Query 014445
Match_columns 424
No_of_seqs 186 out of 941
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 05:11:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014445.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014445hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02365 NAM: No apical merist 100.0 1.4E-38 3.1E-43 277.6 5.6 127 58-198 1-129 (129)
2 PF09889 DUF2116: Uncharacteri 49.5 9.3 0.0002 30.3 1.3 17 34-50 1-17 (59)
3 PF13248 zf-ribbon_3: zinc-rib 44.4 13 0.00028 24.3 1.2 13 37-49 3-15 (26)
4 PF13240 zinc_ribbon_2: zinc-r 37.2 19 0.00041 23.2 1.0 13 38-50 1-13 (23)
5 PF03604 DNA_RNApol_7kD: DNA d 36.2 22 0.00048 24.8 1.3 16 31-46 12-27 (32)
6 smart00659 RPOLCX RNA polymera 29.7 29 0.00064 25.7 1.2 16 32-47 15-30 (44)
7 PF00301 Rubredoxin: Rubredoxi 29.4 19 0.00041 27.2 0.1 27 38-65 3-29 (47)
8 PF10571 UPF0547: Uncharacteri 27.9 31 0.00068 22.9 0.9 11 35-45 13-23 (26)
9 PF07282 OrfB_Zn_ribbon: Putat 23.1 68 0.0015 24.9 2.2 33 30-63 22-55 (69)
10 COG0777 AccD Acetyl-CoA carbox 22.9 55 0.0012 33.5 2.0 46 33-78 25-71 (294)
11 cd00730 rubredoxin Rubredoxin; 22.5 64 0.0014 24.6 1.9 26 38-64 3-28 (50)
12 CHL00174 accD acetyl-CoA carbo 21.4 47 0.001 34.1 1.3 46 33-78 35-81 (296)
No 1
>PF02365 NAM: No apical meristem (NAM) protein; InterPro: IPR003441 The NAC domain (for Petunia hybrida (Petunia) NAM and for Arabidopsis ATAF1, ATAF2, and CUC2) is an N-terminal module of ~160 amino acids, which is found in proteins of the NAC family of plant-specific transcriptional regulators (no apical meristem (NAM) proteins) []. NAC proteins are involved in developmental processes, including formation of the shoot apical meristem, floral organs and lateral shoots, as well as in plant hormonal control and defence. The NAC domain is accompanied by diverse C-terminal transcriptional activation domains. The NAC domain has been shown to be a DNA-binding domain (DBD) and a dimerization domain [,]. The NAC domain can be subdivided into five subdomains (A-E). Each subdomain is distinguishable by blocks of heterogeneous amino acids or gaps. While the NAC domains were rich in basic amino acids (R, K and H) as a whole, the distribution of positive and negative amino acids in each subdomain were unequal. Subdomains C and D are rich in basic amino acids but poor in acidic amino acids, while subdomain B contains a high proportion of acidic amino acids. Putative nuclear localization signals (NLS) have been detected in subdomains C and D []. The DBD is contained within a 60 amino acid region located within subdomains D and E []. The overall structure of the NAC domain monomer consists of a very twisted antiparallel beta-sheet, which packs against an N-terminal alpha-helix on one side and one shorter helix on the other side surrounded by a few helical elements. The structure suggests that the NAC domain mediates dimerization through conserved interactions including a salt bridge, and DNA binding through the NAC dimer face rich in positive charges [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1UT4_A 3SWM_B 4DUL_B 3SWP_D 1UT7_B 3ULX_A.
Probab=100.00 E-value=1.4e-38 Score=277.57 Aligned_cols=127 Identities=37% Similarity=0.607 Sum_probs=90.2
Q ss_pred CCCCceeCCChHHHHHHHHHhhhcCCCCCCCccccccceeccCCCCCCCCCCCCCC-CCCCCCceEEEeccccccCCCCc
Q 014445 58 LPRGVKFDPSDQEIIWHLLAKAGLEGLNPHPFIDEFIPTVDQDGGICYTHPQNLPG-VKQDGSAAHFFYRAIKAYSTGTR 136 (424)
Q Consensus 58 LPpGfRF~PTDeELI~~YL~kKi~G~~~p~Pli~~~Ip~vD~d~~Iy~~ePwdLPg-~~~dG~~wYFFs~r~kky~~G~R 136 (424)
|||||||+|||+|||.+||++|+.|.+.+ ...+|.++| ||+.|||+||. ....++.||||+++.+++.+|.|
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~---~~~~i~~~D----iy~~~P~~L~~~~~~~~~~~yFF~~~~~~~~~~~r 73 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLP---CEDVIHDVD----IYSAHPWELPAKFKGGDEEWYFFSPRKKKYPNGGR 73 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHC---S-CHSEE------GGGS-GGGCHHHSSS-SSEEEEEEE----------
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCC---cccceeecc----cCccChHHhhhhccCCCceEEEEEecccccCCccc
Confidence 89999999999999999999999998532 126788887 99999999994 23456799999999999999999
Q ss_pred ccccccCCCCCccEEeecCCCceEec-CCeeeeeEEEEEeeeeccCCCCCCCcCeEEEEEEeC
Q 014445 137 KRRKINGDDFGEVRWHKTGRTKPVML-DGVQKGCKKIMVLYMSMVRGGKAEKTNWVMHQYHLG 198 (424)
Q Consensus 137 ~~R~t~~G~~g~G~Wk~tGk~K~I~~-~G~vVG~KKtLvFY~gr~~g~kg~KT~WVMHEY~L~ 198 (424)
++|+++ +|+||.+|+.++|.. +|.+||+||+|+||.++. +++.+|+|+||||+|.
