Query 001377
Match_columns 1090
No_of_seqs 410 out of 956
Neff 5.4
Searched_HMMs 46136
Date Thu Mar 28 23:15:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001377.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001377hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1952 Transcription factor N 100.0 1E-164 2E-169 1433.3 47.9 734 81-858 161-901 (950)
2 KOG1952 Transcription factor N 100.0 3.3E-60 7.3E-65 556.1 17.1 539 237-844 237-858 (950)
3 cd02643 R3H_NF-X1 R3H domain o 99.8 7.5E-19 1.6E-23 158.2 7.2 74 770-844 1-74 (74)
4 cd06006 R3H_unknown_2 R3H doma 99.7 2.3E-17 5E-22 141.7 6.7 59 780-844 1-59 (59)
5 cd02642 R3H_encore_like R3H do 99.4 9.1E-13 2E-17 115.3 7.8 62 777-845 2-63 (63)
6 cd02646 R3H_G-patch R3H domain 99.3 2E-12 4.4E-17 111.4 6.5 57 781-844 2-58 (58)
7 smart00393 R3H Putative single 99.3 4.9E-12 1.1E-16 115.4 5.1 70 769-845 10-79 (79)
8 cd02636 R3H_sperm-antigen R3H 99.2 9.3E-12 2E-16 106.9 5.9 59 781-845 2-61 (61)
9 PF01424 R3H: R3H domain; Int 99.2 1.4E-11 2.9E-16 107.5 6.9 58 781-845 6-63 (63)
10 cd02641 R3H_Smubp-2_like R3H d 99.2 1.8E-11 4E-16 106.2 6.7 58 781-844 2-60 (60)
11 cd06008 NF-X1-zinc-finger Pres 99.2 1.1E-11 2.5E-16 103.2 3.2 49 271-319 1-49 (49)
12 cd02644 R3H_jag R3H domain fou 99.2 2.2E-11 4.7E-16 108.0 4.7 64 781-844 2-66 (67)
13 cd06008 NF-X1-zinc-finger Pres 99.1 6.8E-11 1.5E-15 98.6 3.7 48 393-440 1-48 (49)
14 cd02325 R3H R3H domain. The na 99.1 2.7E-10 5.8E-15 96.2 6.7 58 781-844 2-59 (59)
15 cd02640 R3H_NRF R3H domain of 99.0 1.4E-09 3.1E-14 94.4 6.9 57 782-844 3-60 (60)
16 cd06007 R3H_DEXH_helicase R3H 98.9 1.9E-09 4.2E-14 93.2 6.6 56 782-844 3-59 (59)
17 cd02638 R3H_unknown_1 R3H doma 98.9 3.3E-09 7.1E-14 91.4 6.2 58 782-844 3-61 (62)
18 COG1847 Jag Predicted RNA-bind 98.7 9.7E-09 2.1E-13 108.3 5.4 68 777-844 139-207 (208)
19 cd02645 R3H_AAA R3H domain of 98.6 7.7E-08 1.7E-12 83.7 5.3 41 803-843 19-59 (60)
20 PF13639 zf-RING_2: Ring finge 97.8 1.2E-05 2.5E-10 65.4 1.7 43 113-170 2-44 (44)
21 PF01422 zf-NF-X1: NF-X1 type 97.7 1.9E-05 4E-10 53.8 1.6 20 281-300 1-20 (20)
22 PF01422 zf-NF-X1: NF-X1 type 97.7 2.4E-05 5.3E-10 53.3 1.8 20 498-517 1-20 (20)
23 smart00438 ZnF_NFX Repressor o 97.0 0.0003 6.4E-09 51.3 1.6 22 281-302 1-22 (26)
24 cd02639 R3H_RRM R3H domain of 96.9 0.0013 2.8E-08 57.6 4.5 43 802-844 17-60 (60)
25 smart00438 ZnF_NFX Repressor o 96.7 0.00081 1.8E-08 49.1 1.7 21 498-518 1-21 (26)
26 PF11793 FANCL_C: FANCL C-term 96.3 0.00086 1.9E-08 60.3 -0.6 61 111-174 2-66 (70)
27 PF10309 DUF2414: Protein of u 95.9 0.017 3.7E-07 51.0 5.6 49 883-932 11-62 (62)
28 cd00162 RING RING-finger (Real 95.2 0.014 3E-07 46.0 2.4 44 113-172 1-44 (45)
29 PF12678 zf-rbx1: RING-H2 zinc 95.2 0.017 3.6E-07 52.5 3.2 42 113-170 21-73 (73)
30 PHA02926 zinc finger-like prot 95.2 0.023 5.1E-07 61.3 4.6 72 95-175 153-231 (242)
31 COG5540 RING-finger-containing 94.4 0.045 9.7E-07 61.2 4.7 50 110-173 322-371 (374)
32 PF12861 zf-Apc11: Anaphase-pr 94.3 0.039 8.5E-07 51.5 3.3 52 112-174 22-82 (85)
33 PHA02929 N1R/p28-like protein; 94.1 0.043 9.4E-07 60.5 3.8 66 96-175 158-228 (238)
34 PF13923 zf-C3HC4_2: Zinc fing 93.9 0.061 1.3E-06 42.7 3.2 32 114-148 1-32 (39)
35 PLN03208 E3 ubiquitin-protein 93.6 0.059 1.3E-06 57.5 3.6 62 110-175 17-80 (193)
36 COG5219 Uncharacterized conser 93.1 0.044 9.6E-07 68.5 1.8 58 102-172 1461-1521(1525)
37 COG5243 HRD1 HRD ubiquitin lig 92.8 0.11 2.4E-06 59.5 4.3 60 99-172 275-343 (491)
38 PF00097 zf-C3HC4: Zinc finger 87.6 0.42 9E-06 38.0 2.3 32 114-148 1-32 (41)
39 smart00184 RING Ring finger. E 87.2 0.46 9.9E-06 35.8 2.2 30 114-147 1-30 (39)
40 KOG4628 Predicted E3 ubiquitin 84.8 0.78 1.7E-05 53.3 3.5 48 113-174 231-278 (348)
41 KOG4483 Uncharacterized conser 84.7 1 2.3E-05 52.3 4.4 51 881-931 392-446 (528)
42 PF05883 Baculo_RING: Baculovi 84.6 0.75 1.6E-05 46.6 2.8 49 97-147 12-67 (134)
43 PF00628 PHD: PHD-finger; Int 79.5 0.4 8.6E-06 39.9 -1.0 48 114-170 2-49 (51)
44 KOG4443 Putative transcription 77.8 0.99 2.1E-05 55.6 1.2 51 113-172 20-71 (694)
45 KOG0804 Cytoplasmic Zn-finger 77.6 0.77 1.7E-05 54.2 0.2 48 111-174 175-222 (493)
46 PHA02825 LAP/PHD finger-like p 74.4 2.5 5.3E-05 44.1 2.8 56 108-175 5-60 (162)
47 smart00744 RINGv The RING-vari 74.3 2.3 5E-05 35.9 2.1 45 113-170 1-49 (49)
48 PF13920 zf-C3HC4_3: Zinc fing 74.0 3 6.4E-05 34.8 2.7 44 112-173 3-47 (50)
49 KOG1493 Anaphase-promoting com 73.8 1.2 2.6E-05 40.9 0.3 34 127-173 47-80 (84)
50 KOG0827 Predicted E3 ubiquitin 71.8 2.9 6.2E-05 48.8 2.8 12 730-741 146-157 (465)
51 KOG3970 Predicted E3 ubiquitin 68.7 2.8 6.1E-05 45.6 1.8 66 96-173 37-104 (299)
52 PF14634 zf-RING_5: zinc-RING 68.6 4.6 0.0001 32.9 2.7 44 113-171 1-44 (44)
53 PF08675 RNA_bind: RNA binding 65.9 12 0.00025 35.5 4.9 58 880-938 11-68 (87)
54 smart00249 PHD PHD zinc finger 64.1 3.4 7.3E-05 32.7 1.1 46 114-169 2-47 (47)
55 KOG0823 Predicted E3 ubiquitin 63.6 7.9 0.00017 42.6 4.0 54 107-175 43-96 (230)
56 PF15227 zf-C3HC4_4: zinc fing 63.3 6.6 0.00014 32.0 2.6 42 114-169 1-42 (42)
57 KOG0802 E3 ubiquitin ligase [P 63.1 4.2 9.1E-05 50.3 2.1 55 104-172 284-339 (543)
58 COG5194 APC11 Component of SCF 61.5 4.5 9.8E-05 37.6 1.5 33 114-148 34-69 (88)
59 KOG0317 Predicted E3 ubiquitin 59.5 4.2 9.1E-05 46.0 1.1 50 107-174 235-284 (293)
60 KOG2930 SCF ubiquitin ligase, 58.7 4.8 0.0001 39.1 1.2 31 127-173 77-107 (114)
61 PF15135 UPF0515: Uncharacteri 56.4 19 0.00042 40.1 5.4 20 82-101 64-83 (278)
62 PHA02862 5L protein; Provision 56.1 12 0.00025 38.7 3.4 51 113-175 4-54 (156)
63 KOG2275 Aminoacylase ACY1 and 54.2 37 0.00079 40.7 7.5 55 803-857 38-95 (420)
64 KOG0320 Predicted E3 ubiquitin 52.9 8.2 0.00018 41.0 1.9 53 103-171 123-175 (187)
65 KOG0828 Predicted E3 ubiquitin 50.7 7.7 0.00017 46.7 1.4 53 108-173 568-633 (636)
66 KOG0978 E3 ubiquitin ligase in 49.0 7.6 0.00017 49.0 1.1 61 98-177 632-692 (698)
67 KOG1734 Predicted RING-contain 48.9 5.3 0.00011 44.7 -0.3 49 111-172 224-279 (328)
68 COG5574 PEX10 RING-finger-cont 48.1 12 0.00025 42.1 2.2 47 110-173 214-261 (271)
69 PF07649 C1_3: C1-like domain; 46.6 10 0.00022 28.6 1.0 29 113-142 2-30 (30)
70 PRK03976 rpl37ae 50S ribosomal 46.5 11 0.00024 36.0 1.5 35 104-138 29-65 (90)
71 TIGR00280 L37a ribosomal prote 45.5 12 0.00026 35.9 1.5 35 104-138 28-64 (91)
72 TIGR00599 rad18 DNA repair pro 45.4 16 0.00036 43.5 3.0 47 110-174 25-71 (397)
73 PF03107 C1_2: C1 domain; Int 44.7 9.7 0.00021 28.8 0.7 30 112-142 1-30 (30)
74 cd02637 R3H_PARN R3H domain of 44.6 53 0.0012 29.6 5.4 54 783-843 4-61 (65)
75 PF11608 Limkain-b1: Limkain b 44.3 55 0.0012 31.3 5.6 60 883-943 5-69 (90)
76 PTZ00255 60S ribosomal protein 44.3 14 0.0003 35.4 1.8 34 104-138 29-65 (90)
77 PF13893 RRM_5: RNA recognitio 43.9 75 0.0016 26.5 6.1 46 896-943 3-51 (56)
78 PF12906 RINGv: RING-variant d 41.1 11 0.00025 31.4 0.6 35 114-148 1-38 (47)
79 KOG2164 Predicted E3 ubiquitin 40.0 69 0.0015 39.3 7.0 72 90-174 165-236 (513)
80 smart00362 RRM_2 RNA recogniti 39.5 1.2E+02 0.0026 24.9 6.7 52 891-943 13-69 (72)
81 smart00504 Ubox Modified RING 37.7 36 0.00078 29.2 3.2 44 112-173 2-45 (63)
82 PF00076 RRM_1: RNA recognitio 36.7 92 0.002 26.3 5.7 46 890-936 11-63 (70)
83 cd07135 ALDH_F14-YMR110C Sacch 36.2 2E+02 0.0043 34.8 10.3 129 778-938 263-393 (436)
84 PF14446 Prok-RING_1: Prokaryo 32.4 32 0.00069 30.0 2.0 32 111-142 5-36 (54)
85 COG1997 RPL43A Ribosomal prote 31.5 29 0.00062 33.0 1.7 32 106-137 30-63 (89)
86 PLN03134 glycine-rich RNA-bind 30.5 2.9E+02 0.0062 28.3 9.0 53 890-943 47-106 (144)
87 TIGR00570 cdk7 CDK-activating 30.5 43 0.00093 38.8 3.2 11 742-752 76-86 (309)
88 cd00590 RRM RRM (RNA recogniti 30.0 2.4E+02 0.0052 23.2 7.1 52 891-943 13-70 (74)
89 KOG0107 Alternative splicing f 28.6 1.3E+02 0.0029 32.4 6.1 36 903-938 35-73 (195)
90 KOG1039 Predicted E3 ubiquitin 27.7 61 0.0013 38.1 3.9 66 109-182 159-228 (344)
91 smart00360 RRM RNA recognition 27.1 1.9E+02 0.004 23.5 5.9 53 890-943 9-68 (71)
92 KOG0558 Dihydrolipoamide trans 26.6 62 0.0013 37.9 3.5 232 737-979 173-461 (474)
93 PF08746 zf-RING-like: RING-li 26.3 58 0.0012 26.9 2.4 41 114-169 1-43 (43)
94 cd07133 ALDH_CALDH_CalB Conife 26.3 5.2E+02 0.011 31.2 11.5 24 915-938 367-391 (434)
95 PLN02203 aldehyde dehydrogenas 25.9 3.6E+02 0.0078 33.2 10.2 24 915-938 375-399 (484)
96 KOG1117 Rho- and Arf-GTPase ac 25.7 1.7E+02 0.0036 38.2 7.2 45 906-950 998-1045(1186)
97 PTZ00381 aldehyde dehydrogenas 25.4 4E+02 0.0086 32.9 10.5 25 914-938 369-394 (493)
98 PF10367 Vps39_2: Vacuolar sor 24.7 31 0.00068 32.6 0.7 32 111-144 78-109 (109)
99 cd06396 PB1_NBR1 The PB1 domai 24.3 80 0.0017 29.8 3.2 37 903-939 38-75 (81)
100 KOG0309 Conserved WD40 repeat- 24.1 47 0.001 42.2 2.2 37 111-149 1028-1064(1081)
101 cd06404 PB1_aPKC PB1 domain is 23.9 91 0.002 29.6 3.5 40 903-943 39-78 (83)
102 PF01780 Ribosomal_L37ae: Ribo 22.9 47 0.001 31.9 1.5 33 105-137 29-63 (90)
103 PF14259 RRM_6: RNA recognitio 22.5 2.9E+02 0.0063 23.7 6.4 54 885-940 3-66 (70)
104 PF13445 zf-RING_UBOX: RING-ty 21.6 66 0.0014 26.6 1.9 34 114-149 1-35 (43)
105 PRK11241 gabD succinate-semial 21.2 4.4E+02 0.0095 32.4 9.7 131 778-938 304-439 (482)
106 KOG1941 Acetylcholine receptor 20.7 50 0.0011 39.1 1.4 52 111-174 365-416 (518)
No 1
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=100.00 E-value=1.1e-164 Score=1433.33 Aligned_cols=734 Identities=46% Similarity=0.980 Sum_probs=667.4
Q ss_pred ccCCCccccCCCCCChhHHHHHHHHHhccCcceEeeecccccccCceeeCCCCceeechhHHHHHhcCCCCcchhhhccC
Q 001377 81 ARGENQDKKLPKDLDLPQLLQEIQDKLMKSKVECMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQ 160 (1090)
Q Consensus 81 ~~~~~~~~~~~~d~~~~~l~~~l~e~l~~~~yeC~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~ 160 (1090)
+..++++.-.+.|++..++++.|+++|.++.|||||||+.|+++++||||.+||+||||+||++||++. +++.
T Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~li~~l~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~-------ek~~ 233 (950)
T KOG1952|consen 161 RTPESYEPQNESLDNDLTLTQSLIEQLSNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSS-------EKTG 233 (950)
T ss_pred cchhhhcccccCccchHHHHHHHHHHHhcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHh-------hhcc
Confidence 333444443566777999999999999999999999999999999999999999999999999999982 3345
Q ss_pred CCCCCCCCCCccccCCCCCceeeeecCCccCCCCCCCCCCCCCCCCCCCCccccccCCCCCCCCCCCccccccccCCCCC
Q 001377 161 GFNWRCPGCQSVQLTSSKEIRYVCFCGKRTDPTSDFYLTPHSCGEPCGKPLESKISSAGGSEEDLCPHKCVLQCHPGPCP 240 (1090)
Q Consensus 161 ~~~WrCP~C~~~~~~~~~p~~y~CfCGK~~~p~~~~~~~phSCg~~C~k~l~~~~~~~~~~~~~~C~H~C~l~CHpGpCP 240 (1090)
+..||||+||+++... |..|+|||||+.||+++++++||||||+|+|++. ..|+|+|.|+|||||||
T Consensus 234 ~~~WrCP~Cqsv~~~~--~~~y~C~CGk~~nP~~~~~~~PHSCGE~C~k~~~-----------~~C~H~C~llCHPGPCp 300 (950)
T KOG1952|consen 234 QDGWRCPACQSVSKTV--PKTYLCFCGKVKNPEFSRNELPHSCGEVCGKPRP-----------GGCPHPCTLLCHPGPCP 300 (950)
T ss_pred CccccCCcccchhccC--CcccceecCcccCCCCCCCCCCccccccccCCCC-----------CCCCCcccccccCCCCC
Confidence 6799999999999875 4599999999999999999999999999999876 35999999999999999
Q ss_pred CCcccCCCcccCCCCccceeccCCCCCcccccccccccccCCCcccccccccCCCccCccceeEEEecCCeeeEEecccc
Q 001377 241 PCKAFAPPRLCPCGKKMITTRCFDRKSVLTCGQHCNKHLECWRHKCEKICHVGPCGPCRVLVNASCFCKKKVEVVLCGDM 320 (1090)
Q Consensus 241 pC~~~~~~~~C~CGk~~~~~rC~~~~~~~sC~~~C~K~L~CG~H~C~~~CH~G~C~~C~~~v~~~C~CGk~~~~v~C~~~ 320 (1090)
||.+|+ .++|+||++..+++|+.....+-|+++|+|+|+||+|+|+++||+|+|++|.+++.++||||+..+++.|+..
T Consensus 301 pC~~~v-~~~C~CGk~s~~vrC~~~~~~~~C~~vC~k~L~Cg~H~Ck~~CH~G~C~~C~e~~v~~C~Cgk~~k~v~C~~~ 379 (950)
T KOG1952|consen 301 PCPAFV-TKSCHCGKTSKTVRCGQIQSAVCCGNVCDKLLSCGQHRCKEICHSGECGPCQEQLVQKCYCGKTKKEVPCNRV 379 (950)
T ss_pred chhhhh-hhcccCCCeeeeEEeccccchhhhcccCCCccccccchhhhhcCCCCCCcChhhheeeeccCCcccceecccc
Confidence 999998 6999999999999999976668899999999999999999999999999999999999999999999999886
Q ss_pred cccCcccccccccccccccccccCCCCCeecCcccCCCCCCCCCCCCCceeccCCCcccc---cccccccCCcccccccc
Q 001377 321 AVKGEVKAEAGVFSCSSTCGKKLSCGHHSCGEICHPGPCGDCELLPSKIKSCFCGKMSLQ---EQRKSCLDPIPACSEKC 397 (1090)
Q Consensus 321 ~~~~~~~~~~~~~sC~~~C~k~L~CG~H~C~~~CH~g~C~~C~~~p~~v~tCpCGkt~l~---~~R~~C~dpip~C~~~C 397 (1090)
.. +.|.|+|+|...|+++|.||+|.|.+.||+++|++|++.++.+++||||++.|+ ..|++|.|+||+|+.+|
T Consensus 380 ~~----~~~~g~ysC~~~C~~~~~Cg~H~c~~~Ch~~~c~~c~~~~~~~~~CpCGr~~l~lg~~~rksC~DpiPtC~~vC 455 (950)
T KOG1952|consen 380 RG----KEWFGVYSCDDTCGKMLSCGKHKCSEVCHAGPCGQCPRLPQRVRTCPCGRTPLELGRRQRKSCDDPVPTCGSVC 455 (950)
T ss_pred cc----cccceeEecccccccccccccchhcccccCCccccCccchhhceecCCCCcccccccccccccCCcCCcccccc
Confidence 42 468899999999999999999999999999999999999999999999999953 35899999999999999
Q ss_pred ccccCCCCccCCCCccCCCccccccceeeEecCCCeeeeecCccCCCCccccccccccccccCCCcccCCCccCCCCCCC
Q 001377 398 GKPLACGLHYCDELCHAGNCPPCLAAVTQKCRCGSTSRNVECYRTTGGENFTCEKACGRKKNCGRHRCSERCCPLSSSNS 477 (1090)
Q Consensus 398 ~K~L~CG~H~C~~~CH~G~C~pC~~~v~~~C~CG~t~~~v~C~~~~~~~~~~C~~~C~k~l~CGrH~C~~~CCp~~~~~~ 477 (1090)
+|+|.||.|+|..+||.|+|+||.+.+.++||||.++++|+|.+..+...|.|.+.|+++++||+|+|+++||..
T Consensus 456 ~K~L~Cg~H~C~~~CH~g~C~pC~~~~~v~CRCg~~~~~i~C~~~~~~~~~~C~k~C~~k~sCgrHkC~~~CC~~----- 530 (950)
T KOG1952|consen 456 GKPLPCGIHTCGEKCHEGACPPCSVNVSVKCRCGFSTKQIPCDQLSEDARFMCDKRCTKKRSCGRHKCNERCCSD----- 530 (950)
T ss_pred cCccccccccCCCeeecCCCCCcccccceeeecccccceeecccccccccchhhhhccccccccccccchhhcCC-----
Confidence 999999999999999999999999999999999999999999998778899999999999999999999999975
Q ss_pred CCCCCCCCcccccccccccCCCCccccCcccCCCCCCCccccccceecCCCCcccCCCCCCCCCCCCccCCCCCCCCCCC
Q 001377 478 LLSGDWDPHFCQMACGKKLRCGQHSCESLCHSGHCPPCLETIFTDLTCACGRTSFPPPLPCGTPPPSCQLPCSVPQPCGH 557 (1090)
Q Consensus 478 ~~~~~~~~~~C~~~Cgk~L~CG~H~C~~~CH~G~C~pC~e~~~~~l~C~CG~t~i~ppvpCgt~~p~C~~~C~r~l~CGH 557 (1090)
.+|+|.++|+|+|+||+|.|+.+||.|.||||+|++|++|+|+||+|+|+|||+|||++|.|..||.++.+|||
T Consensus 531 ------~eH~C~~pCnkkLsCG~H~Ce~~CH~G~CPpCleasf~el~C~CG~tvi~pPv~CGt~~P~C~~pC~~~~~C~H 604 (950)
T KOG1952|consen 531 ------REHICPLPCNKKLSCGIHKCEEPCHRGNCPPCLEASFDELTCHCGATVIYPPVPCGTRLPECSQPCSRPHSCDH 604 (950)
T ss_pred ------CcccccccccccccccchhhhcccCCCCCCchhhhccccccccCCCeeecCCccCCCCCCCCCCCCCCCccCCC
Confidence 37999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCC-CCCCCCccceEEecccceeecccCcCCCCccchhccCcccCCCCCCCCCCCCCCCCCCCCCCCCCccCcc
Q 001377 558 SASHSCHFG-DCPPCSVPIAKECIGGHVVLRNVPCGSKDIRCNKLCGKTRQCGMHACGRTCHPPPCDTACNSEPGSKASC 636 (1090)
Q Consensus 558 ~c~~~CH~g-~CPPC~~~v~~~C~cG~~~~~~vpC~~~~~~C~~~C~k~l~CG~H~C~~~Ch~~pC~~~~~~~~~~~~~C 636 (1090)
+..|.||++ +||||+++|++.|.|||.++.||||++.+++|+.+||++|+||.|.|+++||.++|. ....|
T Consensus 605 ~~~H~CH~~~~CPPCt~~v~K~C~ggh~~~~nipC~~~dvsCg~~CgkpL~Cg~H~Cqr~CH~~~c~--------~~e~C 676 (950)
T KOG1952|consen 605 PVYHNCHSEEKCPPCTELVEKPCVGGHEVRENIPCHLTDVSCGLLCGKPLPCGMHKCQRTCHPGECC--------VGEKC 676 (950)
T ss_pred CCCcCCCCCCCCCCCCcceeecccCCceehhcCCccCcccccccccCCccccccceeccccCCCccc--------ccChh
Confidence 999999998 799999999999999999999999999999999999999999999999999999886 24789
Q ss_pred cccccCCCCCCCCCcccCccCCCCCCCCCCcccEeeeccCCCccccccCCCCCCCCCCC-CchhhhhhhhccCCCCCCcc
Q 001377 637 GQVCGAPRRDCRHTCTALCHPSALCPDVRCEFPFTITCSCGRITASVPCDAGGSSSGYS-SDTVYEASIVQKLPAPLQPV 715 (1090)
Q Consensus 637 ~q~C~k~l~~C~H~C~~~CH~g~~CP~~~C~~~v~i~C~Cgr~~~~~~C~~~~~~~~~~-~~~~~~~s~~~~~~~~~~~~ 715 (1090)
.|.|+++|+.|+|+|+++||++.+||++||+++|+|+|+|||+++.|+|++...+.... +..-.+.+..+...-.++..
T Consensus 677 kq~C~k~R~~C~H~C~~pCH~~~pCp~~pCka~V~isCeCGrikk~v~C~~~~~~~~~~~~~~c~~~c~~~~~~~~~~e~ 756 (950)
T KOG1952|consen 677 KQKCGKPRPDCGHPCAAPCHPSSPCPPTPCKALVEISCECGRIKKMVTCDEASDSTDQRIAAICMESCEADMRLKGLKEA 756 (950)
T ss_pred hcccCCCCCCCCCCCCcCCCCCCCCCCccccceeEEEEecCccccceecccccCCcchHHHHHhhhhhhhhcccccccch
Confidence 99999999999999999999999999999999999999999999999999987532111 11122233333333445555
Q ss_pred cccCCcccCCCccCCchHHHHHHHHHHHHHhhhCCCCCCccccCcCCcc-hhHHHHHHHHhChhHHHHHHHHHHHHHhcc
Q 001377 716 ESTGKKIPLGQRKLMCDDECAKLERKRVLADAFEITTPNLDALHFGESA-VTELLADLYRRDPKWVLSVEERCKFLVLGK 794 (1090)
Q Consensus 716 ~~~~~~~~~~~~~l~CddeC~k~~R~~~LA~Al~I~~p~~~~~~f~e~~-yse~Ll~~~~~~~~~~~~vE~~L~~fv~~~ 794 (1090)
........+++..|.||+||.+++|++.||+||.|+........+..++ |+++|.+++++++.|++.+|+++.+|+...
T Consensus 757 ~~~~t~~~~~~~~l~c~~ec~~ler~~~~aea~~i~~~~~~~~~~~~~~~~~e~~~e~~r~~~~f~~sv~~e~~~lv~~~ 836 (950)
T KOG1952|consen 757 SNILTKKELHQVKLECDDECSFLERKRRLAEAFSISEDSDEVNKRSSLSKFSESLKEDARKDLKFVKSVEKELEFLVELV 836 (950)
T ss_pred hcccccchhhhhhhhHHHHHHHHHhhhHHHHHHhhccchhhhhhhhhhhhhhHHHHHHHHhchhhhccchhhhHHHHHHH
Confidence 5566677888999999999999999999999999997654444444444 999999999999999999999999999887
Q ss_pred ccCCccccceEecCCCChhhHHHHHHHHHHcCCceeecCCCCCceEEEEeCCC-CCCCccccccc
Q 001377 795 NRGSTNALKVHVFCPMLKDKRDAVRLIAERWKLAVNPAGWEPKRFIVVHVTPK-SKPPPRVIGVK 858 (1090)
Q Consensus 795 ~~~~~~~~k~~~f~PM~~~kR~fIHeLAe~ygL~S~S~d~EP~R~VvV~kt~~-Sk~P~~lLs~~ 858 (1090)
..+....+++++|+||+.++|++||+||+.|+|.+.|+|.||+|+||+.+..+ +..|..+++..
