Query 014310
Match_columns 427
No_of_seqs 187 out of 934
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 03:53:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014310.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014310hhsearch_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 6.3E-39 1.4E-43 280.1 6.6 127 58-198 1-129 (129)
2 PF09889 DUF2116: Uncharacteri 50.1 8.4 0.00018 30.5 1.1 15 34-48 1-15 (59)
3 PF13248 zf-ribbon_3: zinc-rib 49.9 8.7 0.00019 25.2 1.0 12 37-48 3-14 (26)
4 PF03604 DNA_RNApol_7kD: DNA d 47.0 12 0.00025 26.2 1.3 16 31-46 12-27 (32)
5 PF13240 zinc_ribbon_2: zinc-r 43.3 12 0.00026 24.1 0.9 13 38-50 1-13 (23)
6 smart00659 RPOLCX RNA polymera 42.8 15 0.00032 27.3 1.4 16 32-47 15-30 (44)
7 PF10571 UPF0547: Uncharacteri 32.6 20 0.00044 23.8 0.7 11 37-47 1-11 (26)
8 PF00301 Rubredoxin: Rubredoxi 30.1 21 0.00045 27.0 0.5 27 38-65 3-29 (47)
9 COG0777 AccD Acetyl-CoA carbox 29.1 39 0.00085 34.6 2.3 46 33-78 25-71 (294)
10 PF14149 YhfH: YhfH-like prote 26.3 15 0.00032 26.8 -0.9 14 35-48 12-25 (37)
11 CHL00174 accD acetyl-CoA carbo 26.3 32 0.0007 35.3 1.2 46 33-78 35-81 (296)
12 PRK05654 acetyl-CoA carboxylas 24.8 37 0.0008 34.6 1.3 46 33-78 24-70 (292)
13 TIGR02098 MJ0042_CXXC MJ0042 f 24.3 38 0.00082 23.5 0.9 15 33-47 22-36 (38)
14 COG1996 RPC10 DNA-directed RNA 24.2 41 0.00089 25.8 1.1 15 32-46 20-34 (49)
15 TIGR00515 accD acetyl-CoA carb 21.5 42 0.00091 34.1 0.9 46 32-77 22-68 (285)
16 cd00730 rubredoxin Rubredoxin; 21.4 75 0.0016 24.3 2.1 26 38-64 3-28 (50)
17 PF07282 OrfB_Zn_ribbon: Putat 21.0 76 0.0016 24.6 2.1 32 31-63 23-55 (69)
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=6.3e-39 Score=280.14 Aligned_cols=127 Identities=37% Similarity=0.607 Sum_probs=90.3
Q ss_pred CCCCceeCCChHHHHHHHHHhhhcCCCCCCCcccccccccccCCCCCCCCCCCCCC-CCCCCCceEEEEecccccCCCCc
Q 014310 58 LPRGVKFDPSDQEIIWHLLAKAGLEGLNPHPFIDEFIPTVDQDGGICYTHPQNLPG-VKQDGSAAHFFYRAIKAYSTGTR 136 (427)
Q Consensus 58 LPpGfRF~PTDeELI~hYL~kKi~G~~~p~Pli~~~Ip~vD~d~~Iy~~ePwdLPg-~~~dG~~wYFFs~r~kky~~G~R 136 (427)
|||||||+|||+|||.+||++|+.|.+.+ ...+|+++| ||+.|||+||. ....++.||||+++.+++.+|.|
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 cceeccCCCCCccEEeecCCCceeee-CCeeeEEEEEEEeeeeccCCCCCCCcCeEEEEEEeC
Q 014310 137 KRRKINGDDFGEVRWHKTGRTKPVML-DGVQKGCKKIMVLYMSMVRGGKAEKTNWVMHQYHLG 198 (427)
Q Consensus 137 ~rR~~~~G~~g~G~Wk~tGk~K~I~~-~G~vVG~KKtLvFY~gr~~g~kg~KT~WVMHEY~L~ 198 (427)
++|++. +|+||.+|+.++|.. +|.+||+||+|+||.++. +++.+|+|+||||+|.
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 999774 479999999999998 899999999999997753 5778999999999984
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=50.09 E-value=8.4 Score=30.54 Aligned_cols=15 Identities=40% Similarity=0.862 Sum_probs=12.8
Q ss_pred CCcccCCCCcceecC
Q 014310 34 NPTKACPNCHHVIDN 48 (427)
Q Consensus 34 ~~~~~cp~c~~~id~ 48 (427)
+|++.||+||..|+-
T Consensus 1 e~HkHC~~CG~~Ip~ 15 (59)
T PF09889_consen 1 EPHKHCPVCGKPIPP 15 (59)
T ss_pred CCCCcCCcCCCcCCc
Confidence 478999999998865
No 3
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=49.90 E-value=8.7 Score=25.18 Aligned_cols=12 Identities=50% Similarity=0.955 Sum_probs=8.7
Q ss_pred ccCCCCcceecC
Q 014310 37 KACPNCHHVIDN 48 (427)
Q Consensus 37 ~~cp~c~~~id~ 48 (427)
+.||+|++.|+.
