Query 000390
Match_columns 1585
No_of_seqs 322 out of 1132
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 06:54:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000390.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000390hhsearch_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 8.5E-24 1.9E-28 230.2 1.4 108 245-366 221-331 (336)
2 KOG1512 PHD Zn-finger protein 99.7 2.9E-18 6.3E-23 188.3 1.0 105 246-367 256-364 (381)
3 KOG4443 Putative transcription 99.1 2.1E-11 4.5E-16 146.1 1.7 106 249-374 19-126 (694)
4 KOG0825 PHD Zn-finger protein 99.0 1.2E-10 2.5E-15 140.6 2.4 56 313-368 213-268 (1134)
5 PF00628 PHD: PHD-finger; Int 98.4 7.5E-08 1.6E-12 82.0 0.4 48 317-365 1-50 (51)
6 KOG4299 PHD Zn-finger protein 98.3 3E-07 6.5E-12 111.2 1.7 52 315-367 253-306 (613)
7 cd04718 BAH_plant_2 BAH, or Br 98.1 1.7E-06 3.7E-11 90.2 2.4 28 341-368 2-29 (148)
8 smart00249 PHD PHD zinc finger 98.0 4.2E-06 9.1E-11 67.9 3.3 46 317-363 1-47 (47)
9 KOG1973 Chromatin remodeling p 97.8 6.4E-06 1.4E-10 92.7 2.1 46 316-367 222-269 (274)
10 KOG1245 Chromatin remodeling c 97.8 3.7E-06 8E-11 110.7 -0.9 54 314-368 1107-1160(1404)
11 KOG0383 Predicted helicase [Ge 97.8 1.1E-05 2.3E-10 100.3 2.8 48 313-364 45-92 (696)
12 COG5034 TNG2 Chromatin remodel 97.7 2.2E-05 4.8E-10 87.6 2.9 46 316-365 222-269 (271)
13 KOG0955 PHD finger protein BR1 97.4 6.2E-05 1.3E-09 96.8 2.8 53 313-368 217-271 (1051)
14 KOG0957 PHD finger protein [Ge 97.4 5.2E-05 1.1E-09 90.1 0.9 51 315-366 544-598 (707)
15 KOG4323 Polycomb-like PHD Zn-f 97.3 0.00017 3.6E-09 86.5 3.7 61 306-368 162-226 (464)
16 KOG0954 PHD finger protein [Ge 96.9 0.00035 7.6E-09 86.4 1.1 50 314-366 270-321 (893)
17 COG5141 PHD zinc finger-contai 96.6 0.00073 1.6E-08 80.8 1.6 51 314-367 192-244 (669)
18 KOG1246 DNA-binding protein ju 96.3 0.0025 5.5E-08 82.1 3.9 79 314-396 154-232 (904)
19 KOG0956 PHD finger protein AF1 95.7 0.0048 1E-07 76.4 1.9 46 316-364 6-55 (900)
20 PF13831 PHD_2: PHD-finger; PD 94.6 0.0053 1.1E-07 51.1 -1.6 34 328-364 2-36 (36)
21 KOG1473 Nucleosome remodeling 92.7 0.052 1.1E-06 70.5 1.7 49 315-367 344-392 (1414)
22 PF15446 zf-PHD-like: PHD/FYVE 91.0 0.28 6E-06 53.4 4.6 94 250-350 1-143 (175)
23 KOG1473 Nucleosome remodeling 90.9 0.056 1.2E-06 70.3 -0.7 101 248-366 344-479 (1414)
24 KOG0954 PHD finger protein [Ge 89.9 0.12 2.7E-06 65.1 1.0 103 247-369 270-392 (893)
25 KOG4299 PHD Zn-finger protein 88.9 0.29 6.4E-06 61.1 3.2 45 248-301 253-299 (613)
26 KOG4443 Putative transcription 88.5 0.14 3.1E-06 64.1 0.2 56 314-370 17-75 (694)
27 KOG0957 PHD finger protein [Ge 86.8 0.44 9.6E-06 58.3 2.9 45 247-300 543-591 (707)
28 KOG1244 Predicted transcriptio 86.2 0.36 7.7E-06 55.7 1.6 40 250-300 283-324 (336)
29 PF00628 PHD: PHD-finger; Int 84.3 0.3 6.5E-06 41.9 -0.1 42 250-300 1-44 (51)
30 KOG0825 PHD Zn-finger protein 76.6 1.2 2.6E-05 57.1 1.4 49 241-300 208-259 (1134)
31 KOG0955 PHD finger protein BR1 71.4 3.6 7.7E-05 55.0 3.8 46 245-301 216-263 (1051)
32 KOG0804 Cytoplasmic Zn-finger 69.0 2.2 4.8E-05 52.2 1.2 45 124-168 40-84 (493)
33 COG5141 PHD zinc finger-contai 67.9 4.7 0.0001 49.9 3.6 60 230-301 175-237 (669)
34 smart00249 PHD PHD zinc finger 63.9 6.2 0.00013 32.1 2.5 41 250-300 1-43 (47)
35 PF15446 zf-PHD-like: PHD/FYVE 58.1 4.7 0.0001 44.4 1.1 48 317-365 1-59 (175)
36 KOG4323 Polycomb-like PHD Zn-f 51.1 5.8 0.00013 49.1 0.5 45 249-300 169-217 (464)
37 PF07744 SPOC: SPOC domain; I 48.2 15 0.00033 36.2 2.8 105 846-956 1-119 (119)
38 PF14446 Prok-RING_1: Prokaryo 44.3 13 0.00029 34.4 1.6 35 314-349 4-39 (54)
39 KOG0383 Predicted helicase [Ge 43.5 4.1 8.9E-05 52.5 -2.4 48 315-366 506-554 (696)
40 KOG1245 Chromatin remodeling c 37.8 8.1 0.00018 53.4 -1.1 48 243-301 1103-1152(1404)
41 PF13917 zf-CCHC_3: Zinc knuck 37.1 16 0.00034 32.3 0.9 21 716-736 2-22 (42)
42 KOG1512 PHD Zn-finger protein 36.5 12 0.00025 44.1 -0.0 55 316-371 259-322 (381)
43 KOG3116 Predicted C3H1-type Zn 32.7 16 0.00034 39.8 0.2 21 717-737 26-46 (177)
44 PF07649 C1_3: C1-like domain; 28.9 21 0.00045 28.6 0.3 29 316-345 1-29 (30)
45 PRK14559 putative protein seri 25.6 58 0.0013 42.3 3.5 49 317-367 3-51 (645)
46 PF00098 zf-CCHC: Zinc knuckle 25.0 39 0.00086 24.9 1.1 16 720-735 2-17 (18)
47 PF11793 FANCL_C: FANCL C-term 24.9 14 0.00031 34.8 -1.5 50 317-367 4-65 (70)
48 COG1773 Rubredoxin [Energy pro 24.0 48 0.001 31.0 1.7 39 317-365 5-44 (55)
49 cd00214 Calpain_III Calpain, s 23.6 1.4E+02 0.003 31.6 5.1 70 906-982 65-145 (150)
50 PF13696 zf-CCHC_2: Zinc knuck 20.4 61 0.0013 27.5 1.4 22 717-738 7-28 (32)
51 KOG1632 Uncharacterized PHD Zn 20.0 56 0.0012 39.4 1.7 47 321-368 65-115 (345)
No 1
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=99.87 E-value=8.5e-24 Score=230.19 Aligned_cols=108 Identities=24% Similarity=0.539 Sum_probs=101.9
Q ss_pred cccccccccccccccccCCCCCCCCCCceecCCC--CCCccCCccCcCCC-cccCCCCcCCCCCCccccccccccccccc
Q 000390 245 SSSDVLTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELP-DVQRFPAASGDETDESDIMEQDVKVCDIC 321 (1585)
Q Consensus 245 ~Ts~~~C~~C~~tee~nd~d~~gqpEeLL~Cs~C--s~H~sCLd~~~e~~-~ikky~WQs~DE~d~~DCi~~DckvC~VC 321 (1585)
.-++.+|.||++....|++ .+.||+||+|++| ++||+||+++..|. .+++|.|| |+ +|+.|.+|
T Consensus 221 a~Pn~YCDFclgdsr~nkk--t~~peelvscsdcgrsghpsclqft~nm~~avk~yrwq---------ci--eck~csic 287 (336)
T KOG1244|consen 221 AQPNPYCDFCLGDSRENKK--TGMPEELVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQ---------CI--ECKYCSIC 287 (336)
T ss_pred ccCCcccceeccccccccc--cCCchhhcchhhcCCCCCcchhhhhHHHHHHHHhheee---------ee--ecceeccc
Confidence 5678899999999888886 8999999999999 89999999999988 78889999 87 99999999
Q ss_pred cCCCCCCCceeeCCCCCCCCCccccCcccCCCCCCCccCccCccc
Q 000390 322 GDAGREDLLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECKFA 366 (1585)
Q Consensus 322 g~~gded~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~~ 366 (1585)
|..+++++|||||.|||| ||||||.|||-+.|+|.|.|..|...
