVGNCLVLTSMKIKGKGFQH 161
F+ + W R+ + + + + + G+ ++ T + +
Sbjct: 86 ENFSTSFWIRIPKYFNSISLNNEYTIINCMENNS-GWKVSLNYGEIIWTLQDTQEIKQRV 144
Query: 162 CVKYE------FQPRKWYMIAIVYIYNRWTKSEIKCFVNGQLASSTEMAWFVSTNEPFDK 215
KY +W + I NR S+I ++NG+L ++ + + +
Sbjct: 145 VFKYSQMINISDYINRWIFVTIT--NNRLNNSKI--YINGRLIDQKPISNLGNIHASNN- 199
Query: 216 CYIGATPELDEERVFCGQMAAIYLFNESLSTHQICAMHRLGPGYKVKTGWVEELNSSWGE 275
I + + + LF++ L+ +I ++ + L WG+
Sbjct: 200 --IMFKLDGCRDTHRYIWIKYFNLFDKELNEKEIKDLYDNQSNSGI-------LKDFWGD 250
Query: 276 EL 277
L
Sbjct: 251 YL 252
>3pvn_A C-reactive protein; pentraxin family, immune system; 1.98A {Homo
sapiens} PDB: 1gnh_A 1lj7_A 3l2y_A 1b09_A 3pvo_A
Length = 206
Score = 37.8 bits (87), Expect = 0.002
Identities = 21/188 (11%), Positives = 50/188 (26%), Gaps = 19/188 (10%)
Query: 75 GPDVFFSFPGKKGSAMVLPPLAKWPHENGFTFTTWFRLDPINSVNIEREKPYLYSFKTSK 134
F + PL K FT F + ++ ++S+ T +
Sbjct: 6 RKAFVFPKESDTSYVSLKAPLTKPLKA--FTVCLHFYTELSSTRGY-----SIFSYATKR 58
Query: 135 GVGYTAHFVGNCLVLTSMKIKGKGFQHCVKYEFQPRKWYMIAIVYIYNRWTKSEIKCFVN 194
F G + + I + ++ +V+
Sbjct: 59 QDNEILIFWSKD---IGYSFTVGGSEILFEVPEVTVAPVHICTSW---ESASGIVEFWVD 112
Query: 195 GQLASSTEMAWFVSTNEPFDKCYIGATP-----ELDEERVFCGQMAAIYLFNESLSTHQI 249
G+ + + +G + + G + + +++ LS +I
Sbjct: 113 GKPRVRKSLKKGYTVGAE-ASIILGQEQDSFGGNFEGSQSLVGDIGNVNMWDFVLSPDEI 171
Query: 250 CAMHRLGP 257
++ GP
Sbjct: 172 NTIYLGGP 179
>1a8d_A Tetanus neurotoxin; clostridial, ganglioside binding region; 1.57A
{Clostridium tetani} SCOP: b.29.1.6 b.42.4.2 PDB: 1af9_A
1fv3_A* 1fv2_A* 3hmy_A* 3hn1_A* 1d0h_A* 1dfq_A* 1dll_A*
1yxw_A* 1yyn_A* 1diw_A*
Length = 452
Score = 36.1 bits (82), Expect = 0.009
Identities = 33/207 (15%), Positives = 74/207 (35%), Gaps = 24/207 (11%)
Query: 80 FSFPGKKGSAMVLPPLAKWPHE---NGFTFTTWFRLDPINSVNIEREKPYLYSFKTSKG- 135
+ S +++ + N FT + W R+ +++ ++E+ YS +S
Sbjct: 60 IHLVNNESSEVIVHKAMDIEYNDMFNNFTVSFWLRVPKVSASHLEQYGTNEYSIISSMKK 119
Query: 136 ------VGYTAHFVGNCLVLTSMKIKGKGFQHCVKY------EFQPRKWYMIAIVYIYNR 183
G++ GN L+ T G+ Q + + KW I I +R
Sbjct: 120 HSLSIGSGWSVSLKGNNLIWTLKDSAGEVRQITFRDLPDKFNAYLANKWVFITIT--NDR 177
Query: 184 WTKSEIKCFVNGQLASSTEMAWFVSTNEPFDKCYIGATPELDEERVFCGQMAAIYLFNES 243
+ + + ++NG L S E+ + E + + + + +F ++
Sbjct: 178 LSSANL--YINGVLMGSAEITGLGAIRED-NNITLKLDRCNNNN--QYVSIDKFRIFCKA 232
Query: 244 LSTHQICAMHRLGP-GYKVKTGWVEEL 269
L+ +I ++ ++ W L
Sbjct: 233 LNPKEIEKLYTSYLSITFLRDFWGNPL 259
>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 = 34.6 bits (79), Expect = 0.034
Identities = 29/151 (19%), Positives = 45/151 (29%), Gaps = 49/151 (32%)
Query: 29 MGVLASYSITVKELKLFFAAMKAVNNKWPR---HSTKLLNV-LRQMPQRNGPDVFFSFPG 84
MG +L A + V W R H + + N ++ F G
Sbjct: 1631 MG---------MDLYKTSKAAQDV---WNRADNHFKDTYGFSILDIVINNPVNLTIHFGG 1678
Query: 85 KKGSAMVLPPLAKWPHENGFTFTTWFRLDPINSVNIER------EKPYLYSFKTSKGV-- 136
+KG + EN F + E+ E Y+F++ KG+
Sbjct: 1679 EKGKRI---------RENYSAMI--FETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLS 1727
