Query 000388
Match_columns 1587
No_of_seqs 333 out of 1134
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 06:49:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000388.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000388hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1244 Predicted transcriptio 99.9 2.3E-24 4.9E-29 234.6 1.3 108 244-365 220-330 (336)
2 KOG1512 PHD Zn-finger protein 99.7 1E-17 2.2E-22 184.1 1.2 102 246-364 256-361 (381)
3 KOG4443 Putative transcription 99.1 1.6E-11 3.5E-16 147.0 1.7 106 249-374 19-126 (694)
4 KOG0825 PHD Zn-finger protein 99.0 1.6E-10 3.5E-15 139.5 2.2 56 313-368 213-268 (1134)
5 PF00628 PHD: PHD-finger; Int 98.4 7.6E-08 1.7E-12 81.9 0.3 48 317-365 1-50 (51)
6 KOG4299 PHD Zn-finger protein 98.2 4.2E-07 9E-12 110.0 1.7 53 315-368 253-307 (613)
7 cd04718 BAH_plant_2 BAH, or Br 98.1 1.8E-06 3.9E-11 90.1 3.1 26 341-366 2-27 (148)
8 smart00249 PHD PHD zinc finger 98.0 4.9E-06 1.1E-10 67.5 3.2 46 317-363 1-47 (47)
9 KOG0383 Predicted helicase [Ge 97.9 7.7E-06 1.7E-10 101.5 3.3 48 314-365 46-93 (696)
10 KOG1973 Chromatin remodeling p 97.8 6.7E-06 1.5E-10 92.6 2.0 45 316-366 222-268 (274)
11 KOG1245 Chromatin remodeling c 97.8 3.6E-06 7.9E-11 110.7 -1.0 52 316-368 1109-1160(1404)
12 COG5034 TNG2 Chromatin remodel 97.5 3.4E-05 7.4E-10 86.2 2.0 43 320-365 225-269 (271)
13 KOG0955 PHD finger protein BR1 97.5 4.8E-05 1E-09 97.8 2.8 50 314-366 218-269 (1051)
14 KOG0957 PHD finger protein [Ge 97.4 9.9E-05 2.2E-09 87.9 3.3 49 315-364 544-596 (707)
15 KOG4323 Polycomb-like PHD Zn-f 97.3 0.00014 3E-09 87.1 3.8 59 306-368 162-226 (464)
16 KOG0954 PHD finger protein [Ge 97.0 0.00024 5.2E-09 87.8 1.0 57 314-373 270-333 (893)
17 COG5141 PHD zinc finger-contai 96.7 0.00061 1.3E-08 81.4 1.4 49 315-366 193-243 (669)
18 KOG0956 PHD finger protein AF1 96.5 0.001 2.2E-08 81.9 1.6 46 316-364 6-55 (900)
19 KOG1246 DNA-binding protein ju 96.1 0.0045 9.8E-08 79.9 4.0 80 314-399 154-233 (904)
20 PF13831 PHD_2: PHD-finger; PD 95.3 0.0028 6.1E-08 52.7 -1.4 34 328-364 2-36 (36)
21 KOG1473 Nucleosome remodeling 92.0 0.071 1.5E-06 69.4 1.7 48 316-367 345-392 (1414)
22 PF15446 zf-PHD-like: PHD/FYVE 90.8 0.34 7.5E-06 52.7 5.1 34 250-289 1-36 (175)
23 KOG1473 Nucleosome remodeling 90.7 0.068 1.5E-06 69.6 -0.3 101 248-366 344-479 (1414)
24 KOG4443 Putative transcription 88.3 0.15 3.3E-06 63.8 0.2 58 314-372 17-77 (694)
25 KOG1244 Predicted transcriptio 88.3 0.22 4.7E-06 57.3 1.4 30 269-300 293-324 (336)
26 KOG0957 PHD finger protein [Ge 85.3 0.58 1.3E-05 57.3 2.9 47 246-301 542-592 (707)
27 PF00628 PHD: PHD-finger; Int 84.3 0.32 6.9E-06 41.8 0.1 42 250-300 1-44 (51)
28 KOG0825 PHD Zn-finger protein 76.7 1.2 2.6E-05 57.1 1.4 49 241-300 208-259 (1134)
29 KOG0954 PHD finger protein [Ge 74.1 1.4 3E-05 56.3 1.1 101 246-366 269-389 (893)
30 KOG0804 Cytoplasmic Zn-finger 71.9 1.7 3.6E-05 53.2 1.0 45 124-168 40-84 (493)
31 smart00249 PHD PHD zinc finger 70.0 3.5 7.7E-05 33.5 2.2 32 250-290 1-34 (47)
32 KOG0955 PHD finger protein BR1 69.8 3.6 7.9E-05 54.9 3.4 44 246-300 217-262 (1051)
33 COG5141 PHD zinc finger-contai 68.7 4.2 9E-05 50.3 3.3 60 230-301 175-237 (669)
34 PF15446 zf-PHD-like: PHD/FYVE 58.9 4.3 9.4E-05 44.6 1.0 48 317-365 1-59 (175)
35 KOG4323 Polycomb-like PHD Zn-f 56.3 3.7 8.1E-05 50.7 0.0 44 250-300 170-217 (464)
36 PF07744 SPOC: SPOC domain; I 48.6 15 0.00033 36.2 2.8 105 848-958 1-119 (119)
37 KOG0383 Predicted helicase [Ge 46.8 3.8 8.3E-05 52.8 -1.9 47 315-365 506-553 (696)
38 KOG4299 PHD Zn-finger protein 43.7 15 0.00033 46.8 2.5 47 316-366 48-95 (613)
39 KOG1512 PHD Zn-finger protein 39.4 11 0.00024 44.3 0.4 58 316-374 259-325 (381)
40 PF13917 zf-CCHC_3: Zinc knuck 37.4 15 0.00033 32.4 0.9 21 718-738 2-22 (42)
41 KOG1245 Chromatin remodeling c 36.9 8.4 0.00018 53.2 -1.2 49 242-301 1102-1152(1404)
42 PF14446 Prok-RING_1: Prokaryo 35.8 22 0.00047 33.0 1.6 33 315-348 5-38 (54)
43 PF07649 C1_3: C1-like domain; 33.4 16 0.00035 29.2 0.3 28 317-345 2-29 (30)
44 KOG3116 Predicted C3H1-type Zn 33.0 15 0.00034 39.9 0.2 21 719-739 26-46 (177)
45 COG1773 Rubredoxin [Energy pro 25.8 44 0.00096 31.2 1.8 39 317-365 5-44 (55)
46 PF00098 zf-CCHC: Zinc knuckle 25.2 39 0.00084 25.0 1.1 16 722-737 2-17 (18)
47 PF11793 FANCL_C: FANCL C-term 24.0 15 0.00033 34.7 -1.5 49 317-366 4-64 (70)
48 cd00214 Calpain_III Calpain, s 24.0 1.3E+02 0.0029 31.6 5.2 70 908-984 65-145 (150)
49 PRK14559 putative protein seri 23.9 61 0.0013 42.1 3.2 47 317-365 3-49 (645)
50 PF13901 DUF4206: Domain of un 22.8 60 0.0013 36.2 2.5 27 329-365 171-197 (202)
51 KOG1632 Uncharacterized PHD Zn 21.8 47 0.001 40.0 1.6 38 329-367 74-114 (345)
52 PF13696 zf-CCHC_2: Zinc knuck 20.7 60 0.0013 27.6 1.4 22 719-740 7-28 (32)
No 1
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=99.89 E-value=2.3e-24 Score=234.64 Aligned_cols=108 Identities=24% Similarity=0.531 Sum_probs=101.9
Q ss_pred cccccccccccccccccccCCCCCCCCCccccCCC--CCCCCCCcCCcCCC-cccCCCCCCCCCCCCCcccccccccccc
Q 000388 244 ESSSDVLTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELP-DVQRFPAASGDETDESDIMEQDVKVCDI 320 (1587)
Q Consensus 244 ~~Ts~~~C~~C~~~ee~nk~~~~gepEELL~Cs~C--s~HpSCLd~s~e~s-~ikky~WQs~DE~DedDci~~DckvC~V 320 (1587)
..-++.+|.||+++..+|++ .+.||+||.|++| ++||+||+++..|. .+++|.|| || +|+.|.+
T Consensus 220 ~a~Pn~YCDFclgdsr~nkk--t~~peelvscsdcgrsghpsclqft~nm~~avk~yrwq---------ci--eck~csi 286 (336)
T KOG1244|consen 220 IAQPNPYCDFCLGDSRENKK--TGMPEELVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQ---------CI--ECKYCSI 286 (336)
T ss_pred cccCCcccceeccccccccc--cCCchhhcchhhcCCCCCcchhhhhHHHHHHHHhheee---------ee--ecceecc
Confidence 35678899999999988886 9999999999999 89999999999988 78899999 77 9999999
Q ss_pred cccccCCCCeEEeCCCCCCCCCccccCcccCCCCCCCccCccCcc
Q 000388 321 CGDAGREDLLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECKF 365 (1587)
Q Consensus 321 Cg~~gded~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~ 365 (1587)
||..+++++|||||.|||| ||||||.|||.+.|+|.|.|..|..
