Query psy12937
Match_columns 111
No_of_seqs 111 out of 163
Neff 3.2
Searched_HMMs 46136
Date Fri Aug 16 23:33:07 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12937.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12937hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1763|consensus 100.0 3E-48 6.5E-53 320.4 4.2 90 10-111 92-189 (343)
2 COG5252 Uncharacterized conser 100.0 6.3E-33 1.4E-37 225.7 4.1 76 16-111 97-174 (299)
3 KOG1040|consensus 91.3 0.13 2.7E-06 43.4 1.9 38 7-44 74-119 (325)
4 PF14608 zf-CCCH_2: Zinc finge 90.0 0.16 3.4E-06 26.4 0.9 12 100-111 7-19 (19)
5 PF00642 zf-CCCH: Zinc finger 89.1 0.15 3.2E-06 28.1 0.4 12 16-27 16-27 (27)
6 smart00356 ZnF_C3H1 zinc finge 86.8 0.35 7.5E-06 25.3 1.0 12 16-27 16-27 (27)
7 PF01396 zf-C4_Topoisom: Topoi 80.2 1.2 2.5E-05 26.6 1.5 20 90-109 13-33 (39)
8 COG5175 MOT2 Transcriptional r 79.7 0.73 1.6E-05 40.6 0.6 24 78-110 200-223 (480)
9 KOG1677|consensus 78.8 0.53 1.2E-05 37.5 -0.5 22 80-110 177-199 (332)
10 PF02662 FlpD: Methyl-viologen 58.2 8.8 0.00019 27.6 2.2 27 84-110 43-70 (124)
11 PF13295 DUF4077: Domain of un 53.6 6.1 0.00013 30.7 0.8 23 80-102 25-55 (175)
12 KOG2494|consensus 43.2 14 0.00031 31.8 1.5 25 76-110 33-59 (331)
13 PF14753 DUF4475: Domain of un 37.2 15 0.00033 29.4 0.7 20 87-107 28-48 (196)
14 KOG2295|consensus 37.0 29 0.00064 32.3 2.6 42 60-106 476-517 (648)
15 COG1592 Rubrerythrin [Energy p 34.9 32 0.00069 26.7 2.2 21 85-110 124-144 (166)
16 PF06839 zf-GRF: GRF zinc fing 33.7 26 0.00056 20.9 1.2 17 92-108 19-38 (45)
17 PF07936 Defensin_4: Potassium 33.1 15 0.00032 22.3 0.0 8 97-104 13-22 (34)
18 PF04054 Not1: CCR4-Not comple 32.6 25 0.00055 30.0 1.4 41 59-103 322-362 (379)
19 COG5152 Uncharacterized conser 30.5 18 0.00038 30.1 0.1 12 17-28 155-166 (259)
20 KOG2068|consensus 30.4 43 0.00093 28.8 2.4 44 51-110 140-183 (327)
21 PRK14973 DNA topoisomerase I; 30.0 19 0.00042 34.2 0.3 20 87-108 646-665 (936)
22 PRK07220 DNA topoisomerase I; 29.8 27 0.00058 32.1 1.2 14 93-108 652-665 (740)
23 PF00706 Toxin_4: Anenome neur 28.9 18 0.0004 22.9 -0.0 11 97-107 21-33 (43)
24 PRK11788 tetratricopeptide rep 27.3 26 0.00056 27.1 0.5 7 97-103 367-373 (389)
25 PF09929 DUF2161: Uncharacteri 26.1 29 0.00062 25.9 0.6 9 90-98 92-100 (118)
26 KOG1155|consensus 26.1 52 0.0011 30.2 2.3 34 59-101 167-200 (559)
27 COG0551 TopA Zn-finger domain 24.8 43 0.00093 23.9 1.3 17 92-108 31-48 (140)
28 PF14194 Cys_rich_VLP: Cystein 24.7 46 0.00099 22.1 1.3 11 80-90 42-52 (56)
29 PF02891 zf-MIZ: MIZ/SP-RING z 23.7 50 0.0011 20.4 1.3 15 86-103 32-46 (50)
30 PF13413 HTH_25: Helix-turn-he 23.6 58 0.0013 20.8 1.6 15 82-96 22-36 (62)
31 KOG1813|consensus 23.5 28 0.00061 29.9 0.1 13 16-28 199-211 (313)
32 PF08806 Sep15_SelM: Sep15/Sel 22.8 43 0.00092 22.7 0.9 18 51-68 58-75 (78)
33 KOG2333|consensus 21.7 38 0.00082 31.4 0.6 17 11-29 88-104 (614)
