Query 041820
Match_columns 316
No_of_seqs 94 out of 107
Neff 3.6
Searched_HMMs 29240
Date Mon Mar 25 18:53:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041820.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/041820hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1nc8_A Nucleocapsid protein; H 28.5 21 0.00072 22.1 1.1 19 221-244 8-26 (29)
2 1dsq_A Nucleic acid binding pr 26.5 21 0.00072 21.7 0.9 20 221-245 4-23 (26)
3 1a6b_B Momulv, zinc finger pro 24.0 44 0.0015 22.7 2.1 26 219-249 10-35 (40)
4 1u6p_A GAG polyprotein; MLV, A 18.4 63 0.0022 23.4 2.1 23 220-247 24-46 (56)
5 1yuz_A Nigerythrin; rubrythrin 15.9 61 0.0021 28.3 1.9 31 216-246 168-198 (202)
6 4ggi_A UDP-2,3-diacylglucosami 15.3 64 0.0022 29.4 1.9 25 105-129 221-246 (283)
7 2ysa_A Retinoblastoma-binding 13.6 60 0.0021 23.4 1.0 18 46-68 7-24 (55)
8 4exq_A UPD, URO-D, uroporphyri 13.5 16 0.00054 34.4 -2.7 21 112-134 22-42 (368)
9 1lng_A SRP19, signal recogniti 13.2 1.7E+02 0.0057 22.8 3.5 51 101-151 16-66 (87)
10 3pwf_A Rubrerythrin; non heme 12.8 3.6E+02 0.012 22.8 5.8 28 218-245 137-164 (170)
No 1
>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A
Probab=28.45 E-value=21 Score=22.12 Aligned_cols=19 Identities=42% Similarity=1.008 Sum_probs=14.9
Q ss_pred ccCCCCceeecCCCcccccccCCc
Q 041820 221 TCGYCPEVQVGPKGHRVRNCQAYK 244 (316)
Q Consensus 221 ~C~yC~EVHVG~~GHkir~C~g~k 244 (316)
.|-.| |..||.+++|..++
T Consensus 8 ~C~nC-----gk~GH~ar~C~~pr 26 (29)
T 1nc8_A 8 RCWNC-----GKEGHSARQCRAPR 26 (29)
T ss_dssp BCTTT-----SCBSSCGGGCCSSS
T ss_pred EEEEC-----CccccCHhHCcccc
Confidence 47777 56799999998764
No 2
>1dsq_A Nucleic acid binding protein P14; CCHC type zinc finger, virus/viral protein; NMR {Mouse mammary tumor virus} SCOP: g.40.1.1
Probab=26.54 E-value=21 Score=21.68 Aligned_cols=20 Identities=35% Similarity=0.770 Sum_probs=13.9
Q ss_pred ccCCCCceeecCCCcccccccCCcc
Q 041820 221 TCGYCPEVQVGPKGHRVRNCQAYKH 245 (316)
Q Consensus 221 ~C~yC~EVHVG~~GHkir~C~g~k~ 245 (316)
.|-.| |..||.+|.|...+.
T Consensus 4 ~Cf~C-----G~~GH~ardC~~~~~ 23 (26)
T 1dsq_A 4 VCFSC-----GKTGHIKRDCKEEXX 23 (26)
T ss_dssp BCTTT-----CCBSSCTTTTTCC--
T ss_pred eeEeC-----CCCCcccccCCCccc
Confidence 46566 467999999987653
No 3
>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1
Probab=24.01 E-value=44 Score=22.71 Aligned_cols=26 Identities=31% Similarity=0.750 Sum_probs=19.5
Q ss_pred ccccCCCCceeecCCCcccccccCCcccccc
Q 041820 219 VQTCGYCPEVQVGPKGHRVRNCQAYKHQMRD 249 (316)
Q Consensus 219 V~~C~yC~EVHVG~~GHkir~C~g~k~~~R~ 249 (316)
-..|-+|. ..||.+++|-..+...|.
