Query 017784
Match_columns 366
No_of_seqs 95 out of 107
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 03:24:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017784.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017784hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0825 PHD Zn-finger protein 98.4 9.3E-08 2E-12 101.9 2.0 50 2-52 215-264 (1134)
2 PF00628 PHD: PHD-finger; Int 98.2 5E-07 1.1E-11 63.3 1.5 49 4-53 1-50 (51)
3 smart00249 PHD PHD zinc finger 98.1 2.4E-06 5.3E-11 56.3 3.5 47 4-51 1-47 (47)
4 KOG4443 Putative transcription 97.7 1.2E-05 2.5E-10 84.5 1.8 48 3-52 69-116 (694)
5 KOG0955 PHD finger protein BR1 97.7 2.2E-05 4.7E-10 85.8 3.2 50 2-55 219-270 (1051)
6 KOG1512 PHD Zn-finger protein 97.7 1.5E-05 3.2E-10 78.2 1.6 47 3-53 315-362 (381)
7 KOG0956 PHD finger protein AF1 97.3 7.8E-05 1.7E-09 79.3 1.5 53 1-57 4-60 (900)
8 KOG0954 PHD finger protein [Ge 97.1 0.00016 3.4E-09 77.4 0.8 49 2-54 271-321 (893)
9 PF13831 PHD_2: PHD-finger; PD 96.9 0.00021 4.5E-09 49.8 -0.1 35 15-52 2-36 (36)
10 KOG1245 Chromatin remodeling c 96.8 0.00021 4.5E-09 80.2 -1.2 53 2-56 1108-1160(1404)
11 KOG4299 PHD Zn-finger protein 96.6 0.00081 1.8E-08 70.4 1.0 53 3-57 254-308 (613)
12 COG5141 PHD zinc finger-contai 96.1 0.0022 4.8E-08 66.8 1.1 48 3-54 194-243 (669)
13 cd04718 BAH_plant_2 BAH, or Br 95.9 0.016 3.4E-07 51.8 5.3 27 28-55 2-28 (148)
14 KOG4323 Polycomb-like PHD Zn-f 95.5 0.0058 1.3E-07 62.5 1.3 55 2-57 168-227 (464)
15 KOG0383 Predicted helicase [Ge 91.3 0.073 1.6E-06 56.9 0.7 47 3-54 48-94 (696)
16 KOG0957 PHD finger protein [Ge 90.1 0.15 3.2E-06 54.0 1.5 49 1-51 543-595 (707)
17 PF07649 C1_3: C1-like domain; 78.4 0.93 2E-05 29.8 0.7 29 3-32 1-29 (30)
18 KOG1844 PHD Zn-finger proteins 78.0 1.3 2.9E-05 43.6 1.9 46 6-54 89-135 (508)
19 KOG0957 PHD finger protein [Ge 75.9 2 4.4E-05 45.8 2.6 54 3-57 120-182 (707)
20 KOG1246 DNA-binding protein ju 75.2 2.4 5.1E-05 45.9 3.0 49 3-54 156-204 (904)
21 COG4393 Predicted membrane pro 74.8 0.97 2.1E-05 46.0 0.0 23 4-26 336-360 (405)
22 PF15446 zf-PHD-like: PHD/FYVE 73.9 1.6 3.5E-05 40.4 1.3 31 4-35 1-34 (175)
23 KOG4443 Putative transcription 73.2 0.89 1.9E-05 49.0 -0.7 48 4-52 20-69 (694)
24 PF14446 Prok-RING_1: Prokaryo 69.0 3.5 7.5E-05 31.9 1.9 33 2-35 5-38 (54)
25 PF14569 zf-UDP: Zinc-binding 67.4 0.95 2.1E-05 37.5 -1.5 47 3-54 10-60 (80)
26 PF00130 C1_1: Phorbol esters/ 61.3 8.9 0.00019 27.0 2.6 35 2-37 11-47 (53)
27 PRK14559 putative protein seri 59.5 7.9 0.00017 41.4 3.0 49 3-54 2-50 (645)
28 PLN02400 cellulose synthase 59.3 6.5 0.00014 44.6 2.5 47 3-54 37-87 (1085)
29 PF10080 DUF2318: Predicted me 57.6 5.5 0.00012 33.6 1.2 23 4-26 37-61 (102)
30 PLN02436 cellulose synthase A 56.6 7.1 0.00015 44.4 2.2 48 3-55 37-88 (1094)
31 KOG1244 Predicted transcriptio 54.5 2.7 5.9E-05 41.9 -1.2 51 2-53 224-283 (336)
32 PLN02638 cellulose synthase A 53.1 7.9 0.00017 44.0 1.9 47 3-54 18-68 (1079)
33 PLN02915 cellulose synthase A 49.4 10 0.00023 42.9 2.1 47 3-54 16-66 (1044)
34 PLN02189 cellulose synthase 48.8 11 0.00024 42.7 2.1 48 3-55 35-86 (1040)
35 KOG1512 PHD Zn-finger protein 46.7 5.6 0.00012 40.2 -0.4 48 3-52 259-315 (381)
36 PF03107 C1_2: C1 domain; Int 44.9 21 0.00046 23.6 2.2 29 4-33 2-30 (30)
37 TIGR02098 MJ0042_CXXC MJ0042 f 44.9 18 0.00038 24.4 1.9 26 1-26 1-34 (38)
38 PLN02195 cellulose synthase A 41.9 16 0.00034 41.3 2.0 48 2-54 6-57 (977)
39 cd00729 rubredoxin_SM Rubredox 39.3 12 0.00026 25.8 0.4 26 3-28 3-29 (34)
40 PF01753 zf-MYND: MYND finger; 38.6 24 0.00053 23.8 1.8 23 5-34 1-23 (37)
41 PF14205 Cys_rich_KTR: Cystein 38.3 17 0.00038 28.5 1.2 22 4-25 6-36 (55)
42 PF13248 zf-ribbon_3: zinc-rib 35.7 22 0.00047 23.0 1.2 24 1-25 1-24 (26)
43 PF04216 FdhE: Protein involve 32.0 20 0.00043 33.8 0.7 51 3-54 173-247 (290)
44 cd00029 C1 Protein kinase C co 31.8 35 0.00075 23.1 1.7 35 2-37 11-47 (50)
45 PF02977 CarbpepA_inh: Carboxy 31.5 23 0.00049 27.0 0.8 20 29-52 9-28 (46)
46 PF13719 zinc_ribbon_5: zinc-r 30.7 39 0.00085 23.4 1.9 25 1-25 1-33 (37)
47 KOG1080 Histone H3 (Lys4) meth 30.4 40 0.00087 38.3 2.8 48 3-53 574-623 (1005)
48 smart00109 C1 Protein kinase C 30.3 20 0.00044 23.9 0.4 34 2-36 11-45 (49)
49 KOG4216 Steroid hormone nuclea 28.3 25 0.00055 36.8 0.8 24 2-25 46-71 (479)
50 PF04810 zf-Sec23_Sec24: Sec23 27.9 16 0.00035 25.6 -0.4 34 17-57 2-36 (40)
51 cd00350 rubredoxin_like Rubred 27.9 24 0.00052 23.8 0.4 9 45-53 17-25 (33)
52 PF12773 DZR: Double zinc ribb 27.8 48 0.001 23.2 1.9 38 5-54 1-38 (50)
53 KOG4218 Nuclear hormone recept 27.7 26 0.00055 36.5 0.7 52 3-54 16-76 (475)
54 cd03031 GRX_GRX_like Glutaredo 27.7 69 0.0015 28.3 3.3 43 3-54 100-142 (147)
55 COG1107 Archaea-specific RecJ- 27.6 41 0.00089 36.9 2.2 51 3-54 54-104 (715)
56 PF13832 zf-HC5HC2H_2: PHD-zin 26.3 40 0.00087 26.9 1.5 31 2-35 55-87 (110)
57 PF06827 zf-FPG_IleRS: Zinc fi 26.2 40 0.00086 22.0 1.2 22 3-24 2-28 (30)
58 PRK14714 DNA polymerase II lar 25.8 61 0.0013 38.1 3.2 47 3-54 668-718 (1337)
59 PF13717 zinc_ribbon_4: zinc-r 25.8 54 0.0012 22.8 1.9 25 1-25 1-33 (36)
60 PRK04023 DNA polymerase II lar 25.2 51 0.0011 38.0 2.5 34 3-54 627-660 (1121)
61 KOG4846 Nuclear receptor [Sign 25.1 30 0.00066 36.6 0.7 25 1-25 131-157 (538)
62 PF04438 zf-HIT: HIT zinc fing 25.0 30 0.00065 23.5 0.5 24 2-33 2-25 (30)
63 PRK03564 formate dehydrogenase 24.1 82 0.0018 31.3 3.4 51 3-54 188-261 (309)
64 PF05502 Dynactin_p62: Dynacti 23.7 43 0.00093 34.6 1.5 35 15-56 3-37 (483)
65 PRK06424 transcription factor; 23.3 26 0.00056 31.0 -0.2 7 5-11 3-9 (144)
66 PF13824 zf-Mss51: Zinc-finger 21.3 51 0.0011 25.7 1.1 30 4-36 1-30 (55)
67 TIGR01206 lysW lysine biosynth 21.0 73 0.0016 24.4 1.9 34 1-35 1-39 (54)
No 1
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.41 E-value=9.3e-08 Score=101.87 Aligned_cols=50 Identities=26% Similarity=0.673 Sum_probs=44.6
Q ss_pred CcccccccccCcccceeecCCCCCCCeeeccCCCCCCCCCCCCcccccccc
Q 017784 2 VTVCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCE 52 (366)
Q Consensus 2 VtVCdICGDvGFEElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECq 52 (366)
+.-|.||+.-.-+|+|++|+.|+.+..|+|||+.++-+ ++-+.|||.-|.
