RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5894
(233 letters)
>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 = 50.0 bits (119), Expect = 2e-07
Identities = 55/327 (16%), Positives = 92/327 (28%), Gaps = 137/327 (41%)
Query: 1 MADKLGLNP-DIRELKLGSS-----------FTNANKGSSFHT-----LRYDFK------ 37
A LG P ++R G++ + SF + F
Sbjct: 252 TAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCY 311
Query: 38 ----PASMDPNEVAK-LDVGE---SNQVTVTVPHG-SRETVFK-----GSHKPYQKECVL 83
S+ P+ + L+ E S ++++ ++E V SH P K+ +
Sbjct: 312 EAYPNTSLPPSILEDSLENNEGVPSPMLSIS---NLTQEQVQDYVNKTNSHLPAGKQVEI 368
Query: 84 IIDN------VTGE-ITLEKLSNNIQLKKTRTAPTNKTDTSHVMPSAIPLSRLKKKTSGK 136
+ N V+G +L L N+ L+K + AP+ D S IP S K K S
Sbjct: 369 SLVNGAKNLVVSGPPQSLYGL--NLTLRKAK-APSGL-DQSR-----IPFSERKLKFS-- 417
Query: 137 ANNNHKTKSGNNLSVPPSIPRHSPL-----------------QTSPSYFSPP--HTKS-- 175
N +P + P HS L + P T
Sbjct: 418 -----------NRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGS 466
Query: 176 ------------------------PTAPFKSPS------PGQGSSLSPMVNSLPALGLDD 205
T + PG S L + +
Sbjct: 467 DLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHR-------- 518
Query: 206 IGLIEGT----VTAKVLSSRNRRENED 228
+GT + A + + ++D
Sbjct: 519 --NKDGTGVRVIVA---GTLDINPDDD 540
>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 = 44.5 bits (104), Expect = 2e-05
Identities = 24/132 (18%), Positives = 45/132 (34%), Gaps = 17/132 (12%)
Query: 41 MDPNEVAKLDVGESNQVTVTVPHGSRETVFKGSHKPYQKECVLIIDNVTGEITLEKLSNN 100
+DPN ++ D + ++ + + K KPY + C+L++ NV N
Sbjct: 209 IDPNWTSRSDHSSNIKLRIHSIQAELRRLLK--SKPY-ENCLLVLLNVQNAKAWNAF--N 263
Query: 101 IQ---LKKTRTAPTNKTDTSHVMPSAIPLSRLKKKTSGKANNNHKTKSGNNLSV-----P 152
+ L TR K T + + L + + K+ L P
Sbjct: 264 LSCKILLTTR----FKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLP 319
Query: 153 PSIPRHSPLQTS 164
+ +P + S
Sbjct: 320 REVLTTNPRRLS 331
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 37.7 bits (87), Expect = 0.003
Identities = 26/89 (29%), Positives = 40/89 (44%), Gaps = 6/89 (6%)
Query: 108 TAPTNKTDTSHVMPSAIPLSRLKKKTSGKANNNHKTKSGNNLSVPPSIPRHSPLQTSPSY 167
T+P+ + P++ S TS + + S + S P+ P +SP TSPSY
Sbjct: 1651 TSPSYSPTSPSYSPTSPSYS----PTSPSYSPTSPSYSPTSPSYSPTSPSYSP--TSPSY 1704
Query: 168 FSPPHTKSPTAPFKSPSPGQGSSLSPMVN 196
+ SPT+P SP+ S SP +
Sbjct: 1705 SPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1733
Score = 33.9 bits (77), Expect = 0.049
Identities = 19/41 (46%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 153 PSIPRHSPLQTSPSYFSPPHTKSPTAPFKSPSPGQGSSLSP 193
PS P +SP TSPSY + SPT+P SP+ S+ SP
Sbjct: 1573 PSSPSYSP--TSPSYSPTSPSYSPTSPSYSPTSPSYSATSP 1611
Score = 33.5 bits (76), Expect = 0.053
Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 2/61 (3%)
Query: 133 TSGKANNNHKTKSGNNLSVPPSIPRHSPLQTSPSYFSPPHTKSPTAPFKSPSPGQGSSLS 192
+S + + S + S P+ P +SP TSPSY + + SPT+P SP+ S S
Sbjct: 1574 SSPSYSPTSPSYSPTSPSYSPTSPSYSP--TSPSYSATSPSYSPTSPSYSPTSPSYSPTS 1631
