RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9120
(263 letters)
>2i7x_A Protein CFT2; polyadenylation, metallo-B-lactamase, PRE-mRNA
processing, artemis, V(D)J recombination, double-strand
break repair; 2.50A {Saccharomyces cerevisiae} SCOP:
d.157.1.10
Length = 717
Score = 55.2 bits (132), Expect = 6e-09
Identities = 10/72 (13%), Positives = 22/72 (30%), Gaps = 3/72 (4%)
Query: 23 RLKHFKSIHDDAFNAEFRQPCIVFCGHPSLRFGDSVHFVQLWGSNPLHTIIFTEPDFPYV 82
+ I +++ I F + G++ T+I T+P F
Sbjct: 318 EIGSRIKIIAPNELSKYPGSKICFVSEVG---ALINEVIIKVGNSEKTTLILTKPSFECA 374
Query: 83 EALAPFQPLAMK 94
+L + +
Sbjct: 375 SSLDKILEIVEQ 386
>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 = 42.7 bits (100), Expect = 8e-05
Identities = 39/234 (16%), Positives = 65/234 (27%), Gaps = 111/234 (47%)
Query: 38 EFRQPCI---------------------VFCGHPSLRFGDSVHFVQLWGSNPLHTIIFTE 76
+F QP + F GH SL G E
Sbjct: 1730 QFTQPALTLMEKAAFEDLKSKGLIPADATFAGH-SL--G--------------------E 1766
Query: 77 PDFPYVEALAPFQPLAMKSIHCPIDTSLNFNQANKLIRELKPSTLWSR-RYL----PRWC 131
Y ALA ++ + ++ +++ R + PR
Sbjct: 1767 ----YA-ALA-----SLADV-------MSIESLVEVVFY--------RGMTMQVAVPR-- 1799
Query: 132 SGQGATYLGGVVVKALPPRPM----DQQALKNANVLLLSGLTQTPTSNPDAMLGELC--- 184
+ G++ A+ P + Q+AL+ V + T G L
Sbjct: 1800 -DELGRSNYGMI--AINPGRVAASFSQEALQYV-VERVGKRT-----------GWLVEIV 1844
Query: 185 ------MTVV--GTLRANGKVDRKVLTLKRGEVLKIPLKRKRTRVNMSAEIAEA 230
V G LRA +D L ++ KI + + ++S E E
Sbjct: 1845 NYNVENQQYVAAGDLRA---LDTVTNVLNFIKLQKIDI--IELQKSLSLEEVEG 1893
>3iek_A Ribonuclease TTHA0252; metallo beta lactamase fold, endonuclease,
hydrolase, metal- nuclease, RNA-binding, rRNA
processing; HET: FLC; 2.05A {Thermus thermophilus} PDB:
2dkf_A* 3iel_A* 3iem_A* 2zdf_A* 3idz_A* 2zdd_A* 3ie0_A*
2zde_A* 3ie1_A* 2zdw_A* 3a4y_A* 2yvd_A* 3ie2_A*
Length = 431
Score = 32.8 bits (76), Expect = 0.11
Identities = 14/66 (21%), Positives = 27/66 (40%), Gaps = 6/66 (9%)
Query: 10 EEPFPHAHLVKTGRLKHFKSIHDDAFNAEFRQPCIVFCGHPSLRFGDSVHFVQLWGSNPL 69
+ PF A L + K+++ P +V G L G +H ++ S+P
Sbjct: 280 KNPFRPAGLEVVEHTEASKALNRA------PGPMVVLAGSGMLAGGRILHHLKHGLSDPR 333
Query: 70 HTIIFT 75
+ ++F
Sbjct: 334 NALVFV 339
>3af5_A Putative uncharacterized protein PH1404; archaeal CPSF, beta-CAsp
family, KH domain, ribonuclease, ME beta-lactamase
superfamily, archaea; 2.60A {Pyrococcus horikoshii} PDB:
3af6_A*
Length = 651
Score = 31.2 bits (71), Expect = 0.39
Identities = 14/63 (22%), Positives = 23/63 (36%), Gaps = 8/63 (12%)
Query: 13 FPHAHLVKTGRLKHFKSIHDDAFNAEFRQPCIVFCGHPSLRFGDSVHFVQLWGSNPLHTI 72
H V + + I D +P I+ L G SV + + +P ++I
Sbjct: 494 SEIFHPVAN--SRERQDIIDS------NEPAIIIASSGMLVGGPSVEYFKQLAPDPKNSI 545
Query: 73 IFT 75
IF
Sbjct: 546 IFV 548
>3nuw_A 2-OXO-3-deoxygalactonate kinase; structural genomics, PSI-2,
