Query 041295
Match_columns 209
No_of_seqs 51 out of 53
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 05:44:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041295.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041295hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00249 PHD PHD zinc finger 98.4 2.7E-07 5.9E-12 57.5 3.2 43 42-87 1-47 (47)
2 KOG4299 PHD Zn-finger protein 98.3 1.9E-07 4.2E-12 91.2 0.8 50 40-92 253-307 (613)
3 PF00628 PHD: PHD-finger; Int 98.3 2.9E-07 6.3E-12 60.8 1.1 45 42-89 1-50 (51)
4 KOG0383 Predicted helicase [Ge 97.6 2E-05 4.2E-10 78.4 1.3 54 35-91 42-95 (696)
5 KOG1973 Chromatin remodeling p 97.4 7.2E-05 1.6E-09 66.1 1.9 54 34-90 213-268 (274)
6 COG5141 PHD zinc finger-contai 97.3 7.7E-05 1.7E-09 73.0 1.3 47 40-90 193-243 (669)
7 KOG1244 Predicted transcriptio 97.3 0.00013 2.7E-09 67.2 2.1 47 39-88 280-329 (336)
8 KOG0825 PHD Zn-finger protein 97.1 0.00071 1.5E-08 69.3 5.0 56 33-90 208-266 (1134)
9 KOG0955 PHD finger protein BR1 96.9 0.00056 1.2E-08 71.0 3.2 71 20-94 199-273 (1051)
10 cd04718 BAH_plant_2 BAH, or Br 96.9 0.00051 1.1E-08 57.4 1.8 34 64-97 1-34 (148)
11 PF13831 PHD_2: PHD-finger; PD 96.5 0.0007 1.5E-08 44.1 0.1 32 53-87 4-35 (36)
12 COG5034 TNG2 Chromatin remodel 96.4 0.0018 4E-08 58.7 2.0 46 39-88 220-268 (271)
13 KOG0956 PHD finger protein AF1 95.7 0.0052 1.1E-07 62.3 2.1 44 42-88 7-55 (900)
14 KOG1245 Chromatin remodeling c 95.6 0.0032 7E-08 67.0 -0.0 52 39-92 1107-1160(1404)
15 KOG1512 PHD Zn-finger protein 95.6 0.0059 1.3E-07 57.0 1.6 46 39-88 313-361 (381)
16 KOG0954 PHD finger protein [Ge 95.0 0.012 2.5E-07 60.1 1.9 48 39-90 270-321 (893)
17 KOG4443 Putative transcription 94.6 0.019 4.1E-07 57.7 2.0 50 39-90 67-118 (694)
18 KOG0957 PHD finger protein [Ge 94.4 0.025 5.4E-07 56.1 2.5 47 39-87 543-595 (707)
19 PF13771 zf-HC5HC2H: PHD-like 94.4 0.017 3.6E-07 41.8 1.0 48 39-87 35-86 (90)
20 KOG1473 Nucleosome remodeling 94.4 0.011 2.3E-07 62.6 -0.2 57 33-91 421-480 (1414)
21 KOG0956 PHD finger protein AF1 92.5 0.067 1.5E-06 54.7 1.9 51 40-90 117-180 (900)
22 PF15446 zf-PHD-like: PHD/FYVE 92.1 0.084 1.8E-06 45.6 1.8 44 42-88 1-58 (175)
23 KOG4323 Polycomb-like PHD Zn-f 91.4 0.072 1.6E-06 51.6 0.7 56 43-100 171-234 (464)
24 KOG4299 PHD Zn-finger protein 90.6 0.17 3.6E-06 50.7 2.3 60 21-88 31-90 (613)
25 KOG1473 Nucleosome remodeling 90.6 0.17 3.6E-06 54.1 2.4 49 38-89 342-390 (1414)
26 PF13832 zf-HC5HC2H_2: PHD-zin 90.6 0.12 2.7E-06 38.8 1.1 33 39-72 54-87 (110)
27 KOG0957 PHD finger protein [Ge 83.6 1.4 2.9E-05 44.4 4.1 49 39-90 118-179 (707)
28 KOG1081 Transcription factor N 81.6 1.4 3E-05 42.3 3.2 43 29-72 78-126 (463)
29 PF08746 zf-RING-like: RING-li 78.4 0.49 1.1E-05 31.7 -0.6 34 49-87 10-43 (43)
30 PHA02862 5L protein; Provision 77.5 0.69 1.5E-05 39.5 -0.1 52 40-93 2-54 (156)
31 KOG1734 Predicted RING-contain 73.9 1.8 4E-05 40.5 1.6 55 29-90 213-279 (328)
32 PF11793 FANCL_C: FANCL C-term 73.6 2 4.4E-05 31.1 1.4 52 40-91 2-65 (70)
33 smart00744 RINGv The RING-vari 71.6 1.1 2.4E-05 30.6 -0.3 44 42-87 1-48 (49)
34 PF14446 Prok-RING_1: Prokaryo 68.6 2.8 6.1E-05 30.2 1.2 29 40-71 5-37 (54)
35 KOG0383 Predicted helicase [Ge 67.3 0.88 1.9E-05 46.2 -2.1 53 35-90 501-554 (696)
36 KOG4628 Predicted E3 ubiquitin 65.9 3 6.6E-05 39.3 1.2 41 41-89 230-275 (348)
37 KOG3612 PHD Zn-finger protein 65.6 4.2 9E-05 40.9 2.1 49 39-90 59-108 (588)
38 PF07649 C1_3: C1-like domain; 65.0 2 4.4E-05 26.2 -0.1 27 42-70 2-30 (30)
39 PHA02825 LAP/PHD finger-like p 63.5 2.6 5.7E-05 36.2 0.3 55 38-94 6-61 (162)
40 KOG1829 Uncharacterized conser 61.3 2.9 6.3E-05 41.8 0.2 31 53-92 531-561 (580)
41 COG2824 PhnA Uncharacterized Z 59.7 3.2 7E-05 33.9 0.2 23 73-95 12-34 (112)
42 KOG1246 DNA-binding protein ju 59.4 7.9 0.00017 39.6 2.9 54 35-90 150-204 (904)
43 KOG4443 Putative transcription 59.1 2.3 5.1E-05 43.3 -0.9 54 39-94 17-75 (694)
44 PF00130 C1_1: Phorbol esters/ 56.8 13 0.00028 24.5 2.7 33 39-74 10-47 (53)
45 PF13639 zf-RING_2: Ring finge 55.8 2.5 5.5E-05 27.1 -0.8 41 41-88 1-44 (44)
46 KOG1609 Protein involved in mR 54.9 6.1 0.00013 33.6 1.1 54 39-94 77-136 (323)
47 PF13901 DUF4206: Domain of un 53.1 11 0.00024 32.1 2.4 40 40-90 152-198 (202)
48 cd00029 C1 Protein kinase C co 52.8 11 0.00024 23.9 1.8 31 40-73 11-46 (50)
49 PF04071 zf-like: Cysteine-ric 51.9 43 0.00094 26.0 5.2 63 47-113 18-83 (86)
50 PF11287 DUF3088: Protein of u 50.1 8.3 0.00018 31.4 1.1 37 81-117 21-65 (112)
51 PF03854 zf-P11: P-11 zinc fin 46.1 5 0.00011 28.8 -0.7 42 42-91 4-45 (50)
52 cd00162 RING RING-finger (Real 44.8 4.8 0.00011 24.0 -0.8 42 43-89 2-43 (45)
53 cd07160 NR_DBD_LXR DNA-binding 44.4 37 0.00081 26.5 3.9 54 39-94 17-83 (101)
54 PF03107 C1_2: C1 domain; Int 44.1 15 0.00033 22.6 1.4 27 42-70 2-30 (30)
55 KOG3005 GIY-YIG type nuclease 40.3 8.4 0.00018 35.6 -0.3 51 39-89 184-240 (276)
56 PF06677 Auto_anti-p27: Sjogre 39.7 18 0.00039 24.5 1.3 19 68-87 22-40 (41)
57 KOG1100 Predicted E3 ubiquitin 38.2 24 0.00052 30.7 2.2 18 40-57 158-177 (207)
58 PF12906 RINGv: RING-variant d 37.6 2.9 6.3E-05 28.3 -2.8 43 43-87 1-47 (47)
59 PF12861 zf-Apc11: Anaphase-pr 37.1 12 0.00025 29.1 0.1 29 61-90 52-80 (85)
60 smart00184 RING Ring finger. E 37.0 5.9 0.00013 22.7 -1.2 24 61-87 16-39 (39)
61 cd06962 NR_DBD_FXR DNA-binding 36.9 42 0.0009 25.2 3.0 52 41-94 2-66 (84)
62 smart00451 ZnF_U1 U1-like zinc 36.1 41 0.00089 20.1 2.4 13 80-92 2-14 (35)
63 TIGR00570 cdk7 CDK-activating 35.7 28 0.00061 32.5 2.3 44 39-90 2-52 (309)
64 smart00547 ZnF_RBZ Zinc finger 35.3 18 0.0004 20.9 0.7 15 80-94 1-15 (26)
65 cd00350 rubredoxin_like Rubred 35.2 29 0.00062 21.8 1.6 23 69-91 4-27 (33)
66 PF13920 zf-C3HC4_3: Zinc fing 34.2 3.1 6.7E-05 27.5 -3.1 42 39-89 1-45 (50)
67 PF10235 Cript: Microtubule-as 33.7 21 0.00045 28.0 1.0 24 69-92 47-70 (90)
68 cd03019 DsbA_DsbA DsbA family, 31.3 18 0.00039 27.9 0.3 19 72-90 15-33 (178)
69 COG0266 Nei Formamidopyrimidin 31.3 24 0.00051 32.4 1.1 37 41-88 236-272 (273)
70 cd02972 DsbA_family DsbA famil 31.3 16 0.00034 24.4 -0.0 12 80-91 5-16 (98)
71 smart00109 C1 Protein kinase C 30.8 14 0.00029 23.1 -0.4 30 40-72 11-44 (49)
72 TIGR00686 phnA alkylphosphonat 30.7 18 0.00039 29.5 0.2 23 73-95 11-33 (109)
73 PF12171 zf-C2H2_jaz: Zinc-fin 30.0 22 0.00047 20.9 0.4 14 81-94 1-14 (27)
74 cd03023 DsbA_Com1_like DsbA fa 29.1 19 0.00041 26.6 0.1 17 74-90 7-23 (154)
75 KOG1512 PHD Zn-finger protein 27.4 31 0.00067 32.9 1.2 32 39-72 257-296 (381)
76 PF00641 zf-RanBP: Zn-finger i 27.3 26 0.00055 21.2 0.4 14 79-92 2-15 (30)
77 PF13248 zf-ribbon_3: zinc-rib 26.4 38 0.00083 20.2 1.1 21 68-89 4-24 (26)
78 KOG3408 U1-like Zn-finger-cont 25.8 69 0.0015 26.9 2.8 40 73-112 49-88 (129)
79 PF12678 zf-rbx1: RING-H2 zinc 25.4 11 0.00024 27.2 -1.7 25 60-88 49-73 (73)
80 PF10186 Atg14: UV radiation r 25.4 1.1E+02 0.0025 25.7 4.1 15 77-91 7-21 (302)
81 COG5141 PHD zinc finger-contai 25.3 34 0.00073 34.8 1.0 38 39-76 302-339 (669)
82 PF13240 zinc_ribbon_2: zinc-r 25.3 43 0.00093 19.9 1.1 20 69-89 2-21 (23)
83 PRK10445 endonuclease VIII; Pr 25.3 44 0.00096 29.5 1.7 37 41-88 226-262 (263)
84 COG5415 Predicted integral mem 25.0 40 0.00086 30.9 1.3 30 61-91 195-224 (251)
85 PRK10220 hypothetical protein; 24.0 28 0.00061 28.5 0.2 23 73-95 12-34 (111)
86 TIGR00310 ZPR1_znf ZPR1 zinc f 23.8 33 0.00071 29.7 0.6 40 42-92 2-41 (192)
87 PRK00420 hypothetical protein; 22.9 1.1E+02 0.0024 24.8 3.4 27 60-93 25-52 (112)
88 PRK14873 primosome assembly pr 22.8 64 0.0014 32.6 2.5 44 40-92 383-433 (665)
89 PF00412 LIM: LIM domain; Int 22.5 20 0.00043 23.4 -0.8 28 63-90 20-56 (58)
90 PF08285 DPM3: Dolichol-phosph 22.5 1E+02 0.0022 23.9 3.0 20 93-112 67-86 (91)
91 PF13462 Thioredoxin_4: Thiore 22.4 48 0.001 25.0 1.2 17 74-90 14-30 (162)
92 PF00093 VWC: von Willebrand f 22.2 39 0.00084 23.0 0.6 46 36-87 12-57 (57)
93 KOG0802 E3 ubiquitin ligase [P 22.2 16 0.00035 35.2 -1.7 42 39-89 290-338 (543)
94 PF01323 DSBA: DSBA-like thior 21.9 50 0.0011 25.7 1.2 13 80-92 6-18 (193)
95 PF14260 zf-C4pol: C4-type zin 21.1 2.6E+02 0.0056 19.6 4.7 43 69-112 1-43 (73)
96 cd07158 NR_DBD_Ppar_like The D 20.9 54 0.0012 23.6 1.2 50 43-94 1-64 (73)
No 1
>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 KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.28 E-value=1.9e-07 Score=91.24 Aligned_cols=50 Identities=32% Similarity=0.654 Sum_probs=45.3
Q ss_pred CCceeeccCCCCeE---EeeCCCCCcccccccccCCC--CccCCCCCccccccchhhH
Q 041295 40 EEPCIKCNRRDESL---LVCIQSGCPISVHENCLSCG--VKSDDVGNIYCPYFWYKCE 92 (209)
Q Consensus 40 eD~CikC~kdGq~L---L~Cs~~gCPlAvH~kClg~s--l~~dd~GnfYCPyC~ykka 92 (209)
++.|-.|+..|. . ++|+ +||.+||..||.++ +.-.|.|.||||.|-++-.