T Consensus 288 gtsenddqllfcddcdrg-yhmyclsppm~eppegswsc~KOG~~ 331 (336)
T KOG1244|consen 288 GTSENDDQLLFCDDCDRG-YHMYCLSPPMVEPPEGSWSCHLCLEE 331 (336)
T ss_pred cCcCCCceeEeecccCCc-eeeEecCCCcCCCCCCchhHHHHHHH
Confidence 999999999999999999 89999999999999999999999754
No 2
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=99.69 E-value=2.9e-18 Score=188.27 Aligned_cols=105 Identities=21% Similarity=0.426 Sum_probs=95.8
Q ss_pred ccccccccccccccccCCCCCCCCCCceecCCC--CCCccCCccCcCCC-cccCCCCcCCCCCCcccccccccccccccc
Q 000390 246 SSDVLTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELP-DVQRFPAASGDETDESDIMEQDVKVCDICG 322 (1585)
Q Consensus 246 Ts~~~C~~C~~tee~nd~d~~gqpEeLL~Cs~C--s~H~sCLd~~~e~~-~ikky~WQs~DE~d~~DCi~~DckvC~VCg 322 (1585)
..+..|++|..+.+.++ ++..+.+|.|+.| .+||+|++++++++ .+++|.|+ |+ +|+.|.+|+
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 67889999999877665 8999999999999 89999999999998 67889999 76 999999999
Q ss_pred CCCCCCCceeeCCCCCCCCCccccCcccCCCCCCCccCc-cCcccc
Q 000390 323 DAGREDLLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCE-ECKFAE 367 (1585)
Q Consensus 323 ~~gded~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp-~C~~~~ 367 (1585)
.+..++.++|||.|||| ||+||.+ |..+|.|.|+|. .|....
T Consensus 322 ~P~~E~E~~FCD~CDRG-~HT~CVG--L~~lP~G~WICD~~C~~~~ 364 (381)
T KOG1512|consen 322 GPVIESEHLFCDVCDRG-PHTLCVG--LQDLPRGEWICDMRCREAT 364 (381)
T ss_pred CcccchheeccccccCC-CCccccc--cccccCccchhhhHHHHhc
Confidence 99999999999999999 7999999 999999999998 365443
No 3
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=99.10 E-value=2.1e-11 Score=146.06 Aligned_cols=106 Identities=25% Similarity=0.494 Sum_probs=87.5
Q ss_pred cccccccccccccCCCCCCCCCCceecCCC--CCCccCCccCcCCCcccCCCCcCCCCCCccccccccccccccccCCCC
Q 000390 249 VLTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELPDVQRFPAASGDETDESDIMEQDVKVCDICGDAGR 326 (1585)
Q Consensus 249 ~~C~~C~~tee~nd~d~~gqpEeLL~Cs~C--s~H~sCLd~~~e~~~ikky~WQs~DE~d~~DCi~~DckvC~VCg~~gd 326 (1585)
.+|.+|.... .+.+.-|+.|.+| .||+.|...++..... ...|+ |. +|.+|+.|+..++
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---------CP--SCRVCEACGTTGD 79 (694)
T ss_pred hhhhhhcccc-------ccccCcchhhhhhcccCCcchhhHHHhHHHh-cCCcc---------cC--CceeeeeccccCC
Confidence 3566666642 5677889999999 8999999876654322 23377 53 8999999999999
Q ss_pred CCCceeeCCCCCCCCCccccCcccCCCCCCCccCccCccccchhhhhh
Q 000390 327 EDLLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECKFAEETEKQKQ 374 (1585)
Q Consensus 327 ed~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~~~e~ekk~~ 374 (1585)
+..+++|+.||.. ||.||+.|+++.||.|.|+|+.|..+..|....+
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 9999999999977 8999999999999999999999999988866443
No 4
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=99.00 E-value=1.2e-10 Score=140.63 Aligned_cols=56 Identities=34% Similarity=0.812 Sum_probs=51.9
Q ss_pred ccccccccccCCCCCCCceeeCCCCCCCCCccccCcccCCCCCCCccCccCccccc
Q 000390 313 QDVKVCDICGDAGREDLLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECKFAEE 368 (1585)
Q Consensus 313 ~DckvC~VCg~~gded~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~~~e 368 (1585)
.+...|.+|...+.+++||+||.|+.++||+|||+|+|-++|-+.|||++|..-..
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 46679999999999999999999999999999999999999999999999976543
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=98.38 E-value=7.5e-08 Score=81.97 Aligned_cols=48 Identities=27% Similarity=0.832 Sum_probs=42.7
Q ss_pred ccccccCCCCCCCceeeCCCCCCCCCccccCcccC--CCCCCCccCccCcc
Q 000390 317 VCDICGDAGREDLLAICSRCSDGAEHTYCMKEMLQ--KVPEGDWLCEECKF 365 (1585)
Q Consensus 317 vC~VCg~~gded~LLlCD~CDrGaYH~yCL~PPL~--eVPeGdW~Cp~C~~ 365 (1585)
+|.+|+..+.++.||.||.|++. ||++|++|++. .++.+.|+|+.|..
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 58899998889999999999977 89999999987 66667999999974
No 6
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.25 E-value=3e-07 Score=111.16 Aligned_cols=52 Identities=27% Similarity=0.783 Sum_probs=46.4
Q ss_pred ccccccccCCCCCCCceeeCCCCCCCCCccccCcc--cCCCCCCCccCccCcccc
Q 000390 315 VKVCDICGDAGREDLLAICSRCSDGAEHTYCMKEM--LQKVPEGDWLCEECKFAE 367 (1585)
Q Consensus 315 ckvC~VCg~~gded~LLlCD~CDrGaYH~yCL~PP--L~eVPeGdW~Cp~C~~~~ 367 (1585)
.++|..|+..+.-..+++||+|+++ ||++||.|| .+.+|.|.|+|++|....
T Consensus 253 ~~fCsaCn~~~~F~~~i~CD~Cp~s-FH~~CLePPl~~eniP~g~W~C~ec~~k~ 306 (613)
T KOG4299|consen 253 EDFCSACNGSGLFNDIICCDGCPRS-FHQTCLEPPLEPENIPPGSWFCPECKIKS 306 (613)
T ss_pred HHHHHHhCCccccccceeecCCchH-HHHhhcCCCCCcccCCCCccccCCCeeee
Confidence 4699999999987778999999999 699999999 578999999999997544
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=98.06 E-value=1.7e-06 Score=90.24 Aligned_cols=28 Identities=39% Similarity=1.014 Sum_probs=25.9
Q ss_pred CCccccCcccCCCCCCCccCccCccccc
Q 000390 341 EHTYCMKEMLQKVPEGDWLCEECKFAEE 368 (1585)
Q Consensus 341 YH~yCL~PPL~eVPeGdW~Cp~C~~~~e 368 (1585)
||++||+|||+.+|+|+|+||.|.....
