RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13345
(276 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 = 108 bits (270), Expect = 8e-27
Identities = 28/150 (18%), Positives = 60/150 (40%), Gaps = 23/150 (15%)
Query: 34 IEWMSDKLMKSFEGARN-NPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDLF 92
+EW+S L+K++E N +PF + EL+K P K+ VS ++
Sbjct: 297 LEWLSPSLLKTWENRNNTSPFEIGSRIKIIAPNELSKYPGSKICFVSEVG---ALINEVI 353
Query: 93 FQWCSSPENSIIITNRTSPGTLARDLI-------------------ELGGNRTLTLQVKK 133
+ +S + ++I+T + + D I + +++ K
Sbjct: 354 IKVGNSEKTTLILTKPSFECASSLDKILEIVEQDERNWKTFPEDGKSFLCDNYISIDTIK 413
Query: 134 RIRLEGEELEEYQKKKDKEAKDKQEKEKIP 163
L EE E ++ + ++ +D+ +K +
Sbjct: 414 EEPLSKEETEAFKVQLKEKKRDRNKKILLV 443
Score = 37.1 bits (85), Expect = 0.005
Identities = 3/33 (9%), Positives = 13/33 (39%), Gaps = 2/33 (6%)
Query: 209 VLVSTPDMECGFSRDLFFQWCSSPENSIIITNR 241
+ + ++ + +S + ++I+T
Sbjct: 339 ICFVSEVG--ALINEVIIKVGNSEKTTLILTKP 369
>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 = 70.2 bits (173), Expect = 6e-14
Identities = 23/114 (20%), Positives = 42/114 (36%), Gaps = 16/114 (14%)
Query: 34 IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAE---LAKVPSPKVVLVSTPDM-ECGFSR 89
+ + S+++ F +N PF +++ L + P P VVL + M G
Sbjct: 265 VRYFSEEVQAHFLQGKN-PFRPAGLEVVEHTEASKALNRAPGPMVVL-AGSGMLAGGRIL 322
Query: 90 DLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEELE 143
S P N+++ G L ++I +R+ GEE+
Sbjct: 323 HHLKHGLSDPRNALVFVGYQPQGGLGAEIIA-RP---------PAVRILGEEVP 366
Score = 30.1 bits (69), Expect = 0.70
Identities = 6/32 (18%), Positives = 12/32 (37%), Gaps = 1/32 (3%)
Query: 209 VLVSTPDM-ECGFSRDLFFQWCSSPENSIIIT 239
V+++ M G S P N+++
Sbjct: 308 VVLAGSGMLAGGRILHHLKHGLSDPRNALVFV 339
>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 = 69.2 bits (170), Expect = 1e-13
Identities = 33/111 (29%), Positives = 53/111 (47%), Gaps = 14/111 (12%)
Query: 34 IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDM-ECGFSRDLF 92
+ M+DK+ K NNPF FKH+ S+ P VV+ ++P M + G SR+LF
Sbjct: 286 VNAMNDKIRKQINI--NNPFVFKHISNLKSMDHF-DDIGPSVVM-ASPGMMQSGLSRELF 341
Query: 93 FQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEELE 143
WC+ N +II GTLA+ ++ ++ + G++L
Sbjct: 342 ESWCTDKRNGVIIAGYCVEGTLAKHIMS-EP--------EEITTMSGQKLP 383
Score = 33.4 bits (77), Expect = 0.074
Identities = 13/32 (40%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 209 VLVSTPDM-ECGFSRDLFFQWCSSPENSIIIT 239
V++++P M + G SR+LF WC+ N +II
Sbjct: 324 VVMASPGMMQSGLSRELFESWCTDKRNGVIIA 355
>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 = 68.5 bits (168), Expect = 3e-13
Identities = 27/115 (23%), Positives = 46/115 (40%), Gaps = 15/115 (13%)
Query: 34 IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAE---LAKVPSPKVVLVSTPDM-ECGFSR 89
E++S +L + NPF + + E + P +++ ++ M G S
Sbjct: 473 PEYLSRRLREQIFKEGYNPFLSEIFHPVANSRERQDIIDSNEPAIII-ASSGMLVGGPSV 531