T Consensus 287 cgtsenddqllfcddcdrg-yhmyclsppm~eppegswsc~KOG~ 330 (336)
T KOG1244|consen 287 CGTSENDDQLLFCDDCDRG-YHMYCLSPPMVEPPEGSWSCHLCLE 330 (336)
T ss_pred ccCcCCCceeEeecccCCc-eeeEecCCCcCCCCCCchhHHHHHH
Confidence 9999999999999999999 9999999999999999999999974
No 2
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=99.67 E-value=1e-17 Score=184.10 Aligned_cols=102 Identities=21% Similarity=0.444 Sum_probs=94.3
Q ss_pred cccccccccccccccccCCCCCCCCCccccCCC--CCCCCCCcCCcCCC-cccCCCCCCCCCCCCCcccccccccccccc
Q 000388 246 SSDVLTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELP-DVQRFPAASGDETDESDIMEQDVKVCDICG 322 (1587)
Q Consensus 246 Ts~~~C~~C~~~ee~nk~~~~gepEELL~Cs~C--s~HpSCLd~s~e~s-~ikky~WQs~DE~DedDci~~DckvC~VCg 322 (1587)
-.+.+|++|..+.+.++ ++..+.+|.|..| .+||+|++++++++ .+++|.|+ |+ +|+.|.+|+
T Consensus 256 ~~~~~~~~~~~~~~~~~---~~r~~S~I~C~~C~~~~HP~Ci~M~~elv~~~KTY~W~---------C~--~C~lC~IC~ 321 (381)
T KOG1512|consen 256 QRRNERKHFWDIQTNII---QSRRNSWIVCKPCATRPHPYCVAMIPELVGQYKTYFWK---------CS--SCELCRICL 321 (381)
T ss_pred cchhhhhhhhcchhhhh---hhhhccceeecccccCCCCcchhcCHHHHhHHhhcchh---------hc--ccHhhhccC
Confidence 67789999999887765 8999999999999 89999999999998 67889999 65 899999999
Q ss_pred cccCCCCeEEeCCCCCCCCCccccCcccCCCCCCCccCc-cCc
Q 000388 323 DAGREDLLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCE-ECK 364 (1587)
Q Consensus 323 ~~gded~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp-~C~ 364 (1587)
.+..++.++|||.|||| ||+||.+ |..+|.|.|.|. .|.
T Consensus 322 ~P~~E~E~~FCD~CDRG-~HT~CVG--L~~lP~G~WICD~~C~ 361 (381)
T KOG1512|consen 322 GPVIESEHLFCDVCDRG-PHTLCVG--LQDLPRGEWICDMRCR 361 (381)
T ss_pred CcccchheeccccccCC-CCccccc--cccccCccchhhhHHH
Confidence 99999999999999999 8999999 999999999998 354
No 3
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=99.11 E-value=1.6e-11 Score=147.02 Aligned_cols=106 Identities=25% Similarity=0.501 Sum_probs=88.0
Q ss_pred ccccccccccccccCCCCCCCCCccccCCC--CCCCCCCcCCcCCCcccCCCCCCCCCCCCCcccccccccccccccccC
Q 000388 249 VLTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELPDVQRFPAASGDETDESDIMEQDVKVCDICGDAGR 326 (1587)
Q Consensus 249 ~~C~~C~~~ee~nk~~~~gepEELL~Cs~C--s~HpSCLd~s~e~s~ikky~WQs~DE~DedDci~~DckvC~VCg~~gd 326 (1587)
.+|.+|...+ .+.+.-|+.|.+| .||+.|...++..... ...|+ | .+|.+|+.|+..++
T Consensus 19 ~mc~l~~s~G-------~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l-~~gWr---------C--~~crvCe~c~~~gD 79 (694)
T KOG4443|consen 19 LMCPLCGSSG-------KGRAGRLLACSDCGQKYHPYCVTSWAQHAVL-SGGWR---------C--PSCRVCEACGTTGD 79 (694)
T ss_pred hhhhhhcccc-------ccccCcchhhhhhcccCCcchhhHHHhHHHh-cCCcc---------c--CCceeeeeccccCC
Confidence 3566666643 5677789999999 8999999876543321 23478 5 38999999999999
Q ss_pred CCCeEEeCCCCCCCCCccccCcccCCCCCCCccCccCccccccccccC
Q 000388 327 EDLLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECKFAEETEKQKQ 374 (1587)
Q Consensus 327 ed~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~~~ec~kk~~ 374 (1587)
+..+++|++||.. ||.||+.|+++.||.|.|+|+.|..+..|...-.
T Consensus 80 ~~kf~~Ck~cDvs-yh~yc~~P~~~~v~sg~~~ckk~~~c~qc~~~lp 126 (694)
T KOG4443|consen 80 PKKFLLCKRCDVS-YHCYCQKPPNDKVPSGPWLCKKCTRCRQCDSTLP 126 (694)
T ss_pred ccccccccccccc-ccccccCCccccccCcccccHHHHhhhhcccccc
Confidence 9999999999876 9999999999999999999999999999988655
No 4
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.97 E-value=1.6e-10 Score=139.48 Aligned_cols=56 Identities=34% Similarity=0.812 Sum_probs=51.2
Q ss_pred cccccccccccccCCCCeEEeCCCCCCCCCccccCcccCCCCCCCccCccCccccc
Q 000388 313 QDVKVCDICGDAGREDLLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECKFAEE 368 (1587)
Q Consensus 313 ~DckvC~VCg~~gded~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~~~e 368 (1587)
.+...|.+|...+.+++||+||.|+.++||+|||+|+|.++|.+.|||+.|..-..
T Consensus 213 ~E~~~C~IC~~~DpEdVLLLCDsCN~~~YH~YCLDPdl~eiP~~eWYC~NC~dL~~ 268 (1134)
T KOG0825|consen 213 QEEVKCDICTVHDPEDVLLLCDSCNKVYYHVYCLDPDLSESPVNEWYCTNCSLLEI 268 (1134)
T ss_pred cccccceeeccCChHHhheeecccccceeeccccCcccccccccceecCcchhhhh
Confidence 35668999999999999999999999999999999999999999999999975433
No 5
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=98.37 E-value=7.6e-08 Score=81.91 Aligned_cols=48 Identities=27% Similarity=0.832 Sum_probs=42.5
Q ss_pred cccccccccCCCCeEEeCCCCCCCCCccccCcccC--CCCCCCccCccCcc
Q 000388 317 VCDICGDAGREDLLAICSRCSDGAEHTYCMKEMLQ--KVPEGDWLCEECKF 365 (1587)
Q Consensus 317 vC~VCg~~gded~LLlCD~CDrGaYH~yCL~PPL~--eVPeGdW~Cp~C~~ 365 (1587)
+|.+|+..++++.||.||.|++. ||++|++|++. .++.+.|+|+.|..
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~-~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRW-YHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCE-EETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcCCCChh-hCcccCCCChhhccCCCCcEECcCCcC
Confidence 48999998889999999999876 99999999987 66667999999974
No 6
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.21 E-value=4.2e-07 Score=109.95 Aligned_cols=53 Identities=26% Similarity=0.757 Sum_probs=46.7
Q ss_pred cccccccccccCCCCeEEeCCCCCCCCCccccCcc--cCCCCCCCccCccCccccc
Q 000388 315 VKVCDICGDAGREDLLAICSRCSDGAEHTYCMKEM--LQKVPEGDWLCEECKFAEE 368 (1587)
Q Consensus 315 ckvC~VCg~~gded~LLlCD~CDrGaYH~yCL~PP--L~eVPeGdW~Cp~C~~~~e 368 (1587)
.++|..|+..+.-..+++||+|+++ ||++||.|| .+.+|.|.|+|++|.....
T Consensus 253 ~~fCsaCn~~~~F~~~i~CD~Cp~s-FH~~CLePPl~~eniP~g~W~C~ec~~k~~ 307 (613)
T KOG4299|consen 253 EDFCSACNGSGLFNDIICCDGCPRS-FHQTCLEPPLEPENIPPGSWFCPECKIKSV 307 (613)
T ss_pred HHHHHHhCCccccccceeecCCchH-HHHhhcCCCCCcccCCCCccccCCCeeeee
Confidence 3589999999987778999999999 799999999 5689999999999976543
No 7
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=98.09 E-value=1.8e-06 Score=90.13 Aligned_cols=26 Identities=42% Similarity=1.074 Sum_probs=24.8
Q ss_pred CCccccCcccCCCCCCCccCccCccc
Q 000388 341 EHTYCMKEMLQKVPEGDWLCEECKFA 366 (1587)
Q Consensus 341 YH~yCL~PPL~eVPeGdW~Cp~C~~~ 366 (1587)
||++||.|||..+|+|+|+||.|...