T Consensus 2 ~H~~CL~Ppl~~~P~g~W~Cp~C~~~~~ 29 (148)
T cd04718 2 FHLCCLRPPLKEVPEGDWICPFCEVEKS 29 (148)
T ss_pred cccccCCCCCCCCCCCCcCCCCCcCCCC
Confidence 8999999999999999999999987643
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 KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=97.84 E-value=6.4e-06 Score=92.74 Aligned_cols=46 Identities=28% Similarity=0.711 Sum_probs=38.7
Q ss_pred cccccccCCCCCCCceeeCC--CCCCCCCccccCcccCCCCCCCccCccCcccc
Q 000390 316 KVCDICGDAGREDLLAICSR--CSDGAEHTYCMKEMLQKVPEGDWLCEECKFAE 367 (1585)
Q Consensus 316 kvC~VCg~~gded~LLlCD~--CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~~~ 367 (1585)
++|. |...|. |+-||. |+..|||+.|.+ |...|.|.|||+.|....
T Consensus 222 C~Cn-qvsyg~---Mi~CDn~~C~~eWFH~~CVG--L~~~PkgkWyC~~C~~~~ 269 (274)
T KOG1973|consen 222 CICN-QVSYGK---MIGCDNPGCPIEWFHFTCVG--LKTKPKGKWYCPRCKAEN 269 (274)
T ss_pred EEec-cccccc---ccccCCCCCCcceEEEeccc--cccCCCCcccchhhhhhh
Confidence 3455 555554 999999 998999999999 999999999999998654
No 10
>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=3.7e-06 Score=110.67 Aligned_cols=54 Identities=28% Similarity=0.900 Sum_probs=50.1
Q ss_pred cccccccccCCCCCCCceeeCCCCCCCCCccccCcccCCCCCCCccCccCccccc
Q 000390 314 DVKVCDICGDAGREDLLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECKFAEE 368 (1585)
Q Consensus 314 DckvC~VCg~~gded~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~~~e 368 (1585)
..-.|.+|...+..+.|++||.|+.+ ||+||+.|.+..+|.|+|+|+.|+....
T Consensus 1107 ~~~~c~~cr~k~~~~~m~lc~~c~~~-~h~~C~rp~~~~~~~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1107 VNALCKVCRRKKQDEKMLLCDECLSG-FHLFCLRPALSSVPPGDWMCPSCRKEHR 1160 (1404)
T ss_pred chhhhhhhhhcccchhhhhhHhhhhh-HHHHhhhhhhccCCcCCccCCccchhhh
Confidence 34589999999999999999999998 7999999999999999999999998875
No 11
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=97.78 E-value=1.1e-05 Score=100.29 Aligned_cols=48 Identities=31% Similarity=0.856 Sum_probs=44.0
Q ss_pred ccccccccccCCCCCCCceeeCCCCCCCCCccccCcccCCCCCCCccCccCc
Q 000390 313 QDVKVCDICGDAGREDLLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECK 364 (1585)
Q Consensus 313 ~DckvC~VCg~~gded~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~ 364 (1585)
.+...|.+|+.++. +|+||.|... ||.+|++||+..+|.|+|.|+.|.
T Consensus 45 ~~~e~c~ic~~~g~---~l~c~tC~~s-~h~~cl~~pl~~~p~~~~~c~Rc~ 92 (696)
T KOG0383|consen 45 AEQEACRICADGGE---LLWCDTCPAS-FHASCLGPPLTPQPNGEFICPRCF 92 (696)
T ss_pred hhhhhhhhhcCCCc---EEEeccccHH-HHHHccCCCCCcCCccceeeeeec
Confidence 36679999999997 9999999976 899999999999999999999993
No 12
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=97.68 E-value=2.2e-05 Score=87.63 Aligned_cols=46 Identities=30% Similarity=0.799 Sum_probs=39.8
Q ss_pred cccccccCCCCCCCceeeCC--CCCCCCCccccCcccCCCCCCCccCccCcc
Q 000390 316 KVCDICGDAGREDLLAICSR--CSDGAEHTYCMKEMLQKVPEGDWLCEECKF 365 (1585)
Q Consensus 316 kvC~VCg~~gded~LLlCD~--CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~ 365 (1585)
.+| -|++... ..|+-||. |.+-|||+.|.+ |...|+|.|||+.|..
T Consensus 222 lYC-fCqqvSy-GqMVaCDn~nCkrEWFH~~CVG--Lk~pPKG~WYC~eCk~ 269 (271)
T COG5034 222 LYC-FCQQVSY-GQMVACDNANCKREWFHLECVG--LKEPPKGKWYCPECKK 269 (271)
T ss_pred eEE-Eeccccc-ccceecCCCCCchhheeccccc--cCCCCCCcEeCHHhHh
Confidence 356 5787765 44999997 999999999999 9999999999999974
No 13
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=97.45 E-value=6.2e-05 Score=96.83 Aligned_cols=53 Identities=30% Similarity=0.804 Sum_probs=46.1
Q ss_pred ccccccccccCCCCC--CCceeeCCCCCCCCCccccCcccCCCCCCCccCccCccccc
Q 000390 313 QDVKVCDICGDAGRE--DLLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECKFAEE 368 (1585)
Q Consensus 313 ~DckvC~VCg~~gde--d~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~~~e 368 (1585)
++..+|.||.+..-. +.+|+||.|+.+ +|++|++ ..-+|+|.|+|..|.....
T Consensus 217 ~~D~~C~iC~~~~~~n~n~ivfCD~Cnl~-VHq~Cyg--i~~ipeg~WlCr~Cl~s~~ 271 (1051)
T KOG0955|consen 217 EEDAVCCICLDGECQNSNVIVFCDGCNLA-VHQECYG--IPFIPEGQWLCRRCLQSPQ 271 (1051)
T ss_pred CCCccceeecccccCCCceEEEcCCCcch-hhhhccC--CCCCCCCcEeehhhccCcC
Confidence 366799999998866 899999999987 8999999 6689999999999976543
No 14
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=97.37 E-value=5.2e-05 Score=90.13 Aligned_cols=51 Identities=29% Similarity=0.716 Sum_probs=46.1
Q ss_pred ccccccccCCCCCCCceeeCCCCCCCCCccccCcccCCCCCC----CccCccCccc
Q 000390 315 VKVCDICGDAGREDLLAICSRCSDGAEHTYCMKEMLQKVPEG----DWLCEECKFA 366 (1585)
Q Consensus 315 ckvC~VCg~~gded~LLlCD~CDrGaYH~yCL~PPL~eVPeG----dW~Cp~C~~~ 366 (1585)
...|-+|.+..+.++++.||.|... ||+-||.|||+.+|.- .|.|.+|...