34 KOG1544|consensus 20.2 54 0.0012 29.2 1.2 16 82-97 148-163 (470)
No 1
>KOG1763|consensus
Probab=100.00 E-value=3e-48 Score=320.42 Aligned_cols=90 Identities=63% Similarity=1.272 Sum_probs=85.3
Q ss_pred ceeeee------ccCCccccCCCchhHHHhhhhhhhhcccccCcccchhhhhccHHHHHHHHHhhhcccccCCCcchhhh
Q psy12937 10 YLPCLF------QSGAKCKFSHDLTIERKAEKRSLYVDMRDDGEDVNETMENWDEDKLKEVVEKKHGEAEKKRPTTTIIC 83 (111)
Q Consensus 10 ~~~C~f------~KG~KCKFSHDl~~~rk~eK~dlY~D~Rd~~~e~~dtmd~WDe~kLe~VV~~Khg~~~k~~~~TdiVC 83 (111)
.++|+| +||++|||||||+++|+.+|+|||.|+|++ | ||+++|++||++|||+ ++++|+|||
T Consensus 92 SvvCafFk~g~C~KG~kCKFsHdl~~~~k~eK~dly~d~rde-------m--WD~~kl~~vv~~K~~k---~k~~tdiVC 159 (343)
T KOG1763|consen 92 SVVCAFFKQGTCTKGDKCKFSHDLAVERKKEKIDLYPDTRDE-------M--WDEEKLEEVVLKKHGK---PKPTTDIVC 159 (343)
T ss_pred HHHHHHHhccCCCCCCcccccchHHHhhhccchhccccchhh-------h--hhHHHHHHHHHhhccC---CCCchhHHH
Confidence 478988 689999999999999999999999999975 5 9999999999999994 789999999
Q ss_pred HHHHHHHHccccccceecCCC-C-cccccC
Q psy12937 84 KYFIEAVENSKYGWFWSCPNG-P-CTFENG 111 (111)
Q Consensus 84 K~FLeAvE~~kYGWFW~CPNG-d-C~YRHa 111 (111)
||||||||+|+|||||+|||| + |+||||
T Consensus 160 KfFLeAvE~~kYGWfW~CPnGg~~C~YrHa 189 (343)
T KOG1763|consen 160 KFFLEAVENGKYGWFWECPNGGDKCIYRHA 189 (343)
T ss_pred HHHHHHHhcCCccceeECCCCCCeeeeeec
Confidence 999999999999999999999 6 999997
No 2
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=99.97 E-value=6.3e-33 Score=225.67 Aligned_cols=76 Identities=43% Similarity=0.911 Sum_probs=69.7
Q ss_pred ccCCccccCCCchhHHHhhhhhhhhcccccCcccchhhhhccHHHHHHHHHhhhcccccCCCcchhhhHHHHHHHHcccc
Q psy12937 16 QSGAKCKFSHDLTIERKAEKRSLYVDMRDDGEDVNETMENWDEDKLKEVVEKKHGEAEKKRPTTTIICKYFIEAVENSKY 95 (111)
Q Consensus 16 ~KG~KCKFSHDl~~~rk~eK~dlY~D~Rd~~~e~~dtmd~WDe~kLe~VV~~Khg~~~k~~~~TdiVCK~FLeAvE~~kY 95 (111)
.||+.|||+|+++..|+.||+|||.|.|++++ +++|+ + .+.++||+||||||||+|+|+|
T Consensus 97 ~kg~~ckF~h~~ee~r~~eK~DLYsDvRd~~e--d~pl~----------------k--rP~intd~VCkffieA~e~GkY 156 (299)
T COG5252 97 AKGDACKFAHGKEEARKTEKPDLYSDVRDKEE--DVPLG----------------K--RPWINTDRVCKFFIEAMESGKY 156 (299)
T ss_pred ccCchhhhhcchHHHhhhcccchhhhhhhhhc--cCCcc----------------c--CCCCChhHHHHHHHHHHhcCCc
Confidence 59999999999999999999999999999876 47776 1 1678999999999999999999
Q ss_pred ccceecCCC-C-cccccC
Q psy12937 96 GWFWSCPNG-P-CTFENG 111 (111)
Q Consensus 96 GWFW~CPNG-d-C~YRHa 111 (111)
||||.|||| + |+|+|+
T Consensus 157 gw~W~CPng~~~C~y~H~ 174 (299)
T COG5252 157 GWGWTCPNGNMRCSYIHK 174 (299)
T ss_pred cceeeCCCCCceeeeeec
Confidence 999999999 6 999996
No 3
>KOG1040|consensus
Probab=91.28 E-value=0.13 Score=43.41 Aligned_cols=38 Identities=24% Similarity=0.553 Sum_probs=29.2
Q ss_pred CCCceeeee------ccCCccccCCCchhH--HHhhhhhhhhcccc
Q psy12937 7 YSGYLPCLF------QSGAKCKFSHDLTIE--RKAEKRSLYVDMRD 44 (111)
Q Consensus 7 ~~~~~~C~f------~KG~KCKFSHDl~~~--rk~eK~dlY~D~Rd 44 (111)
-++-++|-+ .||+.|-|+|+.++- |.+-.-++|.+-..
