Query 044718
Match_columns 236
No_of_seqs 46 out of 48
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 06:04:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044718.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044718hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4299 PHD Zn-finger protein 98.5 4.8E-08 1E-12 96.5 1.1 50 34-86 253-307 (613)
2 smart00249 PHD PHD zinc finger 98.3 7E-07 1.5E-11 56.1 3.1 43 36-81 1-47 (47)
3 PF00628 PHD: PHD-finger; Int 98.2 8.3E-07 1.8E-11 59.3 1.5 45 36-83 1-50 (51)
4 KOG0383 Predicted helicase [Ge 97.7 1.4E-05 3.1E-10 80.2 1.5 52 30-84 43-94 (696)
5 KOG1973 Chromatin remodeling p 97.6 3.7E-05 8E-10 68.5 3.1 56 26-84 211-268 (274)
6 cd04718 BAH_plant_2 BAH, or Br 97.5 1.7E-05 3.6E-10 67.0 -0.8 61 58-120 1-61 (148)
7 COG5141 PHD zinc finger-contai 97.2 0.00011 2.4E-09 72.8 1.4 48 33-84 192-243 (669)
8 KOG0955 PHD finger protein BR1 97.1 0.00028 6E-09 74.0 3.0 68 11-86 200-271 (1051)
9 KOG0825 PHD Zn-finger protein 96.7 0.0019 4.1E-08 67.1 4.9 56 27-84 208-266 (1134)
10 KOG1244 Predicted transcriptio 96.6 0.0012 2.6E-08 61.8 2.1 46 34-82 281-329 (336)
11 PF13831 PHD_2: PHD-finger; PD 96.4 0.00092 2E-08 44.2 0.3 32 47-81 4-35 (36)
12 COG5034 TNG2 Chromatin remodel 96.1 0.003 6.5E-08 58.2 2.0 46 33-82 220-268 (271)
13 KOG0956 PHD finger protein AF1 95.1 0.011 2.4E-07 60.9 2.0 62 36-109 7-72 (900)
14 KOG1245 Chromatin remodeling c 95.0 0.0062 1.4E-07 65.6 -0.1 57 26-86 1102-1160(1404)
15 KOG0957 PHD finger protein [Ge 95.0 0.015 3.3E-07 58.4 2.5 67 13-81 523-595 (707)
16 KOG4443 Putative transcription 94.1 0.026 5.7E-07 57.4 1.9 50 32-83 66-117 (694)
17 KOG1512 PHD Zn-finger protein 93.5 0.037 8.1E-07 52.5 1.7 47 32-82 312-361 (381)
18 KOG0954 PHD finger protein [Ge 93.0 0.051 1.1E-06 56.4 1.9 48 33-84 270-321 (893)
19 PF13771 zf-HC5HC2H: PHD-like 92.6 0.058 1.3E-06 39.4 1.1 48 34-82 36-87 (90)
20 KOG4323 Polycomb-like PHD Zn-f 91.6 0.086 1.9E-06 51.7 1.4 67 25-94 160-234 (464)
21 KOG1473 Nucleosome remodeling 91.4 0.078 1.7E-06 57.2 0.9 64 20-85 414-480 (1414)
22 PF15446 zf-PHD-like: PHD/FYVE 90.8 0.12 2.7E-06 45.3 1.4 44 36-82 1-58 (175)
23 KOG1473 Nucleosome remodeling 87.9 0.36 7.7E-06 52.4 2.6 54 27-83 337-390 (1414)
24 PF13832 zf-HC5HC2H_2: PHD-zin 84.2 0.62 1.4E-05 35.3 1.6 33 33-66 54-87 (110)
25 KOG0956 PHD finger protein AF1 82.8 0.64 1.4E-05 48.5 1.5 51 34-84 117-180 (900)
26 KOG0957 PHD finger protein [Ge 75.8 1.8 3.8E-05 44.2 2.1 48 34-84 119-179 (707)
27 KOG4299 PHD Zn-finger protein 74.9 2.1 4.4E-05 43.7 2.3 45 34-83 47-91 (613)
28 KOG1081 Transcription factor N 71.5 2.6 5.5E-05 41.1 2.0 37 29-66 84-126 (463)
29 KOG3612 PHD Zn-finger protein 69.9 4.1 8.9E-05 41.5 3.1 47 33-82 59-106 (588)
30 PF08746 zf-RING-like: RING-li 67.1 1.4 3E-05 30.0 -0.6 31 49-81 13-43 (43)
31 PHA02825 LAP/PHD finger-like p 64.4 2.8 6.1E-05 36.5 0.7 58 29-88 3-61 (162)
32 smart00744 RINGv The RING-vari 61.4 2.6 5.5E-05 29.2 -0.1 44 36-81 1-48 (49)
33 PHA02862 5L protein; Provision 58.8 3 6.5E-05 36.3 -0.1 52 34-87 2-54 (156)
34 KOG1246 DNA-binding protein ju 56.2 13 0.00028 38.5 3.8 54 29-84 150-204 (904)
35 PF11793 FANCL_C: FANCL C-term 55.7 5.5 0.00012 29.2 0.8 51 35-86 3-66 (70)
36 KOG1609 Protein involved in mR 54.3 4.6 9.9E-05 34.7 0.2 53 34-88 78-136 (323)
37 COG2824 PhnA Uncharacterized Z 52.4 5.4 0.00012 33.2 0.3 24 67-90 12-35 (112)
38 PF11287 DUF3088: Protein of u 51.6 7.8 0.00017 32.0 1.2 35 76-110 22-64 (112)
39 KOG0383 Predicted helicase [Ge 51.0 5.7 0.00012 41.1 0.3 52 30-84 502-554 (696)
40 PF07649 C1_3: C1-like domain; 50.9 6.2 0.00013 24.5 0.4 27 36-64 2-30 (30)
41 PF00130 C1_1: Phorbol esters/ 49.1 11 0.00023 25.2 1.3 34 32-68 9-47 (53)
42 cd08059 MPN_prok_mb Mpr1p, Pad 46.9 32 0.0007 25.5 3.8 22 182-203 48-70 (101)
43 PF14446 Prok-RING_1: Prokaryo 46.6 11 0.00025 27.5 1.3 30 33-65 4-37 (54)
44 PF13901 DUF4206: Domain of un 45.6 17 0.00036 31.4 2.3 39 35-84 153-198 (202)
45 KOG4443 Putative transcription 45.1 5.5 0.00012 41.3 -0.8 78 28-108 12-94 (694)
46 KOG1734 Predicted RING-contain 44.5 15 0.00033 35.1 2.0 56 26-84 216-279 (328)
47 PF01323 DSBA: DSBA-like thior 43.8 16 0.00036 28.7 1.9 12 74-85 6-17 (193)
48 cd02972 DsbA_family DsbA famil 42.7 8.4 0.00018 26.0 0.1 12 74-85 5-16 (98)
49 KOG4628 Predicted E3 ubiquitin 42.0 17 0.00036 34.9 1.9 41 35-83 230-275 (348)
50 cd03019 DsbA_DsbA DsbA family, 42.0 9.6 0.00021 29.6 0.3 20 66-85 15-34 (178)
51 PF04071 zf-like: Cysteine-ric 40.5 80 0.0017 25.0 5.2 64 40-107 17-83 (86)
52 KOG1829 Uncharacterized conser 39.7 8.1 0.00018 39.3 -0.5 30 47-85 531-560 (580)
53 cd03023 DsbA_Com1_like DsbA fa 39.3 11 0.00023 28.2 0.1 18 67-84 6-23 (154)
54 PF13462 Thioredoxin_4: Thiore 38.0 5.9 0.00013 30.2 -1.4 17 67-83 13-29 (162)
55 KOG3005 GIY-YIG type nuclease 37.9 10 0.00022 35.6 -0.2 52 33-84 184-241 (276)
56 PF04216 FdhE: Protein involve 37.2 29 0.00063 31.0 2.6 28 33-62 171-210 (290)
57 cd00162 RING RING-finger (Real 35.1 8.5 0.00018 23.1 -0.8 41 37-82 2-42 (45)
58 PF10235 Cript: Microtubule-as 33.5 21 0.00045 28.5 1.0 26 61-86 45-70 (90)
59 PF14410 GH-E: HNH/ENDO VII su 32.2 30 0.00065 25.8 1.6 39 71-109 1-51 (70)
60 PF00412 LIM: LIM domain; Int 32.2 12 0.00025 24.8 -0.5 29 57-85 20-57 (58)
61 PF00641 zf-RanBP: Zn-finger i 31.6 19 0.00041 22.2 0.4 13 73-85 2-14 (30)
62 cd06962 NR_DBD_FXR DNA-binding 30.9 52 0.0011 25.1 2.7 52 35-88 2-66 (84)
63 smart00451 ZnF_U1 U1-like zinc 30.9 52 0.0011 19.9 2.3 14 73-86 1-14 (35)
64 PF03854 zf-P11: P-11 zinc fin 30.4 14 0.0003 27.1 -0.4 44 36-87 4-47 (50)
65 cd00029 C1 Protein kinase C co 30.2 28 0.00061 22.3 1.0 31 33-66 10-45 (50)
66 PF06677 Auto_anti-p27: Sjogre 30.1 30 0.00066 23.8 1.2 20 62-82 22-41 (41)
67 cd03025 DsbA_FrnE_like DsbA fa 29.9 34 0.00073 27.1 1.6 12 75-86 8-19 (193)
68 PF12861 zf-Apc11: Anaphase-pr 29.0 18 0.00039 28.5 -0.0 44 37-84 35-80 (85)
69 PF13240 zinc_ribbon_2: zinc-r 28.8 33 0.00071 20.8 1.1 20 63-83 2-21 (23)
70 PF08285 DPM3: Dolichol-phosph 28.5 68 0.0015 25.2 3.1 20 87-106 67-86 (91)
71 cd03022 DsbA_HCCA_Iso DsbA fam 28.3 34 0.00073 27.0 1.4 12 75-86 6-17 (192)
72 smart00547 ZnF_RBZ Zinc finger 28.3 28 0.0006 20.5 0.7 14 74-87 1-14 (26)
73 cd07168 NR_DBD_DHR4_like DNA-b 27.4 50 0.0011 25.4 2.1 54 33-88 5-71 (90)
74 smart00184 RING Ring finger. E 27.1 11 0.00024 21.7 -1.2 25 54-81 15-39 (39)
75 COG4391 Uncharacterized protei 27.0 39 0.00084 25.7 1.4 13 71-83 44-56 (62)
76 PRK14973 DNA topoisomerase I; 26.8 44 0.00096 35.6 2.3 54 35-89 589-671 (936)
77 PF10497 zf-4CXXC_R1: Zinc-fin 26.7 40 0.00086 26.8 1.5 53 32-85 5-71 (105)
78 cd03024 DsbA_FrnE DsbA family, 26.4 39 0.00085 27.0 1.4 11 74-84 5-15 (201)
79 smart00531 TFIIE Transcription 25.8 31 0.00067 28.2 0.8 15 71-85 119-133 (147)
80 PLN02638 cellulose synthase A 25.7 55 0.0012 35.8 2.8 47 31-82 14-66 (1079)
81 cd00350 rubredoxin_like Rubred 25.3 55 0.0012 20.8 1.7 23 63-85 4-27 (33)
82 smart00109 C1 Protein kinase C 25.0 25 0.00055 22.2 0.1 32 33-66 10-44 (49)
83 TIGR00310 ZPR1_znf ZPR1 zinc f 24.4 33 0.00071 30.1 0.7 40 36-86 2-41 (192)
84 PF03107 C1_2: C1 domain; Int 24.0 71 0.0015 19.9 2.0 27 36-64 2-30 (30)
85 PF13248 zf-ribbon_3: zinc-rib 23.4 48 0.001 20.2 1.1 21 62-83 4-24 (26)
86 COG1310 Predicted metal-depend 23.2 47 0.001 26.1 1.3 19 182-200 60-80 (134)
87 KOG2114 Vacuolar assembly/sort 23.0 76 0.0016 34.3 3.1 58 30-96 836-894 (933)
88 PRK00420 hypothetical protein; 23.0 1.1E+02 0.0024 25.1 3.4 26 68-93 32-58 (112)
89 PF14260 zf-C4pol: C4-type zin 23.0 2.2E+02 0.0049 20.2 4.7 44 63-107 1-44 (73)
90 PF12760 Zn_Tnp_IS1595: Transp 20.9 44 0.00096 22.5 0.7 12 72-84 16-27 (46)
91 PF12171 zf-C2H2_jaz: Zinc-fin 20.9 40 0.00087 20.0 0.4 10 75-84 1-10 (27)
92 COG1634 Uncharacterized Rossma 20.5 56 0.0012 30.1 1.4 38 186-225 110-147 (232)
93 TIGR00570 cdk7 CDK-activating 20.2 82 0.0018 29.9 2.5 42 34-83 3-51 (309)
94 COG1645 Uncharacterized Zn-fin 20.1 42 0.00092 28.4 0.5 17 68-84 37-53 (131)
No 1
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.45 E-value=4.8e-08 Score=96.50 Aligned_cols=50 Identities=32% Similarity=0.633 Sum_probs=44.2
Q ss_pred CccceecCCCCCeE---EeeCCCCccccccccccCCC--CccCCCCCcccccchhchH
Q 044718 34 EEPCIKCNRRDENL---LVCSQSGCLISVHENCLSCG--VEFDDVGNFYRPYCWYKCE 86 (236)
Q Consensus 34 qD~CikC~kdGq~L---L~CSg~GCPlsvH~sCLgss--p~fDD~GnFYCPyC~YKka 86 (236)
+++|-.|++.|. . |+|+ +||.+||+.||.+| +.--|.|.||||.|.++--
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 789999999999 6 9999 89999999999976 3444999999999998843
No 2
>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 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=98.15 E-value=8.3e-07 Score=59.28 Aligned_cols=45 Identities=22% Similarity=0.580 Sum_probs=35.4
Q ss_pred cceecCC---CCCeEEeeCCCCccccccccccCCCCcc--CCCCCcccccchh
Q 044718 36 PCIKCNR---RDENLLVCSQSGCLISVHENCLSCGVEF--DDVGNFYRPYCWY 83 (236)
Q Consensus 36 ~CikC~k---dGq~LL~CSg~GCPlsvH~sCLgssp~f--DD~GnFYCPyC~Y 83 (236)
.|.+|+. +++ +|.|+ +|...||..|++.+... ...+.|+||.|.-
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 3677777 455 99999 99999999999976542 2456999999963
No 4
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=97.68 E-value=1.4e-05 Score=80.24 Aligned_cols=52 Identities=35% Similarity=0.652 Sum_probs=46.7
Q ss_pred CCCCCccceecCCCCCeEEeeCCCCccccccccccCCCCccCCCCCcccccchhc
Q 044718 30 DLLEEEPCIKCNRRDENLLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYCWYK 84 (236)
Q Consensus 30 e~~~qD~CikC~kdGq~LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~YK 84 (236)
++-+++.|..|...|. ||+|+ .||.+||.+|++.+..=.+.|+|.||.|...