T Consensus 544 ~ysCgiCkks~dQHll~~CDtC~lh-YHlGCL~PPLTR~Pkk~kn~gWqCsECdk~ 598 (707)
T KOG0957|consen 544 NYSCGICKKSTDQHLLTQCDTCHLH-YHLGCLSPPLTRLPKKNKNFGWQCSECDKN 598 (707)
T ss_pred ceeeeeeccchhhHHHhhcchhhce-eeccccCCccccCcccccCcceeecccccc
Confidence 5689999999999999999999987 9999999999999985 4999999443
No 15
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=97.28 E-value=0.00017 Score=86.47 Aligned_cols=61 Identities=23% Similarity=0.676 Sum_probs=43.9
Q ss_pred CccccccccccccccccCCCCCCCceeeCCCCCCCCCccccCcccCCC----CCCCccCccCccccc
Q 000390 306 DESDIMEQDVKVCDICGDAGREDLLAICSRCSDGAEHTYCMKEMLQKV----PEGDWLCEECKFAEE 368 (1585)
Q Consensus 306 d~~DCi~~DckvC~VCg~~gded~LLlCD~CDrGaYH~yCL~PPL~eV----PeGdW~Cp~C~~~~e 368 (1585)
|...+++..|.+| .|+..+.-+.||.|++|. .+||..|+.|+.+.. |.+.|||..|....+
T Consensus 162 D~~~~~n~qc~vC-~~g~~~~~NrmlqC~~C~-~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~ 226 (464)
T KOG4323|consen 162 DSGHKVNLQCSVC-YCGGPGAGNRMLQCDKCR-QWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPK 226 (464)
T ss_pred Cccccccceeeee-ecCCcCccceeeeecccc-cHHHHHhccCCCCHhhccCccceEeehhhccchh
Confidence 4555665454444 345555566999999995 679999999997543 667899999986543
No 16
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=96.86 E-value=0.00035 Score=86.39 Aligned_cols=50 Identities=30% Similarity=0.899 Sum_probs=42.8
Q ss_pred cccccccccCCCC--CCCceeeCCCCCCCCCccccCcccCCCCCCCccCccCccc
Q 000390 314 DVKVCDICGDAGR--EDLLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECKFA 366 (1585)
Q Consensus 314 DckvC~VCg~~gd--ed~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~~ 366 (1585)
+...|.||..++. .+.|+|||.|+-. .|+.|++ +.++|+|.|+|..|.-.
T Consensus 270 edviCDvCrspD~e~~neMVfCd~Cn~c-VHqaCyG--Ile~p~gpWlCr~Calg 321 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCDKCNIC-VHQACYG--ILEVPEGPWLCRTCALG 321 (893)
T ss_pred ccceeceecCCCccccceeEEeccchhH-HHHhhhc--eeecCCCCeeehhcccc
Confidence 4558999998853 4579999999876 7999999 99999999999999643
No 17
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=96.65 E-value=0.00073 Score=80.78 Aligned_cols=51 Identities=31% Similarity=0.791 Sum_probs=43.6
Q ss_pred cccccccccCCCCC--CCceeeCCCCCCCCCccccCcccCCCCCCCccCccCcccc
Q 000390 314 DVKVCDICGDAGRE--DLLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECKFAE 367 (1585)
Q Consensus 314 DckvC~VCg~~gde--d~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~~~ 367 (1585)
-+..|.+|...+.+ +.+++||+|+-+ .|..|++ +.-+|+|.|+|..|....
T Consensus 192 ~d~~C~~c~~t~~eN~naiVfCdgC~i~-VHq~CYG--I~f~peG~WlCrkCi~~~ 244 (669)
T COG5141 192 FDDICTKCTSTHNENSNAIVFCDGCEIC-VHQSCYG--IQFLPEGFWLCRKCIYGE 244 (669)
T ss_pred hhhhhHhccccccCCcceEEEecCcchh-hhhhccc--ceecCcchhhhhhhcccc
Confidence 35689999887754 579999999987 7999999 779999999999998654
No 18
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=96.34 E-value=0.0025 Score=82.08 Aligned_cols=79 Identities=28% Similarity=0.633 Sum_probs=67.6
Q ss_pred cccccccccCCCCCCCceeeCCCCCCCCCccccCcccCCCCCCCccCccCccccchhhhhhcccccccCCcccccccccc
Q 000390 314 DVKVCDICGDAGREDLLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECKFAEETEKQKQDIEGKRTNKQSTSTQSSGK 393 (1585)
Q Consensus 314 DckvC~VCg~~gded~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~~~e~ekk~~d~~Gkr~~k~~~s~QsfgK 393 (1585)
+...|..|.+...+. ++.|+.|.+. ||.+|..|+++.+|+|+|.|+.|..... ......+||.+....|+++.|++
T Consensus 154 ~~~~~~~~~k~~~~~-~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~gf~~~~~~yt~~~f~~ 229 (904)
T KOG1246|consen 154 DYPQCNTCSKGKEEK-LLLCDSCDDS-YHTYCLRPPLTRVPDGDWRCPKCIPTPE--SKPNYKFGFEQGSREYTLPKFEE 229 (904)
T ss_pred cchhhhccccCCCcc-ceecccccCc-ccccccCCCCCcCCcCcccCCccccccc--CCcccccCcCCCCCccccchhhh
Confidence 667899999999884 4499999998 8999999999999999999999998733 44555789999999999999887
Q ss_pred ccc
Q 000390 394 RHA 396 (1585)
Q Consensus 394 R~A 396 (1585)
++.
T Consensus 230 ~~~ 232 (904)
T KOG1246|consen 230 YAD 232 (904)
T ss_pred Hhh
Confidence 664
No 19
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=95.68 E-value=0.0048 Score=76.36 Aligned_cols=46 Identities=37% Similarity=0.948 Sum_probs=37.5
Q ss_pred cccccccC-CCC-CCCceeeCC--CCCCCCCccccCcccCCCCCCCccCccCc
Q 000390 316 KVCDICGD-AGR-EDLLAICSR--CSDGAEHTYCMKEMLQKVPEGDWLCEECK 364 (1585)
Q Consensus 316 kvC~VCg~-~gd-ed~LLlCD~--CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~ 364 (1585)
--|-||-+ .|+ |+-|++||+ |.-+ .|..|++ +-.||.|.|||..|.
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 35667754 344 567999997 9876 8999999 889999999999994
No 20
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=94.57 E-value=0.0053 Score=51.11 Aligned_cols=34 Identities=38% Similarity=1.098 Sum_probs=20.1
Q ss_pred CCceeeCCCCCCCCCccccCcccCCCCCC-CccCccCc
Q 000390 328 DLLAICSRCSDGAEHTYCMKEMLQKVPEG-DWLCEECK 364 (1585)
Q Consensus 328 d~LLlCD~CDrGaYH~yCL~PPL~eVPeG-dW~Cp~C~ 364 (1585)
+.||.|+.|.-. .|..|++ +..+|.+ +|+|..|.
