RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy422
(164 letters)
>2wwb_C SEC61BETA, protein transport protein SEC61 subunit beta; ribosome,
protein EXIT tunnel, cotranslational protein
translocation, protein conducting channel; 6.48A {Canis
lupus familiaris}
Length = 96
Score = 67.9 bits (165), Expect = 9e-16
Identities = 53/95 (55%), Positives = 64/95 (67%)
Query: 68 SPAPASSTSVGSGTRSPKAGGPGGRPTGSTVRQRKPTTTTAARSNRTGAGSGGMWRYYTD 127
S T+VGS RSP + +++ + T + T AG+GGMWR+YT+
Sbjct: 2 PGPTPSGTNVGSSGRSPSKAVAARAAGSTVRQRKNASCGTRSAGRTTSAGTGGMWRFYTE 61
Query: 128 DSPGIKVGPVPVLVMSLLFIASVFMLHIWGKYTRS 162
DSPG+KVGPVPVLVMSLLFIASVFMLHIWGKYTRS
Sbjct: 62 DSPGLKVGPVPVLVMSLLFIASVFMLHIWGKYTRS 96
Score = 39.4 bits (91), Expect = 5e-05
Identities = 25/65 (38%), Positives = 36/65 (55%)
Query: 2 APASSTSVGSGTRSPKAGGPGGRPTGSTVRQRKPTTTTAARSNRTGAGSGGMWRYYTDDS 61
S T+VGS RSP + +++ + T + T AG+GGMWR+YT+DS
Sbjct: 4 PTPSGTNVGSSGRSPSKAVAARAAGSTVRQRKNASCGTRSAGRTTSAGTGGMWRFYTEDS 63
Query: 62 PGIKV 66
PG+KV
Sbjct: 64 PGLKV 68
>2ww9_C Protein transport protein SEB2; ribonucleoprotein, transmembrane,
phospho signal sequence, membrane, ribosome, transport;
8.60A {Saccharomyces cerevisiae} PDB: 2wwa_C
Length = 87
Score = 66.0 bits (160), Expect = 4e-15
Identities = 23/69 (33%), Positives = 36/69 (52%)
Query: 92 RPTGSTVRQRKPTTTTAARSNRTGAGSGGMWRYYTDDSPGIKVGPVPVLVMSLLFIASVF 151
R S ++ T T+ R G S + + YTD++ G +V + VL +S+ FI SV
Sbjct: 17 RQAQSIKEKQAKQTPTSTRQAGYGGSSSSILKLYTDEANGFRVDSLVVLFLSVGFIFSVI 76
Query: 152 MLHIWGKYT 160
LH+ K+T
Sbjct: 77 ALHLLTKFT 85
Score = 34.4 bits (78), Expect = 0.003
Identities = 12/43 (27%), Positives = 20/43 (46%)
Query: 24 RPTGSTVRQRKPTTTTAARSNRTGAGSGGMWRYYTDDSPGIKV 66
R S ++ T T+ R G S + + YTD++ G +V
Sbjct: 17 RQAQSIKEKQAKQTPTSTRQAGYGGSSSSILKLYTDEANGFRV 59
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A
1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A*
1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A*
1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 29.7 bits (66), Expect = 0.47
Identities = 20/114 (17%), Positives = 24/114 (21%), Gaps = 8/114 (7%)
Query: 1 PAPASSTSVGSGTRSPKAGGPGGRPTGSTVRQRKPTTTTAARSNRTGAGSGGMWRYYTDD 60
A SP A S G +
Sbjct: 1479 LVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVS 1538
Query: 61 SPGIKVKSPA------PASSTSVGSGTRSPK--AGGPGGRPTGSTVRQRKPTTT 106
SPG SP S TS SP P PT + P+ +
Sbjct: 1539 SPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1592
>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 = 28.4 bits (62), Expect = 0.68
Identities = 6/15 (40%), Positives = 10/15 (66%), Gaps = 1/15 (6%)
Query: 55 RYYTDDS-PGIKVKS 68
+ Y DDS P + +K+
Sbjct: 30 KLYADDSAPALAIKA 44
>1rh5_C Secbeta; protein translocation, SECY, membrane protein, protein
channels, protein transport; 3.20A {Methanocaldococcus
jannaschii} SCOP: f.23.29.1 PDB: 1rhz_C 2yxq_C 2yxr_C
3kcr_C 3dkn_C 3bo1_C 3bo0_C
Length = 53
Score = 26.5 bits (58), Expect = 0.92