T Consensus 43 ~~~~~e~c~ic~~~g~-~l~c~--tC~~s~h~~cl~~pl~~~p~~~~~c~Rc~~p 94 (696)
T KOG0383|consen 43 DDAEQEACRICADGGE-LLWCD--TCPASFHASCLGPPLTPQPNGEFICPRCFCP 94 (696)
T ss_pred chhhhhhhhhhcCCCc-EEEec--cccHHHHHHccCCCCCcCCccceeeeeeccC
Confidence 3568999999999999 99999 9999999999998877778899999999554
No 5
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=97.63 E-value=3.7e-05 Score=68.54 Aligned_cols=56 Identities=25% Similarity=0.434 Sum_probs=43.5
Q ss_pred CCCCCCCCCcccee-cCCCCCeEEeeCCCCcc-ccccccccCCCCccCCCCCcccccchhc
Q 044718 26 FMDVDLLEEEPCIK-CNRRDENLLVCSQSGCL-ISVHENCLSCGVEFDDVGNFYRPYCWYK 84 (236)
Q Consensus 26 ~~~~e~~~qD~Cik-C~kdGq~LL~CSg~GCP-lsvH~sCLgssp~fDD~GnFYCPyC~YK 84 (236)
....+..+...|+= |..-|+ ..-|+..+|| ==||..|+| +...|.|.||||.|.-.
T Consensus 211 ~~~~d~~e~~yC~Cnqvsyg~-Mi~CDn~~C~~eWFH~~CVG--L~~~PkgkWyC~~C~~~ 268 (274)
T KOG1973|consen 211 EEAVDPDEPTYCICNQVSYGK-MIGCDNPGCPIEWFHFTCVG--LKTKPKGKWYCPRCKAE 268 (274)
T ss_pred ccccCCCCCEEEEeccccccc-ccccCCCCCCcceEEEeccc--cccCCCCcccchhhhhh
Confidence 34444556666664 455566 9999999999 668999999 78899999999999744
No 6
>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=97.50 E-value=1.7e-05 Score=66.99 Aligned_cols=61 Identities=11% Similarity=0.144 Sum_probs=41.9
Q ss_pred cccccccCCCCccCCCCCcccccchhchHHHHHHHHHHHHHHHHHHHHhhhccCcccchhhhh
Q 044718 58 SVHENCLSCGVEFDDVGNFYRPYCWYKCELMRTKELRKKAMETKKKLACFIDSKSFSGDKKKE 120 (236)
Q Consensus 58 svH~sCLgssp~fDD~GnFYCPyC~YKkav~~y~eaKKkA~~AKKeLssFL~s~qv~gd~~k~ 120 (236)
+||..||.++++-.|+|+|+||.|..++....+...... .+|.+-..||...+.-+.+++-
T Consensus 1 g~H~~CL~Ppl~~~P~g~W~Cp~C~~~~~~~~~~~~~~~--~~~~~~~~~l~~~~~vArIeki 61 (148)
T cd04718 1 GFHLCCLRPPLKEVPEGDWICPFCEVEKSGQSAMPQLPP--TSRSACEKLLSGDLWLARIEKL 61 (148)
T ss_pred CcccccCCCCCCCCCCCCcCCCCCcCCCCCCcccccCCC--cchhhhhhhccCchHHHHHHHH
Confidence 589999999999899999999999988666555432211 2233445566666655555543
No 7
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=97.24 E-value=0.00011 Score=72.80 Aligned_cols=48 Identities=29% Similarity=0.766 Sum_probs=42.8
Q ss_pred CCccceecCCCCCe----EEeeCCCCccccccccccCCCCccCCCCCcccccchhc
Q 044718 33 EEEPCIKCNRRDEN----LLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYCWYK 84 (236)
Q Consensus 33 ~qD~CikC~kdGq~----LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~YK 84 (236)
=.++|.+|.....+ +++|+ ||.++||.+|-| -+|-|+|.|+|-.|-|.
T Consensus 192 ~d~~C~~c~~t~~eN~naiVfCd--gC~i~VHq~CYG--I~f~peG~WlCrkCi~~ 243 (669)
T COG5141 192 FDDICTKCTSTHNENSNAIVFCD--GCEICVHQSCYG--IQFLPEGFWLCRKCIYG 243 (669)
T ss_pred hhhhhHhccccccCCcceEEEec--Ccchhhhhhccc--ceecCcchhhhhhhccc
Confidence 35799999887652 99999 999999999999 78999999999999886
No 8
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=97.13 E-value=0.00028 Score=73.95 Aligned_cols=68 Identities=21% Similarity=0.423 Sum_probs=53.3
Q ss_pred ccccccccCCCCCCCCCCCCCCCCccceecCCCCC----eEEeeCCCCccccccccccCCCCccCCCCCcccccchhchH
Q 044718 11 GIHIENHSGSGRSGDFMDVDLLEEEPCIKCNRRDE----NLLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYCWYKCE 86 (236)
Q Consensus 11 ~~~i~n~s~~g~S~~~~~~e~~~qD~CikC~kdGq----~LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~YKka 86 (236)
-+.|+|+.-....+ .+......|-.|...-- -+|+|+ +|-++||..|.| .+|.++|.|+|--|-++.+
T Consensus 200 e~~f~~~e~~~~~~----~~~~~D~~C~iC~~~~~~n~n~ivfCD--~Cnl~VHq~Cyg--i~~ipeg~WlCr~Cl~s~~ 271 (1051)
T KOG0955|consen 200 ESYFKNYELGDPKD----ALLEEDAVCCICLDGECQNSNVIVFCD--GCNLAVHQECYG--IPFIPEGQWLCRRCLQSPQ 271 (1051)
T ss_pred HHHhhhhhccCCCc----cccCCCccceeecccccCCCceEEEcC--CCcchhhhhccC--CCCCCCCcEeehhhccCcC
Confidence 34556665555554 44557788999986543 299999 999999999999 7899999999999998754
No 9
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.72 E-value=0.0019 Score=67.14 Aligned_cols=56 Identities=27% Similarity=0.458 Sum_probs=46.1
Q ss_pred CCCCCCCCccceecCCCCCe--EEeeCCCCcccc-ccccccCCCCccCCCCCcccccchhc
Q 044718 27 MDVDLLEEEPCIKCNRRDEN--LLVCSQSGCLIS-VHENCLSCGVEFDDVGNFYRPYCWYK 84 (236)
Q Consensus 27 ~~~e~~~qD~CikC~kdGq~--LL~CSg~GCPls-vH~sCLgssp~fDD~GnFYCPyC~YK 84 (236)
......+..-|..|....-+ ||.|+ +|..+ ||..||...+.--+.+-|||+-|..-
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 34445677789999998875 99999 99999 99999996554468999999999854
No 10
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=96.56 E-value=0.0012 Score=61.79 Aligned_cols=46 Identities=28% Similarity=0.511 Sum_probs=38.7
Q ss_pred CccceecC---CCCCeEEeeCCCCccccccccccCCCCccCCCCCcccccch
Q 044718 34 EEPCIKCN---RRDENLLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYCW 82 (236)
Q Consensus 34 qD~CikC~---kdGq~LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~ 82 (236)
...|-.|+ .++| ||+|+ .|-..||..||.+|..--|+|-|-|-.|-
T Consensus 281 ck~csicgtsenddq-llfcd--dcdrgyhmyclsppm~eppegswsc~KOG 329 (336)
T KOG1244|consen 281 CKYCSICGTSENDDQ-LLFCD--DCDRGYHMYCLSPPMVEPPEGSWSCHLCL 329 (336)
T ss_pred cceeccccCcCCCce-eEeec--ccCCceeeEecCCCcCCCCCCchhHHHHH
Confidence 34455554 4567 99999 99999999999998888899999999995
No 11
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=96.43 E-value=0.00092 Score=44.20 Aligned_cols=32 Identities=28% Similarity=0.699 Sum_probs=17.9
Q ss_pred EEeeCCCCccccccccccCCCCccCCCCCcccccc
Q 044718 47 LLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYC 81 (236)
Q Consensus 47 LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC 81 (236)
||.|+ +|.++||.+|-|.... .+..+|+|-.|
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 9999999999997543 34446999877
No 12
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=96.11 E-value=0.003 Score=58.15 Aligned_cols=46 Identities=26% Similarity=0.672 Sum_probs=37.9
Q ss_pred CCccceecCC--CCCeEEeeCCCCcccc-ccccccCCCCccCCCCCcccccch
Q 044718 33 EEEPCIKCNR--RDENLLVCSQSGCLIS-VHENCLSCGVEFDDVGNFYRPYCW 82 (236)
Q Consensus 33 ~qD~CikC~k--dGq~LL~CSg~GCPls-vH~sCLgssp~fDD~GnFYCPyC~ 82 (236)
++-.| .|.. =|| .+-||+..|++- ||..|+| +.--|.|.||||-|.