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 458999999876 7999999 7788887 89999884
No 21
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=92.67 E-value=0.052 Score=70.53 Aligned_cols=49 Identities=31% Similarity=0.663 Sum_probs=44.6
Q ss_pred ccccccccCCCCCCCceeeCCCCCCCCCccccCcccCCCCCCCccCccCcccc
Q 000390 315 VKVCDICGDAGREDLLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECKFAE 367 (1585)
Q Consensus 315 ckvC~VCg~~gded~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~~~ 367 (1585)
...|.+|++.++ ++||..|++- ||+.|..||+..+|+..|.|..|...+
T Consensus 344 ddhcrf~~d~~~---~lc~Et~prv-vhlEcv~hP~~~~~s~~~e~evc~~hk 392 (1414)
T KOG1473|consen 344 DDHCRFCHDLGD---LLCCETCPRV-VHLECVFHPRFAVPSAFWECEVCNIHK 392 (1414)
T ss_pred cccccccCcccc---eeecccCCce-EEeeecCCccccCCCccchhhhhhhhc
Confidence 468999999998 9999999998 899999999999999999999997443
No 22
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=91.04 E-value=0.28 Score=53.35 Aligned_cols=94 Identities=12% Similarity=0.149 Sum_probs=54.6
Q ss_pred ccccccccccccCCCCCCCCCCceecCCC--CCCccCCccCcCCC-cccC-----CCCcCC---CCCCcccccccccccc
Q 000390 250 LTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELP-DVQR-----FPAASG---DETDESDIMEQDVKVC 318 (1585)
Q Consensus 250 ~C~~C~~tee~nd~d~~gqpEeLL~Cs~C--s~H~sCLd~~~e~~-~ikk-----y~WQs~---DE~d~~DCi~~DckvC 318 (1585)
.|..|..... .-+...||+|..| .||-.||.+-..-. -+.+ +--||- .-.-..|..-.....|
T Consensus 1 ~C~~C~~~g~------~~~kG~Lv~CQGCs~sYHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Cig~~~kKD~~aP~~~~C 74 (175)
T PF15446_consen 1 TCDTCGYEGD------DRNKGPLVYCQGCSSSYHKACLGPRSQREHLVTKVGDDDFVLQCRRCIGIAHKKDPRAPHHGMC 74 (175)
T ss_pred CcccccCCCC------CccCCCeEEcCccChHHHhhhcCCccccceeeEEEcCCceEEechhhcChhhcccCCCCCCCcc
Confidence 4778865211 2245689999999 89999999855322 1112 111110 0000011112356688
Q ss_pred ccccCCCC-------------------------------------C-CCceeeCCCCCCCCCccccCccc
Q 000390 319 DICGDAGR-------------------------------------E-DLLAICSRCSDGAEHTYCMKEML 350 (1585)
Q Consensus 319 ~VCg~~gd-------------------------------------e-d~LLlCD~CDrGaYH~yCL~PPL 350 (1585)
+.|...|. . ++|--|..|-|+ ||+.-|.|+-
T Consensus 75 ~~C~~~G~~c~pfr~r~T~kQEe~~ReeNgG~DPit~Vd~~lvnN~~nVLFRC~~C~Ra-wH~~HLP~~~ 143 (175)
T PF15446_consen 75 QQCKKPGPSCKPFRPRKTPKQEEKLREENGGVDPITPVDPELVNNPDNVLFRCTSCHRA-WHFEHLPPPS 143 (175)
T ss_pred cccCCCCCCCcccCCCCCcHHHHHHHHHcCCCCCCccCCHHHccChhheEEecCCccce-eehhhCCCCc
Confidence 88876431 1 245559999999 7999998764
No 23
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=90.92 E-value=0.056 Score=70.29 Aligned_cols=101 Identities=13% Similarity=-0.004 Sum_probs=65.5
Q ss_pred ccccccccccccccCCCCCCCCCCceecCCC--CCCccCCccCcCCCcccCCCCcCCCCC-----Cccccccc-------
Q 000390 248 DVLTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELPDVQRFPAASGDET-----DESDIMEQ------- 313 (1585)
Q Consensus 248 ~~~C~~C~~tee~nd~d~~gqpEeLL~Cs~C--s~H~sCLd~~~e~~~ikky~WQs~DE~-----d~~DCi~~------- 313 (1585)
+..|.||... .+++.|-.| .+|..|...+..... +.-|+|+=-. ...+|+-.
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 3467777663 467889999 678888887775543 3447752000 00111110
Q ss_pred -----------------cccccccccCCCCCCCceeeCC-CCCCCCCc-cccCcc--cCCCCCCCccCccCccc
Q 000390 314 -----------------DVKVCDICGDAGREDLLAICSR-CSDGAEHT-YCMKEM--LQKVPEGDWLCEECKFA 366 (1585)
Q Consensus 314 -----------------DckvC~VCg~~gded~LLlCD~-CDrGaYH~-yCL~PP--L~eVPeGdW~Cp~C~~~ 366 (1585)
-...|.+|+.. +.+|+|+. |+.. ||+ .||+-. -..+|+|-|+|++|...
T Consensus 410 iR~~~iG~dr~gr~ywfi~rrl~Ie~~d---et~l~yysT~pql-y~ll~cLd~~~~e~~L~d~i~~~~ee~~r 479 (1414)
T KOG1473|consen 410 IRHTPIGRDRYGRKYWFISRRLRIEGMD---ETLLWYYSTCPQL-YHLLRCLDRTYVEMYLCDGIWERREEIIR 479 (1414)
T ss_pred eeccCCCcCccccchhceeeeeEEecCC---CcEEEEecCcHHH-HHHHHHhchHHHHHhhccchhhhHHHHHH
Confidence 13456666643 45999999 9988 899 999933 35789999999999754
No 24
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=89.92 E-value=0.12 Score=65.13 Aligned_cols=103 Identities=19% Similarity=0.347 Sum_probs=67.1
Q ss_pred cccccccccccccccCCCCCCCCCCceecCCC--CCCccCCccCcCCCcccCCCCcCCCCCCccccccccccccccccCC
Q 000390 247 SDVLTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELPDVQRFPAASGDETDESDIMEQDVKVCDICGDA 324 (1585)
Q Consensus 247 s~~~C~~C~~tee~nd~d~~gqpEeLL~Cs~C--s~H~sCLd~~~e~~~ikky~WQs~DE~d~~DCi~~DckvC~VCg~~ 324 (1585)
.+++|.||..+. +++..+||+|..| ..|-.|..... +...+|-|. -|.-.-+-.|..|-..
T Consensus 270 edviCDvCrspD-------~e~~neMVfCd~Cn~cVHqaCyGIle----~p~gpWlCr------~Calg~~ppCvLCPkk 332 (893)
T KOG0954|consen 270 EDVICDVCRSPD-------SEEANEMVFCDKCNICVHQACYGILE----VPEGPWLCR------TCALGIEPPCVLCPKK 332 (893)
T ss_pred ccceeceecCCC-------ccccceeEEeccchhHHHHhhhceee----cCCCCeeeh------hccccCCCCeeecccc
Confidence 688999999863 5678899999999 78999987533 223779964 2544456678888766
Q ss_pred CCCCCceeeCCCCCCCCCcccc--------------Ccc--cCCCCCCCc--cCccCccccch
Q 000390 325 GREDLLAICSRCSDGAEHTYCM--------------KEM--LQKVPEGDW--LCEECKFAEET 369 (1585)
Q Consensus 325 gded~LLlCD~CDrGaYH~yCL--------------~PP--L~eVPeGdW--~Cp~C~~~~e~ 369 (1585)
|. .|-=..-..-|-|.+|- .|. ...||+..| .|..|....+.
T Consensus 333 GG---amK~~~sgT~wAHvsCALwIPEVsie~~ekmePItkfs~IpesRwslvC~LCk~k~GA 392 (893)
T KOG0954|consen 333 GG---AMKPTKSGTKWAHVSCALWIPEVSIECPEKMEPITKFSHIPESRWSLVCNLCKVKSGA 392 (893)
T ss_pred CC---cccccCCCCeeeEeeeeeccceeeccCHhhcCcccccCCCcHHHHHHHHHHhcccCcc
Confidence 63 12111222234577763 122 146788888 68888765543
No 25
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=88.90 E-value=0.29 Score=61.12 Aligned_cols=45 Identities=7% Similarity=-0.064 Sum_probs=32.8
Q ss_pred ccccccccccccccCCCCCCCCCCceecCCC--CCCccCCccCcCCCcccCCCCcC
Q 000390 248 DVLTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELPDVQRFPAAS 301 (1585)
Q Consensus 248 ~~~C~~C~~tee~nd~d~~gqpEeLL~Cs~C--s~H~sCLd~~~e~~~ikky~WQs 301 (1585)
...|..|.+.+.. .++|.|..| ++|..||+++.+...+....|.|
T Consensus 253 ~~fCsaCn~~~~F---------~~~i~CD~Cp~sFH~~CLePPl~~eniP~g~W~C 299 (613)
T KOG4299|consen 253 EDFCSACNGSGLF---------NDIICCDGCPRSFHQTCLEPPLEPENIPPGSWFC 299 (613)
T ss_pred HHHHHHhCCcccc---------ccceeecCCchHHHHhhcCCCCCcccCCCCcccc
Confidence 4489999996543 457999999 89999999995544344445554
No 26
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=88.55 E-value=0.14 Score=64.06 Aligned_cols=56 Identities=32% Similarity=0.815 Sum_probs=44.5
Q ss_pred cccccccccCCC--CCCCceeeCCCCCCCCCccccCcccCCC-CCCCccCccCccccchh
Q 000390 314 DVKVCDICGDAG--REDLLAICSRCSDGAEHTYCMKEMLQKV-PEGDWLCEECKFAEETE 370 (1585)
Q Consensus 314 DckvC~VCg~~g--ded~LLlCD~CDrGaYH~yCL~PPL~eV-PeGdW~Cp~C~~~~e~e 370 (1585)
-|..|.+|+..| .+..|+.|..|..- ||.||+.--+... =.+-|.|+.|+.|..|.