T Consensus 74 ~~~~~vcK~~l~glC~kgD~C~Flhe~~~~k~rec~ff~~~g~c~~ 119 (325)
T KOG1040|consen 74 SRGKVVCKHWLRGLCKKGDQCEFLHEYDLTKMRECKFFSLFGECTN 119 (325)
T ss_pred cCCceeehhhhhhhhhccCcCcchhhhhhccccccccccccccccc
Confidence 456789987 799999999987765 45666777777665
No 4
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=90.04 E-value=0.16 Score=26.43 Aligned_cols=12 Identities=42% Similarity=1.126 Sum_probs=10.3
Q ss_pred ecCCCC-cccccC
Q psy12937 100 SCPNGP-CTFENG 111 (111)
Q Consensus 100 ~CPNGd-C~YRHa 111 (111)
.|+||+ |.|.|.
T Consensus 7 ~C~~~~~C~f~HP 19 (19)
T PF14608_consen 7 NCTNGDNCPFSHP 19 (19)
T ss_pred CCCCCCcCccCCc
Confidence 499995 999994
No 5
>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 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 entry represents C-x8-C-x5-C-x3-H (CCCH) type Zinc finger (Znf) domains. Proteins containing CCCH Znf domains include Znf proteins from eukaryotes involved in cell cycle or growth phase-related regulation, e.g. human TIS11B (butyrate response factor 1), a probable regulatory protein involved in regulating the response to growth factors, and the mouse TTP growth factor-inducible nuclear protein, which has the same function. The mouse TTP protein is induced by growth factors. Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA interactions required for 3' splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3'-untranslated region of various mRNA [, ]. This type of Znf is very often present in two copies. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 1M9O_A 1RGO_A 2CQE_A 2FC6_A 2D9M_A 2E5S_A 2RHK_C 2D9N_A 3D2S_A 3D2Q_C ....
Probab=89.06 E-value=0.15 Score=28.08 Aligned_cols=12 Identities=42% Similarity=0.891 Sum_probs=10.4
Q ss_pred ccCCccccCCCc
Q psy12937 16 QSGAKCKFSHDL 27 (111)
Q Consensus 16 ~KG~KCKFSHDl 27 (111)
..|++|+|+|+.
T Consensus 16 ~~G~~C~f~H~~ 27 (27)
T PF00642_consen 16 PFGDKCRFAHGE 27 (27)
T ss_dssp TTGGGSSSBSSG
T ss_pred CCCCCcCccCCC
Confidence 579999999983
No 6
>smart00356 ZnF_C3H1 zinc finger.
Probab=86.76 E-value=0.35 Score=25.26 Aligned_cols=12 Identities=50% Similarity=1.082 Sum_probs=10.3
Q ss_pred ccCCccccCCCc
Q psy12937 16 QSGAKCKFSHDL 27 (111)
Q Consensus 16 ~KG~KCKFSHDl 27 (111)
..|..|.|+|++
T Consensus 16 ~~g~~C~~~H~~ 27 (27)
T smart00356 16 PYGDRCKFAHPL 27 (27)
T ss_pred CCCCCcCCCCcC
Confidence 579999999984
No 7
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=80.21 E-value=1.2 Score=26.58 Aligned_cols=20 Identities=30% Similarity=0.694 Sum_probs=16.5
Q ss_pred HHccccccceecCCC-Ccccc
Q psy12937 90 VENSKYGWFWSCPNG-PCTFE 109 (111)
Q Consensus 90 vE~~kYGWFW~CPNG-dC~YR 109 (111)
+..+++|.||.|.|= +|.|.