T Consensus 837 ~~~~~~~~k~~~~p~ms~~~rr~vh~~~e~~~l~~~sa~~~pkr~~v~t~ir~~s~~~~~~~~~~ 901 (950)
T KOG1952|consen 837 KRGKNYSKKSHSFPPMSRDKRRLVHELAEVFGLESVSADSEPKRNVVVTAIRGKSVFPATTITGV 901 (950)
T ss_pred hhcccccccccccCchhHHHHHHHHhhhhccCCcccccCCCcccceeeEeecccccCchhhHHHH
Confidence 76666578999999999999999999999999999999999999999999755 56777776654
No 2
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=100.00 E-value=3.3e-60 Score=556.12 Aligned_cols=539 Identities=29% Similarity=0.666 Sum_probs=391.0
Q ss_pred CCCCCCc---c-cCCCcccCCCCccceeccCCCCCcccccccccccc--cCCCcccccccccCCCccCccceeEEEecCC
Q 001377 237 GPCPPCK---A-FAPPRLCPCGKKMITTRCFDRKSVLTCGQHCNKHL--ECWRHKCEKICHVGPCGPCRVLVNASCFCKK 310 (1090)
Q Consensus 237 GpCPpC~---~-~~~~~~C~CGk~~~~~rC~~~~~~~sC~~~C~K~L--~CG~H~C~~~CH~G~C~~C~~~v~~~C~CGk 310 (1090)
|-||.|. . +.....|||||...+ .+.....+++||++|+|.+ .|. |.|.++||+|+|+||..+|+++|.||+
T Consensus 237 WrCP~Cqsv~~~~~~~y~C~CGk~~nP-~~~~~~~PHSCGE~C~k~~~~~C~-H~C~llCHPGPCppC~~~v~~~C~CGk 314 (950)
T KOG1952|consen 237 WRCPACQSVSKTVPKTYLCFCGKVKNP-EFSRNELPHSCGEVCGKPRPGGCP-HPCTLLCHPGPCPPCPAFVTKSCHCGK 314 (950)
T ss_pred ccCCcccchhccCCcccceecCcccCC-CCCCCCCCccccccccCCCCCCCC-CcccccccCCCCCchhhhhhhcccCCC
Confidence 7788998 3 223567999999864 3444456899999999955 587 999999999999999999999999999
Q ss_pred eeeEEecccccccCcccccccccccccccccccCCCCCeecCcccCCCCCCCCCCCCCceeccCCCcccccccccccCC-
Q 001377 311 KVEVVLCGDMAVKGEVKAEAGVFSCSSTCGKKLSCGHHSCGEICHPGPCGDCELLPSKIKSCFCGKMSLQEQRKSCLDP- 389 (1090)
Q Consensus 311 ~~~~v~C~~~~~~~~~~~~~~~~sC~~~C~k~L~CG~H~C~~~CH~g~C~~C~~~p~~v~tCpCGkt~l~~~R~~C~dp- 389 (1090)
+..++.|++.. ..+-|+++|+++|+||.|.|.+.||+|.|++|..+ ++..|+||++..+ ..|...
T Consensus 315 ~s~~vrC~~~~---------~~~~C~~vC~k~L~Cg~H~Ck~~CH~G~C~~C~e~--~v~~C~Cgk~~k~---v~C~~~~ 380 (950)
T KOG1952|consen 315 TSKTVRCGQIQ---------SAVCCGNVCDKLLSCGQHRCKEICHSGECGPCQEQ--LVQKCYCGKTKKE---VPCNRVR 380 (950)
T ss_pred eeeeEEecccc---------chhhhcccCCCccccccchhhhhcCCCCCCcChhh--heeeeccCCcccc---eeccccc
Confidence 99999999853 13789999999999999999999999999999987 5699999999865 456433
Q ss_pred ------ccccccccccccCCCCccCCCCccCCCcccccc--ceeeEecCCCeeeeecCccCCCCccccccccccccccCC
Q 001377 390 ------IPACSEKCGKPLACGLHYCDELCHAGNCPPCLA--AVTQKCRCGSTSRNVECYRTTGGENFTCEKACGRKKNCG 461 (1090)
Q Consensus 390 ------ip~C~~~C~K~L~CG~H~C~~~CH~G~C~pC~~--~v~~~C~CG~t~~~v~C~~~~~~~~~~C~~~C~k~l~CG 461 (1090)
++.|...|+++|.||+|.|.+.||.|+|..|.. ....+|+||++...+ +.. ...+|.
T Consensus 381 ~~~~~g~ysC~~~C~~~~~Cg~H~c~~~Ch~~~c~~c~~~~~~~~~CpCGr~~l~l--------g~~-------~rksC~ 445 (950)
T KOG1952|consen 381 GKEWFGVYSCDDTCGKMLSCGKHKCSEVCHAGPCGQCPRLPQRVRTCPCGRTPLEL--------GRR-------QRKSCD 445 (950)
T ss_pred ccccceeEecccccccccccccchhcccccCCccccCccchhhceecCCCCccccc--------ccc-------cccccC
Confidence 378999999999999999999999999996655 456789999985311 000 001111
Q ss_pred CcccCCCccCCCCCCCCCCCCCCCcccccccccccCCCCccccCcccCCCCCCCccccccceecCCCCcccCC-------
Q 001377 462 RHRCSERCCPLSSSNSLLSGDWDPHFCQMACGKKLRCGQHSCESLCHSGHCPPCLETIFTDLTCACGRTSFPP------- 534 (1090)
Q Consensus 462 rH~C~~~CCp~~~~~~~~~~~~~~~~C~~~Cgk~L~CG~H~C~~~CH~G~C~pC~e~~~~~l~C~CG~t~i~p------- 534 (1090)
.....|..+|+|.|.||.|+|..+||.|+|+||...+ .+.|+||.+...-
T Consensus 446 ---------------------DpiPtC~~vC~K~L~Cg~H~C~~~CH~g~C~pC~~~~--~v~CRCg~~~~~i~C~~~~~ 502 (950)
T KOG1952|consen 446 ---------------------DPVPTCGSVCGKPLPCGIHTCGEKCHEGACPPCSVNV--SVKCRCGFSTKQIPCDQLSE 502 (950)
T ss_pred ---------------------CcCCcccccccCccccccccCCCeeecCCCCCccccc--ceeeecccccceeecccccc
Confidence 1346899999999999999999999999999999865 6899999987530
Q ss_pred ------------CCCCCC----------CCCCccCCCCCCCCCC-CCCCCCCCCCCCCCCCccc--eEEecccce-eecc
Q 001377 535 ------------PLPCGT----------PPPSCQLPCSVPQPCG-HSASHSCHFGDCPPCSVPI--AKECIGGHV-VLRN 588 (1090)
Q Consensus 535 ------------pvpCgt----------~~p~C~~~C~r~l~CG-H~c~~~CH~g~CPPC~~~v--~~~C~cG~~-~~~~ 588 (1090)
...||. ....|..+|.+.|.|| |.|.+.||.|.||||.+.. +-.|.||++ +++.
T Consensus 503 ~~~~~C~k~C~~k~sCgrHkC~~~CC~~~eH~C~~pCnkkLsCG~H~Ce~~CH~G~CPpCleasf~el~C~CG~tvi~pP 582 (950)
T KOG1952|consen 503 DARFMCDKRCTKKRSCGRHKCNERCCSDREHICPLPCNKKLSCGIHKCEEPCHRGNCPPCLEASFDELTCHCGATVIYPP 582 (950)
T ss_pred cccchhhhhccccccccccccchhhcCCCcccccccccccccccchhhhcccCCCCCCchhhhccccccccCCCeeecCC
Confidence 122221 2478999999999999 9999999999999999754 457999987 6788
Q ss_pred cCcCCCCccchhccCcccCCCCCCCCCCCCC----CCCCCCCCC-------------CCCccCcccccccCCCCCCCCCc
Q 001377 589 VPCGSKDIRCNKLCGKTRQCGMHACGRTCHP----PPCDTACNS-------------EPGSKASCGQVCGAPRRDCRHTC 651 (1090)
Q Consensus 589 vpC~~~~~~C~~~C~k~l~CG~H~C~~~Ch~----~pC~~~~~~-------------~~~~~~~C~q~C~k~l~~C~H~C 651 (1090)
|+|++..+.|..+|.+..+|+ |.=...||. |||....+. -.....+|+..|||+|+.+.|.|
T Consensus 583 v~CGt~~P~C~~pC~~~~~C~-H~~~H~CH~~~~CPPCt~~v~K~C~ggh~~~~nipC~~~dvsCg~~CgkpL~Cg~H~C 661 (950)
T KOG1952|consen 583 VPCGTRLPECSQPCSRPHSCD-HPVYHNCHSEEKCPPCTELVEKPCVGGHEVRENIPCHLTDVSCGLLCGKPLPCGMHKC 661 (950)
T ss_pred ccCCCCCCCCCCCCCCCccCC-CCCCcCCCCCCCCCCCCcceeecccCCceehhcCCccCcccccccccCCcccccccee
Confidence 999999999999999999999 777788884 566654320 01234789999999999999999
Q ss_pred ccCccCCCCCCCCCCcccEee-eccCCCccccccCCCCCCCCCCCCchhhhhh-hhccCCCCCCc-ccccCCcccCCCcc
Q 001377 652 TALCHPSALCPDVRCEFPFTI-TCSCGRITASVPCDAGGSSSGYSSDTVYEAS-IVQKLPAPLQP-VESTGKKIPLGQRK 728 (1090)
Q Consensus 652 ~~~CH~g~~CP~~~C~~~v~i-~C~Cgr~~~~~~C~~~~~~~~~~~~~~~~~s-~~~~~~~~~~~-~~~~~~~~~~~~~~ 728 (1090)
+..||+++.|-...|+++... +=.|+|.-+ .+|+...+=+--++....+-+ .-+.+.. ..+ .+.++ ....+..
T Consensus 662 qr~CH~~~c~~~e~Ckq~C~k~R~~C~H~C~-~pCH~~~pCp~~pCka~V~isCeCGrikk-~v~C~~~~~--~~~~~~~ 737 (950)
T KOG1952|consen 662 QRTCHPGECCVGEKCKQKCGKPRPDCGHPCA-APCHPSSPCPPTPCKALVEISCECGRIKK-MVTCDEASD--STDQRIA 737 (950)
T ss_pred ccccCCCcccccChhhcccCCCCCCCCCCCC-cCCCCCCCCCCccccceeEEEEecCcccc-ceecccccC--CcchHHH
Confidence 999999865523345444211 112333332 345543221100111000000 0000000 000 01111 1223346
Q ss_pred CCchHHHHHHHHHHHHHhhhCCCCCCccccCcCCcc-hhHHHHHHHHhChhHHHHHH--------------HHHHHHHhc
Q 001377 729 LMCDDECAKLERKRVLADAFEITTPNLDALHFGESA-VTELLADLYRRDPKWVLSVE--------------ERCKFLVLG 793 (1090)
Q Consensus 729 l~CddeC~k~~R~~~LA~Al~I~~p~~~~~~f~e~~-yse~Ll~~~~~~~~~~~~vE--------------~~L~~fv~~ 793 (1090)
+.|+++|...+|++.|++|++|-++.... ... |-+....|+.++..|.+.++ ..|.+|+.+
T Consensus 738 ~~c~~~c~~~~~~~~~~e~~~~~t~~~~~----~~~l~c~~ec~~ler~~~~aea~~i~~~~~~~~~~~~~~~~~e~~~e 813 (950)
T KOG1952|consen 738 AICMESCEADMRLKGLKEASNILTKKELH----QVKLECDDECSFLERKRRLAEAFSISEDSDEVNKRSSLSKFSESLKE 813 (950)
T ss_pred HHhhhhhhhhcccccccchhcccccchhh----hhhhhHHHHHHHHHhhhHHHHHHhhccchhhhhhhhhhhhhhHHHHH
Confidence 89999999999999999999876542111 111 44444455555555555544 444444444
Q ss_pred cccCCccccceEecCCCChhhHHHHHHHHHHcCCceeecCCCCCceEEEEe
Q 001377 794 KNRGSTNALKVHVFCPMLKDKRDAVRLIAERWKLAVNPAGWEPKRFIVVHV 844 (1090)
Q Consensus 794 ~~~~~~~~~k~~~f~PM~~~kR~fIHeLAe~ygL~S~S~d~EP~R~VvV~k 844 (1090)
.. .+.+.|.+|..+++.|+-+++..+++++......|.++|...+
T Consensus 814 ~~------r~~~~f~~sv~~e~~~lv~~~~~~~~~~~k~~~~p~ms~~~rr 858 (950)
T KOG1952|consen 814 DA------RKDLKFVKSVEKELEFLVELVKRGKNYSKKSHSFPPMSRDKRR 858 (950)
T ss_pred HH------HhchhhhccchhhhHHHHHHHhhcccccccccccCchhHHHHH
Confidence 43 4668899999999999999999888888777777777766443
No 3
>cd02643 R3H_NF-X1 R3H domain of the X1 box binding protein (NF-X1) and related proteins. Human NF-X1 is a transcription factor that regulates the expression of class II major histocompatibility complex (MHC) genes. The Drosophila homolog shuttle craft (STC) has been shown to be a DNA- or RNA-binding protein required for proper axon guidance in the central nervous system and, the yeast homolog FAP1 encodes a dosage suppressor of rapamycin toxicity. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=99.76 E-value=7.5e-19 Score=158.16 Aligned_cols=74 Identities=32% Similarity=0.484 Sum_probs=68.5
Q ss_pred HHHHHhChhHHHHHHHHHHHHHhccccCCccccceEecCCCChhhHHHHHHHHHHcCCceeecCCCCCceEEEEe
Q 001377 770 ADLYRRDPKWVLSVEERCKFLVLGKNRGSTNALKVHVFCPMLKDKRDAVRLIAERWKLAVNPAGWEPKRFIVVHV 844 (1090)
Q Consensus 770 l~~~~~~~~~~~~vE~~L~~fv~~~~~~~~~~~k~~~f~PM~~~kR~fIHeLAe~ygL~S~S~d~EP~R~VvV~k 844 (1090)
++||++|++|+++||++|+.||.+.+.+ ..+.+.+.|+||++.+|+|||+||++|||.|+|+|+||+|+|||.+
T Consensus 1 ~~~~~~~~~~~~~vE~~l~~la~~~~~~-~~~~~~~~l~PM~~~eR~iIH~la~~~~l~S~S~G~ep~R~VvI~~ 74 (74)
T cd02643 1 KNMAKKDPKFVKDVEKDLIELVESVNKG-KQTSRSHSFPPMNREKRRIVHELAEHFGIESVSYDQEPKRNVVATA 74 (74)
T ss_pred CchHHHCHHHHHHHHHHHHHHHHHHHhc-cccCCeeECCCCCHHHHHHHHHHHhhCCCEEEecCCCCCceEEEeC
Confidence 3799999999999999999999987655 5568899999999999999999999999999999999999999963
No 4
>cd06006 R3H_unknown_2 R3H domain of a group of fungal proteins with unknown function. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=99.70 E-value=2.3e-17 Score=141.72 Aligned_cols=59 Identities=22% Similarity=0.287 Sum_probs=54.9
Q ss_pred HHHHHHHHHHHHhccccCCccccceEecCCCChhhHHHHHHHHHHcCCceeecCCCCCceEEEEe
Q 001377 780 VLSVEERCKFLVLGKNRGSTNALKVHVFCPMLKDKRDAVRLIAERWKLAVNPAGWEPKRFIVVHV 844 (1090)
Q Consensus 780 ~~~vE~~L~~fv~~~~~~~~~~~k~~~f~PM~~~kR~fIHeLAe~ygL~S~S~d~EP~R~VvV~k 844 (1090)
+++||++|+.||.+.+ .+++.|+||++.+|+|||+||++|||+|+|+|+||+|||||+|
T Consensus 1 ~~~~E~~l~~fv~d~~------~~~~~f~pM~~~~R~~vHdla~~~gl~SeS~d~Ep~R~V~v~k 59 (59)
T cd06006 1 CQQIESTLRKFINDKS------KRSLRFPPMRSPQRAFIHELAKDYGLYSESQDPEPKRSVFVKK 59 (59)
T ss_pred ChhHHHHHHHHHhCCC------CCceeCCCCCHHHHHHHHHHHHHcCCeeEecCCCCCcEEEEeC
Confidence 3579999999999875 5788999999999999999999999999999999999999975
No 5
>cd02642 R3H_encore_like R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H domain is a potential regulator of DBF1 activity in stress responses. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=99.38 E-value=9.1e-13 Score=115.35 Aligned_cols=62 Identities=18% Similarity=0.154 Sum_probs=57.8
Q ss_pred hhHHHHHHHHHHHHHhccccCCccccceEecCCCChhhHHHHHHHHHHcCCceeecCCCCCceEEEEeC
Q 001377 777 PKWVLSVEERCKFLVLGKNRGSTNALKVHVFCPMLKDKRDAVRLIAERWKLAVNPAGWEPKRFIVVHVT 845 (1090)
Q Consensus 777 ~~~~~~vE~~L~~fv~~~~~~~~~~~k~~~f~PM~~~kR~fIHeLAe~ygL~S~S~d~EP~R~VvV~kt 845 (1090)
..|+.++|+.|..||.+.. ...+.|+||++.+|.|||+||++|||.++|+|.| .|+|+|+||
T Consensus 2 r~~~l~~E~~i~~Fi~~~~------~~~~~f~pm~sy~RllvH~la~~~gL~s~s~~~~-~r~vvv~kt 63 (63)
T cd02642 2 RLFVLKLEKDLLAFIKDST------RQSLELPPMNSYYRLLAHRVAQYYGLDHNVDNSG-GKCVIVNKT 63 (63)
T ss_pred chHHHHHHHHHHHHHhCCC------CCeeEcCCCCcHHHHHHHHHHHHhCCeeEeecCC-ceEEEEEeC
Confidence 4689999999999999864 4678999999999999999999999999999999 999999986
No 6
>cd02646 R3H_G-patch R3H domain of a group of fungal and plant proteins with unknown function, who also contain a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the R3H domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=99.33 E-value=2e-12 Score=111.38 Aligned_cols=57 Identities=23% Similarity=0.353 Sum_probs=52.9
Q ss_pred HHHHHHHHHHHhccccCCccccceEecCCCChhhHHHHHHHHHHcCCceeecCCCCCceEEEEe
Q 001377 781 LSVEERCKFLVLGKNRGSTNALKVHVFCPMLKDKRDAVRLIAERWKLAVNPAGWEPKRFIVVHV 844 (1090)
Q Consensus 781 ~~vE~~L~~fv~~~~~~~~~~~k~~~f~PM~~~kR~fIHeLAe~ygL~S~S~d~EP~R~VvV~k 844 (1090)
+.||++|+.|+.+. ...+.|+||++.+|++||+||+.|||.|+|+|.+|+|+|+|+|
T Consensus 2 ~~i~~~i~~F~~~~-------~~~~~fppm~~~~R~~vH~lA~~~~L~S~S~G~g~~R~v~v~k 58 (58)
T cd02646 2 EDIKDEIEAFLLDS-------RDSLSFPPMDKHGRKTIHKLANCYNLKSKSRGKGKKRFVTVTK 58 (58)
T ss_pred hHHHHHHHHHHhCC-------CceEecCCCCHHHHHHHHHHHHHcCCcccccccCCceEEEEEC
Confidence 56999999999876 4678999999999999999999999999999999999999975
No 7
>smart00393 R3H Putative single-stranded nucleic acids-binding domain.