T Consensus 253 ~~fCsaCn~~~~-F~~~i~CD--~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~k~~ 307 (613)
T KOG4299|consen 253 EDFCSACNGSGL-FNDIICCD--GCPRSFHQTCLEPPLEPENIPPGSWFCPECKIKSV 307 (613)
T ss_pred HHHHHHhCCccc-cccceeec--CCchHHHHhhcCCCCCcccCCCCccccCCCeeeee
Confidence 569999999999 7 9999 89999999999998 7778999999999998743
No 3
>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=98.26 E-value=2.9e-07 Score=60.84 Aligned_cols=45 Identities=24% Similarity=0.568 Sum_probs=36.1
Q ss_pred ceeeccC---CCCeEEeeCCCCCcccccccccCCCCc--cCCCCCccccccch
Q 041295 42 PCIKCNR---RDESLLVCIQSGCPISVHENCLSCGVK--SDDVGNIYCPYFWY 89 (209)
Q Consensus 42 ~CikC~k---dGq~LL~Cs~~gCPlAvH~kClg~sl~--~dd~GnfYCPyC~y 89 (209)
.|.+|+. +++ +|.|+ +|...||..|++.+.. -...+.|+||.|.-
T Consensus 1 ~C~vC~~~~~~~~-~i~C~--~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGD-MIQCD--SCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSS-EEEBS--TTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCC-eEEcC--CCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 3778888 555 99999 9999999999998655 33345999999963
No 4
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=97.61 E-value=2e-05 Score=78.43 Aligned_cols=54 Identities=33% Similarity=0.628 Sum_probs=48.6
Q ss_pred CCCCCCCceeeccCCCCeEEeeCCCCCcccccccccCCCCccCCCCCccccccchhh
Q 041295 35 VDLLEEEPCIKCNRRDESLLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWYKC 91 (209)
Q Consensus 35 ~d~~neD~CikC~kdGq~LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~ykk 91 (209)
-++-+++.|-+|...|+ ||.|+ +||.+||..|++.++.-.+.+.|.||-|....
T Consensus 42 ~~~~~~e~c~ic~~~g~-~l~c~--tC~~s~h~~cl~~pl~~~p~~~~~c~Rc~~p~ 95 (696)
T KOG0383|consen 42 WDDAEQEACRICADGGE-LLWCD--TCPASFHASCLGPPLTPQPNGEFICPRCFCPK 95 (696)
T ss_pred cchhhhhhhhhhcCCCc-EEEec--cccHHHHHHccCCCCCcCCccceeeeeeccCC
Confidence 44568999999999999 99999 99999999999999998999999999995543
No 5
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=97.40 E-value=7.2e-05 Score=66.06 Aligned_cols=54 Identities=30% Similarity=0.532 Sum_probs=42.6
Q ss_pred cCCCCCCCceee-ccCCCCeEEeeCCCCCc-ccccccccCCCCccCCCCCccccccchh
Q 041295 34 DVDLLEEEPCIK-CNRRDESLLVCIQSGCP-ISVHENCLSCGVKSDDVGNIYCPYFWYK 90 (209)
Q Consensus 34 ~~d~~neD~Cik-C~kdGq~LL~Cs~~gCP-lAvH~kClg~sl~~dd~GnfYCPyC~yk 90 (209)
..+.-+.-+|+= |...|+ .+-|+..+|| -=||-.|+| +...|.|.||||.|.-.
T Consensus 213 ~~d~~e~~yC~Cnqvsyg~-Mi~CDn~~C~~eWFH~~CVG--L~~~PkgkWyC~~C~~~ 268 (274)
T KOG1973|consen 213 AVDPDEPTYCICNQVSYGK-MIGCDNPGCPIEWFHFTCVG--LKTKPKGKWYCPRCKAE 268 (274)
T ss_pred ccCCCCCEEEEeccccccc-ccccCCCCCCcceEEEeccc--cccCCCCcccchhhhhh
Confidence 334445566664 444677 9999988999 779999999 78999999999999744
No 6
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=97.33 E-value=7.7e-05 Score=72.97 Aligned_cols=47 Identities=28% Similarity=0.692 Sum_probs=42.8
Q ss_pred CCceeeccCCCCe----EEeeCCCCCcccccccccCCCCccCCCCCccccccchh
Q 041295 40 EEPCIKCNRRDES----LLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWYK 90 (209)
Q Consensus 40 eD~CikC~kdGq~----LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~yk 90 (209)
+++|.+|.....+ +++|+ +|-++||.+|-| -.|.|+|.|+|--|.|.
T Consensus 193 d~~C~~c~~t~~eN~naiVfCd--gC~i~VHq~CYG--I~f~peG~WlCrkCi~~ 243 (669)
T COG5141 193 DDICTKCTSTHNENSNAIVFCD--GCEICVHQSCYG--IQFLPEGFWLCRKCIYG 243 (669)
T ss_pred hhhhHhccccccCCcceEEEec--Ccchhhhhhccc--ceecCcchhhhhhhccc
Confidence 6899999986653 99999 999999999999 78999999999999876
No 7
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=97.28 E-value=0.00013 Score=67.22 Aligned_cols=47 Identities=30% Similarity=0.517 Sum_probs=41.1
Q ss_pred CCCceeeccC---CCCeEEeeCCCCCcccccccccCCCCccCCCCCccccccc
Q 041295 39 EEEPCIKCNR---RDESLLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFW 88 (209)
Q Consensus 39 neD~CikC~k---dGq~LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~ 88 (209)
+=-.|.+|+- ++| ||+|+ .|-+.||-.||.+++.-.|+|-|.|-.|.
T Consensus 280 eck~csicgtsenddq-llfcd--dcdrgyhmyclsppm~eppegswsc~KOG 329 (336)
T KOG1244|consen 280 ECKYCSICGTSENDDQ-LLFCD--DCDRGYHMYCLSPPMVEPPEGSWSCHLCL 329 (336)
T ss_pred ecceeccccCcCCCce-eEeec--ccCCceeeEecCCCcCCCCCCchhHHHHH
Confidence 3445667765 677 99999 99999999999999999999999999996
No 8
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.06 E-value=0.00071 Score=69.31 Aligned_cols=56 Identities=27% Similarity=0.441 Sum_probs=47.5
Q ss_pred ccCCCCCCCceeeccCCCCe--EEeeCCCCCccc-ccccccCCCCccCCCCCccccccchh
Q 041295 33 MDVDLLEEEPCIKCNRRDES--LLVCIQSGCPIS-VHENCLSCGVKSDDVGNIYCPYFWYK 90 (209)
Q Consensus 33 ~~~d~~neD~CikC~kdGq~--LL~Cs~~gCPlA-vH~kClg~sl~~dd~GnfYCPyC~yk 90 (209)
......+.--|.+|.....+ ||.|+ +|-.+ ||..||...+.-.+.+-|||+-|..-
T Consensus 208 ~~~~~~E~~~C~IC~~~DpEdVLLLCD--sCN~~~YH~YCLDPdl~eiP~~eWYC~NC~dL 266 (1134)
T KOG0825|consen 208 ISGLSQEEVKCDICTVHDPEDVLLLCD--SCNKVYYHVYCLDPDLSESPVNEWYCTNCSLL 266 (1134)
T ss_pred ccCcccccccceeeccCChHHhheeec--ccccceeeccccCcccccccccceecCcchhh
Confidence 34444577889999998877 99999 99999 99999998777678999999999843
No 9
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=96.94 E-value=0.00056 Score=70.96 Aligned_cols=71 Identities=21% Similarity=0.318 Sum_probs=53.0
Q ss_pred hhhhcCCCCCCCcccCCCCCCCceeeccCCCCe----EEeeCCCCCcccccccccCCCCccCCCCCccccccchhhHHH
Q 041295 20 IENHRGSGRSRDFMDVDLLEEEPCIKCNRRDES----LLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWYKCELM 94 (209)
Q Consensus 20 ~~~~~~S~~S~Ds~~~d~~neD~CikC~kdGq~----LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~ykka~e 94 (209)
++..|..--..+..+.+.-++..|.+|.++.-. +|+|+ +|-++||..|.| ..|.++|.|.|--|.++.+..
T Consensus 199 ke~~f~~~e~~~~~~~~~~~D~~C~iC~~~~~~n~n~ivfCD--~Cnl~VHq~Cyg--i~~ipeg~WlCr~Cl~s~~~~ 273 (1051)
T KOG0955|consen 199 KESYFKNYELGDPKDALLEEDAVCCICLDGECQNSNVIVFCD--GCNLAVHQECYG--IPFIPEGQWLCRRCLQSPQRP 273 (1051)
T ss_pred HHHHhhhhhccCCCccccCCCccceeecccccCCCceEEEcC--CCcchhhhhccC--CCCCCCCcEeehhhccCcCcc
Confidence 333343333333334555578899999884322 99999 999999999999 789999999999999886544
No 10
>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=96.87 E-value=0.00051 Score=57.41 Aligned_cols=34 Identities=21% Similarity=0.283 Sum_probs=29.3
Q ss_pred cccccccCCCCccCCCCCccccccchhhHHHHHH
Q 041295 64 SVHENCLSCGVKSDDVGNIYCPYFWYKCELMRTK 97 (209)
Q Consensus 64 AvH~kClg~sl~~dd~GnfYCPyC~ykka~eey~ 97 (209)
.||-.||.++++-.|.|+|+||.|..+.......
T Consensus 1 g~H~~CL~Ppl~~~P~g~W~Cp~C~~~~~~~~~~ 34 (148)
T cd04718 1 GFHLCCLRPPLKEVPEGDWICPFCEVEKSGQSAM 34 (148)
T ss_pred CcccccCCCCCCCCCCCCcCCCCCcCCCCCCccc
Confidence 4899999999999999999999999876555443
No 11
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=96.50 E-value=0.0007 Score=44.12 Aligned_cols=32 Identities=28% Similarity=0.637 Sum_probs=17.9
Q ss_pred EEeeCCCCCcccccccccCCCCccCCCCCcccccc
Q 041295 53 LLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYF 87 (209)
Q Consensus 53 LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC 87 (209)
||.|+ +|.++||..|-|.... .+...|+|-.|
T Consensus 4 ll~C~--~C~v~VH~~CYGv~~~-~~~~~W~C~~C 35 (36)
T PF13831_consen 4 LLFCD--NCNVAVHQSCYGVSEV-PDGDDWLCDRC 35 (36)
T ss_dssp EEE-S--SS--EEEHHHHT-SS---SS-----HHH
T ss_pred eEEeC--CCCCcCChhhCCcccC-CCCCcEECCcC
Confidence 99999 9999999999997544 34446999877
No 12
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=96.37 E-value=0.0018 Score=58.69 Aligned_cols=46 Identities=28% Similarity=0.667 Sum_probs=38.7
Q ss_pred CCCceeeccC--CCCeEEeeCCCCCccc-ccccccCCCCccCCCCCccccccc
Q 041295 39 EEEPCIKCNR--RDESLLVCIQSGCPIS-VHENCLSCGVKSDDVGNIYCPYFW 88 (209)
Q Consensus 39 neD~CikC~k--dGq~LL~Cs~~gCPlA-vH~kClg~sl~~dd~GnfYCPyC~ 88 (209)
++-.| .|.. =|+ .+-||+-.|++- ||-.|+| +.-.|.|-||||.|-
T Consensus 220 e~lYC-fCqqvSyGq-MVaCDn~nCkrEWFH~~CVG--Lk~pPKG~WYC~eCk 268 (271)
T COG5034 220 EELYC-FCQQVSYGQ-MVACDNANCKREWFHLECVG--LKEPPKGKWYCPECK 268 (271)
T ss_pred ceeEE-Eeccccccc-ceecCCCCCchhheeccccc--cCCCCCCcEeCHHhH
Confidence 44455 4665 578 999999999996 9999999 788999999999995
No 13
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=95.74 E-value=0.0052 Score=62.35 Aligned_cols=44 Identities=23% Similarity=0.622 Sum_probs=37.0
Q ss_pred ceeeccC-----CCCeEEeeCCCCCcccccccccCCCCccCCCCCccccccc
Q 041295 42 PCIKCNR-----RDESLLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFW 88 (209)
Q Consensus 42 ~CikC~k-----dGq~LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~ 88 (209)
=|.+|.. +-. |+.||+-.|.+|||.-|-| ----|.|.|||-.|-
T Consensus 7 GCCVCSDErGWaeNP-LVYCDG~nCsVAVHQaCYG--IvqVPtGpWfCrKCe 55 (900)
T KOG0956|consen 7 GCCVCSDERGWAENP-LVYCDGHNCSVAVHQACYG--IVQVPTGPWFCRKCE 55 (900)
T ss_pred ceeeecCcCCCccCc-eeeecCCCceeeeehhcce--eEecCCCchhhhhhh
Confidence 4788865 223 9999999999999999999 445789999999996
No 14
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=95.60 E-value=0.0032 Score=67.02 Aligned_cols=52 Identities=25% Similarity=0.520 Sum_probs=46.2
Q ss_pred CCCceeeccCCCCe--EEeeCCCCCcccccccccCCCCccCCCCCccccccchhhH
Q 041295 39 EEEPCIKCNRRDES--LLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWYKCE 92 (209)
Q Consensus 39 neD~CikC~kdGq~--LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~ykka 92 (209)
..-+|-+|...++- ++.|+ +|.-.+|-.|+.+-+...+.|+|+||-|.-..-
T Consensus 1107 ~~~~c~~cr~k~~~~~m~lc~--~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1107 VNALCKVCRRKKQDEKMLLCD--ECLSGFHLFCLRPALSSVPPGDWMCPSCRKEHR 1160 (1404)
T ss_pred chhhhhhhhhcccchhhhhhH--hhhhhHHHHhhhhhhccCCcCCccCCccchhhh
Confidence 57789999987664 89999 999999999999999999999999999985543
No 15
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=95.58 E-value=0.0059 Score=56.99 Aligned_cols=46 Identities=22% Similarity=0.332 Sum_probs=39.1
Q ss_pred CCCceeeccCCCCe--EEeeCCCCCcccccccccCCCCccCCCCCcccc-ccc
Q 041295 39 EEEPCIKCNRRDES--LLVCIQSGCPISVHENCLSCGVKSDDVGNIYCP-YFW 88 (209)
Q Consensus 39 neD~CikC~kdGq~--LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCP-yC~ 88 (209)
+=.+|++|+..-.+ .|+|+ .|-+.||.-|+| +.-.|+|.|.|- ||.
