Query 032109
Match_columns 147
No_of_seqs 64 out of 66
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 09:42:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032109.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032109hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12678 zf-rbx1: RING-H2 zinc 63.7 3.7 8E-05 28.2 1.0 13 133-145 17-29 (73)
2 KOG4628 Predicted E3 ubiquitin 47.9 6.2 0.00014 35.3 0.1 11 136-146 230-240 (348)
3 KOG2164 Predicted E3 ubiquitin 43.3 10 0.00022 35.7 0.7 11 135-145 186-196 (513)
4 PF02132 RecR: RecR protein; 41.3 6.5 0.00014 24.3 -0.6 11 134-144 28-38 (41)
5 PHA02929 N1R/p28-like protein; 34.4 19 0.00042 30.4 1.0 12 134-145 173-184 (238)
6 PF08274 PhnA_Zn_Ribbon: PhnA 33.4 11 0.00024 22.4 -0.4 11 135-145 19-29 (30)
7 PHA02926 zinc finger-like prot 30.5 23 0.0005 30.5 0.8 12 133-144 168-179 (242)
8 PF12861 zf-Apc11: Anaphase-pr 30.1 21 0.00045 26.1 0.4 13 134-146 20-32 (85)
9 COG0353 RecR Recombinational D 29.7 26 0.00057 29.2 1.0 13 133-145 64-76 (198)
10 PF11238 DUF3039: Protein of u 29.3 12 0.00026 25.7 -0.9 12 135-146 44-55 (58)
11 KOG0320 Predicted E3 ubiquitin 29.2 21 0.00046 29.6 0.4 14 133-146 129-142 (187)
12 PF14369 zf-RING_3: zinc-finge 29.1 37 0.0008 20.6 1.3 14 132-145 17-31 (35)
13 cd00729 rubredoxin_SM Rubredox 26.2 29 0.00063 20.8 0.5 9 135-143 18-26 (34)
14 PRK06393 rpoE DNA-directed RNA 24.6 35 0.00076 23.8 0.7 11 134-144 16-26 (64)
15 PF05605 zf-Di19: Drought indu 23.8 32 0.0007 21.9 0.4 11 134-144 30-40 (54)
16 cd00350 rubredoxin_like Rubred 23.7 41 0.00089 19.7 0.8 10 134-143 16-25 (33)
17 PF06484 Ten_N: Teneurin Intra 23.2 82 0.0018 28.7 3.0 32 37-71 321-352 (370)
18 KOG4021 Mitochondrial ribosoma 22.8 34 0.00073 29.1 0.5 11 136-146 109-119 (239)
19 PRK08351 DNA-directed RNA poly 20.7 47 0.001 22.8 0.8 10 134-143 14-23 (61)
No 1
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=63.73 E-value=3.7 Score=28.15 Aligned_cols=13 Identities=38% Similarity=0.874 Sum_probs=10.2
Q ss_pred CcccCCCcccCcc
Q 032109 133 EEEDTCPICLEGV 145 (147)
Q Consensus 133 EeEDVCPtCLEEY 145 (147)
.++|.|.||++.+
T Consensus 17 ~~~d~C~IC~~~l 29 (73)
T PF12678_consen 17 IADDNCAICREPL 29 (73)
T ss_dssp SCCSBETTTTSBT
T ss_pred CcCCcccccChhh
Confidence 3455699999988
No 2
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=47.93 E-value=6.2 Score=35.31 Aligned_cols=11 Identities=64% Similarity=1.186 Sum_probs=9.9
Q ss_pred cCCCcccCccc
Q 032109 136 DTCPICLEGVV 146 (147)
Q Consensus 136 DVCPtCLEEYt 146 (147)
|.|-||||+|.