Probab=99.25 E-value=4.9e-12 Score=115.36 Aligned_cols=70 Identities=21% Similarity=0.225 Sum_probs=61.0
Q ss_pred HHHHHHhChhHHHHHHHHHHHHHhccccCCccccceEecCCCChhhHHHHHHHHHHcCCceeecCCCCCceEEEEeC
Q 001377 769 LADLYRRDPKWVLSVEERCKFLVLGKNRGSTNALKVHVFCPMLKDKRDAVRLIAERWKLAVNPAGWEPKRFIVVHVT 845 (1090)
Q Consensus 769 Ll~~~~~~~~~~~~vE~~L~~fv~~~~~~~~~~~k~~~f~PM~~~kR~fIHeLAe~ygL~S~S~d~EP~R~VvV~kt 845 (1090)
+.++..+...|+..++..+..|+... .+.+.|+||++.+|+|||+||+.|||.|+|+|.||+|+|+|+++
T Consensus 10 ~~~~~~~~~~~l~~~~~~~~~~v~~~-------~~~~~~~pm~~~~R~~iH~~a~~~~l~s~S~g~g~~R~vvv~~~ 79 (79)
T smart00393 10 ALSYRPRRREELIELELEIARFVKST-------KESVELPPMNSYERKIVHELAEKYGLESESFGEGPKRRVVISKK 79 (79)
T ss_pred CCccCHHHHHHHHHHHHHHHHHHhcc-------CCeEEcCCCCHHHHHHHHHHHHHcCCEEEEEcCCCCcEEEEEeC
Confidence 34555667788888999998888754 57899999999999999999999999999999999999999874
No 8
>cd02636 R3H_sperm-antigen R3H domain of a group of metazoan proteins that is related to the sperm-associated antigen 7. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=99.25 E-value=9.3e-12 Score=106.95 Aligned_cols=59 Identities=22% Similarity=0.218 Sum_probs=53.1
Q ss_pred HHHHHHHHHHHhccccCCccccceEecCCCChhhHHHHHHHHHHcCCceeecCCC-CCceEEEEeC
Q 001377 781 LSVEERCKFLVLGKNRGSTNALKVHVFCPMLKDKRDAVRLIAERWKLAVNPAGWE-PKRFIVVHVT 845 (1090)
Q Consensus 781 ~~vE~~L~~fv~~~~~~~~~~~k~~~f~PM~~~kR~fIHeLAe~ygL~S~S~d~E-P~R~VvV~kt 845 (1090)
+.+|+++..|+++.. .....|+||++.+|++||++|+..||.|+|+|.| |.|||||+++
T Consensus 2 ~~~e~~~~~f~~d~~------~~~~~l~pM~~~eRkivHDv~~~~Gl~S~S~Geee~~R~VVv~~k 61 (61)
T cd02636 2 KSMEKEVSKFIKDSV------RTREKFQPMDKVERSIVHDVAEVAGLTSFSFGEDEVDRYVMIFKK 61 (61)
T ss_pred chHHHHHHHHhhccc------ccccccCCCCHHHHHHHHHHHHhcCceeEecCCCCCceEEEEecC
Confidence 569999999999864 3456799999999999999999999999999997 9999999874
No 9
>PF01424 R3H: R3H domain; InterPro: IPR001374 The R3H motif: a domain that binds single-stranded nucleic acids. The most prominent feature of the R3H motif is the presence of an invariant arginine residue and a highly conserved histidine residue that are separated by three residues. The motif also displays a conserved pattern of hydrophobic residues, prolines and glycines. The R3H motif is present in proteins from a diverse range of organisms that includes Eubacteria, green plants, fungi and various groups of metazoans. Intriguingly, it has not yet been identified in Archaea and Escherichia coli. The sequences that contain the R3H domain, many of which are hypothetical proteins predicted from genome sequencing projects, can be grouped into eight families on the basis of similarities outside the R3H region. Three of the families contain ATPase domains either upstream (families II and VII) or downstream of the R3H domain (family VIII). The N-terminal part of members of family VII contains an SF1 helicase domain5. The C-terminal part of family VIII contains an SF2 DEAH helicase domain5. The ATPase domain in the members of family II is similar to the stage-III sporulation protein AA (S3AA_BACSU), the proteasome ATPase, bacterial transcription-termination factor r and the mitochondrial F1-ATPase b subunit (the F5 helicase family5). Family VI contains Cys-rich repeats6, as well as a ring-type zinc finger upstream of the R3H domain. JAG bacterial proteins (family I) contain a KH domain N-terminal to the R3H domain. The functions of other domains in R3H proteins support the notion that the R3H domain might be involved in interactions with single-stranded nucleic acids [].; GO: 0003676 nucleic acid binding; PDB: 1WHR_A 1MSZ_A 1UG8_A 3GKU_B 2CPM_A.
Probab=99.24 E-value=1.4e-11 Score=107.47 Aligned_cols=58 Identities=28% Similarity=0.298 Sum_probs=46.4
Q ss_pred HHHHHHHHHHHhccccCCccccceEecCCCChhhHHHHHHHHHHcCCceeecCCCCCceEEEEeC
Q 001377 781 LSVEERCKFLVLGKNRGSTNALKVHVFCPMLKDKRDAVRLIAERWKLAVNPAGWEPKRFIVVHVT 845 (1090)
Q Consensus 781 ~~vE~~L~~fv~~~~~~~~~~~k~~~f~PM~~~kR~fIHeLAe~ygL~S~S~d~EP~R~VvV~kt 845 (1090)
.++++.+.+|+.+. ...+.|+||++.+|++||+||++|||.|.|+|.||+|+|+|++|
T Consensus 6 ~~~~~~~~~~~~~~-------~~~~~f~pm~~~~R~~iH~~a~~~gL~s~S~g~~~~R~vvv~k~ 63 (63)
T PF01424_consen 6 EKIEEKLIEFFLSS-------GESLEFPPMNSFERKLIHELAEYYGLKSKSEGEGPNRRVVVSKT 63 (63)
T ss_dssp HHHHHHHHHHHHHC-------SSEEEEEC--SHHHHHHHHHHHHCTEEEEEESSSSSSEEEEEES
T ss_pred HHHHHHHHHHHHcC-------CCEEEECCCCHHHHHHHHHHHHHCCCEEEEecCCCCeEEEEEeC
Confidence 34555555555433 22899999999999999999999999999999999999999986
No 10
>cd02641 R3H_Smubp-2_like R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.
Probab=99.22 E-value=1.8e-11 Score=106.17 Aligned_cols=58 Identities=21% Similarity=0.187 Sum_probs=52.9
Q ss_pred HHHHHHHHHHHhccccCCccccceEecCC-CChhhHHHHHHHHHHcCCceeecCCCCCceEEEEe
Q 001377 781 LSVEERCKFLVLGKNRGSTNALKVHVFCP-MLKDKRDAVRLIAERWKLAVNPAGWEPKRFIVVHV 844 (1090)
Q Consensus 781 ~~vE~~L~~fv~~~~~~~~~~~k~~~f~P-M~~~kR~fIHeLAe~ygL~S~S~d~EP~R~VvV~k 844 (1090)
+.+|+.|..|+.+.. ...+.|+| |++.+|++||+||+.|||.++|+|.++.|+|+|.+
T Consensus 2 ~~~~~~i~~F~~~~~------~~~l~F~p~ls~~eR~~vH~lA~~~gL~s~S~G~g~~R~v~v~k 60 (60)
T cd02641 2 KHLKAMVKAFMKDPK------ATELEFPPTLSSHDRLLVHELAEELGLRHESTGEGSDRVITVSK 60 (60)
T ss_pred hhHHHHHHHHHcCCC------cCcEECCCCCCHHHHHHHHHHHHHcCCceEeeCCCCceEEEeeC
Confidence 468999999998863 36789999 99999999999999999999999999999999964
No 11
>cd06008 NF-X1-zinc-finger Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms.
Probab=99.18 E-value=1.1e-11 Score=103.23 Aligned_cols=49 Identities=49% Similarity=1.179 Sum_probs=46.6
Q ss_pred ccccccccccCCCcccccccccCCCccCccceeEEEecCCeeeEEeccc
Q 001377 271 CGQHCNKHLECWRHKCEKICHVGPCGPCRVLVNASCFCKKKVEVVLCGD 319 (1090)
Q Consensus 271 C~~~C~K~L~CG~H~C~~~CH~G~C~~C~~~v~~~C~CGk~~~~v~C~~ 319 (1090)
|+++|+|+|+||.|+|.+.||.|+|++|.++++++|+||++...++|++
T Consensus 1 C~~~C~k~L~Cg~H~C~~~CH~G~C~pC~~~~~~~C~CG~~~~~~~C~~ 49 (49)
T cd06008 1 CGEVCGKPLPCGNHKCEQLCHEGPCPPCPETVKKKCRCGKTTKEVPCGE 49 (49)
T ss_pred CcccccCccCCCCCcCCCcCcCCcCcCcCCccCeEecCCCeecccCCcC
Confidence 7899999999999999999999999999999999999999998888863
No 12
>cd02644 R3H_jag R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with SpoIIIJ. SpoIIIJ is necessary for the third stage of sporulation. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=99.17 E-value=2.2e-11 Score=108.00 Aligned_cols=64 Identities=17% Similarity=0.053 Sum_probs=56.8
Q ss_pred HHHHHHHHHHHhccccCCccccceEecCCCChhhHHHHHHHHHHcC-CceeecCCCCCceEEEEe
Q 001377 781 LSVEERCKFLVLGKNRGSTNALKVHVFCPMLKDKRDAVRLIAERWK-LAVNPAGWEPKRFIVVHV 844 (1090)
Q Consensus 781 ~~vE~~L~~fv~~~~~~~~~~~k~~~f~PM~~~kR~fIHeLAe~yg-L~S~S~d~EP~R~VvV~k 844 (1090)
++.++.|..++...+.++..+.+.+.|+||++.+|+|||++++.|+ |.|+|+|.||+|+|||++
T Consensus 2 ~~r~~~L~~~A~~~a~~v~~tg~~~~l~PM~~~eRrivH~~~~~~~~l~T~S~G~~~~R~vvI~~ 66 (67)
T cd02644 2 ERREETLIRLAERAAEKVRRTGKPVKLEPMNAYERRIIHDALANDEDVETESEGEGPYRRVVISP 66 (67)
T ss_pred cHHHHHHHHHHHHHHHHHHHHCCeeEeCCCCHHHHHHHHHHHHhCCCceEEeecCCCCeEEEEEe
Confidence 4567888888887776666778899999999999999999999888 999999999999999976
No 13
>cd06008 NF-X1-zinc-finger Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms.