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 4664 377 899999999997 6999999 677799999999996
No 13
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=95.13 E-value=0.011 Score=60.92 Aligned_cols=62 Identities=21% Similarity=0.494 Sum_probs=44.4
Q ss_pred cceecCCCCC----eEEeeCCCCccccccccccCCCCccCCCCCcccccchhchHHHHHHHHHHHHHHHHHHHHhhhc
Q 044718 36 PCIKCNRRDE----NLLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYCWYKCELMRTKELRKKAMETKKKLACFID 109 (236)
Q Consensus 36 ~CikC~kdGq----~LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~YKkav~~y~eaKKkA~~AKKeLssFL~ 109 (236)
-|.+|.-.-- -|+.|||-.|.++||.-|-+ ----|.|-|||-.|.- ++.++.-|=+|.=|-|
T Consensus 7 GCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYG--IvqVPtGpWfCrKCes----------qeraarvrCeLCP~kd 72 (900)
T KOG0956|consen 7 GCCVCSDERGWAENPLVYCDGHNCSVAVHQACYG--IVQVPTGPWFCRKCES----------QERAARVRCELCPHKD 72 (900)
T ss_pred ceeeecCcCCCccCceeeecCCCceeeeehhcce--eEecCCCchhhhhhhh----------hhhhccceeecccCcc
Confidence 5777754322 29999999999999999999 3446899999999963 3444444555554433
No 14
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=95.01 E-value=0.0062 Score=65.64 Aligned_cols=57 Identities=23% Similarity=0.527 Sum_probs=49.4
Q ss_pred CCCCCCCCCccceecCCCCC--eEEeeCCCCccccccccccCCCCccCCCCCcccccchhchH
Q 044718 26 FMDVDLLEEEPCIKCNRRDE--NLLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYCWYKCE 86 (236)
Q Consensus 26 ~~~~e~~~qD~CikC~kdGq--~LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~YKka 86 (236)
|.+.. .+-.|-.|...++ .++.|+ +|.-.+|..|+.+.+...+.|+|+||-|.-.+-
T Consensus 1102 w~~s~--~~~~c~~cr~k~~~~~m~lc~--~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1102 WDRSA--VNALCKVCRRKKQDEKMLLCD--ECLSGFHLFCLRPALSSVPPGDWMCPSCRKEHR 1160 (1404)
T ss_pred hcccc--chhhhhhhhhcccchhhhhhH--hhhhhHHHHhhhhhhccCCcCCccCCccchhhh
Confidence 65555 7889999998887 489999 999999999999988889999999999985443
No 15
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=94.98 E-value=0.015 Score=58.35 Aligned_cols=67 Identities=21% Similarity=0.347 Sum_probs=56.4
Q ss_pred ccccccCCCCCCCCCCCCCCCCccceecCCCCC--eEEeeCCCCccccccccccCCCCccCCCCC----cccccc
Q 044718 13 HIENHSGSGRSGDFMDVDLLEEEPCIKCNRRDE--NLLVCSQSGCLISVHENCLSCGVEFDDVGN----FYRPYC 81 (236)
Q Consensus 13 ~i~n~s~~g~S~~~~~~e~~~qD~CikC~kdGq--~LL~CSg~GCPlsvH~sCLgssp~fDD~Gn----FYCPyC 81 (236)
-+.|+..+..|++-.+...-....|..|.+.-+ -|+.|+ .|-+.||--||.+|++--|.-+ |-|..|
T Consensus 523 ~~~~rk~g~~st~~~s~~~a~~ysCgiCkks~dQHll~~CD--tC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsEC 595 (707)
T KOG0957|consen 523 DFNNRKSGSRSTPAISAPKAMNYSCGICKKSTDQHLLTQCD--TCHLHYHLGCLSPPLTRLPKKNKNFGWQCSEC 595 (707)
T ss_pred ccccccccccCCcccccccccceeeeeeccchhhHHHhhcc--hhhceeeccccCCccccCcccccCcceeeccc
Confidence 466777777777777777778899999999876 388999 9999999999998887777766 999999
No 16
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=94.08 E-value=0.026 Score=57.43 Aligned_cols=50 Identities=20% Similarity=0.383 Sum_probs=42.4
Q ss_pred CCCccceecCCCCC--eEEeeCCCCccccccccccCCCCccCCCCCcccccchh
Q 044718 32 LEEEPCIKCNRRDE--NLLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYCWY 83 (236)
Q Consensus 32 ~~qD~CikC~kdGq--~LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~Y 83 (236)
.....|..|+..|+ ++|+|+ +|-++||-.|+-++..--+.|-|+||.|.-
T Consensus 66 ~~crvCe~c~~~gD~~kf~~Ck--~cDvsyh~yc~~P~~~~v~sg~~~ckk~~~ 117 (694)
T KOG4443|consen 66 PSCRVCEACGTTGDPKKFLLCK--RCDVSYHCYCQKPPNDKVPSGPWLCKKCTR 117 (694)
T ss_pred CCceeeeeccccCCcccccccc--cccccccccccCCccccccCcccccHHHHh
Confidence 34567777776666 599999 999999999999887778999999999974
No 17
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=93.51 E-value=0.037 Score=52.53 Aligned_cols=47 Identities=21% Similarity=0.316 Sum_probs=40.7
Q ss_pred CCCccceecCCCCC--eEEeeCCCCccccccccccCCCCccCCCCCcccc-cch
Q 044718 32 LEEEPCIKCNRRDE--NLLVCSQSGCLISVHENCLSCGVEFDDVGNFYRP-YCW 82 (236)
Q Consensus 32 ~~qD~CikC~kdGq--~LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCP-yC~ 82 (236)
.+..+|+.|+++-. +.|+|+ -|-.++|.-|+| +.-.|.|.|.|- ||.
T Consensus 312 ~~C~lC~IC~~P~~E~E~~FCD--~CDRG~HT~CVG--L~~lP~G~WICD~~C~ 361 (381)
T KOG1512|consen 312 SSCELCRICLGPVIESEHLFCD--VCDRGPHTLCVG--LQDLPRGEWICDMRCR 361 (381)
T ss_pred cccHhhhccCCcccchheeccc--cccCCCCccccc--cccccCccchhhhHHH
Confidence 35678999998876 499999 999999999999 777899999997 665
No 18
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=93.04 E-value=0.051 Score=56.37 Aligned_cols=48 Identities=23% Similarity=0.507 Sum_probs=41.4
Q ss_pred CCccceecCCC----CCeEEeeCCCCccccccccccCCCCccCCCCCcccccchhc
Q 044718 33 EEEPCIKCNRR----DENLLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYCWYK 84 (236)
Q Consensus 33 ~qD~CikC~kd----Gq~LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~YK 84 (236)
+.-+|-+|-.+ +.++++|+ -|.+.||..|-| ..-+|+|-|.|--|+.-
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 67788888887 55699999 999999999999 56678999999988753
No 19
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=92.55 E-value=0.058 Score=39.38 Aligned_cols=48 Identities=29% Similarity=0.636 Sum_probs=36.7
Q ss_pred CccceecCCC-CCeEEeeCCCCccccccccccCCCC---ccCCCCCcccccch
Q 044718 34 EEPCIKCNRR-DENLLVCSQSGCLISVHENCLSCGV---EFDDVGNFYRPYCW 82 (236)
Q Consensus 34 qD~CikC~kd-Gq~LL~CSg~GCPlsvH~sCLgssp---~fDD~GnFYCPyC~ 82 (236)
...|..|++. |- .+.|...+|..+||..|.-... .+++...+|..||.
T Consensus 36 ~~~C~~C~~~~Ga-~i~C~~~~C~~~fH~~CA~~~~~~~~~~~~~~~~~~~C~ 87 (90)
T PF13771_consen 36 KLKCSICKKKGGA-CIGCSHPGCSRSFHVPCARKAGCFIEFDEDNGKFRIFCP 87 (90)
T ss_pred CCCCcCCCCCCCe-EEEEeCCCCCcEEChHHHccCCeEEEEccCCCceEEECh
Confidence 4689999999 88 9999999999999999987532 23333345666653
No 20
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=91.56 E-value=0.086 Score=51.73 Aligned_cols=67 Identities=18% Similarity=0.297 Sum_probs=48.6
Q ss_pred CCCCCCCCCCccceecCCC--CC--eEEeeCCCCccccccccccCCCCc----cCCCCCcccccchhchHHHHHHHHH
Q 044718 25 DFMDVDLLEEEPCIKCNRR--DE--NLLVCSQSGCLISVHENCLSCGVE----FDDVGNFYRPYCWYKCELMRTKELR 94 (236)
Q Consensus 25 ~~~~~e~~~qD~CikC~kd--Gq--~LL~CSg~GCPlsvH~sCLgssp~----fDD~GnFYCPyC~YKkav~~y~eaK 94 (236)
+|..-...+.. |..|.-. |. ++|.|+ +|---||.-|.-+..+ =|+...|||-.|-+.........++
T Consensus 160 ~wD~~~~~n~q-c~vC~~g~~~~~NrmlqC~--~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~~~~r~t~~ 234 (464)
T KOG4323|consen 160 DWDSGHKVNLQ-CSVCYCGGPGAGNRMLQCD--KCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPKKVPRLTLR 234 (464)
T ss_pred ccCccccccce-eeeeecCCcCccceeeeec--ccccHHHHHhccCCCCHhhccCccceEeehhhccchhhccccccc
Confidence 34444444444 8888733 32 599999 9999999999985322 2478899999999998777766665
No 21
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=91.38 E-value=0.078 Score=57.18 Aligned_cols=64 Identities=14% Similarity=-0.012 Sum_probs=52.6
Q ss_pred CCCCCCCCCCCCCCCccceecCCCCCeEEeeCCCCccccccc-cccC--CCCccCCCCCcccccchhch
Q 044718 20 SGRSGDFMDVDLLEEEPCIKCNRRDENLLVCSQSGCLISVHE-NCLS--CGVEFDDVGNFYRPYCWYKC 85 (236)
Q Consensus 20 ~g~S~~~~~~e~~~qD~CikC~kdGq~LL~CSg~GCPlsvH~-sCLg--ssp~fDD~GnFYCPyC~YKk 85 (236)
.+..|-....=|+..+-|+.|++++. +|+|. +.||..||. .||+ .--.+...|=|+||.|...+
T Consensus 414 ~iG~dr~gr~ywfi~rrl~Ie~~det-~l~yy-sT~pqly~ll~cLd~~~~e~~L~d~i~~~~ee~~rq 480 (1414)
T KOG1473|consen 414 PIGRDRYGRKYWFISRRLRIEGMDET-LLWYY-STCPQLYHLLRCLDRTYVEMYLCDGIWERREEIIRQ 480 (1414)
T ss_pred CCCcCccccchhceeeeeEEecCCCc-EEEEe-cCcHHHHHHHHHhchHHHHHhhccchhhhHHHHHHh
Confidence 34445577788999999999999999 88888 449999999 9999 33345589999999999774
No 22
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=90.77 E-value=0.12 Score=45.28 Aligned_cols=44 Identities=27% Similarity=0.615 Sum_probs=32.1
Q ss_pred cceecCC------CCCeEEeeCCCCccccccccccCCCCccC------CCCCcc--cccch
Q 044718 36 PCIKCNR------RDENLLVCSQSGCLISVHENCLSCGVEFD------DVGNFY--RPYCW 82 (236)
Q Consensus 36 ~CikC~k------dGq~LL~CSg~GCPlsvH~sCLgssp~fD------D~GnFY--CPyC~ 82 (236)
.|-.|+. .|. |+.|- ||.++||..|||....=+ ..++|- |-+|.
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 3777853 455 99999 999999999999643322 556663 77775
No 23
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=87.88 E-value=0.36 Score=52.42 Aligned_cols=54 Identities=19% Similarity=0.307 Sum_probs=46.2
Q ss_pred CCCCCCCCccceecCCCCCeEEeeCCCCccccccccccCCCCccCCCCCcccccchh
Q 044718 27 MDVDLLEEEPCIKCNRRDENLLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYCWY 83 (236)
Q Consensus 27 ~~~e~~~qD~CikC~kdGq~LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~Y 83 (236)
+.....-.|.|..|...|+ ||||- .||..||-+|.-.+..--++..|-|-.|.+
T Consensus 337 se~~~~~ddhcrf~~d~~~-~lc~E--t~prvvhlEcv~hP~~~~~s~~~e~evc~~ 390 (1414)
T KOG1473|consen 337 SEGEIEYDDHCRFCHDLGD-LLCCE--TCPRVVHLECVFHPRFAVPSAFWECEVCNI 390 (1414)
T ss_pred cccceeecccccccCcccc-eeecc--cCCceEEeeecCCccccCCCccchhhhhhh
Confidence 3445567789999999999 99999 999999999999766656899999999884
No 24
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=84.20 E-value=0.62 Score=35.34 Aligned_cols=33 Identities=24% Similarity=0.615 Sum_probs=28.7
Q ss_pred CCccceecCCC-CCeEEeeCCCCccccccccccCC
Q 044718 33 EEEPCIKCNRR-DENLLVCSQSGCLISVHENCLSC 66 (236)
Q Consensus 33 ~qD~CikC~kd-Gq~LL~CSg~GCPlsvH~sCLgs 66 (236)
-...|..|+.. |- ++.|+..+|..+||..|...