T Consensus 313 ~C~lC~IC~~P~~E~E~~FCD--~CDRG~HT~CVG--L~~lP~G~WICD~~C~ 361 (381)
T KOG1512|consen 313 SCELCRICLGPVIESEHLFCD--VCDRGPHTLCVG--LQDLPRGEWICDMRCR 361 (381)
T ss_pred ccHhhhccCCcccchheeccc--cccCCCCccccc--cccccCccchhhhHHH
Confidence 45689999885443 99999 999999999999 788999999997 564
No 16
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=95.04 E-value=0.012 Score=60.12 Aligned_cols=48 Identities=23% Similarity=0.493 Sum_probs=42.2
Q ss_pred CCCceeeccCC----CCeEEeeCCCCCcccccccccCCCCccCCCCCccccccchh
Q 041295 39 EEEPCIKCNRR----DESLLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWYK 90 (209)
Q Consensus 39 neD~CikC~kd----Gq~LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~yk 90 (209)
|+-+|-+|..+ ++++++|+ -|-+.||..|.| ..-++.|.|.|--|+.-
T Consensus 270 edviCDvCrspD~e~~neMVfCd--~Cn~cVHqaCyG--Ile~p~gpWlCr~Calg 321 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCD--KCNICVHQACYG--ILEVPEGPWLCRTCALG 321 (893)
T ss_pred ccceeceecCCCccccceeEEec--cchhHHHHhhhc--eeecCCCCeeehhcccc
Confidence 77899999987 66699999 999999999999 56678899999888764
No 17
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=94.55 E-value=0.019 Score=57.67 Aligned_cols=50 Identities=20% Similarity=0.365 Sum_probs=42.5
Q ss_pred CCCceeeccCCCCe--EEeeCCCCCcccccccccCCCCccCCCCCccccccchh
Q 041295 39 EEEPCIKCNRRDES--LLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWYK 90 (209)
Q Consensus 39 neD~CikC~kdGq~--LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~yk 90 (209)
.--+|..|+..|+. +++|+ +|-++||-.|+-+...-.++|-|+||-|.-=
T Consensus 67 ~crvCe~c~~~gD~~kf~~Ck--~cDvsyh~yc~~P~~~~v~sg~~~ckk~~~c 118 (694)
T KOG4443|consen 67 SCRVCEACGTTGDPKKFLLCK--RCDVSYHCYCQKPPNDKVPSGPWLCKKCTRC 118 (694)
T ss_pred CceeeeeccccCCcccccccc--cccccccccccCCccccccCcccccHHHHhh
Confidence 44567777766654 99999 9999999999999999999999999998743
No 18
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=94.44 E-value=0.025 Score=56.13 Aligned_cols=47 Identities=23% Similarity=0.415 Sum_probs=42.4
Q ss_pred CCCceeeccCCCCe--EEeeCCCCCcccccccccCCCCccCCCCC----cccccc
Q 041295 39 EEEPCIKCNRRDES--LLVCIQSGCPISVHENCLSCGVKSDDVGN----IYCPYF 87 (209)
Q Consensus 39 neD~CikC~kdGq~--LL~Cs~~gCPlAvH~kClg~sl~~dd~Gn----fYCPyC 87 (209)
-...|.+|.+.-+- |+.|+ +|-+.||--||.++++-.|..+ |-|..|
T Consensus 543 ~~ysCgiCkks~dQHll~~CD--tC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsEC 595 (707)
T KOG0957|consen 543 MNYSCGICKKSTDQHLLTQCD--TCHLHYHLGCLSPPLTRLPKKNKNFGWQCSEC 595 (707)
T ss_pred cceeeeeeccchhhHHHhhcc--hhhceeeccccCCccccCcccccCcceeeccc
Confidence 46889999996554 88999 9999999999999999999888 999999
No 19
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=94.43 E-value=0.017 Score=41.80 Aligned_cols=48 Identities=19% Similarity=0.426 Sum_probs=36.2
Q ss_pred CCCceeeccCC-CCeEEeeCCCCCcccccccccCCCCc---cCCCCCcccccc
Q 041295 39 EEEPCIKCNRR-DESLLVCIQSGCPISVHENCLSCGVK---SDDVGNIYCPYF 87 (209)
Q Consensus 39 neD~CikC~kd-Gq~LL~Cs~~gCPlAvH~kClg~sl~---~dd~GnfYCPyC 87 (209)
-...|..|++. |- .+.|...+|...||..|.-.... +++...++-.||
T Consensus 35 ~~~~C~~C~~~~Ga-~i~C~~~~C~~~fH~~CA~~~~~~~~~~~~~~~~~~~C 86 (90)
T PF13771_consen 35 RKLKCSICKKKGGA-CIGCSHPGCSRSFHVPCARKAGCFIEFDEDNGKFRIFC 86 (90)
T ss_pred hCCCCcCCCCCCCe-EEEEeCCCCCcEEChHHHccCCeEEEEccCCCceEEEC
Confidence 35689999999 98 99999999999999999885332 332234555555
No 20
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=94.36 E-value=0.011 Score=62.61 Aligned_cols=57 Identities=16% Similarity=-0.061 Sum_probs=49.9
Q ss_pred ccCCCCCCCceeeccCCCCeEEeeCCCCCcccccc-cccC--CCCccCCCCCccccccchhh
Q 041295 33 MDVDLLEEEPCIKCNRRDESLLVCIQSGCPISVHE-NCLS--CGVKSDDVGNIYCPYFWYKC 91 (209)
Q Consensus 33 ~~~d~~neD~CikC~kdGq~LL~Cs~~gCPlAvH~-kClg--~sl~~dd~GnfYCPyC~ykk 91 (209)
.+.=|+..+.|++|++++. +|+|. ++||.+||. .||+ .--.+...+-|+||.|..++
T Consensus 421 gr~ywfi~rrl~Ie~~det-~l~yy-sT~pqly~ll~cLd~~~~e~~L~d~i~~~~ee~~rq 480 (1414)
T KOG1473|consen 421 GRKYWFISRRLRIEGMDET-LLWYY-STCPQLYHLLRCLDRTYVEMYLCDGIWERREEIIRQ 480 (1414)
T ss_pred ccchhceeeeeEEecCCCc-EEEEe-cCcHHHHHHHHHhchHHHHHhhccchhhhHHHHHHh
Confidence 3555889999999999999 99998 379999999 9999 56678899999999999764
No 21
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=92.50 E-value=0.067 Score=54.68 Aligned_cols=51 Identities=33% Similarity=0.818 Sum_probs=43.2
Q ss_pred CCceeeccCCCCe-------EEeeCCCCCcccccccccCC-CCccCCCCCc-----cccccchh
Q 041295 40 EEPCIKCNRRDES-------LLVCIQSGCPISVHENCLSC-GVKSDDVGNI-----YCPYFWYK 90 (209)
Q Consensus 40 eD~CikC~kdGq~-------LL~Cs~~gCPlAvH~kClg~-sl~~dd~Gnf-----YCPyC~yk 90 (209)
--.|++|.+.|.+ -+-|...+|-.+||..|.-+ .+-.++.|+. ||-||.|-
T Consensus 117 nKtCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~~GLLCEE~gn~~dNVKYCGYCk~H 180 (900)
T KOG0956|consen 117 NKTCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQRAGLLCEEEGNISDNVKYCGYCKYH 180 (900)
T ss_pred cceeeeecccCCccccccccceecccccchhhhhhhHhhhhccceeccccccccceechhHHHH
Confidence 4579999998765 78999999999999999875 5777777764 99999985
No 22
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=92.13 E-value=0.084 Score=45.65 Aligned_cols=44 Identities=25% Similarity=0.557 Sum_probs=31.1
Q ss_pred ceeeccC------CCCeEEeeCCCCCcccccccccCCCCcc------CCCCCc--cccccc
Q 041295 42 PCIKCNR------RDESLLVCIQSGCPISVHENCLSCGVKS------DDVGNI--YCPYFW 88 (209)
Q Consensus 42 ~CikC~k------dGq~LL~Cs~~gCPlAvH~kClg~sl~~------dd~Gnf--YCPyC~ 88 (209)
.|-.|+. .|. |+.|- ||..+||+.|||....- -...+| -|-+|.
T Consensus 1 ~C~~C~~~g~~~~kG~-Lv~CQ--GCs~sYHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Ci 58 (175)
T PF15446_consen 1 TCDTCGYEGDDRNKGP-LVYCQ--GCSSSYHKACLGPRSQREHLVTKVGDDDFVLQCRRCI 58 (175)
T ss_pred CcccccCCCCCccCCC-eEEcC--ccChHHHhhhcCCccccceeeEEEcCCceEEechhhc
Confidence 3677753 456 99999 99999999999963322 234455 377776
No 23
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=91.39 E-value=0.072 Score=51.61 Aligned_cols=56 Identities=20% Similarity=0.317 Sum_probs=43.3
Q ss_pred eeeccCCC----CeEEeeCCCCCcccccccccCCC----CccCCCCCccccccchhhHHHHHHHHH
Q 041295 43 CIKCNRRD----ESLLVCIQSGCPISVHENCLSCG----VKSDDVGNIYCPYFWYKCELMRTKELR 100 (209)
Q Consensus 43 CikC~kdG----q~LL~Cs~~gCPlAvH~kClg~s----l~~dd~GnfYCPyC~ykka~eey~elk 100 (209)
|.+|.-+| +.+|.|+ +|---||.-|.-+. +.=|....|||-.|.+......-..++
T Consensus 171 c~vC~~g~~~~~NrmlqC~--~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~~~~r~t~~ 234 (464)
T KOG4323|consen 171 CSVCYCGGPGAGNRMLQCD--KCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPKKVPRLTLR 234 (464)
T ss_pred eeeeecCCcCccceeeeec--ccccHHHHHhccCCCCHhhccCccceEeehhhccchhhccccccc
Confidence 99987433 3399999 99999999998863 234667889999999987766655554
No 24
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=90.61 E-value=0.17 Score=50.68 Aligned_cols=60 Identities=20% Similarity=0.202 Sum_probs=46.0
Q ss_pred hhhcCCCCCCCcccCCCCCCCceeeccCCCCeEEeeCCCCCcccccccccCCCCccCCCCCccccccc
Q 041295 21 ENHRGSGRSRDFMDVDLLEEEPCIKCNRRDESLLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFW 88 (209)
Q Consensus 21 ~~~~~S~~S~Ds~~~d~~neD~CikC~kdGq~LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~ 88 (209)
+++|+|+.+. .+...| -..|-.|..+|+ +++|. .||.++|..|....+. +.-.++|--|.
T Consensus 31 ~~ar~s~~~~-~~~~k~--~ts~~~~~~~gn-~~~~~--~~~~s~h~~~~~~~~s--p~~~~~~~~~~ 90 (613)
T KOG4299|consen 31 RRARKSEKEN-RRSGKA--ATSCGICKSGGN-LLCCD--HCPASFHLECDKPPLS--PDLKGSEINCS 90 (613)
T ss_pred hccccccccc-ccccch--hhhcchhhhcCC-ccccc--cCccccchhccCcccC--ccccccccccc
Confidence 4448888873 434444 899999999999 99999 9999999999996544 66666665554
No 25
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=90.58 E-value=0.17 Score=54.11 Aligned_cols=49 Identities=22% Similarity=0.362 Sum_probs=44.4
Q ss_pred CCCCceeeccCCCCeEEeeCCCCCcccccccccCCCCccCCCCCccccccch
Q 041295 38 LEEEPCIKCNRRDESLLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWY 89 (209)
Q Consensus 38 ~neD~CikC~kdGq~LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~y 89 (209)
.=.|.|-.|.+.|. ||||- +||+.||-+|+-.+.---++..|-|-+|.+
T Consensus 342 ~~ddhcrf~~d~~~-~lc~E--t~prvvhlEcv~hP~~~~~s~~~e~evc~~ 390 (1414)
T KOG1473|consen 342 EYDDHCRFCHDLGD-LLCCE--TCPRVVHLECVFHPRFAVPSAFWECEVCNI 390 (1414)
T ss_pred eecccccccCcccc-eeecc--cCCceEEeeecCCccccCCCccchhhhhhh
Confidence 35789999999999 99999 999999999999887778899999999974
No 26
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=90.57 E-value=0.12 Score=38.77 Aligned_cols=33 Identities=21% Similarity=0.599 Sum_probs=29.0
Q ss_pred CCCceeeccCC-CCeEEeeCCCCCcccccccccCC
Q 041295 39 EEEPCIKCNRR-DESLLVCIQSGCPISVHENCLSC 72 (209)
Q Consensus 39 neD~CikC~kd-Gq~LL~Cs~~gCPlAvH~kClg~ 72 (209)
....|..|+.. |- ++.|+..+|..+||..|+-.