T Consensus 13 ~r~~k~g~F~~Cs~yP~C~~~ 33 (39)
T PF01396_consen 13 LRRGKKGKFLGCSNYPECKYT 33 (39)
T ss_pred EEECCCCCEEECCCCCCcCCe
Confidence 346899999999996 59985
No 8
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=79.71 E-value=0.73 Score=40.63 Aligned_cols=24 Identities=29% Similarity=0.683 Sum_probs=17.9
Q ss_pred cchhhhHHHHHHHHccccccceecCCCCccccc
Q psy12937 78 TTTIICKYFIEAVENSKYGWFWSCPNGPCTFEN 110 (111)
Q Consensus 78 ~TdiVCK~FLeAvE~~kYGWFW~CPNGdC~YRH 110 (111)
-|..-|-.+|.- =+|||++|||-|
T Consensus 200 GTTKYCtsYLRn---------~~CpNp~CMyLH 223 (480)
T COG5175 200 GTTKYCTSYLRN---------AVCPNPDCMYLH 223 (480)
T ss_pred CchHHHHHHHcC---------CCCCCCCeeeec
Confidence 355667766642 489999999998
No 9
>KOG1677|consensus
Probab=78.76 E-value=0.53 Score=37.46 Aligned_cols=22 Identities=36% Similarity=0.859 Sum_probs=17.7
Q ss_pred hhhhHHHHHHHHccccccceecCCCC-ccccc
Q psy12937 80 TIICKYFIEAVENSKYGWFWSCPNGP-CTFEN 110 (111)
Q Consensus 80 diVCK~FLeAvE~~kYGWFW~CPNGd-C~YRH 110 (111)
.+.|.+|..- | .||.|. |+|.|
T Consensus 177 t~lC~~f~~t------G---~C~yG~rC~F~H 199 (332)
T KOG1677|consen 177 TKLCPKFQKT------G---LCKYGSRCRFIH 199 (332)
T ss_pred CcCCCccccC------C---CCCCCCcCeecC
Confidence 4679999764 3 799996 99998
No 10
>PF02662 FlpD: Methyl-viologen-reducing hydrogenase, delta subunit; InterPro: IPR003813 Methyl-viologen-reducing hydrogenase (MVH) is one of the enzymes involved in methanogenesis and coded in the mth-flp-mvh-mrt cluster of methane genes in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) []. No specific functions have been assigned to the delta subunit.; GO: 0015948 methanogenesis, 0055114 oxidation-reduction process
Probab=58.20 E-value=8.8 Score=27.59 Aligned_cols=27 Identities=22% Similarity=0.623 Sum_probs=22.5
Q ss_pred HHHHHHHHccccccc-eecCCCCccccc
Q psy12937 84 KYFIEAVENSKYGWF-WSCPNGPCTFEN 110 (111)
Q Consensus 84 K~FLeAvE~~kYGWF-W~CPNGdC~YRH 110 (111)
.+.|+|+++|-=|=+ .-||.|+|+|++
T Consensus 43 ~~il~Af~~GADGV~V~gC~~g~Ch~~~ 70 (124)
T PF02662_consen 43 EFILRAFEKGADGVLVAGCHPGDCHYRE 70 (124)
T ss_pred HHHHHHHHcCCCEEEEeCCCCCCCCcch
Confidence 578999999987744 479998999975
No 11
>PF13295 DUF4077: Domain of unknown function (DUF4077)
Probab=53.59 E-value=6.1 Score=30.71 Aligned_cols=23 Identities=35% Similarity=1.084 Sum_probs=20.5
Q ss_pred hhhhHHHHHHHHcccccc--------ceecC
Q psy12937 80 TIICKYFIEAVENSKYGW--------FWSCP 102 (111)
Q Consensus 80 diVCK~FLeAvE~~kYGW--------FW~CP 102 (111)
--+|.+||--|.-|-||. ||+|.
T Consensus 25 iticsfflgiiaigyygyifteraiafwvcg 55 (175)
T PF13295_consen 25 ITICSFFLGIIAIGYYGYIFTERAIAFWVCG 55 (175)
T ss_pred HHHHHHHHHHHHHhhhheeehhHHHHHHhhc
Confidence 358999999999999998 89995
No 12
>KOG2494|consensus
Probab=43.19 E-value=14 Score=31.76 Aligned_cols=25 Identities=28% Similarity=0.784 Sum_probs=20.0
Q ss_pred CCcchhhhHHHHHHHHccccccceecCCCC--ccccc
Q psy12937 76 RPTTTIICKYFIEAVENSKYGWFWSCPNGP--CTFEN 110 (111)
Q Consensus 76 ~~~TdiVCK~FLeAvE~~kYGWFW~CPNGd--C~YRH 110 (111)
+--|+-||+-||-- +|--|| |+|+|
T Consensus 33 ~wl~~eVCReF~rn----------~C~R~d~~CkfaH 59 (331)
T KOG2494|consen 33 KWLTLEVCREFLRN----------TCSRGDRECKFAH 59 (331)
T ss_pred chhHHHHHHHHHhc----------cccCCCccccccC
Confidence 44799999999964 577773 99988
No 13
>PF14753 DUF4475: Domain of unknown function (DUF4475)
Probab=37.21 E-value=15 Score=29.43 Aligned_cols=20 Identities=30% Similarity=0.647 Sum_probs=17.1
Q ss_pred HHHHHccccccceecCCC-Ccc
Q psy12937 87 IEAVENSKYGWFWSCPNG-PCT 107 (111)
Q Consensus 87 LeAvE~~kYGWFW~CPNG-dC~ 107 (111)
..||.++.|-. |.+|+| ||+
T Consensus 28 p~~~knrlyv~-Wr~~~~~DC~ 48 (196)
T PF14753_consen 28 PLRIKNRLYVS-WRNPTGMDCK 48 (196)
T ss_pred HhhhcCceEEE-EeCCCCccee
Confidence 35899999997 999999 686
No 14
>KOG2295|consensus
