Query psy6200
Match_columns 112
No_of_seqs 26 out of 28
Neff 2.2
Searched_HMMs 46136
Date Fri Aug 16 20:18:09 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6200.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6200hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10588 NADH-G_4Fe-4S_3: NADH 64.5 3 6.5E-05 25.1 0.6 15 71-85 8-22 (41)
2 PF13465 zf-H2C2_2: Zinc-finge 48.1 5.8 0.00012 21.4 -0.1 13 74-86 12-24 (26)
3 PF15186 TEX13: Testis-express 45.3 31 0.00067 27.0 3.5 32 12-43 121-152 (152)
4 PF06353 DUF1062: Protein of u 44.6 9 0.0002 28.8 0.5 18 77-94 14-31 (142)
5 PF13912 zf-C2H2_6: C2H2-type 42.0 8 0.00017 20.0 -0.1 11 76-86 1-11 (27)
6 COG1034 NuoG NADH dehydrogenas 41.4 13 0.00028 34.3 1.1 17 69-85 88-104 (693)
7 PF09237 GAGA: GAGA factor; I 34.6 14 0.00031 24.6 0.2 13 72-84 20-32 (54)
8 PHA00097 K protein K 33.1 42 0.00091 22.5 2.2 22 5-26 23-44 (56)
9 PF04967 HTH_10: HTH DNA bindi 30.0 44 0.00095 21.3 1.9 15 12-26 39-53 (53)
10 PF11500 Cut12: Spindle pole b 29.2 45 0.00097 25.7 2.1 14 74-89 61-74 (152)
11 PF12283 Protein_K: Bacterioph 28.3 60 0.0013 21.8 2.3 22 5-26 23-44 (56)
12 PF00301 Rubredoxin: Rubredoxi 28.0 49 0.0011 20.7 1.8 20 65-87 26-45 (47)
13 PF14728 PHTB1_C: PTHB1 C-term 26.7 87 0.0019 26.6 3.6 22 10-31 223-244 (377)
14 PF14120 YhzD: YhzD-like prote 25.5 16 0.00035 24.8 -0.8 28 55-82 22-52 (61)
15 PF13719 zinc_ribbon_5: zinc-r 24.9 28 0.0006 20.3 0.3 19 69-87 18-36 (37)
16 PF07111 HCR: Alpha helical co 24.8 2E+02 0.0044 27.5 5.8 33 9-41 633-665 (739)
17 PF13695 zf-3CxxC: Zinc-bindin 24.3 36 0.00078 23.2 0.8 14 77-90 6-19 (98)
18 PF07818 HCNGP: HCNGP-like pro 24.1 83 0.0018 22.0 2.5 20 7-26 71-90 (96)
19 PF08614 ATG16: Autophagy prot 23.5 1.7E+02 0.0036 21.9 4.2 31 11-41 154-184 (194)
20 smart00355 ZnF_C2H2 zinc finge 23.2 41 0.00088 15.8 0.6 11 77-87 1-11 (26)
21 PF14353 CpXC: CpXC protein 22.7 42 0.00091 23.2 0.9 14 75-88 37-50 (128)
22 PF13945 NST1: Salt tolerance 21.9 29 0.00062 27.5 -0.1 15 73-87 138-152 (190)
23 PF14803 Nudix_N_2: Nudix N-te 21.8 44 0.00095 19.7 0.7 18 79-96 3-20 (34)
24 PRK07569 bidirectional hydroge 21.6 1.7E+02 0.0037 22.4 4.0 65 14-85 78-154 (234)
25 KOG4102|consensus 21.5 1.6E+02 0.0034 22.4 3.7 30 79-108 90-119 (121)
26 PF12269 zf-CpG_bind_C: CpG bi 21.4 2.4E+02 0.0051 23.2 5.0 35 14-48 35-69 (236)
27 PF06970 RepA_N: Replication i 21.3 51 0.0011 22.1 1.0 25 5-29 50-74 (76)
28 TIGR01973 NuoG NADH-quinone ox 20.8 49 0.0011 28.5 1.1 17 69-85 86-102 (603)
29 PF00096 zf-C2H2: Zinc finger, 20.8 29 0.00062 17.2 -0.2 11 77-87 1-11 (23)
30 PF13894 zf-C2H2_4: C2H2-type 20.4 33 0.00071 16.2 -0.0 12 77-88 1-12 (24)
31 PF09538 FYDLN_acid: Protein o 20.2 1.1E+02 0.0023 22.0 2.5 19 72-90 22-40 (108)
32 cd00730 rubredoxin Rubredoxin; 20.0 67 0.0015 20.3 1.3 19 67-88 28-46 (50)
No 1
>PF10588 NADH-G_4Fe-4S_3: NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; InterPro: IPR019574 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry describes the G subunit (one of 14 subunits, A to N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This family does not contain related subunits from formate dehydrogenase complexes. This entry represents the iron-sulphur binding domain of the G subunit.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3M9S_C 2FUG_L 3IAS_L 2YBB_3 3IAM_3 3I9V_3.
