Query 018282
Match_columns 358
No_of_seqs 125 out of 252
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 07:40:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018282.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018282hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00744 RINGv The RING-vari 99.6 2.8E-15 6.1E-20 109.3 4.1 49 104-160 1-49 (49)
2 KOG1609 Protein involved in mR 99.5 9E-15 2E-19 132.2 4.6 90 97-192 73-162 (323)
3 PHA02825 LAP/PHD finger-like p 99.5 9.2E-15 2E-19 130.5 2.9 58 100-168 6-63 (162)
4 PF12906 RINGv: RING-variant d 99.5 2.8E-15 6.1E-20 108.5 -0.5 47 105-159 1-47 (47)
5 PHA02862 5L protein; Provision 99.4 9.9E-14 2.1E-18 123.1 4.4 53 102-165 2-54 (156)
6 COG5183 SSM4 Protein involved 99.1 1.2E-10 2.7E-15 123.9 4.9 55 102-164 12-66 (1175)
7 KOG3053 Uncharacterized conser 98.5 9.7E-08 2.1E-12 91.8 3.6 64 100-169 18-87 (293)
8 PF13639 zf-RING_2: Ring finge 96.0 0.0019 4E-08 45.0 0.3 44 103-160 1-44 (44)
9 PHA02929 N1R/p28-like protein; 95.2 0.015 3.2E-07 55.3 3.0 63 100-171 172-234 (238)
10 KOG4628 Predicted E3 ubiquitin 94.8 0.019 4.1E-07 57.5 2.6 49 103-164 230-278 (348)
11 PF12861 zf-Apc11: Anaphase-pr 94.3 0.079 1.7E-06 43.9 4.7 59 102-164 21-82 (85)
12 KOG1493 Anaphase-promoting com 93.3 0.063 1.4E-06 44.5 2.4 61 101-165 19-82 (84)
13 smart00504 Ubox Modified RING 93.1 0.13 2.8E-06 37.2 3.6 45 103-164 2-46 (63)
14 PF13920 zf-C3HC4_3: Zinc fing 92.0 0.069 1.5E-06 38.2 0.9 49 102-166 2-50 (50)
15 PF12678 zf-rbx1: RING-H2 zinc 91.7 0.067 1.5E-06 41.7 0.7 54 100-160 17-73 (73)
16 cd00162 RING RING-finger (Real 91.7 0.18 3.9E-06 32.8 2.6 44 104-162 1-44 (45)
17 PLN03208 E3 ubiquitin-protein 91.5 0.28 6.2E-06 45.8 4.6 48 102-164 18-79 (193)
18 PHA02926 zinc finger-like prot 91.5 0.16 3.5E-06 48.9 3.1 68 100-173 168-239 (242)
19 PF11793 FANCL_C: FANCL C-term 91.4 0.051 1.1E-06 42.4 -0.3 53 102-164 2-66 (70)
20 smart00184 RING Ring finger. E 89.9 0.44 9.6E-06 29.8 3.1 31 123-159 9-39 (39)
21 PF08510 PIG-P: PIG-P; InterP 88.8 0.8 1.7E-05 39.1 4.8 45 274-344 11-55 (126)
22 COG5243 HRD1 HRD ubiquitin lig 87.6 0.63 1.4E-05 48.1 4.1 56 99-162 284-343 (491)
23 COG5219 Uncharacterized conser 87.5 0.36 7.7E-06 54.6 2.4 56 100-165 1467-1524(1525)
24 KOG0802 E3 ubiquitin ligase [P 85.9 0.62 1.3E-05 48.1 3.0 49 102-162 291-339 (543)
25 COG5540 RING-finger-containing 82.2 1.1 2.4E-05 45.3 2.9 63 87-163 306-371 (374)
26 PF04564 U-box: U-box domain; 78.6 2.6 5.5E-05 32.6 3.3 55 124-184 16-70 (73)
27 PF05883 Baculo_RING: Baculovi 74.7 2.5 5.3E-05 37.9 2.5 42 102-150 26-68 (134)
28 TIGR00599 rad18 DNA repair pro 69.5 7 0.00015 40.1 4.7 48 101-165 25-72 (397)
29 KOG0827 Predicted E3 ubiquitin 69.2 4.3 9.2E-05 42.3 3.1 23 138-160 29-52 (465)
30 PF13687 DUF4153: Domain of un 68.4 2.5 5.3E-05 38.5 1.1 29 322-350 144-175 (217)
31 PF08113 CoxIIa: Cytochrome c 68.4 3.6 7.9E-05 29.5 1.7 17 335-351 17-33 (34)
32 KOG0828 Predicted E3 ubiquitin 67.8 5 0.00011 43.0 3.3 55 101-163 570-633 (636)
33 COG0341 SecF Preprotein transl 66.9 2.2 4.8E-05 42.1 0.6 33 288-320 123-155 (305)
34 KOG0823 Predicted E3 ubiquitin 65.3 14 0.0003 35.8 5.5 48 102-164 47-95 (230)
35 COG5194 APC11 Component of SCF 62.3 6.4 0.00014 33.2 2.3 27 138-166 57-83 (88)
36 KOG2257 N-acetylglucosaminyltr 62.1 8.8 0.00019 34.6 3.3 45 274-345 15-60 (135)
37 PRK12652 putative monovalent c 57.6 10 0.00022 38.0 3.3 86 253-343 144-235 (357)
38 PF04632 FUSC: Fusaric acid re 53.2 5.1 0.00011 40.9 0.4 45 297-342 385-429 (650)
39 PF08746 zf-RING-like: RING-li 48.9 7.8 0.00017 28.0 0.7 21 139-159 23-43 (43)
40 PF13179 DUF4006: Family of un 45.8 23 0.00051 28.5 3.0 28 261-288 2-30 (66)
41 PF00097 zf-C3HC4: Zinc finger 43.3 19 0.00042 24.2 1.9 29 126-159 13-41 (41)
42 cd02987 Phd_like_Phd Phosducin 43.3 26 0.00056 31.3 3.2 39 177-222 12-53 (175)
43 KOG2927 Membrane component of 42.7 5.7 0.00012 40.7 -1.0 13 336-348 241-257 (372)
44 PRK12596 putative monovalent c 41.0 14 0.0003 33.4 1.2 55 283-344 14-68 (171)
45 KOG0801 Predicted E3 ubiquitin 39.3 17 0.00037 34.4 1.5 24 102-132 177-200 (205)
46 TIGR03826 YvyF flagellar opero 37.9 33 0.00072 30.6 3.0 64 154-218 4-73 (137)
47 PF12732 YtxH: YtxH-like prote 36.6 32 0.00069 26.7 2.4 22 278-299 8-29 (74)
48 KOG2930 SCF ubiquitin ligase, 36.6 29 0.00063 30.6 2.4 25 138-164 84-108 (114)
49 PF02355 SecD_SecF: Protein ex 36.0 6 0.00013 36.0 -1.9 33 288-320 20-52 (189)
50 PF14353 CpXC: CpXC protein 35.6 28 0.00061 29.1 2.1 29 199-230 18-46 (128)
51 KOG1734 Predicted RING-contain 35.4 13 0.00028 37.4 0.2 67 93-164 215-281 (328)
52 PF06197 DUF998: Protein of un 32.9 33 0.00073 29.2 2.2 27 263-291 36-62 (184)
53 PF13894 zf-C2H2_4: C2H2-type 30.8 20 0.00044 20.6 0.4 12 155-166 2-13 (24)
54 cd07922 CarBa CarBa is the A s 30.8 40 0.00088 27.8 2.2 50 169-221 4-53 (81)
55 KOG4265 Predicted E3 ubiquitin 30.3 41 0.00088 34.5 2.6 44 101-164 289-336 (349)
56 TIGR00570 cdk7 CDK-activating 30.0 89 0.0019 31.5 4.9 52 102-164 3-54 (309)
57 PF11872 DUF3392: Protein of u 29.5 42 0.00092 29.1 2.3 23 330-352 84-106 (106)
58 PF13923 zf-C3HC4_2: Zinc fing 29.5 39 0.00084 22.9 1.7 27 126-159 13-39 (39)
59 TIGR00942 2a6301s05 Monovalent 27.8 19 0.0004 31.6 -0.2 42 301-344 10-52 (144)
60 TIGR00869 sec62 protein transl 26.7 33 0.00071 33.2 1.2 29 263-291 106-137 (232)
61 PF01440 Gemini_AL2: Geminivir 26.3 7.8 0.00017 34.7 -2.8 31 124-157 31-61 (134)
62 KOG1645 RING-finger-containing 26.0 66 0.0014 34.0 3.3 52 103-164 5-56 (463)
63 PF10367 Vps39_2: Vacuolar sor 25.3 23 0.00051 27.6 -0.0 34 100-146 76-109 (109)
64 PRK12651 putative monovalent c 25.2 46 0.00099 29.5 1.8 54 284-344 12-66 (158)
65 KOG3970 Predicted E3 ubiquitin 24.6 1.1E+02 0.0025 30.4 4.4 48 103-163 51-104 (299)
66 PF08173 YbgT_YccB: Membrane b 24.3 65 0.0014 22.2 2.0 16 273-288 9-24 (28)
67 KOG2636 Splicing factor 3a, su 24.3 46 0.001 35.4 1.8 62 123-196 374-440 (497)
68 PF00096 zf-C2H2: Zinc finger, 23.7 32 0.00069 20.5 0.4 12 155-166 2-13 (23)
69 COG3304 Predicted membrane pro 23.4 40 0.00086 30.8 1.0 23 331-353 71-93 (145)
70 PF14570 zf-RING_4: RING/Ubox 22.6 54 0.0012 24.8 1.5 33 126-164 14-48 (48)
71 PF13912 zf-C2H2_6: C2H2-type 21.5 60 0.0013 20.1 1.3 12 155-166 3-14 (27)
72 PF09607 BrkDBD: Brinker DNA-b 21.4 55 0.0012 25.8 1.4 21 131-151 23-49 (58)
73 PF03839 Sec62: Translocation 21.1 51 0.0011 31.6 1.3 14 336-349 163-179 (224)
No 1
>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=99.56 E-value=2.8e-15 Score=109.33 Aligned_cols=49 Identities=33% Similarity=0.786 Sum_probs=42.9
Q ss_pred ceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhcCCceeeccc
Q 018282 104 EVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICG 160 (358)
Q Consensus 104 eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC~ 160 (358)
.||||+ +.+ +.++++++||.|+|+++++|++||++|+..+++++||||+
T Consensus 1 ~CrIC~---~~~-----~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICH---DEG-----DEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCC---CCC-----CCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 599998 211 2457789999999999999999999999999999999996
No 2
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=99.51 E-value=9e-15 Score=132.23 Aligned_cols=90 Identities=33% Similarity=0.489 Sum_probs=65.4
Q ss_pred eecCCCCceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhcCCceeeccccccccccchhhHHHHH
Q 018282 97 QFISPDGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGAKNIRVSDFKKVLI 176 (358)
Q Consensus 97 E~~SpE~eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC~~~a~NV~~~dfnkVm~ 176 (358)
+.++.+.+|||||.+ .+... +.+++.||.|+|++++||++|+++|+..||+.+||||++.+++.........-.
