RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14646
(366 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 = 51.2 bits (122), Expect = 3e-07
Identities = 54/306 (17%), Positives = 86/306 (28%), Gaps = 128/306 (41%)
Query: 25 WDLFEAQITD------------QNEFPICSSSPIDLDETGVGCALTIPQLNETKRFALNK 72
W+ F + +P S P L++
Sbjct: 289 WESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILED---------------------- 326
Query: 73 HSSIFHAELFSIPLHLSLTNCTIDR-DSSIDIFFNNKHELKDKLLQQIAYVDINSLQSLN 131
S+ + E P+ LS++N T ++ ++ N H L V+I SL +N
Sbjct: 327 --SLENNEGVPSPM-LSISNLTQEQVQDYVNKT--NSH------LPAGKQVEI-SL--VN 372
Query: 132 HVKELDTRKILIISDSLSSFQAISNLYHPNPLVKKIQEEYSNSQANIK-----------F 180
K L++S S LY N ++K + Q+ I F
Sbjct: 373 ------GAKNLVVSGPPQS------LYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRF 420
Query: 181 L--WCPSHVSISGNERAEECYSNYLASVETAIRSD---PRFFWKYERSMRKDQSLP-KNL 234
L P H S+ L I D + KD +P +
Sbjct: 421 LPVASPFH-------------SHLLVPASDLINKDLVKNNVSFN-----AKDIQIPVYDT 462
Query: 235 HYGSDEATSVKWNTVWTSINPNENKLRRIKNSITPWKTSSQKARL-DEVCLMRL---RIG 290
GSD LR + SI+ R+ D + + +
Sbjct: 463 FDGSD--------------------LRVLSGSISE--------RIVDCIIRLPVKWETTT 494
Query: 291 HTKITH 296
K TH
Sbjct: 495 QFKATH 500
Score = 29.2 bits (65), Expect = 2.7
Identities = 8/36 (22%), Positives = 17/36 (47%), Gaps = 4/36 (11%)
Query: 335 LGNSLSNILSDNPDSISTLMRFLK----RNNFLKHM 366
G S+ +I+ +NP +++ K R N+ +
Sbjct: 1657 YGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMI 1692
Score = 28.1 bits (62), Expect = 6.6
Identities = 29/144 (20%), Positives = 50/144 (34%), Gaps = 32/144 (22%)
Query: 223 SMRKDQSLPKNLHYGSDEATSVKWNTVWTSINPNENKLRRIKNSITPWKTSSQKARLDEV 282
S R P L +GS E V T+ ++L+ N I P T A +
Sbjct: 5 STR-----PLTLSHGSLEHV---LL-VPTASFFIASQLQEQFNKILPEPTEGFAADDEPT 55
Query: 283 CLMRL--R-IGHTKITHSHLFKREERPECDTCHEPVTVEHLLLHCNKLRFRPPSFL-GN- 337
L + +G+ S L + + + D + L F +L GN
Sbjct: 56 TPAELVGKFLGYV----SSLVEPSKVGQFDQV-----LNLCLTE-----FE-NCYLEGND 100
Query: 338 --SL-SNILSDNPDSISTLMRFLK 358
+L + +L +N ++ +K
Sbjct: 101 IHALAAKLLQENDTTLVKTKELIK 124
>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 = 49.9 bits (118), Expect = 1e-06
Identities = 58/349 (16%), Positives = 91/349 (26%), Gaps = 111/349 (31%)
Query: 117 QQIAYVDINSLQSLNHVKELDTRKIL-----IISDS-----LSSFQAISNLY-------- 158
Q Y DI S+ V D + + I+S + S A+S
Sbjct: 14 HQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLS 73
Query: 159 HPNPLVKKIQEEYSNSQANIKFLWCPSHVSISGNERAEECYSNYLASVETAIRSDPRFFW 218
+V+K EE + N KFL P Y + +D + F
Sbjct: 74 KQEEMVQKFVEEVL--RINYKFLMSPIKTEQRQPSMMTRMYIEQR----DRLYNDNQVFA 127
Query: 219 KYERSMRKDQ--SLPKNLH----------YG--------------SDEAT------SVKW 246
KY S R L + L G + W
Sbjct: 128 KYNVS-RLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFW 186
Query: 247 NTVWTSINPNE--NKLRRIKNSITPWKTSSQKARLDEVCLMRLRIGHTKITHSHLFKREE 304
+ +P L+++ I P + +R D ++LRI + L K +
Sbjct: 187 LNLKNCNSPETVLEMLQKLLYQIDP----NWTSRSDHSSNIKLRIHSIQAELRRLLKSKP 242
Query: 305 RPEC-----DTCHEPVTVEHLLLHCNKL---R------------------------FRPP 332
C + + L C L R P
Sbjct: 243 YENCLLVLLNVQN-AKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPD 301
Query: 333 ---SFLGNSLSNILSD--------NPDSISTLMRFLK----RNNFLKHM 366
S L L D NP +S + ++ + KH+
Sbjct: 302 EVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHV 350
>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 = 38.9 bits (91), Expect = 6e-04
Identities = 9/61 (14%), Positives = 17/61 (27%), Gaps = 9/61 (14%)
Query: 140 KILIISDSLSSFQAISNLYHP-----NPLVKKIQEEYSNSQANIKFLWCPSHVSISGNER 194
KI I+ D I+ N + + + + F +H N+
Sbjct: 71 KIRILHDY----AGIAFWATGEWKAKNEFTQAYAKLMNQYRGIYSFEKVKAHSGNEFNDY 126
Query: 195 A 195
Sbjct: 127 V 127
>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 = 31.0 bits (70), Expect = 0.36