T Consensus 3 ~~Cp~Cg~~~~~ 14 (26)
T PF13248_consen 3 MFCPNCGAEIDP 14 (26)
T ss_pred CCCcccCCcCCc
Confidence 578888887654
No 4
>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=46.96 E-value=12 Score=26.20 Aligned_cols=16 Identities=38% Similarity=0.794 Sum_probs=11.8
Q ss_pred ccCCCcccCCCCccee
Q 014310 31 WKSNPTKACPNCHHVI 46 (427)
Q Consensus 31 ~~~~~~~~cp~c~~~i 46 (427)
........||+|+|+|
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 4556678999999987
No 5
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=43.25 E-value=12 Score=24.11 Aligned_cols=13 Identities=38% Similarity=0.953 Sum_probs=10.2
Q ss_pred cCCCCcceecCCC
Q 014310 38 ACPNCHHVIDNSD 50 (427)
Q Consensus 38 ~cp~c~~~id~~~ 50 (427)
.||+|++.|++..
T Consensus 1 ~Cp~CG~~~~~~~ 13 (23)
T PF13240_consen 1 YCPNCGAEIEDDA 13 (23)
T ss_pred CCcccCCCCCCcC
Confidence 4999999987643
No 6
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=42.80 E-value=15 Score=27.30 Aligned_cols=16 Identities=31% Similarity=0.430 Sum_probs=12.9
Q ss_pred cCCCcccCCCCcceec
Q 014310 32 KSNPTKACPNCHHVID 47 (427)
Q Consensus 32 ~~~~~~~cp~c~~~id 47 (427)
+......||+|+|+|-
T Consensus 15 ~~~~~irC~~CG~rIl 30 (44)
T smart00659 15 KSKDVVRCRECGYRIL 30 (44)
T ss_pred CCCCceECCCCCceEE
Confidence 3567789999999974
No 7
>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=32.65 E-value=20 Score=23.84 Aligned_cols=11 Identities=36% Similarity=1.017 Sum_probs=8.0
Q ss_pred ccCCCCcceec
Q 014310 37 KACPNCHHVID 47 (427)
Q Consensus 37 ~~cp~c~~~id 47 (427)
+.||+|+..|-
T Consensus 1 K~CP~C~~~V~ 11 (26)
T PF10571_consen 1 KTCPECGAEVP 11 (26)
T ss_pred CcCCCCcCCch
Confidence 46888888763
No 8
>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=30.11 E-value=21 Score=26.97 Aligned_cols=27 Identities=33% Similarity=0.726 Sum_probs=18.2
Q ss_pred cCCCCcceecCCCcCCCCCCCCCCceeC
Q 014310 38 ACPNCHHVIDNSDVAHEWPGLPRGVKFD 65 (427)
Q Consensus 38 ~cp~c~~~id~~~v~~~~~~LPpGfRF~ 65 (427)
.|+.|+++-|-.. ....-++|||..|.
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 6999999988754 55556889998874
No 9
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=29.07 E-value=39 Score=34.58 Aligned_cols=46 Identities=20% Similarity=0.339 Sum_probs=39.3
Q ss_pred CCCcccCCCCcceecCCCcCCCCCCCC-CCceeCCChHHHHHHHHHh
Q 014310 33 SNPTKACPNCHHVIDNSDVAHEWPGLP-RGVKFDPSDQEIIWHLLAK 78 (427)
Q Consensus 33 ~~~~~~cp~c~~~id~~~v~~~~~~LP-pGfRF~PTDeELI~hYL~k 78 (427)
.+-|..||.|++.|=..|+-....-.| -|+.|+=+-.|.|..+|-.