T Consensus 73 ~~~~~~~~cRIc~~~--~~~~~----~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~~~~~~~~~~~ 146 (323)
T KOG1609|consen 73 ESPSSGPICRICHEE--DEESN----GLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINVGTKLKPLIVI 146 (323)
T ss_pred cCCCCCCcEEEEecc--ccccc----ccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccceecceeecceeeh
Confidence 333445789999932 22111 117999999999999999999999999999999999999999887665444333
Q ss_pred HHHHHHHHHHhhhcCC
Q 018282 177 ALKDFEALRERTATGE 192 (358)
Q Consensus 177 slk~~~alRE~ta~G~ 192 (358)
....+++..+++..+.
T Consensus 147 ~~~~~~~~~~~~~~~~ 162 (323)
T KOG1609|consen 147 SKVRSGALSERTLSGM 162 (323)
T ss_pred hhhhhHhhhheeeehh
Confidence 3344455656666554
No 3
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=99.49 E-value=9.2e-15 Score=130.54 Aligned_cols=58 Identities=21% Similarity=0.531 Sum_probs=48.1
Q ss_pred CCCCceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhcCCceeeccccccccccc
Q 018282 100 SPDGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGAKNIRV 168 (358)
Q Consensus 100 SpE~eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC~~~a~NV~~ 168 (358)
..+++||||+.+ + +....||.|||++++||++|+++|++.+++..||+|++.|...+.
T Consensus 6 ~~~~~CRIC~~~---~--------~~~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~~~ 63 (162)
T PHA02825 6 LMDKCCWICKDE---Y--------DVVTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIKKN 63 (162)
T ss_pred CCCCeeEecCCC---C--------CCccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEEEe
Confidence 347889999811 1 123579999999999999999999999999999999999975543
No 4
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=99.49 E-value=2.8e-15 Score=108.52 Aligned_cols=47 Identities=34% Similarity=0.830 Sum_probs=35.8
Q ss_pred eeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhcCCceeecc
Q 018282 105 VFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEIC 159 (358)
Q Consensus 105 CRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC 159 (358)
||||+ +.+ +++++|+.||.|+|+|+|||++||++|+..+++++||||
T Consensus 1 CrIC~---~~~-----~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICL---EGE-----EEDEPLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTT---EE------SSSS-EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeC---CcC-----CCCCceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 89998 221 122379999999999999999999999999999999998
No 5
>PHA02862 5L protein; Provisional
Probab=99.42 E-value=9.9e-14 Score=123.09 Aligned_cols=53 Identities=21% Similarity=0.532 Sum_probs=44.8
Q ss_pred CCceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhcCCceeecccccccc
Q 018282 102 DGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGAKN 165 (358)
Q Consensus 102 E~eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC~~~a~N 165 (358)
...||||+.+ + +++ ..||.|+|++++||++||++|++.+++..||+|++.|..
T Consensus 2 ~diCWIC~~~-~--------~e~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~I 54 (156)
T PHA02862 2 SDICWICNDV-C--------DER--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNI 54 (156)
T ss_pred CCEEEEecCc-C--------CCC--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEE
Confidence 3579999921 1 111 589999999999999999999999999999999999963
No 6
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=99.05 E-value=1.2e-10 Score=123.86 Aligned_cols=55 Identities=29% Similarity=0.709 Sum_probs=48.2
Q ss_pred CCceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhcCCceeeccccccc
Q 018282 102 DGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGAK 164 (358)
Q Consensus 102 E~eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC~~~a~ 164 (358)
...|||||++ | ..+++|-.||+|+||++|+|++|+..|+.-+++++|||||+.|+
T Consensus 12 ~~~CRICr~e-~-------~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~ 66 (1175)
T COG5183 12 KRSCRICRTE-D-------IRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYK 66 (1175)
T ss_pred chhceeecCC-C-------CCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceee
Confidence 3569999921 1 24678999999999999999999999999999999999999986
No 7
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.47 E-value=9.7e-08 Score=91.80 Aligned_cols=64 Identities=22% Similarity=0.414 Sum_probs=49.8
Q ss_pred CCCCceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhcCC------ceeeccccccccccch
Q 018282 100 SPDGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGS------TACEICGNGAKNIRVS 169 (358)
Q Consensus 100 SpE~eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGn------ttCEIC~~~a~NV~~~ 169 (358)
.+|+.|.||. .+|.+.+ -.....||.|+|+.+.||++|+.+|+..|.- -+|..|+.+|..+-|.
T Consensus 18 e~eR~CWiCF-~TdeDn~-----~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv~P~ 87 (293)
T KOG3053|consen 18 ELERCCWICF-ATDEDNR-----LAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIVFPQ 87 (293)
T ss_pred ccceeEEEEe-ccCcccc-----hhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchheeeccc
Confidence 4578899998 3443321 1236899999999999999999999998754 4899999999765543
No 8
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=96.04 E-value=0.0019 Score=45.01 Aligned_cols=44 Identities=25% Similarity=0.739 Sum_probs=30.8
Q ss_pred CceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhcCCceeeccc
Q 018282 103 GEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICG 160 (358)
Q Consensus 103 ~eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC~ 160 (358)
++|-||+ .+.+. ++..+.++|+ -..|++|+++|++.+ .+|.+|.
T Consensus 1 d~C~IC~--~~~~~-----~~~~~~l~C~-----H~fh~~Ci~~~~~~~--~~CP~CR 44 (44)
T PF13639_consen 1 DECPICL--EEFED-----GEKVVKLPCG-----HVFHRSCIKEWLKRN--NSCPVCR 44 (44)
T ss_dssp -CETTTT--CBHHT-----TSCEEEETTS-----EEEEHHHHHHHHHHS--SB-TTTH
T ss_pred CCCcCCC--hhhcC-----CCeEEEccCC-----CeeCHHHHHHHHHhC--CcCCccC
Confidence 3699998 23321 3466778862 479999999999885 4999884
No 9
>PHA02929 N1R/p28-like protein; Provisional
Probab=95.20 E-value=0.015 Score=55.29 Aligned_cols=63 Identities=22% Similarity=0.329 Sum_probs=40.3
Q ss_pred CCCCceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhcCCceeeccccccccccchhh
Q 018282 100 SPDGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGAKNIRVSDF 171 (358)
Q Consensus 100 SpE~eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC~~~a~NV~~~df 171 (358)
+.+.+|-||++. ..........-.+..+|. -..|+.|+.+|++. ..+|.+|...+..|...+|
T Consensus 172 ~~~~eC~ICle~--~~~~~~~~~~~~vl~~C~-----H~FC~~CI~~Wl~~--~~tCPlCR~~~~~v~~~r~ 234 (238)
T PHA02929 172 SKDKECAICMEK--VYDKEIKNMYFGILSNCN-----HVFCIECIDIWKKE--KNTCPVCRTPFISVIKSRF 234 (238)
T ss_pred CCCCCCccCCcc--cccCccccccceecCCCC-----CcccHHHHHHHHhc--CCCCCCCCCEeeEEeeeee
Confidence 456789999821 111000000012334553 36999999999875 5699999999998877654
No 10
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.79 E-value=0.019 Score=57.46 Aligned_cols=49 Identities=31% Similarity=0.594 Sum_probs=38.3
Q ss_pred CceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhcCCceeeccccccc
Q 018282 103 GEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGAK 164 (358)
Q Consensus 103 ~eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC~~~a~ 164 (358)
..|=||. .|-+. .+.+-.+||+= ..|..|++.||... .+.|.+|++...
T Consensus 230 ~~CaICl--EdY~~-----GdklRiLPC~H-----~FH~~CIDpWL~~~-r~~CPvCK~di~ 278 (348)
T KOG4628|consen 230 DTCAICL--EDYEK-----GDKLRILPCSH-----KFHVNCIDPWLTQT-RTFCPVCKRDIR 278 (348)
T ss_pred ceEEEee--ccccc-----CCeeeEecCCC-----chhhccchhhHhhc-CccCCCCCCcCC
Confidence 3799998 34443 34567799973 58999999999998 778999999654
No 11
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=94.31 E-value=0.079 Score=43.93 Aligned_cols=59 Identities=25% Similarity=0.454 Sum_probs=37.3
Q ss_pred CCceeeecCCCCCCCCCC-C-CCCcceeecccccChhhhhHHHHHHHHHHh-cCCceeeccccccc
Q 018282 102 DGEVFICNTNTDLEMGPC-H-NQDTLIELGCSCRGDLALVHYGCALKWFVN-HGSTACEICGNGAK 164 (358)
Q Consensus 102 E~eCRICh~~~DlEsG~~-~-~~g~lL~lPC~CKGSL~~vHr~ClekWf~~-KGnttCEIC~~~a~ 164 (358)
+..|-||+...|..-... . .++-+|. -+.|+- ..|.+|+.+|++. +.+..|.+|.+.++
T Consensus 21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv-~g~C~H---~FH~hCI~kWl~~~~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 21 DDVCGICRMPFDGCCPDCKFPGDDCPLV-WGKCSH---NFHMHCILKWLSTQSSKGQCPMCRQPWK 82 (85)
T ss_pred CCceeeEecccccCCCCccCCCCCCcee-eccCcc---HHHHHHHHHHHccccCCCCCCCcCCeee
Confidence 667999984322111000 0 0111332 356665 6999999999997 45789999999875
No 12
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=93.29 E-value=0.063 Score=44.53 Aligned_cols=61 Identities=26% Similarity=0.429 Sum_probs=39.4
Q ss_pred CCCceeeecCCCCCCCCC--CCCCCcceeecccccChhhhhHHHHHHHHHHhcCCc-eeecccccccc
Q 018282 101 PDGEVFICNTNTDLEMGP--CHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGST-ACEICGNGAKN 165 (358)
Q Consensus 101 pE~eCRICh~~~DlEsG~--~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnt-tCEIC~~~a~N 165 (358)
|+..|-||+.+.|.---+ .-.++=+|..+ .|+ ...|..|+.+|+..+.+. .|..|.++++.
T Consensus 19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G-~C~---h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~ 82 (84)
T KOG1493|consen 19 PDETCGICRMPFDGCCPDCKLPGDDCPLVWG-YCL---HAFHAHCILKWLNTPTSQGQCPMCRQTWQF 82 (84)
T ss_pred CCCccceEecccCCcCCCCcCCCCCCccHHH-HHH---HHHHHHHHHHHhcCccccccCCcchheeEe
Confidence 344788998432211000 01123356666 554 479999999999988774 89999998864
No 13
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=93.08 E-value=0.13 Score=37.23 Aligned_cols=45 Identities=13% Similarity=0.124 Sum_probs=33.0
Q ss_pred CceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhcCCceeeccccccc
Q 018282 103 GEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGAK 164 (358)
Q Consensus 103 ~eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC~~~a~ 164 (358)
-.|.||. +. + .+++.++|+ -..-++|+++|++. +.+|.+|++.+.