T Consensus 54 ~~~~C~iC~~~~G~-~i~C~~~~C~~~fH~~CA~~ 87 (110)
T PF13832_consen 54 FKLKCSICGKSGGA-CIKCSHPGCSTAFHPTCARK 87 (110)
T ss_pred cCCcCcCCCCCCce-eEEcCCCCCCcCCCHHHHHH
Confidence 46799999995 66 99999888999999999864
No 27
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=83.61 E-value=1.4 Score=44.37 Aligned_cols=49 Identities=27% Similarity=0.518 Sum_probs=36.8
Q ss_pred CCCceeeccC-----CCCeEEeeCCCCCcccccccccCCC-----CccCCC---CCccccccchh
Q 041295 39 EEEPCIKCNR-----RDESLLVCIQSGCPISVHENCLSCG-----VKSDDV---GNIYCPYFWYK 90 (209)
Q Consensus 39 neD~CikC~k-----dGq~LL~Cs~~gCPlAvH~kClg~s-----l~~dd~---GnfYCPyC~yk 90 (209)
.-.+|-+|-. .|+ +|.|+ .|-+.||..|-|+. +...+. ..|||--|.|-
T Consensus 118 k~~iCcVClg~rs~da~e-i~qCd--~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~G 179 (707)
T KOG0957|consen 118 KAVICCVCLGQRSVDAGE-ILQCD--KCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLYG 179 (707)
T ss_pred cceEEEEeecCccccccc-eeecc--ccCceecccccccccccccCCCCccCCCCchhhhhHhcC
Confidence 4458999954 455 99999 99999999999974 222222 67999888764
No 28
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=81.56 E-value=1.4 Score=42.35 Aligned_cols=43 Identities=19% Similarity=0.384 Sum_probs=34.8
Q ss_pred CCCcccCCCCCCCceeeccCCCCeEEeeC------CCCCcccccccccCC
Q 041295 29 SRDFMDVDLLEEEPCIKCNRRDESLLVCI------QSGCPISVHENCLSC 72 (209)
Q Consensus 29 S~Ds~~~d~~neD~CikC~kdGq~LL~Cs------~~gCPlAvH~kClg~ 72 (209)
..+..-..-.+.+.|-+|.++|. |+.|+ ...||.++|..|...
T Consensus 78 ~~~~~~~~~~~~~~c~vc~~ggs-~v~~~s~~~~~~r~c~~~~~~~c~~~ 126 (463)
T KOG1081|consen 78 EPGSRRHPKIEPSECFVCFKGGS-LVTCKSRIQAPHRKCKPAQLEKCSKR 126 (463)
T ss_pred CCCchhccCCCcchhccccCCCc-cceeccccccccccCcCccCcccccC
Confidence 44445555568999999999999 99999 788888888888875
No 29
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=78.42 E-value=0.49 Score=31.71 Aligned_cols=34 Identities=21% Similarity=0.582 Sum_probs=17.5
Q ss_pred CCCeEEeeCCCCCcccccccccCCCCccCCCCCcccccc
Q 041295 49 RDESLLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYF 87 (209)
Q Consensus 49 dGq~LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC 87 (209)
-|+ .|+..+|++.+|..|+. .-+-...+--||-|
T Consensus 10 ~G~---~C~~~~C~~r~H~~C~~--~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 10 QGQ---RCSNRDCNVRLHDDCFK--KYFRHRSNPKCPNC 43 (43)
T ss_dssp SSE---E-SS--S--EE-HHHHH--HHTTT-SS-B-TTT
T ss_pred eec---cCCCCccCchHHHHHHH--HHHhcCCCCCCcCC
Confidence 455 89988999999999998 33333333478876
No 30
>PHA02862 5L protein; Provisional
Probab=77.53 E-value=0.69 Score=39.50 Aligned_cols=52 Identities=17% Similarity=0.219 Sum_probs=40.8
Q ss_pred CCceeeccCCCCe-EEeeCCCCCcccccccccCCCCccCCCCCccccccchhhHH
Q 041295 40 EEPCIKCNRRDES-LLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWYKCEL 93 (209)
Q Consensus 40 eD~CikC~kdGq~-LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~ykka~ 93 (209)
.+.|++|...+++ +-+|-=+|--.-+|.+|+..=. ..++.-+||.|.++...
T Consensus 2 ~diCWIC~~~~~e~~~PC~C~GS~K~VHq~CL~~WI--n~S~k~~CeLCkteY~I 54 (156)
T PHA02862 2 SDICWICNDVCDERNNFCGCNEEYKVVHIKCMQLWI--NYSKKKECNLCKTKYNI 54 (156)
T ss_pred CCEEEEecCcCCCCcccccccCcchhHHHHHHHHHH--hcCCCcCccCCCCeEEE
Confidence 4789999998775 6677655668899999988534 45889999999988654
No 31
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=73.91 E-value=1.8 Score=40.46 Aligned_cols=55 Identities=24% Similarity=0.379 Sum_probs=37.0
Q ss_pred CCCcccCCCCCCCceeeccCCCCe-E-----------EeeCCCCCcccccccccCCCCccCCCCCccccccchh
Q 041295 29 SRDFMDVDLLEEEPCIKCNRRDES-L-----------LVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWYK 90 (209)
Q Consensus 29 S~Ds~~~d~~neD~CikC~kdGq~-L-----------L~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~yk 90 (209)
|++--|.-.+++++|.+|+..=.. + | +|.-+||+-|+.- =..-..--.||||--+
T Consensus 213 s~~glPtkhl~d~vCaVCg~~~~~s~~eegvienty~L-----sCnHvFHEfCIrG--WcivGKkqtCPYCKek 279 (328)
T KOG1734|consen 213 SPSGLPTKHLSDSVCAVCGQQIDVSVDEEGVIENTYKL-----SCNHVFHEFCIRG--WCIVGKKQTCPYCKEK 279 (328)
T ss_pred CCCCCCCCCCCcchhHhhcchheeecchhhhhhhheee-----ecccchHHHhhhh--heeecCCCCCchHHHH
Confidence 666677778899999999973220 1 3 3558999999872 1122334579999644
No 32
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=73.61 E-value=2 Score=31.05 Aligned_cols=52 Identities=29% Similarity=0.273 Sum_probs=19.8
Q ss_pred CCceeeccCC---CCe--EEeeCCCCCcccccccccCCCCcc-------CCCCCccccccchhh
Q 041295 40 EEPCIKCNRR---DES--LLVCIQSGCPISVHENCLSCGVKS-------DDVGNIYCPYFWYKC 91 (209)
Q Consensus 40 eD~CikC~kd---Gq~--LL~Cs~~gCPlAvH~kClg~sl~~-------dd~GnfYCPyC~ykk 91 (209)
+..|.+|-.. +.+ .+.|....|...||..||..-... -..-..-||+|.-+.
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i 65 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPI 65 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEE
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCee
Confidence 3467777652 222 589998999999999999742111 112223599997543
No 33
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=71.60 E-value=1.1 Score=30.60 Aligned_cols=44 Identities=25% Similarity=0.497 Sum_probs=28.0
Q ss_pred ceeeccC---CCCe-EEeeCCCCCcccccccccCCCCccCCCCCcccccc
Q 041295 42 PCIKCNR---RDES-LLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYF 87 (209)
Q Consensus 42 ~CikC~k---dGq~-LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC 87 (209)
.|.+|.. +++. +.+|.=.|--.-||..|+.. =+..++.-.||.|
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~--W~~~~~~~~C~iC 48 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLER--WINESGNKTCEIC 48 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHH--HHHHcCCCcCCCC
Confidence 4778876 3332 55665223336799999983 3344556699988
No 34
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=68.59 E-value=2.8 Score=30.15 Aligned_cols=29 Identities=28% Similarity=0.780 Sum_probs=24.8
Q ss_pred CCceeeccC----CCCeEEeeCCCCCcccccccccC
Q 041295 40 EEPCIKCNR----RDESLLVCIQSGCPISVHENCLS 71 (209)
Q Consensus 40 eD~CikC~k----dGq~LL~Cs~~gCPlAvH~kClg 71 (209)
.-.|..|++ .++ +|+|- .|-..||..|-.
T Consensus 5 ~~~C~~Cg~~~~~~dD-iVvCp--~CgapyHR~C~~ 37 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDD-IVVCP--ECGAPYHRDCWE 37 (54)
T ss_pred CccChhhCCcccCCCC-EEECC--CCCCcccHHHHh
Confidence 457999998 456 99999 999999999974
No 35
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=67.32 E-value=0.88 Score=46.16 Aligned_cols=53 Identities=15% Similarity=0.208 Sum_probs=48.0
Q ss_pred CCCCCCCceeeccCCCCeEEeeCCCCCcccccccccCC-CCccCCCCCccccccchh
Q 041295 35 VDLLEEEPCIKCNRRDESLLVCIQSGCPISVHENCLSC-GVKSDDVGNIYCPYFWYK 90 (209)
Q Consensus 35 ~d~~neD~CikC~kdGq~LL~Cs~~gCPlAvH~kClg~-sl~~dd~GnfYCPyC~yk 90 (209)
.+.+++..|-.|-+.++ +|.|. .|++.+|..|+-. +++.+.-|.|-||-|+-+
T Consensus 501 ~e~~~d~~~~~~~~~l~-~l~~p--~~lrr~k~d~l~~~P~Kte~i~~~~~~~~Q~~ 554 (696)
T KOG0383|consen 501 LEEFHDISCEEQIKKLH-LLLCP--HMLRRLKLDVLKPMPLKTELIGRVELSPCQKK 554 (696)
T ss_pred hhhcchhhHHHHHHhhc-cccCc--hhhhhhhhhhccCCCccceeEEEEecCHHHHH
Confidence 34447999999999999 99999 9999999999998 999999999999999844
No 36
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=65.86 E-value=3 Score=39.30 Aligned_cols=41 Identities=22% Similarity=0.585 Sum_probs=31.1
Q ss_pred CceeeccC---CCCe--EEeeCCCCCcccccccccCCCCccCCCCCccccccch
Q 041295 41 EPCIKCNR---RDES--LLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWY 89 (209)
Q Consensus 41 D~CikC~k---dGq~--LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~y 89 (209)
+.|.+|=. .|++ +|+|+ -.||..|+.+=+.- -+-+||.|--
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~-----H~FH~~CIDpWL~~---~r~~CPvCK~ 275 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCS-----HKFHVNCIDPWLTQ---TRTFCPVCKR 275 (348)
T ss_pred ceEEEeecccccCCeeeEecCC-----CchhhccchhhHhh---cCccCCCCCC
Confidence 59999987 4554 67777 79999999964432 2568999975
No 37
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=65.60 E-value=4.2 Score=40.86 Aligned_cols=49 Identities=27% Similarity=0.364 Sum_probs=39.2
Q ss_pred CCCceeeccCCCCeEEeeCCCCCcccccccccCCCCccC-CCCCccccccchh
Q 041295 39 EEEPCIKCNRRDESLLVCIQSGCPISVHENCLSCGVKSD-DVGNIYCPYFWYK 90 (209)
Q Consensus 39 neD~CikC~kdGq~LL~Cs~~gCPlAvH~kClg~sl~~d-d~GnfYCPyC~yk 90 (209)
.+-.|-.|.++|. +|.|+ .|-++||..|+....... -+-.|-||.|.--
T Consensus 59 ~d~~cfechlpg~-vl~c~--vc~Rs~h~~c~sp~~q~r~~s~p~~~p~p~s~ 108 (588)
T KOG3612|consen 59 IDPFCFECHLPGA-VLKCI--VCHRSFHENCQSPDPQKRNYSVPSDKPQPYSF 108 (588)
T ss_pred CCcccccccCCcc-eeeee--hhhccccccccCcchhhccccccccCCccccc
Confidence 3557999999999 99999 999999999999644332 2456889998643
No 38
>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=64.99 E-value=2 Score=26.22 Aligned_cols=27 Identities=26% Similarity=0.780 Sum_probs=12.4
Q ss_pred ceeeccCCCCe--EEeeCCCCCccccccccc
Q 041295 42 PCIKCNRRDES--LLVCIQSGCPISVHENCL 70 (209)
Q Consensus 42 ~CikC~kdGq~--LL~Cs~~gCPlAvH~kCl 70 (209)
.|-.|++.+.. +..|. .|-..+|.+|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~--~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCS--ECDFDLHEECA 30 (30)
T ss_dssp --TTTS----S--EEE-T--TT-----HHHH
T ss_pred cCCcCCCcCCCCceEECc--cCCCccChhcC
Confidence 47788887653 88999 99999999984
No 39
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=63.49 E-value=2.6 Score=36.20 Aligned_cols=55 Identities=18% Similarity=0.227 Sum_probs=39.3
Q ss_pred CCCCceeeccCCCCe-EEeeCCCCCcccccccccCCCCccCCCCCccccccchhhHHH
Q 041295 38 LEEEPCIKCNRRDES-LLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWYKCELM 94 (209)
Q Consensus 38 ~neD~CikC~kdGq~-LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~ykka~e 94 (209)
..+..|++|..+++. .-+|.=.|=-..+|.+|+.. =.+.+++-.||.|.++....
T Consensus 6 ~~~~~CRIC~~~~~~~~~PC~CkGs~k~VH~sCL~r--Wi~~s~~~~CeiC~~~Y~i~ 61 (162)
T PHA02825 6 LMDKCCWICKDEYDVVTNYCNCKNENKIVHKECLEE--WINTSKNKSCKICNGPYNIK 61 (162)
T ss_pred CCCCeeEecCCCCCCccCCcccCCCchHHHHHHHHH--HHhcCCCCcccccCCeEEEE
Confidence 467899999987642 44555335566889999973 33457999999999875544
No 40
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=61.25 E-value=2.9 Score=41.80 Aligned_cols=31 Identities=23% Similarity=0.442 Sum_probs=23.9
Q ss_pred EEeeCCCCCcccccccccCCCCccCCCCCccccccchhhH
Q 041295 53 LLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWYKCE 92 (209)
Q Consensus 53 LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~ykka 92 (209)
.-.|+ +|-..||.+|+...... ||-|.+.+.
