RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8162
(326 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 = 47.4 bits (112), Expect = 5e-06
Identities = 41/212 (19%), Positives = 75/212 (35%), Gaps = 76/212 (35%)
Query: 123 YSINDVISSSQLNPVNSI--FSAE----LIAIY--LCLEAIT---VHPSDHFLIVSDSRS 171
+SI D++ + NPVN F E + Y + E I + F +++ +
Sbjct: 1659 FSILDIVIN---NPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHST 1715
Query: 172 AL------AALSNVSFTNP---LVSKVYSCWDLLKTLNKDVHFVLKPSQ----------S 212
+ LS FT P L+ + ++ LK+ ++ +
Sbjct: 1716 SYTFRSEKGLLSATQFTQPALTLME--KAAFEDLKS-----KGLIPADATFAGHSLGEYA 1768
Query: 213 ALAALSNV-SFTNPLVSKVYSCWDLLKTLNKDVHFLWCPSHCGIRG---NEAV--DEAAR 266
ALA+L++V S L++ V + RG AV DE R
Sbjct: 1769 ALASLADVMSIE-----------SLVEV----VFY---------RGMTMQVAVPRDELGR 1804
Query: 267 NP-----VNPARLKL-CSPDDFKPIAASMVKK 292
+ +NP R+ S + + + + K+
Sbjct: 1805 SNYGMIAINPGRVAASFSQEALQYVVERVGKR 1836
Score = 38.5 bits (89), Expect = 0.003
Identities = 42/253 (16%), Positives = 73/253 (28%), Gaps = 86/253 (33%)
Query: 18 VLFDQDLTPYNFTTNKPKP---------------LLSRFLSLPNFPNLISSSDIAPYV-R 61
L +Q F P+P L+ +FL YV
Sbjct: 32 QLQEQ------FNKILPEPTEGFAADDEPTTPAELVGKFLG---------------YVSS 70
Query: 62 TVPPWSSSSPPVDLSLGKDRKKDTPPVVFQQLFAGVINSKYVNHTICYT---DGSKTMNS 118
V P L+L F+ + + + H + + T+
Sbjct: 71 LVEPSKVGQFDQVLNLCLTE--------FENCYLEGND---I-HALAAKLLQENDTTLVK 118
Query: 119 TS----CAYSINDVISSSQLNPVNSIF-------SAELIAI---------YLC-LEAI-- 155
T + + NS +A+L+AI Y L +
Sbjct: 119 TKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQ 178
Query: 156 TVHPSDHFLIVSDSRSALAALSNVSFTNPLVSKVYSC-WDLLKTLNKDVHFVLKPSQSAL 214
T H LI + + LS + T KV++ ++L+ L + P + L
Sbjct: 179 TYHVLVGDLI----KFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSN---TPDKDYL 231
Query: 215 AALSNVSFTNPLV 227
+ +S PL+
Sbjct: 232 LS-IPISC--PLI 241
Score = 38.1 bits (88), Expect = 0.004
Identities = 27/203 (13%), Positives = 62/203 (30%), Gaps = 82/203 (40%)
Query: 14 PVQKVLFDQ-D---LTPYNFT-----TNKPKPLLSRFLSLPNFPNLISSSDIAPYVRTVP 64
+ ++++ D Y F+ N P L F
Sbjct: 1640 KAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHF----------------------- 1676
Query: 65 PWSSSSPPVDLSLGKDRKKDTPPVVFQQLFAGVINSKYVNH-------TICYTDGSKTMN 117
GK +++ ++F+ + G + ++ + + + ++
Sbjct: 1677 ---------GGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLS 1727
Query: 118 STSCAYSINDVISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDHFLIVSDSR------- 170
+T Q P ++ E A + L++ LI +D+
Sbjct: 1728 ATQFT----------Q--P--ALTLME-KAAFEDLKS-------KGLIPADATFAGHSLG 1765
Query: 171 --SALAALSNV-SFTN--PLVSK 188
+ALA+L++V S + +V
Sbjct: 1766 EYAALASLADVMSIESLVEVVFY 1788
Score = 36.2 bits (83), Expect = 0.015
Identities = 46/295 (15%), Positives = 86/295 (29%), Gaps = 103/295 (34%)
Query: 67 SSSSPPVDLSLGKDRKK-DTPPVVF---QQL---FAGVINSKYVNHTICYTDGSKTMNST 119
+ S+ P+ LS G P F QL F +K +
Sbjct: 3 AYSTRPLTLSHGSLEHVLLVPTASFFIASQLQEQF------------------NKILPEP 44
Query: 120 SCAYSINDVISSSQLNPVNSIFSAELIAIYL-----------------CLEAITVHPSDH 162
+ ++ +D ++ AEL+ +L L +
Sbjct: 45 TEGFAADDEPTTP----------AELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENC 94
Query: 163 FLIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLKT-------LNKDVHFVLKPSQSAL- 214
+L +D + A L + T + +K +L+K + K S SAL
Sbjct: 95 YLEGNDIHALAAKLLQENDTTLVKTK-----ELIKNYITARIMAKRPFD---KKSNSALF 146
Query: 215 -AALSNVSFTNPLVSKVYS----------CWDLLKTLNKDVHFLWCPSHCGIRGNEAVDE 263
A +++ + ++ L+ L+ H + + +
Sbjct: 147 RAVGEG-------NAQLVAIFGGQGNTDDYFEELRD-------LYQTYHVLVG--DLIKF 190
Query: 264 AARNPVNPARLKLCSPDDFKPI-AASMVKKEWQNQWDIIPITNKLKSIK---PLI 314
+A R + D + + + EW P + L SI PLI