Probab=36.99 E-value=29 Score=32.26 Aligned_cols=42 Identities=21% Similarity=0.328 Sum_probs=31.9
Q ss_pred HHHHHHHhhhcccccCCCcchhhhHHHHHHHHccccccceecCCCCc
Q psy12937 60 KLKEVVEKKHGEAEKKRPTTTIICKYFIEAVENSKYGWFWSCPNGPC 106 (111)
Q Consensus 60 kLe~VV~~Khg~~~k~~~~TdiVCK~FLeAvE~~kYGWFW~CPNGdC 106 (111)
-|+++-.+|-|. +..++-|= -||+-+-..+|+|-|-||-+.|
T Consensus 476 ~lee~eakkkg~----k~~e~eve-~~v~s~t~e~~kdKy~C~lsgc 517 (648)
T KOG2295|consen 476 ELEEEEAKKKGA----KDVEDEVE-NFVDSNTMELDKDKYLCPLSGC 517 (648)
T ss_pred cchHHHHHHhcc----cCHHHHHH-HHHHHHHHHhhcccccCCCcch
Confidence 456777777774 44666654 6889999999999999998655
No 15
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=34.93 E-value=32 Score=26.69 Aligned_cols=21 Identities=33% Similarity=0.960 Sum_probs=16.7
Q ss_pred HHHHHHHccccccceecCCCCccccc
Q psy12937 85 YFIEAVENSKYGWFWSCPNGPCTFEN 110 (111)
Q Consensus 85 ~FLeAvE~~kYGWFW~CPNGdC~YRH 110 (111)
-.|+-+++|+ .|+||- |=|.|
T Consensus 124 ~~Le~~~~~~---~~vC~v--CGy~~ 144 (166)
T COG1592 124 GLLERLEEGK---VWVCPV--CGYTH 144 (166)
T ss_pred HHHHhhhcCC---EEEcCC--CCCcc
Confidence 5689999999 999995 55554
No 16
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 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 presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=33.67 E-value=26 Score=20.94 Aligned_cols=17 Identities=35% Similarity=0.808 Sum_probs=12.8
Q ss_pred ccccccceecCCC-C--ccc
Q psy12937 92 NSKYGWFWSCPNG-P--CTF 108 (111)
Q Consensus 92 ~~kYGWFW~CPNG-d--C~Y 108 (111)
++.--.||.||+. + |.|
T Consensus 19 ~N~GR~Fy~C~~~~~~~C~f 38 (45)
T PF06839_consen 19 PNPGRRFYKCPNYKDKGCNF 38 (45)
T ss_pred CCCCCcceECCCCCCCCcCC
Confidence 3555679999998 3 876
No 17
>PF07936 Defensin_4: Potassium-channel blocking toxin; InterPro: IPR012414 This family features the antihypertensive and antiviral proteins BDS-I (P11494 from SWISSPROT) and BDS-II (P59084 from SWISSPROT) expressed by Anemonia sulcata. BDS-I is organised into a triple-stranded antiparallel beta-sheet, with an additional small antiparallel beta-sheet at the N terminus []. Both peptides are known to specifically block the Kv3.4 potassium channel, and thus bring about a decrease in blood pressure []. Moreover, they inhibit the cytopathic effects of mouse hepatitis virus strain MHV-A59 on mouse liver cells, by an unknown mechanism []. ; GO: 0008200 ion channel inhibitor activity, 0009405 pathogenesis, 0042151 nematocyst; PDB: 2BDS_A 1BDS_A 1WXN_A 1WQK_A.
Probab=33.10 E-value=15 Score=22.26 Aligned_cols=8 Identities=75% Similarity=1.909 Sum_probs=5.1
Q ss_pred cce--ecCCC
Q psy12937 97 WFW--SCPNG 104 (111)
Q Consensus 97 WFW--~CPNG 104 (111)
||| .||+|
T Consensus 13 W~~~~~CP~g 22 (34)
T PF07936_consen 13 WFARGSCPGG 22 (34)
T ss_dssp EESTSS--TT
T ss_pred EEEecCCCCC
Confidence 888 79998
No 18
>PF04054 Not1: CCR4-Not complex component, Not1; InterPro: IPR007196 The Ccr4-Not complex is a global regulator of gene expression that is conserved from yeast to human. It affects genes positively and negatively and is thought to regulate transcription factor IID function. In Saccharomyces cerevisiae, it exists in two prominent forms and consists of at least nine core subunits: the five Not proteins (Not1p to Not5p), Caf1p, Caf40p, Caf130p and Ccr4p []. The Ccr4-Not complex regulates many different cellular functions, including RNA degradation and transcription initiation. It may be a regulatory platform that senses nutrient levels and stress []. Caf1p and Ccr4p, are directly involved in mRNA deadenylation, and Caf1p is associated with Dhh1p, a putative RNA helicase thought to be a component of the decapping complex []. Pop2, a component of the Ccr4-Not complex, functions as a deadenylase []. The Ccr4-Not complex is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID [].