Query: 137 --GYT--AHFVGNCLVLTSM----KIKGKGF 159
+T A L L +K KG
Sbjct: 1728 ATQFTQPA------LTLMEKAAFEDLKSKGL 1752
Score = 26.9 bits (59), Expect = 9.8
Identities = 13/72 (18%), Positives = 20/72 (27%), Gaps = 19/72 (26%)
Query: 19 PVVADLLIDMMGVLASYSITVKELKLFFAAMKAVNNKWPRHSTKLLNVLRQMPQRNGPD- 77
+V DL+ L+ T + + F +L L P PD
Sbjct: 182 VLVGDLIKFSAETLSELIRTTLDAEKVFT-----------QGLNILEWLEN-PSNT-PDK 228
Query: 78 -----VFFSFPG 84
+ S P
Sbjct: 229 DYLLSIPISCPL 240
>3rsj_A BONT/F; clostridium botulinum type F, ganglioside binding site,
GD1A; HET: NGA GAL SIA; 2.00A {Clostridium botulinum}
PDB: 3fuq_A
Length = 413
Score = 34.5 bits (78), Expect = 0.035
Identities = 18/108 (16%), Positives = 33/108 (30%), Gaps = 10/108 (9%)
Query: 102 NGFTFTTWFRLDPINSVNIEREKPYLYSFKTSKGVGYTAHFVGNCLVLTSMKIKGKGFQH 161
F+ + W R+ + + + + G+ N ++ T G +
Sbjct: 67 QNFSISFWVRIPKYFNKVNLNNEYTIIDCIRNNNSGWKISLNYNKIIWTLQDTAGNNQKL 126
Query: 162 CVKYE------FQPRKWYMIAIVYIYNRWTKSEIKCFVNGQLASSTEM 203
Y KW + I NR S I ++NG L +
Sbjct: 127 VFNYTQMISISDYINKWIFVTIT--NNRLGNSRI--YINGNLIDEKSI 170
>3gne_A Val-1; alginate lyase, polysaccharide lyase family 14, chlorella VI
lyase; HET: FLC; 1.20A {Chlorella virus} PDB: 3a0n_A*
3im0_A*
Length = 252
Score = 31.6 bits (71), Expect = 0.19
Identities = 11/61 (18%), Positives = 17/61 (27%), Gaps = 6/61 (9%)
Query: 164 KYEFQPRKWYMIAIVYIYNRWTKS------EIKCFVNGQLASSTEMAWFVSTNEPFDKCY 217
K + W I I N + E VNG+ + W S + +
Sbjct: 157 KNALKYDVWNRIEIGTKMNTFKNGIPQLDGESYVIVNGKKEVLKRINWSRSPDLLISRFD 216
Query: 218 I 218
Sbjct: 217 W 217
>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 = 29.4 bits (65), Expect = 1.5
Identities = 25/178 (14%), Positives = 50/178 (28%), Gaps = 35/178 (19%)
Query: 7 KWRYYSGLPH-ADPVVADL----LIDMM-GVLASYSITVKELKLFFAAMKAVNNKWPRHS 60
+++Y L D V + + DM +L+ +E+ + AV+ +
Sbjct: 15 QYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSK-----EEIDHIIMSKDAVSG-----T 64
Query: 61 TKLLNVLRQMPQRNGPDVFFSFPGKKGSAMVLPPLA---KWPHENGFTFT-----TWFRL 112
+L L Q F + ++ P+ + P + +
Sbjct: 65 LRLFWTLLSK-QEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDN 123
Query: 113 DPINSVNIEREKPY------LYSFKTSKGVGYTAHFVGNC--LVLTSMKIKGKGFQHC 162
N+ R +PY L + +K V V + Q
Sbjct: 124 QVFAKYNVSRLQPYLKLRQALLELRPAKNV--LIDGVLGSGKTWVALDVCLSYKVQCK 179
>3suz_A Amyloid beta A4 precursor protein-binding family 2; APP binding;
2.70A {Rattus norvegicus} PDB: 1u3b_A 1u39_A 1x45_A
1u37_A 1u38_A 2yt8_A
Length = 388
Score = 28.4 bits (62), Expect = 2.9
Identities = 17/77 (22%), Positives = 30/77 (38%), Gaps = 8/77 (10%)
Query: 134 KGVGYTAHFVGNCLVLTSMKIKGKGFQHCVKYEFQPRKWYMIAIVYIYNRWTKSEIKCFV 193
G+ + A+++G+ +L S + K + E R M K + K
Sbjct: 7 DGIIFAANYLGSTQLL-SERNPSKNIRMMQAQEAVSRVKRMQKA-------AKIKKKANS 58
Query: 194 NGQLASSTEMAWFVSTN 210
G + TE+ F+ST
Sbjct: 59 EGDAQTLTEVDLFISTQ 75
>3iln_A Laminarinase; jelly ROW, hydrolase, family 16 glycosyl hydrolase;
1.95A {Rhodothermus marinus}
