RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10399
(442 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 = 44.7 bits (105), Expect = 5e-05
Identities = 78/473 (16%), Positives = 135/473 (28%), Gaps = 189/473 (39%)
Query: 30 FAVGTSPNVSPPNNLKAELTKWTLESR------ISKNHVSSLLRSLR------------- 70
A EL K + +R K S+L R++
Sbjct: 104 LAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQ 163
Query: 71 ----PYHPQLPQD----YRTLLGTPTLVDSIEEM-----NPVSAVCSRYPR---IKHFIC 114
Y +L +D Y L+G L+ E + + I ++
Sbjct: 164 GNTDDYFEEL-RDLYQTYHVLVG--DLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLE 220
Query: 115 D---TPAKGYLLNIKGHTGFSF--IV----AH---------------AAKLRDSTVKMQ- 149
+ TP K YLL+I S I AH + L+ +T Q
Sbjct: 221 NPSNTPDKDYLLSI----PISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQG 276
Query: 150 -------------EHFIFQILQLQGYLLNI--KGHTGFNFIVAHAAKLRDSTKDDDQFHR 194
E F + + L I + + + + L DS ++++
Sbjct: 277 LVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEG--- 333
Query: 195 GPTPLQHLFGFNIIKNVPLDYMHLVCLGIMKKLLVLWQRPKMNHLLPAFKIDAMSDRLLE 254
P+P M L + ++ + + K N LPA K +S L
Sbjct: 334 VPSP-----------------M-LSISNLTQEQVQDYVN-KTNSHLPAGKQVEIS--L-- 370
Query: 255 MKKFTNNDKMQLNQHTWLDLVACG------------KEISFMWCPSHCGISGNEAVDVAA 302
N K LV G ++ PS S
Sbjct: 371 ----VNGAKN---------LVVSGPPQSLYGLNLTLRKAK---APSGLDQS--------- 405
Query: 303 KNP--------SPSFPPLKLCSA---SDY-KPLIKKIVQRNWQS--SWNS----VP---- 340
+ P S F P+ ++ S P I + ++ S+N+ +P
Sbjct: 406 RIPFSERKLKFSNRFLPV---ASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDT 462
Query: 341 -NGNKLKSIKPNIEKWPSSNRKTRLEEVV--LTRMRI-----GHTRLTHSYLF 385
+G+ L+ + +I E +V + R+ + + TH F
Sbjct: 463 FDGSDLRVLSGSI-----------SERIVDCIIRLPVKWETTTQFKATHILDF 504
Score = 29.6 bits (66), Expect = 2.4
Identities = 37/270 (13%), Positives = 69/270 (25%), Gaps = 118/270 (43%)
Query: 192 FHRGPTPLQHLFGF---NIIKNVPLDYMHLVCLGIMKKLLVLW-----QRPKMNHLLPAF 243
++R + +GF +I+ N P L + + +R + N+ A
Sbjct: 1646 WNRADNHFKDTYGFSILDIVINNP------------VNLTIHFGGEKGKRIRENYS--AM 1691
Query: 244 KIDAMSDRLLEMKKFTNNDKMQLNQHTW------LD------------------------ 273
+ + D L+ +K +T+ L
Sbjct: 1692 IFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKG 1751
Query: 274 ------------------LVACGKEISF---------------MWCPSHCGISGNEAVDV 300
L + +S + P G +
Sbjct: 1752 LIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPR--DELGRSNYGM 1809
Query: 301 AAKNPSPSFPPLKLCSASDYKPLIKKI-------VQ------RNWQ----------SSWN 337
A NP S + +++++ V+ N Q +
Sbjct: 1810 IAINPG---RVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVT 1866
Query: 338 SVPNGNKLKSIKPNIEKWPSSNRKTRLEEV 367
+V N KL+ I I + S LEEV
Sbjct: 1867 NVLNFIKLQKID--IIELQKS---LSLEEV 1891
>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 = 36.2 bits (84), Expect = 0.007
Identities = 11/45 (24%), Positives = 15/45 (33%), Gaps = 3/45 (6%)
Query: 259 TNNDKMQLNQHTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAK 303
N+ Q SF +H G N+ VD+ AK
Sbjct: 91 AKNEFTQAYAKLMNQY---RGIYSFEKVKAHSGNEFNDYVDMKAK 132
>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 = 36.1 bits (82), Expect = 0.009
Identities = 11/52 (21%), Positives = 16/52 (30%), Gaps = 25/52 (48%)
Query: 45 KAELTKWTLESRISKNHVSSLLRSLRPYHPQLPQDYRTLLGTPTLV--DSIE 94
K L K L++ SL+ Y D P L ++E