T Consensus 2 ~~Cpi~~---~~-~------~~Pv~~~~G-----~v~~~~~i~~~~~~--~~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISL---EV-M------KDPVILPSG-----QTYERRAIEKWLLS--HGTDPVTGQPLT 46 (63)
T ss_pred cCCcCCC---Cc-C------CCCEECCCC-----CEEeHHHHHHHHHH--CCCCCCCcCCCC
Confidence 3588986 11 1 245777774 45789999999987 568999998863
No 14
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=91.99 E-value=0.069 Score=38.16 Aligned_cols=49 Identities=22% Similarity=0.438 Sum_probs=35.1
Q ss_pred CCceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhcCCceeeccccccccc
Q 018282 102 DGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGAKNI 166 (358)
Q Consensus 102 E~eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC~~~a~NV 166 (358)
+..|.||+ +. ..+.+..||+= ..+-..|+++|++ ....|.+|.+.+..|
T Consensus 2 ~~~C~iC~---~~-------~~~~~~~pCgH----~~~C~~C~~~~~~--~~~~CP~Cr~~i~~V 50 (50)
T PF13920_consen 2 DEECPICF---EN-------PRDVVLLPCGH----LCFCEECAERLLK--RKKKCPICRQPIESV 50 (50)
T ss_dssp HSB-TTTS---SS-------BSSEEEETTCE----EEEEHHHHHHHHH--TTSBBTTTTBB-SEE
T ss_pred cCCCccCC---cc-------CCceEEeCCCC----hHHHHHHhHHhcc--cCCCCCcCChhhcCC
Confidence 46799997 11 23578899962 1266799999999 888999999987653
No 15
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=91.71 E-value=0.067 Score=41.72 Aligned_cols=54 Identities=17% Similarity=0.507 Sum_probs=29.6
Q ss_pred CCCCceeeecCCCCCCC---CCCCCCCcceeecccccChhhhhHHHHHHHHHHhcCCceeeccc
Q 018282 100 SPDGEVFICNTNTDLEM---GPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICG 160 (358)
Q Consensus 100 SpE~eCRICh~~~DlEs---G~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC~ 160 (358)
..++.|-||+.+.+... ....++-.....+|+ =..|..|+++|++.+. +|.+|.
T Consensus 17 ~~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~-----H~FH~~Ci~~Wl~~~~--~CP~CR 73 (73)
T PF12678_consen 17 IADDNCAICREPLEDPCPECQAPQDECPIVWGPCG-----HIFHFHCISQWLKQNN--TCPLCR 73 (73)
T ss_dssp SCCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTS-----EEEEHHHHHHHHTTSS--B-TTSS
T ss_pred CcCCcccccChhhhChhhhhcCCccccceEecccC-----CCEEHHHHHHHHhcCC--cCCCCC
Confidence 34667999984321100 000111222333452 2589999999996644 999984
No 16
>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=91.68 E-value=0.18 Score=32.79 Aligned_cols=44 Identities=25% Similarity=0.696 Sum_probs=30.2
Q ss_pred ceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhcCCceeeccccc
Q 018282 104 EVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNG 162 (358)
Q Consensus 104 eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC~~~ 162 (358)
.|-||+. +. .......+|+- ..|+.|+++|++. ++..|.+|+..
T Consensus 1 ~C~iC~~--~~-------~~~~~~~~C~H-----~~c~~C~~~~~~~-~~~~Cp~C~~~ 44 (45)
T cd00162 1 ECPICLE--EF-------REPVVLLPCGH-----VFCRSCIDKWLKS-GKNTCPLCRTP 44 (45)
T ss_pred CCCcCch--hh-------hCceEecCCCC-----hhcHHHHHHHHHh-CcCCCCCCCCc
Confidence 4889972 11 12334444653 3799999999987 67789999875
No 17
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=91.50 E-value=0.28 Score=45.80 Aligned_cols=48 Identities=23% Similarity=0.484 Sum_probs=34.9
Q ss_pred CCceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhc--------------CCceeeccccccc
Q 018282 102 DGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNH--------------GSTACEICGNGAK 164 (358)
Q Consensus 102 E~eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~K--------------GnttCEIC~~~a~ 164 (358)
+-+|-||+ |.. .+++..+|+ -...+.|+.+|+..+ +...|.+|++.+.
T Consensus 18 ~~~CpICl---d~~-------~dPVvT~CG-----H~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is 79 (193)
T PLN03208 18 DFDCNICL---DQV-------RDPVVTLCG-----HLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVS 79 (193)
T ss_pred ccCCccCC---CcC-------CCcEEcCCC-----chhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCC
Confidence 56799998 221 245777773 357899999999743 3468999999875
No 18
>PHA02926 zinc finger-like protein; Provisional
Probab=91.50 E-value=0.16 Score=48.93 Aligned_cols=68 Identities=24% Similarity=0.373 Sum_probs=44.8
Q ss_pred CCCCceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhc----CCceeeccccccccccchhhHH
Q 018282 100 SPDGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNH----GSTACEICGNGAKNIRVSDFKK 173 (358)
Q Consensus 100 SpE~eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~K----GnttCEIC~~~a~NV~~~dfnk 173 (358)
|.|.+|-||.+.. .+-....+.--.+..+|. =.....|+.+|.+.+ +.+.|.+|...+.++.+++|.+
T Consensus 168 SkE~eCgICmE~I-~eK~~~~eRrFGIL~~Cn-----HsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I~pSrf~~ 239 (242)
T PHA02926 168 SKEKECGICYEVV-YSKRLENDRYFGLLDSCN-----HIFCITCINIWHRTRRETGASDNCPICRTRFRNITMSKFYK 239 (242)
T ss_pred cCCCCCccCcccc-ccccccccccccccCCCC-----chHHHHHHHHHHHhccccCcCCcCCCCcceeeeecccccee
Confidence 6688999997211 110000011123555564 237889999999975 2467999999999999998754
No 19
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=91.37 E-value=0.051 Score=42.35 Aligned_cols=53 Identities=23% Similarity=0.533 Sum_probs=23.0
Q ss_pred CCceeeecCCCCCCCCCCCCCCcceeecc---cccChhhhhHHHHHHHHHHhcCCc---------eeeccccccc
Q 018282 102 DGEVFICNTNTDLEMGPCHNQDTLIELGC---SCRGDLALVHYGCALKWFVNHGST---------ACEICGNGAK 164 (358)
Q Consensus 102 E~eCRICh~~~DlEsG~~~~~g~lL~lPC---~CKGSL~~vHr~ClekWf~~KGnt---------tCEIC~~~a~ 164 (358)
+.+|-||.. ... +.++....-| .|+. ..|..||.+||....+. .|..|.+.++
T Consensus 2 ~~~C~IC~~--~~~-----~~~~~p~~~C~n~~C~~---~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 2 ELECGICYS--YRL-----DDGEIPDVVCPNPSCGK---KFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp --S-SSS----SS------TT-----B--S-TT-------B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred CCCCCcCCc--Eec-----CCCCcCceEcCCcccCC---HHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence 568999982 111 1123334556 5664 79999999999953222 5999988754
No 20
>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=89.94 E-value=0.44 Score=29.76 Aligned_cols=31 Identities=29% Similarity=0.748 Sum_probs=23.3
Q ss_pred CcceeecccccChhhhhHHHHHHHHHHhcCCceeecc
Q 018282 123 DTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEIC 159 (358)
Q Consensus 123 g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC 159 (358)
.+.+.++|.- ..|+.|++.|++ .+...|.+|
T Consensus 9 ~~~~~~~C~H-----~~c~~C~~~~~~-~~~~~CP~C 39 (39)
T smart00184 9 KDPVVLPCGH-----TFCRSCIRKWLK-SGNNTCPIC 39 (39)
T ss_pred CCcEEecCCC-----hHHHHHHHHHHH-hCcCCCCCC
Confidence 3567788754 369999999999 566678766
No 21
>PF08510 PIG-P: PIG-P; InterPro: IPR013717 PIG-P (phosphatidylinositol N-acetylglucosaminyltransferase subunit P) is an enzyme involved in GPI anchor biosynthesis [].
Probab=88.77 E-value=0.8 Score=39.15 Aligned_cols=45 Identities=36% Similarity=0.737 Sum_probs=35.3
Q ss_pred hhhhHhHHHHHHHhhhccccchhhhHHHHHHHhhchhheeeeEEEEeeeeeeeecccchhhHHHHHHHHHh
Q 018282 274 ILLATGLLTVTLAWLIAPRVGKKTAKSGLHILLGGICALTVVVFFRFFVLTRIKYGPARYWAILFVFWFLV 344 (358)
Q Consensus 274 i~la~~l~~v~lawliap~vgkk~a~~~lh~llgg~caltvvi~~rf~v~~ri~yg~~rywailfv~wflv 344 (358)
-++.+-++++.|.|.+.|. .-||-+ =|.|=|.||||+.+=.|+|+
T Consensus 11 ~i~s~~~~~lyl~Wa~lP~-------~~L~~l-------------------gity~P~kyWAlaiP~~~l~ 55 (126)
T PF08510_consen 11 YILSTVAFVLYLLWAFLPD-------EWLHSL-------------------GITYYPDKYWALAIPSWLLM 55 (126)
T ss_pred HHHHHHHHHHHHHHHhcCH-------HHHHhc-------------------CccccCcchHHHHHHHHHHH
Confidence 3456667788899999995 456653 47788999999999888887
No 22
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=87.63 E-value=0.63 Score=48.08 Aligned_cols=56 Identities=23% Similarity=0.489 Sum_probs=38.0
Q ss_pred cCCCCceeeecCCCCCCCC----CCCCCCcceeecccccChhhhhHHHHHHHHHHhcCCceeeccccc
Q 018282 99 ISPDGEVFICNTNTDLEMG----PCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNG 162 (358)
Q Consensus 99 ~SpE~eCRICh~~~DlEsG----~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC~~~ 162 (358)
.+.++.|-||..+ -.+.+ +-...-.+-++||+ -..|-+|+..|+.- ..+|.||+..
T Consensus 284 ~n~D~~C~ICmde-~~h~~~~~~~~~~~~~pKrLpCG-----HilHl~CLknW~ER--qQTCPICr~p 343 (491)
T COG5243 284 TNSDRTCTICMDE-MFHPDHEPLPRGLDMTPKRLPCG-----HILHLHCLKNWLER--QQTCPICRRP 343 (491)
T ss_pred cCCCCeEEEeccc-ccCCCCccCcccccCCccccccc-----ceeeHHHHHHHHHh--ccCCCcccCc
Confidence 3668889999731 12222 11112345678996 36899999999874 5699999987
No 23
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=87.51 E-value=0.36 Score=54.58 Aligned_cols=56 Identities=27% Similarity=0.637 Sum_probs=38.5
Q ss_pred CCCCceeeecCCCC-CCCCCCCCCCcceeeccc-ccChhhhhHHHHHHHHHHhcCCceeecccccccc
Q 018282 100 SPDGEVFICNTNTD-LEMGPCHNQDTLIELGCS-CRGDLALVHYGCALKWFVNHGSTACEICGNGAKN 165 (358)
Q Consensus 100 SpE~eCRICh~~~D-lEsG~~~~~g~lL~lPC~-CKGSL~~vHr~ClekWf~~KGnttCEIC~~~a~N 165 (358)
|--.+|-||-.-.+ .+. .+=...|. ||. ..|-+|+-|||+.+++.+|.+|.+.+..