T Consensus 2 ~H~~CL~Ppl~~~P~g~W~Cp~C~~~ 27 (148)
T cd04718 2 FHLCCLRPPLKEVPEGDWICPFCEVE 27 (148)
T ss_pred cccccCCCCCCCCCCCCcCCCCCcCC
Confidence 89999999999999999999999864
No 8
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG0383 consensus Predicted helicase [General function prediction only]
Probab=97.86 E-value=7.7e-06 Score=101.46 Aligned_cols=48 Identities=31% Similarity=0.852 Sum_probs=43.6
Q ss_pred ccccccccccccCCCCeEEeCCCCCCCCCccccCcccCCCCCCCccCccCcc
Q 000388 314 DVKVCDICGDAGREDLLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECKF 365 (1587)
Q Consensus 314 DckvC~VCg~~gded~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~ 365 (1587)
+...|.+|...+. +|+||.|... ||.+|++||+..+|.|+|.|+.|..
T Consensus 46 ~~e~c~ic~~~g~---~l~c~tC~~s-~h~~cl~~pl~~~p~~~~~c~Rc~~ 93 (696)
T KOG0383|consen 46 EQEACRICADGGE---LLWCDTCPAS-FHASCLGPPLTPQPNGEFICPRCFC 93 (696)
T ss_pred hhhhhhhhcCCCc---EEEeccccHH-HHHHccCCCCCcCCccceeeeeecc
Confidence 5668999999998 9999999865 9999999999999999999999943
No 10
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=97.83 E-value=6.7e-06 Score=92.59 Aligned_cols=45 Identities=29% Similarity=0.720 Sum_probs=38.4
Q ss_pred ccccccccccCCCCeEEeCC--CCCCCCCccccCcccCCCCCCCccCccCccc
Q 000388 316 KVCDICGDAGREDLLAICSR--CSDGAEHTYCMKEMLQKVPEGDWLCEECKFA 366 (1587)
Q Consensus 316 kvC~VCg~~gded~LLlCD~--CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~~ 366 (1587)
++|. |...|. |+-||. |+..|||+.|.+ |...|.|.|||+.|...
T Consensus 222 C~Cn-qvsyg~---Mi~CDn~~C~~eWFH~~CVG--L~~~PkgkWyC~~C~~~ 268 (274)
T KOG1973|consen 222 CICN-QVSYGK---MIGCDNPGCPIEWFHFTCVG--LKTKPKGKWYCPRCKAE 268 (274)
T ss_pred EEec-cccccc---ccccCCCCCCcceEEEeccc--cccCCCCcccchhhhhh
Confidence 3566 555555 999998 998999999999 99999999999999754
No 11
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=97.79 E-value=3.6e-06 Score=110.73 Aligned_cols=52 Identities=29% Similarity=0.967 Sum_probs=48.9
Q ss_pred ccccccccccCCCCeEEeCCCCCCCCCccccCcccCCCCCCCccCccCccccc
Q 000388 316 KVCDICGDAGREDLLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECKFAEE 368 (1587)
Q Consensus 316 kvC~VCg~~gded~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~~~e 368 (1587)
..|.+|...+.++.|++|+.|+.+ ||+||+.|.+..+|.|+|+|+.|+...+
T Consensus 1109 ~~c~~cr~k~~~~~m~lc~~c~~~-~h~~C~rp~~~~~~~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1109 ALCKVCRRKKQDEKMLLCDECLSG-FHLFCLRPALSSVPPGDWMCPSCRKEHR 1160 (1404)
T ss_pred hhhhhhhhcccchhhhhhHhhhhh-HHHHhhhhhhccCCcCCccCCccchhhh
Confidence 479999999999999999999988 8999999999999999999999998765
No 12
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=97.54 E-value=3.4e-05 Score=86.16 Aligned_cols=43 Identities=30% Similarity=0.791 Sum_probs=37.4
Q ss_pred ccccccCCCCeEEeCC--CCCCCCCccccCcccCCCCCCCccCccCcc
Q 000388 320 ICGDAGREDLLAICSR--CSDGAEHTYCMKEMLQKVPEGDWLCEECKF 365 (1587)
Q Consensus 320 VCg~~gded~LLlCD~--CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~ 365 (1587)
-|++... ..|+-||+ |.+-|||+.|.+ |.+.|+|.|||+.|..
T Consensus 225 fCqqvSy-GqMVaCDn~nCkrEWFH~~CVG--Lk~pPKG~WYC~eCk~ 269 (271)
T COG5034 225 FCQQVSY-GQMVACDNANCKREWFHLECVG--LKEPPKGKWYCPECKK 269 (271)
T ss_pred Eeccccc-ccceecCCCCCchhheeccccc--cCCCCCCcEeCHHhHh
Confidence 4777665 34999996 999999999999 9999999999999964
No 13
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=97.49 E-value=4.8e-05 Score=97.79 Aligned_cols=50 Identities=32% Similarity=0.833 Sum_probs=44.3
Q ss_pred ccccccccccccCC--CCeEEeCCCCCCCCCccccCcccCCCCCCCccCccCccc
Q 000388 314 DVKVCDICGDAGRE--DLLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECKFA 366 (1587)
Q Consensus 314 DckvC~VCg~~gde--d~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~~ 366 (1587)
+..+|.||.+..-. +.+|+||.|+.. +|++|++ ..-+|+|.|+|..|...
T Consensus 218 ~D~~C~iC~~~~~~n~n~ivfCD~Cnl~-VHq~Cyg--i~~ipeg~WlCr~Cl~s 269 (1051)
T KOG0955|consen 218 EDAVCCICLDGECQNSNVIVFCDGCNLA-VHQECYG--IPFIPEGQWLCRRCLQS 269 (1051)
T ss_pred CCccceeecccccCCCceEEEcCCCcch-hhhhccC--CCCCCCCcEeehhhccC
Confidence 56789999998866 899999999876 8999999 67899999999999754
No 14
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=97.38 E-value=9.9e-05 Score=87.88 Aligned_cols=49 Identities=31% Similarity=0.769 Sum_probs=44.8
Q ss_pred cccccccccccCCCCeEEeCCCCCCCCCccccCcccCCCCCC----CccCccCc
Q 000388 315 VKVCDICGDAGREDLLAICSRCSDGAEHTYCMKEMLQKVPEG----DWLCEECK 364 (1587)
Q Consensus 315 ckvC~VCg~~gded~LLlCD~CDrGaYH~yCL~PPL~eVPeG----dW~Cp~C~ 364 (1587)
.+.|-||.+..+..+++.||.|... ||+-||.|||+.+|+- .|.|.+|.
T Consensus 544 ~ysCgiCkks~dQHll~~CDtC~lh-YHlGCL~PPLTR~Pkk~kn~gWqCsECd 596 (707)
T KOG0957|consen 544 NYSCGICKKSTDQHLLTQCDTCHLH-YHLGCLSPPLTRLPKKNKNFGWQCSECD 596 (707)
T ss_pred ceeeeeeccchhhHHHhhcchhhce-eeccccCCccccCcccccCcceeecccc
Confidence 4679999999999999999999876 9999999999999985 59999993
No 15
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=97.34 E-value=0.00014 Score=87.14 Aligned_cols=59 Identities=20% Similarity=0.625 Sum_probs=42.6
Q ss_pred CCCccccccccccccccc--ccCCCCeEEeCCCCCCCCCccccCcccCCC----CCCCccCccCccccc
Q 000388 306 DESDIMEQDVKVCDICGD--AGREDLLAICSRCSDGAEHTYCMKEMLQKV----PEGDWLCEECKFAEE 368 (1587)
Q Consensus 306 DedDci~~DckvC~VCg~--~gded~LLlCD~CDrGaYH~yCL~PPL~eV----PeGdW~Cp~C~~~~e 368 (1587)
|...+++.. |.||.. .+.-+.||+|++| +.+||..|+.|+.+.. |.+.|||..|....+
T Consensus 162 D~~~~~n~q---c~vC~~g~~~~~NrmlqC~~C-~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~ 226 (464)
T KOG4323|consen 162 DSGHKVNLQ---CSVCYCGGPGAGNRMLQCDKC-RQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPK 226 (464)
T ss_pred Cccccccce---eeeeecCCcCccceeeeeccc-ccHHHHHhccCCCCHhhccCccceEeehhhccchh
Confidence 344454333 666654 4455699999999 5689999999997643 667899999986544
No 16
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=96.98 E-value=0.00024 Score=87.80 Aligned_cols=57 Identities=28% Similarity=0.743 Sum_probs=45.5
Q ss_pred ccccccccccccC--CCCeEEeCCCCCCCCCccccCcccCCCCCCCccCccCc-----ccccccccc
Q 000388 314 DVKVCDICGDAGR--EDLLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECK-----FAEETEKQK 373 (1587)
Q Consensus 314 DckvC~VCg~~gd--ed~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~-----~~~ec~kk~ 373 (1587)
+...|.||+.++- .+.|+|||.|+-- .|+.|++ +.++|+|.|+|..|. .|.-|.++-
T Consensus 270 edviCDvCrspD~e~~neMVfCd~Cn~c-VHqaCyG--Ile~p~gpWlCr~Calg~~ppCvLCPkkG 333 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCDKCNIC-VHQACYG--ILEVPEGPWLCRTCALGIEPPCVLCPKKG 333 (893)
T ss_pred ccceeceecCCCccccceeEEeccchhH-HHHhhhc--eeecCCCCeeehhccccCCCCeeeccccC
Confidence 3446999998853 4579999999755 8999999 999999999999995 344555543
No 17
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=96.70 E-value=0.00061 Score=81.42 Aligned_cols=49 Identities=31% Similarity=0.829 Sum_probs=42.3
Q ss_pred cccccccccccCC--CCeEEeCCCCCCCCCccccCcccCCCCCCCccCccCccc
Q 000388 315 VKVCDICGDAGRE--DLLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECKFA 366 (1587)
Q Consensus 315 ckvC~VCg~~gde--d~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~~ 366 (1587)
+..|.+|...+.+ +.++|||+|+-. .|..|++ +.-+|+|.|+|..|...