T Consensus 230 ~~CaIClEdY~ 240 (348)
T KOG4628|consen 230 DTCAICLEDYE 240 (348)
T ss_pred ceEEEeecccc
Confidence 49999999996
No 3
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=43.29 E-value=10 Score=35.66 Aligned_cols=11 Identities=55% Similarity=1.165 Sum_probs=9.5
Q ss_pred ccCCCcccCcc
Q 032109 135 EDTCPICLEGV 145 (147)
Q Consensus 135 EDVCPtCLEEY 145 (147)
+..||||||+-
T Consensus 186 ~~~CPICL~~~ 196 (513)
T KOG2164|consen 186 DMQCPICLEPP 196 (513)
T ss_pred CCcCCcccCCC
Confidence 68899999974
No 4
>PF02132 RecR: RecR protein; InterPro: IPR023628 The bacterial protein RecR seems to play a role in a recombinational process of DNA repair []. It may act with RecF and RecO. RecR's structure consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif []. This entry represents the C4-type zinc finger.; PDB: 1VDD_D 2V1C_B.
Probab=41.30 E-value=6.5 Score=24.35 Aligned_cols=11 Identities=55% Similarity=1.135 Sum_probs=7.1
Q ss_pred cccCCCcccCc
Q 032109 134 EEDTCPICLEG 144 (147)
Q Consensus 134 eEDVCPtCLEE 144 (147)
|+|+|+||...
T Consensus 28 e~~~C~IC~d~ 38 (41)
T PF02132_consen 28 EEDPCEICSDP 38 (41)
T ss_dssp SSSS-HHHH-T
T ss_pred CCCcCcCCCCC
Confidence 46799999865
No 5
>PHA02929 N1R/p28-like protein; Provisional
Probab=34.42 E-value=19 Score=30.45 Aligned_cols=12 Identities=42% Similarity=1.118 Sum_probs=9.4
Q ss_pred cccCCCcccCcc
Q 032109 134 EEDTCPICLEGV 145 (147)
Q Consensus 134 eEDVCPtCLEEY 145 (147)
+++.||||||++
T Consensus 173 ~~~eC~ICle~~ 184 (238)
T PHA02929 173 KDKECAICMEKV 184 (238)
T ss_pred CCCCCccCCccc
Confidence 346699999974
No 6
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=33.36 E-value=11 Score=22.44 Aligned_cols=11 Identities=27% Similarity=0.416 Sum_probs=7.8
Q ss_pred ccCCCcccCcc
Q 032109 135 EDTCPICLEGV 145 (147)
Q Consensus 135 EDVCPtCLEEY 145 (147)
--|||+|+-|.
T Consensus 19 ~~vCp~C~~ew 29 (30)
T PF08274_consen 19 LLVCPECGHEW 29 (30)
T ss_dssp SEEETTTTEEE
T ss_pred EEeCCcccccC
Confidence 35788887764
No 7
>PHA02926 zinc finger-like protein; Provisional
Probab=30.52 E-value=23 Score=30.45 Aligned_cols=12 Identities=42% Similarity=0.864 Sum_probs=9.4
Q ss_pred CcccCCCcccCc
Q 032109 133 EEEDTCPICLEG 144 (147)
Q Consensus 133 EeEDVCPtCLEE 144 (147)
.+|++|+||||.
T Consensus 168 SkE~eCgICmE~ 179 (242)
T PHA02926 168 SKEKECGICYEV 179 (242)
T ss_pred cCCCCCccCccc
Confidence 346789999985
No 8
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=30.08 E-value=21 Score=26.09 Aligned_cols=13 Identities=31% Similarity=0.644 Sum_probs=10.8
Q ss_pred cccCCCcccCccc
Q 032109 134 EEDTCPICLEGVV 146 (147)
Q Consensus 134 eEDVCPtCLEEYt 146 (147)
++|+|+||...|+
T Consensus 20 ~dd~CgICr~~fd 32 (85)
T PF12861_consen 20 NDDVCGICRMPFD 32 (85)
T ss_pred CCCceeeEecccc
Confidence 4678999998886
No 9
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=29.74 E-value=26 Score=29.24 Aligned_cols=13 Identities=38% Similarity=0.861 Sum_probs=10.6
Q ss_pred CcccCCCcccCcc
Q 032109 133 EEEDTCPICLEGV 145 (147)
Q Consensus 133 EeEDVCPtCLEEY 145 (147)
.|+|+|.||.+++
T Consensus 64 te~d~C~ICsd~~ 76 (198)
T COG0353 64 TESDPCDICSDES 76 (198)
T ss_pred CCCCcCcCcCCcc
Confidence 4567899999876
No 10
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=29.31 E-value=12 Score=25.74 Aligned_cols=12 Identities=33% Similarity=0.481 Sum_probs=9.9
Q ss_pred ccCCCcccCccc
Q 032109 135 EDTCPICLEGVV 146 (147)
Q Consensus 135 EDVCPtCLEEYt 146 (147)
--|||.|-|-|.