T Consensus 1467 sG~eECaICYsvL~~vdr-------~lPskrC~TCkn---KFH~~CLyKWf~Ss~~s~CPlCRseitf 1524 (1525)
T COG5219 1467 SGHEECAICYSVLDMVDR-------SLPSKRCATCKN---KFHTRCLYKWFASSARSNCPLCRSEITF 1524 (1525)
T ss_pred CCcchhhHHHHHHHHHhc-------cCCccccchhhh---hhhHHHHHHHHHhcCCCCCCcccccccc
Confidence 33457999962122 111 11123353 665 6899999999999999999999988653
No 24
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.91 E-value=0.62 Score=48.11 Aligned_cols=49 Identities=29% Similarity=0.586 Sum_probs=35.8
Q ss_pred CCceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhcCCceeeccccc
Q 018282 102 DGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNG 162 (358)
Q Consensus 102 E~eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC~~~ 162 (358)
+..|.||++. +..++ .-.+-.+||. -..|..|+.+||.. ..+|.+|...
T Consensus 291 ~~~C~IC~e~--l~~~~---~~~~~rL~C~-----Hifh~~CL~~W~er--~qtCP~CR~~ 339 (543)
T KOG0802|consen 291 DELCIICLEE--LHSGH---NITPKRLPCG-----HIFHDSCLRSWFER--QQTCPTCRTV 339 (543)
T ss_pred CCeeeeechh--hcccc---ccccceeecc-----cchHHHHHHHHHHH--hCcCCcchhh
Confidence 5669999822 22111 1235678885 57999999999998 7899999993
No 25
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.23 E-value=1.1 Score=45.34 Aligned_cols=63 Identities=24% Similarity=0.456 Sum_probs=41.3
Q ss_pred cccccCCCceeecCC---CCceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhcCCceeecccccc
Q 018282 87 NLVNNESGYVQFISP---DGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGA 163 (358)
Q Consensus 87 ~~v~~esg~~E~~Sp---E~eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC~~~a 163 (358)
++ .+++-..|-.+. .-+|-||. .+. ...+..+.+||.= -.|+.|+++|+.-- ...|.+|....
T Consensus 306 ~g-~lkpls~e~~~ea~~GveCaICm--s~f-----iK~d~~~vlPC~H-----~FH~~Cv~kW~~~y-~~~CPvCrt~i 371 (374)
T COG5540 306 KG-SLKPLSIERAVEADKGVECAICM--SNF-----IKNDRLRVLPCDH-----RFHVGCVDKWLLGY-SNKCPVCRTAI 371 (374)
T ss_pred Cc-ceeechhHhHHhcCCCceEEEEh--hhh-----cccceEEEeccCc-----eechhHHHHHHhhh-cccCCccCCCC
Confidence 44 344444443322 24699997 222 1345689999963 48999999999832 34799998763
No 26
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=78.62 E-value=2.6 Score=32.63 Aligned_cols=55 Identities=7% Similarity=0.063 Sum_probs=36.0
Q ss_pred cceeecccccChhhhhHHHHHHHHHHhcCCceeeccccccccccchhhHHHHHHHHHHHHH
Q 018282 124 TLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGAKNIRVSDFKKVLIALKDFEAL 184 (358)
Q Consensus 124 ~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC~~~a~NV~~~dfnkVm~slk~~~al 184 (358)
+++.+||+ ...=|+|+++|++. ++.+|.+|++....-...-...+...+++|.+-
T Consensus 16 dPVi~~~G-----~tyer~~I~~~l~~-~~~~~P~t~~~l~~~~l~pn~~Lk~~I~~~~~~ 70 (73)
T PF04564_consen 16 DPVILPSG-----HTYERSAIERWLEQ-NGGTDPFTRQPLSESDLIPNRALKSAIEEWCAE 70 (73)
T ss_dssp SEEEETTS-----EEEEHHHHHHHHCT-TSSB-TTT-SB-SGGGSEE-HHHHHHHHHHHHH
T ss_pred CceeCCcC-----CEEcHHHHHHHHHc-CCCCCCCCCCcCCcccceECHHHHHHHHHHHHH
Confidence 56778765 34668999999998 788999998876543333324566667777654
No 27
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=74.66 E-value=2.5 Score=37.86 Aligned_cols=42 Identities=17% Similarity=0.272 Sum_probs=27.5
Q ss_pred CCceeeecCCCCCCCCCCCCCCcceeecccccChhhh-hHHHHHHHHHHh
Q 018282 102 DGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLAL-VHYGCALKWFVN 150 (358)
Q Consensus 102 E~eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~-vHr~ClekWf~~ 150 (358)
..+|+||... +.. .+..+..+|.-.-.|-- .|.+|++||-+.
T Consensus 26 ~~EC~IC~~~--I~~-----~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~ 68 (134)
T PF05883_consen 26 TVECQICFDR--IDN-----NDGVVYVTDGGTLNLEKMFCADCDKRWRRE 68 (134)
T ss_pred Ceeehhhhhh--hhc-----CCCEEEEecCCeehHHHHHHHHHHHHHHhh
Confidence 6789999822 211 12356677766555544 999999999443
No 28
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=69.54 E-value=7 Score=40.10 Aligned_cols=48 Identities=21% Similarity=0.436 Sum_probs=33.8
Q ss_pred CCCceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhcCCceeecccccccc
Q 018282 101 PDGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGAKN 165 (358)
Q Consensus 101 pE~eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC~~~a~N 165 (358)
.+-.|.||+ +.- .+++..+|. -.....|+..|+..+ ..|.+|+..+..
T Consensus 25 ~~l~C~IC~---d~~-------~~PvitpCg-----H~FCs~CI~~~l~~~--~~CP~Cr~~~~~ 72 (397)
T TIGR00599 25 TSLRCHICK---DFF-------DVPVLTSCS-----HTFCSLCIRRCLSNQ--PKCPLCRAEDQE 72 (397)
T ss_pred cccCCCcCc---hhh-------hCccCCCCC-----CchhHHHHHHHHhCC--CCCCCCCCcccc
Confidence 356799997 221 234567775 235678999999874 489999998763
No 29
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.18 E-value=4.3 Score=42.33 Aligned_cols=23 Identities=35% Similarity=0.911 Sum_probs=20.6
Q ss_pred hhHHHHHHHHHHhcCC-ceeeccc
Q 018282 138 LVHYGCALKWFVNHGS-TACEICG 160 (358)
Q Consensus 138 ~vHr~ClekWf~~KGn-ttCEIC~ 160 (358)
..|..|+..||..--. +.|+||+
T Consensus 29 ifh~~cl~qwfe~~Ps~R~cpic~ 52 (465)
T KOG0827|consen 29 IFHTTCLTQWFEGDPSNRGCPICQ 52 (465)
T ss_pred HHHHHHHHHHHccCCccCCCCcee
Confidence 5899999999997666 6999999
No 30
>PF13687 DUF4153: Domain of unknown function (DUF4153)
Probab=68.44 E-value=2.5 Score=38.51 Aligned_cols=29 Identities=34% Similarity=0.954 Sum_probs=24.3
Q ss_pred eeeee-ecc--cchhhHHHHHHHHHhhhhhcc
Q 018282 322 VLTRI-KYG--PARYWAILFVFWFLVFGIWAS 350 (358)
Q Consensus 322 v~~ri-~yg--~~rywailfv~wflvfgiwas 350 (358)
+.-|| ||| |.|||++++.+|.++.+++..
T Consensus 144 i~~RI~qYGlT~~R~~~~~~~~~~~~~~l~~~ 175 (217)
T PF13687_consen 144 IWLRISQYGLTPNRYYALLLAIFLLIYALYYI 175 (217)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 45566 899 899999999999998887654
No 31
>PF08113 CoxIIa: Cytochrome c oxidase subunit IIa family; InterPro: IPR012538 This family consists of the cytochrome c oxidase subunit IIa family. The bax-type cytochrome c oxidase from Thermus thermophilus is known as a two subunit enzyme. From its crystal structure, it was discovered that an additional transmembrane helix, subunit IIa, spans the membrane. This subunit consists of 34 residues forming one helix across the membrane. The presence of this subunit seems to be important for the function of cytochrome c oxidases [].; PDB: 2QPD_C 3QJR_C 3EH5_C 3BVD_C 3S39_C 3QJU_C 3QJS_C 4EV3_C 3QJT_C 4FA7_C ....
Probab=68.42 E-value=3.6 Score=29.46 Aligned_cols=17 Identities=47% Similarity=1.122 Sum_probs=14.2
Q ss_pred HHHHHHHHHhhhhhccc
Q 018282 335 AILFVFWFLVFGIWASR 351 (358)
Q Consensus 335 ailfv~wflvfgiwasr 351 (358)
++..+|||-||...-+|
T Consensus 17 ~~ILvFWfgvf~~fl~R 33 (34)
T PF08113_consen 17 AFILVFWFGVFALFLAR 33 (34)
T ss_dssp HHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHhheec
Confidence 35678999999998887
No 32
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=67.79 E-value=5 Score=42.97 Aligned_cols=55 Identities=18% Similarity=0.493 Sum_probs=36.3
Q ss_pred CCCceeeecCCCCCCCCCC---------CCCCcceeecccccChhhhhHHHHHHHHHHhcCCceeecccccc
Q 018282 101 PDGEVFICNTNTDLEMGPC---------HNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGA 163 (358)
Q Consensus 101 pE~eCRICh~~~DlEsG~~---------~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC~~~a 163 (358)
.-.+|-||.. +.+.-.. ....+.|..||. -..|+.||++|.... .-.|.+|.+..
T Consensus 570 ~t~dC~ICMt--~I~l~~~~s~~~~~~~~~~~nYm~tPC~-----HifH~~CL~~WMd~y-kl~CPvCR~pL 633 (636)
T KOG0828|consen 570 RTNDCVICMT--PIDLRSTGSDCMVASMMVRRNYMLTPCH-----HIFHRQCLLQWMDTY-KLICPVCRCPL 633 (636)
T ss_pred ccccceEecc--ccceeeccCcchhhhhhhhccccccchH-----HHHHHHHHHHHHhhh-cccCCccCCCC
Confidence 3578999983 3331110 112356777886 479999999999832 25899998763
No 33
>COG0341 SecF Preprotein translocase subunit SecF [Intracellular trafficking and secretion]
Probab=66.89 E-value=2.2 Score=42.07 Aligned_cols=33 Identities=42% Similarity=0.801 Sum_probs=32.0
Q ss_pred hhccccchhhhHHHHHHHhhchhheeeeEEEEe
Q 018282 288 LIAPRVGKKTAKSGLHILLGGICALTVVVFFRF 320 (358)
Q Consensus 288 liap~vgkk~a~~~lh~llgg~caltvvi~~rf 320 (358)
.|.|.|||..++.++=-++.++....|.|+|||
T Consensus 123 ~Vgp~vg~eL~~~~~~Al~~alv~I~iYV~~RF 155 (305)
T COG0341 123 FVGPTVGKELARQGLLALLLALVGILIYVFFRF 155 (305)
T ss_pred EECcchHHHHHHHHHHHHHHHHHHHHHhhheee
Confidence 589999999999999999999999999999999
No 34
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=65.31 E-value=14 Score=35.84 Aligned_cols=48 Identities=21% Similarity=0.505 Sum_probs=34.7
Q ss_pred CCceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhcCCce-eeccccccc
Q 018282 102 DGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTA-CEICGNGAK 164 (358)
Q Consensus 102 E~eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGntt-CEIC~~~a~ 164 (358)
.=+|-||. |. ..+++...|+ -+.==-|+-+|+.++.++. |.+|+..+.