Probab=64.52 E-value=3 Score=25.06 Aligned_cols=15 Identities=33% Similarity=0.924 Sum_probs=7.5
Q ss_pred cccCCCcccccCCCc
Q psy6200 71 FIQNHPHRCLQCGTS 85 (112)
Q Consensus 71 ~~~n~~h~~~~~~~~ 85 (112)
-..||||-|..|.++
T Consensus 8 ll~~H~~dC~~C~~~ 22 (41)
T PF10588_consen 8 LLANHPLDCPTCDKN 22 (41)
T ss_dssp HHTT----TTT-TTG
T ss_pred HHhCCCCcCcCCCCC
Confidence 357999999999864
No 2
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=48.07 E-value=5.8 Score=21.36 Aligned_cols=13 Identities=38% Similarity=1.053 Sum_probs=10.1
Q ss_pred CCCcccccCCCcc
Q psy6200 74 NHPHRCLQCGTSW 86 (112)
Q Consensus 74 n~~h~~~~~~~~~ 86 (112)
.-||.|..||.+-
T Consensus 12 ~k~~~C~~C~k~F 24 (26)
T PF13465_consen 12 EKPYKCPYCGKSF 24 (26)
T ss_dssp SSSEEESSSSEEE
T ss_pred CCCCCCCCCcCee
Confidence 4579999999753
No 3
>PF15186 TEX13: Testis-expressed sequence 13 protein family
Probab=45.30 E-value=31 Score=26.98 Aligned_cols=32 Identities=22% Similarity=0.206 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHHHHHhhchhHHHHHHhhhcC
Q psy6200 12 CFQSVLKSSQRKLLKASRDKSFLLDRLLEYEK 43 (112)
Q Consensus 12 cfq~eLR~aQrKLLkvsRDKsFLLDRLLqYE~ 43 (112)
--.-+|+-+|-.|-+|-+++..|--|||+.|.