T Consensus 531 ~~rC~--~C~avfH~~C~~r~s~~-------CPrC~R~q~ 561 (580)
T KOG1829|consen 531 TRRCS--TCLAVFHKKCLRRKSPC-------CPRCERRQK 561 (580)
T ss_pred ceeHH--HHHHHHHHHHHhccCCC-------CCchHHHHH
Confidence 35688 99999999999964332 999986544
No 41
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=59.70 E-value=3.2 Score=33.89 Aligned_cols=23 Identities=17% Similarity=0.235 Sum_probs=18.8
Q ss_pred CCccCCCCCccccccchhhHHHH
Q 041295 73 GVKSDDVGNIYCPYFWYKCELMR 95 (209)
Q Consensus 73 sl~~dd~GnfYCPyC~ykka~ee 95 (209)
.-.|+|.+.|+||.|++...-.+
T Consensus 12 EytYed~~~~~cpec~~ew~~~~ 34 (112)
T COG2824 12 EYTYEDGGQLICPECAHEWNENE 34 (112)
T ss_pred ceEEecCceEeCchhcccccccc
Confidence 45789999999999999876443
No 42
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=59.37 E-value=7.9 Score=39.57 Aligned_cols=54 Identities=28% Similarity=0.558 Sum_probs=47.8
Q ss_pred CCCCCCCceeeccCCCCe-EEeeCCCCCcccccccccCCCCccCCCCCccccccchh
Q 041295 35 VDLLEEEPCIKCNRRDES-LLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWYK 90 (209)
Q Consensus 35 ~d~~neD~CikC~kdGq~-LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~yk 90 (209)
+.......|..|.++..+ ++.|+ +|--.+|..|...++..-+.|.|.||-|...
T Consensus 150 ~~~~~~~~~~~~~k~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 204 (904)
T KOG1246|consen 150 VEFIDYPQCNTCSKGKEEKLLLCD--SCDDSYHTYCLRPPLTRVPDGDWRCPKCIPT 204 (904)
T ss_pred cccccchhhhccccCCCccceecc--cccCcccccccCCCCCcCCcCcccCCccccc
Confidence 566678899999998865 44888 9999999999999999999999999999876
No 43
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=59.09 E-value=2.3 Score=43.30 Aligned_cols=54 Identities=20% Similarity=0.324 Sum_probs=40.1
Q ss_pred CCCceeeccCCCCe----EEeeCCCCCcccccccccCCCCccC-CCCCccccccchhhHHH
Q 041295 39 EEEPCIKCNRRDES----LLVCIQSGCPISVHENCLSCGVKSD-DVGNIYCPYFWYKCELM 94 (209)
Q Consensus 39 neD~CikC~kdGq~----LL~Cs~~gCPlAvH~kClg~sl~~d-d~GnfYCPyC~ykka~e 94 (209)
....|.+|+..|.. ||.|+ .|-.-||..|+..-..-. =.+-|-||-|..-.+--
T Consensus 17 ~~~mc~l~~s~G~~~ag~m~ac~--~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~c~ 75 (694)
T KOG4443|consen 17 VCLMCPLCGSSGKGRAGRLLACS--DCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEACG 75 (694)
T ss_pred hhhhhhhhccccccccCcchhhh--hhcccCCcchhhHHHhHHHhcCCcccCCceeeeecc
Confidence 56778888887765 99999 999999999998533322 13349999998654443
No 44
>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=56.84 E-value=13 Score=24.48 Aligned_cols=33 Identities=24% Similarity=0.487 Sum_probs=24.0
Q ss_pred CCCceeeccC-----CCCeEEeeCCCCCcccccccccCCCC
Q 041295 39 EEEPCIKCNR-----RDESLLVCIQSGCPISVHENCLSCGV 74 (209)
Q Consensus 39 neD~CikC~k-----dGq~LL~Cs~~gCPlAvH~kClg~sl 74 (209)
.-..|.+|++ ..+ =+.|. .|-+.+|.+|+..-+
T Consensus 10 ~~~~C~~C~~~i~g~~~~-g~~C~--~C~~~~H~~C~~~~~ 47 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQ-GYRCS--WCGLVCHKKCLSKVP 47 (53)
T ss_dssp STEB-TTSSSBECSSSSC-EEEET--TTT-EEETTGGCTSS
T ss_pred CCCCCcccCcccCCCCCC-eEEEC--CCCChHhhhhhhhcC
Confidence 3457888876 344 78999 999999999998643
No 45
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=55.83 E-value=2.5 Score=27.11 Aligned_cols=41 Identities=24% Similarity=0.498 Sum_probs=25.4
Q ss_pred CceeeccC---CCCeEEeeCCCCCcccccccccCCCCccCCCCCccccccc
Q 041295 41 EPCIKCNR---RDESLLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFW 88 (209)
Q Consensus 41 D~CikC~k---dGq~LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~ 88 (209)
|.|.+|-. .++.++.. .|--.||.+|+..-+.. +..||+|.
T Consensus 1 d~C~IC~~~~~~~~~~~~l---~C~H~fh~~Ci~~~~~~----~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVVKL---PCGHVFHRSCIKEWLKR----NNSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHTTSCEEEE---TTSEEEEHHHHHHHHHH----SSB-TTTH
T ss_pred CCCcCCChhhcCCCeEEEc---cCCCeeCHHHHHHHHHh----CCcCCccC
Confidence 45677765 34434443 38899999999854333 34999983
No 46
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=54.90 E-value=6.1 Score=33.64 Aligned_cols=54 Identities=26% Similarity=0.335 Sum_probs=42.3
Q ss_pred CCCceeeccCCCCe------EEeeCCCCCcccccccccCCCCccCCCCCccccccchhhHHH
Q 041295 39 EEEPCIKCNRRDES------LLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWYKCELM 94 (209)
Q Consensus 39 neD~CikC~kdGq~------LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~ykka~e 94 (209)
++..|.+|...+.. +.+|+-.+=+..+|..|+.. =+.-.|+..|.+|+......
T Consensus 77 ~~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~--W~~~~~~~~CeiC~~~~~~~ 136 (323)
T KOG1609|consen 77 SGPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEK--WFSIKGNITCEICKSFFINV 136 (323)
T ss_pred CCCcEEEEecccccccccccccCccccCcHHHHHHHHHHh--hhccccCeeeecccccceec
Confidence 46899999996642 67788667788899999994 44469999999999865544
No 47
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=53.12 E-value=11 Score=32.08 Aligned_cols=40 Identities=25% Similarity=0.503 Sum_probs=29.8
Q ss_pred CCceeeccCCCC-------eEEeeCCCCCcccccccccCCCCccCCCCCccccccchh
Q 041295 40 EEPCIKCNRRDE-------SLLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWYK 90 (209)
Q Consensus 40 eD~CikC~kdGq-------~LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~yk 90 (209)
-.+|-.|+.++- ....|. .|-..||.+|+.. --||-|.-.
T Consensus 152 GfiCe~C~~~~~IfPF~~~~~~~C~--~C~~v~H~~C~~~---------~~CpkC~R~ 198 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQIDTTVRCP--KCKSVFHKSCFRK---------KSCPKCARR 198 (202)
T ss_pred CCCCccCCCCCCCCCCCCCCeeeCC--cCccccchhhcCC---------CCCCCcHhH
Confidence 457788876431 167899 9999999999993 129999744
No 48
>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=52.79 E-value=11 Score=23.89 Aligned_cols=31 Identities=23% Similarity=0.500 Sum_probs=23.9
Q ss_pred CCceeeccC--CC---CeEEeeCCCCCcccccccccCCC
Q 041295 40 EEPCIKCNR--RD---ESLLVCIQSGCPISVHENCLSCG 73 (209)
Q Consensus 40 eD~CikC~k--dG---q~LL~Cs~~gCPlAvH~kClg~s 73 (209)
...|..|.+ .| + =+.|+ .|-+++|.+|...-
T Consensus 11 ~~~C~~C~~~i~~~~~~-~~~C~--~C~~~~H~~C~~~v 46 (50)
T cd00029 11 PTFCDVCRKSIWGLFKQ-GLRCS--WCKVKCHKKCADKV 46 (50)
T ss_pred CCChhhcchhhhccccc-eeEcC--CCCCchhhhhhccC
Confidence 346888866 22 4 67899 99999999999853
No 49
>PF04071 zf-like: Cysteine-rich small domain; InterPro: IPR007212 This is a probable metal-binding domain. It is found in a probable precorrin-3B C17-methyltransferase from Methanobacterium thermoautotrophicum, that catalyses the methylation of C-17 in precorrin-3B to form precorrin-4.
Probab=51.94 E-value=43 Score=26.00 Aligned_cols=63 Identities=16% Similarity=0.224 Sum_probs=50.1
Q ss_pred cCCCCeEEeeCCCCCccc-ccccccCCCCccCCCC--CccccccchhhHHHHHHHHHHHHHHHHHHHHhh
Q 041295 47 NRRDESLLVCIQSGCPIS-VHENCLSCGVKSDDVG--NIYCPYFWYKCELMRTKELRKKAMETKKQLACF 113 (209)
Q Consensus 47 ~kdGq~LL~Cs~~gCPlA-vH~kClg~sl~~dd~G--nfYCPyC~ykka~eey~elkKkA~~AKK~Ls~F 113 (209)
...||.=|+|- ||+- ....|+|. ..+...| -|-|.-|......+-|..+.+..++.-+++...
T Consensus 18 H~~~qnClFCy---CPlY~c~d~~~G~-~~~~~~G~~vw~C~~C~~~H~~e~~~~i~~~~~~~~~~~k~~ 83 (86)
T PF04071_consen 18 HFEGQNCLFCY---CPLYPCGDECGGN-FIYTKNGSKVWDCSDCTLPHRPENYDYIIRKLKEIIEELKKL 83 (86)
T ss_pred cCCCCCcceEe---CCcccccCCCCcc-EEEcCCCCeeeECccCCCccCHHHHHHHHHHHHHHHHHHHHh
Confidence 35555577887 9997 46899985 4445667 999999999999999999998888888777664
No 50
>PF11287 DUF3088: Protein of unknown function (DUF3088); InterPro: IPR021439 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=50.10 E-value=8.3 Score=31.38 Aligned_cols=37 Identities=16% Similarity=0.311 Sum_probs=22.1
Q ss_pred CccccccchhhH-HHHHHHHHHH-------HHHHHHHHHhhcCCC
Q 041295 81 NIYCPYFWYKCE-LMRTKELRKK-------AMETKKQLACFIDPK 117 (209)
Q Consensus 81 nfYCPyC~ykka-~eey~elkKk-------A~~AKK~Ls~Fl~~~ 117 (209)
.||||.|..--- .+-+..++.. ...-|+++.+.|+..
T Consensus 21 ~f~Cp~c~~iEGlLa~~P~l~~~ldV~rV~f~RPR~~vi~llGE~ 65 (112)
T PF11287_consen 21 RFYCPHCAAIEGLLASFPDLRERLDVRRVDFPRPRQAVIALLGEA 65 (112)
T ss_pred eEECCchHHHHhHHhhChhhhhcccEEEeCCCCchHHHHHHhChh
Confidence 399999985432 2333334332 234577888888753
No 51
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=46.14 E-value=5 Score=28.79 Aligned_cols=42 Identities=24% Similarity=0.414 Sum_probs=23.8
Q ss_pred ceeeccCCCCeEEeeCCCCCcccccccccCCCCccCCCCCccccccchhh
Q 041295 42 PCIKCNRRDESLLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWYKC 91 (209)
Q Consensus 42 ~CikC~kdGq~LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~ykk 91 (209)
-|--|+-..+.|+.|+ -|--|+.+ ++.-=+..-+||+|++.-
T Consensus 4 nCKsCWf~~k~Li~C~-------dHYLCl~C-Lt~ml~~s~~C~iC~~~L 45 (50)
T PF03854_consen 4 NCKSCWFANKGLIKCS-------DHYLCLNC-LTLMLSRSDRCPICGKPL 45 (50)
T ss_dssp ---SS-S--SSEEE-S-------S-EEEHHH-HHHT-SSSSEETTTTEE-
T ss_pred cChhhhhcCCCeeeec-------chhHHHHH-HHHHhccccCCCcccCcC
Confidence 4778888888899999 58888876 333334455899999764
No 52
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=44.80 E-value=4.8 Score=23.95 Aligned_cols=42 Identities=21% Similarity=0.407 Sum_probs=25.3
Q ss_pred eeeccCCCCeEEeeCCCCCcccccccccCCCCccCCCCCccccccch
Q 041295 43 CIKCNRRDESLLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWY 89 (209)
Q Consensus 43 CikC~kdGq~LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~y 89 (209)
|.+|...-...+.-. .|--.||..|+..-.. .+...||.|..