T Consensus 47 ~FdCNICL---d~-------akdPVvTlCG-----HLFCWpClyqWl~~~~~~~~cPVCK~~Vs 95 (230)
T KOG0823|consen 47 FFDCNICL---DL-------AKDPVVTLCG-----HLFCWPCLYQWLQTRPNSKECPVCKAEVS 95 (230)
T ss_pred ceeeeeec---cc-------cCCCEEeecc-----cceehHHHHHHHhhcCCCeeCCccccccc
Confidence 44699997 32 2367888885 1233469999999888765 599999875
No 35
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=62.33 E-value=6.4 Score=33.21 Aligned_cols=27 Identities=19% Similarity=0.437 Sum_probs=22.9
Q ss_pred hhHHHHHHHHHHhcCCceeeccccccccc
Q 018282 138 LVHYGCALKWFVNHGSTACEICGNGAKNI 166 (358)
Q Consensus 138 ~vHr~ClekWf~~KGnttCEIC~~~a~NV 166 (358)
..|-+|+.+||+.|| .|.++.+.+.--
T Consensus 57 aFH~HCI~rWL~Tk~--~CPld~q~w~~~ 83 (88)
T COG5194 57 AFHDHCIYRWLDTKG--VCPLDRQTWVLA 83 (88)
T ss_pred HHHHHHHHHHHhhCC--CCCCCCceeEEe
Confidence 589999999999955 899999988643
No 36
>KOG2257 consensus N-acetylglucosaminyltransferase complex, subunit PIG-P, required for phosphatidylinositol biosynthesis [Function unknown]
Probab=62.14 E-value=8.8 Score=34.61 Aligned_cols=45 Identities=33% Similarity=0.690 Sum_probs=34.3
Q ss_pred hhhhHhHHHHHHHhhhcccc-chhhhHHHHHHHhhchhheeeeEEEEeeeeeeeecccchhhHHHHHHHHHhh
Q 018282 274 ILLATGLLTVTLAWLIAPRV-GKKTAKSGLHILLGGICALTVVVFFRFFVLTRIKYGPARYWAILFVFWFLVF 345 (358)
Q Consensus 274 i~la~~l~~v~lawliap~v-gkk~a~~~lh~llgg~caltvvi~~rf~v~~ri~yg~~rywailfv~wflvf 345 (358)
-++.+-+++|.|.|-|-|-- ++. +| |-|=|-||||+..=.||+|-
T Consensus 15 yiv~~~~~ViylIWai~P~~~l~~---------~g------------------i~y~Psk~WalAip~~l~v~ 60 (135)
T KOG2257|consen 15 YIVSWTLFVIYLIWAITPVPILES---------LG------------------ITYYPSKYWALAIPTYLLVA 60 (135)
T ss_pred HHHHHHHHHHHHHhhcccHHHHhh---------cC------------------ceeehHHHHHHHHHHHHHHH
Confidence 45566788899999999942 221 12 88899999999999998874
No 37
>PRK12652 putative monovalent cation/H+ antiporter subunit E; Reviewed
Probab=57.55 E-value=10 Score=38.00 Aligned_cols=86 Identities=20% Similarity=0.254 Sum_probs=49.1
Q ss_pred eeecccccCCC--cceeeeecchhhhhHhHHHHHHHhhhccccchhhhHHHHHHHhhchhheeeeEEEEeeeee---eee
Q 018282 253 VTEDVVAAENP--ATKWAVEGTGILLATGLLTVTLAWLIAPRVGKKTAKSGLHILLGGICALTVVVFFRFFVLT---RIK 327 (358)
Q Consensus 253 ~~~~~~~~~~~--~t~w~~e~tgi~la~~l~~v~lawliap~vgkk~a~~~lh~llgg~caltvvi~~rf~v~~---ri~ 327 (358)
++.+..|.|-+ +++-..+.|+.-+..=.+.+.+.||+-= |.. +-.++++|-+.++.|..++|=+.+. +..
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ll~~~Wllls--g~~---s~~~l~~G~v~~~~v~~~~~~~~~~~~~~~~ 218 (357)
T PRK12652 144 ITYEEAPVERPTRRGRLVRAATLDKFAALFGASFGFYLLLG--DPL---YWFDLLTGAVTALIVAVLLAHVTFSRPPSLR 218 (357)
T ss_pred CceecCCccCccCcccccchhhhhHHHHHHHHHHHHHHHHc--CcC---CHHHHHHHHHHHHHHHHHhcccccCCccccc
Confidence 45566666654 6666666666433222234445565531 222 4589999999998888777643322 224
Q ss_pred cccchhhH-HHHHHHHH
Q 018282 328 YGPARYWA-ILFVFWFL 343 (358)
Q Consensus 328 yg~~rywa-ilfv~wfl 343 (358)
..+.|.|. +.|++|||
T Consensus 219 ~~~~r~~~~~~y~~~~l 235 (357)
T PRK12652 219 RTPLRVLRFLLYVPYLL 235 (357)
T ss_pred cchhhHHHHHHHHHHHH
Confidence 44556554 45666665
No 38
>PF04632 FUSC: Fusaric acid resistance protein family; InterPro: IPR006726 This entry represents the p-hydroxybenzoic acid efflux pump subunit AaeB (pHBA efflux pump protein B) whose substrates are p-hydroxybenzoic acid (pHBA), 6-hydroxy-2-naphthoic and 2-hydroxycinnamate. It could function as a metabolic relief valve, allowing to eliminate certain compounds when they accumulate to high levels in the cell []. This family also includes fusaric acid resistance proteins [], which are likely to be membrane transporter proteins, and uncharacterised transporter YdhK.; GO: 0006810 transport, 0005886 plasma membrane
Probab=53.22 E-value=5.1 Score=40.85 Aligned_cols=45 Identities=22% Similarity=0.318 Sum_probs=33.5
Q ss_pred hhHHHHHHHhhchhheeeeEEEEeeeeeeeecccchhhHHHHHHHH
Q 018282 297 TAKSGLHILLGGICALTVVVFFRFFVLTRIKYGPARYWAILFVFWF 342 (358)
Q Consensus 297 ~a~~~lh~llgg~caltvvi~~rf~v~~ri~yg~~rywailfv~wf 342 (358)
.++...+++.|.+++..+-.++.|+|+|.+.-. .=...+|++|+|
T Consensus 385 P~~~~~~~~~G~l~~~~~a~~~~~~vlP~~~~f-~~L~l~l~~~l~ 429 (650)
T PF04632_consen 385 PAPALRLFLIGALLGAVLAFLYLFFVLPHLDGF-PLLALVLAPFLF 429 (650)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhhccCcH-HHHHHHHHHHHH
Confidence 346678999999999999999999999998763 333444444433
No 39
>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=48.92 E-value=7.8 Score=27.95 Aligned_cols=21 Identities=29% Similarity=0.746 Sum_probs=15.7
Q ss_pred hHHHHHHHHHHhcCCceeecc
Q 018282 139 VHYGCALKWFVNHGSTACEIC 159 (358)
Q Consensus 139 vHr~ClekWf~~KGnttCEIC 159 (358)
.|..|++++|+.+.+..|..|
T Consensus 23 ~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 23 LHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp E-HHHHHHHTTT-SS-B-TTT
T ss_pred HHHHHHHHHHhcCCCCCCcCC
Confidence 999999999999998888876
No 40
>PF13179 DUF4006: Family of unknown function (DUF4006)
Probab=45.77 E-value=23 Score=28.54 Aligned_cols=28 Identities=39% Similarity=0.631 Sum_probs=21.9
Q ss_pred CCCcceeeeec-chhhhhHhHHHHHHHhh
Q 018282 261 ENPATKWAVEG-TGILLATGLLTVTLAWL 288 (358)
Q Consensus 261 ~~~~t~w~~e~-tgi~la~~l~~v~lawl 288 (358)
++.+.-|.+.| ||.|+|+-||..+||-|
T Consensus 2 ~~~r~~f~LnGi~G~LIAvvLLLsIl~~l 30 (66)
T PF13179_consen 2 NNNRSVFGLNGITGMLIAVVLLLSILAFL 30 (66)
T ss_pred CCccceeeecchHhHHHHHHHHHHHHHHH
Confidence 34455577777 89999999999888876
No 41
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 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 C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=43.32 E-value=19 Score=24.16 Aligned_cols=29 Identities=38% Similarity=0.828 Sum_probs=23.6
Q ss_pred eeecccccChhhhhHHHHHHHHHHhcCCceeecc
Q 018282 126 IELGCSCRGDLALVHYGCALKWFVNHGSTACEIC 159 (358)
Q Consensus 126 L~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC 159 (358)
..++|.= ..++.|+++|++.++...|.+|
T Consensus 13 ~~~~C~H-----~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 13 ILLPCGH-----SFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp EETTTSE-----EEEHHHHHHHHHHTSSSBTTTT
T ss_pred EEecCCC-----cchHHHHHHHHHhcCCccCCcC
Confidence 4778752 3889999999999888888877
No 42
>cd02987 Phd_like_Phd Phosducin (Phd)-like family, Phd subfamily; Phd is a cytosolic regulator of G protein functions. It specifically binds G protein betagamma (Gbg)-subunits with high affinity, resulting in the solubilization of Gbg from the plasma membrane. This impedes the formation of a functional G protein trimer (G protein alphabetagamma), thereby inhibiting G protein-mediated signal transduction. Phd also inhibits the GTPase activity of G protein alpha. Phd can be phosphorylated by protein kinase A and G protein-coupled receptor kinase 2, leading to its inactivation. Phd was originally isolated from the retina, where it is highly expressed and has been implicated to play an important role in light adaptation. It is also found in the pineal gland, liver, spleen, striated muscle and the brain. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain.
Probab=43.26 E-value=26 Score=31.29 Aligned_cols=39 Identities=18% Similarity=0.365 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhhhcCCCCCcccccCCCCChH---HHHHHHHhhhhhhhh
Q 018282 177 ALKDFEALRERTATGEPNPAHVHTSSGVDPD---AVAAIRRQRLSEISL 222 (358)
Q Consensus 177 slk~~~alRE~ta~G~~~~~~~~~~sgvdp~---~~aairrqrlsei~~ 222 (358)
=+.+|++.++. +++ ++ ...-+|-| .+..+|+|||.|+..
T Consensus 12 v~~d~~~~~~~--~~~---~~--~~d~~~~~~e~~l~~~R~~R~~el~~ 53 (175)
T cd02987 12 VINDWRKFKQL--KES---EQ--EDDDDDEDKEEFLQQYREQRMQEMHA 53 (175)
T ss_pred hHHHHHHHHhh--hch---hh--hhhhhhhhHHHHHHHHHHHHHHHHHH
Confidence 35788888777 444 22 11233555 899999999999965
No 43
>KOG2927 consensus Membrane component of ER protein translocation complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=42.73 E-value=5.7 Score=40.67 Aligned_cols=13 Identities=54% Similarity=1.160 Sum_probs=8.0
Q ss_pred HHHH-HHHHhh---hhh
Q 018282 336 ILFV-FWFLVF---GIW 348 (358)
Q Consensus 336 ilfv-~wflvf---giw 348 (358)
|||+ .|.|++ |||
T Consensus 241 ILF~I~~il~~g~~g~W 257 (372)
T KOG2927|consen 241 ILFGITWILTGGKHGFW 257 (372)
T ss_pred HHHHHHHHHhCCCCceE
Confidence 5664 466666 566
No 44
>PRK12596 putative monovalent cation/H+ antiporter subunit E; Reviewed
Probab=40.96 E-value=14 Score=33.37 Aligned_cols=55 Identities=13% Similarity=0.190 Sum_probs=31.8
Q ss_pred HHHHhhhccccchhhhHHHHHHHhhchhheeeeEEEEeeeeeeeecccchhhHHHHHHHHHh
Q 018282 283 VTLAWLIAPRVGKKTAKSGLHILLGGICALTVVVFFRFFVLTRIKYGPARYWAILFVFWFLV 344 (358)
Q Consensus 283 v~lawliap~vgkk~a~~~lh~llgg~caltvvi~~rf~v~~ri~yg~~rywailfv~wflv 344 (358)
.++.|++-= | . +-.++++|-+.++.+..++|-+.-.+..+.+ -.+++.|++||+.
