Query gi|254780937|ref|YP_003065350.1| DNA-directed RNA polymerase subunit omega [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 122
No_of_seqs 138 out of 474
Neff 4.1
Searched_HMMs 13730
Date Wed Jun 1 10:42:37 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780937.hhm -d /home/congqian_1/database/scop/scop70_1_75.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 d1twff_ a.143.1.2 (F:) RPB6 {B 97.5 6.4E-05 4.7E-09 45.5 5.5 47 14-60 14-61 (84)
2 d1qkla_ a.143.1.2 (A:) RPB6 {H 97.5 6.2E-05 4.5E-09 45.5 4.9 47 14-60 57-104 (127)
3 d1smye_ a.143.1.1 (E:) RNA pol 96.1 0.0061 4.5E-07 34.3 6.0 54 7-60 6-74 (95)
4 d2p0la1 d.104.1.3 (A:4-272) Li 12.9 38 0.0028 12.9 5.4 54 23-76 191-244 (269)
5 d1ekza_ d.50.1.1 (A:) Staufen, 10.3 47 0.0034 12.4 1.6 18 39-56 2-19 (76)
6 d1tzyc_ a.22.1.1 (C:) Histone 9.3 42 0.0031 12.7 0.7 13 27-39 11-23 (95)
7 d2cpna1 d.50.1.1 (A:150-225) T 6.4 70 0.0051 11.4 1.9 19 36-54 1-19 (76)
8 d2uubm1 a.156.1.1 (M:2-126) Ri 5.9 76 0.0055 11.2 1.1 17 38-54 6-22 (125)
9 d1h8ba_ a.39.1.7 (A:) alpha-Ac 5.7 78 0.0057 11.2 1.8 21 46-66 10-32 (73)
10 d2dw4a1 a.4.1.18 (A:172-273) L 5.1 85 0.0062 11.0 0.8 27 48-74 23-53 (102)
No 1
>d1twff_ a.143.1.2 (F:) RPB6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
Probab=97.54 E-value=6.4e-05 Score=45.46 Aligned_cols=47 Identities=17% Similarity=0.294 Sum_probs=41.3
Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHH-HHHHHHHCCCCCH
Q ss_conf 7899999999999999857887767744685411-5675654058799
Q gi|254780937|r 14 DNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTV-VALREIASGTLSP 60 (122)
Q Consensus 14 ~nrf~LVllAa~RArql~~G~~~~v~~~ndK~~V-iALREIa~gki~~ 60 (122)
=++|+..-+-+.||.||+.|++|+|+.++..+++ ||..|.-.|++-+
T Consensus 14 LTkYE~ariiG~Ra~Ql~~Ga~p~I~~~~~~d~~~IA~~El~~~kiP~ 61 (84)
T d1twff_ 14 MTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPL 61 (84)
T ss_dssp CCHHHHHHHHHHHHHHHHTTCCCSSCCSSCCSHHHHHHHHHHTTCCCE
T ss_pred CCHHHHHHHHHHHHHHHHCCCCCEECCCCCCCHHHHHHHHHHCCCCCE
T ss_conf 229999999999999997699824547888799999999998399877
No 2
>d1qkla_ a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId: 9606]}
Probab=97.49 E-value=6.2e-05 Score=45.54 Aligned_cols=47 Identities=11% Similarity=0.244 Sum_probs=41.1
Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCH-HHHHHHHHCCCCCH
Q ss_conf 789999999999999985788776774468541-15675654058799
Q gi|254780937|r 14 DNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNT-VVALREIASGTLSP 60 (122)
Q Consensus 14 ~nrf~LVllAa~RArql~~G~~~~v~~~ndK~~-ViALREIa~gki~~ 60 (122)
=++|+..-+-+.||.||+.|++|+|+.++...+ .||+.|...+||-+
T Consensus 57 lTkYE~arilG~Ra~Qi~~ga~~~i~~~~~~d~~~IA~~EL~~kkiPf 104 (127)
T d1qkla_ 57 MTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPI 104 (127)
T ss_dssp CCHHHHHHHHHHHHHHHHHSCCSSSCSSSSCSSSHHHHHHHHHTCCCE
T ss_pred CCHHHHHHHHHHHHHHHHCCCCCEECCCCCCCHHHHHHHHHHCCCCCE
T ss_conf 219899999999999985699835668888799999999998399877
No 3
>d1smye_ a.143.1.1 (E:) RNA polymerase omega subunit {Thermus thermophilus [TaxId: 274]}
Probab=96.15 E-value=0.0061 Score=34.32 Aligned_cols=54 Identities=24% Similarity=0.449 Sum_probs=40.2
Q ss_pred HHHHCCCCCHHHHHHHHHHHHHH-HHCCCC-CCCCCC------------CCCCHH-HHHHHHHCCCCCH
Q ss_conf 99851287899999999999999-857887-767744------------685411-5675654058799
Q gi|254780937|r 7 EDCIDKVDNRFLLVLLASHRTRH-LSQGAK-PTVDVG------------KDKNTV-VALREIASGTLSP 60 (122)
Q Consensus 7 Edcl~kv~nrf~LVllAa~RArq-l~~G~~-~~v~~~------------ndK~~V-iALREIa~gki~~ 60 (122)
...+.-.+|||.|.++.++||-| |.+|.+ .+++.+ .|-|+| .|.+|..-|++..