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 35789999996 55 99999999999999999864
No 25
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=82.81 E-value=0.64 Score=48.54 Aligned_cols=51 Identities=31% Similarity=0.757 Sum_probs=41.5
Q ss_pred CccceecCCCCCe-------EEeeCCCCccccccccccCC-CCccCCCCC-----cccccchhc
Q 044718 34 EEPCIKCNRRDEN-------LLVCSQSGCLISVHENCLSC-GVEFDDVGN-----FYRPYCWYK 84 (236)
Q Consensus 34 qD~CikC~kdGq~-------LL~CSg~GCPlsvH~sCLgs-sp~fDD~Gn-----FYCPyC~YK 84 (236)
...|+.|+..|.. -+.|...+|--+||..|.-+ .+-++++|+ -||-||.|-
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 4579999998773 78999999999999999865 355566666 499999885
No 26
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=75.77 E-value=1.8 Score=44.17 Aligned_cols=48 Identities=27% Similarity=0.535 Sum_probs=35.6
Q ss_pred CccceecCCC-----CCeEEeeCCCCccccccccccCCC-----CccCCC---CCcccccchhc
Q 044718 34 EEPCIKCNRR-----DENLLVCSQSGCLISVHENCLSCG-----VEFDDV---GNFYRPYCWYK 84 (236)
Q Consensus 34 qD~CikC~kd-----Gq~LL~CSg~GCPlsvH~sCLgss-----p~fDD~---GnFYCPyC~YK 84 (236)
-++|-+|-.. |+ +|.|+ .|-+.||..|-|+. +.--.. .-|||--|.|-
T Consensus 119 ~~iCcVClg~rs~da~e-i~qCd--~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~G 179 (707)
T KOG0957|consen 119 AVICCVCLGQRSVDAGE-ILQCD--KCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLYG 179 (707)
T ss_pred ceEEEEeecCccccccc-eeecc--ccCceecccccccccccccCCCCccCCCCchhhhhHhcC
Confidence 3589999643 34 99999 99999999999964 222222 56999888765
No 27
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=74.89 E-value=2.1 Score=43.75 Aligned_cols=45 Identities=22% Similarity=0.332 Sum_probs=36.8
Q ss_pred CccceecCCCCCeEEeeCCCCccccccccccCCCCccCCCCCcccccchh
Q 044718 34 EEPCIKCNRRDENLLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYCWY 83 (236)
Q Consensus 34 qD~CikC~kdGq~LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~Y 83 (236)
-+.|-.|...|. +|+|+ .||.++|..|-+.. +.++-.++|--|..
T Consensus 47 ~ts~~~~~~~gn-~~~~~--~~~~s~h~~~~~~~--~sp~~~~~~~~~~~ 91 (613)
T KOG4299|consen 47 ATSCGICKSGGN-LLCCD--HCPASFHLECDKPP--LSPDLKGSEINCSR 91 (613)
T ss_pred hhhcchhhhcCC-ccccc--cCccccchhccCcc--cCcccccccccccC
Confidence 689999999999 99999 99999999999954 44666666665553
No 28
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=71.52 E-value=2.6 Score=41.05 Aligned_cols=37 Identities=22% Similarity=0.501 Sum_probs=32.0
Q ss_pred CCCCCCccceecCCCCCeEEeeC------CCCccccccccccCC
Q 044718 29 VDLLEEEPCIKCNRRDENLLVCS------QSGCLISVHENCLSC 66 (236)
Q Consensus 29 ~e~~~qD~CikC~kdGq~LL~CS------g~GCPlsvH~sCLgs 66 (236)
..-.+.+.|.+|..+|. |+.|+ -.+||.++|.+|...
T Consensus 84 ~~~~~~~~c~vc~~ggs-~v~~~s~~~~~~r~c~~~~~~~c~~~ 126 (463)
T KOG1081|consen 84 HPKIEPSECFVCFKGGS-LVTCKSRIQAPHRKCKPAQLEKCSKR 126 (463)
T ss_pred ccCCCcchhccccCCCc-cceeccccccccccCcCccCcccccC
Confidence 34456789999999999 99999 899999999999886
No 29
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=69.87 E-value=4.1 Score=41.47 Aligned_cols=47 Identities=26% Similarity=0.383 Sum_probs=38.2
Q ss_pred CCccceecCCCCCeEEeeCCCCccccccccccCCCCccC-CCCCcccccch
Q 044718 33 EEEPCIKCNRRDENLLVCSQSGCLISVHENCLSCGVEFD-DVGNFYRPYCW 82 (236)
Q Consensus 33 ~qD~CikC~kdGq~LL~CSg~GCPlsvH~sCLgssp~fD-D~GnFYCPyC~ 82 (236)
..-.|..|..+|. +|+|+ .|-.++|..|+...+..- -+--|-||.|.
T Consensus 59 ~d~~cfechlpg~-vl~c~--vc~Rs~h~~c~sp~~q~r~~s~p~~~p~p~ 106 (588)
T KOG3612|consen 59 IDPFCFECHLPGA-VLKCI--VCHRSFHENCQSPDPQKRNYSVPSDKPQPY 106 (588)
T ss_pred CCcccccccCCcc-eeeee--hhhccccccccCcchhhccccccccCCccc
Confidence 4558999999999 99999 999999999999644433 34567888886
No 30
>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=67.10 E-value=1.4 Score=29.97 Aligned_cols=31 Identities=29% Similarity=0.694 Sum_probs=16.0
Q ss_pred eeCCCCccccccccccCCCCccCCCCCcccccc
Q 044718 49 VCSQSGCLISVHENCLSCGVEFDDVGNFYRPYC 81 (236)
Q Consensus 49 ~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC 81 (236)
.|+..+|++.+|..|+. --|-...+--||-|
T Consensus 13 ~C~~~~C~~r~H~~C~~--~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 13 RCSNRDCNVRLHDDCFK--KYFRHRSNPKCPNC 43 (43)
T ss_dssp E-SS--S--EE-HHHHH--HHTTT-SS-B-TTT
T ss_pred cCCCCccCchHHHHHHH--HHHhcCCCCCCcCC
Confidence 89988999999999998 33333333378876
No 31
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=64.43 E-value=2.8 Score=36.53 Aligned_cols=58 Identities=17% Similarity=0.175 Sum_probs=40.8
Q ss_pred CCCCCCccceecCCCCCe-EEeeCCCCccccccccccCCCCccCCCCCcccccchhchHHH
Q 044718 29 VDLLEEEPCIKCNRRDEN-LLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYCWYKCELM 88 (236)
Q Consensus 29 ~e~~~qD~CikC~kdGq~-LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~YKkav~ 88 (236)
+-+.....|+.|..+++. .-.|.=.|=.-.+|.+||. -=.+.+|+-.||.|-++-.+.
T Consensus 3 ~~s~~~~~CRIC~~~~~~~~~PC~CkGs~k~VH~sCL~--rWi~~s~~~~CeiC~~~Y~i~ 61 (162)
T PHA02825 3 DVSLMDKCCWICKDEYDVVTNYCNCKNENKIVHKECLE--EWINTSKNKSCKICNGPYNIK 61 (162)
T ss_pred CcCCCCCeeEecCCCCCCccCCcccCCCchHHHHHHHH--HHHhcCCCCcccccCCeEEEE
Confidence 334567899999888752 2344433556688999998 345568999999998875544
No 32
>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=61.41 E-value=2.6 Score=29.20 Aligned_cols=44 Identities=27% Similarity=0.548 Sum_probs=27.9
Q ss_pred cceecCC---CCCe-EEeeCCCCccccccccccCCCCccCCCCCcccccc
Q 044718 36 PCIKCNR---RDEN-LLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYC 81 (236)
Q Consensus 36 ~CikC~k---dGq~-LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC 81 (236)
.|+.|.. +++. ++.|.=.|-.--||.+||. .=+...++-.||.|
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~--~W~~~~~~~~C~iC 48 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLE--RWINESGNKTCEIC 48 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhHHHHHHHH--HHHHHcCCCcCCCC
Confidence 4777775 3332 4455523334679999998 34445667799988
No 33
>PHA02862 5L protein; Provisional
Probab=58.79 E-value=3 Score=36.27 Aligned_cols=52 Identities=17% Similarity=0.243 Sum_probs=39.5
Q ss_pred CccceecCCCCCe-EEeeCCCCccccccccccCCCCccCCCCCcccccchhchHH
Q 044718 34 EEPCIKCNRRDEN-LLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYCWYKCEL 87 (236)
Q Consensus 34 qD~CikC~kdGq~-LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~YKkav 87 (236)
.+.|+.|...++. +=.|-=.|-.--+|.+||.- =+..++.-+||.|.++-.+
T Consensus 2 ~diCWIC~~~~~e~~~PC~C~GS~K~VHq~CL~~--WIn~S~k~~CeLCkteY~I 54 (156)
T PHA02862 2 SDICWICNDVCDERNNFCGCNEEYKVVHIKCMQL--WINYSKKKECNLCKTKYNI 54 (156)
T ss_pred CCEEEEecCcCCCCcccccccCcchhHHHHHHHH--HHhcCCCcCccCCCCeEEE
Confidence 4789999998874 44555446688899999884 3345889999999988654
No 34
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=56.18 E-value=13 Score=38.50 Aligned_cols=54 Identities=28% Similarity=0.573 Sum_probs=47.0
Q ss_pred CCCCCCccceecCCCCCe-EEeeCCCCccccccccccCCCCccCCCCCcccccchhc
Q 044718 29 VDLLEEEPCIKCNRRDEN-LLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYCWYK 84 (236)
Q Consensus 29 ~e~~~qD~CikC~kdGq~-LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~YK 84 (236)
........|..|.++... ++.|+ +|--++|..|+..+++.-+.|.|.||-|...
T Consensus 150 ~~~~~~~~~~~~~k~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 204 (904)
T KOG1246|consen 150 VEFIDYPQCNTCSKGKEEKLLLCD--SCDDSYHTYCLRPPLTRVPDGDWRCPKCIPT 204 (904)
T ss_pred cccccchhhhccccCCCccceecc--cccCcccccccCCCCCcCCcCcccCCccccc
Confidence 566678899999998853 44888 9999999999999999899999999999866
No 35
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=55.73 E-value=5.5 Score=29.22 Aligned_cols=51 Identities=27% Similarity=0.301 Sum_probs=19.2
Q ss_pred ccceecCCC----CC-eEEeeCCCCccccccccccCCC--------CccCCCCCcccccchhchH
Q 044718 35 EPCIKCNRR----DE-NLLVCSQSGCLISVHENCLSCG--------VEFDDVGNFYRPYCWYKCE 86 (236)
Q Consensus 35 D~CikC~kd----Gq-~LL~CSg~GCPlsvH~sCLgss--------p~fDD~GnFYCPyC~YKka 86 (236)
..|..|-.. ++ -.++|....|...+|..||..- ..|. .-..-||||.-+..
T Consensus 3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~-~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 3 LECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFI-PIFGECPYCSSPIS 66 (70)
T ss_dssp -S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT---EEE-TTT-SEEE
T ss_pred CCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeec-ccccCCcCCCCeee
Confidence 456667642 22 1589999999999999999731 1111 11234999975543
No 36
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=54.26 E-value=4.6 Score=34.69 Aligned_cols=53 Identities=30% Similarity=0.413 Sum_probs=40.7
Q ss_pred CccceecCCCCC------eEEeeCCCCccccccccccCCCCccCCCCCcccccchhchHHH
Q 044718 34 EEPCIKCNRRDE------NLLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYCWYKCELM 88 (236)
Q Consensus 34 qD~CikC~kdGq------~LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~YKkav~ 88 (236)
+..|+.|...+. -+..|+-.|=+.-+|..|+.. =+.-.|+..|..|+...+..
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~--W~~~~~~~~CeiC~~~~~~~ 136 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEK--WFSIKGNITCEICKSFFINV 136 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHh--hhccccCeeeecccccceec
Confidence 578999999664 156677667788899999994 44579999999999764443
No 37
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=52.38 E-value=5.4 Score=33.17 Aligned_cols=24 Identities=17% Similarity=0.297 Sum_probs=19.2
Q ss_pred CCccCCCCCcccccchhchHHHHH
Q 044718 67 GVEFDDVGNFYRPYCWYKCELMRT 90 (236)
Q Consensus 67 sp~fDD~GnFYCPyC~YKkav~~y 90 (236)
.-.|+|.+.|+||.||+.+.-.+.