T Consensus 121 eaa~qL~~~~a~L~~v~~ERD~Lr~kLlqae~ 152 (152)
T PF15186_consen 121 EAAFQLQLTQAALQEVQKERDLLRWKLLQAEL 152 (152)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 45567899999999999999999999999873
No 4
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=44.56 E-value=9 Score=28.75 Aligned_cols=18 Identities=22% Similarity=0.488 Sum_probs=13.7
Q ss_pred cccccCCCcccccCCCCC
Q psy6200 77 HRCLQCGTSWANKGPTGT 94 (112)
Q Consensus 77 h~~~~~~~~~~~~~~~~t 94 (112)
+||..||+.|.+--=.++
T Consensus 14 YrC~~C~~TwN~ti~eR~ 31 (142)
T PF06353_consen 14 YRCEKCDYTWNMTIFERV 31 (142)
T ss_pred EEcccCcCccccceEeec
Confidence 689999999987544433
No 5
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=42.04 E-value=8 Score=20.02 Aligned_cols=11 Identities=36% Similarity=1.223 Sum_probs=8.8
Q ss_pred CcccccCCCcc
Q psy6200 76 PHRCLQCGTSW 86 (112)
Q Consensus 76 ~h~~~~~~~~~ 86 (112)
||+|..|+..-
T Consensus 1 ~~~C~~C~~~F 11 (27)
T PF13912_consen 1 PFECDECGKTF 11 (27)
T ss_dssp SEEETTTTEEE
T ss_pred CCCCCccCCcc
Confidence 68999998754
No 6
>COG1034 NuoG NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75 kD subunit (chain G) [Energy production and conversion]
Probab=41.39 E-value=13 Score=34.25 Aligned_cols=17 Identities=29% Similarity=0.729 Sum_probs=13.7
Q ss_pred cccccCCCcccccCCCc
Q psy6200 69 YLFIQNHPHRCLQCGTS 85 (112)
Q Consensus 69 ~~~~~n~~h~~~~~~~~ 85 (112)
+.-.-||||.|..|+..
T Consensus 88 E~LLiNHPlDCpiCD~g 104 (693)
T COG1034 88 EFLLINHPLDCPVCDKG 104 (693)
T ss_pred HHHHhcCCCCCCccCCC
Confidence 44456999999999875
No 7
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=34.57 E-value=14 Score=24.60 Aligned_cols=13 Identities=31% Similarity=0.846 Sum_probs=6.6
Q ss_pred ccCCCcccccCCC
Q psy6200 72 IQNHPHRCLQCGT 84 (112)
Q Consensus 72 ~~n~~h~~~~~~~ 84 (112)
..++||.|..||.
T Consensus 20 ~S~~PatCP~C~a 32 (54)
T PF09237_consen 20 QSEQPATCPICGA 32 (54)
T ss_dssp TTS--EE-TTT--
T ss_pred ccCCCCCCCcchh
Confidence 3578999999986
No 8
>PHA00097 K protein K
Probab=33.09 E-value=42 Score=22.52 Aligned_cols=22 Identities=41% Similarity=0.353 Sum_probs=17.6
Q ss_pred ehhhhhHHHHHHHHHHHHHHHH
Q psy6200 5 FIFQENECFQSVLKSSQRKLLK 26 (112)
Q Consensus 5 fLvYEnEcfq~eLR~aQrKLLk 26 (112)
.|+-|||-.|.+|.+..+-||.
T Consensus 23 gllveneeiqs~lk~le~lll~ 44 (56)
T PHA00097 23 GLLVENEEIQSQLKKLEKLLLC 44 (56)
T ss_pred cceeccHHHHHHHHHHHHHHhh
Confidence 4667899999999988876663
No 9
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=29.98 E-value=44 Score=21.30 Aligned_cols=15 Identities=27% Similarity=0.516 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHHHHH
Q psy6200 12 CFQSVLKSSQRKLLK 26 (112)
Q Consensus 12 cfq~eLR~aQrKLLk 26 (112)
-|.+-||++++||++
T Consensus 39 t~~~~LRrae~kli~ 53 (53)
T PF04967_consen 39 TVSEHLRRAERKLIE 53 (53)
T ss_pred HHHHHHHHHHHHHhC
Confidence 367889999999974
No 10
>PF11500 Cut12: Spindle pole body formation-associated protein; InterPro: IPR021589 This is the central coiled-coil region of cut12 also found in other fungi, barring S. cerevisiae. The full protein has two predicted coiled-coil regions, and one consensus phosphorylation site for p34cdc2 and two for MAP kinase. During Schizosaccharomyces japonicus yFS275 mitosis, the duplicated spindle pole bodies (SPBs) nucleate microtubule arrays that interdigitate to form the mitotic spindle. Cut12 is localised to the SPB throughout the cell cycle, predominantly around the inner face of the interphase SPB, adjacent to the nucleus []. Cut12 associates with Fin1 and is important in this context for the activity of Plo1 [].