Probab=99.08 E-value=6.8e-11 Score=98.63 Aligned_cols=48 Identities=58% Similarity=1.430 Sum_probs=46.1
Q ss_pred cccccccccCCCCccCCCCccCCCccccccceeeEecCCCeeeeecCc
Q 001377 393 CSEKCGKPLACGLHYCDELCHAGNCPPCLAAVTQKCRCGSTSRNVECY 440 (1090)
Q Consensus 393 C~~~C~K~L~CG~H~C~~~CH~G~C~pC~~~v~~~C~CG~t~~~v~C~ 440 (1090)
|+++|+|+|+||.|+|.+.||.|+|+||.++++++|+||++...++|+
T Consensus 1 C~~~C~k~L~Cg~H~C~~~CH~G~C~pC~~~~~~~C~CG~~~~~~~C~ 48 (49)
T cd06008 1 CGEVCGKPLPCGNHKCEQLCHEGPCPPCPETVKKKCRCGKTTKEVPCG 48 (49)
T ss_pred CcccccCccCCCCCcCCCcCcCCcCcCcCCccCeEecCCCeecccCCc
Confidence 788999999999999999999999999999999999999999989886
No 14
>cd02325 R3H R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich repeats, ring-type zinc fingers, and KH domains. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=99.07 E-value=2.7e-10 Score=96.18 Aligned_cols=58 Identities=22% Similarity=0.213 Sum_probs=53.4
Q ss_pred HHHHHHHHHHHhccccCCccccceEecCCCChhhHHHHHHHHHHcCCceeecCCCCCceEEEEe
Q 001377 781 LSVEERCKFLVLGKNRGSTNALKVHVFCPMLKDKRDAVRLIAERWKLAVNPAGWEPKRFIVVHV 844 (1090)
Q Consensus 781 ~~vE~~L~~fv~~~~~~~~~~~k~~~f~PM~~~kR~fIHeLAe~ygL~S~S~d~EP~R~VvV~k 844 (1090)
..+|+.|..|+.+.. ...+.|+||++.+|++||+||+.|||.++|+|.|++|+|+|++
T Consensus 2 ~~~~~~l~~f~~~~~------~~~~~~~p~~~~~R~~vH~la~~~~L~s~s~g~~~~r~v~i~~ 59 (59)
T cd02325 2 EEREEELEAFAKDAA------GKSLELPPMNSYERKLIHDLAEYYGLKSESEGEGPNRRVVITK 59 (59)
T ss_pred hHHHHHHHHHHHhhc------CCeEEcCCCCHHHHHHHHHHHHHCCCEEEEecCCCCcEEEEeC
Confidence 568999999998874 5678999999999999999999999999999999999999974
No 15
>cd02640 R3H_NRF R3H domain of the NF-kappaB-repression factor (NRF). NRF is a nuclear inhibitor of NF-kappaB proteins that can silence the IFNbeta promoter via binding to a negative regulatory element (NRE). Beside R3H NRF also contains a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=98.96 E-value=1.4e-09 Score=94.38 Aligned_cols=57 Identities=19% Similarity=0.371 Sum_probs=51.0
Q ss_pred HHHHHHHHHHhccccCCccccceEecCC-CChhhHHHHHHHHHHcCCceeecCCCCCceEEEEe
Q 001377 782 SVEERCKFLVLGKNRGSTNALKVHVFCP-MLKDKRDAVRLIAERWKLAVNPAGWEPKRFIVVHV 844 (1090)
Q Consensus 782 ~vE~~L~~fv~~~~~~~~~~~k~~~f~P-M~~~kR~fIHeLAe~ygL~S~S~d~EP~R~VvV~k 844 (1090)
.+++.|.+|+.+.. ...+.|+| |++.+|++||+||+.+||.|.|+|.++.|+|+|++
T Consensus 3 ~~~~~i~~F~~s~~------~~~l~f~p~lt~~eR~~vH~~a~~~gL~s~S~G~g~~R~v~v~k 60 (60)
T cd02640 3 DYRQIIQNYAHSDD------IRDMVFSPEFSKEERALIHQIAQKYGLKSRSYGSGNDRYLVISK 60 (60)
T ss_pred hHHHHHHHHHcCCc------cceEEcCCCCCHHHHHHHHHHHHHcCCceeeEeCCCCeEEEEeC
Confidence 46788899997753 46789999 99999999999999999999999999999999964
No 16
>cd06007 R3H_DEXH_helicase R3H domain of a group of proteins which also contain a DEXH-box helicase domain, and may function as ATP-dependent DNA or RNA helicases. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=98.93 E-value=1.9e-09 Score=93.25 Aligned_cols=56 Identities=11% Similarity=0.129 Sum_probs=50.7
Q ss_pred HHHHHHHHHHhccccCCccccceEecCC-CChhhHHHHHHHHHHcCCceeecCCCCCceEEEEe
Q 001377 782 SVEERCKFLVLGKNRGSTNALKVHVFCP-MLKDKRDAVRLIAERWKLAVNPAGWEPKRFIVVHV 844 (1090)
Q Consensus 782 ~vE~~L~~fv~~~~~~~~~~~k~~~f~P-M~~~kR~fIHeLAe~ygL~S~S~d~EP~R~VvV~k 844 (1090)
.|++.|.+|+.+. ...+.|+| |++.+|++||+||+.+||.+.|+|.++.|+|+|+|
T Consensus 3 ~i~~~i~~F~~~~-------~~~l~Fpp~ls~~eR~~vH~~a~~~gL~s~S~G~g~~R~v~v~K 59 (59)
T cd06007 3 AINKALEDFRASD-------NEEYEFPSSLTNHERAVIHRLCRKLGLKSKSKGKGSNRRLSVYK 59 (59)
T ss_pred cHHHHHHHHHcCc-------ccEEEcCCCCCHHHHHHHHHHHHHcCCCceeecCCCCeEEEEeC
Confidence 4788899998765 35689999 99999999999999999999999999999999975
No 17
>cd02638 R3H_unknown_1 R3H domain of a group of eukaryotic proteins with unknown function. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=98.88 E-value=3.3e-09 Score=91.44 Aligned_cols=58 Identities=22% Similarity=0.289 Sum_probs=49.6
Q ss_pred HHHHHHHHHHhccccCCccccceEecCCCChhhHHHHH-HHHHHcCCceeecCCCCCceEEEEe
Q 001377 782 SVEERCKFLVLGKNRGSTNALKVHVFCPMLKDKRDAVR-LIAERWKLAVNPAGWEPKRFIVVHV 844 (1090)
Q Consensus 782 ~vE~~L~~fv~~~~~~~~~~~k~~~f~PM~~~kR~fIH-eLAe~ygL~S~S~d~EP~R~VvV~k 844 (1090)
.+.+.|..|+.... -++.+.|+||++.+|++|| .|+++-++.|+|.|.||+|+|||..
T Consensus 3 ~~~~~~~~f~~~~~-----~~r~v~LePM~~~ERkIIH~~Lq~~~~v~T~S~G~ep~RrVVI~~ 61 (62)
T cd02638 3 RVSEELEIFLLSFQ-----RYRVLLFPPLNSRRRYLIHQTVENRFLLSTFSVGEGWARRTVVCY 61 (62)
T ss_pred hhHHHHHHHHHhcc-----cCCeEecCCCChHHHHHHHHHHhcCCCceEEEccCCCCcEEEEee
Confidence 45677777776542 2678999999999999999 8899999999999999999999964
No 18
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=98.73 E-value=9.7e-09 Score=108.31 Aligned_cols=68 Identities=18% Similarity=0.103 Sum_probs=63.5
Q ss_pred hhHHHHHHHHHHHHHhccccCCccccceEecCCCChhhHHHHH-HHHHHcCCceeecCCCCCceEEEEe
Q 001377 777 PKWVLSVEERCKFLVLGKNRGSTNALKVHVFCPMLKDKRDAVR-LIAERWKLAVNPAGWEPKRFIVVHV 844 (1090)
Q Consensus 777 ~~~~~~vE~~L~~fv~~~~~~~~~~~k~~~f~PM~~~kR~fIH-eLAe~ygL~S~S~d~EP~R~VvV~k 844 (1090)
-+|+.+++++|..|+...+.++..+.+++.++||++.+|++|| .|.++-|+.|+|.|.||+|+|||..
T Consensus 139 ~~yRerR~e~L~~LA~~~A~rV~~tg~~v~L~pM~~~ERkIVH~~l~~~~~V~T~SeG~ep~R~vVV~~ 207 (208)
T COG1847 139 GDYRERRKETLIKLAERAAERVLETGRSVELEPMPPFERKIVHTALSANPGVETYSEGEEPNRRVVVRP 207 (208)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHhhCCeeecCCCCHHHHHHHHHHHHhcCCcceeecCCCCceEEEEec
Confidence 4899999999999999988888888999999999999999999 7788888999999999999999964
No 19
>cd02645 R3H_AAA R3H domain of a group of proteins with unknown function, who also contain a AAA-ATPase (AAA) domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to be binding ssDNA or ssRNA in a sequence-specific manner.
Probab=98.57 E-value=7.7e-08 Score=83.67 Aligned_cols=41 Identities=22% Similarity=0.244 Sum_probs=39.3
Q ss_pred ceEecCCCChhhHHHHHHHHHHcCCceeecCCCCCceEEEE
Q 001377 803 KVHVFCPMLKDKRDAVRLIAERWKLAVNPAGWEPKRFIVVH 843 (1090)
Q Consensus 803 k~~~f~PM~~~kR~fIHeLAe~ygL~S~S~d~EP~R~VvV~ 843 (1090)
+.+.|.||++..|++||+|++.|||.|+|+|.||+|+|+|+
T Consensus 19 ~~veL~Pm~~~eRri~H~~v~~~~l~s~S~G~ep~RrvvI~ 59 (60)
T cd02645 19 EPVELLPRSAYIRRLQHDLVERYQLRSESFGSEPNRRLRIL 59 (60)
T ss_pred ceEEcCCCCHHHHHHHHHHHHHCCCeEEEecCCCCcEEEEe
Confidence 67899999999999999999999999999999999999996
No 20
>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=97.75 E-value=1.2e-05 Score=65.41 Aligned_cols=43 Identities=35% Similarity=0.856 Sum_probs=36.9
Q ss_pred eEeeecccccccCceeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCC
Q 001377 113 ECMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQ 170 (1090)
Q Consensus 113 eC~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~ 170 (1090)
+|+||++.+...+.+.... |.++||..||++|.+.. -.||-||
T Consensus 2 ~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~~~~~--------------~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLP-CGHVFHRSCIKEWLKRN--------------NSCPVCR 44 (44)
T ss_dssp CETTTTCBHHTTSCEEEET-TSEEEEHHHHHHHHHHS--------------SB-TTTH
T ss_pred CCcCCChhhcCCCeEEEcc-CCCeeCHHHHHHHHHhC--------------CcCCccC
Confidence 6999999999888888887 99999999999999752 2899885
No 21
>PF01422 zf-NF-X1: NF-X1 type zinc finger; InterPro: IPR000967 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a domain presumed to be a zinc binding domain. The following pattern describes the zinc finger: C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C where X can be any amino acid, and numbers in brackets indicate the number of residues. The two position can be either His or Cys. This domain is found in the human transcriptional repressor NK-X1, a repressor of HLA-DRA transcription; the Drosophila shuttle craft protein, which plays an essential role during the late stages of embryonic neurogenesis; and a yeast hypothetical protein YNL023C. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=97.69 E-value=1.9e-05 Score=53.84 Aligned_cols=20 Identities=50% Similarity=1.462 Sum_probs=18.5
Q ss_pred CCCcccccccccCCCccCcc
Q 001377 281 CWRHKCEKICHVGPCGPCRV 300 (1090)
Q Consensus 281 CG~H~C~~~CH~G~C~~C~~ 300 (1090)
||+|+|+++||.|+|++|.+
T Consensus 1 CG~H~C~~~CH~G~C~pC~~ 20 (20)
T PF01422_consen 1 CGNHTCQQLCHPGPCPPCPQ 20 (20)
T ss_pred CCCcccCCcccCCcCCCCCC
Confidence 78999999999999999963
No 22
>PF01422 zf-NF-X1: NF-X1 type zinc finger; InterPro: IPR000967 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a domain presumed to be a zinc binding domain. The following pattern describes the zinc finger: C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C where X can be any amino acid, and numbers in brackets indicate the number of residues. The two position can be either His or Cys. This domain is found in the human transcriptional repressor NK-X1, a repressor of HLA-DRA transcription; the Drosophila shuttle craft protein, which plays an essential role during the late stages of embryonic neurogenesis; and a yeast hypothetical protein YNL023C. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=97.66 E-value=2.4e-05 Score=53.29 Aligned_cols=20 Identities=60% Similarity=1.742 Sum_probs=18.6
Q ss_pred CCCccccCcccCCCCCCCcc
Q 001377 498 CGQHSCESLCHSGHCPPCLE 517 (1090)
Q Consensus 498 CG~H~C~~~CH~G~C~pC~e 517 (1090)
||+|+|+++||.|+|+||.+
T Consensus 1 CG~H~C~~~CH~G~C~pC~~ 20 (20)
T PF01422_consen 1 CGNHTCQQLCHPGPCPPCPQ 20 (20)
T ss_pred CCCcccCCcccCCcCCCCCC
Confidence 78999999999999999974
No 23
>smart00438 ZnF_NFX Repressor of transcription.
Probab=97.04 E-value=0.0003 Score=51.30 Aligned_cols=22 Identities=55% Similarity=1.413 Sum_probs=19.5
Q ss_pred CCCcccccccccCCCccCccce
Q 001377 281 CWRHKCEKICHVGPCGPCRVLV 302 (1090)
Q Consensus 281 CG~H~C~~~CH~G~C~~C~~~v 302 (1090)
||+|+|++.||+|+|++|.+..
T Consensus 1 CG~H~C~~~CH~G~C~pC~~~~ 22 (26)
T smart00438 1 CGIHKCQKLCHPGPCPPCKQXX 22 (26)
T ss_pred CCCCcCCCCCCCCcCcCccccc
Confidence 7899999999999999998543
No 24
>cd02639 R3H_RRM R3H domain of mainly fungal proteins which are associated with a RNA recognition motif (RRM) domain. Present in this group is the RNA-binding post-transcriptional regulator Cip2 (Csx1-interacting protein 2) involved in counteracting Csx1 function. Csx1 plays a central role in controlling gene expression during oxidative stress. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=96.89 E-value=0.0013 Score=57.62 Aligned_cols=43 Identities=21% Similarity=0.224 Sum_probs=39.4
Q ss_pred cceEecCC-CChhhHHHHHHHHHHcCCceeecCCCCCceEEEEe
Q 001377 802 LKVHVFCP-MLKDKRDAVRLIAERWKLAVNPAGWEPKRFIVVHV 844 (1090)
Q Consensus 802 ~k~~~f~P-M~~~kR~fIHeLAe~ygL~S~S~d~EP~R~VvV~k 844 (1090)
...+.|+| .++.+|++||.||..+||.+.|.|..-.|.|+|++
T Consensus 17 ~~eL~Fp~~ls~~eRriih~la~~lGL~~~s~G~g~~R~v~v~k 60 (60)
T cd02639 17 RDELAFPSSLSPAERRIVHLLASRLGLNHVSDGTGERRQVQITK 60 (60)
T ss_pred ceEEEcCCCCCHHHHHHHHHHHHHcCCceEEeCCCceEEEeecC
Confidence 45688988 99999999999999999999999999999999875
No 25
>smart00438 ZnF_NFX Repressor of transcription.