T Consensus 12 EytYed~~~~~cpec~~ew~~~~~ 35 (112)
T COG2824 12 EYTYEDGGQLICPECAHEWNENEA 35 (112)
T ss_pred ceEEecCceEeCchhccccccccc
Confidence 346789999999999998875443
No 38
>PF11287 DUF3088: Protein of unknown function (DUF3088); InterPro: IPR021439 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=51.62 E-value=7.8 Score=32.02 Aligned_cols=35 Identities=20% Similarity=0.389 Sum_probs=20.8
Q ss_pred cccccchhchHH-HHHHHHHHHH-------HHHHHHHHhhhcc
Q 044718 76 FYRPYCWYKCEL-MRTKELRKKA-------METKKKLACFIDS 110 (236)
Q Consensus 76 FYCPyC~YKkav-~~y~eaKKkA-------~~AKKeLssFL~s 110 (236)
||||.|..-.-+ +.+-.++... ...|+++.+.++-
T Consensus 22 f~Cp~c~~iEGlLa~~P~l~~~ldV~rV~f~RPR~~vi~llGE 64 (112)
T PF11287_consen 22 FYCPHCAAIEGLLASFPDLRERLDVRRVDFPRPRQAVIALLGE 64 (112)
T ss_pred EECCchHHHHhHHhhChhhhhcccEEEeCCCCchHHHHHHhCh
Confidence 999999854322 2222333322 2567788888875
No 39
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=51.05 E-value=5.7 Score=41.07 Aligned_cols=52 Identities=17% Similarity=0.278 Sum_probs=47.3
Q ss_pred CCCCCccceecCCCCCeEEeeCCCCccccccccccCC-CCccCCCCCcccccchhc
Q 044718 30 DLLEEEPCIKCNRRDENLLVCSQSGCLISVHENCLSC-GVEFDDVGNFYRPYCWYK 84 (236)
Q Consensus 30 e~~~qD~CikC~kdGq~LL~CSg~GCPlsvH~sCLgs-sp~fDD~GnFYCPyC~YK 84 (236)
+.+.+..|-.|-+.++ +|.|. -|+..+|..||.. +++...-|.|-||-|+-+
T Consensus 502 e~~~d~~~~~~~~~l~-~l~~p--~~lrr~k~d~l~~~P~Kte~i~~~~~~~~Q~~ 554 (696)
T KOG0383|consen 502 EEFHDISCEEQIKKLH-LLLCP--HMLRRLKLDVLKPMPLKTELIGRVELSPCQKK 554 (696)
T ss_pred hhcchhhHHHHHHhhc-cccCc--hhhhhhhhhhccCCCccceeEEEEecCHHHHH
Confidence 4467789999999999 99999 9999999999998 889999999999999844
No 40
>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=50.87 E-value=6.2 Score=24.46 Aligned_cols=27 Identities=30% Similarity=0.789 Sum_probs=12.1
Q ss_pred cceecCCCCCe--EEeeCCCCcccccccccc
Q 044718 36 PCIKCNRRDEN--LLVCSQSGCLISVHENCL 64 (236)
Q Consensus 36 ~CikC~kdGq~--LL~CSg~GCPlsvH~sCL 64 (236)
.|-.|++.+.. ...|. .|-..+|.+|.
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 47778888873 88898 99999999884
No 41
>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=49.08 E-value=11 Score=25.21 Aligned_cols=34 Identities=26% Similarity=0.442 Sum_probs=24.5
Q ss_pred CCCccceecCCC-----CCeEEeeCCCCccccccccccCCCC
Q 044718 32 LEEEPCIKCNRR-----DENLLVCSQSGCLISVHENCLSCGV 68 (236)
Q Consensus 32 ~~qD~CikC~kd-----Gq~LL~CSg~GCPlsvH~sCLgssp 68 (236)
..-..|..|++. .+ =+.|. .|-+.+|.+|+..-+
T Consensus 9 ~~~~~C~~C~~~i~g~~~~-g~~C~--~C~~~~H~~C~~~~~ 47 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWGLGKQ-GYRCS--WCGLVCHKKCLSKVP 47 (53)
T ss_dssp SSTEB-TTSSSBECSSSSC-EEEET--TTT-EEETTGGCTSS
T ss_pred CCCCCCcccCcccCCCCCC-eEEEC--CCCChHhhhhhhhcC
Confidence 455678888754 34 68999 999999999998543
No 42
>cd08059 MPN_prok_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); prokaryotic. This family contains bacterial and archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These catalytically active domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=46.91 E-value=32 Score=25.54 Aligned_cols=22 Identities=36% Similarity=0.370 Sum_probs=16.9
Q ss_pred HHHHhhhCCCCce-eccCCCCCC
Q 044718 182 FKRALESQSDPLA-VHSHPGDKI 203 (236)
Q Consensus 182 ~~~~~~~~~~~~~-~~~~~~~~~ 203 (236)
|+.|++.....++ +||||.-.-
T Consensus 48 ~~~a~~~~~~~v~i~HsHP~g~~ 70 (101)
T cd08059 48 DLAALEIGMKVVGLVHSHPSGSC 70 (101)
T ss_pred HHHHhhCCCcEEEEEecCcCCCC
Confidence 8999998876654 799996533
No 43
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=46.55 E-value=11 Score=27.53 Aligned_cols=30 Identities=30% Similarity=0.837 Sum_probs=24.9
Q ss_pred CCccceecCCC----CCeEEeeCCCCccccccccccC
Q 044718 33 EEEPCIKCNRR----DENLLVCSQSGCLISVHENCLS 65 (236)
Q Consensus 33 ~qD~CikC~kd----Gq~LL~CSg~GCPlsvH~sCLg 65 (236)
..-.|..|++. ++ +++|- .|-..||..|-.
T Consensus 4 ~~~~C~~Cg~~~~~~dD-iVvCp--~CgapyHR~C~~ 37 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDD-IVVCP--ECGAPYHRDCWE 37 (54)
T ss_pred cCccChhhCCcccCCCC-EEECC--CCCCcccHHHHh
Confidence 34679999874 45 99999 999999999974
No 44
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=45.64 E-value=17 Score=31.43 Aligned_cols=39 Identities=26% Similarity=0.505 Sum_probs=28.9
Q ss_pred ccceecCCCCC-------eEEeeCCCCccccccccccCCCCccCCCCCcccccchhc
Q 044718 35 EPCIKCNRRDE-------NLLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYCWYK 84 (236)
Q Consensus 35 D~CikC~kdGq-------~LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~YK 84 (236)
.+|-.|+.++- ....|. .|-..+|.+|+.. --||.|.-.
T Consensus 153 fiCe~C~~~~~IfPF~~~~~~~C~--~C~~v~H~~C~~~---------~~CpkC~R~ 198 (202)
T PF13901_consen 153 FICEICNSDDIIFPFQIDTTVRCP--KCKSVFHKSCFRK---------KSCPKCARR 198 (202)
T ss_pred CCCccCCCCCCCCCCCCCCeeeCC--cCccccchhhcCC---------CCCCCcHhH
Confidence 46777776531 267899 9999999999993 129999743
No 45
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=45.10 E-value=5.5 Score=41.29 Aligned_cols=78 Identities=22% Similarity=0.284 Sum_probs=53.5
Q ss_pred CCCCCCCccceecCCCCC----eEEeeCCCCccccccccccCCCCcc-CCCCCcccccchhchHHHHHHHHHHHHHHHHH
Q 044718 28 DVDLLEEEPCIKCNRRDE----NLLVCSQSGCLISVHENCLSCGVEF-DDVGNFYRPYCWYKCELMRTKELRKKAMETKK 102 (236)
Q Consensus 28 ~~e~~~qD~CikC~kdGq----~LL~CSg~GCPlsvH~sCLgssp~f-DD~GnFYCPyC~YKkav~~y~eaKKkA~~AKK 102 (236)
.........|..|+..|+ +||.|+ .|-.-||..|+..-..- +=.+-|-||-|..-.+-. ....=++.+.-+.
T Consensus 12 ~~~~~~~~mc~l~~s~G~~~ag~m~ac~--~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~c~-~~gD~~kf~~Ck~ 88 (694)
T KOG4443|consen 12 DKAIIVCLMCPLCGSSGKGRAGRLLACS--DCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEACG-TTGDPKKFLLCKR 88 (694)
T ss_pred chhhhhhhhhhhhccccccccCcchhhh--hhcccCCcchhhHHHhHHHhcCCcccCCceeeeecc-ccCCccccccccc
Confidence 334456778999999888 399999 99999999999853221 224459999998654444 3333445555566
Q ss_pred HHHhhh
Q 044718 103 KLACFI 108 (236)
Q Consensus 103 eLssFL 108 (236)
-..+|-
T Consensus 89 cDvsyh 94 (694)
T KOG4443|consen 89 CDVSYH 94 (694)
T ss_pred cccccc
Confidence 666665
No 46
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=44.52 E-value=15 Score=35.11 Aligned_cols=56 Identities=21% Similarity=0.299 Sum_probs=34.3
Q ss_pred CCCCCCCCCccceecCCCCCeEEe--------eCCCCccccccccccCCCCccCCCCCcccccchhc
Q 044718 26 FMDVDLLEEEPCIKCNRRDENLLV--------CSQSGCLISVHENCLSCGVEFDDVGNFYRPYCWYK 84 (236)
Q Consensus 26 ~~~~e~~~qD~CikC~kdGq~LL~--------CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~YK 84 (236)
=.+.--++++.|.+|++.=+ .-. =-.-.|.-++|+-|+.- =.--.---.||||.-+
T Consensus 216 glPtkhl~d~vCaVCg~~~~-~s~~eegvienty~LsCnHvFHEfCIrG--WcivGKkqtCPYCKek 279 (328)
T KOG1734|consen 216 GLPTKHLSDSVCAVCGQQID-VSVDEEGVIENTYKLSCNHVFHEFCIRG--WCIVGKKQTCPYCKEK 279 (328)
T ss_pred CCCCCCCCcchhHhhcchhe-eecchhhhhhhheeeecccchHHHhhhh--heeecCCCCCchHHHH
Confidence 34556678899999987644 100 00014668999999872 1112334579999754
No 47
>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=43.81 E-value=16 Score=28.72 Aligned_cols=12 Identities=25% Similarity=0.780 Sum_probs=9.5
Q ss_pred CCcccccchhch
Q 044718 74 GNFYRPYCWYKC 85 (236)
Q Consensus 74 GnFYCPyC~YKk 85 (236)
.|+.||||+.-.
T Consensus 6 ~D~~Cp~cy~~~ 17 (193)
T PF01323_consen 6 FDFICPWCYLAS 17 (193)
T ss_dssp EBTTBHHHHHHH
T ss_pred EeCCCHHHHHHH
Confidence 478999999643
No 48
>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=42.67 E-value=8.4 Score=25.97 Aligned_cols=12 Identities=25% Similarity=0.437 Sum_probs=9.2
Q ss_pred CCcccccchhch
Q 044718 74 GNFYRPYCWYKC 85 (236)
Q Consensus 74 GnFYCPyC~YKk 85 (236)
.|+.||+|+.-.
T Consensus 5 ~d~~Cp~C~~~~ 16 (98)
T cd02972 5 FDPLCPYCYLFE 16 (98)
T ss_pred ECCCCHhHHhhh
Confidence 478999999543
No 49
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.01 E-value=17 Score=34.94 Aligned_cols=41 Identities=24% Similarity=0.586 Sum_probs=30.3
Q ss_pred ccceecCCC---CC--eEEeeCCCCccccccccccCCCCccCCCCCcccccchh
Q 044718 35 EPCIKCNRR---DE--NLLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYCWY 83 (236)
Q Consensus 35 D~CikC~kd---Gq--~LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~Y 83 (236)
+.|..|=.+ |+ ++|.|+ -.||..|+.+- +-.- .-+||.|.-
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~-----H~FH~~CIDpW--L~~~-r~~CPvCK~ 275 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCS-----HKFHVNCIDPW--LTQT-RTFCPVCKR 275 (348)
T ss_pred ceEEEeecccccCCeeeEecCC-----Cchhhccchhh--Hhhc-CccCCCCCC
Confidence 699999765 44 378888 89999999943 3233 557999974
No 50
>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=41.95 E-value=9.6 Score=29.64 Aligned_cols=20 Identities=15% Similarity=0.097 Sum_probs=14.6
Q ss_pred CCCccCCCCCcccccchhch
Q 044718 66 CGVEFDDVGNFYRPYCWYKC 85 (236)
Q Consensus 66 ssp~fDD~GnFYCPyC~YKk 85 (236)
.++.+..-.||.||+|+--.