Sbjct: 191 SAETLSELIR----TTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLI 241
>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO
enzyme, structural genomics, protein structure
initiative; NMR {Desulfitobacterium hafniense dcb-2}
PDB: 2kw4_A
Length = 147
Score = 42.7 bits (101), Expect = 3e-05
Identities = 8/33 (24%), Positives = 12/33 (36%)
Query: 234 WDLLKTLNKDVHFLWCPSHCGIRGNEAVDEAAR 266
L+ F +H G N+ VD A+
Sbjct: 100 AKLMNQYRGIYSFEKVKAHSGNEFNDYVDMKAK 132
>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV,
RNAse H, reverse transcriptase, transcription; 1.50A
{Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A
3v1r_A* 2hb5_A
Length = 165
Score = 42.5 bits (100), Expect = 4e-05
Identities = 37/174 (21%), Positives = 54/174 (31%), Gaps = 58/174 (33%)
Query: 105 HTICYTDGSKTMNS--TSCAYSI---NDVISSSQLNPVNSIFSAELIAIYLCLEAITVHP 159
+T YTDGS + ++ +VI + L S AELIA+ L+
Sbjct: 24 YTW-YTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA---E 79
Query: 160 SDHFLIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLKTLNKDVHFVLKPSQSALAALSN 219
+ +DSR A A S + +K + +
Sbjct: 80 GKKLNVYTDSRYAFATAHVHSEGREIKNK-----NEI----------------------- 111
Query: 220 VSFTNPLVSKVYSCWDLLKTLNK--DVHFLWCPSHCG-----IRGNEAVDEAAR 266
LLK L + + CP H RGN D+AAR
Sbjct: 112 --------------LALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAR 151
>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 = 6e-04
Identities = 44/340 (12%), Positives = 92/340 (27%), Gaps = 127/340 (37%)
Query: 12 FNPVQKVLFDQDLTPYNFTTNKPKPLLSRFLSLPNFPN-LISSSDIAPYVRTVPPWSSSS 70
+P D + + L R L + N L+ ++ ++
Sbjct: 209 IDPNWTSRSDHSSNIK-LRIHSIQAELRRLLKSKPYENCLLVLLNV---------QNAK- 257
Query: 71 PPVDLSLGKDRKKDTPPVVFQQLFAGVINSKYVNHTICYTDGSKTMNSTSCAYSINDVIS 130
N+ + K + +T + D +S
Sbjct: 258 --------------------------AWNA--------FNLSCKILLTTRFK-QVTDFLS 282
Query: 131 SSQ-----LNPVNSIF----SAELIAIYL-----CL--EAITVHPSDHFLIVSDSRSALA 174
++ L+ + L+ YL L E +T +P + S +A
Sbjct: 283 AATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNP---RRL-----SIIA 334
Query: 175 ALSNVSFTNPLVSKVYSCWDLLKTLNKDVHFVLKPSQSALAALSNVSFTNPLVSKVYSCW 234
+ + WD K +N D + +S+L L P + +
Sbjct: 335 E---------SIRDGLATWDNWKHVNCDK--LTTIIESSLNVL------EPAEYR--KMF 375
Query: 235 DLLKTLNKDVH-------FLWCPSHCGIRGNEAVDEAARNPVNPARLKLCSPDDFKPIAA 287
D L H +W + + VN KL
Sbjct: 376 DRLSVFPPSAHIPTILLSLIWF---------DVIKSDVMVVVN----KLHK--------Y 414
Query: 288 SMVKKEWQN--------QWDIIPITNKLKSI-KPLIEHWN 318
S+V+K+ + ++ ++ + +++H+N
Sbjct: 415 SLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYN 454
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 36.0 bits (84), Expect = 0.005
Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 234 WDLLKTLNK--DVHFLWCPSHCGIRGNEAVDEAARN 267
+ L+ L + D+ ++ P H G GNE D AR
Sbjct: 112 FVALERLTQGMDIQWMHVPGHSGFIGNEEADRLARE 147
>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase,
hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} PDB:
3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A
Length = 150
Score = 33.7 bits (78), Expect = 0.030
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 243 DVHFLWCPSHCGIRGNEAVDEAARN 267
V+ W P+H GI GNE VD+
Sbjct: 119 KVYLAWVPAHKGIGGNEQVDKLVSA 143
>2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI,
nonnucleoside inhibitor, AIDS, HIV, rilpivirine,
diarylpyrimidine, DAPY, DNA recombination; HET: T27;
1.80A {Human immunodeficiency virus 1} PDB: 3is9_A*
3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_A* 1dlo_A
1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A*
2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* ...