T Consensus 215 ~~~C~IC~~~DpEdVLLLCDsCN~~~YH~YCLDPdl~e-iP~~eWYC~NC~ 264 (1134)
T KOG0825|consen 215 EVKCDICTVHDPEDVLLLCDSCNKVYYHVYCLDPDLSE-SPVNEWYCTNCS 264 (1134)
T ss_pred cccceeeccCChHHhheeecccccceeeccccCccccc-ccccceecCcch
Confidence 46799999999999999999999988999999996533 667899999994
No 2
>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=98.22 E-value=5e-07 Score=63.33 Aligned_cols=49 Identities=27% Similarity=0.658 Sum_probs=40.3
Q ss_pred ccccccccCcccceeecCCCCCCCeeeccCCCCCCC-CCCCCccccccccC
Q 017784 4 VCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPAS-FEDDVLWYCEDCEP 53 (366)
Q Consensus 4 VCdICGDvGFEElLv~CdkCrvgAEHTYCLdv~pve-fvppg~WfCEECqs 53 (366)
+|.+||..+..+.|+.|+.|+. ..|.+|+++.... ..+...|+|..|+.
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~-~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNR-WYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSC-EEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcCCCCh-hhCcccCCCChhhccCCCCcEECcCCcC
Confidence 5899999999999999999997 6999999995421 12235899999974
No 3
>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 KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=97.74 E-value=1.2e-05 Score=84.50 Aligned_cols=48 Identities=27% Similarity=0.752 Sum_probs=43.3
Q ss_pred cccccccccCcccceeecCCCCCCCeeeccCCCCCCCCCCCCcccccccc
Q 017784 3 TVCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCE 52 (366)
Q Consensus 3 tVCdICGDvGFEElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECq 52 (366)
+||..||-.|++..+++|++|++ +.|+||+.+. ...++.+.|+|.||.
T Consensus 69 rvCe~c~~~gD~~kf~~Ck~cDv-syh~yc~~P~-~~~v~sg~~~ckk~~ 116 (694)
T KOG4443|consen 69 RVCEACGTTGDPKKFLLCKRCDV-SYHCYCQKPP-NDKVPSGPWLCKKCT 116 (694)
T ss_pred eeeeeccccCCcccccccccccc-cccccccCCc-cccccCcccccHHHH
Confidence 68999999999999999999999 6999999994 445888999999984
No 5
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=97.69 E-value=2.2e-05 Score=85.76 Aligned_cols=50 Identities=30% Similarity=0.688 Sum_probs=43.4
Q ss_pred CcccccccccCcc--cceeecCCCCCCCeeeccCCCCCCCCCCCCccccccccCCc
Q 017784 2 VTVCQQCGDKGFY--EALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPKV 55 (366)
Q Consensus 2 VtVCdICGDvGFE--ElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECqse~ 55 (366)
-.+|+||-|..-. +.+++||+|+. +.|+||+++ + +.|+|.|+|-.|....
T Consensus 219 D~~C~iC~~~~~~n~n~ivfCD~Cnl-~VHq~Cygi-~--~ipeg~WlCr~Cl~s~ 270 (1051)
T KOG0955|consen 219 DAVCCICLDGECQNSNVIVFCDGCNL-AVHQECYGI-P--FIPEGQWLCRRCLQSP 270 (1051)
T ss_pred CccceeecccccCCCceEEEcCCCcc-hhhhhccCC-C--CCCCCcEeehhhccCc
Confidence 4689999887555 99999999999 699999997 4 7899999999997653
No 6
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.69 E-value=1.5e-05 Score=78.21 Aligned_cols=47 Identities=19% Similarity=0.524 Sum_probs=41.1
Q ss_pred cccccccccCcccceeecCCCCCCCeeeccCCCCCCCCCCCCccccc-cccC
Q 017784 3 TVCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCE-DCEP 53 (366)
Q Consensus 3 tVCdICGDvGFEElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCE-ECqs 53 (366)
..|-|||..--|+.++|||.|+++ -|+||.++. ..|.|.|+|+ .|..
T Consensus 315 ~lC~IC~~P~~E~E~~FCD~CDRG-~HT~CVGL~---~lP~G~WICD~~C~~ 362 (381)
T KOG1512|consen 315 ELCRICLGPVIESEHLFCDVCDRG-PHTLCVGLQ---DLPRGEWICDMRCRE 362 (381)
T ss_pred HhhhccCCcccchheeccccccCC-CCccccccc---cccCccchhhhHHHH
Confidence 469999999999999999999997 999999995 3678999999 3543
No 7
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=97.33 E-value=7.8e-05 Score=79.32 Aligned_cols=53 Identities=32% Similarity=0.772 Sum_probs=45.4
Q ss_pred CCccccccccc-Cc-ccceeecCC--CCCCCeeeccCCCCCCCCCCCCccccccccCCcCC
Q 017784 1 MVTVCQQCGDK-GF-YEALIGCEK--CQTTAVHIYCLPVLPASFEDDVLWYCEDCEPKVAK 57 (366)
Q Consensus 1 mVtVCdICGDv-GF-EElLv~Cdk--CrvgAEHTYCLdv~pvefvppg~WfCEECqse~~k 57 (366)
||-=|++|-|- |+ |+-|+|||+ |.+ |.|+-|-++. .+|.|.|||--|++....
T Consensus 4 MVGGCCVCSDErGWaeNPLVYCDG~nCsV-AVHQaCYGIv---qVPtGpWfCrKCesqera 60 (900)
T KOG0956|consen 4 MVGGCCVCSDERGWAENPLVYCDGHNCSV-AVHQACYGIV---QVPTGPWFCRKCESQERA 60 (900)
T ss_pred cccceeeecCcCCCccCceeeecCCCcee-eeehhcceeE---ecCCCchhhhhhhhhhhh
Confidence 78889999986 77 678999985 999 7999999995 488999999999877443
No 8
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=97.10 E-value=0.00016 Score=77.39 Aligned_cols=49 Identities=24% Similarity=0.625 Sum_probs=41.5
Q ss_pred Cccccccccc--CcccceeecCCCCCCCeeeccCCCCCCCCCCCCccccccccCC
Q 017784 2 VTVCQQCGDK--GFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPK 54 (366)
Q Consensus 2 VtVCdICGDv--GFEElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECqse 54 (366)
..+|++|-.. ...+.|+||++|+.. .|.-|-++. .+|++.|+|-+|...
T Consensus 271 dviCDvCrspD~e~~neMVfCd~Cn~c-VHqaCyGIl---e~p~gpWlCr~Calg 321 (893)
T KOG0954|consen 271 DVICDVCRSPDSEEANEMVFCDKCNIC-VHQACYGIL---EVPEGPWLCRTCALG 321 (893)
T ss_pred cceeceecCCCccccceeEEeccchhH-HHHhhhcee---ecCCCCeeehhcccc
Confidence 4689999654 556789999999996 999999994 478899999999765
No 9
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=96.92 E-value=0.00021 Score=49.79 Aligned_cols=35 Identities=37% Similarity=0.851 Sum_probs=19.1
Q ss_pred cceeecCCCCCCCeeeccCCCCCCCCCCCCcccccccc
Q 017784 15 EALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCE 52 (366)
Q Consensus 15 ElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECq 52 (366)
+.|++|++|+. +.|..|-++.. ......|+|+.|+
T Consensus 2 n~ll~C~~C~v-~VH~~CYGv~~--~~~~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDNCNV-AVHQSCYGVSE--VPDGDDWLCDRCE 36 (36)
T ss_dssp CEEEE-SSS---EEEHHHHT-SS----SS-----HHH-
T ss_pred CceEEeCCCCC-cCChhhCCccc--CCCCCcEECCcCC
Confidence 57999999999 69999999953 2233479999985
No 10
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=96.81 E-value=0.00021 Score=80.15 Aligned_cols=53 Identities=23% Similarity=0.599 Sum_probs=46.9
Q ss_pred CcccccccccCcccceeecCCCCCCCeeeccCCCCCCCCCCCCccccccccCCcC
Q 017784 2 VTVCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPKVA 56 (366)
Q Consensus 2 VtVCdICGDvGFEElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECqse~~ 56 (366)
+..|.+|-..+..+.++.|+.|..+ .|.||+++.+. .++++.|+|.+|+.+..