protein structure initiative, MI center for structural
genomics, MCSG; HET: MSE; 2.09A {Klebsiella pneumoniae}
PDB: 3r1x_A*
Length = 295
Score = 30.8 bits (69), Expect = 0.39
Identities = 17/113 (15%), Positives = 32/113 (28%), Gaps = 9/113 (7%)
Query: 89 QPLAMKSIHCPIDTSLNFNQANKLIRELKPSTLWSRRYLPRWCSG-----QGATYLGGVV 143
+ L + + + A L + W P +G G +
Sbjct: 27 ECLESRQSEAGVTRLNGRSPAAVLAEITQH---WRDGATPVVMAGMVGSNVGWKIAPYLP 83
Query: 144 VKALPPRPMDQQALKNANVLLLSGLTQTPTSNPDAMLGELCMTVVGTLRANGK 196
+ A Q N+ ++ GL + N + M GE ++G
Sbjct: 84 LPAAFSDIGQQLTAVGDNIWIIPGLCVSRDDNHNVMRGE-ETQLLGARALAPS 135
>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 = 29.9 bits (66), Expect = 0.45
Identities = 9/37 (24%), Positives = 17/37 (45%), Gaps = 9/37 (24%)
Query: 211 KIPLKRKRTRVNMSAEIAEAVEPCELRPGLAI-ASIK 246
K LK+ + + + A + P LAI A+++
Sbjct: 19 KQALKKLQASLKLYA-------D-DSAPALAIKATME 47
>2ycb_A Beta-CAsp RNAse, cleavage and polyadenylation specificity factor;
hydrolase, KH, metallo-beta-lactamase; 3.10A
{Methanothermobacter thermautotrophicusorganism_taxid}
Length = 636
Score = 30.4 bits (69), Expect = 0.66
Identities = 10/63 (15%), Positives = 24/63 (38%), Gaps = 9/63 (14%)
Query: 13 FPHAHLVKTGRLKHFKSIHDDAFNAEFRQPCIVFCGHPSLRFGDSVHFVQLWGSNPLHTI 72
H V + + I + +P I+ L G+S+ + + +P +++
Sbjct: 480 SDIFHKVNG--MDERREIVE-------GEPSIILSTSGMLTGGNSLEYFKWLCEDPDNSL 530
Query: 73 IFT 75
+F
Sbjct: 531 VFV 533
>2xr1_A Cleavage and polyadenylation specificity factor 1 subunit;
hydrolase, metallo-beta-lactamase, beta-CAsp, RNA
processing; 2.59A {Methanosarcina mazei}
Length = 640
Score = 29.6 bits (67), Expect = 1.1
Identities = 9/63 (14%), Positives = 24/63 (38%), Gaps = 8/63 (12%)
Query: 13 FPHAHLVKTGRLKHFKSIHDDAFNAEFRQPCIVFCGHPSLRFGDSVHFVQLWGSNPLHTI 72
V + + + I + QPC++ + G + + + + +P +T+
Sbjct: 483 SECFKPVDS--HEARQKIIQN------PQPCVILATSGMMNGGPVMEYFKAFAEDPRNTL 534
Query: 73 IFT 75
+F
Sbjct: 535 VFV 537
>2x36_A LON protease homolog, mitochondrial; hydrolase, catalytic DYAD,
transit peptide; 2.00A {Homo sapiens}
Length = 207
Score = 27.9 bits (63), Expect = 2.7
Identities = 16/55 (29%), Positives = 20/55 (36%), Gaps = 14/55 (25%)
Query: 164 LLSGLTQTPTSNPDAMLGELCMTVVGTLRANGKVDR------KVLTLKRGEVLKI 212
LLS P AM GE+ +L GK+ K + KR V I
Sbjct: 112 LLSLAMGRPVRQNLAMTGEV------SLT--GKILPVGGIKEKTIAAKRAGVTCI 158
>2i7t_A Cleavage and polyadenylation specificity factor 73 kDa subunit;
metallo-B-lactamase, PRE-mRNA processing, artemis, V(D)J
recombination; 2.10A {Homo sapiens} SCOP: d.157.1.10
PDB: 2i7v_A
Length = 459
Score = 28.0 bits (63), Expect = 3.7
Identities = 8/51 (15%), Positives = 19/51 (37%), Gaps = 1/51 (1%)
Query: 25 KHFKSIHDDAFNAEFRQPCIVFCGHPSLRFGDSVHFVQLWGSNPLHTIIFT 75
KH ++ + P +V ++ G S + W ++ + +I
Sbjct: 306 KHISNLKSMDHFDD-IGPSVVMASPGMMQSGLSRELFESWCTDKRNGVIIA 355