T Consensus 10 ~~~C~~Cg-----k~GH~ardCP~~~~~~r~ 35 (40)
T 1a6b_B 10 RDQCAYCK-----EKGHWAKDCPKKPRGPRG 35 (40)
T ss_dssp SSSCSSSC-----CTTCCTTSCSSSCCCTTC
T ss_pred CCeeeECC-----CCCcchhhCcCCcccCCC
Confidence 35688885 579999999987665554
No 4
>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger, NC, viral protein-RN; HET: AP7; NMR {Moloney murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A 1wwg_A
Probab=18.35 E-value=63 Score=23.37 Aligned_cols=23 Identities=35% Similarity=0.866 Sum_probs=18.0
Q ss_pred cccCCCCceeecCCCcccccccCCcccc
Q 041820 220 QTCGYCPEVQVGPKGHRVRNCQAYKHQM 247 (316)
Q Consensus 220 ~~C~yC~EVHVG~~GHkir~C~g~k~~~ 247 (316)
-.|-+|.| .||.++.|--.+...
T Consensus 24 ~~C~~Cge-----~GH~ardCp~~~~~~ 46 (56)
T 1u6p_A 24 DQCAYCKE-----KGHWAKDCPKKPRGP 46 (56)
T ss_dssp TBCSSSCC-----BSSCGGGCTTCCCSS
T ss_pred CcceeCCC-----CCcccccCcCCcccc
Confidence 45999966 799999998765543
No 5
>1yuz_A Nigerythrin; rubrythrin, rubredoxin, hemerythrin, electron transfer, DIIR center, oxidoreductase; 1.40A {Desulfovibrio vulgaris subsp} SCOP: a.25.1.1 g.41.5.1 PDB: 1yv1_A 1yux_A
Probab=15.93 E-value=61 Score=28.32 Aligned_cols=31 Identities=16% Similarity=0.280 Sum_probs=21.8
Q ss_pred ceeccccCCCCceeecCCCcccccccCCccc
Q 041820 216 KYAVQTCGYCPEVQVGPKGHRVRNCQAYKHQ 246 (316)
Q Consensus 216 vypV~~C~yC~EVHVG~~GHkir~C~g~k~~ 246 (316)
....+.|..|.-+|.|...-+=..|++.|..
T Consensus 168 ~~~~~~C~~CG~i~~g~~p~~CP~C~~~k~~ 198 (202)
T 1yuz_A 168 DDKFHLCPICGYIHKGEDFEKCPICFRPKDT 198 (202)
T ss_dssp SCCEEECSSSCCEEESSCCSBCTTTCCBGGG
T ss_pred CCcEEEECCCCCEEcCcCCCCCCCCCCChHH
Confidence 4568999999999998433344567766543
No 6
>4ggi_A UDP-2,3-diacylglucosamine pyrophosphatase LPXI; structural genomics, PSI-biology; HET: UDG; 2.52A {Caulobacter crescentus} PDB: 4ggm_X*
Probab=15.30 E-value=64 Score=29.39 Aligned_cols=25 Identities=20% Similarity=0.248 Sum_probs=19.9
Q ss_pred ccccccccCCCc-hhHHHHHHHhCCC
Q 041820 105 VSHNERLQVDQI-PAVNELCIQAGID 129 (316)
Q Consensus 105 I~H~eRf~~~RI-PAivELCiQAGvd 129 (316)
...|-||++|-| |.-+|+|.+||+.