T Consensus 1108 ~~~c~~cr~k~~~~~m~lc~~c~~~-~h~~C~rp~~~-~~~~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1108 NALCKVCRRKKQDEKMLLCDECLSG-FHLFCLRPALS-SVPPGDWMCPSCRKEHR 1160 (1404)
T ss_pred hhhhhhhhhcccchhhhhhHhhhhh-HHHHhhhhhhc-cCCcCCccCCccchhhh
Confidence 3579999999999999999999996 99999999754 48889999999998753
No 11
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.55 E-value=0.00081 Score=70.44 Aligned_cols=53 Identities=26% Similarity=0.770 Sum_probs=45.2
Q ss_pred cccccccccCcccceeecCCCCCCCeeeccCCCCC--CCCCCCCccccccccCCcCC
Q 017784 3 TVCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLP--ASFEDDVLWYCEDCEPKVAK 57 (366)
Q Consensus 3 tVCdICGDvGFEElLv~CdkCrvgAEHTYCLdv~p--vefvppg~WfCEECqse~~k 57 (366)
.+|..|+..|.-..++.|+.|.. .=|.||++. | .+-.|+|.|+|.+|.-....
T Consensus 254 ~fCsaCn~~~~F~~~i~CD~Cp~-sFH~~CLeP-Pl~~eniP~g~W~C~ec~~k~~i 308 (613)
T KOG4299|consen 254 DFCSACNGSGLFNDIICCDGCPR-SFHQTCLEP-PLEPENIPPGSWFCPECKIKSVI 308 (613)
T ss_pred HHHHHhCCccccccceeecCCch-HHHHhhcCC-CCCcccCCCCccccCCCeeeeec
Confidence 47999999998899999999998 599999999 5 33477899999999876433
No 12
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=96.08 E-value=0.0022 Score=66.81 Aligned_cols=48 Identities=25% Similarity=0.736 Sum_probs=40.6
Q ss_pred ccccccccc--CcccceeecCCCCCCCeeeccCCCCCCCCCCCCccccccccCC
Q 017784 3 TVCQQCGDK--GFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPK 54 (366)
Q Consensus 3 tVCdICGDv--GFEElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECqse 54 (366)
-.|-+|-.. .+.+.|++|++|+. +.|+-|-++ + |.|+|.|+|--|.-.
T Consensus 194 ~~C~~c~~t~~eN~naiVfCdgC~i-~VHq~CYGI-~--f~peG~WlCrkCi~~ 243 (669)
T COG5141 194 DICTKCTSTHNENSNAIVFCDGCEI-CVHQSCYGI-Q--FLPEGFWLCRKCIYG 243 (669)
T ss_pred hhhHhccccccCCcceEEEecCcch-hhhhhcccc-e--ecCcchhhhhhhccc
Confidence 357788766 45789999999998 699999999 4 899999999999744
No 13
>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=95.86 E-value=0.016 Score=51.82 Aligned_cols=27 Identities=26% Similarity=0.488 Sum_probs=22.9
Q ss_pred eeeccCCCCCCCCCCCCccccccccCCc
Q 017784 28 VHIYCLPVLPASFEDDVLWYCEDCEPKV 55 (366)
Q Consensus 28 EHTYCLdv~pvefvppg~WfCEECqse~ 55 (366)
.|.||++.. ...+|+|+|+|..|+...
T Consensus 2 ~H~~CL~Pp-l~~~P~g~W~Cp~C~~~~ 28 (148)
T cd04718 2 FHLCCLRPP-LKEVPEGDWICPFCEVEK 28 (148)
T ss_pred cccccCCCC-CCCCCCCCcCCCCCcCCC
Confidence 599999994 456888999999999773
No 14
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=95.48 E-value=0.0058 Score=62.51 Aligned_cols=55 Identities=24% Similarity=0.513 Sum_probs=40.9
Q ss_pred Cccccccc--ccCcccceeecCCCCCCCeeeccCCCCCCC---CCCCCccccccccCCcCC
Q 017784 2 VTVCQQCG--DKGFYEALIGCEKCQTTAVHIYCLPVLPAS---FEDDVLWYCEDCEPKVAK 57 (366)
Q Consensus 2 VtVCdICG--DvGFEElLv~CdkCrvgAEHTYCLdv~pve---fvppg~WfCEECqse~~k 57 (366)
+..|.+|. -.|..+.|++|++|+.. .|+-|+...... .++...|||+.|......
T Consensus 168 n~qc~vC~~g~~~~~NrmlqC~~C~~~-fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~~ 227 (464)
T KOG4323|consen 168 NLQCSVCYCGGPGAGNRMLQCDKCRQW-YHQACHQPLIKDELAGDPFYEWFCDVCNRGPKK 227 (464)
T ss_pred cceeeeeecCCcCccceeeeecccccH-HHHHhccCCCCHhhccCccceEeehhhccchhh
Confidence 34577775 55667899999999995 999999883211 255589999999877443
No 15
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=91.33 E-value=0.073 Score=56.92 Aligned_cols=47 Identities=26% Similarity=0.610 Sum_probs=36.7
Q ss_pred cccccccccCcccceeecCCCCCCCeeeccCCCCCCCCCCCCccccccccCC
Q 017784 3 TVCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPK 54 (366)
Q Consensus 3 tVCdICGDvGFEElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECqse 54 (366)
.-|.||+|.|. ++.|+.|.. .-|-||++..... .+.+.|.|..|...
T Consensus 48 e~c~ic~~~g~---~l~c~tC~~-s~h~~cl~~pl~~-~p~~~~~c~Rc~~p 94 (696)
T KOG0383|consen 48 EACRICADGGE---LLWCDTCPA-SFHASCLGPPLTP-QPNGEFICPRCFCP 94 (696)
T ss_pred hhhhhhcCCCc---EEEeccccH-HHHHHccCCCCCc-CCccceeeeeeccC
Confidence 35999999874 555999996 7999999985433 55566999999655
No 16
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=90.08 E-value=0.15 Score=54.00 Aligned_cols=49 Identities=27% Similarity=0.635 Sum_probs=40.9
Q ss_pred CCcccccccccCcccceeecCCCCCCCeeeccCCCCCCCCCC----CCccccccc
Q 017784 1 MVTVCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFED----DVLWYCEDC 51 (366)
Q Consensus 1 mVtVCdICGDvGFEElLv~CdkCrvgAEHTYCLdv~pvefvp----pg~WfCEEC 51 (366)
|+.-|-||-..-+.++|+.||-|+- ..|.=|++. |....| --.|.|.+|
T Consensus 543 ~~ysCgiCkks~dQHll~~CDtC~l-hYHlGCL~P-PLTR~Pkk~kn~gWqCsEC 595 (707)
T KOG0957|consen 543 MNYSCGICKKSTDQHLLTQCDTCHL-HYHLGCLSP-PLTRLPKKNKNFGWQCSEC 595 (707)
T ss_pred cceeeeeeccchhhHHHhhcchhhc-eeeccccCC-ccccCcccccCcceeeccc
Confidence 4667999999999999999999998 699999998 333333 247999999
No 17
>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=78.43 E-value=0.93 Score=29.78 Aligned_cols=29 Identities=24% Similarity=0.528 Sum_probs=12.8
Q ss_pred cccccccccCcccceeecCCCCCCCeeecc
Q 017784 3 TVCQQCGDKGFYEALIGCEKCQTTAVHIYC 32 (366)
Q Consensus 3 tVCdICGDvGFEElLv~CdkCrvgAEHTYC 32 (366)
.+|.+||..+..+....|..|+.. -|.-|
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 379999999999999999999984 78766
No 18
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=78.01 E-value=1.3 Score=43.58 Aligned_cols=46 Identities=24% Similarity=0.510 Sum_probs=38.9
Q ss_pred ccccccCc-ccceeecCCCCCCCeeeccCCCCCCCCCCCCccccccccCC
Q 017784 6 QQCGDKGF-YEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPK 54 (366)
Q Consensus 6 dICGDvGF-EElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECqse 54 (366)
++||-... ..++..|+.|.. .+|.+|++.... +.+..-.|+.|..+
T Consensus 89 c~c~~~~~~~g~~i~c~~c~~-Wqh~~C~g~~~~--~~p~~y~c~~c~~~ 135 (508)
T KOG1844|consen 89 CDCGLEDDMEGLMIQCDWCGR-WQHKICCGSFKS--TKPDKYVCEICTPR 135 (508)
T ss_pred cccccccCCCceeeCCcccCc-ccCceeeeecCC--CCchhceeeeeccc
Confidence 47998888 899999999998 699999999652 34678889999877
No 19
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=75.87 E-value=2 Score=45.84 Aligned_cols=54 Identities=33% Similarity=0.753 Sum_probs=38.4
Q ss_pred cccccc-ccc-CcccceeecCCCCCCCeeeccCCCC-----CCCCCC--CCccccccccCCcCC
Q 017784 3 TVCQQC-GDK-GFYEALIGCEKCQTTAVHIYCLPVL-----PASFED--DVLWYCEDCEPKVAK 57 (366)
Q Consensus 3 tVCdIC-GDv-GFEElLv~CdkCrvgAEHTYCLdv~-----pvefvp--pg~WfCEECqse~~k 57 (366)
..|++| |+. .+.+-++.|++|... .|--|-++. +..... ...|||+-|.--+..
T Consensus 120 ~iCcVClg~rs~da~ei~qCd~CGi~-VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~Gvs~ 182 (707)
T KOG0957|consen 120 VICCVCLGQRSVDAGEILQCDKCGIN-VHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLYGVSL 182 (707)
T ss_pred eEEEEeecCccccccceeeccccCce-ecccccccccccccCCCCccCCCCchhhhhHhcCCCC
Confidence 368888 333 556789999999995 999999996 211111 158999999866543
No 20
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=75.23 E-value=2.4 Score=45.90 Aligned_cols=49 Identities=29% Similarity=0.658 Sum_probs=41.2
Q ss_pred cccccccccCcccceeecCCCCCCCeeeccCCCCCCCCCCCCccccccccCC
Q 017784 3 TVCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPK 54 (366)
Q Consensus 3 tVCdICGDvGFEElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECqse 54 (366)
..|..|+....+.++ .|+.|+. ..|+||.+.- ....+.+.|.|..|...