T Consensus 15 ~~~~i~~f~D~~Cp~C~~~~ 34 (178)
T cd03019 15 GKPEVIEFFSYGCPHCYNFE 34 (178)
T ss_pred CCcEEEEEECCCCcchhhhh
Confidence 34556677899999998443
No 51
>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=40.53 E-value=80 Score=24.95 Aligned_cols=64 Identities=17% Similarity=0.290 Sum_probs=50.4
Q ss_pred cCCCCCeEEeeCCCCcccc-ccccccCCCCccCCCC--CcccccchhchHHHHHHHHHHHHHHHHHHHHhh
Q 044718 40 CNRRDENLLVCSQSGCLIS-VHENCLSCGVEFDDVG--NFYRPYCWYKCELMRTKELRKKAMETKKKLACF 107 (236)
Q Consensus 40 C~kdGq~LL~CSg~GCPls-vH~sCLgssp~fDD~G--nFYCPyC~YKkav~~y~eaKKkA~~AKKeLssF 107 (236)
|...||.=|.|= ||+- .-..|+|. ......| -|-|.-|.+...-+-|....++.++.-+++.+.
T Consensus 17 CH~~~qnClFCy---CPlY~c~d~~~G~-~~~~~~G~~vw~C~~C~~~H~~e~~~~i~~~~~~~~~~~k~~ 83 (86)
T PF04071_consen 17 CHFEGQNCLFCY---CPLYPCGDECGGN-FIYTKNGSKVWDCSDCTLPHRPENYDYIIRKLKEIIEELKKL 83 (86)
T ss_pred CcCCCCCcceEe---CCcccccCCCCcc-EEEcCCCCeeeECccCCCccCHHHHHHHHHHHHHHHHHHHHh
Confidence 447777778887 9997 46899974 3445677 999999999999888888888888777776654
No 52
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=39.68 E-value=8.1 Score=39.26 Aligned_cols=30 Identities=30% Similarity=0.533 Sum_probs=23.8
Q ss_pred EEeeCCCCccccccccccCCCCccCCCCCcccccchhch
Q 044718 47 LLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYCWYKC 85 (236)
Q Consensus 47 LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~YKk 85 (236)
.-.|+ .|-..||.+|+...... ||.|.+-+
T Consensus 531 ~~rC~--~C~avfH~~C~~r~s~~-------CPrC~R~q 560 (580)
T KOG1829|consen 531 TRRCS--TCLAVFHKKCLRRKSPC-------CPRCERRQ 560 (580)
T ss_pred ceeHH--HHHHHHHHHHHhccCCC-------CCchHHHH
Confidence 35788 99999999999965332 99998654
No 53
>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=39.28 E-value=11 Score=28.20 Aligned_cols=18 Identities=17% Similarity=0.239 Sum_probs=13.0
Q ss_pred CCccCCCCCcccccchhc
Q 044718 67 GVEFDDVGNFYRPYCWYK 84 (236)
Q Consensus 67 sp~fDD~GnFYCPyC~YK 84 (236)
++.+..-.||.||+|+--
T Consensus 6 ~~~i~~f~D~~Cp~C~~~ 23 (154)
T cd03023 6 DVTIVEFFDYNCGYCKKL 23 (154)
T ss_pred CEEEEEEECCCChhHHHh
Confidence 345556679999999843
No 54
>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=37.98 E-value=5.9 Score=30.24 Aligned_cols=17 Identities=18% Similarity=0.307 Sum_probs=12.4
Q ss_pred CCccCCCCCcccccchh
Q 044718 67 GVEFDDVGNFYRPYCWY 83 (236)
Q Consensus 67 sp~fDD~GnFYCPyC~Y 83 (236)
++.+..-.||+||+|.-
T Consensus 13 ~~~v~~f~d~~Cp~C~~ 29 (162)
T PF13462_consen 13 PITVTEFFDFQCPHCAK 29 (162)
T ss_dssp SEEEEEEE-TTSHHHHH
T ss_pred CeEEEEEECCCCHhHHH
Confidence 45566778999999985
No 55
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=37.86 E-value=10 Score=35.59 Aligned_cols=52 Identities=25% Similarity=0.284 Sum_probs=38.3
Q ss_pred CCccceecC-CCCCeEEeeCCCCccccccccccCCCCccCCCCCcc-----cccchhc
Q 044718 33 EEEPCIKCN-RRDENLLVCSQSGCLISVHENCLSCGVEFDDVGNFY-----RPYCWYK 84 (236)
Q Consensus 33 ~qD~CikC~-kdGq~LL~CSg~GCPlsvH~sCLgssp~fDD~GnFY-----CPyC~YK 84 (236)
...+|.++- ..+..++.|-..+|+.-.|..||.....-+..|+-+ ||.|.--
T Consensus 184 ~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~ 241 (276)
T KOG3005|consen 184 ECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKF 241 (276)
T ss_pred hhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhce
Confidence 456666665 455568999999999999999999744444555544 9999743
No 56
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=37.19 E-value=29 Score=30.98 Aligned_cols=28 Identities=21% Similarity=0.331 Sum_probs=16.1
Q ss_pred CCccceecCCC------------CCeEEeeCCCCcccccccc
Q 044718 33 EEEPCIKCNRR------------DENLLVCSQSGCLISVHEN 62 (236)
Q Consensus 33 ~qD~CikC~kd------------Gq~LL~CSg~GCPlsvH~s 62 (236)
+...|-+||.. |.+.|.|+ -|--.+|..
T Consensus 171 ~~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs--~C~t~W~~~ 210 (290)
T PF04216_consen 171 QRGYCPVCGSPPVLSVLRGGEREGKRYLHCS--LCGTEWRFV 210 (290)
T ss_dssp T-SS-TTT---EEEEEEE------EEEEEET--TT--EEE--
T ss_pred cCCcCCCCCCcCceEEEecCCCCccEEEEcC--CCCCeeeec
Confidence 45799999975 77899999 999999864
No 57
>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=35.09 E-value=8.5 Score=23.12 Aligned_cols=41 Identities=20% Similarity=0.340 Sum_probs=24.3
Q ss_pred ceecCCCCCeEEeeCCCCccccccccccCCCCccCCCCCcccccch
Q 044718 37 CIKCNRRDENLLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYCW 82 (236)
Q Consensus 37 CikC~kdGq~LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~ 82 (236)
|..|...-...+.-. .|--.||..|+..-. ..+...||.|.
T Consensus 2 C~iC~~~~~~~~~~~--~C~H~~c~~C~~~~~---~~~~~~Cp~C~ 42 (45)
T cd00162 2 CPICLEEFREPVVLL--PCGHVFCRSCIDKWL---KSGKNTCPLCR 42 (45)
T ss_pred CCcCchhhhCceEec--CCCChhcHHHHHHHH---HhCcCCCCCCC
Confidence 445554432123333 466788899987322 23778899986
No 58
>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=33.49 E-value=21 Score=28.46 Aligned_cols=26 Identities=27% Similarity=0.534 Sum_probs=19.2
Q ss_pred ccccCCCCccCCCCCcccccchhchH
Q 044718 61 ENCLSCGVEFDDVGNFYRPYCWYKCE 86 (236)
Q Consensus 61 ~sCLgssp~fDD~GnFYCPyC~YKka 86 (236)
.+|.-+.-.+...|.-||..|+|++-
T Consensus 45 ~~C~~CK~~v~q~g~~YCq~CAYkkG 70 (90)
T PF10235_consen 45 SKCKICKTKVHQPGAKYCQTCAYKKG 70 (90)
T ss_pred ccccccccccccCCCccChhhhcccC
Confidence 35555556666678899999999864
No 59
>PF14410 GH-E: HNH/ENDO VII superfamily nuclease with conserved GHE residues
Probab=32.22 E-value=30 Score=25.81 Aligned_cols=39 Identities=21% Similarity=0.173 Sum_probs=26.2
Q ss_pred CCCCCcccccchhch---------HHHHHHHHHHHHH---HHHHHHHhhhc
Q 044718 71 DDVGNFYRPYCWYKC---------ELMRTKELRKKAM---ETKKKLACFID 109 (236)
Q Consensus 71 DD~GnFYCPyC~YKk---------av~~y~eaKKkA~---~AKKeLssFL~ 109 (236)
|+.|.|+||-|++.. ..-++..+...|. ..+|++..|+.
T Consensus 1 ~~~G~~~~~~~~~~i~~~~dmgH~~~~e~~~~~~~~~~~~~t~ke~~d~~n 51 (70)
T PF14410_consen 1 DPDGKVRDPNTGYPIEGPWDMGHKPGVEYWRLVGRAEEGGITRKEFLDWYN 51 (70)
T ss_pred CCCCeEecCCCCCCCCCCCCccCchHHHHHHHHHHHHhcCCCHHHHHHHHh
Confidence 578999999999885 4556666666664 33455554443
No 60
>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=32.18 E-value=12 Score=24.85 Aligned_cols=29 Identities=28% Similarity=0.574 Sum_probs=19.3
Q ss_pred ccccccccCC---------CCccCCCCCcccccchhch
Q 044718 57 ISVHENCLSC---------GVEFDDVGNFYRPYCWYKC 85 (236)
Q Consensus 57 lsvH~sCLgs---------sp~fDD~GnFYCPyC~YKk 85 (236)
..||..|+.+ ..-+.-.|.+||..|..++
T Consensus 20 ~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~ 57 (58)
T PF00412_consen 20 KFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKR 57 (58)
T ss_dssp EEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHH
T ss_pred cEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhh
Confidence 4688888774 1134456788998887653
No 61
>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=31.62 E-value=19 Score=22.21 Aligned_cols=13 Identities=23% Similarity=0.560 Sum_probs=10.8
Q ss_pred CCCcccccchhch
Q 044718 73 VGNFYRPYCWYKC 85 (236)
Q Consensus 73 ~GnFYCPyC~YKk 85 (236)
.|+|.||.|.+..
T Consensus 2 ~g~W~C~~C~~~N 14 (30)
T PF00641_consen 2 EGDWKCPSCTFMN 14 (30)
T ss_dssp SSSEEETTTTEEE
T ss_pred CcCccCCCCcCCc
Confidence 5899999998764
No 62
>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=30.86 E-value=52 Score=25.08 Aligned_cols=52 Identities=21% Similarity=0.371 Sum_probs=33.5
Q ss_pred ccceecCCCCCe----EEeeCCCCcccccccc--------ccCC-CCccCCCCCcccccchhchHHH
Q 044718 35 EPCIKCNRRDEN----LLVCSQSGCLISVHEN--------CLSC-GVEFDDVGNFYRPYCWYKCELM 88 (236)
Q Consensus 35 D~CikC~kdGq~----LL~CSg~GCPlsvH~s--------CLgs-sp~fDD~GnFYCPyC~YKkav~ 88 (236)
..|.+|+..... ++.|. +|-.=|+.+ |... .-..+..+.+.|++|.|++-++
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 469999876552 78898 887655443 3211 1122345678999999987554
No 63
>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=30.86 E-value=52 Score=19.90 Aligned_cols=14 Identities=29% Similarity=0.596 Sum_probs=10.3
Q ss_pred CCCcccccchhchH
Q 044718 73 VGNFYRPYCWYKCE 86 (236)
Q Consensus 73 ~GnFYCPyC~YKka 86 (236)
.|.|||.+|-..-.
T Consensus 1 ~~~~~C~~C~~~~~ 14 (35)
T smart00451 1 TGGFYCKLCNVTFT 14 (35)
T ss_pred CcCeEccccCCccC
Confidence 37899999975433
No 64
>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=30.38 E-value=14 Score=27.06 Aligned_cols=44 Identities=25% Similarity=0.426 Sum_probs=22.4
Q ss_pred cceecCCCCCeEEeeCCCCccccccccccCCCCccCCCCCcccccchhchHH
Q 044718 36 PCIKCNRRDENLLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYCWYKCEL 87 (236)
Q Consensus 36 ~CikC~kdGq~LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~YKkav 87 (236)
.|-.|--..++|+.|+ -|-=|+++ ++.-=.-.-+||.|++.-+.
T Consensus 4 nCKsCWf~~k~Li~C~-------dHYLCl~C-Lt~ml~~s~~C~iC~~~LPt 47 (50)
T PF03854_consen 4 NCKSCWFANKGLIKCS-------DHYLCLNC-LTLMLSRSDRCPICGKPLPT 47 (50)
T ss_dssp ---SS-S--SSEEE-S-------S-EEEHHH-HHHT-SSSSEETTTTEE---
T ss_pred cChhhhhcCCCeeeec-------chhHHHHH-HHHHhccccCCCcccCcCcc
Confidence 3566666667799999 68878776 22222334579999987553
No 65
>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=30.15 E-value=28 Score=22.29 Aligned_cols=31 Identities=26% Similarity=0.590 Sum_probs=23.4
Q ss_pred CCccceecCCC--C---CeEEeeCCCCccccccccccCC
Q 044718 33 EEEPCIKCNRR--D---ENLLVCSQSGCLISVHENCLSC 66 (236)
Q Consensus 33 ~qD~CikC~kd--G---q~LL~CSg~GCPlsvH~sCLgs 66 (236)
....|..|++. | + =|.|+ .|-+.+|.+|...