Probab=96.74 E-value=0.00081 Score=49.07 Aligned_cols=21 Identities=57% Similarity=1.540 Sum_probs=19.3
Q ss_pred CCCccccCcccCCCCCCCccc
Q 001377 498 CGQHSCESLCHSGHCPPCLET 518 (1090)
Q Consensus 498 CG~H~C~~~CH~G~C~pC~e~ 518 (1090)
||+|.|+..||.|+|+||.+.
T Consensus 1 CG~H~C~~~CH~G~C~pC~~~ 21 (26)
T smart00438 1 CGIHKCQKLCHPGPCPPCKQX 21 (26)
T ss_pred CCCCcCCCCCCCCcCcCcccc
Confidence 788999999999999999864
No 26
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=96.27 E-value=0.00086 Score=60.34 Aligned_cols=61 Identities=30% Similarity=0.554 Sum_probs=28.3
Q ss_pred cceEeeeccccccc--CceeeCC--CCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCcccc
Q 001377 111 KVECMICYDMVKRS--APIWSCS--SCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQSVQL 174 (1090)
Q Consensus 111 ~yeC~IC~~~i~~~--~~vWsC~--~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~~~~ 174 (1090)
..+|.||++.+... .++=.|. .|..+||+.|+.+|.+....... .-....+.||.|.....
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~---~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQ---SFIPIFGECPYCSSPIS 66 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS----TTT--EEE-TTT-SEEE
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCe---eecccccCCcCCCCeee
Confidence 36899999997633 3567887 99999999999999985322110 01234688999997643
No 27
>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function.
Probab=95.90 E-value=0.017 Score=51.00 Aligned_cols=49 Identities=29% Similarity=0.450 Sum_probs=40.7
Q ss_pred EEecCcccchhhhHHHHhh---cCeeeEEEecCCceEEEecChhhHHHHHHhh
Q 001377 883 VSFLDLPRESDISALVLRF---GGECELVWLNDKNALAVFSDPARAATATRRL 932 (1090)
Q Consensus 883 v~~~dl~~~~~i~~~~~~f---~g~~el~wi~d~~~l~vF~~p~~~~~a~~~l 932 (1090)
-.+++| ...||..++.+| ++-+.++||||..+-+||.++.-|..||.+|
T Consensus 11 rGvd~l-sT~dI~~y~~~y~~~~~~~~IEWIdDtScNvvf~d~~~A~~AL~~L 62 (62)
T PF10309_consen 11 RGVDEL-STDDIKAYFSEYFDEEGPFRIEWIDDTSCNVVFKDEETAARALVAL 62 (62)
T ss_pred EcCCCC-CHHHHHHHHHHhcccCCCceEEEecCCcEEEEECCHHHHHHHHHcC
Confidence 445777 556788888776 2567899999999999999999999999876
No 28
>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=95.19 E-value=0.014 Score=45.97 Aligned_cols=44 Identities=32% Similarity=0.671 Sum_probs=34.3
Q ss_pred eEeeecccccccCceeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCcc
Q 001377 113 ECMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQSV 172 (1090)
Q Consensus 113 eC~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~~ 172 (1090)
+|.||.+.+ ...+.-..|.++||..|++.|.+. ...+||.|+..
T Consensus 1 ~C~iC~~~~---~~~~~~~~C~H~~c~~C~~~~~~~-------------~~~~Cp~C~~~ 44 (45)
T cd00162 1 ECPICLEEF---REPVVLLPCGHVFCRSCIDKWLKS-------------GKNTCPLCRTP 44 (45)
T ss_pred CCCcCchhh---hCceEecCCCChhcHHHHHHHHHh-------------CcCCCCCCCCc
Confidence 589999998 334444569999999999999875 25679999864
No 29
>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=95.18 E-value=0.017 Score=52.46 Aligned_cols=42 Identities=36% Similarity=1.027 Sum_probs=30.9
Q ss_pred eEeeecccccccC---------c--eeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCC
Q 001377 113 ECMICYDMVKRSA---------P--IWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQ 170 (1090)
Q Consensus 113 eC~IC~~~i~~~~---------~--vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~ 170 (1090)
.|.||.+.+.... - +| ..|-++||+.||.+|.+. ...||-|+
T Consensus 21 ~C~IC~~~l~~~~~~~~~~~~~~~i~~--~~C~H~FH~~Ci~~Wl~~--------------~~~CP~CR 73 (73)
T PF12678_consen 21 NCAICREPLEDPCPECQAPQDECPIVW--GPCGHIFHFHCISQWLKQ--------------NNTCPLCR 73 (73)
T ss_dssp BETTTTSBTTSTTCCHHHCTTTS-EEE--ETTSEEEEHHHHHHHHTT--------------SSB-TTSS
T ss_pred cccccChhhhChhhhhcCCccccceEe--cccCCCEEHHHHHHHHhc--------------CCcCCCCC
Confidence 4999999993321 1 33 369999999999999975 23799886
No 30
>PHA02926 zinc finger-like protein; Provisional
Probab=95.15 E-value=0.023 Score=61.32 Aligned_cols=72 Identities=31% Similarity=0.619 Sum_probs=51.8
Q ss_pred ChhHHHHHHHHHhccC-cceEeeecccccccCceeeC------CCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCC
Q 001377 95 DLPQLLQEIQDKLMKS-KVECMICYDMVKRSAPIWSC------SSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCP 167 (1090)
Q Consensus 95 ~~~~l~~~l~e~l~~~-~yeC~IC~~~i~~~~~vWsC------~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP 167 (1090)
+++.+.++-.+..+.. ..+|.||++.|-... .=+. +.|-|+|.+.||++|.+.... ......||
T Consensus 153 ~i~~il~~ye~~~~~SkE~eCgICmE~I~eK~-~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~--------~~~~rsCP 223 (242)
T PHA02926 153 DIIKILDKYEDVYRVSKEKECGICYEVVYSKR-LENDRYFGLLDSCNHIFCITCINIWHRTRRE--------TGASDNCP 223 (242)
T ss_pred chhHHHHHHHHHHhccCCCCCccCcccccccc-ccccccccccCCCCchHHHHHHHHHHHhccc--------cCcCCcCC
Confidence 6777777777766654 489999999984321 1122 279999999999999985321 13468899
Q ss_pred CCCccccC
Q 001377 168 GCQSVQLT 175 (1090)
Q Consensus 168 ~C~~~~~~ 175 (1090)
-|+.....
T Consensus 224 iCR~~f~~ 231 (242)
T PHA02926 224 ICRTRFRN 231 (242)
T ss_pred CCcceeee
Confidence 99987654
No 31
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.41 E-value=0.045 Score=61.22 Aligned_cols=50 Identities=28% Similarity=0.740 Sum_probs=40.8
Q ss_pred CcceEeeecccccccCceeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCccc
Q 001377 110 SKVECMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQSVQ 173 (1090)
Q Consensus 110 ~~yeC~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~~~ 173 (1090)
+-.||.||++.+-..++ .-=-=|-|+||-.||.||... ..-.||-|+++.
T Consensus 322 ~GveCaICms~fiK~d~-~~vlPC~H~FH~~Cv~kW~~~-------------y~~~CPvCrt~i 371 (374)
T COG5540 322 KGVECAICMSNFIKNDR-LRVLPCDHRFHVGCVDKWLLG-------------YSNKCPVCRTAI 371 (374)
T ss_pred CCceEEEEhhhhcccce-EEEeccCceechhHHHHHHhh-------------hcccCCccCCCC
Confidence 44999999999988777 333458999999999999873 356799999874
No 32
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=94.27 E-value=0.039 Score=51.54 Aligned_cols=52 Identities=31% Similarity=0.629 Sum_probs=36.6
Q ss_pred ceEeeecccccccCce-----eeC----CCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCcccc
Q 001377 112 VECMICYDMVKRSAPI-----WSC----SSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQSVQL 174 (1090)
Q Consensus 112 yeC~IC~~~i~~~~~v-----WsC----~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~~~~ 174 (1090)
-+|-||...+....+. =.| ..|-+.||+.||.+|...+.+ .=.||-|+.+..
T Consensus 22 d~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~-----------~~~CPmCR~~w~ 82 (85)
T PF12861_consen 22 DVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSS-----------KGQCPMCRQPWK 82 (85)
T ss_pred CceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccC-----------CCCCCCcCCeee
Confidence 4678887777744430 112 269999999999999987532 348999998653
No 33
>PHA02929 N1R/p28-like protein; Provisional
Probab=94.12 E-value=0.043 Score=60.52 Aligned_cols=66 Identities=26% Similarity=0.601 Sum_probs=44.2
Q ss_pred hhHHHHHHHHHhc-cCcceEeeecccccccCc----eeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCC
Q 001377 96 LPQLLQEIQDKLM-KSKVECMICYDMVKRSAP----IWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQ 170 (1090)
Q Consensus 96 ~~~l~~~l~e~l~-~~~yeC~IC~~~i~~~~~----vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~ 170 (1090)
+|.+.++..+... +...+|.||.+.+..... +=-=..|.|+||..||.+|.+.. -.||-|+
T Consensus 158 lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~--------------~tCPlCR 223 (238)
T PHA02929 158 IPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEK--------------NTCPVCR 223 (238)
T ss_pred cchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcC--------------CCCCCCC
Confidence 4444444443322 356899999999865430 11123799999999999998642 2699999
Q ss_pred ccccC
Q 001377 171 SVQLT 175 (1090)
Q Consensus 171 ~~~~~ 175 (1090)
.....
T Consensus 224 ~~~~~ 228 (238)
T PHA02929 224 TPFIS 228 (238)
T ss_pred CEeeE
Confidence 87653
No 34
>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=93.86 E-value=0.061 Score=42.65 Aligned_cols=32 Identities=28% Similarity=0.606 Sum_probs=27.1
Q ss_pred EeeecccccccCceeeCCCCceeechhHHHHHhcC
Q 001377 114 CMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWARA 148 (1090)
Q Consensus 114 C~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~~ 148 (1090)
|+||.+.+.. .+--..|.++|...||.+|.++
T Consensus 1 C~iC~~~~~~---~~~~~~CGH~fC~~C~~~~~~~ 32 (39)
T PF13923_consen 1 CPICLDELRD---PVVVTPCGHSFCKECIEKYLEK 32 (39)
T ss_dssp ETTTTSB-SS---EEEECTTSEEEEHHHHHHHHHC
T ss_pred CCCCCCcccC---cCEECCCCCchhHHHHHHHHHC
Confidence 7899998876 6667789999999999999875
No 35
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=93.64 E-value=0.059 Score=57.50 Aligned_cols=62 Identities=27% Similarity=0.585 Sum_probs=43.1
Q ss_pred CcceEeeecccccccCceeeCCCCceeechhHHHHHhcCCCCcch-hh-hccCCCCCCCCCCCccccC
Q 001377 110 SKVECMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWARAPTSADL-SA-ERSQGFNWRCPGCQSVQLT 175 (1090)
Q Consensus 110 ~~yeC~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~~~~s~~~-~~-~~~~~~~WrCP~C~~~~~~ 175 (1090)
+.++|.||.+.++ ++|= ..|-|+|...||.+|...+....+ .. -.......+||-|+.....
T Consensus 17 ~~~~CpICld~~~--dPVv--T~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 17 GDFDCNICLDQVR--DPVV--TLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred CccCCccCCCcCC--CcEE--cCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 6799999999874 5554 479999999999999875421111 00 0112346899999988654
No 36
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=93.06 E-value=0.044 Score=68.45 Aligned_cols=58 Identities=38% Similarity=0.868 Sum_probs=48.4
Q ss_pred HHHHHhccCcceEeeeccc---ccccCceeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCcc
Q 001377 102 EIQDKLMKSKVECMICYDM---VKRSAPIWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQSV 172 (1090)
Q Consensus 102 ~l~e~l~~~~yeC~IC~~~---i~~~~~vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~~ 172 (1090)
.|++++ +|.-||.|||+- |.|+=|-=.|..|-+-||-.|+-||++.+. .-+||-|+++
T Consensus 1461 Ni~~~f-sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~------------~s~CPlCRse 1521 (1525)
T COG5219 1461 NIDEKF-SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSA------------RSNCPLCRSE 1521 (1525)
T ss_pred hhhhhc-CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcC------------CCCCCccccc
Confidence 344433 589999999975 568888889999999999999999999865 5689999976
No 37
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=92.80 E-value=0.11 Score=59.51 Aligned_cols=60 Identities=28% Similarity=0.628 Sum_probs=48.6
Q ss_pred HHHHHHHHhccCcceEeeeccccccc--CceeeCC-------CCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCC
Q 001377 99 LLQEIQDKLMKSKVECMICYDMVKRS--APIWSCS-------SCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGC 169 (1090)
Q Consensus 99 l~~~l~e~l~~~~yeC~IC~~~i~~~--~~vWsC~-------~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C 169 (1090)
+.+...|+|.++--.|.||++++-.. ++.|-=. -|-++|||.|.|-|...+ --||-|
T Consensus 275 ~~t~t~eql~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERq--------------QTCPIC 340 (491)
T COG5243 275 YPTATEEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ--------------QTCPIC 340 (491)
T ss_pred cchhhhhhhcCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhc--------------cCCCcc
Confidence 56778899999999999999996444 4566532 489999999999999763 359999
Q ss_pred Ccc
Q 001377 170 QSV 172 (1090)
Q Consensus 170 ~~~ 172 (1090)
+..