T Consensus 193 d~~C~~c~~t~~eN~naiVfCdgC~i~-VHq~CYG--I~f~peG~WlCrkCi~~ 243 (669)
T COG5141 193 DDICTKCTSTHNENSNAIVFCDGCEIC-VHQSCYG--IQFLPEGFWLCRKCIYG 243 (669)
T ss_pred hhhhHhccccccCCcceEEEecCcchh-hhhhccc--ceecCcchhhhhhhccc
Confidence 4679999887754 579999999876 8999999 88999999999999743
No 18
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=96.49 E-value=0.001 Score=81.90 Aligned_cols=46 Identities=35% Similarity=0.905 Sum_probs=38.2
Q ss_pred cccccccccc--CCCCeEEeCC--CCCCCCCccccCcccCCCCCCCccCccCc
Q 000388 316 KVCDICGDAG--REDLLAICSR--CSDGAEHTYCMKEMLQKVPEGDWLCEECK 364 (1587)
Q Consensus 316 kvC~VCg~~g--ded~LLlCD~--CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~ 364 (1587)
--|.||-+.. -|+-|++||+ |.-+ .|..|++ +-.||.|.|||..|.
T Consensus 6 GGCCVCSDErGWaeNPLVYCDG~nCsVA-VHQaCYG--IvqVPtGpWfCrKCe 55 (900)
T KOG0956|consen 6 GGCCVCSDERGWAENPLVYCDGHNCSVA-VHQACYG--IVQVPTGPWFCRKCE 55 (900)
T ss_pred cceeeecCcCCCccCceeeecCCCceee-eehhcce--eEecCCCchhhhhhh
Confidence 3588887643 3667999986 9765 8999999 999999999999994
No 19
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=96.06 E-value=0.0045 Score=79.85 Aligned_cols=80 Identities=29% Similarity=0.652 Sum_probs=64.0
Q ss_pred ccccccccccccCCCCeEEeCCCCCCCCCccccCcccCCCCCCCccCccCccccccccccCCCCccccccccCCcccCCc
Q 000388 314 DVKVCDICGDAGREDLLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECKFAEETEKQKQGSDIEGKRTNKQSTSTQSS 393 (1587)
Q Consensus 314 DckvC~VCg~~gded~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~~~ec~kk~~~~~~egk~~~~~sst~Qss 393 (1587)
+...|..|.++..+..+ .|+.|++. ||.+|..|++..+|+|+|.|+.|... .+.+....++|++. ...|+.+.+
T Consensus 154 ~~~~~~~~~k~~~~~~~-~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~gf~~~---~~~yt~~~f 227 (904)
T KOG1246|consen 154 DYPQCNTCSKGKEEKLL-LCDSCDDS-YHTYCLRPPLTRVPDGDWRCPKCIPT-PESKPNYKFGFEQG---SREYTLPKF 227 (904)
T ss_pred cchhhhccccCCCccce-ecccccCc-ccccccCCCCCcCCcCcccCCccccc-ccCCcccccCcCCC---CCccccchh
Confidence 55679999999988444 99999988 89999999999999999999999976 44444444566654 668888888
Q ss_pred cccccc
Q 000388 394 GKRHAE 399 (1587)
Q Consensus 394 gkr~a~ 399 (1587)
++++..
T Consensus 228 ~~~~~~ 233 (904)
T KOG1246|consen 228 EEYADN 233 (904)
T ss_pred hhHhhh
Confidence 865543
No 20
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=95.28 E-value=0.0028 Score=52.70 Aligned_cols=34 Identities=38% Similarity=1.098 Sum_probs=20.2
Q ss_pred CCeEEeCCCCCCCCCccccCcccCCCCCC-CccCccCc
Q 000388 328 DLLAICSRCSDGAEHTYCMKEMLQKVPEG-DWLCEECK 364 (1587)
Q Consensus 328 d~LLlCD~CDrGaYH~yCL~PPL~eVPeG-dW~Cp~C~ 364 (1587)
+.||+|+.|.-. .|..|++ +..+|.+ +|+|..|.
T Consensus 2 n~ll~C~~C~v~-VH~~CYG--v~~~~~~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDNCNVA-VHQSCYG--VSEVPDGDDWLCDRCE 36 (36)
T ss_dssp CEEEE-SSS--E-EEHHHHT---SS--SS-----HHH-
T ss_pred CceEEeCCCCCc-CChhhCC--cccCCCCCcEECCcCC
Confidence 469999999765 8999999 8888888 89999884
No 21
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=91.97 E-value=0.071 Score=69.39 Aligned_cols=48 Identities=31% Similarity=0.697 Sum_probs=44.0
Q ss_pred ccccccccccCCCCeEEeCCCCCCCCCccccCcccCCCCCCCccCccCcccc
Q 000388 316 KVCDICGDAGREDLLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECKFAE 367 (1587)
Q Consensus 316 kvC~VCg~~gded~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~~~ 367 (1587)
..|.+|++.++ +++|..|++- ||+.|..||+..+|.-.|-|.-|..++
T Consensus 345 dhcrf~~d~~~---~lc~Et~prv-vhlEcv~hP~~~~~s~~~e~evc~~hk 392 (1414)
T KOG1473|consen 345 DHCRFCHDLGD---LLCCETCPRV-VHLECVFHPRFAVPSAFWECEVCNIHK 392 (1414)
T ss_pred ccccccCcccc---eeecccCCce-EEeeecCCccccCCCccchhhhhhhhc
Confidence 47999999988 9999999987 999999999999999999999998544
No 22
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=90.80 E-value=0.34 Score=52.67 Aligned_cols=34 Identities=3% Similarity=-0.080 Sum_probs=24.8
Q ss_pred cccccccccccccCCCCCCCCCccccCCC--CCCCCCCcCCc
Q 000388 250 LTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLA 289 (1587)
Q Consensus 250 ~C~~C~~~ee~nk~~~~gepEELL~Cs~C--s~HpSCLd~s~ 289 (1587)
.|..|..... .-+...||+|..| .||-.||.+-.
T Consensus 1 ~C~~C~~~g~------~~~kG~Lv~CQGCs~sYHk~CLG~Rs 36 (175)
T PF15446_consen 1 TCDTCGYEGD------DRNKGPLVYCQGCSSSYHKACLGPRS 36 (175)
T ss_pred CcccccCCCC------CccCCCeEEcCccChHHHhhhcCCcc
Confidence 4788865211 2245689999999 89999999855
No 23
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=90.67 E-value=0.068 Score=69.59 Aligned_cols=101 Identities=13% Similarity=0.005 Sum_probs=64.1
Q ss_pred cccccccccccccccCCCCCCCCCccccCCC--CCCCCCCcCCcCCCcccCCCCCCCCCC-----CCCcccc--------
Q 000388 248 DVLTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELPDVQRFPAASGDET-----DESDIME-------- 312 (1587)
Q Consensus 248 ~~~C~~C~~~ee~nk~~~~gepEELL~Cs~C--s~HpSCLd~s~e~s~ikky~WQs~DE~-----DedDci~-------- 312 (1587)
+..|.||... ..++.|-.| .+|..|...+..... +..|+++--. ..-+|+-
T Consensus 344 ddhcrf~~d~------------~~~lc~Et~prvvhlEcv~hP~~~~~--s~~~e~evc~~hkvngvvd~vl~~~K~~~~ 409 (1414)
T KOG1473|consen 344 DDHCRFCHDL------------GDLLCCETCPRVVHLECVFHPRFAVP--SAFWECEVCNIHKVNGVVDCVLPPSKNVDS 409 (1414)
T ss_pred cccccccCcc------------cceeecccCCceEEeeecCCccccCC--CccchhhhhhhhccCcccccccChhhcccc
Confidence 3567777763 357888899 678888777665433 3347652100 0000000
Q ss_pred ----------------cccccccccccccCCCCeEEeCC-CCCCCCCc-cccCc--ccCCCCCCCccCccCccc
Q 000388 313 ----------------QDVKVCDICGDAGREDLLAICSR-CSDGAEHT-YCMKE--MLQKVPEGDWLCEECKFA 366 (1587)
Q Consensus 313 ----------------~DckvC~VCg~~gded~LLlCD~-CDrGaYH~-yCL~P--PL~eVPeGdW~Cp~C~~~ 366 (1587)
.-...|.+|+. ++.+|+|+. |+.. ||. .||+- --..+|+|-|+|+.|...