T Consensus 14 L~~~WllL~--~-~---~~~~ll~G~~v~~~v~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 68 (171)
T PRK12596 14 LVLFWLLLN--S-F---TRAQFILGLVIAFGACRVMMALEPQKNHIRS-PRMMIWLLYAASI 68 (171)
T ss_pred HHHHHHHHH--c-c---cHHHHHHHHHHHHHHHHHhcccCCCCccccc-HHHHHHHHHHHHH
Confidence 356677662 4 2 3348899999998887766532212222333 3345667777653
No 45
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.27 E-value=17 Score=34.40 Aligned_cols=24 Identities=54% Similarity=1.031 Sum_probs=18.5
Q ss_pred CCceeeecCCCCCCCCCCCCCCcceeecccc
Q 018282 102 DGEVFICNTNTDLEMGPCHNQDTLIELGCSC 132 (358)
Q Consensus 102 E~eCRICh~~~DlEsG~~~~~g~lL~lPC~C 132 (358)
.+||-||. .|+|.| +.+-++||-|
T Consensus 177 kGECvICL--EdL~~G-----dtIARLPCLC 200 (205)
T KOG0801|consen 177 KGECVICL--EDLEAG-----DTIARLPCLC 200 (205)
T ss_pred CCcEEEEh--hhccCC-----CceeccceEE
Confidence 57899998 566643 4577899988
No 46
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=37.87 E-value=33 Score=30.60 Aligned_cols=64 Identities=20% Similarity=0.294 Sum_probs=40.0
Q ss_pred ceeeccccccccccchhh-HH-HHHHHHHHHHHHHhhhcCCC--CC-cccccCCCCChHHHHH-HHHhhhh
Q 018282 154 TACEICGNGAKNIRVSDF-KK-VLIALKDFEALRERTATGEP--NP-AHVHTSSGVDPDAVAA-IRRQRLS 218 (358)
Q Consensus 154 ttCEIC~~~a~NV~~~df-nk-Vm~slk~~~alRE~ta~G~~--~~-~~~~~~sgvdp~~~aa-irrqrls 218 (358)
..|..||..|.. ...++ .. .=..-++|+..|++..+..- .. ..+...+||++..+.. ||+-||.
T Consensus 4 ~nC~~CgklF~~-~~~~iCp~C~~~~e~~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL~ 73 (137)
T TIGR03826 4 ANCPKCGRLFVK-TGRDVCPSCYEEEEREFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGRLQ 73 (137)
T ss_pred ccccccchhhhh-cCCccCHHHhHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCee
Confidence 367777777764 23343 11 01123677888888774432 12 2288899999887665 8889997
No 47
>PF12732 YtxH: YtxH-like protein; InterPro: IPR024623 This family of uncharacterised proteins is found in bacteria. Proteins in this family are typically between 100 and 143 amino acids in length. The N-terminal region is the most conserved.
Probab=36.59 E-value=32 Score=26.66 Aligned_cols=22 Identities=27% Similarity=0.395 Sum_probs=16.5
Q ss_pred HhHHHHHHHhhhccccchhhhH
Q 018282 278 TGLLTVTLAWLIAPRVGKKTAK 299 (358)
Q Consensus 278 ~~l~~v~lawliap~vgkk~a~ 299 (358)
=+++-++++-|.||+-||++=+
T Consensus 8 Ga~~Ga~~glL~aP~sG~e~R~ 29 (74)
T PF12732_consen 8 GAAAGAAAGLLFAPKSGKETRE 29 (74)
T ss_pred HHHHHHHHHHHhCCCCcHHHHH
Confidence 3445567788999999998744
No 48
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=36.58 E-value=29 Score=30.61 Aligned_cols=25 Identities=16% Similarity=0.558 Sum_probs=21.0
Q ss_pred hhHHHHHHHHHHhcCCceeeccccccc
Q 018282 138 LVHYGCALKWFVNHGSTACEICGNGAK 164 (358)
Q Consensus 138 ~vHr~ClekWf~~KGnttCEIC~~~a~ 164 (358)
..|..|+.+|++.+ ..|.+|.+...
T Consensus 84 aFH~hCisrWlktr--~vCPLdn~eW~ 108 (114)
T KOG2930|consen 84 AFHFHCISRWLKTR--NVCPLDNKEWV 108 (114)
T ss_pred HHHHHHHHHHHhhc--CcCCCcCccee
Confidence 58999999999884 58999988754
No 49
>PF02355 SecD_SecF: Protein export membrane protein; InterPro: IPR022813 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. The chaperone protein SecB [] is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion []. Together with SecY and SecG, SecE forms a multimeric channel through which preproteins are translocated, using both proton motive forces and ATP-driven secretion. The latter is mediated by SecA. The structure of the Escherichia coli SecYEG assembly revealed a sandwich of two membranes interacting through the extensive cytoplasmic domains []. Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15 transmembrane helices. The SecD and SecF equivalents of the Gram-positive bacterium Bacillus subtilis are jointly present in one polypeptide, denoted SecDF, that is required to maintain a high capacity for protein secretion. Unlike the SecD subunit of the pre-protein translocase of E. coli, SecDF of B. subtilis was not required for the release of a mature secretory protein from the membrane, indicating that SecDF is involved in earlier translocation steps []. Comparison with SecD and SecF proteins from other organisms revealed the presence of 10 conserved regions in SecDF, some of which appear to be important for SecDF function. Interestingly, the SecDF protein of B. subtilis has 12 putative transmembrane domains. Thus, SecDF does not only show sequence similarity but also structural similarity to secondary solute transporters []. This entry represents bacterial SecD and SecF protein export membrane proteins and their archaeal homologues []. It is found in association with PF07549 from PFAM SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC []. SecD and SecF are required to maintain a proton motive force []. ; PDB: 3AQP_A 2RRN_A 3AQO_B.
Probab=35.97 E-value=6 Score=36.02 Aligned_cols=33 Identities=30% Similarity=0.579 Sum_probs=30.0
Q ss_pred hhccccchhhhHHHHHHHhhchhheeeeEEEEe
Q 018282 288 LIAPRVGKKTAKSGLHILLGGICALTVVVFFRF 320 (358)
Q Consensus 288 liap~vgkk~a~~~lh~llgg~caltvvi~~rf 320 (358)
.|.|-+|+...++++..++.++-+..+++++||
T Consensus 20 ~Vgp~~g~~~~~~~~~a~~~al~~i~iyi~~rf 52 (189)
T PF02355_consen 20 TVGPTLGSDLLKSALIALIIALIAILIYIFLRF 52 (189)
T ss_dssp EE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred EEChhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 478999999999999999999999999999999
No 50
>PF14353 CpXC: CpXC protein
Probab=35.57 E-value=28 Score=29.12 Aligned_cols=29 Identities=14% Similarity=0.235 Sum_probs=24.3
Q ss_pred ccCCCCChHHHHHHHHhhhhhhhhhcccCCCC
Q 018282 199 HTSSGVDPDAVAAIRRQRLSEISLWFSPHSSN 230 (358)
Q Consensus 199 ~~~sgvdp~~~aairrqrlsei~~wf~ph~~~ 230 (358)
..|+..||++..+|... ++-++=|||..+
T Consensus 18 ~I~~~~~p~l~e~il~g---~l~~~~CP~Cg~ 46 (128)
T PF14353_consen 18 SINADEDPELKEKILDG---SLFSFTCPSCGH 46 (128)
T ss_pred EEcCcCCHHHHHHHHcC---CcCEEECCCCCC
Confidence 56778899999999988 566788999965
No 51
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.45 E-value=13 Score=37.38 Aligned_cols=67 Identities=18% Similarity=0.372 Sum_probs=43.5
Q ss_pred CCceeecCCCCceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhcCCceeeccccccc
Q 018282 93 SGYVQFISPDGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGAK 164 (358)
Q Consensus 93 sg~~E~~SpE~eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC~~~a~ 164 (358)
+|+|.=--.+..|-||-...|.+.....--++.-.+-|+ --.|.-|+.-|+..-...+|.-|++...
T Consensus 215 ~glPtkhl~d~vCaVCg~~~~~s~~eegvienty~LsCn-----HvFHEfCIrGWcivGKkqtCPYCKekVd 281 (328)
T KOG1734|consen 215 SGLPTKHLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCN-----HVFHEFCIRGWCIVGKKQTCPYCKEKVD 281 (328)
T ss_pred CCCCCCCCCcchhHhhcchheeecchhhhhhhheeeecc-----cchHHHhhhhheeecCCCCCchHHHHhh
Confidence 444443234678999964333322111011355566664 2589999999999999999999998863
No 52
>PF06197 DUF998: Protein of unknown function (DUF998); InterPro: IPR009339 This is a family of proteins with no known function.
Probab=32.87 E-value=33 Score=29.17 Aligned_cols=27 Identities=15% Similarity=0.220 Sum_probs=17.4
Q ss_pred CcceeeeecchhhhhHhHHHHHHHhhhcc
Q 018282 263 PATKWAVEGTGILLATGLLTVTLAWLIAP 291 (358)
Q Consensus 263 ~~t~w~~e~tgi~la~~l~~v~lawliap 291 (358)
..++|-. .+-++..|++.+..+|.+..
T Consensus 36 ~p~~~~~--~~~~~~~g~~~~~~a~~l~~ 62 (184)
T PF06197_consen 36 SPYAWLF--NIGFILSGVLFLAFAVGLFR 62 (184)
T ss_pred CCcHHHH--HHHHHHHHHHHHHHHHHHHH
Confidence 3445555 34566778888888887743
No 53
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=30.77 E-value=20 Score=20.64 Aligned_cols=12 Identities=33% Similarity=0.924 Sum_probs=8.4
Q ss_pred eeeccccccccc
Q 018282 155 ACEICGNGAKNI 166 (358)
Q Consensus 155 tCEIC~~~a~NV 166 (358)
.|++|++.|.+.
T Consensus 2 ~C~~C~~~~~~~ 13 (24)
T PF13894_consen 2 QCPICGKSFRSK 13 (24)
T ss_dssp E-SSTS-EESSH
T ss_pred CCcCCCCcCCcH
Confidence 699999998865
No 54
>cd07922 CarBa CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. 2-aminophenol 1,6-dioxygenase is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, the enzyme has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=30.77 E-value=40 Score=27.75 Aligned_cols=50 Identities=22% Similarity=0.330 Sum_probs=42.3
Q ss_pred hhhHHHHHHHHHHHHHHHhhhcCCCCCcccccCCCCChHHHHHHHHhhhhhhh
Q 018282 169 SDFKKVLIALKDFEALRERTATGEPNPAHVHTSSGVDPDAVAAIRRQRLSEIS 221 (358)
Q Consensus 169 ~dfnkVm~slk~~~alRE~ta~G~~~~~~~~~~sgvdp~~~aairrqrlsei~ 221 (358)
.++|+++.++..-.++||++..- |-.+....|+.+...+++|+-....|.