Query: 193 P 193
P
Sbjct: 1632 P 1632
Score = 32.7 bits (74), Expect = 0.094
Identities = 26/74 (35%), Positives = 34/74 (45%), Gaps = 2/74 (2%)
Query: 121 PSAIPLSRLKKKTSGKANNNHKTKSGNNLSVPPSIPRHSPLQTSPSYFSPPHTKSPTAPF 180
PS P S TS + + S + S P+ P +SP TSPSY + SPT+P
Sbjct: 1674 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP--TSPSYSPTSPSYSPTSPS 1731
Query: 181 KSPSPGQGSSLSPM 194
SP+ S SP
Sbjct: 1732 YSPTSPSYSPTSPS 1745
Score = 32.7 bits (74), Expect = 0.11
Identities = 17/41 (41%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 153 PSIPRHSPLQTSPSYFSPPHTKSPTAPFKSPSPGQGSSLSP 193
+ P +SP TSPSY + SPT+P SP+ S SP
Sbjct: 1608 ATSPSYSP--TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1646
Score = 32.4 bits (73), Expect = 0.14
Identities = 20/49 (40%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 145 SGNNLSVPPSIPRHSPLQTSPSYFSPPHTKSPTAPFKSPSPGQGSSLSP 193
S + S P+ P +SP TSPSY + SPT+P SP+ S SP
Sbjct: 1621 SPTSPSYSPTSPSYSP--TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1667
Score = 30.0 bits (67), Expect = 0.83
Identities = 26/73 (35%), Positives = 34/73 (46%), Gaps = 2/73 (2%)
Query: 121 PSAIPLSRLKKKTSGKANNNHKTKSGNNLSVPPSIPRHSPLQTSPSYFSPPHTKSPTAPF 180
PS P S TS + + S + S P+ P +SP TSPSY + SPT+P
Sbjct: 1632 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP--TSPSYSPTSPSYSPTSPS 1689
Query: 181 KSPSPGQGSSLSP 193
SP+ S SP
Sbjct: 1690 YSPTSPSYSPTSP 1702
Score = 29.3 bits (65), Expect = 1.3
Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 152 PPSIPRHSPLQTSPSYFSPPHTKSPTAPFKSP-SPGQGSSLSPMVNS 197
P SP TSP + T+P SP SPG +S + M +S
Sbjct: 1529 SPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPAYMPSS 1575
Score = 28.5 bits (63), Expect = 2.6
Identities = 20/58 (34%), Positives = 28/58 (48%), Gaps = 3/58 (5%)
Query: 145 SGNNLSVPPSIPRHSPLQTSPSYFSPPHTKSPTAPFKSP-SPGQGSSLSPMVNSLPAL 201
S + S P+ P +SP TSPSY + SPT+P SP SP + + P+
Sbjct: 1614 SPTSPSYSPTSPSYSP--TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1669
Score = 27.3 bits (60), Expect = 5.2
Identities = 15/32 (46%), Positives = 20/32 (62%), Gaps = 2/32 (6%)
Query: 153 PSIPRHSPLQTSPSYFSPPHTKSPTAPFKSPS 184
P+ P +SP TSPSY + SPT+P SP+
Sbjct: 1720 PTSPSYSP--TSPSYSPTSPSYSPTSPSYSPT 1749
Score = 27.3 bits (60), Expect = 5.4
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 4/53 (7%)
Query: 145 SGNNLSVPPSIPRHSP----LQTSPSYFSPPHTKSPTAPFKSPSPGQGSSLSP 193
S + + P +SP TSP+Y + SPT+P SP+ S SP
Sbjct: 1545 SAMSPGYGLTSPSYSPSSPGYSTSPAYMPSSPSYSPTSPSYSPTSPSYSPTSP 1597
>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 = 36.2 bits (83), Expect = 0.008
Identities = 26/79 (32%), Positives = 34/79 (43%), Gaps = 5/79 (6%)
Query: 121 PSAIPLSRLKKKTSGKANNNHKTKSGNNLSVPPSIPRHSPLQ-----TSPSYFSPPHTKS 175
PS P S TS + + S + S P+ P +SP TSPSY + S
Sbjct: 1575 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1634
Query: 176 PTAPFKSPSPGQGSSLSPM 194
PT+P SP+ S SP
Sbjct: 1635 PTSPSYSPTSPSYSPTSPS 1653