Probab=29.15 E-value=45 Score=25.70 Aligned_cols=14 Identities=43% Similarity=0.933 Sum_probs=10.1
Q ss_pred CCCcccccCCCccccc
Q psy6200 74 NHPHRCLQCGTSWANK 89 (112)
Q Consensus 74 n~~h~~~~~~~~~~~~ 89 (112)
|-|| |++|.-|+..
T Consensus 61 ~eP~--SqSGkYWK~e 74 (152)
T PF11500_consen 61 NEPH--SQSGKYWKEE 74 (152)
T ss_pred CCCc--ccccchHHHH
Confidence 4556 7779999853
No 11
>PF12283 Protein_K: Bacteriophage protein K; InterPro: IPR020962 This family of proteins is found in the microviridae (isometric ssDNA phages) and are approximately 60 amino acids in length. The function of these proteins are unknown. In phi X174 site-directed mutagenesis of gene K produces small plaques on su- hosts. The mutant phage has an identical latent period, but a more reduced burst size than that of the wild-type phi X174. The reduced burst size in the gene K mutant suggests that the gene K protein, although not essential, has a role in increasing infectivity by increasing the burst size three to six fold [].
Probab=28.27 E-value=60 Score=21.83 Aligned_cols=22 Identities=41% Similarity=0.437 Sum_probs=17.3
Q ss_pred ehhhhhHHHHHHHHHHHHHHHH
Q psy6200 5 FIFQENECFQSVLKSSQRKLLK 26 (112)
Q Consensus 5 fLvYEnEcfq~eLR~aQrKLLk 26 (112)
.|+-|||-.|.+|.+..+-||+
T Consensus 23 gllvene~i~~~l~~le~lllr 44 (56)
T PF12283_consen 23 GLLVENEEIQSQLKQLEKLLLR 44 (56)
T ss_pred ccccccHHHHHHHHHHHHHHhh
Confidence 4667899999999888776664
No 12
>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=28.01 E-value=49 Score=20.73 Aligned_cols=20 Identities=25% Similarity=0.381 Sum_probs=11.5
Q ss_pred cCcccccccCCCcccccCCCccc
Q psy6200 65 VDFRYLFIQNHPHRCLQCGTSWA 87 (112)
Q Consensus 65 ~~~~~~~~~n~~h~~~~~~~~~~ 87 (112)
+++.+++-+ .+|..||.+|.
T Consensus 26 t~F~~Lp~~---w~CP~C~a~K~ 45 (47)
T PF00301_consen 26 TPFEDLPDD---WVCPVCGAPKS 45 (47)
T ss_dssp --GGGS-TT----B-TTTSSBGG
T ss_pred CCHHHCCCC---CcCcCCCCccc
Confidence 345577666 89999998874
No 13
>PF14728 PHTB1_C: PTHB1 C-terminus
Probab=26.72 E-value=87 Score=26.63 Aligned_cols=22 Identities=27% Similarity=0.326 Sum_probs=19.2
Q ss_pred hHHHHHHHHHHHHHHHHHhhch
Q psy6200 10 NECFQSVLKSSQRKLLKASRDK 31 (112)
Q Consensus 10 nEcfq~eLR~aQrKLLkvsRDK 31 (112)
-++...++|..||+||---|||
T Consensus 223 L~~~a~QfRaIQrrlL~r~kd~ 244 (377)
T PF14728_consen 223 LDERAQQFRAIQRRLLTRFKDK 244 (377)
T ss_pred HHHHHHHHHHHHHHHHHHhccC
Confidence 3567889999999999999998
No 14
>PF14120 YhzD: YhzD-like protein
Probab=25.51 E-value=16 Score=24.76 Aligned_cols=28 Identities=25% Similarity=0.409 Sum_probs=19.1
Q ss_pred ccCCcccccccCcc---cccccCCCcccccC
Q psy6200 55 TESSDEEHKRVDFR---YLFIQNHPHRCLQC 82 (112)
Q Consensus 55 T~SSd~e~~~~~~~---~~~~~n~~h~~~~~ 82 (112)
+.++|++.+..-.. +-..-+|+|||-+.