T Consensus 341 r~p 343 (491)
T COG5243 341 RRP 343 (491)
T ss_pred cCc
Confidence 887
No 38
>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=87.56 E-value=0.42 Score=37.95 Aligned_cols=32 Identities=25% Similarity=0.693 Sum_probs=26.0
Q ss_pred EeeecccccccCceeeCCCCceeechhHHHHHhcC
Q 001377 114 CMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWARA 148 (1090)
Q Consensus 114 C~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~~ 148 (1090)
|.||.+.+.....+ ..|.|.|...||++|.++
T Consensus 1 C~iC~~~~~~~~~~---~~C~H~fC~~C~~~~~~~ 32 (41)
T PF00097_consen 1 CPICLEPFEDPVIL---LPCGHSFCRDCLRKWLEN 32 (41)
T ss_dssp ETTTSSBCSSEEEE---TTTSEEEEHHHHHHHHHH
T ss_pred CCcCCccccCCCEE---ecCCCcchHHHHHHHHHh
Confidence 77898887665533 458999999999999996
No 39
>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=87.22 E-value=0.46 Score=35.79 Aligned_cols=30 Identities=37% Similarity=0.906 Sum_probs=23.4
Q ss_pred EeeecccccccCceeeCCCCceeechhHHHHHhc
Q 001377 114 CMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWAR 147 (1090)
Q Consensus 114 C~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~ 147 (1090)
|.||.+.. ...+.. .|.++||..||++|.+
T Consensus 1 C~iC~~~~--~~~~~~--~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 1 CPICLEEL--KDPVVL--PCGHTFCRSCIRKWLK 30 (39)
T ss_pred CCcCccCC--CCcEEe--cCCChHHHHHHHHHHH
Confidence 67888882 344443 5999999999999987
No 40
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.81 E-value=0.78 Score=53.27 Aligned_cols=48 Identities=25% Similarity=0.634 Sum_probs=39.7
Q ss_pred eEeeecccccccCceeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCcccc
Q 001377 113 ECMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQSVQL 174 (1090)
Q Consensus 113 eC~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~~~~ 174 (1090)
.|.||+|.-...+++=- =-|-|.||.+||..|...- .--||-|.....
T Consensus 231 ~CaIClEdY~~GdklRi-LPC~H~FH~~CIDpWL~~~-------------r~~CPvCK~di~ 278 (348)
T KOG4628|consen 231 TCAICLEDYEKGDKLRI-LPCSHKFHVNCIDPWLTQT-------------RTFCPVCKRDIR 278 (348)
T ss_pred eEEEeecccccCCeeeE-ecCCCchhhccchhhHhhc-------------CccCCCCCCcCC
Confidence 99999999999999766 6799999999999998741 123999987644
No 41
>KOG4483 consensus Uncharacterized conserved protein [Function unknown]
Probab=84.74 E-value=1 Score=52.29 Aligned_cols=51 Identities=33% Similarity=0.527 Sum_probs=40.2
Q ss_pred eEEEecCcccc---hhhhHHHHhhc-CeeeEEEecCCceEEEecChhhHHHHHHh
Q 001377 881 LVVSFLDLPRE---SDISALVLRFG-GECELVWLNDKNALAVFSDPARAATATRR 931 (1090)
Q Consensus 881 ~~v~~~dl~~~---~~i~~~~~~f~-g~~el~wi~d~~~l~vF~~p~~~~~a~~~ 931 (1090)
.||-|-|++.+ .||..+...|+ +.|.+.|++|..||.||....+|++||..
T Consensus 392 HVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDdthalaVFss~~~AaeaLt~ 446 (528)
T KOG4483|consen 392 HVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDDTHALAVFSSVNRAAEALTL 446 (528)
T ss_pred ceeEeccCchhhccHHHHHHHHHhhcCCceeEEeecceeEEeecchHHHHHHhhc
Confidence 55666666543 55555555566 88999999999999999999999999975
No 42
>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=84.59 E-value=0.75 Score=46.58 Aligned_cols=49 Identities=27% Similarity=0.583 Sum_probs=35.8
Q ss_pred hHHHHHHHHHhccCcceEeeecccccccCc-eeeCCCCc------eeechhHHHHHhc
Q 001377 97 PQLLQEIQDKLMKSKVECMICYDMVKRSAP-IWSCSSCF------SIFHLSCIKKWAR 147 (1090)
Q Consensus 97 ~~l~~~l~e~l~~~~yeC~IC~~~i~~~~~-vWsC~~C~------~vfHL~CikkWa~ 147 (1090)
..|-+-|.++..+-..||.||+++|....- |-- .|+ ++||-.|+++|.+
T Consensus 12 ~~l~~lf~~~w~~~~~EC~IC~~~I~~~~GvV~v--t~~g~lnLEkmfc~~C~~rw~~ 67 (134)
T PF05883_consen 12 YYLERLFNDQWPRCTVECQICFDRIDNNDGVVYV--TDGGTLNLEKMFCADCDKRWRR 67 (134)
T ss_pred HHHHHHHHHHccccCeeehhhhhhhhcCCCEEEE--ecCCeehHHHHHHHHHHHHHHh
Confidence 345566667777779999999999998333 322 344 3899999999964
No 43
>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=79.52 E-value=0.4 Score=39.95 Aligned_cols=48 Identities=29% Similarity=0.823 Sum_probs=34.5
Q ss_pred EeeecccccccCceeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCC
Q 001377 114 CMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQ 170 (1090)
Q Consensus 114 C~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~ 170 (1090)
|.||.. ......+=.|..|-..||+.|+.- +... +......|.||.|+
T Consensus 2 C~vC~~-~~~~~~~i~C~~C~~~~H~~C~~~----~~~~----~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 2 CPVCGQ-SDDDGDMIQCDSCNRWYHQECVGP----PEKA----EEIPSGDWYCPNCR 49 (51)
T ss_dssp BTTTTS-SCTTSSEEEBSTTSCEEETTTSTS----SHSH----HSHHSSSBSSHHHH
T ss_pred CcCCCC-cCCCCCeEEcCCCChhhCcccCCC----Chhh----ccCCCCcEECcCCc
Confidence 678888 778888999999999999999831 1110 11112389999885
No 44
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=77.85 E-value=0.99 Score=55.56 Aligned_cols=51 Identities=31% Similarity=0.794 Sum_probs=38.7
Q ss_pred eEeeecccccccCc-eeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCcc
Q 001377 113 ECMICYDMVKRSAP-IWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQSV 172 (1090)
Q Consensus 113 eC~IC~~~i~~~~~-vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~~ 172 (1090)
-|.||...=.-... +=+|..|+-.||=.|++-|+..-. ....||||.|+.-
T Consensus 20 mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~---------l~~gWrC~~crvC 71 (694)
T KOG4443|consen 20 MCPLCGSSGKGRAGRLLACSDCGQKYHPYCVTSWAQHAV---------LSGGWRCPSCRVC 71 (694)
T ss_pred hhhhhccccccccCcchhhhhhcccCCcchhhHHHhHHH---------hcCCcccCCceee
Confidence 46677666544444 889999999999999999997531 1346999999754
No 45
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=77.64 E-value=0.77 Score=54.24 Aligned_cols=48 Identities=29% Similarity=0.609 Sum_probs=39.0
Q ss_pred cceEeeecccccccCceeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCcccc
Q 001377 111 KVECMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQSVQL 174 (1090)
Q Consensus 111 ~yeC~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~~~~ 174 (1090)
.-.|+||.++++.+-..--=..|+|-||-.|+.+|... .||-|+..+.
T Consensus 175 LPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~~----------------scpvcR~~q~ 222 (493)
T KOG0804|consen 175 LPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWDS----------------SCPVCRYCQS 222 (493)
T ss_pred CCCcchhHhhcCccccceeeeecccccchHHHhhcccC----------------cChhhhhhcC
Confidence 56799999999987754444579999999999999764 4888888765
No 46
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=74.36 E-value=2.5 Score=44.08 Aligned_cols=56 Identities=21% Similarity=0.404 Sum_probs=39.9
Q ss_pred ccCcceEeeecccccccCceeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCccccC
Q 001377 108 MKSKVECMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQSVQLT 175 (1090)
Q Consensus 108 ~~~~yeC~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~~~~~ 175 (1090)
.....+|-||.++-+.....=.|..=....|.+|+++|+..+ ...+|+-|+..|..
T Consensus 5 s~~~~~CRIC~~~~~~~~~PC~CkGs~k~VH~sCL~rWi~~s------------~~~~CeiC~~~Y~i 60 (162)
T PHA02825 5 SLMDKCCWICKDEYDVVTNYCNCKNENKIVHKECLEEWINTS------------KNKSCKICNGPYNI 60 (162)
T ss_pred CCCCCeeEecCCCCCCccCCcccCCCchHHHHHHHHHHHhcC------------CCCcccccCCeEEE
Confidence 445679999998854222222233334588999999999964 36789999999875
No 47
>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=74.27 E-value=2.3 Score=35.89 Aligned_cols=45 Identities=24% Similarity=0.640 Sum_probs=29.9
Q ss_pred eEeeecccccccCceee----CCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCC
Q 001377 113 ECMICYDMVKRSAPIWS----CSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQ 170 (1090)
Q Consensus 113 eC~IC~~~i~~~~~vWs----C~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~ 170 (1090)
.|-||++. ...+.+|- |..-..++|..|+++|...+. ..+||-|+
T Consensus 1 ~CrIC~~~-~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~------------~~~C~iC~ 49 (49)
T smart00744 1 ICRICHDE-GDEGDPLVSPCRCKGSLKYVHQECLERWINESG------------NKTCEICK 49 (49)
T ss_pred CccCCCCC-CCCCCeeEeccccCCchhHHHHHHHHHHHHHcC------------CCcCCCCC
Confidence 37899882 23333443 333358999999999998753 34788774
No 48
>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=74.03 E-value=3 Score=34.82 Aligned_cols=44 Identities=23% Similarity=0.638 Sum_probs=32.8
Q ss_pred ceEeeecccccccCceeeCCCCcee-echhHHHHHhcCCCCcchhhhccCCCCCCCCCCCccc
Q 001377 112 VECMICYDMVKRSAPIWSCSSCFSI-FHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQSVQ 173 (1090)
Q Consensus 112 yeC~IC~~~i~~~~~vWsC~~C~~v-fHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~~~ 173 (1090)
.+|.||.+.... --++ -|-|+ |-..|+.+|.+. ..+||-|+...
T Consensus 3 ~~C~iC~~~~~~-~~~~---pCgH~~~C~~C~~~~~~~--------------~~~CP~Cr~~i 47 (50)
T PF13920_consen 3 EECPICFENPRD-VVLL---PCGHLCFCEECAERLLKR--------------KKKCPICRQPI 47 (50)
T ss_dssp SB-TTTSSSBSS-EEEE---TTCEEEEEHHHHHHHHHT--------------TSBBTTTTBB-
T ss_pred CCCccCCccCCc-eEEe---CCCChHHHHHHhHHhccc--------------CCCCCcCChhh
Confidence 579999998542 2233 56788 999999999983 57899999764
No 49
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=73.82 E-value=1.2 Score=40.94 Aligned_cols=34 Identities=41% Similarity=1.039 Sum_probs=27.4
Q ss_pred eeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCccc
Q 001377 127 IWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQSVQ 173 (1090)
Q Consensus 127 vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~~~ 173 (1090)
||- .|-+.||+.||.+|...++++ -.||-|+...
T Consensus 47 v~G--~C~h~fh~hCI~~wl~~~tsq-----------~~CPmcRq~~ 80 (84)
T KOG1493|consen 47 VWG--YCLHAFHAHCILKWLNTPTSQ-----------GQCPMCRQTW 80 (84)
T ss_pred HHH--HHHHHHHHHHHHHHhcCcccc-----------ccCCcchhee
Confidence 565 788999999999999987653 4699888654
No 50
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=71.79 E-value=2.9 Score=48.84 Aligned_cols=12 Identities=25% Similarity=0.340 Sum_probs=7.6
Q ss_pred CchHHHHHHHHH
Q 001377 730 MCDDECAKLERK 741 (1090)
Q Consensus 730 ~CddeC~k~~R~ 741 (1090)
.=|++|..+|-+
T Consensus 146 q~~~et~~lqE~ 157 (465)
T KOG0827|consen 146 QFDPETLELQEN 157 (465)
T ss_pred hhCHHHHHHHHh
Confidence 346777777654
No 51
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=68.72 E-value=2.8 Score=45.58 Aligned_cols=66 Identities=23% Similarity=0.551 Sum_probs=48.4
Q ss_pred hhHHHHHHHHHhccCcc--eEeeecccccccCceeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCccc
Q 001377 96 LPQLLQEIQDKLMKSKV--ECMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQSVQ 173 (1090)
Q Consensus 96 ~~~l~~~l~e~l~~~~y--eC~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~~~ 173 (1090)
++.+.|-|++ .-| -|-.|--.+-..+-|-- .||++||..|+-.||.+--. .+.....+||.|..+.
T Consensus 37 VQSYLqWL~D----sDY~pNC~LC~t~La~gdt~RL--vCyhlfHW~ClneraA~lPa------nTAPaGyqCP~Cs~ei 104 (299)
T KOG3970|consen 37 VQSYLQWLQD----SDYNPNCRLCNTPLASGDTTRL--VCYHLFHWKCLNERAANLPA------NTAPAGYQCPCCSQEI 104 (299)
T ss_pred HHHHHHHHhh----cCCCCCCceeCCccccCcceee--hhhhhHHHHHhhHHHhhCCC------cCCCCcccCCCCCCcc
Confidence 4556666666 555 58889888777665543 69999999999999986321 2346789999998764
No 52
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=68.56 E-value=4.6 Score=32.92 Aligned_cols=44 Identities=30% Similarity=0.638 Sum_probs=33.5
Q ss_pred eEeeecccccccCceeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCc
Q 001377 113 ECMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQS 171 (1090)
Q Consensus 113 eC~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~ 171 (1090)
+|.||++........|- ..|.++|-..||+++.. ..-.||-|+.
T Consensus 1 ~C~~C~~~~~~~~~~~l-~~CgH~~C~~C~~~~~~--------------~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRL-TSCGHIFCEKCLKKLKG--------------KSVKCPICRK 44 (44)
T ss_pred CCcCcCccccCCCCeEE-cccCCHHHHHHHHhhcC--------------CCCCCcCCCC
Confidence 58999999944444454 57999999999999981 1567998873
No 53
>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN). ; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.