Length = 557
Score = 33.6 bits (77), Expect = 0.081
Identities = 14/42 (33%), Positives = 25/42 (59%), Gaps = 6/42 (14%)
Query: 223 TNPLVSKVYSCWDLLKTLNKD-VHFLWCPSHCGIRGNEAVDE 263
+ LV+++ + + + K+ V+ W P+H GI GNE VD+
Sbjct: 516 ESELVNQI-----IEQLIKKEKVYLAWVPAHKGIGGNEQVDK 552
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus
thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
Length = 166
Score = 32.6 bits (75), Expect = 0.098
Identities = 14/50 (28%), Positives = 16/50 (32%), Gaps = 2/50 (4%)
Query: 234 WDLLKTLNK--DVHFLWCPSHCGIRGNEAVDEAARNPVNPARLKLCSPDD 281
W+ L V F + H G NE VD AR C P
Sbjct: 109 WEALLLAMAPHRVRFHFVKGHTGHPENERVDREARRQAQSQAKTPCPPRA 158
>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 = 9/21 (42%), Positives = 11/21 (52%), Gaps = 4/21 (19%)
Query: 272 ARLKLCSPDDFKP---IAASM 289
A LKL + D P I A+M
Sbjct: 27 ASLKLYADDS-APALAIKATM 46
>1jl1_A Ribonuclease HI; RNAse HI, protein stability, thermostability,
hydrogen exchange, cooperativity, hydrolase; 1.30A
{Escherichia coli} SCOP: c.55.3.1 PDB: 1f21_A 1jxb_A
1g15_A 1rch_A 1rdd_A 1rnh_A* 2rn2_A 1rda_A 1law_A 1rdb_A
1lav_A 3aa4_A 1rbu_A 1gob_A 1rdc_A 1kvc_A 3aa3_A 3aa2_A
3aa5_X 1rbv_A ...
Length = 155
Score = 30.9 bits (71), Expect = 0.29
Identities = 11/36 (30%), Positives = 13/36 (36%), Gaps = 2/36 (5%)
Query: 234 WDLLKTLNK--DVHFLWCPSHCGIRGNEAVDEAARN 267
W L + + W H G NE DE AR
Sbjct: 104 WQRLDAALGQHQIKWEWVKGHAGHPENERADELARA 139
>1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase, drug
design, transferase; 2.35A {Human immunodeficiency virus
2} SCOP: c.55.3.1 e.8.1.2 PDB: 1mu2_B
Length = 555
Score = 31.6 bits (72), Expect = 0.34
Identities = 11/42 (26%), Positives = 24/42 (57%), Gaps = 6/42 (14%)
Query: 223 TNPLVSKVYSCWDLLKTLNKD-VHFLWCPSHCGIRGNEAVDE 263
+ +V+++ + + + K+ ++ W P+H GI GN+ VD
Sbjct: 513 ESKIVNQI-----IEEMIKKEAIYVAWVPAHKGIGGNQEVDH 549
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease,
hydrolase, magnesium, metal-binding; 1.60A
{Chlorobaculum tepidum}
Length = 146
Score = 30.5 bits (70), Expect = 0.38
Identities = 10/35 (28%), Positives = 11/35 (31%), Gaps = 2/35 (5%)
Query: 234 WDLLKTLNK--DVHFLWCPSHCGIRGNEAVDEAAR 266
W + L V F H N DE AR
Sbjct: 105 WQEILKLTTLHRVTFHKVKGHSDNPYNSRADELAR 139
>3noy_A 4-hydroxy-3-methylbut-2-EN-1-YL diphosphate synth; iron-sulfur
protein, non-mevalonate pathway, terpene biosynt
isoprenoid biosynthesis; 2.70A {Aquifex aeolicus}
Length = 366
Score = 30.6 bits (70), Expect = 0.64
Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 4/38 (10%)
Query: 220 VSFTNPLVSKVYSCWDLLKTLN---KDVHFLWCPSHCG 254
VS T+ V +V + +++LK+L + V + CP+ CG
Sbjct: 242 VSLTDDPVVEVETAYEILKSLGLRRRGVEIVACPT-CG 278
>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A
{Shewanella oneidensis} PDB: 2zqb_A
Length = 158
Score = 29.4 bits (67), Expect = 0.80
Identities = 10/36 (27%), Positives = 14/36 (38%), Gaps = 2/36 (5%)
Query: 234 WDLLKTLNK--DVHFLWCPSHCGIRGNEAVDEAARN 267
W L + + + W H G NE D+ AR
Sbjct: 106 WKRLDKAAQLHQIDWRWVKGHAGHAENERCDQLARA 141
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR;