T Consensus 22 eA~~D~eAK~~G~~~L~Ek~~~~~THR~v~~ 52 (61)
T PF14120_consen 22 EAANDEEAKEIGEQKLKEKGYEEKTHRCVSS 52 (61)
T ss_pred ecCCHHHHHHHHHHHHHHCChhhcceeeeCC
Confidence 44666666655444 66778999999754
No 15
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=24.93 E-value=28 Score=20.27 Aligned_cols=19 Identities=26% Similarity=0.525 Sum_probs=12.5
Q ss_pred cccccCCCcccccCCCccc
Q psy6200 69 YLFIQNHPHRCLQCGTSWA 87 (112)
Q Consensus 69 ~~~~~n~~h~~~~~~~~~~ 87 (112)
.+....-.-||+.|+..|.
T Consensus 18 ~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 18 KLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred HcccCCcEEECCCCCcEee
Confidence 3444445578999988763
No 16
>PF07111 HCR: Alpha helical coiled-coil rod protein (HCR); InterPro: IPR009800 This family consists of several mammalian alpha helical coiled-coil rod HCR proteins. The function of HCR is unknown but it has been implicated in psoriasis in humans and is thought to affect keratinocyte proliferation [].; GO: 0030154 cell differentiation, 0005634 nucleus, 0005737 cytoplasm
Probab=24.76 E-value=2e+02 Score=27.48 Aligned_cols=33 Identities=27% Similarity=0.402 Sum_probs=28.5
Q ss_pred hhHHHHHHHHHHHHHHHHHhhchhHHHHHHhhh
Q psy6200 9 ENECFQSVLKSSQRKLLKASRDKSFLLDRLLEY 41 (112)
Q Consensus 9 EnEcfq~eLR~aQrKLLkvsRDKsFLLDRLLqY 41 (112)
..|.+.++..+..++|=.+-|||+.+|-||+.-
T Consensus 633 q~e~~~~e~~rl~~rlqelerdkNl~l~rl~~~ 665 (739)
T PF07111_consen 633 QEEARKEEGQRLTQRLQELERDKNLMLQRLLAV 665 (739)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHh
Confidence 356777788889999999999999999999874
No 17
>PF13695 zf-3CxxC: Zinc-binding domain
Probab=24.35 E-value=36 Score=23.25 Aligned_cols=14 Identities=21% Similarity=0.918 Sum_probs=11.4
Q ss_pred cccccCCCcccccC
Q psy6200 77 HRCLQCGTSWANKG 90 (112)
Q Consensus 77 h~~~~~~~~~~~~~ 90 (112)
++|+.|+++|.+.-
T Consensus 6 F~C~~C~~~W~S~~ 19 (98)
T PF13695_consen 6 FQCSKCSRGWTSAK 19 (98)
T ss_pred EECCCCCCCCccCE
Confidence 57999999998764
No 18
>PF07818 HCNGP: HCNGP-like protein; InterPro: IPR012479 This family comprises sequences bearing significant similarity to the mouse transcriptional regulator protein HCNGP (Q02614 from SWISSPROT). This protein is localised to the nucleus and is thought to be involved in the regulation of beta-2-microglobulin genes.
Probab=24.09 E-value=83 Score=22.04 Aligned_cols=20 Identities=15% Similarity=0.124 Sum_probs=16.5
Q ss_pred hhhhHHHHHHHHHHHHHHHH
Q psy6200 7 FQENECFQSVLKSSQRKLLK 26 (112)
Q Consensus 7 vYEnEcfq~eLR~aQrKLLk 26 (112)
.|--|+|-++|+++|++...