T Consensus 10 ~~~~C~~C~~~i~~~~~~-~~~C~--~C~~~~H~~C~~~ 45 (50)
T cd00029 10 KPTFCDVCRKSIWGLFKQ-GLRCS--WCKVKCHKKCADK 45 (50)
T ss_pred CCCChhhcchhhhccccc-eeEcC--CCCCchhhhhhcc
Confidence 34568888543 1 4 57899 9999999999985
No 66
>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=30.11 E-value=30 Score=23.75 Aligned_cols=20 Identities=25% Similarity=0.479 Sum_probs=13.3
Q ss_pred cccCCCCccCCCCCcccccch
Q 044718 62 NCLSCGVEFDDVGNFYRPYCW 82 (236)
Q Consensus 62 sCLgssp~fDD~GnFYCPyC~ 82 (236)
.| +.|+-=+..|..|||.|.
T Consensus 22 ~C-~~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 22 DC-GTPLMRDKDGKIYCVSCG 41 (41)
T ss_pred CC-CCeeEEecCCCEECCCCC
Confidence 46 333333478999999983
No 67
>cd03025 DsbA_FrnE_like DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins.
Probab=29.94 E-value=34 Score=27.14 Aligned_cols=12 Identities=8% Similarity=0.099 Sum_probs=9.8
Q ss_pred CcccccchhchH
Q 044718 75 NFYRPYCWYKCE 86 (236)
Q Consensus 75 nFYCPyC~YKka 86 (236)
|+.||+||.-..
T Consensus 8 D~~cp~c~~~~~ 19 (193)
T cd03025 8 DPLCGWCYGFEP 19 (193)
T ss_pred CCCCchhhCchH
Confidence 789999997654
No 68
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=29.04 E-value=18 Score=28.53 Aligned_cols=44 Identities=18% Similarity=0.376 Sum_probs=28.7
Q ss_pred ceecCCCCCe--EEeeCCCCccccccccccCCCCccCCCCCcccccchhc
Q 044718 37 CIKCNRRDEN--LLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYCWYK 84 (236)
Q Consensus 37 CikC~kdGq~--LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~YK 84 (236)
|..|..+|+. |+.+. |.-.||.-|+.-=+.. +.++-.||.|.-.
T Consensus 35 Cp~Ck~Pgd~Cplv~g~---C~H~FH~hCI~kWl~~-~~~~~~CPmCR~~ 80 (85)
T PF12861_consen 35 CPDCKFPGDDCPLVWGK---CSHNFHMHCILKWLST-QSSKGQCPMCRQP 80 (85)
T ss_pred CCCccCCCCCCceeecc---CccHHHHHHHHHHHcc-ccCCCCCCCcCCe
Confidence 5557777763 43333 8889999998743332 2456799999743
No 69
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=28.83 E-value=33 Score=20.78 Aligned_cols=20 Identities=35% Similarity=0.858 Sum_probs=10.9
Q ss_pred ccCCCCccCCCCCcccccchh
Q 044718 63 CLSCGVEFDDVGNFYRPYCWY 83 (236)
Q Consensus 63 CLgssp~fDD~GnFYCPyC~Y 83 (236)
|-.+...+++ +.-|||+|-.
T Consensus 2 Cp~CG~~~~~-~~~fC~~CG~ 21 (23)
T PF13240_consen 2 CPNCGAEIED-DAKFCPNCGT 21 (23)
T ss_pred CcccCCCCCC-cCcchhhhCC
Confidence 3334445544 4445998854
No 70
>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=28.50 E-value=68 Score=25.20 Aligned_cols=20 Identities=35% Similarity=0.307 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q 044718 87 LMRTKELRKKAMETKKKLAC 106 (236)
Q Consensus 87 v~~y~eaKKkA~~AKKeLss 106 (236)
-++++|+++...+||+.|.+
T Consensus 67 peA~~eL~~eI~eAK~dLr~ 86 (91)
T PF08285_consen 67 PEAAKELQKEIKEAKADLRK 86 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 47899999999999999864
No 71
>cd03022 DsbA_HCCA_Iso DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1,2-dihydroxynapthalene by a dioxygenase, into cis-o-hydroxybenzylidenepyruvate (cHBPA). This is the fourth reaction in a six-step pathway that converts napthalene into salicylate. HCCA isomerase is unique to bacteria that degrade polycyclic aromatic compounds. It is closely related to the eukaryotic protein, GSH transferase kappa (GSTK).
Probab=28.32 E-value=34 Score=27.03 Aligned_cols=12 Identities=33% Similarity=0.794 Sum_probs=9.4
Q ss_pred CcccccchhchH
Q 044718 75 NFYRPYCWYKCE 86 (236)
Q Consensus 75 nFYCPyC~YKka 86 (236)
|+-|||||.-..
T Consensus 6 D~~cP~cy~~~~ 17 (192)
T cd03022 6 DFSSPYSYLAHE 17 (192)
T ss_pred eCCChHHHHHHH
Confidence 678999997543
No 72
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=28.25 E-value=28 Score=20.51 Aligned_cols=14 Identities=21% Similarity=0.406 Sum_probs=10.5
Q ss_pred CCcccccchhchHH
Q 044718 74 GNFYRPYCWYKCEL 87 (236)
Q Consensus 74 GnFYCPyC~YKkav 87 (236)
|+|.||.|-+....
T Consensus 1 g~W~C~~C~~~N~~ 14 (26)
T smart00547 1 GDWECPACTFLNFA 14 (26)
T ss_pred CcccCCCCCCcChh
Confidence 68999999766443
No 73
>cd07168 NR_DBD_DHR4_like DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4
Probab=27.40 E-value=50 Score=25.41 Aligned_cols=54 Identities=15% Similarity=0.400 Sum_probs=34.1
Q ss_pred CCccceecCCCCCe----EEeeCCCCccccccccc--------cCC-CCccCCCCCcccccchhchHHH
Q 044718 33 EEEPCIKCNRRDEN----LLVCSQSGCLISVHENC--------LSC-GVEFDDVGNFYRPYCWYKCELM 88 (236)
Q Consensus 33 ~qD~CikC~kdGq~----LL~CSg~GCPlsvH~sC--------Lgs-sp~fDD~GnFYCPyC~YKkav~ 88 (236)
....|.+|+..... ++.|. +|-.=|...- ... .-.++......|++|.|++-++
T Consensus 5 ~~~~C~VCg~~~~g~hyGv~sC~--aCk~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~ 71 (90)
T cd07168 5 SPKLCSICEDKATGLHYGIITCE--GCKGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCRFRKCIR 71 (90)
T ss_pred cCCCCcccCCcCcceEECceehh--hhhHhhhhhhcCCCCccCCCCCCccccccccccccccchhhhhh
Confidence 44579999876553 78899 9977654433 311 1122345567899999887443
No 74
>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=27.13 E-value=11 Score=21.67 Aligned_cols=25 Identities=24% Similarity=0.472 Sum_probs=15.7
Q ss_pred CccccccccccCCCCccCCCCCcccccc
Q 044718 54 GCLISVHENCLSCGVEFDDVGNFYRPYC 81 (236)
Q Consensus 54 GCPlsvH~sCLgssp~fDD~GnFYCPyC 81 (236)
.|--.+|..|+..- +. .+..-||.|
T Consensus 15 ~C~H~~c~~C~~~~--~~-~~~~~CP~C 39 (39)
T smart00184 15 PCGHTFCRSCIRKW--LK-SGNNTCPIC 39 (39)
T ss_pred cCCChHHHHHHHHH--HH-hCcCCCCCC
Confidence 35567888888732 22 456668876
No 75
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.96 E-value=39 Score=25.65 Aligned_cols=13 Identities=38% Similarity=0.741 Sum_probs=11.0
Q ss_pred CCCCCcccccchh
Q 044718 71 DDVGNFYRPYCWY 83 (236)
Q Consensus 71 DD~GnFYCPyC~Y 83 (236)
.++|.--||||.-
T Consensus 44 g~~gev~CPYC~t 56 (62)
T COG4391 44 GDEGEVVCPYCST 56 (62)
T ss_pred CCCCcEecCcccc
Confidence 4899999999973
No 76
>PRK14973 DNA topoisomerase I; Provisional
Probab=26.76 E-value=44 Score=35.57 Aligned_cols=54 Identities=20% Similarity=0.423 Sum_probs=32.9
Q ss_pred ccceecCC--------CCCeEEeeCC-CCccccc--c-----------ccccCCCC---ccCCCCC---cc-cccchhch
Q 044718 35 EPCIKCNR--------RDENLLVCSQ-SGCLISV--H-----------ENCLSCGV---EFDDVGN---FY-RPYCWYKC 85 (236)
Q Consensus 35 D~CikC~k--------dGq~LL~CSg-~GCPlsv--H-----------~sCLgssp---~fDD~Gn---FY-CPyC~YKk 85 (236)
-.|.+|+. .|. .+-|++ .+|-..+ + ..|-.+.. .+--.|. |. ||.|.|.+
T Consensus 589 ~~CP~CG~~l~ik~~k~gk-FigCS~Yp~Ck~t~~L~~~~~g~~~~~~~~Cp~CG~p~~~~~r~Gr~g~fl~CP~C~~~~ 667 (936)
T PRK14973 589 GPCPVCGKDLRIKHIGSSQ-FIGCSGYPDCTFNIGLPGTTWGWAIRTDEVCPIHHLNHVRLIRKGARPWDIGCPLCSHIE 667 (936)
T ss_pred ccCCcccccceeecccCce-eEECCCCCCCCccccCCccccccCCCCCCCCCCCCCCceEEeecCCCcccccCccccchh
Confidence 57999974 234 688995 4576431 1 23655542 2324444 55 99999987
Q ss_pred HHHH
Q 044718 86 ELMR 89 (236)
Q Consensus 86 av~~ 89 (236)
...+
T Consensus 668 ~~~~ 671 (936)
T PRK14973 668 SNTE 671 (936)
T ss_pred hccc
Confidence 7555
No 77
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=26.71 E-value=40 Score=26.82 Aligned_cols=53 Identities=25% Similarity=0.511 Sum_probs=30.3
Q ss_pred CCCccceecCCC--CCeEEee----CCCCc---cccccccccCCC-----CccCCCCCcccccchhch
Q 044718 32 LEEEPCIKCNRR--DENLLVC----SQSGC---LISVHENCLSCG-----VEFDDVGNFYRPYCWYKC 85 (236)
Q Consensus 32 ~~qD~CikC~kd--Gq~LL~C----Sg~GC---PlsvH~sCLgss-----p~fDD~GnFYCPyC~YKk 85 (236)
..-..|+.|-.. +. ...| ....| ...|=..||.-. ...-..++|-||.|.=.+
T Consensus 5 ~~g~~CHqCrqKt~~~-~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~CrgiC 71 (105)
T PF10497_consen 5 VNGKTCHQCRQKTLDF-KTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGIC 71 (105)
T ss_pred CCCCCchhhcCCCCCC-ceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCCee
Confidence 344567777652 22 3456 22355 777777776621 112257899999987543
No 78
>cd03024 DsbA_FrnE DsbA family, FrnE subfamily; FrnE is a DsbA-like protein containing a CXXC motif. It is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins.
Probab=26.37 E-value=39 Score=27.05 Aligned_cols=11 Identities=18% Similarity=0.754 Sum_probs=8.9
Q ss_pred CCcccccchhc
Q 044718 74 GNFYRPYCWYK 84 (236)
Q Consensus 74 GnFYCPyC~YK 84 (236)
-||.||||+.-
T Consensus 5 ~D~~cP~cyl~ 15 (201)
T cd03024 5 SDVVCPWCYIG 15 (201)
T ss_pred ecCcCccHHHH
Confidence 47899999954
No 79
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=25.76 E-value=31 Score=28.16 Aligned_cols=15 Identities=33% Similarity=0.425 Sum_probs=11.7
Q ss_pred CCCCCcccccchhch
Q 044718 71 DDVGNFYRPYCWYKC 85 (236)
Q Consensus 71 DD~GnFYCPyC~YKk 85 (236)
|+.|.|.||.|-..-
T Consensus 119 d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 119 DMDGTFTCPRCGEEL 133 (147)
T ss_pred CCCCcEECCCCCCEE
Confidence 467889999997553
No 80
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=25.72 E-value=55 Score=35.84 Aligned_cols=47 Identities=23% Similarity=0.465 Sum_probs=36.6
Q ss_pred CCCCccceecCCC------CCeEEeeCCCCccccccccccCCCCccCCCCCcccccch
Q 044718 31 LLEEEPCIKCNRR------DENLLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYCW 82 (236)
Q Consensus 31 ~~~qD~CikC~kd------Gq~LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~ 82 (236)
..+--+|..|+.+ |+-.+-|- .|..-|=..|..-. ..+|+-.||-|.