T Consensus 410 iR~~~iG~dr~gr~ywfi~rrl~Ie~~---det~l~yysT~pql-y~ll~cLd~~~~e~~L~d~i~~~~ee~~r 479 (1414)
T KOG1473|consen 410 IRHTPIGRDRYGRKYWFISRRLRIEGM---DETLLWYYSTCPQL-YHLLRCLDRTYVEMYLCDGIWERREEIIR 479 (1414)
T ss_pred eeccCCCcCccccchhceeeeeEEecC---CCcEEEEecCcHHH-HHHHHHhchHHHHHhhccchhhhHHHHHH
Confidence 01235667763 456999998 9987 899 99993 335789999999999643
No 24
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=88.32 E-value=0.15 Score=63.83 Aligned_cols=58 Identities=31% Similarity=0.791 Sum_probs=44.7
Q ss_pred cccccccccccc--CCCCeEEeCCCCCCCCCccccCcccCCC-CCCCccCccCccccccccc
Q 000388 314 DVKVCDICGDAG--REDLLAICSRCSDGAEHTYCMKEMLQKV-PEGDWLCEECKFAEETEKQ 372 (1587)
Q Consensus 314 DckvC~VCg~~g--ded~LLlCD~CDrGaYH~yCL~PPL~eV-PeGdW~Cp~C~~~~ec~kk 372 (1587)
-|..|.+|+..| .+..|+.|..|.. +||.||+.--+... =.+-|.|+.|+.|..|+.-
T Consensus 17 ~~~mc~l~~s~G~~~ag~m~ac~~c~~-~yH~~cvt~~~~~~~l~~gWrC~~crvCe~c~~~ 77 (694)
T KOG4443|consen 17 VCLMCPLCGSSGKGRAGRLLACSDCGQ-KYHPYCVTSWAQHAVLSGGWRCPSCRVCEACGTT 77 (694)
T ss_pred hhhhhhhhccccccccCcchhhhhhcc-cCCcchhhHHHhHHHhcCCcccCCceeeeecccc
Confidence 566788898766 4667999999975 59999999655443 2234999999999999843
No 25
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=88.28 E-value=0.22 Score=57.31 Aligned_cols=30 Identities=17% Similarity=0.046 Sum_probs=24.6
Q ss_pred CCCccccCCC--CCCCCCCcCCcCCCcccCCCCC
Q 000388 269 PDEALKCLDK--DKEELTSTQLAELPDVQRFPAA 300 (1587)
Q Consensus 269 pEELL~Cs~C--s~HpSCLd~s~e~s~ikky~WQ 300 (1587)
-+.||+|.+| .||..||.+++..++.. .|.
T Consensus 293 ddqllfcddcdrgyhmyclsppm~eppeg--sws 324 (336)
T KOG1244|consen 293 DDQLLFCDDCDRGYHMYCLSPPMVEPPEG--SWS 324 (336)
T ss_pred CceeEeecccCCceeeEecCCCcCCCCCC--chh
Confidence 3689999999 79999999988776643 387
No 26
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=85.33 E-value=0.58 Score=57.32 Aligned_cols=47 Identities=9% Similarity=-0.073 Sum_probs=35.3
Q ss_pred cccccccccccccccccCCCCCCCCCccccCCC--CCCCCCCcCCcCCCcc--cCCCCCC
Q 000388 246 SSDVLTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELPDV--QRFPAAS 301 (1587)
Q Consensus 246 Ts~~~C~~C~~~ee~nk~~~~gepEELL~Cs~C--s~HpSCLd~s~e~s~i--kky~WQs 301 (1587)
..+..|++|-+.. +.--++.|..| .||-.||++++.-.+. +.|.|||
T Consensus 542 a~~ysCgiCkks~---------dQHll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqC 592 (707)
T KOG0957|consen 542 AMNYSCGICKKST---------DQHLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQC 592 (707)
T ss_pred ccceeeeeeccch---------hhHHHhhcchhhceeeccccCCccccCcccccCcceee
Confidence 4567899999953 22357899999 7899999998865433 4599993
No 27
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=84.34 E-value=0.32 Score=41.81 Aligned_cols=42 Identities=7% Similarity=-0.023 Sum_probs=31.8
Q ss_pred cccccccccccccCCCCCCCCCccccCCC--CCCCCCCcCCcCCCcccCCCCC
Q 000388 250 LTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELPDVQRFPAA 300 (1587)
Q Consensus 250 ~C~~C~~~ee~nk~~~~gepEELL~Cs~C--s~HpSCLd~s~e~s~ikky~WQ 300 (1587)
+|.+|.+. +..+++|.|..| .||..|+.++..........|.
T Consensus 1 ~C~vC~~~---------~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~ 44 (51)
T PF00628_consen 1 YCPVCGQS---------DDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWY 44 (51)
T ss_dssp EBTTTTSS---------CTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBS
T ss_pred eCcCCCCc---------CCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEE
Confidence 47888883 356789999999 7999999998765444334677
No 28
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=76.67 E-value=1.2 Score=57.11 Aligned_cols=49 Identities=14% Similarity=-0.058 Sum_probs=37.3
Q ss_pred ccccccccccccccccccccccCCCCCCCCCccccCCC---CCCCCCCcCCcCCCcccCCCCC
Q 000388 241 RLVESSSDVLTKVHQKSEAETDRDNGEPPDEALKCLDK---DKEELTSTQLAELPDVQRFPAA 300 (1587)
Q Consensus 241 ~L~~~Ts~~~C~~C~~~ee~nk~~~~gepEELL~Cs~C---s~HpSCLd~s~e~s~ikky~WQ 300 (1587)
.+...+....|.+|... +.+|-||.|..| .||..||++.+-..++ ..|+
T Consensus 208 ~~~~~~E~~~C~IC~~~---------DpEdVLLLCDsCN~~~YH~YCLDPdl~eiP~--~eWY 259 (1134)
T KOG0825|consen 208 ISGLSQEEVKCDICTVH---------DPEDVLLLCDSCNKVYYHVYCLDPDLSESPV--NEWY 259 (1134)
T ss_pred ccCcccccccceeeccC---------ChHHhheeecccccceeeccccCcccccccc--ccee
Confidence 34566777899999985 367789999999 4999999987644443 3487
No 29
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=74.12 E-value=1.4 Score=56.29 Aligned_cols=101 Identities=20% Similarity=0.360 Sum_probs=63.6
Q ss_pred cccccccccccccccccCCCCCCCCCccccCCC--CCCCCCCcCCcCCCcccCCCCCCCCCCCCCccccccccccccccc
Q 000388 246 SSDVLTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELPDVQRFPAASGDETDESDIMEQDVKVCDICGD 323 (1587)
Q Consensus 246 Ts~~~C~~C~~~ee~nk~~~~gepEELL~Cs~C--s~HpSCLd~s~e~s~ikky~WQs~DE~DedDci~~DckvC~VCg~ 323 (1587)
..+++|.||..+. +++..+|++|..| ..|-.|+.... +...+|-|.. |.-.-+-.|..|-.
T Consensus 269 dedviCDvCrspD-------~e~~neMVfCd~Cn~cVHqaCyGIle----~p~gpWlCr~------Calg~~ppCvLCPk 331 (893)
T KOG0954|consen 269 DEDVICDVCRSPD-------SEEANEMVFCDKCNICVHQACYGILE----VPEGPWLCRT------CALGIEPPCVLCPK 331 (893)
T ss_pred cccceeceecCCC-------ccccceeEEeccchhHHHHhhhceee----cCCCCeeehh------ccccCCCCeeeccc
Confidence 3778999999863 5678899999999 78999988633 2236798632 33223456777876
Q ss_pred ccCCCCeEEeCCCCCCCCCcccc--------------Ccc--cCCCCCCCc--cCccCccc
Q 000388 324 AGREDLLAICSRCSDGAEHTYCM--------------KEM--LQKVPEGDW--LCEECKFA 366 (1587)
Q Consensus 324 ~gded~LLlCD~CDrGaYH~yCL--------------~PP--L~eVPeGdW--~Cp~C~~~ 366 (1587)
.|.. |-=..-..-|-|.+|- .|. ...||+..| .|..|...