T Consensus 156 ~~~~~~~k~~~~~~~-~~~~~~~-~~~~~~~~~~-~~~~~~~~~~~~~~~~~ 204 (904)
T KOG1246|consen 156 PQCNTCSKGKEEKLL-LCDSCDD-SYHTYCLRPP-LTRVPDGDWRCPKCIPT 204 (904)
T ss_pred hhhhccccCCCccce-ecccccC-cccccccCCC-CCcCCcCcccCCccccc
Confidence 468899998888666 9999999 5999999994 44477799999999876
No 21
>COG4393 Predicted membrane protein [Function unknown]
Probab=74.81 E-value=0.97 Score=45.97 Aligned_cols=23 Identities=30% Similarity=0.931 Sum_probs=20.3
Q ss_pred ccccccccCc--ccceeecCCCCCC
Q 017784 4 VCQQCGDKGF--YEALIGCEKCQTT 26 (366)
Q Consensus 4 VCdICGDvGF--EElLv~CdkCrvg 26 (366)
.|++|||.|+ ++--+.|-+|+++
T Consensus 336 AC~iCGd~GYv~e~dqvICv~C~Vr 360 (405)
T COG4393 336 ACDICGDQGYVMEGDQVICVRCDVR 360 (405)
T ss_pred HHHhccccceEeECCEEEEEEccEE
Confidence 5999999998 6678899999985
No 22
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=73.94 E-value=1.6 Score=40.42 Aligned_cols=31 Identities=32% Similarity=0.765 Sum_probs=26.9
Q ss_pred ccccc---cccCcccceeecCCCCCCCeeeccCCC
Q 017784 4 VCQQC---GDKGFYEALIGCEKCQTTAVHIYCLPV 35 (366)
Q Consensus 4 VCdIC---GDvGFEElLv~CdkCrvgAEHTYCLdv 35 (366)
+|++| |+.-..-.|++|-+|-. +.|.-|++.
T Consensus 1 ~C~~C~~~g~~~~kG~Lv~CQGCs~-sYHk~CLG~ 34 (175)
T PF15446_consen 1 TCDTCGYEGDDRNKGPLVYCQGCSS-SYHKACLGP 34 (175)
T ss_pred CcccccCCCCCccCCCeEEcCccCh-HHHhhhcCC
Confidence 68999 56667789999999998 699999987
No 23
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=73.19 E-value=0.89 Score=49.04 Aligned_cols=48 Identities=27% Similarity=0.705 Sum_probs=35.2
Q ss_pred ccccccccC--cccceeecCCCCCCCeeeccCCCCCCCCCCCCcccccccc
Q 017784 4 VCQQCGDKG--FYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCE 52 (366)
Q Consensus 4 VCdICGDvG--FEElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECq 52 (366)
-|.+||..| -+..|+.|..|.. .+|.||........+..+-|-|..|.
T Consensus 20 mc~l~~s~G~~~ag~m~ac~~c~~-~yH~~cvt~~~~~~~l~~gWrC~~cr 69 (694)
T KOG4443|consen 20 MCPLCGSSGKGRAGRLLACSDCGQ-KYHPYCVTSWAQHAVLSGGWRCPSCR 69 (694)
T ss_pred hhhhhccccccccCcchhhhhhcc-cCCcchhhHHHhHHHhcCCcccCCce
Confidence 366677664 5778999999998 69999999644333445668888874
No 24
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=68.99 E-value=3.5 Score=31.91 Aligned_cols=33 Identities=24% Similarity=0.509 Sum_probs=28.5
Q ss_pred CcccccccccCc-ccceeecCCCCCCCeeeccCCC
Q 017784 2 VTVCQQCGDKGF-YEALIGCEKCQTTAVHIYCLPV 35 (366)
Q Consensus 2 VtVCdICGDvGF-EElLv~CdkCrvgAEHTYCLdv 35 (366)
...|..||+.=. ++-++.|..|..+ .|+-|-..
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~Cgap-yHR~C~~~ 38 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAP-YHRDCWEK 38 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCc-ccHHHHhh
Confidence 468999999854 8999999999985 99999765
No 25
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=67.42 E-value=0.95 Score=37.54 Aligned_cols=47 Identities=26% Similarity=0.617 Sum_probs=24.4
Q ss_pred ccccccccc----CcccceeecCCCCCCCeeeccCCCCCCCCCCCCccccccccCC
Q 017784 3 TVCQQCGDK----GFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPK 54 (366)
Q Consensus 3 tVCdICGDv----GFEElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECqse 54 (366)
.+|+||||. ...++.+-|..|..+ .=+-|+.+- -.++.-.|..|.+.
T Consensus 10 qiCqiCGD~VGl~~~Ge~FVAC~eC~fP-vCr~CyEYE----rkeg~q~CpqCkt~ 60 (80)
T PF14569_consen 10 QICQICGDDVGLTENGEVFVACHECAFP-VCRPCYEYE----RKEGNQVCPQCKTR 60 (80)
T ss_dssp -B-SSS--B--B-SSSSB--S-SSS------HHHHHHH----HHTS-SB-TTT--B
T ss_pred cccccccCccccCCCCCEEEEEcccCCc-cchhHHHHH----hhcCcccccccCCC
Confidence 589999997 568899999999995 666677762 34688899999866
No 26
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=61.30 E-value=8.9 Score=27.02 Aligned_cols=35 Identities=31% Similarity=0.650 Sum_probs=28.6
Q ss_pred Cccccccccc--CcccceeecCCCCCCCeeeccCCCCC
Q 017784 2 VTVCQQCGDK--GFYEALIGCEKCQTTAVHIYCLPVLP 37 (366)
Q Consensus 2 VtVCdICGDv--GFEElLv~CdkCrvgAEHTYCLdv~p 37 (366)
.+.|++|+.. |....-+.|..|+. ..|.-|+...+
T Consensus 11 ~~~C~~C~~~i~g~~~~g~~C~~C~~-~~H~~C~~~~~ 47 (53)
T PF00130_consen 11 PTYCDVCGKFIWGLGKQGYRCSWCGL-VCHKKCLSKVP 47 (53)
T ss_dssp TEB-TTSSSBECSSSSCEEEETTTT--EEETTGGCTSS
T ss_pred CCCCcccCcccCCCCCCeEEECCCCC-hHhhhhhhhcC
Confidence 4679999998 68888999999998 59999999864
No 27
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=59.54 E-value=7.9 Score=41.39 Aligned_cols=49 Identities=22% Similarity=0.321 Sum_probs=38.2
Q ss_pred cccccccccCcccceeecCCCCCCCeeeccCCCCCCCCCCCCccccccccCC
Q 017784 3 TVCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPK 54 (366)
Q Consensus 3 tVCdICGDvGFEElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECqse 54 (366)
.+|..||.. +++---||.+|.....|..|..=- . ..+++.-||.+|-..
T Consensus 2 ~~Cp~Cg~~-n~~~akFC~~CG~~l~~~~Cp~CG-~-~~~~~~~fC~~CG~~ 50 (645)
T PRK14559 2 LICPQCQFE-NPNNNRFCQKCGTSLTHKPCPQCG-T-EVPVDEAHCPNCGAE 50 (645)
T ss_pred CcCCCCCCc-CCCCCccccccCCCCCCCcCCCCC-C-CCCcccccccccCCc
Confidence 589999987 455556999999988888888762 2 366789999999655
No 28
>PLN02400 cellulose synthase
Probab=59.32 E-value=6.5 Score=44.63 Aligned_cols=47 Identities=26% Similarity=0.644 Sum_probs=37.9
Q ss_pred ccccccccc----CcccceeecCCCCCCCeeeccCCCCCCCCCCCCccccccccCC
Q 017784 3 TVCQQCGDK----GFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPK 54 (366)
Q Consensus 3 tVCdICGDv----GFEElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECqse 54 (366)
.+|+||||. -+.|.-+-|+.|..+ .=+=|..+ .-.+|.-.|..|...
