RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16693
(196 letters)
>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 = 53.9 bits (130), Expect = 8e-10
Identities = 12/45 (26%), Positives = 19/45 (42%), Gaps = 2/45 (4%)
Query: 50 NPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEAL 94
N + L+++ + F V +H G N+ D AK AL
Sbjct: 93 NEFTQAYAKLMNQYRG--IYSFEKVKAHSGNEFNDYVDMKAKSAL 135
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 44.1 bits (105), Expect = 3e-06
Identities = 15/34 (44%), Positives = 20/34 (58%)
Query: 60 LDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEA 93
L++ + + VP H G GNEEADRLA+E
Sbjct: 115 LERLTQGMDIQWMHVPGHSGFIGNEEADRLAREG 148
>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 = 42.9 bits (102), Expect = 7e-06
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 4/37 (10%)
Query: 59 LLDK--NKHVFSLHFTWVPSHVGIAGNEEADRLAKEA 93
++++ K L WVP+H GI GNE+ D+L
Sbjct: 110 IIEQLIKKEKVYLA--WVPAHKGIGGNEQVDKLVSAG 144
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease,
hydrolase, magnesium, metal-binding; 1.60A
{Chlorobaculum tepidum}
Length = 146
Score = 41.3 bits (98), Expect = 3e-05
Identities = 12/39 (30%), Positives = 17/39 (43%)
Query: 60 LDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSNS 98
+ K + + F V H N AD LA+ A+ NS
Sbjct: 108 ILKLTTLHRVTFHKVKGHSDNPYNSRADELARLAIKENS 146
>2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, D stranded
RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus
tokodaii} PDB: 3aly_A
Length = 149
Score = 40.8 bits (96), Expect = 4e-05
Identities = 13/51 (25%), Positives = 19/51 (37%), Gaps = 8/51 (15%)
Query: 50 NPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSNSPP 100
P+ + L K + WVP N+EADRL++ A
Sbjct: 96 IPLYEKAIELKKK----LNATLIWVPR----EENKEADRLSRVAYELVRRG 138
>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 = 40.6 bits (96), Expect = 7e-05
Identities = 13/41 (31%), Positives = 18/41 (43%)
Query: 60 LDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSNSPP 100
LD + + WV H G NE AD LA+ A + +
Sbjct: 107 LDAALGQHQIKWEWVKGHAGHPENERADELARAAAMNPTLE 147
>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A
{Shewanella oneidensis} PDB: 2zqb_A
Length = 158
Score = 40.6 bits (96), Expect = 7e-05
Identities = 16/44 (36%), Positives = 24/44 (54%)
Query: 60 LDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSNSPPVNT 103
LDK + + + WV H G A NE D+LA+ A +N ++T
Sbjct: 109 LDKAAQLHQIDWRWVKGHAGHAENERCDQLARAAAEANPTQIDT 152
>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 = 40.2 bits (94), Expect = 9e-05
Identities = 15/59 (25%), Positives = 19/59 (32%), Gaps = 5/59 (8%)
Query: 51 PIAREIRNLLDKNKHVFSLHFTWVPSHVG-----IAGNEEADRLAKEALSSNSPPVNTI 104
EI LL L P H GN AD+ A+EA +T+
Sbjct: 106 KNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAVLETSTL 164
>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 = 41.4 bits (96), Expect = 9e-05
Identities = 19/148 (12%), Positives = 45/148 (30%), Gaps = 50/148 (33%)
Query: 55 EIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSNSPPVNTI---------- 104
+ +++ D K + S EE D + V+
Sbjct: 34 DCKDVQDMPKSILS--------------KEEIDHIIMS-----KDAVSGTLRLFWTLLSK 74
Query: 105 PINDFKRFFKSK-------ILTTWNTEWANLADNKLRQIKEENRPWN-----PPFSMSRK 152
++F + +++ TE + I++ +R +N +++SR