T Consensus 332 kGGa---mK~~~sgT~wAHvsCALwIPEVsie~~ekmePItkfs~IpesRwslvC~LCk~k 389 (893)
T KOG0954|consen 332 KGGA---MKPTKSGTKWAHVSCALWIPEVSIECPEKMEPITKFSHIPESRWSLVCNLCKVK 389 (893)
T ss_pred cCCc---ccccCCCCeeeEeeeeeccceeeccCHhhcCcccccCCCcHHHHHHHHHHhccc
Confidence 6541 1111111234566663 221 246777888 68888653
No 30
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=71.86 E-value=1.7 Score=53.21 Aligned_cols=45 Identities=9% Similarity=0.020 Sum_probs=30.3
Q ss_pred CCccccCCcccccccccccccccCCCCCCCccCCCCcccccccCC
Q 000388 124 GTAEGQISPKLEIGLDQRISLNKYDDPKGAEGLDDNISCVSRAND 168 (1587)
Q Consensus 124 ~~a~~~~~~~~~~~~d~~~l~n~~~~~~~~E~~dD~~SCis~~~~ 168 (1587)
.+..-+++|..+..|+=..|..+.......+..-+.+.||-..-.
T Consensus 40 ~~~~~sgnp~ve~t~GiiHLyk~n~~~s~~~~~~~~mLcilaVP~ 84 (493)
T KOG0804|consen 40 QIKYSSGNPSVEETHGIIHLYKKNSHSSLKNASSSTMLCILAVPA 84 (493)
T ss_pred cccccCCCCceeeeceeEEEEecCcccccccCCCCcEEEEEeccc
Confidence 455556777777777776677666666666666688888855544
No 31
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=69.76 E-value=3.6 Score=54.94 Aligned_cols=44 Identities=9% Similarity=0.046 Sum_probs=34.0
Q ss_pred cccccccccccccccccCCCCCCCCCccccCCC--CCCCCCCcCCcCCCcccCCCCC
Q 000388 246 SSDVLTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELPDVQRFPAA 300 (1587)
Q Consensus 246 Ts~~~C~~C~~~ee~nk~~~~gepEELL~Cs~C--s~HpSCLd~s~e~s~ikky~WQ 300 (1587)
.....|.||..++- ..-+.+|+|..| .+|-.|+. .+.+....|-
T Consensus 217 ~~D~~C~iC~~~~~-------~n~n~ivfCD~Cnl~VHq~Cyg----i~~ipeg~Wl 262 (1051)
T KOG0955|consen 217 EEDAVCCICLDGEC-------QNSNVIVFCDGCNLAVHQECYG----IPFIPEGQWL 262 (1051)
T ss_pred CCCccceeeccccc-------CCCceEEEcCCCcchhhhhccC----CCCCCCCcEe
Confidence 45568999999863 355789999999 89999998 3345556687
No 33
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=68.67 E-value=4.2 Score=50.35 Aligned_cols=60 Identities=8% Similarity=-0.023 Sum_probs=39.9
Q ss_pred cCCCCCCCccccc-ccccccccccccccccccccCCCCCCCCCccccCCC--CCCCCCCcCCcCCCcccCCCCCC
Q 000388 230 RSPVPDSQSDKRL-VESSSDVLTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELPDVQRFPAAS 301 (1587)
Q Consensus 230 ~~~l~~~ns~k~L-~~~Ts~~~C~~C~~~ee~nk~~~~gepEELL~Cs~C--s~HpSCLd~s~e~s~ikky~WQs 301 (1587)
.+++|+-+ .+.+ +.+.....|.+|.++..+ ..+.+++|..| ..|-+|+.... +....|-|
T Consensus 175 e~~lp~k~-vepi~~~d~~d~~C~~c~~t~~e-------N~naiVfCdgC~i~VHq~CYGI~f----~peG~WlC 237 (669)
T COG5141 175 EHGLPDKH-VEPIEPSDEFDDICTKCTSTHNE-------NSNAIVFCDGCEICVHQSCYGIQF----LPEGFWLC 237 (669)
T ss_pred hccCcccc-ccccCCchhhhhhhHhccccccC-------CcceEEEecCcchhhhhhccccee----cCcchhhh
Confidence 44455522 2233 444567789999987643 56789999999 89999988644 23345773
No 34
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=58.93 E-value=4.3 Score=44.60 Aligned_cols=48 Identities=33% Similarity=0.708 Sum_probs=33.8
Q ss_pred cccccc---cccCCCCeEEeCCCCCCCCCccccCccc------CCCCCCC--ccCccCcc
Q 000388 317 VCDICG---DAGREDLLAICSRCSDGAEHTYCMKEML------QKVPEGD--WLCEECKF 365 (1587)
Q Consensus 317 vC~VCg---~~gded~LLlCD~CDrGaYH~yCL~PPL------~eVPeGd--W~Cp~C~~ 365 (1587)
+|.+|+ ....-..|++|-+|-.+ ||-.||+|.. ++|-.++ .-|..|+.
T Consensus 1 ~C~~C~~~g~~~~kG~Lv~CQGCs~s-YHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Cig 59 (175)
T PF15446_consen 1 TCDTCGYEGDDRNKGPLVYCQGCSSS-YHKACLGPRSQREHLVTKVGDDDFVLQCRRCIG 59 (175)
T ss_pred CcccccCCCCCccCCCeEEcCccChH-HHhhhcCCccccceeeEEEcCCceEEechhhcC
Confidence 477774 44445679999999876 9999999874 3454444 35777763
No 35
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=56.34 E-value=3.7 Score=50.68 Aligned_cols=44 Identities=9% Similarity=-0.079 Sum_probs=30.5
Q ss_pred cccccccccccccCCCCCCCCCccccCCC--CCCCCCCcCCcCCC--cccCCCCC
Q 000388 250 LTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELP--DVQRFPAA 300 (1587)
Q Consensus 250 ~C~~C~~~ee~nk~~~~gepEELL~Cs~C--s~HpSCLd~s~e~s--~ikky~WQ 300 (1587)
.|-||..+. .+.-..||.|..| .||..|-.+..+.. ....|.|+
T Consensus 170 qc~vC~~g~-------~~~~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~ 217 (464)
T KOG4323|consen 170 QCSVCYCGG-------PGAGNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWF 217 (464)
T ss_pred eeeeeecCC-------cCccceeeeecccccHHHHHhccCCCCHhhccCccceEe
Confidence 499999753 3344589999999 79999988765422 23345555
No 36
>PF07744 SPOC: SPOC domain; InterPro: IPR012921 Spen (split end) proteins regulate the expression of key transcriptional effectors in diverse signalling pathways. They are large proteins characterised by N-terminal RNA-binding motifs and a highly conserved C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. The function of the SPOC domain is unknown, but the SPOC domain of the SHARP Spen protein has been implicated in the interaction of SHARP with the SMRT/NcoR corepressor, where SHARP plays an essential role in the repressor complex []. The SPOC domain is folded into a single compact domain consisting of a beta-barrel with seven strands framed by six alpha helices. A number of deep grooves and clefts in the surface, plus two nonpolar loops, render the SPOC domain well suited to protein-protein interactions; most of the conserved residues occur on the protein surface rather than in the core. Other proteins containing a SPOC domain include drosophila Split ends, which promotes sclerite development in the head and restricts it in the thorax, and mouse MINT (homologue of SHARP), which is involved in skeletal and neuronal development via its repression of Msx2.; PDB: 1OW1_A.
Probab=48.60 E-value=15 Score=36.22 Aligned_cols=105 Identities=19% Similarity=0.328 Sum_probs=58.3
Q ss_pred eEEEEEEecCCCCCccccccceecCccccHHHH----HHHhcCCCccccc-cccCCCCCccccccCCCCCCceEEEee-c
Q 000388 848 WQGGFEVHRGEKLPNLCDGIQAHLSSCASSKVL----EVVSKFPQRIRLK-EVPRVSTWPTMFHESGAKEENIALYFF-A 921 (1587)
Q Consensus 848 W~G~F~V~~~~~~~~~~dGL~AHLSskAc~KV~----E~Sk~LP~vL~lE-~LPRl~vWPksF~~~gPtdddIaLYFF-P 921 (1587)
|+|.+.+..-. .....||+=+.. .... .-....|..|.+. -|+...+|.-.-+......-.|-++=| .