T Consensus 44 ~PVCP~Ck~iye 55 (58)
T PF11238_consen 44 FPVCPECKEIYE 55 (58)
T ss_pred CCCCcCHHHHHH
Confidence 578999998775
No 11
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=29.18 E-value=21 Score=29.59 Aligned_cols=14 Identities=50% Similarity=1.049 Sum_probs=10.3
Q ss_pred CcccCCCcccCccc
Q 032109 133 EEEDTCPICLEGVV 146 (147)
Q Consensus 133 EeEDVCPtCLEEYt 146 (147)
|.---|||||+-|.
T Consensus 129 ~~~~~CPiCl~~~s 142 (187)
T KOG0320|consen 129 EGTYKCPICLDSVS 142 (187)
T ss_pred ccccCCCceecchh
Confidence 33356999999874
No 12
>PF14369 zf-RING_3: zinc-finger
Probab=29.08 E-value=37 Score=20.55 Aligned_cols=14 Identities=43% Similarity=0.987 Sum_probs=10.0
Q ss_pred CCcccC-CCcccCcc
Q 032109 132 SEEEDT-CPICLEGV 145 (147)
Q Consensus 132 sEeEDV-CPtCLEEY 145 (147)
..+++| ||.|-.++
T Consensus 17 ~~~~~~~CP~C~~gF 31 (35)
T PF14369_consen 17 SPDSDVACPRCHGGF 31 (35)
T ss_pred CCCCCcCCcCCCCcE
Confidence 356677 99997654
No 13
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=26.17 E-value=29 Score=20.75 Aligned_cols=9 Identities=44% Similarity=1.202 Sum_probs=7.1
Q ss_pred ccCCCcccC
Q 032109 135 EDTCPICLE 143 (147)
Q Consensus 135 EDVCPtCLE 143 (147)
.++||+|.-
T Consensus 18 p~~CP~Cg~ 26 (34)
T cd00729 18 PEKCPICGA 26 (34)
T ss_pred CCcCcCCCC
Confidence 479999974
No 14
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=24.62 E-value=35 Score=23.75 Aligned_cols=11 Identities=36% Similarity=0.742 Sum_probs=7.9
Q ss_pred cccCCCcccCc
Q 032109 134 EEDTCPICLEG 144 (147)
Q Consensus 134 eEDVCPtCLEE 144 (147)
++++||+|--+
T Consensus 16 ~~~~Cp~Cgs~ 26 (64)
T PRK06393 16 PEKTCPVHGDE 26 (64)
T ss_pred CCCcCCCCCCC
Confidence 45699999643
No 15
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=23.75 E-value=32 Score=21.94 Aligned_cols=11 Identities=36% Similarity=0.936 Sum_probs=8.1
Q ss_pred cccCCCcccCc
Q 032109 134 EEDTCPICLEG 144 (147)
Q Consensus 134 eEDVCPtCLEE 144 (147)
..-|||||-..