T Consensus 221 ~~qD~~fd~P~iG~dti~~~~~ag~~ 246 (283)
T 4ggi_A 221 PIQETRVALPTIGVATIHRAARAGLA 246 (283)
T ss_dssp CC---CCCCCEECHHHHHHHHHTTCC
T ss_pred cccccccCCccccHHHHHHHHHcCCe
Confidence 457999999999 9999999999984
No 7
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=13.58 E-value=60 Score=23.39 Aligned_cols=18 Identities=50% Similarity=1.086 Sum_probs=14.4
Q ss_pred eccCCCCCceeecCCCccccccc
Q 041820 46 IYTCSLCGEVHVGHPPHKIRTCN 68 (316)
Q Consensus 46 V~~C~~C~EvhVG~~gH~i~tC~ 68 (316)
-+.|--| |..||-|+.|-
T Consensus 7 ~~~C~kC-----Gk~GH~~k~Cp 24 (55)
T 2ysa_A 7 GYTCFRC-----GKPGHYIKNCP 24 (55)
T ss_dssp SCCCTTT-----CCTTSCGGGCS
T ss_pred CCccccC-----CCcCcccccCC
Confidence 4568788 46899999996
No 8
>4exq_A UPD, URO-D, uroporphyrinogen decarboxylase; ssgcid, NIH, SBRI, heme biosynthesis, structural GENO niaid; 1.65A {Burkholderia thailandensis}
Probab=13.55 E-value=16 Score=34.36 Aligned_cols=21 Identities=38% Similarity=0.518 Sum_probs=19.0
Q ss_pred cCCCchhHHHHHHHhCCCCCCCC
Q 041820 112 QVDQIPAVNELCIQAGIDIPQYP 134 (316)
Q Consensus 112 ~~~RIPAivELCiQAGvdipeyp 134 (316)
.+||+|-. ++.|||-.+|||=
T Consensus 22 ~~dr~Pvw--~mrqaGr~lpey~ 42 (368)
T 4exq_A 22 PTDYTPIW--LMRQAGRYLPEYN 42 (368)
T ss_dssp CCSSCCBC--CTTSSSTTSHHHH
T ss_pred CCCCCCEE--eeHhhhhccHHHH
Confidence 69999986 7999999999995
No 9
>1lng_A SRP19, signal recognition particle 19 kDa protein; protein-RNA complex, signaling protein/RNA complex; 2.30A {Methanocaldococcus jannaschii} SCOP: d.201.1.1 PDB: 2v3c_A 3ndb_A 1l9a_A*
Probab=13.22 E-value=1.7e+02 Score=22.77 Aligned_cols=51 Identities=16% Similarity=0.251 Sum_probs=36.8
Q ss_pred cCCcccccccccCCCchhHHHHHHHhCCCCCCCCcccccccccccCCeeec
Q 041820 101 IGRAVSHNERLQVDQIPAVNELCIQAGIDIPQYPTRRRVFPAYNLAGKVID 151 (316)
Q Consensus 101 ~g~~I~H~eRf~~~RIPAivELCiQAGvdipeyptkrr~~Pi~~i~~r~~d 151 (316)
-||+|+-+.=-+-|.+--|.+-|.+.|++.--++.|+=-+--....||+..
T Consensus 16 eGRrv~k~~aV~~P~~~EI~~a~~~lgl~~~~E~~K~yPr~w~~~~GRVrV 66 (87)
T 1lng_A 16 EGRKVPEELAIEKPSLKDIEKALKKLGLEPKIYRDKRYPRQHWEICGCVEV 66 (87)
T ss_dssp TTCCSCTTTCBSSCCHHHHHHHHHHTTCCCEEETTCCCGGGTTSCCCEEEC
T ss_pred hcCccCHHHhccCCCHHHHHHHHHHcCCCeEEccCCCCCcccccCCceEEE
Confidence 588899998889999999999999999998555554322222233366664
No 10
>3pwf_A Rubrerythrin; non heme iron peroxidases, oxidative stress, oxidoreductase; 1.64A {Pyrococcus furiosus} PDB: 3mps_A 3pza_A 3qvd_A 1nnq_A 2hr5_A
Probab=12.79 E-value=3.6e+02 Score=22.81 Aligned_cols=28 Identities=25% Similarity=0.320 Sum_probs=21.7
Q ss_pred eccccCCCCceeecCCCcccccccCCcc
Q 041820 218 AVQTCGYCPEVQVGPKGHRVRNCQAYKH 245 (316)
Q Consensus 218 pV~~C~yC~EVHVG~~GHkir~C~g~k~ 245 (316)
..+.|.-|.-||.|...-+=..|++++.
T Consensus 137 ~~~~C~~CG~i~~~~~p~~CP~Cg~~~~ 164 (170)
T 3pwf_A 137 KVYICPICGYTAVDEAPEYCPVCGAPKE 164 (170)
T ss_dssp CEEECTTTCCEEESCCCSBCTTTCCBGG
T ss_pred CeeEeCCCCCeeCCCCCCCCCCCCCCHH
Confidence 4788999999999865556677777654
Done!