T Consensus 37 qiCqICGD~VG~t~dGe~FVAC~eCaFP-VCRpCYEY----ERkeGnq~CPQCkTr 87 (1085)
T PLN02400 37 QICQICGDDVGVTETGDVFVACNECAFP-VCRPCYEY----ERKDGTQCCPQCKTR 87 (1085)
T ss_pred ceeeecccccCcCCCCCEEEEEccCCCc-cccchhhe----ecccCCccCcccCCc
Confidence 489999998 557788999999985 65667766 245789999999877
No 29
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=57.57 E-value=5.5 Score=33.63 Aligned_cols=23 Identities=30% Similarity=0.892 Sum_probs=20.0
Q ss_pred ccccccccCc--ccceeecCCCCCC
Q 017784 4 VCQQCGDKGF--YEALIGCEKCQTT 26 (366)
Q Consensus 4 VCdICGDvGF--EElLv~CdkCrvg 26 (366)
.|++||+.|| +.--+.|..|+.+
T Consensus 37 aCeiC~~~GY~q~g~~lvC~~C~~~ 61 (102)
T PF10080_consen 37 ACEICGPKGYYQEGDQLVCKNCGVR 61 (102)
T ss_pred eccccCCCceEEECCEEEEecCCCE
Confidence 5999999999 4567899999986
No 30
>PLN02436 cellulose synthase A
Probab=56.62 E-value=7.1 Score=44.39 Aligned_cols=48 Identities=25% Similarity=0.561 Sum_probs=38.2
Q ss_pred ccccccccc----CcccceeecCCCCCCCeeeccCCCCCCCCCCCCccccccccCCc
Q 017784 3 TVCQQCGDK----GFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPKV 55 (366)
Q Consensus 3 tVCdICGDv----GFEElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECqse~ 55 (366)
.+|+||||. -+.|+-+-|+.|..+ .=+-|..+ - ..++.-.|..|...-
T Consensus 37 ~iCqICGD~Vg~t~dGe~FVACn~C~fp-vCr~Cyey-e---r~eg~~~Cpqckt~Y 88 (1094)
T PLN02436 37 QTCQICGDEIELTVDGEPFVACNECAFP-VCRPCYEY-E---RREGNQACPQCKTRY 88 (1094)
T ss_pred ccccccccccCcCCCCCEEEeeccCCCc-cccchhhh-h---hhcCCccCcccCCch
Confidence 489999997 457788999999985 66677766 2 347899999998773
No 31
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=54.53 E-value=2.7 Score=41.94 Aligned_cols=51 Identities=29% Similarity=0.714 Sum_probs=38.4
Q ss_pred Ccccccc-ccc------CcccceeecCCCCCCCeeeccCCCCCC--CCCCCCccccccccC
Q 017784 2 VTVCQQC-GDK------GFYEALIGCEKCQTTAVHIYCLPVLPA--SFEDDVLWYCEDCEP 53 (366)
Q Consensus 2 VtVCdIC-GDv------GFEElLv~CdkCrvgAEHTYCLdv~pv--efvppg~WfCEECqs 53 (366)
+..|++| ||. |.+|-|+.|..|.+ .-|--|+.+.+. ..+..--|.|-+|..
T Consensus 224 n~YCDFclgdsr~nkkt~~peelvscsdcgr-sghpsclqft~nm~~avk~yrwqcieck~ 283 (336)
T KOG1244|consen 224 NPYCDFCLGDSRENKKTGMPEELVSCSDCGR-SGHPSCLQFTANMIAAVKTYRWQCIECKY 283 (336)
T ss_pred CcccceeccccccccccCCchhhcchhhcCC-CCCcchhhhhHHHHHHHHhheeeeeecce
Confidence 4568888 444 89999999999998 599999987321 113345799999963
No 32
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=53.12 E-value=7.9 Score=43.98 Aligned_cols=47 Identities=32% Similarity=0.595 Sum_probs=37.5
Q ss_pred ccccccccc----CcccceeecCCCCCCCeeeccCCCCCCCCCCCCccccccccCC
Q 017784 3 TVCQQCGDK----GFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPK 54 (366)
Q Consensus 3 tVCdICGDv----GFEElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECqse 54 (366)
.+|+||||. -+.|.-+-|+.|..+ .=+=|-.+ .-.+|.-.|..|...
T Consensus 18 qiCqICGD~vg~~~~Ge~FVAC~eC~FP-VCrpCYEY----Er~eG~q~CPqCktr 68 (1079)
T PLN02638 18 QVCQICGDNVGKTVDGEPFVACDVCAFP-VCRPCYEY----ERKDGNQSCPQCKTK 68 (1079)
T ss_pred ceeeecccccCcCCCCCEEEEeccCCCc-cccchhhh----hhhcCCccCCccCCc
Confidence 489999998 557788999999985 55567655 244789999999877
No 33
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=49.36 E-value=10 Score=42.93 Aligned_cols=47 Identities=21% Similarity=0.552 Sum_probs=36.4
Q ss_pred ccccccccc----CcccceeecCCCCCCCeeeccCCCCCCCCCCCCccccccccCC
Q 017784 3 TVCQQCGDK----GFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPK 54 (366)
Q Consensus 3 tVCdICGDv----GFEElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECqse 54 (366)
.+|+||||. -+.|.-+-|+.|..+ .=+=|..+- ..+|.-.|..|...
T Consensus 16 ~~c~iCGd~vg~~~~Ge~FVAC~eC~fp-vCr~cyeye----~~~g~~~cp~c~t~ 66 (1044)
T PLN02915 16 KTCRVCGDEVGVKEDGQPFVACHVCGFP-VCKPCYEYE----RSEGNQCCPQCNTR 66 (1044)
T ss_pred chhhccccccCcCCCCCEEEEeccCCCc-cccchhhhh----hhcCCccCCccCCc
Confidence 589999998 557788999999985 555566552 34788999999755
No 34
>PLN02189 cellulose synthase
Probab=48.75 E-value=11 Score=42.73 Aligned_cols=48 Identities=23% Similarity=0.573 Sum_probs=38.6
Q ss_pred ccccccccc----CcccceeecCCCCCCCeeeccCCCCCCCCCCCCccccccccCCc
Q 017784 3 TVCQQCGDK----GFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPKV 55 (366)
Q Consensus 3 tVCdICGDv----GFEElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECqse~ 55 (366)
.+|+||||. -+.+.-+-|..|..+ .=+-|..+ - ..+|.-.|..|...-
T Consensus 35 ~~C~iCgd~vg~~~~g~~fvaC~~C~fp-vCr~Cyey-e---r~eg~q~CpqCkt~Y 86 (1040)
T PLN02189 35 QVCEICGDEIGLTVDGDLFVACNECGFP-VCRPCYEY-E---RREGTQNCPQCKTRY 86 (1040)
T ss_pred ccccccccccCcCCCCCEEEeeccCCCc-cccchhhh-h---hhcCCccCcccCCch
Confidence 489999998 567888999999985 66677765 2 447899999998773
No 35
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=46.67 E-value=5.6 Score=40.16 Aligned_cols=48 Identities=27% Similarity=0.659 Sum_probs=36.8
Q ss_pred ccccccccc------CcccceeecCCCCCCCeeeccCCCCCCCC---CCCCcccccccc
Q 017784 3 TVCQQCGDK------GFYEALIGCEKCQTTAVHIYCLPVLPASF---EDDVLWYCEDCE 52 (366)
Q Consensus 3 tVCdICGDv------GFEElLv~CdkCrvgAEHTYCLdv~pvef---vppg~WfCEECq 52 (366)
..|.+|=|+ |-.+-|+.|.-|.. +-|-||++.-+ +. ...-.|-|.+|.
T Consensus 259 ~~~~~~~~~~~~~~~~r~~S~I~C~~C~~-~~HP~Ci~M~~-elv~~~KTY~W~C~~C~ 315 (381)
T KOG1512|consen 259 NERKHFWDIQTNIIQSRRNSWIVCKPCAT-RPHPYCVAMIP-ELVGQYKTYFWKCSSCE 315 (381)
T ss_pred hhhhhhhcchhhhhhhhhccceeeccccc-CCCCcchhcCH-HHHhHHhhcchhhcccH
Confidence 457777665 77889999999998 69999998732 21 334689999996
No 36
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=44.92 E-value=21 Score=23.64 Aligned_cols=29 Identities=24% Similarity=0.487 Sum_probs=23.2
Q ss_pred ccccccccCcccceeecCCCCCCCeeeccC
Q 017784 4 VCQQCGDKGFYEALIGCEKCQTTAVHIYCL 33 (366)
Q Consensus 4 VCdICGDvGFEElLv~CdkCrvgAEHTYCL 33 (366)
.|++|+...+....-.|..|.. .-|.-|.
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~f-~lh~~Ca 30 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECCF-TLHVRCA 30 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCCC-eEcCccC
Confidence 5999999876665889999995 6888773
No 37
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=44.87 E-value=18 Score=24.40 Aligned_cols=26 Identities=23% Similarity=0.507 Sum_probs=18.4
Q ss_pred CCccccccccc---C-----cccceeecCCCCCC
Q 017784 1 MVTVCQQCGDK---G-----FYEALIGCEKCQTT 26 (366)
Q Consensus 1 mVtVCdICGDv---G-----FEElLv~CdkCrvg 26 (366)
|...|+.||.. . .....+.|.+|...
T Consensus 1 M~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 1 MRIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHV 34 (38)
T ss_pred CEEECCCCCCEEEeCHHHcCCCCCEEECCCCCCE
Confidence 67789999883 2 23446889999864
No 38
>PLN02195 cellulose synthase A
Probab=41.89 E-value=16 Score=41.32 Aligned_cols=48 Identities=23% Similarity=0.542 Sum_probs=37.6
Q ss_pred Cccccccccc----CcccceeecCCCCCCCeeeccCCCCCCCCCCCCccccccccCC
Q 017784 2 VTVCQQCGDK----GFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPK 54 (366)
Q Consensus 2 VtVCdICGDv----GFEElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECqse 54 (366)
..+|.||||. .+.+.-+-|+.|..+ .=+=|..+ ...+|.-.|..|...