Length = 251
Score = 27.3 bits (61), Expect = 5.9
Identities = 10/37 (27%), Positives = 14/37 (37%), Gaps = 5/37 (13%)
Query: 184 WTKSEIKCFVNGQL-----ASSTEMAWFVSTNEPFDK 215
WT EI+ FV+ L + PFD+
Sbjct: 174 WTPEEIRWFVDDSLYYRFPNERLTNPEADWRHWPFDQ 210
>3r8s_G 50S ribosomal protein L6; protein biosynthesis, RNA, tRNA, transfer
RNA, 23S ribosomal subunit, ribosome recycling factor,
RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_E
1p86_E 2awb_G 2aw4_G 2i2v_G 2j28_G 2i2t_G* 2qao_G*
2qba_G* 2qbc_G* 2qbe_G 2qbg_G 2qbi_G* 2qbk_G* 2qov_G
2qox_G 2qoz_G* 2qp1_G* 2rdo_G 2vhm_G ...
Length = 176
Score = 26.7 bits (60), Expect = 6.3
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 6/32 (18%)
Query: 135 GVGYTAHFVGNCLVLTSMKIKGKGFQHCVKYE 166
GVGY A GN + L+ GF H V ++
Sbjct: 90 GVGYRAAVKGNVINLSL------GFSHPVDHQ 115
>3bbo_I Ribosomal protein L6; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 223
Score = 26.8 bits (60), Expect = 7.3
Identities = 14/32 (43%), Positives = 15/32 (46%), Gaps = 6/32 (18%)
Query: 135 GVGYTAHFVGNCLVLTSMKIKGKGFQHCVKYE 166
GVGY A G LVL GF H VK +
Sbjct: 134 GVGYRATVDGKELVLNL------GFSHPVKMQ 159
>1hkq_A REPA, replication protein; DNA binding protein, winged-helix,
PPS10 plasmid, replication initiator dimer.; 2.75A
{Pseudomonas syringae PV} SCOP: a.4.5.10
Length = 132
Score = 26.3 bits (58), Expect = 7.6
Identities = 5/23 (21%), Positives = 15/23 (65%)
Query: 33 ASYSITVKELKLFFAAMKAVNNK 55
+S+++T+ E +L A ++++
Sbjct: 15 SSHTLTLNEKRLVLCAASLIDSR 37
>2nra_C PI protein; protein-DNA complex, DNA replication, replication-DNA
comple; 3.10A {Escherichia coli} SCOP: a.4.5.10
a.4.5.10
Length = 276
Score = 27.0 bits (59), Expect = 7.8
Identities = 3/36 (8%), Positives = 15/36 (41%)
Query: 31 VLASYSITVKELKLFFAAMKAVNNKWPRHSTKLLNV 66
+ + ++ + A+ +++K P ++ +
Sbjct: 22 NHTLAQLPLPAKRVMYMALALIDSKEPLERGRVFKI 57
>1rl6_A Protein (ribosomal protein L6); RNA-binding protein, gentamicin
resistance, alpha/beta protein; 2.00A {Geobacillus
stearothermophilus} SCOP: d.141.1.1 d.141.1.1 PDB:
1giy_H 1ml5_h* 1c04_B 1yl3_H 2b66_H 2b9n_H 2b9p_H 1eg0_J
487d_J
Length = 177
Score = 26.3 bits (59), Expect = 8.0
Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 6/32 (18%)
Query: 135 GVGYTAHFVGNCLVLTSMKIKGKGFQHCVKYE 166
GVGY A G LVL+ G+ H V+ E
Sbjct: 90 GVGYRASKQGKKLVLSV------GYSHPVEIE 115
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 0.136 0.441
Gapped
Lambda K H
0.267 0.0510 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,397,611
Number of extensions: 251443
Number of successful extensions: 473
Number of sequences better than 10.0: 1
Number of HSP's gapped: 471
Number of HSP's successfully gapped: 27
Length of query: 277
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 185
Effective length of database: 4,133,061
Effective search space: 764616285
Effective search space used: 764616285
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: 57 (26.3 bits)