T Consensus 17 ~~~mc~l~~s~G~~~ag~m~ac~~c~~~-yH~~cvt~~~~~~~l~~gWrC~~crvCe~c~ 75 (694)
T KOG4443|consen 17 VCLMCPLCGSSGKGRAGRLLACSDCGQK-YHPYCVTSWAQHAVLSGGWRCPSCRVCEACG 75 (694)
T ss_pred hhhhhhhhccccccccCcchhhhhhccc-CCcchhhHHHhHHHhcCCcccCCceeeeecc
Confidence 566899998766 46679999999865 9999999665544 22349999999999986
No 27
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=86.80 E-value=0.44 Score=58.28 Aligned_cols=45 Identities=9% Similarity=-0.089 Sum_probs=35.0
Q ss_pred cccccccccccccccCCCCCCCCCCceecCCC--CCCccCCccCcCCCc--ccCCCCc
Q 000390 247 SDVLTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELPD--VQRFPAA 300 (1585)
Q Consensus 247 s~~~C~~C~~tee~nd~d~~gqpEeLL~Cs~C--s~H~sCLd~~~e~~~--ikky~WQ 300 (1585)
++..|++|-+.. +.--++.|..| .||-.||++++.-.+ .+.|.||
T Consensus 543 ~~ysCgiCkks~---------dQHll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWq 591 (707)
T KOG0957|consen 543 MNYSCGICKKST---------DQHLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQ 591 (707)
T ss_pred cceeeeeeccch---------hhHHHhhcchhhceeeccccCCccccCcccccCccee
Confidence 467999999953 23457899999 889999999886553 3359999
No 28
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=86.23 E-value=0.36 Score=55.66 Aligned_cols=40 Identities=18% Similarity=0.075 Sum_probs=30.3
Q ss_pred ccccccccccccCCCCCCCCCCceecCCC--CCCccCCccCcCCCcccCCCCc
Q 000390 250 LTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELPDVQRFPAA 300 (1585)
Q Consensus 250 ~C~~C~~tee~nd~d~~gqpEeLL~Cs~C--s~H~sCLd~~~e~~~ikky~WQ 300 (1585)
.|.+|+.++ .-+.||+|.+| .||.+||.++|..++... |.
T Consensus 283 ~csicgtse---------nddqllfcddcdrgyhmyclsppm~eppegs--ws 324 (336)
T KOG1244|consen 283 YCSICGTSE---------NDDQLLFCDDCDRGYHMYCLSPPMVEPPEGS--WS 324 (336)
T ss_pred eeccccCcC---------CCceeEeecccCCceeeEecCCCcCCCCCCc--hh
Confidence 455565543 33789999999 899999999997776544 87
No 29
>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=84.30 E-value=0.3 Score=41.94 Aligned_cols=42 Identities=7% Similarity=-0.023 Sum_probs=31.8
Q ss_pred ccccccccccccCCCCCCCCCCceecCCC--CCCccCCccCcCCCcccCCCCc
Q 000390 250 LTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELPDVQRFPAA 300 (1585)
Q Consensus 250 ~C~~C~~tee~nd~d~~gqpEeLL~Cs~C--s~H~sCLd~~~e~~~ikky~WQ 300 (1585)
.|.+|.+. +..+++|.|..| .+|..|+.++.....+....|.
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 7899999998764433334687
No 30
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=76.60 E-value=1.2 Score=57.11 Aligned_cols=49 Identities=14% Similarity=-0.058 Sum_probs=37.4
Q ss_pred cccccccccccccccccccccCCCCCCCCCCceecCCC---CCCccCCccCcCCCcccCCCCc
Q 000390 241 RLVESSSDVLTKVHQKSEAETDRDNGEPPDEALKCLDK---DKEELTSTQLAELPDVQRFPAA 300 (1585)
Q Consensus 241 ~L~~~Ts~~~C~~C~~tee~nd~d~~gqpEeLL~Cs~C---s~H~sCLd~~~e~~~ikky~WQ 300 (1585)
.+...+....|.+|... |.+|-||.|..| .||.+||++..-..++ ..|+
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 467889999999 5899999987744444 3477
No 31
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=71.38 E-value=3.6 Score=55.04 Aligned_cols=46 Identities=9% Similarity=0.011 Sum_probs=35.5
Q ss_pred cccccccccccccccccCCCCCCCCCCceecCCC--CCCccCCccCcCCCcccCCCCcC
Q 000390 245 SSSDVLTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELPDVQRFPAAS 301 (1585)
Q Consensus 245 ~Ts~~~C~~C~~tee~nd~d~~gqpEeLL~Cs~C--s~H~sCLd~~~e~~~ikky~WQs 301 (1585)
......|.||..++ +......|+|..| .+|-.|+. .+.+....|.|
T Consensus 216 ~~~D~~C~iC~~~~-------~~n~n~ivfCD~Cnl~VHq~Cyg----i~~ipeg~WlC 263 (1051)
T KOG0955|consen 216 LEEDAVCCICLDGE-------CQNSNVIVFCDGCNLAVHQECYG----IPFIPEGQWLC 263 (1051)
T ss_pred cCCCccceeecccc-------cCCCceEEEcCCCcchhhhhccC----CCCCCCCcEee
Confidence 35567899999976 3456789999999 89999988 33455677873
No 32
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=68.99 E-value=2.2 Score=52.21 Aligned_cols=45 Identities=9% Similarity=0.020 Sum_probs=30.2
Q ss_pred CCccccCCcccccccccccccccCCCCCCCccCCCCcccccccCC
Q 000390 124 GTAEGQISPKLEIGLDQRISLNKYDDPKGAEGLDDNISCVSRAND 168 (1585)
Q Consensus 124 ~~a~~~~~~~~~~~~d~~~l~n~~~~~~~~E~~dD~~SCis~~~~ 168 (1585)
.+..-+++|..+..|+=..|..+.......+..-+.+.||-..-.
T Consensus 40 ~~~~~sgnp~ve~t~GiiHLyk~n~~~s~~~~~~~~mLcilaVP~ 84 (493)
T KOG0804|consen 40 QIKYSSGNPSVEETHGIIHLYKKNSHSSLKNASSSTMLCILAVPA 84 (493)
T ss_pred cccccCCCCceeeeceeEEEEecCcccccccCCCCcEEEEEeccc
Confidence 455556777777777776676666666666666688888855544
No 33
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=67.89 E-value=4.7 Score=49.89 Aligned_cols=60 Identities=8% Similarity=-0.023 Sum_probs=40.3
Q ss_pred cCCCCCCCccccc-cccccccccccccccccccCCCCCCCCCCceecCCC--CCCccCCccCcCCCcccCCCCcC
Q 000390 230 RSPVPDSQSDKRL-VESSSDVLTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELPDVQRFPAAS 301 (1585)
Q Consensus 230 ~~~lp~~n~~k~L-~~~Ts~~~C~~C~~tee~nd~d~~gqpEeLL~Cs~C--s~H~sCLd~~~e~~~ikky~WQs 301 (1585)
.+++|+-+ .+.+ +.+.....|.+|.++..+ ..+.+++|..| ..|-+|..-.. +....|-|
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 44455532 2333 455678899999987643 56889999999 88999987533 23345874
No 34
>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 PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=58.05 E-value=4.7 Score=44.35 Aligned_cols=48 Identities=33% Similarity=0.708 Sum_probs=34.3
Q ss_pred cccccc---CCCCCCCceeeCCCCCCCCCccccCccc------CCCCCCC--ccCccCcc
Q 000390 317 VCDICG---DAGREDLLAICSRCSDGAEHTYCMKEML------QKVPEGD--WLCEECKF 365 (1585)
Q Consensus 317 vC~VCg---~~gded~LLlCD~CDrGaYH~yCL~PPL------~eVPeGd--W~Cp~C~~ 365 (1585)
+|.+|+ ....-..|++|-+|-.+ ||-.||+|-. ++|-+++ -.|..|+.