Query: 90 DLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEELEE 144
+ F Q P+NSII + + GTL R + G + I + GEE
Sbjct: 532 EYFKQLAPDPKNSIIFVSYQAEGTLGRQVQS-GI---------REIPMVGEEGRT 576
Score = 31.2 bits (71), Expect = 0.40
Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 209 VLVSTPDM-ECGFSRDLFFQWCSSPENSIIIT 239
+++++ M G S + F Q P+NSII
Sbjct: 517 IIIASSGMLVGGPSVEYFKQLAPDPKNSIIFV 548
>2xr1_A Cleavage and polyadenylation specificity factor 1 subunit;
hydrolase, metallo-beta-lactamase, beta-CAsp, RNA
processing; 2.59A {Methanosarcina mazei}
Length = 640
Score = 67.3 bits (165), Expect = 6e-13
Identities = 22/100 (22%), Positives = 43/100 (43%), Gaps = 7/100 (7%)
Query: 34 IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAE---LAKVPSPKVVLVSTPDM-ECGFSR 89
E++++ L K NPF + K S + + P P V+L +T M G
Sbjct: 462 PEYLNNDLRKLIFQKGQNPFLSECFKPVDSHEARQKIIQNPQPCVIL-ATSGMMNGGPVM 520
Query: 90 DLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTL 129
+ F + P N+++ + GT+ R + + G + + +
Sbjct: 521 EYFKAFAEDPRNTLVFVGYQADGTIGRRIQK--GWKEIPM 558
Score = 30.7 bits (70), Expect = 0.58
Identities = 7/32 (21%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 209 VLVSTPDM-ECGFSRDLFFQWCSSPENSIIIT 239
V+++T M G + F + P N+++
Sbjct: 506 VILATSGMMNGGPVMEYFKAFAEDPRNTLVFV 537
>2ycb_A Beta-CAsp RNAse, cleavage and polyadenylation specificity factor;
hydrolase, KH, metallo-beta-lactamase; 3.10A
{Methanothermobacter thermautotrophicusorganism_taxid}
Length = 636
Score = 66.6 bits (163), Expect = 1e-12
Identities = 27/114 (23%), Positives = 47/114 (41%), Gaps = 14/114 (12%)
Query: 34 IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKV--PSPKVVLVSTPDM-ECGFSRD 90
E++S L +NPF + + E ++ P ++L ST M G S +
Sbjct: 459 PEYLSKDLRDQIFHMGHNPFISDIFHKVNGMDERREIVEGEPSIIL-STSGMLTGGNSLE 517
Query: 91 LFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEELEE 144
F C P+NS++ + G+L R + + G K I L+ E+ +
Sbjct: 518 YFKWLCEDPDNSLVFVGYQAEGSLGRRIQK-G---------WKEIPLKDEDDKM 561
Score = 30.7 bits (70), Expect = 0.51
Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 209 VLVSTPDM-ECGFSRDLFFQWCSSPENSIIIT 239
+++ST M G S + F C P+NS++
Sbjct: 502 IILSTSGMLTGGNSLEYFKWLCEDPDNSLVFV 533
>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 = 48.3 bits (114), Expect = 2e-06
Identities = 39/319 (12%), Positives = 90/319 (28%), Gaps = 106/319 (33%)
Query: 35 EWMSDKL----------MKSFEGARNN------PFHFKHV-------KLCHSLAELAKVP 71
+++ + + + R+ F +V KL +L EL P
Sbjct: 92 KFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELR--P 149
Query: 72 SPKVVL---------------VSTPDMECGFSRDLFFQW-----CSSPENSIIITNRTSP 111
+ V++ + ++C +F W C+SPE + + +
Sbjct: 150 AKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIF--WLNLKNCNSPETVLEMLQKL-- 205
Query: 112 GTLARDLIELGGNRTLTLQVKKRIRLEGEELEEYQKKKDKEAKDKQEKEKIPPHDTSFIN 171
L ++ N T I+L ++ ++ K P++
Sbjct: 206 ------LYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKS----------KPYENCL-- 247