Sbjct: 19 KQALKK--LQA------------SLKLYAD----D-----SAPALAIKATME 47
Score = 27.6 bits (60), Expect = 5.9
Identities = 9/27 (33%), Positives = 11/27 (40%), Gaps = 7/27 (25%)
Query: 224 MKKL---LVLWQRPKMNHLLPAFKIDA 247
+KKL L L+ PA I A
Sbjct: 22 LKKLQASLKLYA-DDS---APALAIKA 44
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 35.2 bits (82), Expect = 0.015
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 259 TNNDKMQLNQHTW--LDLVACGKEISFMWCPSHCGISGNEAVDVAAKN 304
T+ K +N+ + L+ + G +I +M P H G GNE D A+
Sbjct: 100 TSAGKEVINKEDFVALERLTQGMDIQWMHVPGHSGFIGNEEADRLARE 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 = 33.3 bits (77), Expect = 0.058
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 3/49 (6%)
Query: 259 TNNDKMQLNQHTW---LDLVACGKEISFMWCPSHCGISGNEAVDVAAKN 304
T + K N ++ + +++ W P+H GI GNE VD
Sbjct: 95 TADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSA 143
>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 = 33.3 bits (76), Expect = 0.079
Identities = 13/63 (20%), Positives = 21/63 (33%), Gaps = 8/63 (12%)
Query: 249 SDRLLEMKKFTNNDKMQLNQHTW---LDLVACGKEISFMWCPSHCG-----ISGNEAVDV 300
S + + N++ L + K +S + CP H GN D
Sbjct: 89 SRYAFATAHVHSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQ 148
Query: 301 AAK 303
AA+
Sbjct: 149 AAR 151
>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 = 30.2 bits (69), Expect = 0.67
Identities = 17/54 (31%), Positives = 21/54 (38%), Gaps = 6/54 (11%)
Query: 259 TNNDKMQLNQHTW--LDLVACGKEISFMWCPSHCGISGNEAVDV----AAKNPS 306
T + K N W LD +I + W H G NE D AA NP+
Sbjct: 92 TADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELARAAAMNPT 145
>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 = 30.9 bits (70), Expect = 0.84
Identities = 12/23 (52%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 278 GKE-ISFMWCPSHCGISGNEAVD 299
KE + W P+H GI GNE VD
Sbjct: 529 KKEKVYLAWVPAHKGIGGNEQVD 551
>3e6u_A LANC-like protein 1; alpha barrel, cytoplasm, signaling protein;
2.60A {Homo sapiens} PDB: 3e73_A*
Length = 411
Score = 30.5 bits (68), Expect = 1.2
Identities = 36/287 (12%), Positives = 83/287 (28%), Gaps = 39/287 (13%)
Query: 29 DFAVGTSPNVSPPNNLKAELTKWTLESRISKNHVSSLLRSLRPYHPQLPQDYRTLLGTPT 88
D+ + L ++I + + + R L+ P+ Y G
Sbjct: 24 DYNKSLAEGYFDAAGRLTPEFSQRLTNKI-RELLQQMERGLKSADPRDGTGYTGWAGIAV 82
Query: 89 LVDSIEEMNPVSAVCSRYPRIKHFICDTPAKGYLLNIKGHTGFSFIVAHAAKLRDSTVKM 148
L + ++ A + K + + G G + A ++ K
Sbjct: 83 LYLHLYDVFGDPAYLQLAHGYVKQSLNCLTKRSITFLCGDAGPLAVAAVLYHKMNNE-KQ 141
Query: 149 QEHFIFQILQLQ---------------GY---LLNIKGHTG-----FNFIVAHAAKLRDS 185
E I +++ L GY LL + + G + I + S
Sbjct: 142 AEDCITRLIHLNKIDPHAPNEMLYGRIGYIYALLFVNKNFGVEKIPQSHIQQICETILTS 201
Query: 186 TKDDDQFHRGPTPLQHLFGFNIIKNVPLDYMHLVCLGIMKKLLVLWQRPKMNHLLPAFKI 245
++ + ++ + + + H + GI L+ + L +
Sbjct: 202 GENLARKRNFTAKSPLMYEWY--QEYYVGAAHGLA-GIYYYLMQPSLQVSQGKLHSL--V 256
Query: 246 DAMSDRLLEMKKFTNNDKMQLNQHTWLDLVACGKEISFMWCPSHCGI 292
D + ++K + N + + +++ WC G+
Sbjct: 257 KPSVDYVCQLKFPSGN---------YPPCIGDNRDLLVHWCHGAPGV 294
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease,
hydrolase, magnesium, metal-binding; 1.60A
{Chlorobaculum tepidum}
Length = 146
Score = 29.0 bits (66), Expect = 1.6
Identities = 11/54 (20%), Positives = 15/54 (27%), Gaps = 6/54 (11%)
Query: 259 TNNDKMQLNQHTW--LDLVACGKEISFMWCPSHCGISGNEAVDV----AAKNPS 306