T Consensus 30 ~~v~CPiC~~~ 40 (54)
T PF05605_consen 30 KNVVCPICSSR 40 (54)
T ss_pred CCccCCCchhh
Confidence 35789999754
No 16
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=23.70 E-value=41 Score=19.73 Aligned_cols=10 Identities=30% Similarity=0.787 Sum_probs=7.7
Q ss_pred cccCCCcccC
Q 032109 134 EEDTCPICLE 143 (147)
Q Consensus 134 eEDVCPtCLE 143 (147)
+..+||+|-.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 5678999954
No 17
>PF06484 Ten_N: Teneurin Intracellular Region; InterPro: IPR009471 Teneurins are a family of phylogenetically conserved transmembrane glycoproteins expressed during pattern formation and morphogenesis []. Originally discovered as ten-m and ten-a in Drosophila melanogaster, the teneurin family is conserved from Caenorhabditis elegans (ten-1) to vertebrates, in which four paralogs exist (teneurin-1 to -4 or odz-1 to -4). Their distinct domain architecture is highly conserved between invertebrate and vertebrate teneurins, particularly in the extracellular part. The intracellular domains of Ten-a, Ten-m/Odz and C. elegans Ten-1 are significantly different, both in size and structure, from the comparable domains of vertebrate teneurins, but the extracellular domains of all of these proteins are remarkably similar. The large C-terminal extracellular domain consists of eight EGF-like repeats (see PDOC00021 from PROSITEDOC), a region of conserved cysteines and unique YD-repeats. The N-terminal intracellular domain of vertebrate teneurins contains two EF-hand-like calcium-binding motifs and two polyproline regions involved in protein-protein interactions, followed by a single-span transmembrane domain. The intracellular domain is linked to the cytoskeleton through its interaction with the adaptor protein CAP/ponsin and can be cleaved near (or possibly in) the transmembrane domain and transported to the nucleus [, ], giving teneurins the potential to act as transcription factors [, ]. There is considerable divergence between intracellular domains of invertebrate and vertebrate teneurins as well as between different invertebrate proteins [, , , , ]. This domain is found in the intracellular N-terminal region of the Teneurin family.; GO: 0007165 signal transduction, 0016021 integral to membrane
Probab=23.24 E-value=82 Score=28.66 Aligned_cols=32 Identities=25% Similarity=0.508 Sum_probs=19.5
Q ss_pred CCCCcccccceeeccCCCCCCCCCCCCCCCCCccc
Q 032109 37 GTASTFTRGLLVDFHLEASTPDTFRAPPLPLPYDV 71 (147)
Q Consensus 37 ~aas~~St~~~vd~nldtS~pDTyr~PP~PlPYDv 71 (147)
|.++++++.. -+.---..-.|-+||||||-..
T Consensus 321 Gttplf~~as---Pgy~~~s~tvYSpPpRplpRnt 352 (370)
T PF06484_consen 321 GTTPLFSTAS---PGYTMTSGTVYSPPPRPLPRNT 352 (370)
T ss_pred CCCcccccCC---CCCcccCCcccCCCCCCCcccc
Confidence 5666665543 1121223456999999999874
No 18
>KOG4021 consensus Mitochondrial ribosomal protein S18b [Translation, ribosomal structure and biogenesis]
Probab=22.79 E-value=34 Score=29.15 Aligned_cols=11 Identities=36% Similarity=1.129 Sum_probs=9.0
Q ss_pred cCCCcccCccc
Q 032109 136 DTCPICLEGVV 146 (147)
Q Consensus 136 DVCPtCLEEYt 146 (147)
-.||||-+||-
T Consensus 109 npCPICRDeyL 119 (239)
T KOG4021|consen 109 NPCPICRDEYL 119 (239)
T ss_pred CCCCccccceE
Confidence 34999999983
No 19
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=20.66 E-value=47 Score=22.83 Aligned_cols=10 Identities=50% Similarity=1.248 Sum_probs=7.3
Q ss_pred cccCCCcccC
Q 032109 134 EEDTCPICLE 143 (147)
Q Consensus 134 eEDVCPtCLE 143 (147)
++++||+|-.
T Consensus 14 ~~~~CP~Cgs 23 (61)
T PRK08351 14 TEDRCPVCGS 23 (61)
T ss_pred CCCcCCCCcC
Confidence 4568999954
Done!