T Consensus 74 ~~R~~~-----~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~--~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 74 PNRVTG-----GGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKS--PNGKKTGWVMHEYSLE 129 (129)
T ss_dssp S-EEET-----TEEEEEECEEEEEEE-TTCEEEEEEEEEEEESST--TS-EEEEEEEEEEEE-
T ss_pred cccccc-----ceEEeecccccccccccceeeeeEEEEEEEeccC--CCCCcCCeEEEEEEeC
Confidence 999764 479999999999998 899999999999997753 4778999999999984
No 2
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=49.51 E-value=9.3 Score=30.26 Aligned_cols=17 Identities=35% Similarity=0.823 Sum_probs=14.1
Q ss_pred CCCccCCCCCccccCCC
Q 014445 34 NPTKACPNCHHVIDNSD 50 (424)
Q Consensus 34 ~~~~~c~~c~~~id~s~ 50 (424)
.+++.||+||..|+.+.
T Consensus 1 e~HkHC~~CG~~Ip~~~ 17 (59)
T PF09889_consen 1 EPHKHCPVCGKPIPPDE 17 (59)
T ss_pred CCCCcCCcCCCcCCcch
Confidence 37899999999988643
No 3
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=44.41 E-value=13 Score=24.34 Aligned_cols=13 Identities=46% Similarity=0.894 Sum_probs=9.3
Q ss_pred ccCCCCCccccCC
Q 014445 37 KACPNCHHVIDNS 49 (424)
Q Consensus 37 ~~c~~c~~~id~s 49 (424)
+.||+|++.|+.+
T Consensus 3 ~~Cp~Cg~~~~~~ 15 (26)
T PF13248_consen 3 MFCPNCGAEIDPD 15 (26)
T ss_pred CCCcccCCcCCcc
Confidence 5788888876543
No 4
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=37.19 E-value=19 Score=23.21 Aligned_cols=13 Identities=38% Similarity=0.953 Sum_probs=10.3
Q ss_pred cCCCCCccccCCC
Q 014445 38 ACPNCHHVIDNSD 50 (424)
Q Consensus 38 ~c~~c~~~id~s~ 50 (424)
.||+|++.|++..
T Consensus 1 ~Cp~CG~~~~~~~ 13 (23)
T PF13240_consen 1 YCPNCGAEIEDDA 13 (23)
T ss_pred CCcccCCCCCCcC
Confidence 4999999987643
No 5
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=36.21 E-value=22 Score=24.83 Aligned_cols=16 Identities=38% Similarity=0.794 Sum_probs=11.8
Q ss_pred ccCCCCccCCCCCccc
Q 014445 31 WKSNPTKACPNCHHVI 46 (424)
Q Consensus 31 ~~~~~~~~c~~c~~~i 46 (424)
...+....|++|+|+|
T Consensus 12 ~~~~~~irC~~CG~RI 27 (32)
T PF03604_consen 12 LKPGDPIRCPECGHRI 27 (32)
T ss_dssp BSTSSTSSBSSSS-SE
T ss_pred cCCCCcEECCcCCCeE
Confidence 4556678999999986
No 6
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=29.75 E-value=29 Score=25.71 Aligned_cols=16 Identities=31% Similarity=0.430 Sum_probs=12.8
Q ss_pred cCCCCccCCCCCcccc
Q 014445 32 KSNPTKACPNCHHVID 47 (424)
Q Consensus 32 ~~~~~~~c~~c~~~id 47 (424)
+......||+|+|.|-
T Consensus 15 ~~~~~irC~~CG~rIl 30 (44)
T smart00659 15 KSKDVVRCRECGYRIL 30 (44)
T ss_pred CCCCceECCCCCceEE
Confidence 3567789999999973
No 7
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=29.40 E-value=19 Score=27.17 Aligned_cols=27 Identities=33% Similarity=0.726 Sum_probs=18.5
Q ss_pred cCCCCCccccCCCcCCCCCCCCCCceeC
Q 014445 38 ACPNCHHVIDNSDVAHEWPGLPRGVKFD 65 (424)
Q Consensus 38 ~c~~c~~~id~s~v~~~~~~LPpGfRF~ 65 (424)
.|+.|+++-|... .-..-++|||..|.