T Consensus 1 W~G~i~m~~~~-----~f~~~a~~v~G~-~~~~~~~l~~~~~~p~~i~i~gRl~~~~~~~yl~~i~~s~~~~v~v~~~~~ 74 (119)
T PF07744_consen 1 WQGTISMKSVA-----SFSARAHFVSGN-CDLLDNVLPWQQLPPKKIDIRGRLDPEKVWDYLRQIRKSRSKDVCVVALSS 74 (119)
T ss_dssp EEEEEEETT-E-----EEEEEEEEEEE--HHHHHHHS-------EEE-EEEE-SHHHHHHHHHHTSSTTT-EEEEEEE-S
T ss_pred CceEEEcCCCC-----eEEEEEEEEEcc-hhHhhhhcccccCCCcEEEEEeecCHHHHHHHHHhcccCCCceEEEEEEcC
Confidence 99999998522 123445542221 2221 1112337777776 466666666665665555556666666 1
Q ss_pred C--CcccchhhHHHHHHHHHhccceeeeecc------ceeEEeec
Q 000388 922 K--DFESYGRNYKILVDSMMKNDLALMGNLD------GIELLIFP 958 (1587)
Q Consensus 922 ~--d~er~Ek~~d~LVd~Mi~~DlaLRavI~------~aELLIFp 958 (1587)
. +.......|..|++++..++-+=-+.++ ..+|-|||
T Consensus 75 ~~~~~~~~~~~~~~l~~Yl~~k~r~GVv~~~~~~~~~~~dlYl~P 119 (119)
T PF07744_consen 75 PESDSNSDRRPFQKLVDYLKSKQRAGVVSVGNSPSGQVKDLYLFP 119 (119)
T ss_dssp SHHHHHHHHHHHHHTHHHHHHHTEEEEEEE--TT--S-EEEEEE-
T ss_pred CcccCHHHHHHHHHHHHHHhhCCEEEEEecCCCCCCceeEEEEcC
Confidence 1 3455667899999999999876555565 47788887
No 37
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=46.83 E-value=3.8 Score=52.78 Aligned_cols=47 Identities=15% Similarity=0.094 Sum_probs=42.5
Q ss_pred cccccccccccCCCCeEEeCCCCCCCCCccccCc-ccCCCCCCCccCccCcc
Q 000388 315 VKVCDICGDAGREDLLAICSRCSDGAEHTYCMKE-MLQKVPEGDWLCEECKF 365 (1587)
Q Consensus 315 ckvC~VCg~~gded~LLlCD~CDrGaYH~yCL~P-PL~eVPeGdW~Cp~C~~ 365 (1587)
...|..|.+... .++|+.|-|. ||..|+.| |++..+.|.|.|+.|+.
T Consensus 506 d~~~~~~~~~l~---~l~~p~~lrr-~k~d~l~~~P~Kte~i~~~~~~~~Q~ 553 (696)
T KOG0383|consen 506 DISCEEQIKKLH---LLLCPHMLRR-LKLDVLKPMPLKTELIGRVELSPCQK 553 (696)
T ss_pred hhhHHHHHHhhc---cccCchhhhh-hhhhhccCCCccceeEEEEecCHHHH
Confidence 447999999887 8899999887 99999999 99999999999999974
No 38
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=43.72 E-value=15 Score=46.82 Aligned_cols=47 Identities=28% Similarity=0.637 Sum_probs=39.0
Q ss_pred ccccccccccCCCCeEEeCCCCCCCCCccccCcccC-CCCCCCccCccCccc
Q 000388 316 KVCDICGDAGREDLLAICSRCSDGAEHTYCMKEMLQ-KVPEGDWLCEECKFA 366 (1587)
Q Consensus 316 kvC~VCg~~gded~LLlCD~CDrGaYH~yCL~PPL~-eVPeGdW~Cp~C~~~ 366 (1587)
..|.+|..+++ ++.|+.|+.+ +|..|.++++. ..+.+.|.|..|...
T Consensus 48 ts~~~~~~~gn---~~~~~~~~~s-~h~~~~~~~~sp~~~~~~~~~~~~~~~ 95 (613)
T KOG4299|consen 48 TSCGICKSGGN---LLCCDHCPAS-FHLECDKPPLSPDLKGSEINCSRCPKG 95 (613)
T ss_pred hhcchhhhcCC---ccccccCccc-cchhccCcccCcccccccccccCCCcc
Confidence 36999999998 8999999866 89999999987 334468999999764
No 39
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=39.38 E-value=11 Score=44.30 Aligned_cols=58 Identities=17% Similarity=0.401 Sum_probs=42.3
Q ss_pred ccccccccc------cCCCCeEEeCCCCCCCCCccccCcccC---CCCCCCccCccCccccccccccC
Q 000388 316 KVCDICGDA------GREDLLAICSRCSDGAEHTYCMKEMLQ---KVPEGDWLCEECKFAEETEKQKQ 374 (1587)
Q Consensus 316 kvC~VCg~~------gded~LLlCD~CDrGaYH~yCL~PPL~---eVPeGdW~Cp~C~~~~ec~kk~~ 374 (1587)
..|.+|.++ +..+-|+.|..|.-. ||.+|+.-+.+ .+-...|.|-.|..|.-|.++-.
T Consensus 259 ~~~~~~~~~~~~~~~~r~~S~I~C~~C~~~-~HP~Ci~M~~elv~~~KTY~W~C~~C~lC~IC~~P~~ 325 (381)
T KOG1512|consen 259 NERKHFWDIQTNIIQSRRNSWIVCKPCATR-PHPYCVAMIPELVGQYKTYFWKCSSCELCRICLGPVI 325 (381)
T ss_pred hhhhhhhcchhhhhhhhhccceeecccccC-CCCcchhcCHHHHhHHhhcchhhcccHhhhccCCccc
Confidence 346666553 345679999999755 99999985433 23346899999999988887654
No 40
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=37.38 E-value=15 Score=32.36 Aligned_cols=21 Identities=43% Similarity=0.786 Sum_probs=18.5
Q ss_pred CCccchhhccccCcccccccC
Q 000388 718 SKGVLCQKCKEVGHDVESCPL 738 (1587)
Q Consensus 718 ~~~~~cqkcke~gh~~e~c~~ 738 (1587)
.....||+|.+.||.+--|+.
T Consensus 2 ~~~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 2 NARVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCCCcCcccCCCCcchhhCCC
Confidence 356789999999999999996
No 41
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=36.93 E-value=8.4 Score=53.24 Aligned_cols=49 Identities=12% Similarity=0.016 Sum_probs=39.2
Q ss_pred cccccccccccccccccccccCCCCCCCCCccccCCC--CCCCCCCcCCcCCCcccCCCCCC
Q 000388 242 LVESSSDVLTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELPDVQRFPAAS 301 (1587)
Q Consensus 242 L~~~Ts~~~C~~C~~~ee~nk~~~~gepEELL~Cs~C--s~HpSCLd~s~e~s~ikky~WQs 301 (1587)
+..+..+..|.+|... ++.+.++.|..| .+|..|+.+.+...+. ..|+|
T Consensus 1102 w~~s~~~~~c~~cr~k---------~~~~~m~lc~~c~~~~h~~C~rp~~~~~~~--~dW~C 1152 (1404)
T KOG1245|consen 1102 WDRSAVNALCKVCRRK---------KQDEKMLLCDECLSGFHLFCLRPALSSVPP--GDWMC 1152 (1404)
T ss_pred hccccchhhhhhhhhc---------ccchhhhhhHhhhhhHHHHhhhhhhccCCc--CCccC
Confidence 3567788899999983 466899999999 7899999988776654 44983
No 42
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=35.77 E-value=22 Score=33.05 Aligned_cols=33 Identities=24% Similarity=0.666 Sum_probs=26.3
Q ss_pred cccccccccccC-CCCeEEeCCCCCCCCCccccCc
Q 000388 315 VKVCDICGDAGR-EDLLAICSRCSDGAEHTYCMKE 348 (1587)
Q Consensus 315 ckvC~VCg~~gd-ed~LLlCD~CDrGaYH~yCL~P 348 (1587)
-..|.+|+..-. .+.+++|..|. +-||..|+..
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~Cg-apyHR~C~~~ 38 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECG-APYHRDCWEK 38 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCC-CcccHHHHhh
Confidence 347999998763 56699999996 4599999974
No 43
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=33.39 E-value=16 Score=29.23 Aligned_cols=28 Identities=32% Similarity=0.680 Sum_probs=12.3
Q ss_pred cccccccccCCCCeEEeCCCCCCCCCccc
Q 000388 317 VCDICGDAGREDLLAICSRCSDGAEHTYC 345 (1587)
Q Consensus 317 vC~VCg~~gded~LLlCD~CDrGaYH~yC 345 (1587)
.|.+|+........-.|..|+-. .|..|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~-lH~~C 29 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFD-LHEEC 29 (30)
T ss_dssp --TTTS----S--EEE-TTT------HHH
T ss_pred cCCcCCCcCCCCceEECccCCCc-cChhc
Confidence 69999999887678889999876 58776
No 44
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=33.00 E-value=15 Score=39.87 Aligned_cols=21 Identities=33% Similarity=0.615 Sum_probs=18.1
Q ss_pred CccchhhccccCcccccccCC
Q 000388 719 KGVLCQKCKEVGHDVESCPLG 739 (1587)
Q Consensus 719 ~~~~cqkcke~gh~~e~c~~~ 739 (1587)
..++||+|-+|||.+--|..-
T Consensus 26 ~~~rCQKClq~GHWtYECk~k 46 (177)
T KOG3116|consen 26 SSARCQKCLQAGHWTYECKNK 46 (177)
T ss_pred cchhHHHHHhhccceeeecCc
Confidence 456999999999999998754
No 45
>COG1773 Rubredoxin [Energy production and conversion]
Probab=25.77 E-value=44 Score=31.24 Aligned_cols=39 Identities=28% Similarity=0.810 Sum_probs=25.0
Q ss_pred cccccccccCCCC-eEEeCCCCCCCCCccccCcccCCCCCCCccCccCcc
Q 000388 317 VCDICGDAGREDL-LAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECKF 365 (1587)
Q Consensus 317 vC~VCg~~gded~-LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~ 365 (1587)
.|.+|+-.-++++ ---|+.|+ | -+.+.+|+ +|.||.|-.