Query: 172 ELQLSDF--KQTLQRNGIDCEFMDGVLICCRGT-----VAVRRVVLVSTPDMECGF---- 220
L L + + + C+ +L+ R ++ +S
Sbjct: 248 -LVLLNVQNAKAWNAFNLSCK----ILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDE 302
Query: 221 SRDLFFQWCSSPEN--------------SII----ITNRNRAD-----DSDSNVIVLEGC 257
+ L ++ SII D + D ++E
Sbjct: 303 VKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESS 362
Query: 258 LSDEYYRVQQLLYDQYAIL 276
L+ + ++D+ ++
Sbjct: 363 LNVLEPAEYRKMFDRLSVF 381
Score = 28.3 bits (62), Expect = 3.7
Identities = 12/66 (18%), Positives = 27/66 (40%), Gaps = 5/66 (7%)
Query: 131 VKKRIRLEGEELEEYQKKKDKEAKDKQEKEKIPPHDTSF---INELQLSDFKQTLQRNGI 187
++++IR + + + K K I +D + +N + DF ++ N I
Sbjct: 503 LEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAIL--DFLPKIEENLI 560
Query: 188 DCEFMD 193
++ D
Sbjct: 561 CSKYTD 566
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 35.1 bits (80), Expect = 0.013
Identities = 6/31 (19%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 133 KRIRLEGEELEEYQKKKDK--EAKDKQEKEK 161
R+ E E + ++++++ K + D K
Sbjct: 78 DRLTQEPESIRKWREEQRKRLQELDAASKVM 108
Score = 33.2 bits (75), Expect = 0.048
Identities = 8/30 (26%), Positives = 18/30 (60%), Gaps = 4/30 (13%)
Query: 132 KKRIRLEGEELEEYQKKKDKEAKDKQEKEK 161
+KR+ +EL+ K ++E ++K +K+
Sbjct: 95 RKRL----QELDAASKVMEQEWREKAKKDL 120
Score = 30.1 bits (67), Expect = 0.60
Identities = 7/46 (15%), Positives = 20/46 (43%), Gaps = 11/46 (23%)
Query: 132 KKRIRLEGE-ELEE----YQKKKDKEAKDKQEKEKIPPHDTSFINE 172
++ R + + +LEE ++ +K + + +K +F +
Sbjct: 109 EQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADK------AFYQQ 148
>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 = 31.2 bits (70), Expect = 0.40
Identities = 28/172 (16%), Positives = 57/172 (33%), Gaps = 54/172 (31%)
Query: 4 KLMKSFEGARNNPFHFKHVKLC-HSLAE---LAKIEWMSDKLMKSFEGARNNPFHFKHVK 59
+ +KS +G F HSL E LA + +D + S E V+
Sbjct: 1745 EDLKS-KGLIPADATF-----AGHSLGEYAALASL---ADVM--SIESL---------VE 1784
Query: 60 LCH---SLAELAKVP-------SPKVVLVSTPDMECGFSRDLFFQWC---SSPENSII-I 105
+ ++A VP + ++ ++ + FS++ ++ I
Sbjct: 1785 VVFYRGMTMQVA-VPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEI 1843
Query: 106 TNRTSPG-------------TLARDLIELGGNRTLTLQVKKRIRLEGEELEE 144
N T+ L + + ++++K + L EE+E
Sbjct: 1844 VNYNVENQQYVAAGDLRALDTVTNVLNFIKLQKIDIIELQKSLSL--EEVEG 1893
>3cqb_A Probable protease HTPX homolog; heat shock protein HTPX domain,
PSI-2, protein structure INI structural genomics; HET:
MSE; 1.86A {Vibrio parahaemolyticus rimd 2210633}
Length = 107
Score = 29.5 bits (67), Expect = 0.44
Identities = 8/51 (15%), Positives = 16/51 (31%), Gaps = 5/51 (9%)
Query: 38 SDKLMKSFEGAR-----NNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDM 83
S + G N ++ A+ A + P V + + D+
Sbjct: 4 SKGMALRSVGGMVIESPRNETEHWLLETVGRQAQQAGIGMPTVAIYDSADI 54
>1gef_A Holliday junction resolvase; HJC, hydrolase; 2.00A {Pyrococcus
furiosus} SCOP: c.52.1.18 PDB: 1ipi_A