Sbjct: 75 QEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRL 134
Query: 153 EQV-----SITRLRIGPCIS-HGSPPML 174
+ ++ LR + G +L
Sbjct: 135 QPYLKLRQALLELRPAKNVLIDG---VL 159
Score = 30.2 bits (67), Expect = 0.53
Identities = 29/184 (15%), Positives = 56/184 (30%), Gaps = 56/184 (30%)
Query: 10 EHIYYQVDLTGTAEKSECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSL 69
+ + YQ+D T+ D+S + I ++ + E+R LL + L
Sbjct: 203 QKLLYQIDPNWTSR---------SDHSSNIKLRIHSIQA------ELRRLLKSKPYENCL 247
Query: 70 HFTWVPSHVGIAGNEEADRLAKEALSSNSPPVNTIPINDFKRFFKSKIL-TTWNTEWAN- 127
V +V + N F KIL TT + +
Sbjct: 248 ---LVLLNV------------------QNAKA----WNAFN--LSCKILLTTRFKQVTDF 280
Query: 128 LADNKLRQIKEENRPWNPPFSMSRKEQVSITRLRIGPCISHGSPPMLELPATKKPIVSPK 187
L+ I ++ + + + + L P +LP +P+
Sbjct: 281 LSAATTTHISLDHHSM--TLTPDEVKSLLLKYLDCRP---------QDLPREVLTT-NPR 328
Query: 188 KLCL 191
+L +
Sbjct: 329 RLSI 332
>3hst_B Protein RV2228C/MT2287; ribonuclease H1, RV2228C N-terminal domain,
fusion protein, maltose binding protein, HYDR; HET: MLR
TAR; 2.25A {Mycobacterium tuberculosis}
Length = 141
Score = 39.2 bits (92), Expect = 1e-04
Identities = 11/51 (21%), Positives = 23/51 (45%), Gaps = 7/51 (13%)
Query: 51 PIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSNSPPV 101
+ + + L + + + ++ WVP N ADRLA +A+ + +
Sbjct: 95 KLYVQAQALASQFRRI---NYEWVPRA----RNTYADRLANDAMDAAAQSA 138
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus
thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
Length = 166
Score = 39.5 bits (93), Expect = 2e-04
Identities = 11/39 (28%), Positives = 15/39 (38%)
Query: 60 LDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSNS 98
L + F +V H G NE DR A+ S +
Sbjct: 112 LLLAMAPHRVRFHFVKGHTGHPENERVDREARRQAQSQA 150
>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 = 40.5 bits (95), Expect = 2e-04
Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 48 SSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRL 89
S + + +I L K + V + WVP+H GI GNE+ D+L
Sbjct: 515 SESELVNQIIEQLIKKEKV---YLAWVPAHKGIGGNEQVDKL 553
>3u3g_D Ribonuclease H, RNAse H1; hydrolase, cleave the RNA strand of
RNA/DNA hybrid; 1.40A {Uncultured organism}
Length = 140
Score = 37.5 bits (88), Expect = 6e-04
Identities = 9/45 (20%), Positives = 15/45 (33%), Gaps = 6/45 (13%)
Query: 50 NPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEAL 94
+I ++ + V H+ N AD L EA+
Sbjct: 97 KEKFAKIAHIKMER------VPNLVFVHIPREKNARADELVNEAI 135
>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 = 38.9 bits (91), Expect = 6e-04
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 3/42 (7%)
Query: 48 SSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRL 89
S + I +I + K + ++ WVP+H GI GN+E D L
Sbjct: 512 SESKIVNQIIEEMIKKEAIY---VAWVPAHKGIGGNQEVDHL 550
>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 = 37.0 bits (85), Expect = 0.003
Identities = 40/223 (17%), Positives = 68/223 (30%), Gaps = 86/223 (38%)
Query: 1 MLGIPDTCDEHIYYQVDLTGTAEKSECQVYL----TPDN--------SLSALQSIQNVSS 48
ML I + E + V+ T + + QV + N SL L
Sbjct: 338 MLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGL-------- 389
Query: 49 SNPIAREIR--NLLDKNKHVFS---LHFTW------VPSH---VGIAGNEEADRLAKEAL 94
N R+ + + LD+++ FS L F+ P H + A + L K +
Sbjct: 390 -NLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNV 448