T Consensus 71 ~~~~~~y~e~L~k~Qk~~~~ 90 (96)
T PF07818_consen 71 GFPEEDYYEELAKAQKEEME 90 (96)
T ss_pred CCCHHHHHHHHHHHHHHHHH
Confidence 35679999999999998753
No 19
>PF08614 ATG16: Autophagy protein 16 (ATG16); InterPro: IPR013923 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. This entry represents auotphagy protein 16 (Apg16), which is required for the function of the Apg12p-Apg5p conjugate.; PDB: 3A7O_D 3A7P_B.
Probab=23.55 E-value=1.7e+02 Score=21.91 Aligned_cols=31 Identities=23% Similarity=0.312 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHHHHHhhchhHHHHHHhhh
Q psy6200 11 ECFQSVLKSSQRKLLKASRDKSFLLDRLLEY 41 (112)
Q Consensus 11 Ecfq~eLR~aQrKLLkvsRDKsFLLDRLLqY 41 (112)
..++-++-.++.|+=++..+..=|++|+|++
T Consensus 154 ~~L~l~~~~~e~k~~~l~~En~~Lv~Rwm~~ 184 (194)
T PF08614_consen 154 QALQLQLNMLEEKLRKLEEENRELVERWMQR 184 (194)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344455566678888999999999999986
No 20
>smart00355 ZnF_C2H2 zinc finger.
Probab=23.18 E-value=41 Score=15.82 Aligned_cols=11 Identities=36% Similarity=1.023 Sum_probs=7.7
Q ss_pred cccccCCCccc
Q psy6200 77 HRCLQCGTSWA 87 (112)
Q Consensus 77 h~~~~~~~~~~ 87 (112)
++|..|+.+-.
T Consensus 1 ~~C~~C~~~f~ 11 (26)
T smart00355 1 YRCPECGKVFK 11 (26)
T ss_pred CCCCCCcchhC
Confidence 57888986543
No 21
>PF14353 CpXC: CpXC protein
Probab=22.70 E-value=42 Score=23.19 Aligned_cols=14 Identities=21% Similarity=0.650 Sum_probs=11.0
Q ss_pred CCcccccCCCcccc
Q psy6200 75 HPHRCLQCGTSWAN 88 (112)
Q Consensus 75 ~~h~~~~~~~~~~~ 88 (112)
+.|.|.+||..-..
T Consensus 37 ~~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 37 FSFTCPSCGHKFRL 50 (128)
T ss_pred CEEECCCCCCceec
Confidence 45899999987654
No 22
>PF13945 NST1: Salt tolerance down-regulator
Probab=21.95 E-value=29 Score=27.48 Aligned_cols=15 Identities=33% Similarity=0.740 Sum_probs=12.3
Q ss_pred cCCCcccccCCCccc
Q psy6200 73 QNHPHRCLQCGTSWA 87 (112)
Q Consensus 73 ~n~~h~~~~~~~~~~ 87 (112)
|.|.-.|+.||+...
T Consensus 138 q~h~C~C~vCgr~~~ 152 (190)
T PF13945_consen 138 QKHSCSCSVCGRKRT 152 (190)
T ss_pred hccCcccHHHhchhh
Confidence 568889999999863
No 23
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=21.77 E-value=44 Score=19.73 Aligned_cols=18 Identities=39% Similarity=0.767 Sum_probs=8.1
Q ss_pred cccCCCcccccCCCCCCC
Q psy6200 79 CLQCGTSWANKGPTGTFR 96 (112)
Q Consensus 79 ~~~~~~~~~~~~~~~t~~ 96 (112)
|++||..-..+.|.|-.+
T Consensus 3 C~~CG~~l~~~ip~gd~r 20 (34)
T PF14803_consen 3 CPQCGGPLERRIPEGDDR 20 (34)
T ss_dssp -TTT--B-EEE--TT-SS
T ss_pred cccccChhhhhcCCCCCc
Confidence 899999887777766543
No 24
>PRK07569 bidirectional hydrogenase complex protein HoxU; Validated
Probab=21.63 E-value=1.7e+02 Score=22.43 Aligned_cols=65 Identities=14% Similarity=0.045 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHHHhhchhHH------------HHHHhhhcCCCCCCCCCcccccCCcccccccCcccccccCCCccccc
Q psy6200 14 QSVLKSSQRKLLKASRDKSFL------------LDRLLEYEKPVWSDSSDGEATESSDEEHKRVDFRYLFIQNHPHRCLQ 81 (112)
Q Consensus 14 q~eLR~aQrKLLkvsRDKsFL------------LDRLLqYE~v~~~~SSDsdaT~SSd~e~~~~~~~~~~~~n~~h~~~~ 81 (112)
..+++..++.+|....+.+.+ |..+..+=.+. .. .- +.... ...++.+.+.+.-.+.||-.