Score = 35.8 bits (82), Expect = 0.010
Identities = 27/92 (29%), Positives = 40/92 (43%), Gaps = 5/92 (5%)
Query: 106 TRTAPTNKTDTSHVMPSAI---PLSRLKKKTSGKANNNHKTKSGNNLSVPPSIPRHSPLQ 162
+ T+P+ + P++ P S TS + + S + S P+ P +SP
Sbjct: 1627 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSP-- 1684
Query: 163 TSPSYFSPPHTKSPTAPFKSPSPGQGSSLSPM 194
TSPSY SPT+P SP+ S SP
Sbjct: 1685 TSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPA 1716
Score = 32.8 bits (74), Expect = 0.094
Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 153 PSIPRHSPLQTSPSYFSPPHTKSPTAPFKSPSPGQGSSLSPMVN 196
P+ P +SP TSP+Y + SPT+P SP+ S SP +
Sbjct: 1544 PTSPTYSP--TSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1585
Score = 30.1 bits (67), Expect = 0.72
Identities = 26/80 (32%), Positives = 35/80 (43%), Gaps = 2/80 (2%)
Query: 117 SHVMPSAIPLSRLKKKTSGKANNNHKTKSGNNLSVPPSIPRHSPLQTSPSYFSPPHTKSP 176
S PS P S TS + + S + S P+ P +SP S S SP + SP
Sbjct: 1606 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAY--SP 1663
Query: 177 TAPFKSPSPGQGSSLSPMVN 196
T+P SP+ S SP +
Sbjct: 1664 TSPSYSPTSPSYSPTSPSYS 1683
Score = 30.1 bits (67), Expect = 0.84
Identities = 16/45 (35%), Positives = 21/45 (46%), Gaps = 2/45 (4%)
Query: 145 SGNNLSVPPSIPRHSPLQTSPSYFSPPHTKSPTAPFKSPSPGQGS 189
S + S P+ P +SP TSPSY SP +P SP +
Sbjct: 1683 SPTSPSYSPTSPNYSP--TSPSYSPTSPGYSPGSPAYSPKQDEQK 1725
Score = 28.9 bits (64), Expect = 1.6
Identities = 12/44 (27%), Positives = 16/44 (36%)
Query: 150 SVPPSIPRHSPLQTSPSYFSPPHTKSPTAPFKSPSPGQGSSLSP 193
+ TSP + SPT+P SP+ S SP
Sbjct: 1518 EATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSP 1561
Score = 28.5 bits (63), Expect = 2.3
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 145 SGNNLSVPPSIPRHSPLQTSPSYFSPPHTKSPTAPFKSPSPGQGSSLSPMVNS 197
S + S P+ P +SP S S SP + SPT+P SP+ S SP +
Sbjct: 1585 SPTSPSYSPTSPSYSPTSPSYSPTSPSY--SPTSPSYSPTSPSYSPTSPSYSP 1635
Score = 27.8 bits (61), Expect = 3.7
Identities = 18/46 (39%), Positives = 23/46 (50%), Gaps = 5/46 (10%)
Query: 153 PSIPRHSPLQ-----TSPSYFSPPHTKSPTAPFKSPSPGQGSSLSP 193
P+ P +SP TSPSY + SPT+P SP+ S SP
Sbjct: 1558 PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1603
Score = 27.8 bits (61), Expect = 4.6
Identities = 11/37 (29%), Positives = 16/37 (43%), Gaps = 2/37 (5%)
Query: 153 PSIPRHSPLQTSPSYFSPPHTKSPTAPFKSPSPGQGS 189
P+ P +SP TSP Y SP + + + S
Sbjct: 1698 PTSPSYSP--TSPGYSPGSPAYSPKQDEQKHNENENS 1732
Score = 27.4 bits (60), Expect = 5.1
Identities = 15/51 (29%), Positives = 21/51 (41%), Gaps = 6/51 (11%)
Query: 145 SGNNLSVPPSIPRHSPLQTSPSY--FSPPHTKSPTAPFKSPSPGQGSSLSP 193
P+ P +SP + SP + SPT+P SP+ S SP
Sbjct: 1522 PFGAYGEAPTSPGFGV--SSPGFSPTSPTY--SPTSPAYSPTSPSYSPTSP 1568
>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor,
chromophore, glycoprotein, lipoprotein, membrane,
palmitate phosphorylation; HET: BOG RET PLM TWT PC1;
2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A*