T Consensus 4 y~~nrli~~L~~dp~~rerF~~D---Pea~~~~~gLt~eE~~aL~~~D~~~L~ 53 (81)
T cd07922 4 YPVNRLIQELFKDPGLIERFQDD---PSAVFEEYGLTPAERAALREGTFGALT 53 (81)
T ss_pred HHHHHHHHHHhcCHHHHHHHHHC---HHHHHHHcCCCHHHHHHHHccCHHHHH
Confidence 46799999999999999999864 478899999999999999987766554
No 55
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.27 E-value=41 Score=34.49 Aligned_cols=44 Identities=27% Similarity=0.622 Sum_probs=29.6
Q ss_pred CCCceeeecCCCCCCCCCCCCCCcceeeccc----ccChhhhhHHHHHHHHHHhcCCceeeccccccc
Q 018282 101 PDGEVFICNTNTDLEMGPCHNQDTLIELGCS----CRGDLALVHYGCALKWFVNHGSTACEICGNGAK 164 (358)
Q Consensus 101 pE~eCRICh~~~DlEsG~~~~~g~lL~lPC~----CKGSL~~vHr~ClekWf~~KGnttCEIC~~~a~ 164 (358)
...+|=||+ . +.-+.+.+||+ |+| |++.--- -.+.|.||.+.+.
T Consensus 289 ~gkeCVICl--s--------e~rdt~vLPCRHLCLCs~--------Ca~~Lr~--q~n~CPICRqpi~ 336 (349)
T KOG4265|consen 289 SGKECVICL--S--------ESRDTVVLPCRHLCLCSG--------CAKSLRY--QTNNCPICRQPIE 336 (349)
T ss_pred CCCeeEEEe--c--------CCcceEEecchhhehhHh--------HHHHHHH--hhcCCCccccchH
Confidence 357899998 1 23467899986 554 6655431 2357999999875
No 56
>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=30.01 E-value=89 Score=31.49 Aligned_cols=52 Identities=25% Similarity=0.385 Sum_probs=33.0
Q ss_pred CCceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhcCCceeeccccccc
Q 018282 102 DGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGAK 164 (358)
Q Consensus 102 E~eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC~~~a~ 164 (358)
+..|-||. ++.-..+ .-..+..+|+ - -.=+.|+++.|. +|...|..|+..++
T Consensus 3 ~~~CP~Ck--~~~y~np---~~kl~i~~CG--H---~~C~sCv~~l~~-~~~~~CP~C~~~lr 54 (309)
T TIGR00570 3 DQGCPRCK--TTKYRNP---SLKLMVNVCG--H---TLCESCVDLLFV-RGSGSCPECDTPLR 54 (309)
T ss_pred CCCCCcCC--CCCccCc---ccccccCCCC--C---cccHHHHHHHhc-CCCCCCCCCCCccc
Confidence 45799998 3322211 1234666663 1 234689999875 47789999998764
No 57
>PF11872 DUF3392: Protein of unknown function (DUF3392); InterPro: IPR021813 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 110 amino acids in length.
Probab=29.55 E-value=42 Score=29.06 Aligned_cols=23 Identities=26% Similarity=0.587 Sum_probs=16.9
Q ss_pred cchhhHHHHHHHHHhhhhhcccc
Q 018282 330 PARYWAILFVFWFLVFGIWASRT 352 (358)
Q Consensus 330 ~~rywailfv~wflvfgiwasrt 352 (358)
|..|=+...+..|++.|+||-|.
T Consensus 84 ~~~~l~~~vl~~F~~iG~lAqR~ 106 (106)
T PF11872_consen 84 PNYWLAPVVLLSFILIGVLAQRN 106 (106)
T ss_pred CchHHHHHHHHHHHHHHHHhccC
Confidence 44444556677899999999883
No 58
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=29.51 E-value=39 Score=22.93 Aligned_cols=27 Identities=19% Similarity=0.562 Sum_probs=19.7
Q ss_pred eeecccccChhhhhHHHHHHHHHHhcCCceeecc
Q 018282 126 IELGCSCRGDLALVHYGCALKWFVNHGSTACEIC 159 (358)
Q Consensus 126 L~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC 159 (358)
+.++|+ -...++|+++|++. +..|.+|
T Consensus 13 ~~~~CG-----H~fC~~C~~~~~~~--~~~CP~C 39 (39)
T PF13923_consen 13 VVTPCG-----HSFCKECIEKYLEK--NPKCPVC 39 (39)
T ss_dssp EECTTS-----EEEEHHHHHHHHHC--TSB-TTT
T ss_pred EECCCC-----CchhHHHHHHHHHC--cCCCcCC
Confidence 567774 24789999999988 4788776
No 59
>TIGR00942 2a6301s05 Monovalent Cation (K+ or Na+):Proton Antiporter-3 (CPA3) subfamily.
Probab=27.81 E-value=19 Score=31.56 Aligned_cols=42 Identities=24% Similarity=0.166 Sum_probs=24.9
Q ss_pred HHHHHhhchhheeeeEEEEeeeeeeeecccchhh-HHHHHHHHHh
Q 018282 301 GLHILLGGICALTVVVFFRFFVLTRIKYGPARYW-AILFVFWFLV 344 (358)
Q Consensus 301 ~lh~llgg~caltvvi~~rf~v~~ri~yg~~ryw-ailfv~wflv 344 (358)
-.|+++|.+.++.|..++|-+...| .=+-|.+ ++.|++||+.
T Consensus 10 ~~~l~~G~vv~l~v~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~ 52 (144)
T TIGR00942 10 PGSIVLGLIFSTVLAWVTLNLQPAR--SRLHRWSRIIGFILRFLG 52 (144)
T ss_pred HHHHHHHHHHHHHHHHHHhhccCCC--CCcccHHHHHHHHHHHHH
Confidence 3578888888888876666432223 1123333 4557777764
No 60
>TIGR00869 sec62 protein translocation protein, Sec62 family. protein secretary systems of yeast microsomes. They are also the non-selective cation (NS) channels of the mammalian cytoplasmic membrane. The yeast Sec62 protein has been shown to be essential for cell growth. The mammalian NS channel proteins has been implicated in platelet derived growth factor(PGDF) dependent single channel current in fibroblasts. These channels are essentially closed in serum deprived tissue-culture cells and are specifically opened by exposure to PDGF. These channels are reported to exhibit equal selectivity for Na+, K+ and Cs+ with low permeability to Ca2+, and no permeability to anions.
Probab=26.72 E-value=33 Score=33.21 Aligned_cols=29 Identities=17% Similarity=0.306 Sum_probs=17.3
Q ss_pred Ccceeeeecch---hhhhHhHHHHHHHhhhcc
Q 018282 263 PATKWAVEGTG---ILLATGLLTVTLAWLIAP 291 (358)
Q Consensus 263 ~~t~w~~e~tg---i~la~~l~~v~lawliap 291 (358)
..--|.-|++- .+++++++++++|--.-|
T Consensus 106 ~~YvW~ye~~~~~~~l~~~~~~~~ila~~lFP 137 (232)
T TIGR00869 106 MYYVWNYNPRPYMDYLIVILVVSIILALVLFP 137 (232)
T ss_pred ceEEEEecCCcHHHHHHHHHHHHHHHHHhhcc
Confidence 35567777653 456666666666654444
No 61
>PF01440 Gemini_AL2: Geminivirus AL2 protein; InterPro: IPR000942 Geminiviruses are characterised by a genome of circular single-stranded DNA encapsidated in twinned (geminate) quasi-isometric particles, from which the group derives its name []. Most geminiviruses can be divided into two subgroups on the basis of host range and/or insect vector: i.e. those that infect dicotyledenous plants and are transmitted by the same whitefly species, and those that infect monocotyledenous plants and are transmitted by different leafhopper vectors. The genomes of the whitefly-transmitted African cassava mosaic virus, Tomato golden mosaic virus (TGMV) and Bean golden mosaic virus (BGMV) possess a bipartite genome. By contrast, only a single DNA component has been identified for the leafhopper-transmitted Maize streak virus (MSV) and Wheat dwarf virus (WDV) [, ]. Beet curly top virus (BCTV), and Tobacco yellow dwarf virus belong to a third possible subgroup. Like MSV and WDV, BCTV is transmitted by a specific leafhopper species, yet like the whitefly-transmitted geminiviruses it has a host range confined to dicotyledenous plants. Sequence comparison of the whitefly-transmitted Squash leaf curl virus (SqLCV) and Tomato yellow leaf curl virus (TYLCV) with the genomic components of TGMV and BGMV reveals a close evolutionary relationship [, , ]. Amino acid sequence alignments of Potato yellow mosaic virus (PYMV) proteins with those encoded by other geminiviruses show that PYMV is closely related to geminiviruses isolated from the New World, especially in the putative coat protein gene regions []. Comparison of MSV DNA-encoded proteins with those of other geminiviruses infecting monocotyledonous plants, including Panicum streak virus [] and Miscanthus streak virus (MiSV) [], reveal high levels of similarity.; GO: 0005198 structural molecule activity, 0019028 viral capsid
Probab=26.28 E-value=7.8 Score=34.67 Aligned_cols=31 Identities=29% Similarity=0.715 Sum_probs=27.9
Q ss_pred cceeecccccChhhhhHHHHHHHHHHhcCCceee
Q 018282 124 TLIELGCSCRGDLALVHYGCALKWFVNHGSTACE 157 (358)
Q Consensus 124 ~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCE 157 (358)
..+.++|+|.= |+|-.|....|..+|+..|-
T Consensus 31 RRIDL~CGCSy---yihinC~~hGFTHRGthhCs 61 (134)
T PF01440_consen 31 RRIDLPCGCSY---YIHINCHNHGFTHRGTHHCS 61 (134)
T ss_pred CccccCCCCEE---EeecccCCCCcCCCcCccCC
Confidence 56889999985 89999999999999999884
No 62
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=25.95 E-value=66 Score=34.04 Aligned_cols=52 Identities=21% Similarity=0.486 Sum_probs=33.1
Q ss_pred CceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHhcCCceeeccccccc
Q 018282 103 GEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVNHGSTACEICGNGAK 164 (358)
Q Consensus 103 ~eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~KGnttCEIC~~~a~ 164 (358)
..|-||. ...++... .....+-|. -..-.+|+|+|+-.+-...|..|.-.+.