T Consensus 2 C~iC~~~~~~~~~~~--~C~H~~c~~C~~~~~~---~~~~~Cp~C~~ 43 (45)
T cd00162 2 CPICLEEFREPVVLL--PCGHVFCRSCIDKWLK---SGKNTCPLCRT 43 (45)
T ss_pred CCcCchhhhCceEec--CCCChhcHHHHHHHHH---hCcCCCCCCCC
Confidence 566665442123333 4667888889874222 26778999863
No 53
>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq
Probab=44.36 E-value=37 Score=26.52 Aligned_cols=54 Identities=20% Similarity=0.354 Sum_probs=34.9
Q ss_pred CCCceeeccCCCCe----EEeeCCCCCccccccc--------ccCCC-CccCCCCCccccccchhhHHH
Q 041295 39 EEEPCIKCNRRDES----LLVCIQSGCPISVHEN--------CLSCG-VKSDDVGNIYCPYFWYKCELM 94 (209)
Q Consensus 39 neD~CikC~kdGq~----LL~Cs~~gCPlAvH~k--------Clg~s-l~~dd~GnfYCPyC~ykka~e 94 (209)
....|.+|+....+ ++.|. +|-.=|+.. |.... =..+..+...|++|.|++-.+
T Consensus 17 ~~~~C~VCg~~a~g~hyGv~sC~--aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~ 83 (101)
T cd07160 17 GNEVCSVCGDKASGFHYNVLSCE--GCKGFFRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRLRKCRE 83 (101)
T ss_pred CCCCCeecCCcCcceEECcceeh--hhhhhhhhcccccCccccCCCCccccCCcccccCccchhHHHHH
Confidence 56689999986554 78899 887666543 32211 111244567899999887554
No 54
>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=44.08 E-value=15 Score=22.58 Aligned_cols=27 Identities=26% Similarity=0.689 Sum_probs=20.4
Q ss_pred ceeeccCCCCe--EEeeCCCCCccccccccc
Q 041295 42 PCIKCNRRDES--LLVCIQSGCPISVHENCL 70 (209)
Q Consensus 42 ~CikC~kdGq~--LL~Cs~~gCPlAvH~kCl 70 (209)
.|-+|++..+. .-.|+ .|...+|.+|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~--~c~f~lh~~Ca 30 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCS--ECCFTLHVRCA 30 (30)
T ss_pred CCCCCCCCcCCCEeEEeC--CCCCeEcCccC
Confidence 47778775543 45787 89999999995
No 55
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=40.25 E-value=8.4 Score=35.61 Aligned_cols=51 Identities=27% Similarity=0.367 Sum_probs=39.6
Q ss_pred CCCceeecc-CCCCeEEeeCCCCCcccccccccCCCCccCCCCCcc-----ccccch
Q 041295 39 EEEPCIKCN-RRDESLLVCIQSGCPISVHENCLSCGVKSDDVGNIY-----CPYFWY 89 (209)
Q Consensus 39 neD~CikC~-kdGq~LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfY-----CPyC~y 89 (209)
+..+|.++- ..+.+++.|-..+|+.-.|-+||+....-+..|+.+ ||.|--
T Consensus 184 ~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~ 240 (276)
T KOG3005|consen 184 ECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEK 240 (276)
T ss_pred hhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhc
Confidence 456666666 566668999999999999999999855556666654 999964
No 56
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=39.67 E-value=18 Score=24.47 Aligned_cols=19 Identities=32% Similarity=0.714 Sum_probs=13.1
Q ss_pred cccCCCCccCCCCCcccccc
Q 041295 68 NCLSCGVKSDDVGNIYCPYF 87 (209)
Q Consensus 68 kClg~sl~~dd~GnfYCPyC 87 (209)
.| +.++--+..|..|||.|
T Consensus 22 ~C-~~PL~~~k~g~~~Cv~C 40 (41)
T PF06677_consen 22 DC-GTPLMRDKDGKIYCVSC 40 (41)
T ss_pred CC-CCeeEEecCCCEECCCC
Confidence 46 44444347889999998
No 57
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.18 E-value=24 Score=30.66 Aligned_cols=18 Identities=39% Similarity=0.881 Sum_probs=14.9
Q ss_pred CCceeeccCCCCe--EEeeC
Q 041295 40 EEPCIKCNRRDES--LLVCI 57 (209)
Q Consensus 40 eD~CikC~kdGq~--LL~Cs 57 (209)
...|.+|+..+-. ||+|.
T Consensus 158 ~~~Cr~C~~~~~~VlllPCr 177 (207)
T KOG1100|consen 158 MRSCRKCGEREATVLLLPCR 177 (207)
T ss_pred cccceecCcCCceEEeeccc
Confidence 3449999999888 88888
No 58
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=37.58 E-value=2.9 Score=28.27 Aligned_cols=43 Identities=28% Similarity=0.486 Sum_probs=21.6
Q ss_pred eeeccCCCCe----EEeeCCCCCcccccccccCCCCccCCCCCcccccc
Q 041295 43 CIKCNRRDES----LLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYF 87 (209)
Q Consensus 43 CikC~kdGq~----LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC 87 (209)
|.+|..+... +.+|.=.|=-.-+|.+||..= +...++..|+.|
T Consensus 1 CrIC~~~~~~~~~li~pC~C~Gs~~~vH~~CL~~W--~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEEDEPLISPCRCKGSMKYVHRSCLERW--IRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSSS-EE-SSS-SSCCGSEECCHHHHH--HHHHT-SB-TTT
T ss_pred CeEeCCcCCCCCceecccccCCCcchhHHHHHHHH--HHhcCCCcCCCC
Confidence 4455554322 456662233338999999842 222666667766
No 59
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=37.06 E-value=12 Score=29.11 Aligned_cols=29 Identities=17% Similarity=0.390 Sum_probs=20.8
Q ss_pred CcccccccccCCCCccCCCCCccccccchh
Q 041295 61 CPISVHENCLSCGVKSDDVGNIYCPYFWYK 90 (209)
Q Consensus 61 CPlAvH~kClg~sl~~dd~GnfYCPyC~yk 90 (209)
|.-+||--|+--=+... +.+-.||.|.-.
T Consensus 52 C~H~FH~hCI~kWl~~~-~~~~~CPmCR~~ 80 (85)
T PF12861_consen 52 CSHNFHMHCILKWLSTQ-SSKGQCPMCRQP 80 (85)
T ss_pred CccHHHHHHHHHHHccc-cCCCCCCCcCCe
Confidence 77789999987544433 446799999743
No 60
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=37.00 E-value=5.9 Score=22.65 Aligned_cols=24 Identities=29% Similarity=0.610 Sum_probs=14.7
Q ss_pred CcccccccccCCCCccCCCCCcccccc
Q 041295 61 CPISVHENCLSCGVKSDDVGNIYCPYF 87 (209)
Q Consensus 61 CPlAvH~kClg~sl~~dd~GnfYCPyC 87 (209)
|--.||..|+..-.. .+..-||.|
T Consensus 16 C~H~~c~~C~~~~~~---~~~~~CP~C 39 (39)
T smart00184 16 CGHTFCRSCIRKWLK---SGNNTCPIC 39 (39)
T ss_pred CCChHHHHHHHHHHH---hCcCCCCCC
Confidence 446678888763222 455668876
No 61
>cd06962 NR_DBD_FXR DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. FXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. FXR is a member of the nuclear receptor family of ligand activated transcription factors. Bile acids are endogenous ligands for FXRs. Upon binding of a ligand, FXR binds to FXR response element (FXRE), which is an inverted repeat of TGACCT spaced by one nucleotide, either as a monomer or as a heterodimer with retinoid X receptor (RXR), to regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, FXR has a central well conserved
Probab=36.94 E-value=42 Score=25.22 Aligned_cols=52 Identities=21% Similarity=0.381 Sum_probs=33.0
Q ss_pred CceeeccCCCCe----EEeeCCCCCccccccc--------ccCCC-CccCCCCCccccccchhhHHH
Q 041295 41 EPCIKCNRRDES----LLVCIQSGCPISVHEN--------CLSCG-VKSDDVGNIYCPYFWYKCELM 94 (209)
Q Consensus 41 D~CikC~kdGq~----LL~Cs~~gCPlAvH~k--------Clg~s-l~~dd~GnfYCPyC~ykka~e 94 (209)
..|.+|+....+ ++.|. +|-.=|+.. |.... -..+..+.+.|++|.|++-.+
T Consensus 2 ~~C~VCg~~a~g~hyGv~sC~--aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~ 66 (84)
T cd06962 2 ELCVVCGDKASGYHYNALTCE--GCKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRLRKCKE 66 (84)
T ss_pred CCCeecCCcCcceEECcceee--cceeeeeeeeccCCceecCCCCcCccCccccccCccchhhHHHH
Confidence 569999875544 77888 887655433 32111 112345578999999987655
No 62
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=36.15 E-value=41 Score=20.07 Aligned_cols=13 Identities=23% Similarity=0.524 Sum_probs=10.4
Q ss_pred CCccccccchhhH
Q 041295 80 GNIYCPYFWYKCE 92 (209)
Q Consensus 80 GnfYCPyC~ykka 92 (209)
|+|||.+|-....
T Consensus 2 ~~~~C~~C~~~~~ 14 (35)
T smart00451 2 GGFYCKLCNVTFT 14 (35)
T ss_pred cCeEccccCCccC
Confidence 6899999986655
No 63
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=35.75 E-value=28 Score=32.52 Aligned_cols=44 Identities=30% Similarity=0.477 Sum_probs=29.3
Q ss_pred CCCceeeccCCC---Ce--EE--eeCCCCCcccccccccCCCCccCCCCCccccccchh
Q 041295 39 EEEPCIKCNRRD---ES--LL--VCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWYK 90 (209)
Q Consensus 39 neD~CikC~kdG---q~--LL--~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~yk 90 (209)
+++.|.+|..+- .+ |+ .|. |.-|-.+-..+-..|...||.|...
T Consensus 2 d~~~CP~Ck~~~y~np~~kl~i~~CG--------H~~C~sCv~~l~~~~~~~CP~C~~~ 52 (309)
T TIGR00570 2 DDQGCPRCKTTKYRNPSLKLMVNVCG--------HTLCESCVDLLFVRGSGSCPECDTP 52 (309)
T ss_pred CCCCCCcCCCCCccCcccccccCCCC--------CcccHHHHHHHhcCCCCCCCCCCCc
Confidence 567899998842 21 33 254 7777776555555677799999543
No 64
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=35.28 E-value=18 Score=20.92 Aligned_cols=15 Identities=20% Similarity=0.260 Sum_probs=11.0
Q ss_pred CCccccccchhhHHH
Q 041295 80 GNIYCPYFWYKCELM 94 (209)
Q Consensus 80 GnfYCPyC~ykka~e 94 (209)
|+|.||.|-+.....
T Consensus 1 g~W~C~~C~~~N~~~ 15 (26)
T smart00547 1 GDWECPACTFLNFAS 15 (26)
T ss_pred CcccCCCCCCcChhh
Confidence 689999997765443
No 65
>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=35.24 E-value=29 Score=21.78 Aligned_cols=23 Identities=26% Similarity=0.413 Sum_probs=14.5
Q ss_pred ccCCCCccCCC-CCccccccchhh
Q 041295 69 CLSCGVKSDDV-GNIYCPYFWYKC 91 (209)
Q Consensus 69 Clg~sl~~dd~-GnfYCPyC~ykk 91 (209)
|..+.-.+++. .+|.||.|-..+
T Consensus 4 C~~CGy~y~~~~~~~~CP~Cg~~~ 27 (33)
T cd00350 4 CPVCGYIYDGEEAPWVCPVCGAPK 27 (33)
T ss_pred CCCCCCEECCCcCCCcCcCCCCcH
Confidence 33344444443 799999997644
No 66
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=34.16 E-value=3.1 Score=27.47 Aligned_cols=42 Identities=29% Similarity=0.515 Sum_probs=22.2
Q ss_pred CCCceeeccCCCCe--EEeeCCCCCcccccc-cccCCCCccCCCCCccccccch
Q 041295 39 EEEPCIKCNRRDES--LLVCIQSGCPISVHE-NCLSCGVKSDDVGNIYCPYFWY 89 (209)
Q Consensus 39 neD~CikC~kdGq~--LL~Cs~~gCPlAvH~-kClg~sl~~dd~GnfYCPyC~y 89 (209)
++..|.+|...-.. +++|. |. -|......+.. ....||+|.-
T Consensus 1 ~~~~C~iC~~~~~~~~~~pCg--------H~~~C~~C~~~~~~-~~~~CP~Cr~ 45 (50)
T PF13920_consen 1 EDEECPICFENPRDVVLLPCG--------HLCFCEECAERLLK-RKKKCPICRQ 45 (50)
T ss_dssp -HSB-TTTSSSBSSEEEETTC--------EEEEEHHHHHHHHH-TTSBBTTTTB
T ss_pred CcCCCccCCccCCceEEeCCC--------ChHHHHHHhHHhcc-cCCCCCcCCh
Confidence 35678888876443 55555 44 33332222211 6778999864
No 67
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=33.71 E-value=21 Score=28.03 Aligned_cols=24 Identities=33% Similarity=0.613 Sum_probs=15.6
Q ss_pred ccCCCCccCCCCCccccccchhhH
Q 041295 69 CLSCGVKSDDVGNIYCPYFWYKCE 92 (209)
Q Consensus 69 Clg~sl~~dd~GnfYCPyC~ykka 92 (209)
|.-+.......|.-||+-|+|++-
T Consensus 47 C~~CK~~v~q~g~~YCq~CAYkkG 70 (90)
T PF10235_consen 47 CKICKTKVHQPGAKYCQTCAYKKG 70 (90)
T ss_pred ccccccccccCCCccChhhhcccC
Confidence 444444445567888999988864
No 68
>cd03019 DsbA_DsbA DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol oxidant known, due to the unusual stability of the thiolate anion form of the first cysteine in the CXXC motif. The highly unstable oxidized form of DsbA directly donates disulfide bonds to reduced proteins secreted into the bacterial periplasm. This rapid and unidirectional process helps to catalyze the folding of newly-synthesized polypeptides. To regain catalytic activity, reduced DsbA is then reoxidized by the membrane protein DsbB, which generates its disulfides from oxidized quinones, which in turn are reoxidized by the electron transport chain.
Probab=31.30 E-value=18 Score=27.89 Aligned_cols=19 Identities=11% Similarity=0.016 Sum_probs=13.9
Q ss_pred CCCccCCCCCccccccchh
Q 041295 72 CGVKSDDVGNIYCPYFWYK 90 (209)
Q Consensus 72 ~sl~~dd~GnfYCPyC~yk 90 (209)
.++....-.+|.||+|+.-
T Consensus 15 ~~~~i~~f~D~~Cp~C~~~ 33 (178)
T cd03019 15 GKPEVIEFFSYGCPHCYNF 33 (178)
T ss_pred CCcEEEEEECCCCcchhhh
Confidence 3455666778999999854
No 69
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=31.27 E-value=24 Score=32.38 Aligned_cols=37 Identities=22% Similarity=0.439 Sum_probs=22.9
Q ss_pred CceeeccCCCCeEEeeCCCCCcccccccccCCCCccCCCCCccccccc
Q 041295 41 EPCIKCNRRDESLLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFW 88 (209)
Q Consensus 41 D~CikC~kdGq~LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~ 88 (209)
..=.+=+..|+ +|- .|-=.+. ...+..++.||||.|+
T Consensus 236 ~~l~VYgR~Ge---pC~--~CGt~I~------k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 236 QELKVYGRAGE---PCR--RCGTPIE------KIKLGGRSTFYCPVCQ 272 (273)
T ss_pred eeEEEecCCCC---CCC--ccCCEeE------EEEEcCCcCEeCCCCC
Confidence 33345566677 555 3322222 3566789999999997
No 70
>cd02972 DsbA_family DsbA family; consists of DsbA and DsbA-like proteins, including DsbC, DsbG, glutathione (GSH) S-transferase kappa (GSTK), 2-hydroxychromene-2-carboxylate (HCCA) isomerase, an oxidoreductase (FrnE) presumed to be involved in frenolicin biosynthesis, a 27-kDa outer membrane protein, and similar proteins. Members of this family contain a redox active CXXC motif (except GSTK and HCCA isomerase) imbedded in a TRX fold, and an alpha helical insert of about 75 residues (shorter in DsbC and DsbG) relative to TRX. DsbA is involved in the oxidative protein folding pathway in prokaryotes, catalyzing disulfide bond formation of proteins secreted into the bacterial periplasm. DsbC and DsbG function as protein disulfide isomerases and chaperones to correct non-native disulfide bonds formed by DsbA and prevent aggregation of incorrectly folded proteins.