T Consensus 78 ~~~~~~~rk~~l~~ll~~h~~~C~~C~~~g~C~Lq~~a~~~g~~-~~-~~---~~~~~--~~~~d~s~~~i~~d~~kCi~ 150 (234)
T PRK07569 78 TPRLQEYRRMIVELLFAEGNHVCAVCVANGNCELQDLAIEVGMD-HV-RF---PYLFP--RRPVDISHPRFGIDHNRCVL 150 (234)
T ss_pred CHHHHHHHHHHHHHHHHhccccCcccCCCCCcHHHHHHHHhCCC-Cc-cc---CcccC--CcccccCCCcEEeehhhCcC
Confidence 367888888888876665444 66665544444 11 10 00011 11222333444445689999
Q ss_pred CCCc
Q psy6200 82 CGTS 85 (112)
Q Consensus 82 ~~~~ 85 (112)
||+=
T Consensus 151 Cg~C 154 (234)
T PRK07569 151 CTRC 154 (234)
T ss_pred ccHH
Confidence 9873
No 25
>KOG4102|consensus
Probab=21.51 E-value=1.6e+02 Score=22.44 Aligned_cols=30 Identities=30% Similarity=0.511 Sum_probs=19.3
Q ss_pred cccCCCcccccCCCCCCCCCCCCCCCCCCC
Q psy6200 79 CLQCGTSWANKGPTGTFRGPGAASLPKSPK 108 (112)
Q Consensus 79 ~~~~~~~~~~~~~~~t~~~p~~~~~p~~p~ 108 (112)
|..|--..++..|.|.--+|....+|.-||
T Consensus 90 crgh~~~~~~~~p~~~~~~~d~~~~~~e~k 119 (121)
T KOG4102|consen 90 CRGHTEKRKNAKPNGPEIGPDYSQPPQEPK 119 (121)
T ss_pred cccccchhhccCCCCCCCCCccccCCcccc
Confidence 666666666667777766666655555554
No 26
>PF12269 zf-CpG_bind_C: CpG binding protein zinc finger C terminal domain; InterPro: IPR022056 This domain family is found in eukaryotes, and is approximately 240 amino acids in length. This domain is the zinc finger domain of a CpG binding DNA methyltransferase protein. It contains a CxxC motif which forms the zinc finger and binds to DNA.
Probab=21.38 E-value=2.4e+02 Score=23.19 Aligned_cols=35 Identities=6% Similarity=-0.023 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHHHhhchhHHHHHHhhhcCCCCCC
Q psy6200 14 QSVLKSSQRKLLKASRDKSFLLDRLLEYEKPVWSD 48 (112)
Q Consensus 14 q~eLR~aQrKLLkvsRDKsFLLDRLLqYE~v~~~~ 48 (112)
..+...++.+|..+.+.-..|-.=+..-....+..