Probab=32.56 E-value=25 Score=29.99 Aligned_cols=41 Identities=27% Similarity=0.519 Sum_probs=25.8
Q ss_pred HHHHHHHHhhhcccccCCCcchhhhHHHHHHHHccccccceecCC
Q psy12937 59 DKLKEVVEKKHGEAEKKRPTTTIICKYFIEAVENSKYGWFWSCPN 103 (111)
Q Consensus 59 ~kLe~VV~~Khg~~~k~~~~TdiVCK~FLeAvE~~kYGWFW~CPN 103 (111)
|.+--|+.++.=- +++.| =-+=--|+|-|.+.+|+ ||++|-
T Consensus 322 EqItRVLLERliv-~rPHP--WGllitfiELikN~~y~-f~~~pF 362 (379)
T PF04054_consen 322 EQITRVLLERLIV-NRPHP--WGLLITFIELIKNPKYN-FWELPF 362 (379)
T ss_pred HHHHHHHHHHHhc-CCCCC--ccHHHHHHHHHhCccCC-cccCcc
Confidence 4455566666521 22332 22223799999999999 999985
No 19
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=30.51 E-value=18 Score=30.09 Aligned_cols=12 Identities=50% Similarity=0.946 Sum_probs=10.4
Q ss_pred cCCccccCCCch
Q psy12937 17 SGAKCKFSHDLT 28 (111)
Q Consensus 17 KG~KCKFSHDl~ 28 (111)
=|+-|||+|+-+
T Consensus 155 YGDsCKflH~R~ 166 (259)
T COG5152 155 YGDSCKFLHDRS 166 (259)
T ss_pred CCchhhhhhhhh
Confidence 489999999866
No 20
>KOG2068|consensus
Probab=30.36 E-value=43 Score=28.81 Aligned_cols=44 Identities=18% Similarity=0.320 Sum_probs=29.9
Q ss_pred hhhhhccHHHHHHHHHhhhcccccCCCcchhhhHHHHHHHHccccccceecCCCCccccc
Q psy12937 51 ETMENWDEDKLKEVVEKKHGEAEKKRPTTTIICKYFIEAVENSKYGWFWSCPNGPCTFEN 110 (111)
Q Consensus 51 dtmd~WDe~kLe~VV~~Khg~~~k~~~~TdiVCK~FLeAvE~~kYGWFW~CPNGdC~YRH 110 (111)
.-+++||.-.+-=-.++.+ -.|.+-|-+||.-. .|||.+|||-|
T Consensus 140 rci~~v~g~~~dg~~lka~-------~gttkycs~~l~~~---------~c~~~~cmylh 183 (327)
T KOG2068|consen 140 RCIDDVDGFVDDGRALKAS-------LGTTKYCSFYLRND---------ICQNPDCMYLH 183 (327)
T ss_pred hHHHHhhhHHhhhhhhHHh-------hCCCcchhHHhhhh---------cccCccccccc
Confidence 4488998766544333332 24667888887643 59998899988
No 21
>PRK14973 DNA topoisomerase I; Provisional
Probab=30.01 E-value=19 Score=34.22 Aligned_cols=20 Identities=20% Similarity=0.675 Sum_probs=15.4
Q ss_pred HHHHHccccccceecCCCCccc
Q psy12937 87 IEAVENSKYGWFWSCPNGPCTF 108 (111)
Q Consensus 87 LeAvE~~kYGWFW~CPNGdC~Y 108 (111)
+-.+..|.||||.-||. |+|
T Consensus 646 ~~~~r~Gr~g~fl~CP~--C~~ 665 (936)
T PRK14973 646 VRLIRKGARPWDIGCPL--CSH 665 (936)
T ss_pred eEEeecCCCcccccCcc--ccc
Confidence 44458899999999974 665
No 22
>PRK07220 DNA topoisomerase I; Validated
Probab=29.83 E-value=27 Score=32.05 Aligned_cols=14 Identities=43% Similarity=1.151 Sum_probs=11.0
Q ss_pred cccccceecCCCCccc
Q psy12937 93 SKYGWFWSCPNGPCTF 108 (111)
Q Consensus 93 ~kYGWFW~CPNGdC~Y 108 (111)
++.+|||.||+ |.|
T Consensus 652 g~~~~~~~Cp~--C~~ 665 (740)
T PRK07220 652 GKRPWDLGCPQ--CNF 665 (740)
T ss_pred CCccceeeCCC--CCC
Confidence 56789999986 655
No 23
>PF00706 Toxin_4: Anenome neurotoxin; InterPro: IPR000693 Sea anemones produce many different neurotoxins with related structure and function. Proteins belonging to this family include the neurotoxins, of which there are several, including calitoxin and anthopleurin. The neurotoxins bind specifically to the sodium channel, thereby delaying its inactivation during signal transduction, resulting in strong stimulation of mammalian cardiac muscle contraction. Calitoxin 1 has been found in neuromuscular prearations of crustaceans, where it increases transmitter release, causing firing of the axons. Three disulphide bonds are present in this protein [, , ].; GO: 0009966 regulation of signal transduction, 0005576 extracellular region; PDB: 2H9X_A 1AHL_A 1APF_A 1SHI_A 1SH1_A 2SH1_A 1ATX_A.