fatty acid synthase, acyl-carrier-protein, beta-ketoacyl
RED beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 29.5 bits (66), Expect = 2.2
Identities = 14/67 (20%), Positives = 23/67 (34%), Gaps = 10/67 (14%)
Query: 252 HCGIR--GNEAVDEAARNPVNPARLKLCSPD-DFKPIAAS-----MVKKEWQNQWDIIPI 303
H GIR E + P ++ + D +P AS K + ++ DI I
Sbjct: 901 HSGIRLIEPELFNGYN--PEKKEMIQEVIVEEDLEPFEASKETAEQFKHQHGDKVDIFEI 958
Query: 304 TNKLKSI 310
+
Sbjct: 959 PETGEYS 965
>1j3b_A ATP-dependent phosphoenolpyruvate carboxykinase; adenosine
triphosphate, T thermophilus; 2.00A {Thermus
thermophilus} SCOP: c.91.1.1 c.109.1.1 PDB: 1xkv_A*
2pc9_A*
Length = 529
Score = 28.5 bits (64), Expect = 3.1
Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 5/42 (11%)
Query: 104 NHTICYTDGSKTMNSTSCAYSI----NDVISSSQLNPVNSIF 141
+ + + D SKT N T +Y I N V S +P F
Sbjct: 304 SRRVQWDDDSKTEN-TRSSYPIAHLENVVESGVAGHPRAIFF 344
>3tt9_A Plakophilin-2; cell adhesion; 1.55A {Homo sapiens}
Length = 233
Score = 28.0 bits (62), Expect = 3.6
Identities = 13/63 (20%), Positives = 22/63 (34%), Gaps = 13/63 (20%)
Query: 170 RSALAALSNVSFTNPLVSKVYSCW-------DLLKTLNKDVHFVLKPSQSALAALSNVSF 222
+A + + F K + LLK N+DV ++ AL N+ F
Sbjct: 28 SAAATFIQHECFQKSEARKRVNQLRGILKLLQLLKVQNEDVQ------RAVCGALRNLVF 81
Query: 223 TNP 225
+
Sbjct: 82 EDN 84
>2xzm_O RPS13E; ribosome, translation; 3.93A {Tetrahymena thermophila}
PDB: 2xzn_O 1ysh_E 3jyv_O* 1s1h_O
Length = 153
Score = 27.2 bits (60), Expect = 5.2
Identities = 8/21 (38%), Positives = 11/21 (52%), Gaps = 1/21 (4%)
Query: 51 ISSSDIAPYVRTVPPWSSSSP 71
IS S + P+ R P W +P
Sbjct: 13 ISGSAL-PFKRRSPKWLHMTP 32
>3u5c_N S27A, YS15, 40S ribosomal protein S13; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_O 3o30_G 3o2z_G 3u5g_N 3iz6_O
3jyv_O* 1ysh_E 1s1h_O
Length = 151
Score = 27.1 bits (60), Expect = 5.8
Identities = 11/21 (52%), Positives = 11/21 (52%), Gaps = 1/21 (4%)
Query: 51 ISSSDIAPYVRTVPPWSSSSP 71
ISSS I PY R P W S
Sbjct: 11 ISSSAI-PYSRNAPAWFKLSS 30
>2hy7_A Glucuronosyltransferase GUMK; glycosyltransferases, xanthan,
membrane-associated proteins; 1.90A {Xanthomonas
campestris} PDB: 2q6v_A* 3cv3_A* 3cuy_A*
Length = 406
Score = 27.0 bits (59), Expect = 8.9
Identities = 16/60 (26%), Positives = 25/60 (41%), Gaps = 2/60 (3%)
Query: 164 LIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLKTLNKDVHFVLKPSQSALAALSNVSFT 223
+IV +S A+A + NP VY D L T+N V ++ +A +V
Sbjct: 127 VIVFESGIAVAFIELAKRVNPAAKLVYRASDGLSTIN--VASYIEREFDRVAPTLDVIAL 184
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
0.318 0.132 0.408
Gapped
Lambda K H
0.267 0.0612 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,854,000
Number of extensions: 270493
Number of successful extensions: 436
Number of sequences better than 10.0: 1
Number of HSP's gapped: 433
Number of HSP's successfully gapped: 27
Length of query: 326
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 232
Effective length of database: 4,077,219
Effective search space: 945914808
Effective search space used: 945914808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (26.0 bits)