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 44455679999999987 8999999875 3555544 35777764
No 36
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=51.10 E-value=5.8 Score=49.11 Aligned_cols=45 Identities=9% Similarity=-0.064 Sum_probs=31.6
Q ss_pred cccccccccccccCCCCCCCCCCceecCCC--CCCccCCccCcCCC--cccCCCCc
Q 000390 249 VLTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELP--DVQRFPAA 300 (1585)
Q Consensus 249 ~~C~~C~~tee~nd~d~~gqpEeLL~Cs~C--s~H~sCLd~~~e~~--~ikky~WQ 300 (1585)
..|-||..+. -+.-..||.|..| .||..|-.+..+.. ....|-|+
T Consensus 169 ~qc~vC~~g~-------~~~~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~ 217 (464)
T KOG4323|consen 169 LQCSVCYCGG-------PGAGNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWF 217 (464)
T ss_pred ceeeeeecCC-------cCccceeeeecccccHHHHHhccCCCCHhhccCccceEe
Confidence 3499999753 3344589999999 89999988766422 33446666
No 37
>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=48.22 E-value=15 Score=36.18 Aligned_cols=105 Identities=19% Similarity=0.328 Sum_probs=58.3
Q ss_pred eEEEEEEecCCCCCccccccceecCccccHHHH----HHHhcCCCccccc-cccCCCCCccccccCCCCCCceEEEee-c
Q 000390 846 WQGGFEVHRGEKLPNLCDGIQAHLSSCASSKVL----EVVSKFPQRIRLK-EVPRVSTWPTMFHESGAKEENIALYFF-A 919 (1585)
Q Consensus 846 W~G~F~V~~~~~~~~~~dGL~AHLSskAc~KV~----E~Sk~LP~vL~lE-~LPRl~vWPksF~~~gPtdddIaLYFF-P 919 (1585)
|+|.+.+..-. .....||+=+.. .... .-....|..|.+. -|+...+|.-.-+......-.|-++=| .
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 000390 920 K--DFESYGRNYKILVDSMMKNDLALMGNLD------GIELLIFP 956 (1585)
Q Consensus 920 ~--d~er~Ek~~d~LVd~Mi~~DlaLRavI~------~aELLIFp 956 (1585)
. +.......|..|++++..++-+=-+.++ ..+|-|||
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 3455667899999999999876555555 47788887
No 38
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=44.27 E-value=13 Score=34.36 Aligned_cols=35 Identities=23% Similarity=0.621 Sum_probs=27.4
Q ss_pred cccccccccCCCC-CCCceeeCCCCCCCCCccccCcc
Q 000390 314 DVKVCDICGDAGR-EDLLAICSRCSDGAEHTYCMKEM 349 (1585)
Q Consensus 314 DckvC~VCg~~gd-ed~LLlCD~CDrGaYH~yCL~PP 349 (1585)
.-..|.+|++.-. .+.++.|..|.-- ||..|+...
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~Cgap-yHR~C~~~~ 39 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAP-YHRDCWEKA 39 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCc-ccHHHHhhC
Confidence 3458999998763 5669999999755 999999743
No 39
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=43.50 E-value=4.1 Score=52.50 Aligned_cols=48 Identities=15% Similarity=0.090 Sum_probs=43.3
Q ss_pred ccccccccCCCCCCCceeeCCCCCCCCCccccCc-ccCCCCCCCccCccCccc
Q 000390 315 VKVCDICGDAGREDLLAICSRCSDGAEHTYCMKE-MLQKVPEGDWLCEECKFA 366 (1585)
Q Consensus 315 ckvC~VCg~~gded~LLlCD~CDrGaYH~yCL~P-PL~eVPeGdW~Cp~C~~~ 366 (1585)
...|..|.+... .++|+.|-|. ||..|+.| |++..+.|.|.|+.|...
T Consensus 506 d~~~~~~~~~l~---~l~~p~~lrr-~k~d~l~~~P~Kte~i~~~~~~~~Q~~ 554 (696)
T KOG0383|consen 506 DISCEEQIKKLH---LLLCPHMLRR-LKLDVLKPMPLKTELIGRVELSPCQKK 554 (696)
T ss_pred hhhHHHHHHhhc---cccCchhhhh-hhhhhccCCCccceeEEEEecCHHHHH
Confidence 458999998887 8899999988 89999999 999999999999999854
No 40
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=37.84 E-value=8.1 Score=53.39 Aligned_cols=48 Identities=13% Similarity=0.042 Sum_probs=38.8
Q ss_pred cccccccccccccccccccCCCCCCCCCCceecCCC--CCCccCCccCcCCCcccCCCCcC
Q 000390 243 VESSSDVLTKVHQKSEAETDRDNGEPPDEALKCLDK--DKEELTSTQLAELPDVQRFPAAS 301 (1585)
Q Consensus 243 ~~~Ts~~~C~~C~~tee~nd~d~~gqpEeLL~Cs~C--s~H~sCLd~~~e~~~ikky~WQs 301 (1585)
..+..+..|.+|.. .++.+.++.|..| .+|..|+.+.+..++.. .|+|
T Consensus 1103 ~~s~~~~~c~~cr~---------k~~~~~m~lc~~c~~~~h~~C~rp~~~~~~~~--dW~C 1152 (1404)
T KOG1245|consen 1103 DRSAVNALCKVCRR---------KKQDEKMLLCDECLSGFHLFCLRPALSSVPPG--DWMC 1152 (1404)
T ss_pred ccccchhhhhhhhh---------cccchhhhhhHhhhhhHHHHhhhhhhccCCcC--CccC
Confidence 55677889999998 3467899999999 88999999988776554 4983
No 41
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=37.13 E-value=16 Score=32.32 Aligned_cols=21 Identities=43% Similarity=0.786 Sum_probs=18.5
Q ss_pred CCccchhhccccCcccccccC
Q 000390 716 SKGVLCQKCKEVGHDVESCPL 736 (1585)
Q Consensus 716 ~~~~~cqkcke~gh~~e~c~~ 736 (1585)
.....||+|.+.||.+--|+.
T Consensus 2 ~~~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 2 NARVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCCCcCcccCCCCcchhhCCC
Confidence 356789999999999999996
No 42
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=36.46 E-value=12 Score=44.15 Aligned_cols=55 Identities=18% Similarity=0.424 Sum_probs=38.7
Q ss_pred cccccccCC------CCCCCceeeCCCCCCCCCccccCcccCC---CCCCCccCccCccccchhh
Q 000390 316 KVCDICGDA------GREDLLAICSRCSDGAEHTYCMKEMLQK---VPEGDWLCEECKFAEETEK 371 (1585)
Q Consensus 316 kvC~VCg~~------gded~LLlCD~CDrGaYH~yCL~PPL~e---VPeGdW~Cp~C~~~~e~ek 371 (1585)
..|-+|.++ +..+-|+.|..|.-+ ||.+|+.-+..- +-...|.|..|..|.-|..