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 778999999999999999877666666 7999999999999987643
No 10
>PF14149 YhfH: YhfH-like protein
Probab=26.33 E-value=15 Score=26.75 Aligned_cols=14 Identities=36% Similarity=0.937 Sum_probs=12.3
Q ss_pred CcccCCCCcceecC
Q 014310 35 PTKACPNCHHVIDN 48 (427)
Q Consensus 35 ~~~~cp~c~~~id~ 48 (427)
|.+.|+.||+.|+-
T Consensus 12 p~K~C~~CG~~i~E 25 (37)
T PF14149_consen 12 PPKKCTECGKEIEE 25 (37)
T ss_pred CCcccHHHHHHHHH
Confidence 88999999999863
No 11
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=26.29 E-value=32 Score=35.27 Aligned_cols=46 Identities=15% Similarity=0.102 Sum_probs=36.9
Q ss_pred CCCcccCCCCcceecCCCcCCCCCCCC-CCceeCCChHHHHHHHHHh
Q 014310 33 SNPTKACPNCHHVIDNSDVAHEWPGLP-RGVKFDPSDQEIIWHLLAK 78 (427)
Q Consensus 33 ~~~~~~cp~c~~~id~~~v~~~~~~LP-pGfRF~PTDeELI~hYL~k 78 (427)
.+.|..||+|++.|...++.....--| =|+.|.-|-.|-|..+|-+
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 346899999999998888666555556 7999999999999986643
No 12
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=24.85 E-value=37 Score=34.60 Aligned_cols=46 Identities=22% Similarity=0.337 Sum_probs=36.8
Q ss_pred CCCcccCCCCcceecCCCcCCCCCCCC-CCceeCCChHHHHHHHHHh
Q 014310 33 SNPTKACPNCHHVIDNSDVAHEWPGLP-RGVKFDPSDQEIIWHLLAK 78 (427)
Q Consensus 33 ~~~~~~cp~c~~~id~~~v~~~~~~LP-pGfRF~PTDeELI~hYL~k 78 (427)
.+.|..||+|++.|-..++.....--| =|+.|.-|-.|-|..+|-+
T Consensus 24 ~~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl~areRi~~L~D~ 70 (292)
T PRK05654 24 EGLWTKCPSCGQVLYRKELEANLNVCPKCGHHMRISARERLDLLLDE 70 (292)
T ss_pred CCCeeECCCccchhhHHHHHhcCCCCCCCCCCeeCCHHHHHHHHccC
Confidence 456999999999998888755544455 6899999999999987743
No 13
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=24.34 E-value=38 Score=23.51 Aligned_cols=15 Identities=27% Similarity=0.514 Sum_probs=11.0
Q ss_pred CCCcccCCCCcceec
Q 014310 33 SNPTKACPNCHHVID 47 (427)
Q Consensus 33 ~~~~~~cp~c~~~id 47 (427)
.+....||+|++.|.
T Consensus 22 ~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 22 NGGKVRCGKCGHVWY 36 (38)
T ss_pred CCCEEECCCCCCEEE
Confidence 345678999998864
No 14
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=24.23 E-value=41 Score=25.84 Aligned_cols=15 Identities=27% Similarity=0.603 Sum_probs=12.3
Q ss_pred cCCCcccCCCCccee
Q 014310 32 KSNPTKACPNCHHVI 46 (427)
Q Consensus 32 ~~~~~~~cp~c~~~i 46 (427)
.......||.|+|.|
T Consensus 20 ~~~~~irCp~Cg~rI 34 (49)
T COG1996 20 QETRGIRCPYCGSRI 34 (49)
T ss_pred hccCceeCCCCCcEE
Confidence 345778999999997
No 15
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=21.48 E-value=42 Score=34.13 Aligned_cols=46 Identities=20% Similarity=0.311 Sum_probs=36.7
Q ss_pred cCCCcccCCCCcceecCCCcCCCCCCCC-CCceeCCChHHHHHHHHH
Q 014310 32 KSNPTKACPNCHHVIDNSDVAHEWPGLP-RGVKFDPSDQEIIWHLLA 77 (427)
Q Consensus 32 ~~~~~~~cp~c~~~id~~~v~~~~~~LP-pGfRF~PTDeELI~hYL~ 77 (427)
..+.|..||+|+..|-..++.....--| =|+.|.-|--|-|..++-
T Consensus 22 ~~~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl~areRi~~L~D 68 (285)
T TIGR00515 22 PEGVWTKCPKCGQVLYTKELERNLEVCPKCDHHMRMDARERIESLLD 68 (285)
T ss_pred CCCCeeECCCCcchhhHHHHHhhCCCCCCCCCcCcCCHHHHHHHcee
Confidence 3456999999999998888655555556 799999999999987654
No 16
>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=21.43 E-value=75 Score=24.26 Aligned_cols=26 Identities=27% Similarity=0.635 Sum_probs=19.9
Q ss_pred cCCCCcceecCCCcCCCCCCCCCCcee
Q 014310 38 ACPNCHHVIDNSDVAHEWPGLPRGVKF 64 (427)
Q Consensus 38 ~cp~c~~~id~~~v~~~~~~LPpGfRF 64 (427)
.|..|+++.|-.. ....-++|||-.|
T Consensus 3 ~C~~CgyiYd~~~-Gd~~~~i~pGt~f 28 (50)
T cd00730 3 ECRICGYIYDPAE-GDPDEGIPPGTPF 28 (50)
T ss_pred CCCCCCeEECCCC-CCcccCcCCCCCH
Confidence 6999999998643 4455678888877
No 17
>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=20.98 E-value=76 Score=24.63 Aligned_cols=32 Identities=19% Similarity=0.350 Sum_probs=19.5
Q ss_pred ccCCCcccCCCCcceecCCCcCCCCCCCC-CCce
Q 014310 31 WKSNPTKACPNCHHVIDNSDVAHEWPGLP-RGVK 63 (427)
Q Consensus 31 ~~~~~~~~cp~c~~~id~~~v~~~~~~LP-pGfR 63 (427)
....+.+.||.|++.... ........-| =|+.
T Consensus 23 ~~~~TSq~C~~CG~~~~~-~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 23 DEAYTSQTCPRCGHRNKK-RRSGRVFTCPNCGFE 55 (69)
T ss_pred CCCCCccCccCccccccc-ccccceEEcCCCCCE
Confidence 345578899999998766 3333344444 4554
Done!