T Consensus 6 ~~~c~~cgd~~~~~~~g~~fvaC~eC~~p-vCrpCyey----er~eg~q~CpqCkt~ 57 (977)
T PLN02195 6 APICATCGEEVGVDSNGEAFVACHECSYP-LCKACLEY----EIKEGRKVCLRCGGP 57 (977)
T ss_pred CccceecccccCcCCCCCeEEEeccCCCc-cccchhhh----hhhcCCccCCccCCc
Confidence 4589999994 567888999999985 66667765 245789999999765
No 39
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=39.29 E-value=12 Score=25.82 Aligned_cols=26 Identities=31% Similarity=0.402 Sum_probs=18.1
Q ss_pred cccccccccCccc-ceeecCCCCCCCe
Q 017784 3 TVCQQCGDKGFYE-ALIGCEKCQTTAV 28 (366)
Q Consensus 3 tVCdICGDvGFEE-lLv~CdkCrvgAE 28 (366)
-+|.+||..-..+ ..-.|-.|....+
T Consensus 3 ~~C~~CG~i~~g~~~p~~CP~Cg~~~~ 29 (34)
T cd00729 3 WVCPVCGYIHEGEEAPEKCPICGAPKE 29 (34)
T ss_pred EECCCCCCEeECCcCCCcCcCCCCchH
Confidence 4799999884433 5568888887543
No 40
>PF01753 zf-MYND: MYND finger; InterPro: IPR002893 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 MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [, , ]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif []. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions []. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [, ]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein []. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression []. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3QWW_A 3QWV_A 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3RU0_A ....
Probab=38.65 E-value=24 Score=23.82 Aligned_cols=23 Identities=39% Similarity=1.102 Sum_probs=16.0
Q ss_pred cccccccCcccceeecCCCCCCCeeeccCC
Q 017784 5 CQQCGDKGFYEALIGCEKCQTTAVHIYCLP 34 (366)
Q Consensus 5 CdICGDvGFEElLv~CdkCrvgAEHTYCLd 34 (366)
|..||. ..+..|.+|+.. .||..
T Consensus 1 C~~C~~----~~~~~C~~C~~~---~YCs~ 23 (37)
T PF01753_consen 1 CAVCGK----PALKRCSRCKSV---YYCSE 23 (37)
T ss_dssp -TTTSS----CSSEEETTTSSS---EESSH
T ss_pred CcCCCC----CcCCcCCCCCCE---EecCH
Confidence 678888 344499999875 67764
No 41
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=38.26 E-value=17 Score=28.49 Aligned_cols=22 Identities=27% Similarity=0.765 Sum_probs=14.1
Q ss_pred ccccccc---------cCcccceeecCCCCC
Q 017784 4 VCQQCGD---------KGFYEALIGCEKCQT 25 (366)
Q Consensus 4 VCdICGD---------vGFEElLv~CdkCrv 25 (366)
.|++||. .-..+..+||.+|+.
T Consensus 6 ~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~ 36 (55)
T PF14205_consen 6 LCPICGNKTRLKIREDTVLKNFPLYCPKCKQ 36 (55)
T ss_pred ECCCCCCccceeeecCceeccccccCCCCCc
Confidence 5777773 334566677777775
No 42
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=35.68 E-value=22 Score=22.99 Aligned_cols=24 Identities=25% Similarity=0.593 Sum_probs=16.6
Q ss_pred CCcccccccccCcccceeecCCCCC
Q 017784 1 MVTVCQQCGDKGFYEALIGCEKCQT 25 (366)
Q Consensus 1 mVtVCdICGDvGFEElLv~CdkCrv 25 (366)
|.+.|.-||. ..++---+|..|..
T Consensus 1 m~~~Cp~Cg~-~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 1 MEMFCPNCGA-EIDPDAKFCPNCGA 24 (26)
T ss_pred CcCCCcccCC-cCCcccccChhhCC
Confidence 5677888887 45555667777764
No 43
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=31.99 E-value=20 Score=33.77 Aligned_cols=51 Identities=25% Similarity=0.511 Sum_probs=25.9
Q ss_pred ccccccccc-------Cc---ccceeecCCCCCCCeee------ccCCCCCCC---C-----CCCCccccccccCC
Q 017784 3 TVCQQCGDK-------GF---YEALIGCEKCQTTAVHI------YCLPVLPAS---F-----EDDVLWYCEDCEPK 54 (366)
Q Consensus 3 tVCdICGDv-------GF---EElLv~CdkCrvgAEHT------YCLdv~pve---f-----vppg~WfCEECqse 54 (366)
..|++||.. +. ....++|.-|.. .||- ||-+..... + .....-.|+.|.+-
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t-~W~~~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~Y 247 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGT-EWRFVRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSY 247 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT---EEE--TTS-TTT---SS-EEE--------SEEEEEETTTTEE
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCC-eeeecCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccch
Confidence 579999986 22 359999999997 4775 887764321 1 11246689999865
No 44
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=31.77 E-value=35 Score=23.15 Aligned_cols=35 Identities=26% Similarity=0.713 Sum_probs=25.6
Q ss_pred Cccccccccc--CcccceeecCCCCCCCeeeccCCCCC
Q 017784 2 VTVCQQCGDK--GFYEALIGCEKCQTTAVHIYCLPVLP 37 (366)
Q Consensus 2 VtVCdICGDv--GFEElLv~CdkCrvgAEHTYCLdv~p 37 (366)
.+.|.+|+.. |....-+.|..|+. ..|.=|.+..+
T Consensus 11 ~~~C~~C~~~i~~~~~~~~~C~~C~~-~~H~~C~~~v~ 47 (50)
T cd00029 11 PTFCDVCRKSIWGLFKQGLRCSWCKV-KCHKKCADKVP 47 (50)
T ss_pred CCChhhcchhhhccccceeEcCCCCC-chhhhhhccCC
Confidence 3568888876 33467778999987 58888888743
No 45
>PF02977 CarbpepA_inh: Carboxypeptidase A inhibitor; InterPro: IPR004231 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. This family is represented by the well-characterised metallocarboxypeptidase A inhibitor (MCPI) from potatoes, which belongs to the MEROPS inhibitor family I37, clan IE. It inhibits metallopeptidases belonging to MEROPS peptidase family M14, carboxypeptidase A. In Russet Burbank potatoes, it is a mixture of approximately equal amounts of two polypeptide chains containing 38 or 39 amino acid residues. The chains differ in their amino terminal sequence only [] and are resistant to fragmentation by proteases []. The structure of the complex between bovine carboxypeptidase A and the 39-amino-acid carboxypeptidase A inhibitor from potatoes has been determined at 2.5-A resolution []. The potato inhibitor is synthesised as a precursor, having a 29 residue N-terminal signal peptide, a 27 residue pro-peptide, the 39 residue mature inhibitor region and a 7 residue C-terminal extension. The 7 residue C-terminal extension is involved in inhibitor inactivation and may be required for targeting to the vacuole where the mature active inhibitor accumulates []. The N-terminal region and the mature inhibitor are weakly related to other solananaceous proteins found in this entry, from potato, tomato and henbane, which have been incorrectly described as metallocarboxipeptidase inhibitors [].; GO: 0008191 metalloendopeptidase inhibitor activity; PDB: 4CPA_I 1H20_A 2HLG_A.
Probab=31.49 E-value=23 Score=27.04 Aligned_cols=20 Identities=20% Similarity=0.363 Sum_probs=12.1
Q ss_pred eeccCCCCCCCCCCCCcccccccc
Q 017784 29 HIYCLPVLPASFEDDVLWYCEDCE 52 (366)
Q Consensus 29 HTYCLdv~pvefvppg~WfCEECq 52 (366)
|-||.-- .+=.+.|||.||-
T Consensus 9 n~~C~t~----sDC~g~tlC~~C~ 28 (46)
T PF02977_consen 9 NKYCNTN----SDCSGITLCQWCW 28 (46)
T ss_dssp T-B-SSS----CCCTTSSSS-EE-
T ss_pred CCccccC----ccccceeehHHHH
Confidence 4477766 3557999999994
No 46
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=30.71 E-value=39 Score=23.41 Aligned_cols=25 Identities=24% Similarity=0.628 Sum_probs=18.6
Q ss_pred CCccccccccc--------CcccceeecCCCCC
Q 017784 1 MVTVCQQCGDK--------GFYEALIGCEKCQT 25 (366)
Q Consensus 1 mVtVCdICGDv--------GFEElLv~CdkCrv 25 (366)
|.+.|+.|+-. +.....+.|.+|+.
T Consensus 1 M~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~ 33 (37)
T PF13719_consen 1 MIITCPNCQTRFRVPDDKLPAGGRKVRCPKCGH 33 (37)
T ss_pred CEEECCCCCceEEcCHHHcccCCcEEECCCCCc
Confidence 67788888854 34566888998875
No 47
>KOG1080 consensus Histone H3 (Lys4) methyltransferase complex, subunit SET1 and related methyltransferases [Chromatin structure and dynamics; Transcription]
Probab=30.44 E-value=40 Score=38.31 Aligned_cols=48 Identities=31% Similarity=0.676 Sum_probs=40.0
Q ss_pred ccccccccc--CcccceeecCCCCCCCeeeccCCCCCCCCCCCCccccccccC
Q 017784 3 TVCQQCGDK--GFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEP 53 (366)
Q Consensus 3 tVCdICGDv--GFEElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECqs 53 (366)
..|.+|++. +..++.+.|++|.. .-|+=|.+..+ ......|.|+.|+.