Identities = 13/52 (25%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 108 AARSNRTGAGSGGMWRYYTDDSPGIKVGPVPVLVMSLLFIASVFMLHIWGKY 159
+ R A S G+ RY + I+V P V+ +++ F+ +L +G++
Sbjct: 2 SKREETGLATSAGLIRYMDETFSKIRVKPEHVIGVTVAFVIIEAILT-YGRF 52
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 27.7 bits (61), Expect = 2.1
Identities = 26/108 (24%), Positives = 40/108 (37%), Gaps = 7/108 (6%)
Query: 1 PAPAS-STSVGSGTRSPKAGGPGGRPTGSTVRQRKPT-TTTAARSNRTGAGSGGMWRYYT 58
+P S S S S + SP P PT + P+ + T+ + T Y+
Sbjct: 1634 YSPTSPSYSPTSPSYSP--TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1691
Query: 59 DDSPGIKVKSPAPASSTSVGSGTRSPKAGG--PGGRPTGSTVRQRKPT 104
SP SP+ + ++ S T SP P PT + P+
Sbjct: 1692 PTSPSYSPTSPSYSPTSPSYSPT-SPSYSPTSPSYSPTSPSYSPTSPS 1738
>1m1j_A Fibrinogen alpha subunit; coiled coils, disulfide rings,
fibrinogen, blood clotting; HET: NDG NAG; 2.70A {Gallus
gallus} SCOP: h.1.8.1 PDB: 1ei3_A
Length = 491
Score = 27.6 bits (60), Expect = 2.1
Identities = 21/124 (16%), Positives = 35/124 (28%), Gaps = 6/124 (4%)
Query: 5 SSTSVGSGTRSPKAGGPGGRPTGSTVRQRKPTTTTAARSNRTGAGSGGMWRYYTDDSPGI 64
+ + S R + S+V + T T S G + + + D
Sbjct: 264 TGKLITSSHRRESPSLVDKTSSASSVHRCTRTVTKKVISGPDGPREEIVEKMVSSDGSDC 323
Query: 65 KVKSPAPASSTSVGSGTRSPKAGGP------GGRPTGSTVRQRKPTTTTAARSNRTGAGS 118
ST SGT S + + ++ S+ TGAGS
Sbjct: 324 SHLQGGREGSTYHFSGTGDFHKLDRLLPDLESFFTHDSVSTSSRHSIGSSTSSHVTGAGS 383
Query: 119 GGMW 122
+
Sbjct: 384 SHLG 387
>3ugj_A Phosphoribosylformylglycinamidine synthase; amidotransferase,
glutaminase, thioester intermediate, ligas; HET: ADP;
1.78A {Salmonella enterica subsp} PDB: 1t3t_A* 3ujn_A*
3umm_A*
Length = 1303
Score = 27.3 bits (60), Expect = 2.7
Identities = 11/31 (35%), Positives = 14/31 (45%)
Query: 68 SPAPASSTSVGSGTRSPKAGGPGGRPTGSTV 98
SP P ++T G R A G G +P V
Sbjct: 311 SPWPGAATGSGGEIRDEGATGRGAKPKAGLV 341
Score = 26.2 bits (57), Expect = 7.3
Identities = 10/30 (33%), Positives = 13/30 (43%)
Query: 1 PAPASSTSVGSGTRSPKAGGPGGRPTGSTV 30
P P ++T G R A G G +P V
Sbjct: 312 PWPGAATGSGGEIRDEGATGRGAKPKAGLV 341
>1hkh_A Gamma lactamase; hydrolase, alpha/beta hydrolase, CO-factor free
haloperoxidase,; 1.73A {Microbacterium} SCOP: c.69.1.12
PDB: 1hl7_A*
Length = 279
Score = 25.8 bits (57), Expect = 8.0
Identities = 3/18 (16%), Positives = 8/18 (44%)
Query: 125 YTDDSPGIKVGPVPVLVM 142
+ D ++ P L++
Sbjct: 208 FRSDVEAVRAAGKPTLIL 225
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
0.309 0.127 0.384
Gapped
Lambda K H
0.267 0.0545 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,432,970
Number of extensions: 140087
Number of successful extensions: 279
Number of sequences better than 10.0: 1
Number of HSP's gapped: 265
Number of HSP's successfully gapped: 37
Length of query: 164
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 78
Effective length of database: 4,300,587
Effective search space: 335445786
Effective search space used: 335445786
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 53 (24.6 bits)