RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17175
(285 letters)
>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 = 40.6 bits (94), Expect = 4e-04
Identities = 36/205 (17%), Positives = 60/205 (29%), Gaps = 45/205 (21%)
Query: 36 GLCQYYLKVIKP--TIEYWSTSNQNKRFQEVILTRMRIGHTRLTHNHLFTKTDPPLCQCG 93
C V++ + Y N R ++RI + L C
Sbjct: 190 KNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC--- 246
Query: 94 AAL-------SVRHI----LSCHTKI---DPPLCQCGAALSVRHILFCHQHDNAAGVESL 139
L + + LSC + + +A + HI H E
Sbjct: 247 --LLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVK 304
Query: 140 FLLNAVLNSWIYKLCTTEDLK-------PFISFLI-------TSEWQNQWNHIPNTNKL- 184
LL L+ C +DL P +I + W N W H+ N +KL
Sbjct: 305 SLLLKYLD------CRPQDLPREVLTTNPRRLSIIAESIRDGLATWDN-WKHV-NCDKLT 356
Query: 185 KVIKPTIEYWSTSNQNKRFQE-VIL 208
+I+ ++ + K F +
Sbjct: 357 TIIESSLNVLEPAEYRKMFDRLSVF 381
>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 = 31.5 bits (70), Expect = 0.17
Identities = 8/29 (27%), Positives = 14/29 (48%), Gaps = 7/29 (24%)
Query: 248 QHVN-IRNSL-----DTPPSLEDNAAGVE 270
Q + ++ SL D+ P+L A +E
Sbjct: 20 QALKKLQASLKLYADDSAPALAIKAT-ME 47
>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP,
translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A
Length = 504
Score = 31.8 bits (73), Expect = 0.27
Identities = 12/52 (23%), Positives = 18/52 (34%), Gaps = 23/52 (44%)
Query: 56 NQNKRFQE------VILTRMRIGHTRLTHNHLFTKTDPPLCQCGAALSVRHI 101
Q K F++ VI+T++ GH + G ALS
Sbjct: 231 AQAKAFKDKVDVASVIVTKLD-GHAK----------------GGGALSAVAA 265
Score = 31.8 bits (73), Expect = 0.27
Identities = 12/52 (23%), Positives = 18/52 (34%), Gaps = 23/52 (44%)
Query: 198 NQNKRFQE------VILTRMRIGHTRLTHNHLFTKIDPPLCQCGAALSVRHI 243
Q K F++ VI+T++ GH + G ALS
Sbjct: 231 AQAKAFKDKVDVASVIVTKLD-GHAK----------------GGGALSAVAA 265
>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal
recognition particle, SRP-GTPase, protein targeting,
cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus
furiosus}
Length = 443
Score = 31.0 bits (71), Expect = 0.45
Identities = 11/52 (21%), Positives = 17/52 (32%), Gaps = 23/52 (44%)
Query: 56 NQNKRFQE------VILTRMRIGHTRLTHNHLFTKTDPPLCQCGAALSVRHI 101
NQ F+E +I+T++ G + G ALS
Sbjct: 230 NQALAFKEATPIGSIIVTKLD-GSAK----------------GGGALSAVAA 264
Score = 31.0 bits (71), Expect = 0.45
Identities = 11/52 (21%), Positives = 17/52 (32%), Gaps = 23/52 (44%)
Query: 198 NQNKRFQE------VILTRMRIGHTRLTHNHLFTKIDPPLCQCGAALSVRHI 243
NQ F+E +I+T++ G + G ALS
Sbjct: 230 NQALAFKEATPIGSIIVTKLD-GSAK----------------GGGALSAVAA 264
>2csh_A Zinc finger protein 297B; ZF-C2H2 domain, zinc finger and BTB
domain containing protein 22B, structural genomics,
NPPSFA; NMR {Homo sapiens} SCOP: g.37.1.1 g.37.1.1
Length = 110
Score = 28.9 bits (66), Expect = 0.60
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 5/45 (11%)
Query: 90 CQCGAALSVRHILSCHTKI----DPPLC-QCGAALSVRHILFCHQ 129
CQCG + + + H + P C CG ++H L H