Query: 95 SSNSPPVNTIPINDFKRFFKSKILTTWNTE-WANLADNKLRQIKEENRPWNPPFSMSRKE 153
S N+ + IP+ ++T ++L R
Sbjct: 449 SFNAKDIQ-IPV--------------YDTFDGSDL----------------------RVL 471
Query: 154 QVSITRLRIGPCISHGSPPMLELPATKKPIVSPKKLCLQTHHL 196
SI+ RI CI + P+ + H+
Sbjct: 472 SGSISE-RIVDCI------------IRLPVKWETTTQFKATHI 501
Score = 30.4 bits (68), Expect = 0.45
Identities = 28/175 (16%), Positives = 46/175 (26%), Gaps = 63/175 (36%)
Query: 41 QSIQNV-------SSSNPIAREIRNLLDKNKHV-----FSL-------------HFTWVP 75
Q Q +S A+++ N D H FS+ HF
Sbjct: 1624 QGSQEQGMGMDLYKTS-KAAQDVWNRAD--NHFKDTYGFSILDIVINNPVNLTIHFG--- 1677
Query: 76 SHVGIAGNEEADRLAK-------EALSSNSPPVNTIPINDFKRFFKS--KILT-TWNTEW 125
G G + + + I + F+S +L+ T T+
Sbjct: 1678 ---GEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQP 1734
Query: 126 ANLADNK--LRQIKEE-NRPWNPPF----------------SMSRKEQVSITRLR 161
A K +K + P + F MS + V + R
Sbjct: 1735 ALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYR 1789
Score = 26.6 bits (58), Expect = 6.9
Identities = 7/32 (21%), Positives = 13/32 (40%), Gaps = 4/32 (12%)
Query: 75 PSHVGIAGNEEADRLAKEALSSNSP----PVN 102
P V + ++EA + E + + VN
Sbjct: 1814 PGRVAASFSQEALQYVVERVGKRTGWLVEIVN 1845
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 30.9 bits (69), Expect = 0.19
Identities = 6/32 (18%), Positives = 11/32 (34%)
Query: 124 EWANLADNKLRQIKEENRPWNPPFSMSRKEQV 155
EW ++ + K NR + F +
Sbjct: 122 EWNQRQSEQVEKNKINNRIADKAFYQQPDADI 153
>2bon_A Lipid kinase; DAG kinase, transferase; 1.90A {Escherichia coli}
SCOP: e.52.1.2 PDB: 2jgr_A 2p1r_A
Length = 332
Score = 31.2 bits (71), Expect = 0.20
Identities = 14/56 (25%), Positives = 18/56 (32%), Gaps = 9/56 (16%)
Query: 43 IQN-VSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSN 97
I N S+ N RE LL + + TW A R +EA
Sbjct: 35 ILNGKSTDNLPLREAIMLLREEGMTIHVRVTWEKGD--------AARYVEEARKFG 82
>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 = 28.8 bits (63), Expect = 0.76
Identities = 7/32 (21%), Positives = 13/32 (40%), Gaps = 9/32 (28%)
Query: 153 EQVSI----TRLRI-GPCISHGSPPMLELPAT 179
E+ ++ L++ S P L + AT
Sbjct: 18 EKQALKKLQASLKLYAD----DSAPALAIKAT 45
>3iyg_B T-complex protein 1 subunit beta; TRIC/CCT, asymmetric, cryo-EM,
subunit arrangement, acetylation, ATP-binding,
chaperone, cytoplasm, isopeptide bond; 4.00A {Bos
taurus} PDB: 3ktt_B 4a0o_A 4a0v_A 4a0w_A 4a13_A
Length = 513
Score = 27.9 bits (63), Expect = 2.2
Identities = 20/83 (24%), Positives = 34/83 (40%), Gaps = 17/83 (20%)
Query: 54 REIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSNSPPVNTIPINDFKRFF 113
RE +L+ K H P + IAG EA + A++AL +++ + + +
Sbjct: 98 REAESLIAKKIH---------PQTI-IAGWREATKAARQALLNSAVDHGSDEVKFRQDLM 147
Query: 114 K-------SKILTTWNTEWANLA 129
SK+LT + LA
Sbjct: 148 NIAGTTLSSKLLTHHKDHFTKLA 170
>2j7n_A RNA-dependent RNA polymerase; RNAI response, RNA-directed RNA
polymerase, hydrolase; 2.30A {Neurospora crassa} PDB:
2j7o_A
Length = 1022
Score = 27.2 bits (59), Expect = 4.9
Identities = 17/142 (11%), Positives = 32/142 (22%), Gaps = 4/142 (2%)
Query: 33 PDNSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKE 92
P + ++ VS E+ L +H + W AG + R +
Sbjct: 161 PSPTSTSPSVPPVVSKQPAAVEEVIQWLTMGQHSL-VGRQWRAFFAKDAGYRKPLREFQL 219
Query: 93 ALSSNSP-PVNTIP--INDFKRFFKSKILTTWNTEWANLADNKLRQIKEENRPWNPPFSM 149
P + F T + + + W