T Consensus 574 ~~c~~~~~~~~~~~n~~~~~~~~~~-~~~s~~~g~~~--~~~~~~~~~~~~~~ 623 (1005)
T KOG1080|consen 574 ERCAVCRDDEDWEKNVSIICDRCTR-SVHSECYGNLK--SYDGTSWVCDSCET 623 (1005)
T ss_pred ccccccccccccccceeeeeccccc-cCCCcccccCC--CCCCCcchhhcccc
Confidence 358899988 66888999999998 69999999965 23456999999997
No 48
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=30.27 E-value=20 Score=23.90 Aligned_cols=34 Identities=21% Similarity=0.380 Sum_probs=23.7
Q ss_pred CcccccccccCcc-cceeecCCCCCCCeeeccCCCC
Q 017784 2 VTVCQQCGDKGFY-EALIGCEKCQTTAVHIYCLPVL 36 (366)
Q Consensus 2 VtVCdICGDvGFE-ElLv~CdkCrvgAEHTYCLdv~ 36 (366)
.+.|.+|++.=.. ..-+.|..|+. ..|.-|+...
T Consensus 11 ~~~C~~C~~~i~~~~~~~~C~~C~~-~~H~~C~~~v 45 (49)
T smart00109 11 PTKCCVCRKSIWGSFQGLRCSWCKV-KCHKKCAEKV 45 (49)
T ss_pred CCCccccccccCcCCCCcCCCCCCc-hHHHHHHhhc
Confidence 3568888876221 13577999987 5888888874
No 49
>KOG4216 consensus Steroid hormone nuclear receptor [Transcription]
Probab=28.26 E-value=25 Score=36.83 Aligned_cols=24 Identities=42% Similarity=0.994 Sum_probs=19.5
Q ss_pred Cccccccccc--CcccceeecCCCCC
Q 017784 2 VTVCQQCGDK--GFYEALIGCEKCQT 25 (366)
Q Consensus 2 VtVCdICGDv--GFEElLv~CdkCrv 25 (366)
|.+|.||||. |---=..+|-+|+.
T Consensus 46 vIPCKiCGDKSSGiHYGVITCEGCKG 71 (479)
T KOG4216|consen 46 IIPCKICGDKSSGIHYGVITCEGCKG 71 (479)
T ss_pred EEeeeeccCCCCcceeeeEeeccchH
Confidence 6799999998 55556788999985
No 50
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=27.90 E-value=16 Score=25.64 Aligned_cols=34 Identities=26% Similarity=0.845 Sum_probs=16.0
Q ss_pred eeecCCCCCCCeeeccCCCCCCCCCC-CCccccccccCCcCC
Q 017784 17 LIGCEKCQTTAVHIYCLPVLPASFED-DVLWYCEDCEPKVAK 57 (366)
Q Consensus 17 Lv~CdkCrvgAEHTYCLdv~pvefvp-pg~WfCEECqse~~k 57 (366)
++.|.+|+.+ ---|| .++. ...|.|.-|...+..
T Consensus 2 p~rC~~C~ay-lNp~~------~~~~~~~~w~C~~C~~~N~l 36 (40)
T PF04810_consen 2 PVRCRRCRAY-LNPFC------QFDDGGKTWICNFCGTKNPL 36 (40)
T ss_dssp S-B-TTT--B-S-TTS------EEETTTTEEEETTT--EEE-
T ss_pred ccccCCCCCE-ECCcc------eEcCCCCEEECcCCCCcCCC
Confidence 4679999875 22222 1233 469999999876443
No 51
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=27.88 E-value=24 Score=23.85 Aligned_cols=9 Identities=33% Similarity=1.106 Sum_probs=5.4
Q ss_pred ccccccccC
Q 017784 45 LWYCEDCEP 53 (366)
Q Consensus 45 ~WfCEECqs 53 (366)
.|.|..|..
T Consensus 17 ~~~CP~Cg~ 25 (33)
T cd00350 17 PWVCPVCGA 25 (33)
T ss_pred CCcCcCCCC
Confidence 566666643
No 52
>PF12773 DZR: Double zinc ribbon
Probab=27.79 E-value=48 Score=23.25 Aligned_cols=38 Identities=24% Similarity=0.517 Sum_probs=22.5
Q ss_pred cccccccCcccceeecCCCCCCCeeeccCCCCCCCCCCCCccccccccCC
Q 017784 5 CQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPK 54 (366)
Q Consensus 5 CdICGDvGFEElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECqse 54 (366)
|..||.. .++-..+|..|..... ......++|..|-..
T Consensus 1 Cp~Cg~~-~~~~~~fC~~CG~~l~-----------~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 1 CPHCGTP-NPDDAKFCPHCGTPLP-----------PPDQSKKICPNCGAE 38 (50)
T ss_pred CCCcCCc-CCccccCChhhcCChh-----------hccCCCCCCcCCcCC
Confidence 6677766 3444667888877533 012346777777655
No 53
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=27.68 E-value=26 Score=36.47 Aligned_cols=52 Identities=25% Similarity=0.584 Sum_probs=32.4
Q ss_pred ccccccccc--CcccceeecCCCCCCC-------eeeccCCCCCCCCCCCCccccccccCC
Q 017784 3 TVCQQCGDK--GFYEALIGCEKCQTTA-------VHIYCLPVLPASFEDDVLWYCEDCEPK 54 (366)
Q Consensus 3 tVCdICGDv--GFEElLv~CdkCrvgA-------EHTYCLdv~pvefvppg~WfCEECqse 54 (366)
..|++|||. |+---|++|..|+.-+ -|--|....--.-+..----|.-|+-.
T Consensus 16 ElCPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRFQ 76 (475)
T KOG4218|consen 16 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRFQ 76 (475)
T ss_pred cccccccCccccceeeeeehhhhhhHHHHHhhcCcceecccccccccchHhhccCCchhHH
Confidence 469999998 9999999999998522 233455442111122344567777543
No 54
>cd03031 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive.
Probab=27.67 E-value=69 Score=28.27 Aligned_cols=43 Identities=21% Similarity=0.707 Sum_probs=28.6
Q ss_pred cccccccccCcccceeecCCCCCCCeeeccCCCCCCCCCCCCccccccccCC
Q 017784 3 TVCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPK 54 (366)
Q Consensus 3 tVCdICGDvGFEElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECqse 54 (366)
.+|..||+.+| +.|..|+.. --.|-.+. +...+..-|.+|-++
T Consensus 100 ~~C~~Cgg~rf----v~C~~C~Gs-~k~~~~~~----~~~~~~~rC~~Cnen 142 (147)
T cd03031 100 GVCEGCGGARF----VPCSECNGS-CKVFAENA----TAAGGFLRCPECNEN 142 (147)
T ss_pred CCCCCCCCcCe----EECCCCCCc-ceEEeccC----cccccEEECCCCCcc
Confidence 37999999886 789999974 33333221 112356789999743
No 55
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=27.59 E-value=41 Score=36.90 Aligned_cols=51 Identities=22% Similarity=0.380 Sum_probs=35.8
Q ss_pred cccccccccCcccceeecCCCCCCCeeeccCCCCCCCCCCCCccccccccCC
Q 017784 3 TVCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPK 54 (366)
Q Consensus 3 tVCdICGDvGFEElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECqse 54 (366)
.||..|--.|--..+..|..|...-.=--|--. ..++.+..+.+|.+|+.+
T Consensus 54 ~pc~~c~gkG~V~v~~~c~~c~G~gkv~~c~~c-G~~~~~~~~~lc~~c~~~ 104 (715)
T COG1107 54 IPCPKCRGKGTVTVYDTCPECGGTGKVLTCDIC-GDIIVPWEEGLCPECRRK 104 (715)
T ss_pred CCCCeeccceeEEEEeecccCCCceeEEeeccc-cceecCcccccChhHhhC
Confidence 589999988999999999999875333334333 233444445589999866
No 56
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=26.26 E-value=40 Score=26.92 Aligned_cols=31 Identities=35% Similarity=0.656 Sum_probs=26.3
Q ss_pred CcccccccccCcccceeecCC--CCCCCeeeccCCC
Q 017784 2 VTVCQQCGDKGFYEALIGCEK--CQTTAVHIYCLPV 35 (366)
Q Consensus 2 VtVCdICGDvGFEElLv~Cdk--CrvgAEHTYCLdv 35 (366)
...|.+|+.. .-.++.|.. |.. +-|.+|...
T Consensus 55 ~~~C~iC~~~--~G~~i~C~~~~C~~-~fH~~CA~~ 87 (110)
T PF13832_consen 55 KLKCSICGKS--GGACIKCSHPGCST-AFHPTCARK 87 (110)
T ss_pred CCcCcCCCCC--CceeEEcCCCCCCc-CCCHHHHHH
Confidence 4689999998 556999999 998 599999866
No 57
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=26.18 E-value=40 Score=22.00 Aligned_cols=22 Identities=23% Similarity=0.406 Sum_probs=10.0
Q ss_pred cccccccccCcccc-----eeecCCCC
Q 017784 3 TVCQQCGDKGFYEA-----LIGCEKCQ 24 (366)
Q Consensus 3 tVCdICGDvGFEEl-----Lv~CdkCr 24 (366)
.+|+.||..--... ..+|.+|.