Probab=31.26 E-value=16 Score=24.39 Aligned_cols=12 Identities=25% Similarity=0.509 Sum_probs=8.8
Q ss_pred CCccccccchhh
Q 041295 80 GNIYCPYFWYKC 91 (209)
Q Consensus 80 GnfYCPyC~ykk 91 (209)
.++.||+|+.-.
T Consensus 5 ~d~~Cp~C~~~~ 16 (98)
T cd02972 5 FDPLCPYCYLFE 16 (98)
T ss_pred ECCCCHhHHhhh
Confidence 367899998543
No 71
>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=30.82 E-value=14 Score=23.15 Aligned_cols=30 Identities=23% Similarity=0.615 Sum_probs=23.2
Q ss_pred CCceeeccC--CC--CeEEeeCCCCCcccccccccCC
Q 041295 40 EEPCIKCNR--RD--ESLLVCIQSGCPISVHENCLSC 72 (209)
Q Consensus 40 eD~CikC~k--dG--q~LL~Cs~~gCPlAvH~kClg~ 72 (209)
...|.+|.+ .+ + =+.|. .|.+.+|.+|+..
T Consensus 11 ~~~C~~C~~~i~~~~~-~~~C~--~C~~~~H~~C~~~ 44 (49)
T smart00109 11 PTKCCVCRKSIWGSFQ-GLRCS--WCKVKCHKKCAEK 44 (49)
T ss_pred CCCccccccccCcCCC-CcCCC--CCCchHHHHHHhh
Confidence 456888876 22 3 46899 9999999999975
No 72
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=30.67 E-value=18 Score=29.48 Aligned_cols=23 Identities=17% Similarity=0.288 Sum_probs=20.0
Q ss_pred CCccCCCCCccccccchhhHHHH
Q 041295 73 GVKSDDVGNIYCPYFWYKCELMR 95 (209)
Q Consensus 73 sl~~dd~GnfYCPyC~ykka~ee 95 (209)
.-.|.|...|-||.|.|.++.++
T Consensus 11 eytY~dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 11 EYTYHDGTQLICPSCLYEWNENE 33 (109)
T ss_pred cceEecCCeeECccccccccccc
Confidence 46899999999999999987764
No 73
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=30.02 E-value=22 Score=20.86 Aligned_cols=14 Identities=14% Similarity=0.079 Sum_probs=9.1
Q ss_pred CccccccchhhHHH
Q 041295 81 NIYCPYFWYKCELM 94 (209)
Q Consensus 81 nfYCPyC~ykka~e 94 (209)
+|||+.|-.....+
T Consensus 1 q~~C~~C~k~f~~~ 14 (27)
T PF12171_consen 1 QFYCDACDKYFSSE 14 (27)
T ss_dssp -CBBTTTTBBBSSH
T ss_pred CCCcccCCCCcCCH
Confidence 58999997554433
No 74
>cd03023 DsbA_Com1_like DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC motif, assumed to be imbedded in a DsbA-like structure. Its homology to DsbA suggests that the protein is a protein disulfide oxidoreductase. The role of such a protein in pathogenesis is unknown.
Probab=29.12 E-value=19 Score=26.61 Aligned_cols=17 Identities=18% Similarity=0.114 Sum_probs=12.2
Q ss_pred CccCCCCCccccccchh
Q 041295 74 VKSDDVGNIYCPYFWYK 90 (209)
Q Consensus 74 l~~dd~GnfYCPyC~yk 90 (209)
+....-.++.||+|+.-
T Consensus 7 ~~i~~f~D~~Cp~C~~~ 23 (154)
T cd03023 7 VTIVEFFDYNCGYCKKL 23 (154)
T ss_pred EEEEEEECCCChhHHHh
Confidence 34455678999999844
No 75
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=27.40 E-value=31 Score=32.95 Aligned_cols=32 Identities=19% Similarity=0.350 Sum_probs=25.9
Q ss_pred CCCceeeccCCCC--------eEEeeCCCCCcccccccccCC
Q 041295 39 EEEPCIKCNRRDE--------SLLVCIQSGCPISVHENCLSC 72 (209)
Q Consensus 39 neD~CikC~kdGq--------~LL~Cs~~gCPlAvH~kClg~ 72 (209)
--+.|-+|.+.-. ++++|. .|..++|..|+.-
T Consensus 257 ~~~~~~~~~~~~~~~~~~r~~S~I~C~--~C~~~~HP~Ci~M 296 (381)
T KOG1512|consen 257 RRNERKHFWDIQTNIIQSRRNSWIVCK--PCATRPHPYCVAM 296 (381)
T ss_pred chhhhhhhhcchhhhhhhhhccceeec--ccccCCCCcchhc
Confidence 4578888887433 399999 9999999999984
No 76
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 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 zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=27.31 E-value=26 Score=21.25 Aligned_cols=14 Identities=21% Similarity=0.413 Sum_probs=11.3
Q ss_pred CCCccccccchhhH
Q 041295 79 VGNIYCPYFWYKCE 92 (209)
Q Consensus 79 ~GnfYCPyC~ykka 92 (209)
.|+|.||.|-+...
T Consensus 2 ~g~W~C~~C~~~N~ 15 (30)
T PF00641_consen 2 EGDWKCPSCTFMNP 15 (30)
T ss_dssp SSSEEETTTTEEEE
T ss_pred CcCccCCCCcCCch
Confidence 57999999987643
No 77
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=26.39 E-value=38 Score=20.23 Aligned_cols=21 Identities=29% Similarity=0.604 Sum_probs=14.1
Q ss_pred cccCCCCccCCCCCccccccch
Q 041295 68 NCLSCGVKSDDVGNIYCPYFWY 89 (209)
Q Consensus 68 kClg~sl~~dd~GnfYCPyC~y 89 (209)
.|-.+.. ..+.+.-|||+|-.
T Consensus 4 ~Cp~Cg~-~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 4 FCPNCGA-EIDPDAKFCPNCGA 24 (26)
T ss_pred CCcccCC-cCCcccccChhhCC
Confidence 3445544 46778889999964
No 78
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=25.78 E-value=69 Score=26.90 Aligned_cols=40 Identities=13% Similarity=0.027 Sum_probs=28.9
Q ss_pred CCccCCCCCccccccchhhHHHHHHHHHHHHHHHHHHHHh
Q 041295 73 GVKSDDVGNIYCPYFWYKCELMRTKELRKKAMETKKQLAC 112 (209)
Q Consensus 73 sl~~dd~GnfYCPyC~ykka~eey~elkKkA~~AKK~Ls~ 112 (209)
-+.....|+|||-.|.--...+.....-.+.-.=|+.|..
T Consensus 49 D~dlPG~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~ 88 (129)
T KOG3408|consen 49 DPDLPGGGQFYCIECARYFIDAKALKTHFKTKVHKRRVKE 88 (129)
T ss_pred CCCCCCCceeehhhhhhhhcchHHHHHHHhccHHHHHHHh
Confidence 3677789999999999777766666665555555666655
No 79
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 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 domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=25.44 E-value=11 Score=27.23 Aligned_cols=25 Identities=32% Similarity=0.518 Sum_probs=16.6
Q ss_pred CCcccccccccCCCCccCCCCCccccccc
Q 041295 60 GCPISVHENCLSCGVKSDDVGNIYCPYFW 88 (209)
Q Consensus 60 gCPlAvH~kClg~sl~~dd~GnfYCPyC~ 88 (209)
.|.-.||..|+..=+.. +.-||.|.
T Consensus 49 ~C~H~FH~~Ci~~Wl~~----~~~CP~CR 73 (73)
T PF12678_consen 49 PCGHIFHFHCISQWLKQ----NNTCPLCR 73 (73)
T ss_dssp TTSEEEEHHHHHHHHTT----SSB-TTSS
T ss_pred ccCCCEEHHHHHHHHhc----CCcCCCCC
Confidence 57789999999743322 22899983
No 80
>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking. In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy
Probab=25.41 E-value=1.1e+02 Score=25.70 Aligned_cols=15 Identities=13% Similarity=0.290 Sum_probs=12.4
Q ss_pred CCCCCccccccchhh
Q 041295 77 DDVGNIYCPYFWYKC 91 (209)
Q Consensus 77 dd~GnfYCPyC~ykk 91 (209)
.....|||+.|.-.+
T Consensus 7 ~~~~~~~C~~C~~~~ 21 (302)
T PF10186_consen 7 NSRRRFYCANCVNNR 21 (302)
T ss_pred CCCCCeECHHHHHHH
Confidence 457899999999776
No 81
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=25.34 E-value=34 Score=34.79 Aligned_cols=38 Identities=16% Similarity=0.303 Sum_probs=30.7
Q ss_pred CCCceeeccCCCCeEEeeCCCCCcccccccccCCCCcc
Q 041295 39 EEEPCIKCNRRDESLLVCIQSGCPISVHENCLSCGVKS 76 (209)
Q Consensus 39 neD~CikC~kdGq~LL~Cs~~gCPlAvH~kClg~sl~~ 76 (209)
..-.|..|.+.|---+.|+..-|-+|||..|....--|
T Consensus 302 wkl~C~iCk~~~GtcIqCs~~nC~~aYHVtCArrag~f 339 (669)
T COG5141 302 WKLGCLICKEFGGTCIQCSYFNCTRAYHVTCARRAGYF 339 (669)
T ss_pred HhheeeEEcccCcceeeecccchhhhhhhhhhhhcchh
Confidence 46689999985444899999999999999999864333
No 82
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=25.28 E-value=43 Score=19.88 Aligned_cols=20 Identities=30% Similarity=0.815 Sum_probs=10.6
Q ss_pred ccCCCCccCCCCCccccccch
Q 041295 69 CLSCGVKSDDVGNIYCPYFWY 89 (209)
Q Consensus 69 Clg~sl~~dd~GnfYCPyC~y 89 (209)
|-.+....++ +.-|||+|-.
T Consensus 2 Cp~CG~~~~~-~~~fC~~CG~ 21 (23)
T PF13240_consen 2 CPNCGAEIED-DAKFCPNCGT 21 (23)
T ss_pred CcccCCCCCC-cCcchhhhCC
Confidence 3334444444 4445888854
No 83
>PRK10445 endonuclease VIII; Provisional
Probab=25.25 E-value=44 Score=29.49 Aligned_cols=37 Identities=16% Similarity=0.185 Sum_probs=24.1
Q ss_pred CceeeccCCCCeEEeeCCCCCcccccccccCCCCccCCCCCccccccc
Q 041295 41 EPCIKCNRRDESLLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFW 88 (209)
Q Consensus 41 D~CikC~kdGq~LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~ 88 (209)
...++.+..|+ .|- .|--.+. ...+..++.||||-|+
T Consensus 226 ~~~~Vy~r~g~---~Cp--~Cg~~I~------~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 226 FRFKVFHRDGE---ACE--RCGGIIE------KTTLSSRPFYWCPGCQ 262 (263)
T ss_pred ceEEEeCCCCC---CCC--CCCCEeE------EEEECCCCcEECCCCc
Confidence 35677888888 444 2322221 3455679999999996
No 84
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=24.96 E-value=40 Score=30.86 Aligned_cols=30 Identities=27% Similarity=0.404 Sum_probs=18.1
Q ss_pred CcccccccccCCCCccCCCCCccccccchhh
Q 041295 61 CPISVHENCLSCGVKSDDVGNIYCPYFWYKC 91 (209)
Q Consensus 61 CPlAvH~kClg~sl~~dd~GnfYCPyC~ykk 91 (209)
||-.+|.+=+.. +.--|.-.|+||+|-...
T Consensus 195 C~~C~hhngl~~-~~ek~~~efiC~~Cn~~n 224 (251)
T COG5415 195 CPQCHHHNGLYR-LAEKPIIEFICPHCNHKN 224 (251)
T ss_pred cccccccccccc-cccccchheecccchhhc
Confidence 334455544443 344455589999998665
No 85
>PRK10220 hypothetical protein; Provisional
Probab=23.98 E-value=28 Score=28.47 Aligned_cols=23 Identities=17% Similarity=0.163 Sum_probs=19.9
Q ss_pred CCccCCCCCccccccchhhHHHH
Q 041295 73 GVKSDDVGNIYCPYFWYKCELMR 95 (209)
Q Consensus 73 sl~~dd~GnfYCPyC~ykka~ee 95 (209)
.-.|.|...|-||.|.|.+..++
T Consensus 12 eytY~d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 12 EYTYEDNGMYICPECAHEWNDAE 34 (111)
T ss_pred cceEcCCCeEECCcccCcCCccc
Confidence 46899999999999999887664
No 86
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=23.78 E-value=33 Score=29.66 Aligned_cols=40 Identities=18% Similarity=0.337 Sum_probs=29.4
Q ss_pred ceeeccCCCCeEEeeCCCCCcccccccccCCCCccCCCCCccccccchhhH
Q 041295 42 PCIKCNRRDESLLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWYKCE 92 (209)
Q Consensus 42 ~CikC~kdGq~LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~ykka 92 (209)
.|+.|+..|. ...+--.. +-|..+++-. -|.||.|-|+..