Identities = 11/71 (15%), Positives = 22/71 (30%), Gaps = 9/71 (12%)
Query: 134 KELDTRKILIISDS--LSSFQAISNLYHPNPLVKKIQEEYSNSQA--NIKFLWCPSHVS- 188
K + +K+ + +DS + + + +I + + CP H
Sbjct: 76 KMAEGKKLNVYTDSRYAFATAHVHSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKG 135
Query: 189 ----ISGNERA 195
GN A
Sbjct: 136 NSAEARGNRMA 146
>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 = 31.3 bits (71), Expect = 0.51
Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 7/63 (11%)
Query: 143 IISDSLSSFQAISNLYHP----NPLVKKIQEEYSNSQANIKFLWCPSHVSISGNERAEEC 198
I++DS + I P + LV +I E+ + + W P+H I GNE+ ++
Sbjct: 497 IVTDSQYALGIIQA--QPDKSESELVNQIIEQLIKKEK-VYLAWVPAHKGIGGNEQVDKL 553
Query: 199 YSN 201
S
Sbjct: 554 VSA 556
>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 = 30.9 bits (70), Expect = 0.73
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 7/62 (11%)
Query: 143 IISDSLSSFQAISNLYHP----NPLVKKIQEEYSNSQANIKFLWCPSHVSISGNERAEEC 198
II DS +++ P + +V +I EE +A I W P+H I GN+ +
Sbjct: 494 IIVDSQYVMGIVAS--QPTESESKIVNQIIEEMIKKEA-IYVAWVPAHKGIGGNQEVDHL 550
Query: 199 YS 200
S
Sbjct: 551 VS 552
>1gxj_A SMC, chromosome segregation SMC protein; SMC dimerisation domain,
anti parallel coiled coil, SMC proteins; 2.0A
{Thermotoga maritima} SCOP: d.215.1.1 PDB: 1gxk_A
Length = 186
Score = 29.5 bits (67), Expect = 1.1
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 335 LGNSLSNILSDNPDSISTLMRFLKRNN 361
LG + NI+ N D+ ++ FLK+N
Sbjct: 54 LGGTAQNIVVRNVDTAKAIVEFLKQNE 80
>3nwc_A SMC protein; structural maintenance of chromosomes (SMC), SMC hinge
domai dimerization, DNA binding, cell cycle; 1.70A
{Pyrococcus furiosus}
Length = 189
Score = 28.8 bits (65), Expect = 1.9
Identities = 6/27 (22%), Positives = 14/27 (51%)
Query: 335 LGNSLSNILSDNPDSISTLMRFLKRNN 361
LGN N++ ++ +++LK +
Sbjct: 59 LGNRADNVVVEDELVAEKAIKYLKEHK 85
>1gxl_A SMC, chromosome segregation SMC protein; SMC dimerisation domain,
anti parallel coiled coil, SMC proteins; 3.0A
{Thermotoga maritima} SCOP: d.215.1.1
Length = 213
Score = 28.8 bits (65), Expect = 2.2
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 335 LGNSLSNILSDNPDSISTLMRFLKRNN 361
LG + NI+ N D+ ++ FLK+N
Sbjct: 66 LGGTAQNIVVRNVDTAKAIVEFLKQNE 92
>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 = 27.5 bits (62), Expect = 3.8
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 8/50 (16%)
Query: 163 LVKKIQEEYSNSQANIKFLWCPSHVSISGNERAEECYSNYLASVETAIRS 212
LV +I E+ + + W P+H I GNE+ ++ L S IR
Sbjct: 106 LVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK-----LVS--AGIRK 147
>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG;
2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A*
Length = 680
Score = 27.7 bits (62), Expect = 7.8
Identities = 9/53 (16%), Positives = 20/53 (37%), Gaps = 9/53 (16%)
Query: 318 EHLLLHCNKLRFRPPSFLGNSLSNI----LSDNP-----DSISTLMRFLKRNN 361
+ L L N + G + N+ + NP +SI+ + ++ +
Sbjct: 587 KSLNLQKNLITSVEKKVFGPAFRNLTELDMRFNPFDCTCESIAWFVNWINETH 639
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 26.4 bits (59), Expect = 9.8
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 173 NSQANIKFLWCPSHVSISGNERA 195
+I+++ P H GNE A
Sbjct: 119 TQGMDIQWMHVPGHSGFIGNEEA 141
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
0.319 0.133 0.405
Gapped
Lambda K H
0.267 0.0811 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,378,566
Number of extensions: 299932
Number of successful extensions: 965
Number of sequences better than 10.0: 1
Number of HSP's gapped: 956
Number of HSP's successfully gapped: 57
Length of query: 366
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 271
Effective length of database: 4,049,298
Effective search space: 1097359758
Effective search space used: 1097359758
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: 58 (26.0 bits)