Sbjct: 13 CQCGKSFTHKSQRDRHMSMHLGLRPYGCGVCGKKFKMKHHLVGHM 57
>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition
particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A
{Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A
Length = 433
Score = 30.6 bits (70), Expect = 0.61
Identities = 11/52 (21%), Positives = 16/52 (30%), Gaps = 23/52 (44%)
Query: 56 NQNKRFQE------VILTRMRIGHTRLTHNHLFTKTDPPLCQCGAALSVRHI 101
+ RF + VI+T+M G + G ALS
Sbjct: 229 DLASRFHQASPIGSVIITKMD-GTAK----------------GGGALSAVVA 263
Score = 30.6 bits (70), Expect = 0.61
Identities = 11/52 (21%), Positives = 16/52 (30%), Gaps = 23/52 (44%)
Query: 198 NQNKRFQE------VILTRMRIGHTRLTHNHLFTKIDPPLCQCGAALSVRHI 243
+ RF + VI+T+M G + G ALS
Sbjct: 229 DLASRFHQASPIGSVIITKMD-GTAK----------------GGGALSAVVA 263
>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding,
signal recognition particle, GTP-binding, RNA-binding;
2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B
Length = 432
Score = 30.2 bits (69), Expect = 0.78
Identities = 11/53 (20%), Positives = 17/53 (32%), Gaps = 24/53 (45%)
Query: 56 NQNKRFQE-------VILTRMRIGHTRLTHNHLFTKTDPPLCQCGAALSVRHI 101
Q K F+E +I+T++ G + G ALS
Sbjct: 228 IQAKAFKEAVGEIGSIIVTKLD-GSAK----------------GGGALSAVAE 263
Score = 30.2 bits (69), Expect = 0.78
Identities = 11/53 (20%), Positives = 17/53 (32%), Gaps = 24/53 (45%)
Query: 198 NQNKRFQE-------VILTRMRIGHTRLTHNHLFTKIDPPLCQCGAALSVRHI 243
Q K F+E +I+T++ G + G ALS
Sbjct: 228 IQAKAFKEAVGEIGSIIVTKLD-GSAK----------------GGGALSAVAE 263
>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A
{Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB:
1j8y_F
Length = 297
Score = 29.8 bits (68), Expect = 1.0
Identities = 9/52 (17%), Positives = 16/52 (30%), Gaps = 23/52 (44%)
Query: 56 NQNKRFQE------VILTRMRIGHTRLTHNHLFTKTDPPLCQCGAALSVRHI 101
+ +F + +I+T+M G + G ALS
Sbjct: 230 DLASKFNQASKIGTIIITKMD-GTAK----------------GGGALSAVAA 264
Score = 29.8 bits (68), Expect = 1.0
Identities = 9/52 (17%), Positives = 16/52 (30%), Gaps = 23/52 (44%)
Query: 198 NQNKRFQE------VILTRMRIGHTRLTHNHLFTKIDPPLCQCGAALSVRHI 243
+ +F + +I+T+M G + G ALS
Sbjct: 230 DLASKFNQASKIGTIIITKMD-GTAK----------------GGGALSAVAA 264
>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA
binding protein, hydrolase, gtpas; HET: GCP; 3.94A
{Escherichia coli} PDB: 2j28_9
Length = 433
Score = 29.4 bits (67), Expect = 1.5
Identities = 16/49 (32%), Positives = 20/49 (40%), Gaps = 23/49 (46%)
Query: 59 KRFQE------VILTRMRIGHTRLTHNHLFTKTDPPLCQCGAALSVRHI 101
K F E V+LT++ G R GAALS+RHI
Sbjct: 234 KAFNEALPLTGVVLTKVD-GDAR----------------GGAALSIRHI 265
Score = 29.4 bits (67), Expect = 1.5
Identities = 16/49 (32%), Positives = 20/49 (40%), Gaps = 23/49 (46%)
Query: 201 KRFQE------VILTRMRIGHTRLTHNHLFTKIDPPLCQCGAALSVRHI 243
K F E V+LT++ G R GAALS+RHI
Sbjct: 234 KAFNEALPLTGVVLTKVD-GDAR----------------GGAALSIRHI 265
>1pbi_A Bowman-BIRK proteinase inhibitor; bowman-BIRK inhibitor, trypsin