T Consensus 6 D~ll~ltDSkYRLsvVvakRA~QlLr~g~~ntvL~pde~p~~~tleg~~~dpN~vt~AMkEL~tGrl~~ 74 (95)
T d1smye_ 6 DKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNAETWAMKELLTGRLVF 74 (95)
T ss_dssp HHHHHTSSSHHHHHHHHHHHHHHHHHTCTTCCSCCSSSCCCCSSSSGGGTSSCSHHHHHHHHTTTCEEE
T ss_pred HHHHHCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCEEE
T ss_conf 778631444224413548989999871798563696562556402556799758899999987373553
No 4
>d2p0la1 d.104.1.3 (A:4-272) Lipoate-protein ligase A {Streptococcus agalactiae [TaxId: 1311]}
Probab=12.92 E-value=38 Score=12.92 Aligned_cols=54 Identities=13% Similarity=0.175 Sum_probs=36.0
Q ss_pred HHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf 999999985788776774468541156756540587999999999999841164
Q gi|254780937|r 23 ASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDDLEEDFIHSLQKHVE 76 (122)
Q Consensus 23 Aa~RArql~~G~~~~v~~~ndK~~ViALREIa~gki~~~~l~e~~I~~lq~~~e 76 (122)
...+..-+.....+..-.+-+...|..|+++-...++++.+.+.++..++.+-.
T Consensus 191 ~~~~~~~~~~~~~~~~~~~~~~~~vtsL~~~L~~~~s~e~v~~~l~~~f~~~~~ 244 (269)
T d2p0la1 191 SDFYKIGLGDTGSPIAYPNVDPEIMANLSDLLDCPMTVEDVIDRMLISLKQVGF 244 (269)
T ss_dssp HHHHHHHHTTTCCSSCCCCCCTTSBCCHHHHTTCCCCHHHHHHHHHHHHHHHTC
T ss_pred HHHHHHCCCCCCCCCCCCCCCHHHEEEHHHHCCCCCCHHHHHHHHHHHHHHHCC
T ss_conf 777763046445433357655012135998739999999999999999999728
No 5
>d1ekza_ d.50.1.1 (A:) Staufen, domain III {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}
Probab=10.32 E-value=47 Score=12.42 Aligned_cols=18 Identities=28% Similarity=0.447 Sum_probs=13.1
Q ss_pred CCCCCCCHHHHHHHHHCC
Q ss_conf 744685411567565405
Q gi|254780937|r 39 DVGKDKNTVVALREIASG 56 (122)
Q Consensus 39 ~~~ndK~~ViALREIa~g 56 (122)
+..+.|+||..|.|++..