Probab=28.90 E-value=18 Score=22.86 Aligned_cols=11 Identities=45% Similarity=1.733 Sum_probs=8.7
Q ss_pred cceecCCC-C-cc
Q psy12937 97 WFWSCPNG-P-CT 107 (111)
Q Consensus 97 WFW~CPNG-d-C~ 107 (111)
|+|-||.| . |.
T Consensus 21 w~~~CpsGWh~C~ 33 (43)
T PF00706_consen 21 WLFGCPSGWHKCK 33 (43)
T ss_dssp ETSSS-TTEEECC
T ss_pred eecCCCchhhhhh
Confidence 99999999 5 86
No 24
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=27.32 E-value=26 Score=27.13 Aligned_cols=7 Identities=43% Similarity=1.825 Sum_probs=6.2
Q ss_pred cceecCC
Q psy12937 97 WFWSCPN 103 (111)
Q Consensus 97 WFW~CPN 103 (111)
|+|.|||
T Consensus 367 ~~~~c~~ 373 (389)
T PRK11788 367 LYWHCPS 373 (389)
T ss_pred ceeECcC
Confidence 8899998
No 25
>PF09929 DUF2161: Uncharacterized conserved protein (DUF2161); InterPro: IPR018679 This family of various hypothetical prokaryotic proteins has no known function.
Probab=26.11 E-value=29 Score=25.90 Aligned_cols=9 Identities=44% Similarity=1.534 Sum_probs=7.7
Q ss_pred HHccccccc
Q psy12937 90 VENSKYGWF 98 (111)
Q Consensus 90 vE~~kYGWF 98 (111)
+-+|-||||
T Consensus 92 L~~N~YGWF 100 (118)
T PF09929_consen 92 LRDNHYGWF 100 (118)
T ss_pred HHhCcccce
Confidence 567999999
No 26
>KOG1155|consensus
Probab=26.11 E-value=52 Score=30.25 Aligned_cols=34 Identities=38% Similarity=0.676 Sum_probs=24.8
Q ss_pred HHHHHHHHhhhcccccCCCcchhhhHHHHHHHHccccccceec
Q psy12937 59 DKLKEVVEKKHGEAEKKRPTTTIICKYFIEAVENSKYGWFWSC 101 (111)
Q Consensus 59 ~kLe~VV~~Khg~~~k~~~~TdiVCK~FLeAvE~~kYGWFW~C 101 (111)
-=|.-||.+++|+.. .-=+.|+++| +.|-|||.|
T Consensus 167 lYL~Gvv~k~~~~~s-------~A~~sfv~~v--~~~P~~W~A 200 (559)
T KOG1155|consen 167 LYLYGVVLKELGLLS-------LAIDSFVEVV--NRYPWFWSA 200 (559)
T ss_pred HHHHHHHHHhhchHH-------HHHHHHHHHH--hcCCcchHH
Confidence 457888888888621 2235788888 579999986
No 27
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=24.78 E-value=43 Score=23.90 Aligned_cols=17 Identities=47% Similarity=1.091 Sum_probs=14.3
Q ss_pred ccccccceecCCCC-ccc
Q psy12937 92 NSKYGWFWSCPNGP-CTF 108 (111)
Q Consensus 92 ~~kYGWFW~CPNGd-C~Y 108 (111)
.++||||+.|-|-. |.|
T Consensus 31 ~~~~g~f~gCs~yP~C~~ 48 (140)
T COG0551 31 FGKYGIFLGCSNYPKCDY 48 (140)
T ss_pred EccCCeEEEeCCCCCCCC
Confidence 47889999999984 875
No 28
>PF14194 Cys_rich_VLP: Cysteine-rich VLP
Probab=24.70 E-value=46 Score=22.11 Aligned_cols=11 Identities=45% Similarity=1.195 Sum_probs=10.1
Q ss_pred hhhhHHHHHHH
Q psy12937 80 TIICKYFIEAV 90 (111)
Q Consensus 80 diVCK~FLeAv 90 (111)
.+.|+||.+||
T Consensus 42 s~~CryFr~AV 52 (56)
T PF14194_consen 42 SLLCRYFRAAV 52 (56)
T ss_pred cHHHHHHHHhh
Confidence 78899999998
No 29
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 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 entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=23.70 E-value=50 Score=20.37 Aligned_cols=15 Identities=33% Similarity=0.970 Sum_probs=7.3
Q ss_pred HHHHHHccccccceecCC
Q psy12937 86 FIEAVENSKYGWFWSCPN 103 (111)
Q Consensus 86 FLeAvE~~kYGWFW~CPN 103 (111)
||+..++... |.||-
T Consensus 32 fl~~~~~~~~---W~CPi 46 (50)
T PF02891_consen 32 FLESNQRTPK---WKCPI 46 (50)
T ss_dssp HHHHHHHS------B-TT
T ss_pred HHHHhhccCC---eECcC
Confidence 5666665555 99993
No 30
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=23.59 E-value=58 Score=20.77 Aligned_cols=15 Identities=33% Similarity=0.689 Sum_probs=10.4
Q ss_pred hhHHHHHHHHccccc
Q psy12937 82 ICKYFIEAVENSKYG 96 (111)
Q Consensus 82 VCK~FLeAvE~~kYG 96 (111)
|=..+|+|||++.|.