T Consensus 14 ~~~~qiCqICGD~vg~~~~Ge~FVAC~--eC~FPVCrpCYEYE---r~eG~q~CPqCk 66 (1079)
T PLN02638 14 HGGGQVCQICGDNVGKTVDGEPFVACD--VCAFPVCRPCYEYE---RKDGNQSCPQCK 66 (1079)
T ss_pred ccCCceeeecccccCcCCCCCEEEEec--cCCCccccchhhhh---hhcCCccCCccC
Confidence 3445599999976 66345677 99999999998743 369999999997
No 81
>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=25.28 E-value=55 Score=20.81 Aligned_cols=23 Identities=26% Similarity=0.563 Sum_probs=14.5
Q ss_pred ccCCCCccCCC-CCcccccchhch
Q 044718 63 CLSCGVEFDDV-GNFYRPYCWYKC 85 (236)
Q Consensus 63 CLgssp~fDD~-GnFYCPyC~YKk 85 (236)
|..+.-.+++. .+|.||.|-..+
T Consensus 4 C~~CGy~y~~~~~~~~CP~Cg~~~ 27 (33)
T cd00350 4 CPVCGYIYDGEEAPWVCPVCGAPK 27 (33)
T ss_pred CCCCCCEECCCcCCCcCcCCCCcH
Confidence 33333344443 799999997654
No 82
>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=25.03 E-value=25 Score=22.17 Aligned_cols=32 Identities=25% Similarity=0.531 Sum_probs=23.2
Q ss_pred CCccceecCCCCCe---EEeeCCCCccccccccccCC
Q 044718 33 EEEPCIKCNRRDEN---LLVCSQSGCLISVHENCLSC 66 (236)
Q Consensus 33 ~qD~CikC~kdGq~---LL~CSg~GCPlsvH~sCLgs 66 (236)
....|..|++.=.. =|.|. .|-+.+|.+|+..
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~C~--~C~~~~H~~C~~~ 44 (49)
T smart00109 10 KPTKCCVCRKSIWGSFQGLRCS--WCKVKCHKKCAEK 44 (49)
T ss_pred CCCCccccccccCcCCCCcCCC--CCCchHHHHHHhh
Confidence 34568888653221 36898 9999999999874
No 83
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=24.36 E-value=33 Score=30.06 Aligned_cols=40 Identities=18% Similarity=0.330 Sum_probs=28.8
Q ss_pred cceecCCCCCeEEeeCCCCccccccccccCCCCccCCCCCcccccchhchH
Q 044718 36 PCIKCNRRDENLLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYCWYKCE 86 (236)
Q Consensus 36 ~CikC~kdGq~LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~YKka 86 (236)
.|..|+..|. ...+-... +-|..+++-. .|.||.|-|+..
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 4999999998 55554222 5667777763 389999999854
No 84
>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=23.96 E-value=71 Score=19.89 Aligned_cols=27 Identities=30% Similarity=0.758 Sum_probs=19.9
Q ss_pred cceecCCCCCe--EEeeCCCCcccccccccc
Q 044718 36 PCIKCNRRDEN--LLVCSQSGCLISVHENCL 64 (236)
Q Consensus 36 ~CikC~kdGq~--LL~CSg~GCPlsvH~sCL 64 (236)
.|-.|++.... .-.|+ .|...+|.+|.
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 36667766652 56797 88899999984
No 85
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=23.40 E-value=48 Score=20.17 Aligned_cols=21 Identities=29% Similarity=0.498 Sum_probs=13.7
Q ss_pred cccCCCCccCCCCCcccccchh
Q 044718 62 NCLSCGVEFDDVGNFYRPYCWY 83 (236)
Q Consensus 62 sCLgssp~fDD~GnFYCPyC~Y 83 (236)
.|-.+.. ..+.+.-|||+|-.
T Consensus 4 ~Cp~Cg~-~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 4 FCPNCGA-EIDPDAKFCPNCGA 24 (26)
T ss_pred CCcccCC-cCCcccccChhhCC
Confidence 3445543 35678889999954
No 86
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=23.22 E-value=47 Score=26.15 Aligned_cols=19 Identities=42% Similarity=0.552 Sum_probs=12.7
Q ss_pred HHHHhhhC-CCCcee-ccCCC
Q 044718 182 FKRALESQ-SDPLAV-HSHPG 200 (236)
Q Consensus 182 ~~~~~~~~-~~~~~~-~~~~~ 200 (236)
|..+.+.+ ...+.+ |||||
T Consensus 60 ~~~~~~~~g~~vvg~yHSHP~ 80 (134)
T COG1310 60 FYLAAEDAGEVVVGWYHSHPG 80 (134)
T ss_pred HHHHHhhCCCEEEEEEcCCCC
Confidence 66666665 445555 99998
No 87
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=23.03 E-value=76 Score=34.35 Aligned_cols=58 Identities=21% Similarity=0.322 Sum_probs=39.1
Q ss_pred CCCCCccceecCCCCCeEEeeCCCCccccccccccCCCCccCCCCCcccccchh-chHHHHHHHHHHH
Q 044718 30 DLLEEEPCIKCNRRDENLLVCSQSGCLISVHENCLSCGVEFDDVGNFYRPYCWY-KCELMRTKELRKK 96 (236)
Q Consensus 30 e~~~qD~CikC~kdGq~LL~CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~Y-Kkav~~y~eaKKk 96 (236)
-..+...|-.|+..=+ | .=--=.|--+||.-|++ .+.+-||.|.- -+.+++..+++..
T Consensus 836 ~i~q~skCs~C~~~Ld-l-P~VhF~CgHsyHqhC~e-------~~~~~CP~C~~e~~~~m~l~~s~~q 894 (933)
T KOG2114|consen 836 QIFQVSKCSACEGTLD-L-PFVHFLCGHSYHQHCLE-------DKEDKCPKCLPELRGVMDLKRSQEQ 894 (933)
T ss_pred ceeeeeeecccCCccc-c-ceeeeecccHHHHHhhc-------cCcccCCccchhhhhhHHHHHHHHH
Confidence 3456678999998888 3 22223577899999999 77889999986 1233444444333
No 88
>PRK00420 hypothetical protein; Validated
Probab=22.99 E-value=1.1e+02 Score=25.12 Aligned_cols=26 Identities=15% Similarity=0.046 Sum_probs=17.2
Q ss_pred CccC-CCCCcccccchhchHHHHHHHH
Q 044718 68 VEFD-DVGNFYRPYCWYKCELMRTKEL 93 (236)
Q Consensus 68 p~fD-D~GnFYCPyC~YKkav~~y~ea 93 (236)
|-|. ..|.-|||.|--...+..-.+.
T Consensus 32 pLf~lk~g~~~Cp~Cg~~~~v~~~ee~ 58 (112)
T PRK00420 32 PLFELKDGEVVCPVHGKVYIVKSDEEE 58 (112)
T ss_pred cceecCCCceECCCCCCeeeeccHHHH
Confidence 3444 7999999999866555443333
No 89
>PF14260 zf-C4pol: C4-type zinc-finger of DNA polymerase delta
Probab=22.97 E-value=2.2e+02 Score=20.24 Aligned_cols=44 Identities=16% Similarity=0.289 Sum_probs=26.8
Q ss_pred ccCCCCccCCCCCcccccchhchHHHHHHHHHHHHHHHHHHHHhh
Q 044718 63 CLSCGVEFDDVGNFYRPYCWYKCELMRTKELRKKAMETKKKLACF 107 (236)
Q Consensus 63 CLgssp~fDD~GnFYCPyC~YKkav~~y~eaKKkA~~AKKeLssF 107 (236)
|+.+...........|+.|.-..+...+ .+..+...+.+++...
T Consensus 1 C~~C~~~~~~~~~~lC~~C~~~~~~~~~-~l~~~~~~~E~~~~~l 44 (73)
T PF14260_consen 1 CLVCGAKTQEGESPLCSNCRSDPQQTIY-NLLSRLRELERRFNEL 44 (73)
T ss_pred CCCCCCcCCCCCCCcCcccCcChHHHHH-HHHHHHHHHHHHHHHH
Confidence 4444444444445999999976665555 6666666666655543
No 90
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=20.89 E-value=44 Score=22.45 Aligned_cols=12 Identities=33% Similarity=0.495 Sum_probs=9.0
Q ss_pred CCCCcccccchhc
Q 044718 72 DVGNFYRPYCWYK 84 (236)
Q Consensus 72 D~GnFYCPyC~YK 84 (236)
+.| |.||.|--+
T Consensus 16 ~~g-~~CP~Cg~~ 27 (46)
T PF12760_consen 16 PDG-FVCPHCGST 27 (46)
T ss_pred CCC-CCCCCCCCe
Confidence 345 899999865
No 91
>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=20.89 E-value=40 Score=20.04 Aligned_cols=10 Identities=30% Similarity=0.418 Sum_probs=7.0
Q ss_pred Ccccccchhc
Q 044718 75 NFYRPYCWYK 84 (236)
Q Consensus 75 nFYCPyC~YK 84 (236)
.|||+.|...
T Consensus 1 q~~C~~C~k~ 10 (27)
T PF12171_consen 1 QFYCDACDKY 10 (27)
T ss_dssp -CBBTTTTBB
T ss_pred CCCcccCCCC
Confidence 4899999743
No 92
>COG1634 Uncharacterized Rossmann fold enzyme [General function prediction only]
Probab=20.54 E-value=56 Score=30.08 Aligned_cols=38 Identities=29% Similarity=0.388 Sum_probs=30.1
Q ss_pred hhhCCCCceeccCCCCCCCCCCCCCCCcccccccccCCCC
Q 044718 186 LESQSDPLAVHSHPGDKINNSRDKTPGIGSLVNYTSKERP 225 (236)
Q Consensus 186 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 225 (236)
+.+|.-+++||.| ||-|..-+.-.|-+. .|-+|+.-+|
T Consensus 110 ~~~~g~i~VVHAH-GDNi~~i~~~~~~~~-~vigTtQ~~P 147 (232)
T COG1634 110 CTAKGSIVVVHAH-GDNIWRIPKVVPVLD-RVIGTTQVRP 147 (232)
T ss_pred hhccCCEEEEEec-CcCHHHhhccccccc-eeecccccCC
Confidence 3568889999999 888887777777666 6778888888
No 93
>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=20.19 E-value=82 Score=29.94 Aligned_cols=42 Identities=29% Similarity=0.504 Sum_probs=26.2
Q ss_pred CccceecCCCCC-----eEEe--eCCCCccccccccccCCCCccCCCCCcccccchh
Q 044718 34 EEPCIKCNRRDE-----NLLV--CSQSGCLISVHENCLSCGVEFDDVGNFYRPYCWY 83 (236)
Q Consensus 34 qD~CikC~kdGq-----~LL~--CSg~GCPlsvH~sCLgssp~fDD~GnFYCPyC~Y 83 (236)
...|..|..+-- .||+ |. |.-|..|--.+-..|..-||.|.-
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CG--------H~~C~sCv~~l~~~~~~~CP~C~~ 51 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCG--------HTLCESCVDLLFVRGSGSCPECDT 51 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCC--------CcccHHHHHHHhcCCCCCCCCCCC
Confidence 468999988522 1443 54 666655533444467779999953
No 94
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=20.14 E-value=42 Score=28.39 Aligned_cols=17 Identities=29% Similarity=0.680 Sum_probs=14.3
Q ss_pred CccCCCCCcccccchhc
Q 044718 68 VEFDDVGNFYRPYCWYK 84 (236)
Q Consensus 68 p~fDD~GnFYCPyC~YK 84 (236)
|-|.-.|+-|||.|-|+
T Consensus 37 PLF~KdG~v~CPvC~~~ 53 (131)
T COG1645 37 PLFRKDGEVFCPVCGYR 53 (131)
T ss_pred cceeeCCeEECCCCCce
Confidence 45667999999999975
Done!