T Consensus 3 ~C~~CgyvYd~~~-Gd~~~~i~pGt~F~ 29 (47)
T PF00301_consen 3 QCPVCGYVYDPEK-GDPENGIPPGTPFE 29 (47)
T ss_dssp EETTTSBEEETTT-BBGGGTB-TT--GG
T ss_pred CCCCCCEEEcCCc-CCcccCcCCCCCHH
Confidence 6999999998865 44556889998874
No 8
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=27.89 E-value=31 Score=22.94 Aligned_cols=11 Identities=36% Similarity=0.824 Sum_probs=5.9
Q ss_pred CCccCCCCCcc
Q 014445 35 PTKACPNCHHV 45 (424)
Q Consensus 35 ~~~~c~~c~~~ 45 (424)
..+.||.|||.
T Consensus 13 ~~~~Cp~CG~~ 23 (26)
T PF10571_consen 13 SAKFCPHCGYD 23 (26)
T ss_pred hcCcCCCCCCC
Confidence 44555555554
No 9
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=23.12 E-value=68 Score=24.90 Aligned_cols=33 Identities=18% Similarity=0.323 Sum_probs=20.6
Q ss_pred cccCCCCccCCCCCccccCCCcCCCCCCCC-CCce
Q 014445 30 KWKSNPTKACPNCHHVIDNSDVAHEWPGLP-RGVK 63 (424)
Q Consensus 30 ~~~~~~~~~c~~c~~~id~s~v~~~~~~LP-pGfR 63 (424)
+....+++.||.|++.... ........-| =|+.
T Consensus 22 v~~~~TSq~C~~CG~~~~~-~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 22 VDEAYTSQTCPRCGHRNKK-RRSGRVFTCPNCGFE 55 (69)
T ss_pred ECCCCCccCccCccccccc-ccccceEEcCCCCCE
Confidence 3355588999999999766 3333344444 4554
No 10
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=22.90 E-value=55 Score=33.53 Aligned_cols=46 Identities=20% Similarity=0.339 Sum_probs=39.1
Q ss_pred CCCCccCCCCCccccCCCcCCCCCCCC-CCceeCCChHHHHHHHHHh
Q 014445 33 SNPTKACPNCHHVIDNSDVAHEWPGLP-RGVKFDPSDQEIIWHLLAK 78 (424)
Q Consensus 33 ~~~~~~c~~c~~~id~s~v~~~~~~LP-pGfRF~PTDeELI~~YL~k 78 (424)
.+-|..||+|++.+=..|+-....-.| -|+.|+=+-.|.|..+|-.
T Consensus 25 e~lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ri~A~~Ri~~llD~ 71 (294)
T COG0777 25 EGLWTKCPSCGEMLYRKELESNLKVCPKCGHHMRISARERLEALLDE 71 (294)
T ss_pred CCceeECCCccceeeHHHHHhhhhcccccCcccccCHHHHHHHhhCC
Confidence 788999999999998888877666667 7999999999999987643
No 11
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=22.50 E-value=64 Score=24.62 Aligned_cols=26 Identities=27% Similarity=0.635 Sum_probs=20.2
Q ss_pred cCCCCCccccCCCcCCCCCCCCCCcee
Q 014445 38 ACPNCHHVIDNSDVAHEWPGLPRGVKF 64 (424)
Q Consensus 38 ~c~~c~~~id~s~v~~~~~~LPpGfRF 64 (424)
.|..|+++.|... -...-++|||-.|
T Consensus 3 ~C~~CgyiYd~~~-Gd~~~~i~pGt~f 28 (50)
T cd00730 3 ECRICGYIYDPAE-GDPDEGIPPGTPF 28 (50)
T ss_pred CCCCCCeEECCCC-CCcccCcCCCCCH
Confidence 6999999999754 4445678888877
No 12
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=21.43 E-value=47 Score=34.09 Aligned_cols=46 Identities=15% Similarity=0.102 Sum_probs=36.9
Q ss_pred CCCCccCCCCCccccCCCcCCCCCCCC-CCceeCCChHHHHHHHHHh
Q 014445 33 SNPTKACPNCHHVIDNSDVAHEWPGLP-RGVKFDPSDQEIIWHLLAK 78 (424)
Q Consensus 33 ~~~~~~c~~c~~~id~s~v~~~~~~LP-pGfRF~PTDeELI~~YL~k 78 (424)
.+-|..||+|++.|...++.....--| =|+.|.-|-.|-|..+|-+
T Consensus 35 ~~lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h~rltAreRI~~L~D~ 81 (296)
T CHL00174 35 KHLWVQCENCYGLNYKKFLKSKMNICEQCGYHLKMSSSDRIELLIDP 81 (296)
T ss_pred CCCeeECCCccchhhHHHHHHcCCCCCCCCCCcCCCHHHHHHHHccC
Confidence 346899999999998888755555556 7999999999999977643
Done!