T Consensus 5 ~tcpicl--ds~~~~g~---hr~vsl~cg-----hlFgs~cie~wl~k~~~~~cp~c~~kat 56 (463)
T KOG1645|consen 5 TTCPICL--DSYTTAGN---HRIVSLQCG-----HLFGSQCIEKWLGKKTKMQCPLCSGKAT 56 (463)
T ss_pred ccCceee--eeeeecCc---eEEeeeccc-----ccccHHHHHHHHhhhhhhhCcccCChhH
Confidence 4599997 22233211 123333342 2455799999998666789999998875
No 63
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=25.31 E-value=23 Score=27.62 Aligned_cols=34 Identities=21% Similarity=0.621 Sum_probs=21.8
Q ss_pred CCCCceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHH
Q 018282 100 SPDGEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALK 146 (358)
Q Consensus 100 SpE~eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~Clek 146 (358)
.++..|.+|+... +. +.-...||+ ..+|+.|+.|
T Consensus 76 ~~~~~C~vC~k~l----~~----~~f~~~p~~-----~v~H~~C~~r 109 (109)
T PF10367_consen 76 TESTKCSVCGKPL----GN----SVFVVFPCG-----HVVHYSCIKR 109 (109)
T ss_pred CCCCCccCcCCcC----CC----ceEEEeCCC-----eEEecccccC
Confidence 5577799998322 11 244566664 5789999754
No 64
>PRK12651 putative monovalent cation/H+ antiporter subunit E; Reviewed
Probab=25.18 E-value=46 Score=29.46 Aligned_cols=54 Identities=31% Similarity=0.406 Sum_probs=32.5
Q ss_pred HHHhhhccccchhhhHHHHHHHhhchhheeeeEEEEeeeeeeeecccch-hhHHHHHHHHHh
Q 018282 284 TLAWLIAPRVGKKTAKSGLHILLGGICALTVVVFFRFFVLTRIKYGPAR-YWAILFVFWFLV 344 (358)
Q Consensus 284 ~lawliap~vgkk~a~~~lh~llgg~caltvvi~~rf~v~~ri~yg~~r-ywailfv~wflv 344 (358)
++.|++.= |. .+-.++++|-+.++.+..+++.+...+. -+-| ..++.|++||+.
T Consensus 12 ~~~W~lL~--g~---~~~~~l~~G~~v~~~v~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~ 66 (158)
T PRK12651 12 AVLWLFLT--GS---FSLGNFIIGFILGLFVLFLFRRLLPARF--YLRRIYKLIKLVPIFLK 66 (158)
T ss_pred HHHHHHHh--CC---cCHHHHHHHHHHHHHHHHHHhhccCCCc--ccccHHHHHHHHHHHHH
Confidence 55666542 22 2457899999988887777776443332 2334 335556777764
No 65
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.63 E-value=1.1e+02 Score=30.42 Aligned_cols=48 Identities=25% Similarity=0.482 Sum_probs=35.0
Q ss_pred CceeeecCCCCCCCCCCCCCCcceeecccccChhhhhHHHHHHHHHHh-cCC-----ceeecccccc
Q 018282 103 GEVFICNTNTDLEMGPCHNQDTLIELGCSCRGDLALVHYGCALKWFVN-HGS-----TACEICGNGA 163 (358)
Q Consensus 103 ~eCRICh~~~DlEsG~~~~~g~lL~lPC~CKGSL~~vHr~ClekWf~~-KGn-----ttCEIC~~~a 163 (358)
.-||.|. +.+++ ++.+.+-| +-+.|-+|+..|-.. -.| -.|.-|.+++
T Consensus 51 pNC~LC~--t~La~------gdt~RLvC-----yhlfHW~ClneraA~lPanTAPaGyqCP~Cs~ei 104 (299)
T KOG3970|consen 51 PNCRLCN--TPLAS------GDTTRLVC-----YHLFHWKCLNERAANLPANTAPAGYQCPCCSQEI 104 (299)
T ss_pred CCCceeC--Ccccc------Ccceeehh-----hhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCcc
Confidence 4599996 56654 45577877 467999999999764 222 3899998875
No 66
>PF08173 YbgT_YccB: Membrane bound YbgT-like protein; InterPro: IPR012994 This family contains a set of membrane proteins, typically 33 amino acids long. The family has no known function, but the protein is found in the operon CydAB in Escherichia coli. Members have a consensus motif (MWYFXW), which is rich in aromatic residues. The protein forms a single membrane-spanning helix. This family seems to be restricted to proteobacteria [].
Probab=24.33 E-value=65 Score=22.21 Aligned_cols=16 Identities=38% Similarity=0.744 Sum_probs=14.3
Q ss_pred hhhhhHhHHHHHHHhh
Q 018282 273 GILLATGLLTVTLAWL 288 (358)
Q Consensus 273 gi~la~~l~~v~lawl 288 (358)
|++||..+.++...|+
T Consensus 9 G~~lA~~~~i~~a~wl 24 (28)
T PF08173_consen 9 GVLLACAFGILNAMWL 24 (28)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 8899999999988886
No 67
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=24.26 E-value=46 Score=35.44 Aligned_cols=62 Identities=24% Similarity=0.378 Sum_probs=40.8
Q ss_pred CcceeecccccChhhhhHHHHHHHHH-HhcC---Cceeeccc-cccccccchhhHHHHHHHHHHHHHHHhhhcCCCCCc
Q 018282 123 DTLIELGCSCRGDLALVHYGCALKWF-VNHG---STACEICG-NGAKNIRVSDFKKVLIALKDFEALRERTATGEPNPA 196 (358)
Q Consensus 123 g~lL~lPC~CKGSL~~vHr~ClekWf-~~KG---nttCEIC~-~~a~NV~~~dfnkVm~slk~~~alRE~ta~G~~~~~ 196 (358)
.+++.+|=+=.|.- +=-|| +.+| .-.||||| ++|.--...+ +-|.+||--+=++--|-|+-.
T Consensus 374 ynp~~lPLGwDGkP-------iPyWLyKLHGL~~ey~CEICGNy~Y~GrkaF~-----RHF~EwRH~hGmrCLGIpnt~ 440 (497)
T KOG2636|consen 374 YNPKNLPLGWDGKP-------IPYWLYKLHGLDIEYNCEICGNYVYKGRKAFD-----RHFNEWRHAHGMRCLGIPNTS 440 (497)
T ss_pred CCcccCCCCCCCCc-------CchHHHhhcCCCcccceeeccCccccCcHHHH-----HHhHHHHHhhcceecCCCCcH
Confidence 45666666555531 22354 3555 56899999 8887766655 667888888888888875433
No 68
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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 C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=23.73 E-value=32 Score=20.54 Aligned_cols=12 Identities=33% Similarity=0.847 Sum_probs=10.1
Q ss_pred eeeccccccccc
Q 018282 155 ACEICGNGAKNI 166 (358)
Q Consensus 155 tCEIC~~~a~NV 166 (358)
.|++|+..|.+-
T Consensus 2 ~C~~C~~~f~~~ 13 (23)
T PF00096_consen 2 KCPICGKSFSSK 13 (23)
T ss_dssp EETTTTEEESSH
T ss_pred CCCCCCCccCCH
Confidence 699999998754
No 69
>COG3304 Predicted membrane protein [Function unknown]
Probab=23.36 E-value=40 Score=30.81 Aligned_cols=23 Identities=35% Similarity=0.824 Sum_probs=18.2
Q ss_pred chhhHHHHHHHHHhhhhhccccc
Q 018282 331 ARYWAILFVFWFLVFGIWASRTH 353 (358)
Q Consensus 331 ~rywailfv~wflvfgiwasrt~ 353 (358)
--.=+++=++||+.||.|-.=.|
T Consensus 71 ~~~g~l~NiiWfil~G~WLal~H 93 (145)
T COG3304 71 GTGGALLNIIWFILFGWWLALGH 93 (145)
T ss_pred CchHHHHHHHHHHHHHHHHHHHH
Confidence 34568999999999999975544
No 70
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=22.55 E-value=54 Score=24.84 Aligned_cols=33 Identities=18% Similarity=0.287 Sum_probs=17.5
Q ss_pred eeecccccChhhhhHHHHHHHHHHhc--CCceeeccccccc
Q 018282 126 IELGCSCRGDLALVHYGCALKWFVNH--GSTACEICGNGAK 164 (358)
Q Consensus 126 L~lPC~CKGSL~~vHr~ClekWf~~K--GnttCEIC~~~a~ 164 (358)
-..||.|. ++-|..=|..++ ++..|.-|++.|.
T Consensus 14 ~~~PC~Cg------f~IC~~C~~~i~~~~~g~CPgCr~~Y~ 48 (48)
T PF14570_consen 14 DFYPCECG------FQICRFCYHDILENEGGRCPGCREPYK 48 (48)
T ss_dssp T--SSTTS----------HHHHHHHTTSS-SB-TTT--B--
T ss_pred ccccCcCC------CcHHHHHHHHHHhccCCCCCCCCCCCC
Confidence 35899996 466888888887 4789999998873
No 71
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=21.50 E-value=60 Score=20.06 Aligned_cols=12 Identities=25% Similarity=0.855 Sum_probs=10.6
Q ss_pred eeeccccccccc
Q 018282 155 ACEICGNGAKNI 166 (358)
Q Consensus 155 tCEIC~~~a~NV 166 (358)
.|++|+..|.++
T Consensus 3 ~C~~C~~~F~~~ 14 (27)
T PF13912_consen 3 ECDECGKTFSSL 14 (27)
T ss_dssp EETTTTEEESSH
T ss_pred CCCccCCccCCh
Confidence 699999999876
No 72
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=21.44 E-value=55 Score=25.81 Aligned_cols=21 Identities=24% Similarity=0.477 Sum_probs=14.1
Q ss_pred cccChhhh------hHHHHHHHHHHhc
Q 018282 131 SCRGDLAL------VHYGCALKWFVNH 151 (358)
Q Consensus 131 ~CKGSL~~------vHr~ClekWf~~K 151 (358)
.|+|+... +++.|+++|++.+
T Consensus 23 nc~~~~RAaarkf~V~r~~Vr~W~kqe 49 (58)
T PF09607_consen 23 NCKGNQRAAARKFNVSRRQVRKWRKQE 49 (58)
T ss_dssp TTTT-HHHHHHHTTS-HHHHHHHHTTH
T ss_pred chhhhHHHHHHHhCccHHHHHHHHHHH
Confidence 46665554 6999999999864
No 73
>PF03839 Sec62: Translocation protein Sec62; InterPro: IPR004728 Members of the NSCC2 family have been sequenced from various yeast, fungal and animals species including Saccharomyces cerevisiae, Drosophila melanogaster and Homo sapiens. These proteins are the Sec62 proteins, believed to be associated with the Sec61 and Sec63 constituents of the general protein secretary systems of yeast microsomes. They are also the non-selective cation (NS) channels of the mammalian cytoplasmic membrane. The yeast Sec62 protein has been shown to be essential for cell growth. The mammalian NS channel proteins have been implicated in platelet derived growth factor(PGDF) dependent single channel current in fibroblasts. These channels are essentially closed in serum deprived tissue-culture cells and are specifically opened by exposure to PDGF. These channels are reported to exhibit equal selectivity for Na+, K+ and Cs+ with low permeability to Ca2+, and no permeability to anions.; GO: 0008565 protein transporter activity, 0015031 protein transport, 0016021 integral to membrane
Probab=21.06 E-value=51 Score=31.63 Aligned_cols=14 Identities=29% Similarity=1.101 Sum_probs=9.3
Q ss_pred HHHHHHHHhhh---hhc
Q 018282 336 ILFVFWFLVFG---IWA 349 (358)
Q Consensus 336 ilfv~wflvfg---iwa 349 (358)
|-.+.|++++| +|-
T Consensus 163 lf~i~w~~~~g~~~fWl 179 (224)
T PF03839_consen 163 LFLITWFFTGGKHGFWL 179 (224)
T ss_pred HHHHHHHHhcCCCCEEe
Confidence 34567888855 773
Done!