T K N W + + ++F H N D A K S
Sbjct: 93 TAAKKPVENIDLWQEILKLTTLHRVTFHKVKGHSDNPYNSRADELARLAIKENS 146
>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 = 29.3 bits (66), Expect = 2.6
Identities = 11/23 (47%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 278 GKEISFM-WCPSHCGISGNEAVD 299
KE ++ W P+H GI GN+ VD
Sbjct: 526 KKEAIYVAWVPAHKGIGGNQEVD 548
>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 = 29.1 bits (64), Expect = 4.1
Identities = 24/154 (15%), Positives = 45/154 (29%), Gaps = 32/154 (20%)
Query: 137 HAAKLRDS--TVKMQEHFIFQILQLQGYLLNIKGHTGFNFIVAHAAKLRDSTKDDDQFHR 194
H + D K + L Y ++ I H + + + F
Sbjct: 446 HR-SIVDHYNIPKTFDSDDLIPPYLDQYF--------YSHIGHHLKNI-EHPERMTLF-- 493
Query: 195 GPTPLQHL-FGF--NIIKNVPLDYMHLVCLGIMKKLLVLWQRPKMNHLLPAFKIDAMSDR 251
+ L F F I++ I+ L L + ++ D +R
Sbjct: 494 ---RMVFLDFRFLEQKIRHD--STAWNASGSILNTLQQL--KFYKPYI---CDNDPKYER 543
Query: 252 LL-EMKKFTNNDKMQLNQHTWLDLVACGKEISFM 284
L+ + F + L + DL+ I+ M
Sbjct: 544 LVNAILDFLPKIEENLICSKYTDLL----RIALM 573
>3st7_A Capsular polysaccharide synthesis enzyme CAP5F; rossmann fold,
cupid domain, short-chain dehydrogenase/reduc NADPH;
2.45A {Staphylococcus aureus} PDB: 2zkl_A 3vhr_A
Length = 369
Score = 28.3 bits (63), Expect = 4.7
Identities = 18/160 (11%), Positives = 44/160 (27%), Gaps = 17/160 (10%)
Query: 231 WQRPKMNHLLPAFKIDAMSDRLLEMKKFTNNDKMQLNQHTWLDLVACGKEISFMWCPSHC 290
W +P N ++ F ++ ++ ND+ ++D + + + P+
Sbjct: 137 WCKPNYNSVIATF-----CYKIARNEEIQVNDRNVELTLNYVDDIVAEIKRAIEGTPTIE 191
Query: 291 GISGNEAVDVAAKNPSPSFPPLKLCSASDYKP---------LIKKIVQRNWQSSWNSVPN 341
+ L + L +K + + S S
Sbjct: 192 NGVPTVPNV---FKVTLGEIVDLLYKFKQSRLDRTLPKLDNLFEKDLYSTYLSYLPSTDF 248
Query: 342 GNKLKSIKPNIEKWPSSNRKTRLEEVVLTRMRIGHTRLTH 381
L + + + +V + + G T+ H
Sbjct: 249 SYPLLMNVDDRGSFTEFIKTPDRGQVSVNISKPGITKGNH 288
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus
thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
Length = 166
Score = 27.2 bits (61), Expect = 7.0
Identities = 15/59 (25%), Positives = 22/59 (37%), Gaps = 6/59 (10%)
Query: 259 TNNDKMQLNQHTW--LDLVACGKEISFMWCPSHCGISGNEAVDV----AAKNPSPSFPP 311
T K N+ W L L + F + H G NE VD A++ + + P
Sbjct: 97 TAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGHTGHPENERVDREARRQAQSQAKTPCP 155
>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double
chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces
cerevisiae}
Length = 800
Score = 28.2 bits (63), Expect = 7.2
Identities = 12/30 (40%), Positives = 14/30 (46%), Gaps = 5/30 (16%)
Query: 59 KNHVSSLLRSLRPYHPQLPQDYRTLL-GTP 87
KN SSL SL + R L+ GTP
Sbjct: 380 KNAESSLYESLNSFK----VANRMLITGTP 405
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 0.134 0.413
Gapped
Lambda K H
0.267 0.0590 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,655,717
Number of extensions: 384996
Number of successful extensions: 570
Number of sequences better than 10.0: 1
Number of HSP's gapped: 569
Number of HSP's successfully gapped: 22
Length of query: 442
Length of database: 6,701,793
Length adjustment: 97
Effective length of query: 345
Effective length of database: 3,993,456
Effective search space: 1377742320
Effective search space used: 1377742320
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: 59 (26.8 bits)