Sbjct: 220 RAEDPKPIIKERVHFFAETGITFRPDVFKTRSVVPAEEPVEQRTEFKVSQMLDWLLQLDN 279
Query: 150 SRKEQVSITRLRIGPCISHGSP 171
+ + RI +S
Sbjct: 280 NTWQPHLKLFSRIQLGLSKTYA 301
>3m89_A FTSZ/tubulin-related protein; partition, TUBZ, GTP-binding,
nucleotide-BIND structural protein; HET: GSP; 2.00A
{Bacillus thuringiensis} PDB: 3m8k_A 2xka_A* 2xkb_A*
Length = 427
Score = 26.8 bits (58), Expect = 5.2
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 78 VGIAGNEEADRLAKEALSSNSPPVNTIPIN 107
G GN+EAD A S+ + T+ +N
Sbjct: 50 AGQKGNKEADLFAGYKFSNGTTCYPTLAVN 79
>1rw7_A YDR533CP; alpha-beta sandwich, DJ-1/THIJ/PFPI superfamily, unknown
function; 1.80A {Saccharomyces cerevisiae} SCOP:
c.23.16.2 PDB: 1qvv_A* 1qvz_A 1qvw_A
Length = 243
Score = 26.5 bits (58), Expect = 6.1
Identities = 5/22 (22%), Positives = 10/22 (45%)
Query: 44 QNVSSSNPIAREIRNLLDKNKH 65
N +S++ A + L + H
Sbjct: 219 VNPASAHSTAVRSIDALKNHHH 240
>3icv_A Lipase B, CALB; circular permutation, cleavage on PAIR of basic
residues, glycoprotein, hydrolase, lipid degradation,
zymogen, disulf; HET: NAG BTB; 1.49A {Candida
antarctica} PDB: 3icw_A*
Length = 316
Score = 26.3 bits (57), Expect = 6.8
Identities = 6/30 (20%), Positives = 13/30 (43%)
Query: 74 VPSHVGIAGNEEADRLAKEALSSNSPPVNT 103
V H G ++ + + + AL S + +
Sbjct: 255 VIDHAGSLTSQFSYVVGRSALRSTTGQARS 284
>3k32_A Uncharacterized protein MJ0690; predicted subunit of tRNA
methyltransferase, methanocaldococcus jannaschii DSM ,
PSI- 2; 2.50A {Methanocaldococcus jannaschii}
Length = 203
Score = 25.9 bits (57), Expect = 7.3
Identities = 6/36 (16%), Positives = 12/36 (33%)
Query: 82 GNEEADRLAKEALSSNSPPVNTIPINDFKRFFKSKI 117
G + LA E T +D++ + +
Sbjct: 142 GYKTLRHLASEFFILEEIKSGTKLSSDYEAEIRHIL 177
>3gt5_A N-acetylglucosamine 2-epimerase; structural genomics, isomerase,
PSI-2; 1.70A {Xylella fastidiosa}
Length = 402
Score = 26.3 bits (57), Expect = 7.3
Identities = 8/36 (22%), Positives = 11/36 (30%), Gaps = 1/36 (2%)
Query: 60 LDKNKHVFSLHF-TWVPSHVGIAGNEEADRLAKEAL 94
D H + L F S G ++A E
Sbjct: 106 EDDTNHCYGLAFVMLAYSCGLKVGIKQAREWMDETW 141
>2d4g_A Hypothetical protein BSU11850; beta barrel, alpha helix, structural
genomics, unknown function; 2.30A {Bacillus subtilis}
Length = 171
Score = 25.9 bits (57), Expect = 8.1
Identities = 16/106 (15%), Positives = 39/106 (36%), Gaps = 18/106 (16%)
Query: 55 EIRNLLDKNKHVFSLHFTWVPSHV-----GIAGNEEADRLAK--EALSSNSPPVNTIPIN 107
++++L + + + ++ +P H+ E+AD+L ++ S P+ + +
Sbjct: 12 KLQDLANSYRKRYDPSYSLIPPHLTLRASFECAEEKADQLVSHLRNIAKESHPL-VLKMT 70
Query: 108 DFKRFFKSKILTTW-----NTEWANLADNKLRQ---IKEENRPWNP 145
+ F + E L + KL E+ + P
Sbjct: 71 KY-SSFAPVNNVIYIKAEPTEELKTLNE-KLYTGVLAGEQEYNFVP 114
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
0.316 0.131 0.400
Gapped
Lambda K H
0.267 0.0810 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,969,875
Number of extensions: 157411
Number of successful extensions: 335
Number of sequences better than 10.0: 1
Number of HSP's gapped: 333
Number of HSP's successfully gapped: 30
Length of query: 196
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 107
Effective length of database: 4,216,824
Effective search space: 451200168
Effective search space used: 451200168
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 (21.6 bits)
S2: 55 (24.8 bits)