>3t69_A Putative 2-dehydro-3-deoxygalactonokinase; structural genomics,
PSI-biology, NEW YORK structural genomi research
consortium, nysgrc; 2.55A {Sinorhizobium meliloti}
Length = 330
Score = 27.4 bits (60), Expect = 5.3
Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 1/39 (2%)
Query: 161 NVLLLSGLTQTPTSNPDAMLGELCMTVVGTLRANGKVDR 199
++ +L GL Q +PD M GE ++G G
Sbjct: 107 DIRILPGLAQRDRRHPDVMRGEETQ-LLGAAAHLGAGSH 144
>3ldv_A Orotidine 5'-phosphate decarboxylase; structural genomics,
infectious diseases; 1.77A {Vibrio cholerae o1 biovar el
tor} PDB: 3uwq_A*
Length = 255
Score = 26.8 bits (60), Expect = 6.4
Identities = 10/39 (25%), Positives = 15/39 (38%), Gaps = 3/39 (7%)
Query: 86 APFQPLAMKS--IHCPIDTSLNFNQANKLIRELKPSTLW 122
FQ AM + +D N A + ++ PST
Sbjct: 18 LYFQSNAMNDPKVIVALDYD-NLADALAFVDKIDPSTCR 55
>1y5o_A TFB1, RNA polymerase II transcription factor B 73 kDa subunit;
TFIIH, PH domain, phosphoinositides, VP16; NMR
{Saccharomyces cerevisiae} SCOP: b.55.1.9 PDB: 2gs0_A
2k2u_A 2l2i_A 2lox_A*
Length = 115
Score = 26.2 bits (57), Expect = 6.5
Identities = 9/35 (25%), Positives = 13/35 (37%)
Query: 146 ALPPRPMDQQALKNANVLLLSGLTQTPTSNPDAML 180
L R D + + + L TP S+ ML
Sbjct: 26 ELTWRSTDGDKVHTVVLSTIDKLQATPASSEKMML 60
>3npg_A Uncharacterized DUF364 family protein; protein with unknown
function from DUF364 family, structural genomics; 2.70A
{Pyrococcus horikoshii}
Length = 249
Score = 26.5 bits (58), Expect = 8.3
Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 4/46 (8%)
Query: 100 IDTSLNFNQANKLIRELKPSTLWSRRYLPRWCSGQGATYLGGVVVK 145
+D L+ + KLI P+ LP + G T+L + V
Sbjct: 180 LDMILDRAKKAKLIVITGPTGQL----LPEFLKGTKVTHLASMKVT 221
>1rre_A ATP-dependent protease LA; catalytic Ser-Lys DYAD, hydrolase; HET:
MSE; 1.75A {Escherichia coli} SCOP: d.14.1.10 PDB:
1rr9_A*
Length = 200
Score = 26.3 bits (59), Expect = 9.5
Identities = 23/76 (30%), Positives = 32/76 (42%), Gaps = 14/76 (18%)
Query: 164 LLSGLTQTPTSNPDAMLGELCMTVVGTLRAN----GKVDRKVLTLKRG---EVLKIPLKR 216
L+S LT P AM GE+ TLR G + K+L RG VL IP +
Sbjct: 104 LVSCLTGNPVRADVAMTGEI------TLRGQVLPIGGLKEKLLAAHRGGIKTVL-IPFEN 156
Query: 217 KRTRVNMSAEIAEAVE 232
KR + + ++
Sbjct: 157 KRDLEEIPDNVIADLD 172
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 0.137 0.427
Gapped
Lambda K H
0.267 0.0833 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,062,154
Number of extensions: 236533
Number of successful extensions: 453
Number of sequences better than 10.0: 1
Number of HSP's gapped: 451
Number of HSP's successfully gapped: 25
Length of query: 263
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 171
Effective length of database: 4,133,061
Effective search space: 706753431
Effective search space used: 706753431
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 (25.2 bits)