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTTC
T ss_pred CcCccCCCcceEeEecCCCCeECcCCc
Confidence 36777777633333 36777775
No 58
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=25.79 E-value=61 Score=38.06 Aligned_cols=47 Identities=23% Similarity=0.634 Sum_probs=27.8
Q ss_pred cccccccccCcccceeecCCCCCCCeeec-c---CCCCCCCCCCCCccccccccCC
Q 017784 3 TVCQQCGDKGFYEALIGCEKCQTTAVHIY-C---LPVLPASFEDDVLWYCEDCEPK 54 (366)
Q Consensus 3 tVCdICGDvGFEElLv~CdkCrvgAEHTY-C---Ldv~pvefvppg~WfCEECqse 54 (366)
..|+-||-..+. .+|..|.......| | -...+ .++.+.-+|..|-.+
T Consensus 668 rkCPkCG~~t~~---~fCP~CGs~te~vy~CPsCGaev~--~des~a~~CP~CGtp 718 (1337)
T PRK14714 668 RRCPSCGTETYE---NRCPDCGTHTEPVYVCPDCGAEVP--PDESGRVECPRCDVE 718 (1337)
T ss_pred EECCCCCCcccc---ccCcccCCcCCCceeCccCCCccC--CCccccccCCCCCCc
Confidence 579999998765 39999997643332 3 22211 122224467777655
No 59
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=25.77 E-value=54 Score=22.78 Aligned_cols=25 Identities=28% Similarity=0.646 Sum_probs=17.3
Q ss_pred CCccccccccc--------CcccceeecCCCCC
Q 017784 1 MVTVCQQCGDK--------GFYEALIGCEKCQT 25 (366)
Q Consensus 1 mVtVCdICGDv--------GFEElLv~CdkCrv 25 (366)
|..+|+-|+-. ...-..+.|.+|+.
T Consensus 1 M~i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 1 MIITCPNCQAKYEIDDEKIPPKGRKVRCSKCGH 33 (36)
T ss_pred CEEECCCCCCEEeCCHHHCCCCCcEEECCCCCC
Confidence 66778888754 33456788888875
No 60
>PRK04023 DNA polymerase II large subunit; Validated
Probab=25.17 E-value=51 Score=37.99 Aligned_cols=34 Identities=24% Similarity=0.667 Sum_probs=24.4
Q ss_pred cccccccccCcccceeecCCCCCCCeeeccCCCCCCCCCCCCccccccccCC
Q 017784 3 TVCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPK 54 (366)
Q Consensus 3 tVCdICGDvGFEElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECqse 54 (366)
..|.-||..+ ..+.|..|... ....|+|.+|...
T Consensus 627 RfCpsCG~~t---~~frCP~CG~~---------------Te~i~fCP~CG~~ 660 (1121)
T PRK04023 627 RKCPSCGKET---FYRRCPFCGTH---------------TEPVYRCPRCGIE 660 (1121)
T ss_pred ccCCCCCCcC---CcccCCCCCCC---------------CCcceeCccccCc
Confidence 4699999887 44789999863 1346788888655
No 61
>KOG4846 consensus Nuclear receptor [Signal transduction mechanisms]
Probab=25.11 E-value=30 Score=36.59 Aligned_cols=25 Identities=40% Similarity=1.066 Sum_probs=22.1
Q ss_pred CCccccccccc--CcccceeecCCCCC
Q 017784 1 MVTVCQQCGDK--GFYEALIGCEKCQT 25 (366)
Q Consensus 1 mVtVCdICGDv--GFEElLv~CdkCrv 25 (366)
|+..|.+|||+ ||--=..-|-+|+.
T Consensus 131 ~~~lCkVCgDkASGfHYGV~aCEGCKG 157 (538)
T KOG4846|consen 131 AISLCKVCGDKASGFHYGVTACEGCKG 157 (538)
T ss_pred eeEeehhhccccccceeceeecccchH
Confidence 46789999999 89888999999985
No 62
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=24.97 E-value=30 Score=23.51 Aligned_cols=24 Identities=33% Similarity=0.975 Sum_probs=15.2
Q ss_pred CcccccccccCcccceeecCCCCCCCeeeccC
Q 017784 2 VTVCQQCGDKGFYEALIGCEKCQTTAVHIYCL 33 (366)
Q Consensus 2 VtVCdICGDvGFEElLv~CdkCrvgAEHTYCL 33 (366)
...|.+||. ...-.|.+|+.. ||.
T Consensus 2 ~~~C~vC~~----~~kY~Cp~C~~~----~CS 25 (30)
T PF04438_consen 2 RKLCSVCGN----PAKYRCPRCGAR----YCS 25 (30)
T ss_dssp -EEETSSSS----EESEE-TTT--E----ESS
T ss_pred cCCCccCcC----CCEEECCCcCCc----eeC
Confidence 467899987 556689999885 774
No 63
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=24.12 E-value=82 Score=31.32 Aligned_cols=51 Identities=22% Similarity=0.462 Sum_probs=33.9
Q ss_pred cccccccccC----------cccceeecCCCCCCCeee------ccCCCCCCCC--CCC-----CccccccccCC
Q 017784 3 TVCQQCGDKG----------FYEALIGCEKCQTTAVHI------YCLPVLPASF--EDD-----VLWYCEDCEPK 54 (366)
Q Consensus 3 tVCdICGDvG----------FEElLv~CdkCrvgAEHT------YCLdv~pvef--vpp-----g~WfCEECqse 54 (366)
..|++||..- .....+.|.-|.. .||. ||-.-....+ .++ ..-.|+.|.+-
T Consensus 188 ~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~t-eW~~~R~~C~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~~Y 261 (309)
T PRK03564 188 QFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCES-EWHVVRVKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGTY 261 (309)
T ss_pred CCCCCCCCcchhheeeccCCCCceEEEcCCCCC-cccccCccCCCCCCCCceeeeeecCCCcceEeeeccccccc
Confidence 5799999872 3467899999997 4774 8876422111 111 23679999876
No 64
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=23.70 E-value=43 Score=34.60 Aligned_cols=35 Identities=29% Similarity=0.542 Sum_probs=25.3
Q ss_pred cceeecCCCCCCCeeeccCCCCCCCCCCCCccccccccCCcC
Q 017784 15 EALIGCEKCQTTAVHIYCLPVLPASFEDDVLWYCEDCEPKVA 56 (366)
Q Consensus 15 ElLv~CdkCrvgAEHTYCLdv~pvefvppg~WfCEECqse~~ 56 (366)
+.|+||..|.. .-..||...- -..|||.-|..++.
T Consensus 3 ~~L~fC~~C~~-irc~~c~~~E------i~~~yCp~CL~~~p 37 (483)
T PF05502_consen 3 EELYFCEHCHK-IRCPRCVSEE------IDSYYCPNCLFEVP 37 (483)
T ss_pred ccceecccccc-cCChhhcccc------cceeECccccccCC
Confidence 46899999998 4667777662 23788888876643
No 65
>PRK06424 transcription factor; Provisional
Probab=23.26 E-value=26 Score=31.04 Aligned_cols=7 Identities=57% Similarity=1.616 Sum_probs=5.4
Q ss_pred ccccccc
Q 017784 5 CQQCGDK 11 (366)
Q Consensus 5 CdICGDv 11 (366)
|+|||..
T Consensus 3 CE~CG~~ 9 (144)
T PRK06424 3 CEMCGKK 9 (144)
T ss_pred ccccCcc
Confidence 8888864
No 66
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=21.26 E-value=51 Score=25.69 Aligned_cols=30 Identities=17% Similarity=0.380 Sum_probs=24.8
Q ss_pred ccccccccCcccceeecCCCCCCCeeeccCCCC
Q 017784 4 VCQQCGDKGFYEALIGCEKCQTTAVHIYCLPVL 36 (366)
Q Consensus 4 VCdICGDvGFEElLv~CdkCrvgAEHTYCLdv~ 36 (366)
.|.+|+...-...-+.|..|..+ +||....
T Consensus 1 ~Cpv~~~~~~~~v~~~Cp~cGip---thcS~eh 30 (55)
T PF13824_consen 1 LCPVCKKDLPAHVNFECPDCGIP---THCSEEH 30 (55)
T ss_pred CCCCCccccccccCCcCCCCCCc---CccCHHH
Confidence 48899988888888999999987 7887763
No 67
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=21.05 E-value=73 Score=24.44 Aligned_cols=34 Identities=24% Similarity=0.521 Sum_probs=22.3
Q ss_pred CCccccccccc-----CcccceeecCCCCCCCeeeccCCC
Q 017784 1 MVTVCQQCGDK-----GFYEALIGCEKCQTTAVHIYCLPV 35 (366)
Q Consensus 1 mVtVCdICGDv-----GFEElLv~CdkCrvgAEHTYCLdv 35 (366)
|...|..||.. .....++.|..|....+ ....+.
T Consensus 1 ~~~~CP~CG~~iev~~~~~GeiV~Cp~CGaele-Vv~~~p 39 (54)
T TIGR01206 1 MQFECPDCGAEIELENPELGELVICDECGAELE-VVSLDP 39 (54)
T ss_pred CccCCCCCCCEEecCCCccCCEEeCCCCCCEEE-EEeCCC
Confidence 56689999964 33456889999987532 344443
Done!