Length = 448
Score = 31.0 bits (70), Expect = 0.27
Identities = 21/104 (20%), Positives = 31/104 (29%), Gaps = 4/104 (3%)
Query: 104 KKTRTAPTNKTDTSHVMPSAIPLSRLKKKTSGKANNNHKTKSGNNLSVPPSIPRHSPLQT 163
K+T +T+ S S + K + + P P Q
Sbjct: 342 KETEDDKDAETEIPAGESSDAAPSADAAQMKEMMAMMQKMQQQQ--AAYPPQGYAPPPQG 399
Query: 164 SPSYFSPPHTKSPTA--PFKSPSPGQGSSLSPMVNSLPALGLDD 205
P PP P P P P QG+ + P G+D+
Sbjct: 400 YPPQGYPPQGYPPQGYPPQGYPPPPQGAPPQGAPPAAPPQGVDN 443
>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 = 1.3
Identities = 7/25 (28%), Positives = 12/25 (48%), Gaps = 3/25 (12%)
Query: 93 TLEKLSNNIQLKKTRTAPT---NKT 114
L+KL +++L +AP T
Sbjct: 21 ALKKLQASLKLYADDSAPALAIKAT 45
Score = 28.0 bits (61), Expect = 1.7
Identities = 8/28 (28%), Positives = 13/28 (46%), Gaps = 11/28 (39%)
Query: 189 SSL---SPMVNSLPALGLDDIGLIEGTV 213
+SL + +S PAL I+ T+
Sbjct: 27 ASLKLYAD--DSAPALA------IKATM 46
>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 = 28.5 bits (63), Expect = 2.0
Identities = 12/41 (29%), Positives = 14/41 (34%), Gaps = 1/41 (2%)
Query: 152 PPSIPRHSPLQTSPSYFSPPHTKSPTAPFKSPSPGQGSSLS 192
+ P P P SP SP + SP G G S
Sbjct: 32 SMAAPSLHP-SLGPGIGSPGQLHSPISTLSSPINGMGPPFS 71
Score = 27.4 bits (60), Expect = 5.1
Identities = 16/86 (18%), Positives = 22/86 (25%)
Query: 145 SGNNLSVPPSIPRHSPLQTSPSYFSPPHTKSPTAPFKSPSPGQGSSLSPMVNSLPALGLD 204
S + P P S P PT P S G SPM + +
Sbjct: 54 SPISTLSSPINGMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIK 113
Query: 205 DIGLIEGTVTAKVLSSRNRRENEDRL 230
+ G + S N +
Sbjct: 114 PPLGLNGVLKVPAHPSGNMASFTKHI 139
>3ffv_A Protein SYD; membrane, translocon, secyeg, nanodisc, cell inner
membrane, cell membrane, protein binding; 2.00A
{Escherichia coli}
Length = 181
Score = 26.8 bits (59), Expect = 4.9
Identities = 6/16 (37%), Positives = 11/16 (68%)
Query: 82 VLIIDNVTGEITLEKL 97
V+ + N++GE+ E L
Sbjct: 143 VISVCNLSGEVCKETL 158
>1pk8_A RAT synapsin I; ATP binding, ATP grAsp, calcium (II) ION, membrane
protein; HET: ATP; 2.10A {Rattus norvegicus} SCOP:
c.30.1.5 d.142.1.3 PDB: 1px2_A*
Length = 422
Score = 27.1 bits (59), Expect = 5.5
Identities = 9/51 (17%), Positives = 17/51 (33%)
Query: 150 SVPPSIPRHSPLQTSPSYFSPPHTKSPTAPFKSPSPGQGSSLSPMVNSLPA 200
P + + ++ + T +P A +PSPG + A
Sbjct: 34 PPPSAASPGATPGSAAASAERASTAAPVASPAAPSPGSSGGGGFFSSLSNA 84
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
0.308 0.126 0.356
Gapped
Lambda K H
0.267 0.0749 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,244,701
Number of extensions: 175476
Number of successful extensions: 375
Number of sequences better than 10.0: 1
Number of HSP's gapped: 340
Number of HSP's successfully gapped: 42
Length of query: 233
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 143
Effective length of database: 4,188,903
Effective search space: 599013129
Effective search space used: 599013129
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 (21.6 bits)
S2: 56 (25.3 bits)