T Consensus 35 r~kq~~v~~~l~eLe~~~~el~~~i~~~k~~~~~~ 69 (236)
T PF12269_consen 35 RKKQQKVRNRLQELEKRFKELEAIIARAKQFTVDQ 69 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCc
Confidence 33444555666666665555544444444444333
No 27
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids []. Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=21.29 E-value=51 Score=22.07 Aligned_cols=25 Identities=24% Similarity=0.401 Sum_probs=21.7
Q ss_pred ehhhhhHHHHHHHHHHHHHHHHHhh
Q psy6200 5 FIFQENECFQSVLKSSQRKLLKASR 29 (112)
Q Consensus 5 fLvYEnEcfq~eLR~aQrKLLkvsR 29 (112)
|++|.+|-+++.|...+.++.++-+
T Consensus 50 Yi~~s~eel~~~L~~s~~tv~~~~k 74 (76)
T PF06970_consen 50 YIIFSIEELMELLNCSKSTVIKAKK 74 (76)
T ss_pred EEEeeHHHHHHHHCCCHHHHHHHHH
Confidence 7899999999999999988887654
No 28
>TIGR01973 NuoG NADH-quinone oxidoreductase, chain G. This model represents the G subunit (one of 14: A-N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This model excludes related subunits from formate dehydrogenase complexes.
Probab=20.83 E-value=49 Score=28.54 Aligned_cols=17 Identities=29% Similarity=0.720 Sum_probs=14.4
Q ss_pred cccccCCCcccccCCCc
Q psy6200 69 YLFIQNHPHRCLQCGTS 85 (112)
Q Consensus 69 ~~~~~n~~h~~~~~~~~ 85 (112)
++-.-||||.|..|+..
T Consensus 86 e~ll~~h~~dC~~C~~~ 102 (603)
T TIGR01973 86 EFLLINHPLDCPICDQG 102 (603)
T ss_pred HHHHhcCCCCCCcCCCC
Confidence 56668999999999975
No 29
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=20.81 E-value=29 Score=17.20 Aligned_cols=11 Identities=36% Similarity=0.996 Sum_probs=8.1
Q ss_pred cccccCCCccc
Q psy6200 77 HRCLQCGTSWA 87 (112)
Q Consensus 77 h~~~~~~~~~~ 87 (112)
|+|..||++-.
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 57899987644
No 30
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=20.44 E-value=33 Score=16.25 Aligned_cols=12 Identities=33% Similarity=0.916 Sum_probs=6.9
Q ss_pred cccccCCCcccc
Q psy6200 77 HRCLQCGTSWAN 88 (112)
Q Consensus 77 h~~~~~~~~~~~ 88 (112)
|.|..||..-.+
T Consensus 1 ~~C~~C~~~~~~ 12 (24)
T PF13894_consen 1 FQCPICGKSFRS 12 (24)
T ss_dssp EE-SSTS-EESS
T ss_pred CCCcCCCCcCCc
Confidence 578899876543
No 31
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=20.21 E-value=1.1e+02 Score=22.05 Aligned_cols=19 Identities=26% Similarity=0.740 Sum_probs=14.7
Q ss_pred ccCCCcccccCCCcccccC
Q psy6200 72 IQNHPHRCLQCGTSWANKG 90 (112)
Q Consensus 72 ~~n~~h~~~~~~~~~~~~~ 90 (112)
.|..|-.|..||+.+..-.
T Consensus 22 Lnk~PivCP~CG~~~~~~~ 40 (108)
T PF09538_consen 22 LNKDPIVCPKCGTEFPPEP 40 (108)
T ss_pred CCCCCccCCCCCCccCccc
Confidence 3557788999999987763
No 32
>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=20.05 E-value=67 Score=20.27 Aligned_cols=19 Identities=26% Similarity=0.428 Sum_probs=12.7
Q ss_pred cccccccCCCcccccCCCcccc
Q psy6200 67 FRYLFIQNHPHRCLQCGTSWAN 88 (112)
Q Consensus 67 ~~~~~~~n~~h~~~~~~~~~~~ 88 (112)
+.+++.. .+|..||..|..
T Consensus 28 f~~Lp~~---w~CP~C~a~K~~ 46 (50)
T cd00730 28 FEDLPDD---WVCPVCGAGKDD 46 (50)
T ss_pred HhHCCCC---CCCCCCCCcHHH
Confidence 3355554 789999877653
Done!