T Consensus 2 d~~~~k~Pvs~L~E~~q~ 19 (76)
T d1ekza_ 2 DEGDKKSPISQVHEIGIK 19 (76)
T ss_dssp CCCCCSCHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHH
T ss_conf 877788989999999996
No 6
>d1tzyc_ a.22.1.1 (C:) Histone H3 {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]}
Probab=9.32 E-value=42 Score=12.68 Aligned_cols=13 Identities=8% Similarity=0.202 Sum_probs=4.9
Q ss_pred HHHHHCCCCCCCC
Q ss_conf 9998578877677
Q gi|254780937|r 27 TRHLSQGAKPTVD 39 (122)
Q Consensus 27 Arql~~G~~~~v~ 39 (122)
-|.+..+..++++
T Consensus 11 IRk~Qkst~lLIp 23 (95)
T d1tzyc_ 11 IRRYQKSTELLIR 23 (95)
T ss_dssp HHHHHHCCSCCSC
T ss_pred HHHHHCCCCCCCC
T ss_conf 9988177533514
No 7
>d2cpna1 d.50.1.1 (A:150-225) TAR RNA-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}
Probab=6.45 E-value=70 Score=11.44 Aligned_cols=19 Identities=32% Similarity=0.384 Sum_probs=14.5
Q ss_pred CCCCCCCCCCHHHHHHHHH
Q ss_conf 7677446854115675654
Q gi|254780937|r 36 PTVDVGKDKNTVVALREIA 54 (122)
Q Consensus 36 ~~v~~~ndK~~ViALREIa 54 (122)
|+.+....+|++..|.|++
T Consensus 1 p~~~~~~~~npks~LqE~~ 19 (76)
T d2cpna1 1 PVSPQQSECNPVGALQELV 19 (76)
T ss_dssp CCCCCCCCCCHHHHHHHHH
T ss_pred CCCCCCCCCCHHHHHHHHH
T ss_conf 9797667889789999999
No 8
>d2uubm1 a.156.1.1 (M:2-126) Ribosomal protein S13 {Thermus thermophilus [TaxId: 274]}
Probab=5.85 E-value=76 Score=11.24 Aligned_cols=17 Identities=35% Similarity=0.429 Sum_probs=13.4
Q ss_pred CCCCCCCCHHHHHHHHH
Q ss_conf 77446854115675654
Q gi|254780937|r 38 VDVGKDKNTVVALREIA 54 (122)
Q Consensus 38 v~~~ndK~~ViALREIa 54 (122)
++.+.+|+..+||.-|-
T Consensus 6 ~di~~~K~v~~ALt~I~ 22 (125)
T d2uubm1 6 VEIPRNKRVDVALTYIY 22 (125)
T ss_dssp TCCCCSSBHHHHHTTST
T ss_pred CCCCCCCEEEEEEEEEE
T ss_conf 66999978887632055
No 9
>d1h8ba_ a.39.1.7 (A:) alpha-Actinin {Human (Homo sapiens) [TaxId: 9606]}
Probab=5.71 E-value=78 Score=11.19 Aligned_cols=21 Identities=19% Similarity=0.474 Sum_probs=12.7
Q ss_pred HHHHHHHHHCCC--CCHHHHHHH
Q ss_conf 115675654058--799999999
Q gi|254780937|r 46 TVVALREIASGT--LSPDDLEED 66 (122)
Q Consensus 46 ~ViALREIa~gk--i~~~~l~e~ 66 (122)
+.-|.|.+|.|| |+.++|+..
T Consensus 10 v~~aFr~lA~~KpyVT~~dL~~~ 32 (73)
T d1h8ba_ 10 VIASFRILASDKPYILAEELRRE 32 (73)
T ss_dssp HHHHHHHHTTSCSSBCHHHHHHH
T ss_pred HHHHHHHHHCCCCEECHHHHHHH
T ss_conf 99999999689982079999966
No 10
>d2dw4a1 a.4.1.18 (A:172-273) Lysine-specific histone demethylase 1, LSD1 {Human (Homo sapiens) [TaxId: 9606]}
Probab=5.12 E-value=85 Score=10.97 Aligned_cols=27 Identities=11% Similarity=0.058 Sum_probs=13.7
Q ss_pred HHHHHHHCCCC----CHHHHHHHHHHHHHHC
Q ss_conf 56756540587----9999999999998411
Q gi|254780937|r 48 VALREIASGTL----SPDDLEEDFIHSLQKH 74 (122)
Q Consensus 48 iALREIa~gki----~~~~l~e~~I~~lq~~ 74 (122)
.+|.|+..|.- .+-.+++.++...+..
T Consensus 23 ~~fpe~~~~~~~~~~~Yl~iRN~Il~~w~~n 53 (102)
T d2dw4a1 23 ACFPDIISGPQQTQKVFLFIRNRTLQLWLDN 53 (102)
T ss_dssp HHCHHHHTSCHHHHHHHHHHHHHHHHHHHHC
T ss_pred HHCHHHHCCCCCCHHHHHHHHHHHHHHHHHC
T ss_conf 8786963599977899999999999999819
Done!