T Consensus 259 ~~~~~~~~~~~~~~~~r~~S~I~C~~C~~~-~HP~Ci~M~~elv~~~KTY~W~C~~C~lC~IC~~ 322 (381)
T KOG1512|consen 259 NERKHFWDIQTNIIQSRRNSWIVCKPCATR-PHPYCVAMIPELVGQYKTYFWKCSSCELCRICLG 322 (381)
T ss_pred hhhhhhhcchhhhhhhhhccceeecccccC-CCCcchhcCHHHHhHHhhcchhhcccHhhhccCC
Confidence 355666543 345679999999866 899999855332 2335799999987776644
No 43
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=32.73 E-value=16 Score=39.82 Aligned_cols=21 Identities=33% Similarity=0.615 Sum_probs=18.1
Q ss_pred CccchhhccccCcccccccCC
Q 000390 717 KGVLCQKCKEVGHDVESCPLG 737 (1585)
Q Consensus 717 ~~~~cqkcke~gh~~e~c~~~ 737 (1585)
..++||+|-+|||.+--|..-
T Consensus 26 ~~~rCQKClq~GHWtYECk~k 46 (177)
T KOG3116|consen 26 SSARCQKCLQAGHWTYECKNK 46 (177)
T ss_pred cchhHHHHHhhccceeeecCc
Confidence 456999999999999998754
No 44
>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=28.86 E-value=21 Score=28.62 Aligned_cols=29 Identities=31% Similarity=0.619 Sum_probs=12.2
Q ss_pred cccccccCCCCCCCceeeCCCCCCCCCccc
Q 000390 316 KVCDICGDAGREDLLAICSRCSDGAEHTYC 345 (1585)
Q Consensus 316 kvC~VCg~~gded~LLlCD~CDrGaYH~yC 345 (1585)
+.|.+|++....+..-.|..|+-. .|..|
T Consensus 1 ~~C~~C~~~~~~~~~Y~C~~Cdf~-lH~~C 29 (30)
T PF07649_consen 1 FRCDACGKPIDGGWFYRCSECDFD-LHEEC 29 (30)
T ss_dssp ---TTTS----S--EEE-TTT------HHH
T ss_pred CcCCcCCCcCCCCceEECccCCCc-cChhc
Confidence 368999999887678889999977 58776
No 45
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=25.58 E-value=58 Score=42.29 Aligned_cols=49 Identities=20% Similarity=0.508 Sum_probs=29.0
Q ss_pred ccccccCCCCCCCceeeCCCCCCCCCccccCcccCCCCCCCccCccCcccc
Q 000390 317 VCDICGDAGREDLLAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECKFAE 367 (1585)
Q Consensus 317 vC~VCg~~gded~LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~~~ 367 (1585)
.|..|+..- ++...||..|+...-|..|-.-. ..+|.|.=||+.|-...
T Consensus 3 ~Cp~Cg~~n-~~~akFC~~CG~~l~~~~Cp~CG-~~~~~~~~fC~~CG~~~ 51 (645)
T PRK14559 3 ICPQCQFEN-PNNNRFCQKCGTSLTHKPCPQCG-TEVPVDEAHCPNCGAET 51 (645)
T ss_pred cCCCCCCcC-CCCCccccccCCCCCCCcCCCCC-CCCCcccccccccCCcc
Confidence 566666654 23355677775443334454433 45777888899986543
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=24.95 E-value=39 Score=24.92 Aligned_cols=16 Identities=44% Similarity=1.014 Sum_probs=14.4
Q ss_pred chhhccccCccccccc
Q 000390 720 LCQKCKEVGHDVESCP 735 (1585)
Q Consensus 720 ~cqkcke~gh~~e~c~ 735 (1585)
.|.+|.+.||..-.|+
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=24.93 E-value=14 Score=34.85 Aligned_cols=50 Identities=22% Similarity=0.413 Sum_probs=21.3
Q ss_pred ccccccCCC---CCCCceeeC--CCCCCCCCccccCcccCCCCCC-------CccCccCcccc
Q 000390 317 VCDICGDAG---REDLLAICS--RCSDGAEHTYCMKEMLQKVPEG-------DWLCEECKFAE 367 (1585)
Q Consensus 317 vC~VCg~~g---ded~LLlCD--~CDrGaYH~yCL~PPL~eVPeG-------dW~Cp~C~~~~ 367 (1585)
.|.+|.... .+...++|+ .|... ||+.||.--+...+.+ .+.||.|...-
T Consensus 4 ~C~IC~~~~~~~~~~p~~~C~n~~C~~~-fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i 65 (70)
T PF11793_consen 4 ECGICYSYRLDDGEIPDVVCPNPSCGKK-FHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPI 65 (70)
T ss_dssp S-SSS--SS-TT-----B--S-TT-----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEE
T ss_pred CCCcCCcEecCCCCcCceEcCCcccCCH-HHHHHHHHHHHHcccCCeeecccccCCcCCCCee
Confidence 466776542 233468898 89887 7999998665443332 36799997543
No 48
>COG1773 Rubredoxin [Energy production and conversion]
Probab=23.99 E-value=48 Score=31.01 Aligned_cols=39 Identities=28% Similarity=0.810 Sum_probs=24.4
Q ss_pred ccccccCCCCCCC-ceeeCCCCCCCCCccccCcccCCCCCCCccCccCcc
Q 000390 317 VCDICGDAGREDL-LAICSRCSDGAEHTYCMKEMLQKVPEGDWLCEECKF 365 (1585)
Q Consensus 317 vC~VCg~~gded~-LLlCD~CDrGaYH~yCL~PPL~eVPeGdW~Cp~C~~ 365 (1585)
.|.+|+-.-++++ ---|+.|+ | -+-+.+|+ +|.||.|-.
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 4778876544332 22355554 2 33567776 899999986
No 49
>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=23.61 E-value=1.4e+02 Score=31.57 Aligned_cols=70 Identities=21% Similarity=0.285 Sum_probs=48.0
Q ss_pred CCCCCCceEEEeecCCcc--cchhhHHHHHHH---------HHhccceeeeeccceeEEeecCCCCCccccccccceeEE
Q 000390 906 SGAKEENIALYFFAKDFE--SYGRNYKILVDS---------MMKNDLALMGNLDGIELLIFPSNQLPENCQRWNLLFFLW 974 (1585)
Q Consensus 906 ~gPtdddIaLYFFP~d~e--r~Ek~~d~LVd~---------Mi~~DlaLRavI~~aELLIFpS~lLP~~~Qrf~gk~YLW 974 (1585)
.++....||++.|-.+.+ .....| |+.+ .-.+...++..+.-.+.+|.||+..|.+. |+|.|.
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 000390 975 GVFRVRKV 982 (1585)
Q Consensus 975 GVFR~rK~ 982 (1585)
||-.+..
T Consensus 139 -Vfs~~~~ 145 (150)
T cd00214 139 -VFSEKSI 145 (150)
T ss_pred -EEecCCC
Confidence 7776654
No 50
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=20.41 E-value=61 Score=27.51 Aligned_cols=22 Identities=32% Similarity=0.961 Sum_probs=19.3
Q ss_pred CccchhhccccCcccccccCCC
Q 000390 717 KGVLCQKCKEVGHDVESCPLGS 738 (1585)
Q Consensus 717 ~~~~cqkcke~gh~~e~c~~~~ 738 (1585)
.+..|..|...||..+.|+..+
T Consensus 7 ~~Y~C~~C~~~GH~i~dCP~~~ 28 (32)
T PF13696_consen 7 PGYVCHRCGQKGHWIQDCPTNK 28 (32)
T ss_pred CCCEeecCCCCCccHhHCCCCC
Confidence 5678999999999999999853
No 51
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=20.05 E-value=56 Score=39.42 Aligned_cols=47 Identities=30% Similarity=0.638 Sum_probs=36.0
Q ss_pred ccCCCCCC-CceeeCCCCCCCCCccc--cCcccCCCCC-CCccCccCccccc
Q 000390 321 CGDAGRED-LLAICSRCSDGAEHTYC--MKEMLQKVPE-GDWLCEECKFAEE 368 (1585)
Q Consensus 321 Cg~~gded-~LLlCD~CDrGaYH~yC--L~PPL~eVPe-GdW~Cp~C~~~~e 368 (1585)
|....+++ .|+-|+.|... ||..| .+.+-.++|. -.|+|..|.....
T Consensus 65 ~~~~~~p~~~~~~cd~C~~~-~~~ec~~v~~~~~e~p~~~~~~c~~c~~~~~ 115 (345)
T KOG1632|consen 65 CYKPCDPDDLMEQCDLCEDW-YHGECWEVGTAEKEAPKEDPKVCDECKEAQD 115 (345)
T ss_pred cccccCchhhhhcccccccc-ccccccccCchhhcCCccccccccccchhhh
Confidence 44444443 78999999987 89999 8888777765 5899999986643
Done!