T Consensus 2 ~Cp~C~~~~~-~~~~~~~~--IP~F~evii~--------sf~C~~CGyr~~ 41 (192)
T TIGR00310 2 DCPSCGGECE-TVMKTVND--IPYFGEVLET--------STICEHCGYRSN 41 (192)
T ss_pred cCCCCCCCCE-EEEEEEcC--CCCcceEEEE--------EEECCCCCCccc
Confidence 4999999888 66665222 6667777763 389999999854
No 87
>PRK00420 hypothetical protein; Validated
Probab=22.89 E-value=1.1e+02 Score=24.75 Aligned_cols=27 Identities=22% Similarity=0.465 Sum_probs=18.3
Q ss_pred CCcccccccccCCCCccC-CCCCccccccchhhHH
Q 041295 60 GCPISVHENCLSCGVKSD-DVGNIYCPYFWYKCEL 93 (209)
Q Consensus 60 gCPlAvH~kClg~sl~~d-d~GnfYCPyC~ykka~ 93 (209)
.||. |-. +-|. ..|.-|||.|--...+
T Consensus 25 ~CP~-----Cg~--pLf~lk~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 25 HCPV-----CGL--PLFELKDGEVVCPVHGKVYIV 52 (112)
T ss_pred CCCC-----CCC--cceecCCCceECCCCCCeeee
Confidence 5665 554 3343 7999999999765444
No 88
>PRK14873 primosome assembly protein PriA; Provisional
Probab=22.83 E-value=64 Score=32.58 Aligned_cols=44 Identities=23% Similarity=0.560 Sum_probs=31.6
Q ss_pred CCceeeccCCCCeEEeeCCCCC--ccccccc-----ccCCCCccCCCCCccccccchhhH
Q 041295 40 EEPCIKCNRRDESLLVCIQSGC--PISVHEN-----CLSCGVKSDDVGNIYCPYFWYKCE 92 (209)
Q Consensus 40 eD~CikC~kdGq~LL~Cs~~gC--PlAvH~k-----Clg~sl~~dd~GnfYCPyC~ykka 92 (209)
--.|..|+ . ++.|. .| |+.||.. |-.|.-.. ..|.||.|--+..
T Consensus 383 ~l~C~~Cg---~-~~~C~--~C~~~L~~h~~~~~l~Ch~CG~~~---~p~~Cp~Cgs~~l 433 (665)
T PRK14873 383 SLACARCR---T-PARCR--HCTGPLGLPSAGGTPRCRWCGRAA---PDWRCPRCGSDRL 433 (665)
T ss_pred eeEhhhCc---C-eeECC--CCCCceeEecCCCeeECCCCcCCC---cCccCCCCcCCcc
Confidence 44566664 5 77888 67 6889975 88887542 4899999976543
No 89
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=22.49 E-value=20 Score=23.42 Aligned_cols=28 Identities=29% Similarity=0.575 Sum_probs=18.8
Q ss_pred ccccccccCC---------CCccCCCCCccccccchh
Q 041295 63 ISVHENCLSC---------GVKSDDVGNIYCPYFWYK 90 (209)
Q Consensus 63 lAvH~kClg~---------sl~~dd~GnfYCPyC~yk 90 (209)
..+|..|+.+ +.-+.-.|.+||..|..+
T Consensus 20 ~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~ 56 (58)
T PF00412_consen 20 KFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQK 56 (58)
T ss_dssp EEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHH
T ss_pred cEEEccccccCCCCCccCCCeeEeECCEEECHHHHhh
Confidence 5688888763 223445678889888765
No 90
>PF08285 DPM3: Dolichol-phosphate mannosyltransferase subunit 3 (DPM3); InterPro: IPR013174 This family corresponds to subunit 3 of dolichol-phosphate mannosyltransferase, an enzyme which generates mannosyl donors for glycosylphosphatidylinositols, N-glycan and protein O- and C-mannosylation. DPM3 is an integral membrane protein and plays a role in stabilising the dolichol-phosphate mannosyl transferase complex [].
Probab=22.46 E-value=1e+02 Score=23.88 Aligned_cols=20 Identities=35% Similarity=0.313 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q 041295 93 LMRTKELRKKAMETKKQLAC 112 (209)
Q Consensus 93 ~eey~elkKkA~~AKK~Ls~ 112 (209)
-++++++++...+||+.|.+
T Consensus 67 peA~~eL~~eI~eAK~dLr~ 86 (91)
T PF08285_consen 67 PEAAKELQKEIKEAKADLRK 86 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 47899999999999999975
No 91
>PF13462 Thioredoxin_4: Thioredoxin; PDB: 3FEU_A 3HZ8_A 3DVW_A 3A3T_E 3GMF_A 1Z6M_A 3GYK_C 3BCK_A 3BD2_A 3BCI_A ....
Probab=22.35 E-value=48 Score=25.02 Aligned_cols=17 Identities=12% Similarity=0.166 Sum_probs=11.8
Q ss_pred CccCCCCCccccccchh
Q 041295 74 VKSDDVGNIYCPYFWYK 90 (209)
Q Consensus 74 l~~dd~GnfYCPyC~yk 90 (209)
+.+..-.+|+||+|..-
T Consensus 14 ~~v~~f~d~~Cp~C~~~ 30 (162)
T PF13462_consen 14 ITVTEFFDFQCPHCAKF 30 (162)
T ss_dssp EEEEEEE-TTSHHHHHH
T ss_pred eEEEEEECCCCHhHHHH
Confidence 44555678999999854
No 92
>PF00093 VWC: von Willebrand factor type C domain; InterPro: IPR001007 The vWF domain is found in various plasma proteins: complement factors B, C2, CR3 and CR4; the integrins (I-domains); collagen types VI, VII, XII and XIV; and other extracellular proteins [, , ]. Although the majority of VWA-containing proteins are extracellular, the most ancient ones present in all eukaryotes are all intracellular proteins involved in functions such as transcription, DNA repair, ribosomal and membrane transport and the proteasome. A common feature appears to be involvement in multiprotein complexes. Proteins that incorporate vWF domains participate in numerous biological events (e.g. cell adhesion, migration, homing, pattern formation, and signal transduction), involving interaction with a large array of ligands []. A number of human diseases arise from mutations in VWA domains. Secondary structure prediction from 75 aligned vWF sequences has revealed a largely alternating sequence of alpha-helices and beta-strands []. The domain is named after the von Willebrand factor (VWF) type C repeat which is found in multidomain protein/multifunctional proteins involved in maintaining homeostasis [, ]. For the von Willebrand factor the duplicated VWFC domain is thought to participate in oligomerization, but not in the initial dimerization step []. The presence of this region in a number of other complex-forming proteins points to the possible involvment of the VWFC domain in complex formation.; GO: 0005515 protein binding; PDB: 1U5M_A.
Probab=22.23 E-value=39 Score=23.02 Aligned_cols=46 Identities=22% Similarity=0.528 Sum_probs=19.4
Q ss_pred CCCCCCceeeccCCCCeEEeeCCCCCcccccccccCCCCccCCCCCcccccc
Q 041295 36 DLLEEEPCIKCNRRDESLLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYF 87 (209)
Q Consensus 36 d~~neD~CikC~kdGq~LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC 87 (209)
+.+..+.|..|.=.+- -+.|....||. ..|... .+...-.-.||.|
T Consensus 12 ~~w~~~~C~~C~C~~G-~v~C~~~~Cp~---~~C~~~--~~~~~~g~CCp~C 57 (57)
T PF00093_consen 12 ESWHPDPCTTCTCQDG-EVQCSRIQCPP---LDCPNP--ELVKPPGECCPVC 57 (57)
T ss_dssp -EE-S-SSEEEEEETT-EEEEEE---S----SS-S---------SS-S--S-
T ss_pred CEECCCCCcEeEecCC-EEEEcCCCCcC---CCCCCC--ceecCCCCcCCCC
Confidence 3445666999876444 57999999998 667664 3344556678776
No 93
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.20 E-value=16 Score=35.25 Aligned_cols=42 Identities=26% Similarity=0.458 Sum_probs=31.6
Q ss_pred CCCceeeccCCCC-------eEEeeCCCCCcccccccccCCCCccCCCCCccccccch
Q 041295 39 EEEPCIKCNRRDE-------SLLVCIQSGCPISVHENCLSCGVKSDDVGNIYCPYFWY 89 (209)
Q Consensus 39 neD~CikC~kdGq-------~LL~Cs~~gCPlAvH~kClg~sl~~dd~GnfYCPyC~y 89 (209)
..+.|++|..... .+|.|. -.||..|+-.=.. ..-.||.|..
T Consensus 290 ~~~~C~IC~e~l~~~~~~~~~rL~C~-----Hifh~~CL~~W~e----r~qtCP~CR~ 338 (543)
T KOG0802|consen 290 SDELCIICLEELHSGHNITPKRLPCG-----HIFHDSCLRSWFE----RQQTCPTCRT 338 (543)
T ss_pred cCCeeeeechhhccccccccceeecc-----cchHHHHHHHHHH----HhCcCCcchh
Confidence 4899999998433 277777 7899999985222 2678999986
No 94
>PF01323 DSBA: DSBA-like thioredoxin domain; InterPro: IPR001853 DSBA is a sub-family of the Thioredoxin family []. The efficient and correct folding of bacterial disulphide bonded proteins in vivo is dependent upon a class of periplasmic oxidoreductase proteins called DsbA, after the Escherichia coli enzyme. The bacterial protein-folding factor DsbA is the most oxidizing of the thioredoxin family. DsbA catalyses disulphide-bond formation during the folding of secreted proteins. The extremely oxidizing nature of DsbA has been proposed to result from either domain motion or stabilising active-site interactions in the reduced form. DsbA's highly oxidizing nature is a result of hydrogen bond, electrostatic and helix-dipole interactions that favour the thiolate over the disulphide at the active site []. In the pathogenic bacterium Vibrio cholerae, the DsbA homologue (TcpG) is responsible for the folding, maturation and secretion of virulence factors. While the overall architecture of TcpG and DsbA is similar and the surface features are retained in TcpG, there are significant differences. For example, the kinked active site helix results from a three-residue loop in DsbA, but is caused by a proline in TcpG (making TcpG more similar to thioredoxin in this respect). Furthermore, the proposed peptide binding groove of TcpG is substantially shortened compared with that of DsbA due to a six-residue deletion. Also, the hydrophobic pocket of TcpG is more shallow and the acidic patch is much less extensive than that of E. coli DsbA [].; GO: 0015035 protein disulfide oxidoreductase activity; PDB: 3GL5_A 3DKS_D 3RPP_C 3RPN_B 1YZX_A 3L9V_C 2IMD_A 2IME_A 2IMF_A 2B3S_B ....
Probab=21.91 E-value=50 Score=25.74 Aligned_cols=13 Identities=15% Similarity=0.590 Sum_probs=9.7
Q ss_pred CCccccccchhhH
Q 041295 80 GNIYCPYFWYKCE 92 (209)
Q Consensus 80 GnfYCPyC~ykka 92 (209)
-++.||+|+....
T Consensus 6 ~D~~Cp~cy~~~~ 18 (193)
T PF01323_consen 6 FDFICPWCYLASP 18 (193)
T ss_dssp EBTTBHHHHHHHH
T ss_pred EeCCCHHHHHHHH
Confidence 3689999996543
No 95
>PF14260 zf-C4pol: C4-type zinc-finger of DNA polymerase delta
Probab=21.14 E-value=2.6e+02 Score=19.64 Aligned_cols=43 Identities=19% Similarity=0.335 Sum_probs=25.9
Q ss_pred ccCCCCccCCCCCccccccchhhHHHHHHHHHHHHHHHHHHHHh
Q 041295 69 CLSCGVKSDDVGNIYCPYFWYKCELMRTKELRKKAMETKKQLAC 112 (209)
Q Consensus 69 Clg~sl~~dd~GnfYCPyC~ykka~eey~elkKkA~~AKK~Ls~ 112 (209)
|+.+.....+.....|+.|........+ .+..+...+.+.+..
T Consensus 1 C~~C~~~~~~~~~~lC~~C~~~~~~~~~-~l~~~~~~~E~~~~~ 43 (73)
T PF14260_consen 1 CLVCGAKTQEGESPLCSNCRSDPQQTIY-NLLSRLRELERRFNE 43 (73)
T ss_pred CCCCCCcCCCCCCCcCcccCcChHHHHH-HHHHHHHHHHHHHHH
Confidence 4444444444446899999977766666 555555555555544
No 96
>cd07158 NR_DBD_Ppar_like The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family. The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. These domains interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. This family includes three known types of nuclear receptors: peroxisome proliferator-activated receptors (PPAR), REV-ERB receptors and Drosophila ecdysone-induced protein 78 (E78). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=20.92 E-value=54 Score=23.58 Aligned_cols=50 Identities=24% Similarity=0.496 Sum_probs=27.1
Q ss_pred eeeccCCCCe----EEeeCCCCCcccccc---------cccCCCC-ccCCCCCccccccchhhHHH
Q 041295 43 CIKCNRRDES----LLVCIQSGCPISVHE---------NCLSCGV-KSDDVGNIYCPYFWYKCELM 94 (209)
Q Consensus 43 CikC~kdGq~----LL~Cs~~gCPlAvH~---------kClg~sl-~~dd~GnfYCPyC~ykka~e 94 (209)
|.+|+....+ ++.|. +|-.=|.. .|..... ..+..+...|++|.+++-.+
T Consensus 1 C~VCg~~~~g~hyGv~~C~--aC~~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~ 64 (73)
T cd07158 1 CKVCGDKASGFHYGVHSCE--GCKGFFRRTIQHNLTYRRCLNGGKCVIQRKNRNRCQYCRFKKCLS 64 (73)
T ss_pred CcccCccCcceEECcchhh--HHHHHHhhhhcCCCCcccCCCCCCcCCCccccccCccchhhhhhH
Confidence 5666664443 55666 66543321 3332111 12345578899999987443
Done!