T Consensus 22 I~~~~l~aiE~~~~~ 36 (62)
T PF13413_consen 22 ISVSYLEAIENGDFD 36 (62)
T ss_dssp --HHHHHHHHCT-GC
T ss_pred CCHHHHHHHHCcChh
Confidence 445899999999875
No 31
>KOG1813|consensus
Probab=23.53 E-value=28 Score=29.86 Aligned_cols=13 Identities=46% Similarity=0.848 Sum_probs=11.3
Q ss_pred ccCCccccCCCch
Q psy12937 16 QSGAKCKFSHDLT 28 (111)
Q Consensus 16 ~KG~KCKFSHDl~ 28 (111)
..|+-|||.||..
T Consensus 199 g~gdSckFlh~r~ 211 (313)
T KOG1813|consen 199 GYGDSCKFLHDRS 211 (313)
T ss_pred cccchhhhhhhhh
Confidence 4789999999976
No 32
>PF08806 Sep15_SelM: Sep15/SelM redox domain; InterPro: IPR014912 Sep15 and SelM are eukaryotic selenoproteins that have a thioredoxin-like domain and a surface accessible active site redox motif []. This suggests that they function as thiol-disulphide isomerases involved in disulphide bond formation in the endoplasmic reticulum []. ; PDB: 2A4H_A 2A2P_A.
Probab=22.83 E-value=43 Score=22.65 Aligned_cols=18 Identities=28% Similarity=0.741 Sum_probs=14.5
Q ss_pred hhhhhccHHHHHHHHHhh
Q psy12937 51 ETMENWDEDKLKEVVEKK 68 (111)
Q Consensus 51 dtmd~WDe~kLe~VV~~K 68 (111)
=.+++|+.+.+++.+.+|
T Consensus 58 i~i~~w~~d~i~efL~~k 75 (78)
T PF08806_consen 58 INIEKWKTDEIEEFLNEK 75 (78)
T ss_dssp EE-SSSSHCHHHHHHHHH
T ss_pred EEcccCCHHHHHHHHHHh
Confidence 458999999999998765
No 33
>KOG2333|consensus
Probab=21.74 E-value=38 Score=31.35 Aligned_cols=17 Identities=41% Similarity=1.050 Sum_probs=13.2
Q ss_pred eeeeeccCCccccCCCchh
Q psy12937 11 LPCLFQSGAKCKFSHDLTI 29 (111)
Q Consensus 11 ~~C~f~KG~KCKFSHDl~~ 29 (111)
..|.| |++|+|-||++.
T Consensus 88 ~~C~f--~d~Crf~HDi~a 104 (614)
T KOG2333|consen 88 SKCSF--GDNCRFVHDIEA 104 (614)
T ss_pred ccCcc--cccccccccHHH
Confidence 44555 799999999875
No 34
>KOG1544|consensus
Probab=20.18 E-value=54 Score=29.25 Aligned_cols=16 Identities=38% Similarity=0.887 Sum_probs=13.6
Q ss_pred hhHHHHHHHHcccccc
Q psy12937 82 ICKYFIEAVENSKYGW 97 (111)
Q Consensus 82 VCK~FLeAvE~~kYGW 97 (111)
|=.-.||+|.+|.|||
T Consensus 148 v~Pd~iE~in~G~YgW 163 (470)
T KOG1544|consen 148 VDPDMIEAINQGNYGW 163 (470)
T ss_pred cCHHHHHHHhcCCccc
Confidence 3356899999999998
Done!