Length = 123
Score = 27.7 bits (61), Expect = 2.1
Identities = 8/39 (20%), Positives = 17/39 (43%), Gaps = 4/39 (10%)
Query: 110 SPGTLARDLIELGGNRTLTLQVK----KRIRLEGEELEE 144
S G+ DL+ G + L ++VK + + ++
Sbjct: 26 SAGSKKVDLVAGNGKKYLCIEVKVTKKDHLYVGKRDMGR 64
>3u5c_G RP9, S10, YS4, 40S ribosomal protein S6-A; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3j16_C 3u5g_G
Length = 236
Score = 27.4 bits (60), Expect = 4.3
Identities = 6/33 (18%), Positives = 15/33 (45%), Gaps = 3/33 (9%)
Query: 132 KKRIRLEGEELEEYQK---KKDKEAKDKQEKEK 161
+ + + E EY + K+ E K ++ + +
Sbjct: 195 VRNAQAQREAAAEYAQLLAKRLSERKAEKAEIR 227
>4dgw_B PRE-mRNA-splicing factor PRP21; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 152
Score = 27.3 bits (60), Expect = 4.4
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 141 ELEEYQKKKDKEAKDKQEKEKI 162
+ E++K KD+E E KI
Sbjct: 84 QYWEFEKDKDREHDKLVELCKI 105
>1w36_B RECB, exodeoxyribonuclease V beta chain; recombination, helicase,
hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli}
SCOP: c.37.1.19 c.37.1.19 c.52.1.24 PDB: 3k70_B*
Length = 1180
Score = 27.6 bits (61), Expect = 5.5
Identities = 11/52 (21%), Positives = 17/52 (32%), Gaps = 8/52 (15%)
Query: 223 DLFFQWCSSPENSIII----TNRNRADDSDSNVIVLEGCLSDEYYRVQQLLY 270
DL F+ E + +N D S + + Y +Q LY
Sbjct: 1067 DLVFRH----EGRYYLLDYKSNWLGEDSSAYTQQAMAAAMQAHRYDLQYQLY 1114
>1zym_A Enzyme I; phosphotransferase; 2.50A {Escherichia coli} SCOP:
a.60.10.1 c.8.1.2 PDB: 1eza_A 1ezb_A 1ezc_A 1ezd_A
2eza_A 2ezb_A 2ezc_A 3ezb_A 3eze_A 3eza_A
Length = 258
Score = 26.8 bits (60), Expect = 7.0
Identities = 5/23 (21%), Positives = 14/23 (60%)
Query: 140 EELEEYQKKKDKEAKDKQEKEKI 162
E +++ + +++ A +K E K+
Sbjct: 234 EVIDKMRAVQEQVASEKAELAKL 256
>3mmz_A Putative HAD family hydrolase; structural genomics, protein
structure initiative, NEW YORK structural genomix
research consortium; 1.84A {Streptomyces avermitilis}
Length = 176
Score = 26.4 bits (59), Expect = 9.3
Identities = 10/69 (14%), Positives = 20/69 (28%), Gaps = 22/69 (31%)
Query: 104 IITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEELEEYQKKKDKEA--KDKQEKEK 161
I++ +P AR +L + K+ K E++
Sbjct: 60 ILSTEQNPVVAAR-ARKLK-------------------IPVLHGIDRKDLALKQWCEEQG 99
Query: 162 IPPHDTSFI 170
I P ++
Sbjct: 100 IAPERVLYV 108
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
0.320 0.135 0.408
Gapped
Lambda K H
0.267 0.0562 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,236,695
Number of extensions: 248762
Number of successful extensions: 755
Number of sequences better than 10.0: 1
Number of HSP's gapped: 739
Number of HSP's successfully gapped: 39
Length of query: 276
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 184
Effective length of database: 4,133,061
Effective search space: 760483224
Effective search space used: 760483224
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 (21.8 bits)
S2: 57 (26.1 bits)