T Consensus 5 ~C~~CG~vYd~e~Gdp~~gi~p-g--------T~fedlPd-~w~CP~Cg~ 44 (55)
T COG1773 5 RCSVCGYVYDPEKGDPRCGIAP-G--------TPFEDLPD-DWVCPECGV 44 (55)
T ss_pred EecCCceEeccccCCccCCCCC-C--------CchhhCCC-ccCCCCCCC
Confidence 4888886554332 22355553 2 34677876 899999975
No 46
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 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 the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. 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: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=25.22 E-value=39 Score=24.97 Aligned_cols=16 Identities=44% Similarity=1.014 Sum_probs=14.4
Q ss_pred chhhccccCccccccc
Q 000388 722 LCQKCKEVGHDVESCP 737 (1587)
Q Consensus 722 ~cqkcke~gh~~e~c~ 737 (1587)
.|.+|.+.||..-.|+
T Consensus 2 ~C~~C~~~GH~~~~Cp 17 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCP 17 (18)
T ss_dssp BCTTTSCSSSCGCTSS
T ss_pred cCcCCCCcCcccccCc
Confidence 5899999999998886
No 47
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=24.03 E-value=15 Score=34.67 Aligned_cols=49 Identities=22% Similarity=0.440 Sum_probs=21.1
Q ss_pred ccccccccc---CCCCeEEeC--CCCCCCCCccccCcccCCCCCC-------CccCccCccc
Q 000388 317 VCDICGDAG---REDLLAICS--RCSDGAEHTYCMKEMLQKVPEG-------DWLCEECKFA 366 (1587)
Q Consensus 317 vC~VCg~~g---ded~LLlCD--~CDrGaYH~yCL~PPL~eVPeG-------dW~Cp~C~~~ 366 (1587)
.|.||-..- ++...++|+ .|... ||+.||.--+...+.+ .+.||.|...
T Consensus 4 ~C~IC~~~~~~~~~~p~~~C~n~~C~~~-fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~ 64 (70)
T PF11793_consen 4 ECGICYSYRLDDGEIPDVVCPNPSCGKK-FHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSP 64 (70)
T ss_dssp S-SSS--SS-TT-----B--S-TT-----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SE
T ss_pred CCCcCCcEecCCCCcCceEcCCcccCCH-HHHHHHHHHHHHcccCCeeecccccCCcCCCCe
Confidence 367776542 233468898 89876 8999998665443332 3679999754
No 48
>cd00214 Calpain_III Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains.
Probab=23.99 E-value=1.3e+02 Score=31.63 Aligned_cols=70 Identities=21% Similarity=0.285 Sum_probs=48.1
Q ss_pred CCCCCCceEEEeecCCcc--cchhhHHHHHHH---------HHhccceeeeeccceeEEeecCCCCCccccccccceeEE
Q 000388 908 SGAKEENIALYFFAKDFE--SYGRNYKILVDS---------MMKNDLALMGNLDGIELLIFPSNQLPENCQRWNLLFFLW 976 (1587)
Q Consensus 908 ~gPtdddIaLYFFP~d~e--r~Ek~~d~LVd~---------Mi~~DlaLRavI~~aELLIFpS~lLP~~~Qrf~gk~YLW 976 (1587)
.++....||++.|-.+.+ .....| |+.+ .-.+...++..+.-.+.+|.||+..|.+. |+|.|.
T Consensus 65 ~~~~~~~IGf~v~~~~~~~~~~~~~~--~~~~~~~~~s~~~~~~rev~~~~~L~pG~YvIIPsT~~p~~~----g~F~Lr 138 (150)
T cd00214 65 KGLDLLTIGFHVYKVPGENRHLRRDF--FLHKAPRARSSTFINTREVSLRFRLPPGEYVIVPSTFEPGEE----GEFLLR 138 (150)
T ss_pred cCCCcceEEEEEEEeCCcCcccChhh--hhccCcccccCccccccEEEEEEEcCCCCEEEEeeecCCCCc----ccEEEE
Confidence 356677899999986542 122222 3322 23467888888888899999999999665 777777
Q ss_pred Eeeeeccc
Q 000388 977 GVFRVRKV 984 (1587)
Q Consensus 977 GVFR~rK~ 984 (1587)
||-.+..
T Consensus 139 -Vfs~~~~ 145 (150)
T cd00214 139 -VFSEKSI 145 (150)
T ss_pred -EEecCCC
Confidence 7776654
No 49
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=23.87 E-value=61 Score=42.10 Aligned_cols=47 Identities=21% Similarity=0.521 Sum_probs=28.8
Q ss_pred cccccccccCCCCeEEeCCCCCCCCCccccCcccCCCCCCCccCccCcc
Q 000388 317 VCDICGDAGREDLLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECKF 365 (1587)
Q Consensus 317 vC~VCg~~gded~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~ 365 (1587)
.|..|+..-. +...||..|+...-|..|-.- -..+|.|.=||+.|-.
T Consensus 3 ~Cp~Cg~~n~-~~akFC~~CG~~l~~~~Cp~C-G~~~~~~~~fC~~CG~ 49 (645)
T PRK14559 3 ICPQCQFENP-NNNRFCQKCGTSLTHKPCPQC-GTEVPVDEAHCPNCGA 49 (645)
T ss_pred cCCCCCCcCC-CCCccccccCCCCCCCcCCCC-CCCCCcccccccccCC
Confidence 5777766542 335577777544333455543 2557778888888853
No 50
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=22.82 E-value=60 Score=36.21 Aligned_cols=27 Identities=22% Similarity=0.662 Sum_probs=20.3
Q ss_pred CeEEeCCCCCCCCCccccCcccCCCCCCCccCccCcc
Q 000388 329 LLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECKF 365 (1587)
Q Consensus 329 ~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~ 365 (1587)
....|..|. +.||..|+.. =.||.|..
T Consensus 171 ~~~~C~~C~-~v~H~~C~~~---------~~CpkC~R 197 (202)
T PF13901_consen 171 TTVRCPKCK-SVFHKSCFRK---------KSCPKCAR 197 (202)
T ss_pred CeeeCCcCc-cccchhhcCC---------CCCCCcHh
Confidence 467899995 5599999993 12999964
No 51
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=21.80 E-value=47 Score=40.04 Aligned_cols=38 Identities=32% Similarity=0.676 Sum_probs=31.7
Q ss_pred CeEEeCCCCCCCCCccc--cCcccCCCCC-CCccCccCcccc
Q 000388 329 LLAICSRCSDGAEHTYC--MKEMLQKVPE-GDWLCEECKFAE 367 (1587)
Q Consensus 329 ~LLlCD~CDrGaYH~yC--L~PPL~eVPe-GdW~Cp~C~~~~ 367 (1587)
.|+-|+.|... ||..| .+.+-.++|. -.|+|..|..+.
T Consensus 74 ~~~~cd~C~~~-~~~ec~~v~~~~~e~p~~~~~~c~~c~~~~ 114 (345)
T KOG1632|consen 74 LMEQCDLCEDW-YHGECWEVGTAEKEAPKEDPKVCDECKEAQ 114 (345)
T ss_pred hhhcccccccc-ccccccccCchhhcCCccccccccccchhh
Confidence 68899999876 99999 8888777765 589999997653
No 52
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=20.70 E-value=60 Score=27.57 Aligned_cols=22 Identities=32% Similarity=0.961 Sum_probs=19.3
Q ss_pred CccchhhccccCcccccccCCC
Q 000388 719 KGVLCQKCKEVGHDVESCPLGS 740 (1587)
Q Consensus 719 ~~~~cqkcke~gh~~e~c~~~~ 740 (1587)
.+..|..|...||..+.|+..+
T Consensus 7 ~~Y~C~~C~~~GH~i~dCP~~~ 28 (32)
T PF13696_consen 7 PGYVCHRCGQKGHWIQDCPTNK 28 (32)
T ss_pred CCCEeecCCCCCccHhHCCCCC
Confidence 5678999999999999999853
Done!