inhibitor, chymotrypsin inhib; 2.70A {Pisum sativum}
SCOP: g.3.13.1 PDB: 2aih_A
Length = 72
Score = 26.4 bits (58), Expect = 2.7
Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 13/41 (31%)
Query: 83 TKTDPPLCQCGAALSVRHILSCH--------TKIDPPLCQC 115
TK++PP C+C +CH +PP CQC
Sbjct: 15 TKSNPPTCRCVDVGE-----TCHSACLSCICAYSNPPKCQC 50
>2g81_I BTCI, bowman-BIRK type SEED trypsin and chymotrypsin inhibitor;
proteinase inhibitor, protein structure, bowman-BIRK
inhibitor; HET: P6G PGE; 1.55A {Vigna unguiculata} SCOP:
g.3.13.1 PDB: 1h34_A 1tab_I 2r33_A 1bbi_A 2bbi_A 1d6r_I
1k9b_A 1pi2_A
Length = 83
Score = 26.1 bits (57), Expect = 5.1
Identities = 15/41 (36%), Positives = 18/41 (43%), Gaps = 12/41 (29%)
Query: 83 TKTDPPLCQCGAALSVRHILSCH--------TKIDPPLCQC 115
TK+ PP C+C VR + SCH T P C C
Sbjct: 25 TKSIPPQCRC---SDVR-LNSCHSACKSCACTFSIPAQCFC 61
>2fj8_A BBBI, bowman-BIRK type trypsin inhibitor; all-beta, hydrolase
inhibitor; 1.19A {Hordeum vulgare} SCOP: g.3.13.1 PDB:
1tx6_I 1c2a_A
Length = 125
Score = 26.6 bits (58), Expect = 5.2
Identities = 8/36 (22%), Positives = 16/36 (44%), Gaps = 3/36 (8%)
Query: 83 TKTDPPLCQCGAALSVRH--ILSC-HTKIDPPLCQC 115
T+++PP C+C + +C ++ P C
Sbjct: 75 TRSNPPTCRCVDEVKKCAPTCKTCLPSRSRPSRRVC 110
>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 = 27.7 bits (61), Expect = 5.5
Identities = 6/26 (23%), Positives = 11/26 (42%), Gaps = 2/26 (7%)
Query: 237 ALSVRHILFCHQHVNIRNSLDTPPSL 262
A S R + H ++ + L P +
Sbjct: 3 AYSTRPLTL--SHGSLEHVLLVPTAS 26
>1t5j_A Hypothetical protein MJ1187; putative hydrolase, structural
genomics, PSI, protein structure initiative; 2.70A
{Methanocaldococcus jannaschii} SCOP: a.209.1.1
Length = 313
Score = 27.2 bits (61), Expect = 5.6
Identities = 8/39 (20%), Positives = 12/39 (30%), Gaps = 10/39 (25%)
Query: 74 TRLTHNHLFTKTDPPLCQCGA---ALSVRHILSCHTKID 109
+++THN+ GA A V L
Sbjct: 152 SKITHNN-------KTAIAGALAIAFFVSSALKDRKDFS 183
>1df9_C Bowman-BIRK type trypsin inhibitor; beta barrels, catalytic triad,
inhibitor complex, multiple conformation, virus/viral
protein/inhibitor; 2.10A {Vigna radiata var} SCOP:
g.3.13.1 PDB: 2qid_C 3myw_I
Length = 72
Score = 25.3 bits (55), Expect = 6.4
Identities = 13/41 (31%), Positives = 17/41 (41%), Gaps = 12/41 (29%)
Query: 83 TKTDPPLCQCGAALSVRHILSCH--------TKIDPPLCQC 115
TK+ PP C C + SCH T+ P C+C
Sbjct: 19 TKSIPPQCHCANI----RLNSCHSACKSCICTRSMPGKCRC 55
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
0.324 0.137 0.444
Gapped
Lambda K H
0.267 0.0584 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,314,232
Number of extensions: 239971
Number of successful extensions: 598
Number of sequences better than 10.0: 1
Number of HSP's gapped: 582
Number of HSP's successfully gapped: 27
Length of query: 285
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 192
Effective length of database: 4,105,140
Effective search space: 788186880
Effective search space used: 788186880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 57 (26.1 bits)