Probab=65.85 E-value=12 Score=35.49 Aligned_cols=58 Identities=26% Similarity=0.432 Sum_probs=44.5
Q ss_pred ceEEEecCcccchhhhHHHHhhcCeeeEEEecCCceEEEecChhhHHHHHHhhcCcccc
Q 001377 880 RLVVSFLDLPRESDISALVLRFGGECELVWLNDKNALAVFSDPARAATATRRLDHGSVY 938 (1090)
Q Consensus 880 ~~~v~~~dl~~~~~i~~~~~~f~g~~el~wi~d~~~l~vF~~p~~~~~a~~~l~~~~~~ 938 (1090)
.|=|+|...=...||..|-.-| |-..+.||||-.|.+...+...+..|+..+...+.|
T Consensus 11 VFhltFPkeWK~~DI~qlFspf-G~I~VsWi~dTSAfV~l~~r~~~~~v~~~~~~~~~y 68 (87)
T PF08675_consen 11 VFHLTFPKEWKTSDIYQLFSPF-GQIYVSWINDTSAFVALHNRDQAKVVMNTLKKNSSY 68 (87)
T ss_dssp EEEEE--TT--HHHHHHHCCCC-CCEEEEEECTTEEEEEECCCHHHHHHHHHHTT-SSS
T ss_pred EEEEeCchHhhhhhHHHHhccC-CcEEEEEEcCCcEEEEeecHHHHHHHHHHhccCCce
Confidence 3668887776667777666556 577899999999999999999999999999987777
No 54
>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 KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=63.59 E-value=7.9 Score=42.63 Aligned_cols=54 Identities=24% Similarity=0.604 Sum_probs=43.3
Q ss_pred hccCcceEeeecccccccCceeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCccccC
Q 001377 107 LMKSKVECMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQSVQLT 175 (1090)
Q Consensus 107 l~~~~yeC~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~~~~~ 175 (1090)
-..+.|+|-||+|..+ ++|=++ |-|.|=..||-+|..... ..--||-|...-..
T Consensus 43 ~~~~~FdCNICLd~ak--dPVvTl--CGHLFCWpClyqWl~~~~-----------~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 43 RDGGFFDCNICLDLAK--DPVVTL--CGHLFCWPCLYQWLQTRP-----------NSKECPVCKAEVSI 96 (230)
T ss_pred CCCCceeeeeeccccC--CCEEee--cccceehHHHHHHHhhcC-----------CCeeCCcccccccc
Confidence 4579999999999764 888886 999999999999987543 23457999887554
No 56
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=63.26 E-value=6.6 Score=32.02 Aligned_cols=42 Identities=36% Similarity=0.903 Sum_probs=27.6
Q ss_pred EeeecccccccCceeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCC
Q 001377 114 CMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGC 169 (1090)
Q Consensus 114 C~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C 169 (1090)
|.||.+-++ ++|.- .|-++|=+.||.+|.+... ...+.||-|
T Consensus 1 CpiC~~~~~--~Pv~l--~CGH~FC~~Cl~~~~~~~~----------~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFK--DPVSL--PCGHSFCRSCLERLWKEPS----------GSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-S--SEEE---SSSSEEEHHHHHHHHCCSS----------SST---SSS
T ss_pred CCccchhhC--Ccccc--CCcCHHHHHHHHHHHHccC----------CcCCCCcCC
Confidence 678877765 44443 7999999999999998753 223899976
No 57
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=63.13 E-value=4.2 Score=50.32 Aligned_cols=55 Identities=31% Similarity=0.678 Sum_probs=41.7
Q ss_pred HHHhccCcceEeeecccccccCceeeCC-CCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCcc
Q 001377 104 QDKLMKSKVECMICYDMVKRSAPIWSCS-SCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQSV 172 (1090)
Q Consensus 104 ~e~l~~~~yeC~IC~~~i~~~~~vWsC~-~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~~ 172 (1090)
++.+..+.-.|.||.+++...+.+=... .|-++||..|+++|.+.. =-||-|+..
T Consensus 284 ~~~~~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~--------------qtCP~CR~~ 339 (543)
T KOG0802|consen 284 ERGLALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQ--------------QTCPTCRTV 339 (543)
T ss_pred HhhhhhcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHh--------------CcCCcchhh
Confidence 3347778889999999998863322222 478999999999999973 259999984
No 58
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=61.52 E-value=4.5 Score=37.57 Aligned_cols=33 Identities=27% Similarity=0.716 Sum_probs=22.8
Q ss_pred EeeecccccccCc---eeeCCCCceeechhHHHHHhcC
Q 001377 114 CMICYDMVKRSAP---IWSCSSCFSIFHLSCIKKWARA 148 (1090)
Q Consensus 114 C~IC~~~i~~~~~---vWsC~~C~~vfHL~CikkWa~~ 148 (1090)
|+-|...+...+. +|- .|-+.||+.||.+|...
T Consensus 34 C~eCq~~~~~~~eC~v~wG--~CnHaFH~HCI~rWL~T 69 (88)
T COG5194 34 CPECQFGMTPGDECPVVWG--VCNHAFHDHCIYRWLDT 69 (88)
T ss_pred CcccccCCCCCCcceEEEE--ecchHHHHHHHHHHHhh
Confidence 4444444433333 553 79999999999999875
No 59
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=59.55 E-value=4.2 Score=45.98 Aligned_cols=50 Identities=26% Similarity=0.661 Sum_probs=40.7
Q ss_pred hccCcceEeeecccccccCceeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCcccc
Q 001377 107 LMKSKVECMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQSVQL 174 (1090)
Q Consensus 107 l~~~~yeC~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~~~~ 174 (1090)
+..+++.|.||.+....- ||.-|-|||=-+||..|+..-. -||-|+....
T Consensus 235 i~~a~~kC~LCLe~~~~p----SaTpCGHiFCWsCI~~w~~ek~--------------eCPlCR~~~~ 284 (293)
T KOG0317|consen 235 IPEATRKCSLCLENRSNP----SATPCGHIFCWSCILEWCSEKA--------------ECPLCREKFQ 284 (293)
T ss_pred CCCCCCceEEEecCCCCC----CcCcCcchHHHHHHHHHHcccc--------------CCCcccccCC
Confidence 345889999999998543 5788999999999999998532 1999998754
No 60
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=58.68 E-value=4.8 Score=39.07 Aligned_cols=31 Identities=29% Similarity=0.774 Sum_probs=25.3
Q ss_pred eeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCccc
Q 001377 127 IWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQSVQ 173 (1090)
Q Consensus 127 vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~~~ 173 (1090)
+| ..|-+-||+.||.+|.+. .-+||-+|.+-
T Consensus 77 aW--G~CNHaFH~hCisrWlkt--------------r~vCPLdn~eW 107 (114)
T KOG2930|consen 77 AW--GVCNHAFHFHCISRWLKT--------------RNVCPLDNKEW 107 (114)
T ss_pred Ee--eecchHHHHHHHHHHHhh--------------cCcCCCcCcce
Confidence 55 379999999999999985 35788888764
No 61
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=56.36 E-value=19 Score=40.10 Aligned_cols=20 Identities=15% Similarity=0.378 Sum_probs=12.7
Q ss_pred cCCCccccCCCCCChhHHHH
Q 001377 82 RGENQDKKLPKDLDLPQLLQ 101 (1090)
Q Consensus 82 ~~~~~~~~~~~d~~~~~l~~ 101 (1090)
|.+.+.+.+.+|.|+..+++
T Consensus 64 ~~~~~~~~~~~d~dIq~va~ 83 (278)
T PF15135_consen 64 REDMKQNEMSADQDIQAVAS 83 (278)
T ss_pred hcccccccCCCcccHHHHHh
Confidence 33444556677888877773
No 62
>PHA02862 5L protein; Provisional
Probab=56.08 E-value=12 Score=38.70 Aligned_cols=51 Identities=20% Similarity=0.600 Sum_probs=40.1
Q ss_pred eEeeecccccccCceeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCccccC
Q 001377 113 ECMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQSVQLT 175 (1090)
Q Consensus 113 eC~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~~~~~ 175 (1090)
.|=||.++-...-.-=.|+.=....|.+|+++|.+.+. .=.|+-|+.+|..
T Consensus 4 iCWIC~~~~~e~~~PC~C~GS~K~VHq~CL~~WIn~S~------------k~~CeLCkteY~I 54 (156)
T PHA02862 4 ICWICNDVCDERNNFCGCNEEYKVVHIKCMQLWINYSK------------KKECNLCKTKYNI 54 (156)
T ss_pred EEEEecCcCCCCcccccccCcchhHHHHHHHHHHhcCC------------CcCccCCCCeEEE
Confidence 68999998765545555667788999999999996542 4579999999875
No 63
>KOG2275 consensus Aminoacylase ACY1 and related metalloexopeptidases [Amino acid transport and metabolism]
Probab=54.16 E-value=37 Score=40.66 Aligned_cols=55 Identities=16% Similarity=0.162 Sum_probs=49.2
Q ss_pred ceEecCCCCh-hhHHHHHHHHHHcCCceeecCCCCCceEEEEeCCCC--CCCcccccc
Q 001377 803 KVHVFCPMLK-DKRDAVRLIAERWKLAVNPAGWEPKRFIVVHVTPKS--KPPPRVIGV 857 (1090)
Q Consensus 803 k~~~f~PM~~-~kR~fIHeLAe~ygL~S~S~d~EP~R~VvV~kt~~S--k~P~~lLs~ 857 (1090)
.++.+.||.. .-+.|+-..|+.+++.....-.+|.++++|+..+.| .+|+.+|..
T Consensus 38 ~Tv~p~~dy~~a~~~Fl~~~a~~l~l~~~~i~~~p~~~~~l~T~~GS~P~L~silL~S 95 (420)
T KOG2275|consen 38 PTVQPNPDYTIACADFLKKYAKSLGLTVQKIESEPGKYVLLYTWLGSDPELPSILLNS 95 (420)
T ss_pred cccccCCCccHHHHHHHHHHHHhcCCceeEEEecCceeEEEEEeeCCCCCccceeeec
Confidence 3566789998 999999999999999999999999999999998887 789988875
No 64
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.94 E-value=8.2 Score=41.01 Aligned_cols=53 Identities=26% Similarity=0.656 Sum_probs=42.6
Q ss_pred HHHHhccCcceEeeecccccccCceeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCc
Q 001377 103 IQDKLMKSKVECMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQS 171 (1090)
Q Consensus 103 l~e~l~~~~yeC~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~ 171 (1090)
+++.-..+.|-|+||++.+....+| =..|-|||=-.|||.-.++ +-.||-|+.
T Consensus 123 v~~~~~~~~~~CPiCl~~~sek~~v--sTkCGHvFC~~Cik~alk~--------------~~~CP~C~k 175 (187)
T KOG0320|consen 123 VDPLRKEGTYKCPICLDSVSEKVPV--STKCGHVFCSQCIKDALKN--------------TNKCPTCRK 175 (187)
T ss_pred ccccccccccCCCceecchhhcccc--ccccchhHHHHHHHHHHHh--------------CCCCCCccc
Confidence 3444456899999999999887774 3489999999999987765 567999985
No 65
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=50.66 E-value=7.7 Score=46.65 Aligned_cols=53 Identities=25% Similarity=0.744 Sum_probs=43.2
Q ss_pred ccCcceEeeecccccccCceeeCC-------------CCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCccc
Q 001377 108 MKSKVECMICYDMVKRSAPIWSCS-------------SCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQSVQ 173 (1090)
Q Consensus 108 ~~~~yeC~IC~~~i~~~~~vWsC~-------------~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~~~ 173 (1090)
.+.+.+|+||+..|.-++..=-|. =|-+|||-.|.+.|-.. ..-.||-|+...
T Consensus 568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~-------------ykl~CPvCR~pL 633 (636)
T KOG0828|consen 568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDT-------------YKLICPVCRCPL 633 (636)
T ss_pred hhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhh-------------hcccCCccCCCC
Confidence 567899999999998887776663 59999999999999762 246799998764
No 66
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=48.99 E-value=7.6 Score=49.00 Aligned_cols=61 Identities=18% Similarity=0.515 Sum_probs=45.4
Q ss_pred HHHHHHHHHhccCcceEeeecccccccCceeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCccccCCC
Q 001377 98 QLLQEIQDKLMKSKVECMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQSVQLTSS 177 (1090)
Q Consensus 98 ~l~~~l~e~l~~~~yeC~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~~~~~~~ 177 (1090)
.|+++|.+ -++...|.+|- .+..+.|-+ .|||||=.+||+.-.. .+.-+||+|+......+
T Consensus 632 ~L~EElk~--yK~~LkCs~Cn--~R~Kd~vI~--kC~H~FC~~Cvq~r~e-------------tRqRKCP~Cn~aFganD 692 (698)
T KOG0978|consen 632 VLAEELKE--YKELLKCSVCN--TRWKDAVIT--KCGHVFCEECVQTRYE-------------TRQRKCPKCNAAFGAND 692 (698)
T ss_pred HHHHHHHH--HHhceeCCCcc--CchhhHHHH--hcchHHHHHHHHHHHH-------------HhcCCCCCCCCCCCccc
Confidence 34444444 34889999998 566666655 7999999999988655 34789999998876543
No 67
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=48.88 E-value=5.3 Score=44.74 Aligned_cols=49 Identities=27% Similarity=0.659 Sum_probs=37.5
Q ss_pred cceEeeecccccccC-------ceeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCcc
Q 001377 111 KVECMICYDMVKRSA-------PIWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQSV 172 (1090)
Q Consensus 111 ~yeC~IC~~~i~~~~-------~vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~~ 172 (1090)
.-.|+||...|.++. .++. -+|-+|||--||+-|...+. .=-||.|...
T Consensus 224 d~vCaVCg~~~~~s~~eegvienty~-LsCnHvFHEfCIrGWcivGK------------kqtCPYCKek 279 (328)
T KOG1734|consen 224 DSVCAVCGQQIDVSVDEEGVIENTYK-LSCNHVFHEFCIRGWCIVGK------------KQTCPYCKEK 279 (328)
T ss_pred cchhHhhcchheeecchhhhhhhhee-eecccchHHHhhhhheeecC------------CCCCchHHHH
Confidence 346999999998887 4443 24789999999999998753 3458988644
No 68
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=48.07 E-value=12 Score=42.13 Aligned_cols=47 Identities=28% Similarity=0.759 Sum_probs=39.2
Q ss_pred CcceEeeecccccccCceeeCCCCceeechhHHHH-HhcCCCCcchhhhccCCCCCCCCCCCccc
Q 001377 110 SKVECMICYDMVKRSAPIWSCSSCFSIFHLSCIKK-WARAPTSADLSAERSQGFNWRCPGCQSVQ 173 (1090)
Q Consensus 110 ~~yeC~IC~~~i~~~~~vWsC~~C~~vfHL~Cikk-Wa~~~~s~~~~~~~~~~~~WrCP~C~~~~ 173 (1090)
+.|+|.||.+.+- +-+|..|-+||=+.||-. |-++. .-.||-|+...
T Consensus 214 ~d~kC~lC~e~~~----~ps~t~CgHlFC~~Cl~~~~t~~k-------------~~~CplCRak~ 261 (271)
T COG5574 214 ADYKCFLCLEEPE----VPSCTPCGHLFCLSCLLISWTKKK-------------YEFCPLCRAKV 261 (271)
T ss_pred cccceeeeecccC----CcccccccchhhHHHHHHHHHhhc-------------cccCchhhhhc
Confidence 5899999999875 678999999999999988 98763 34699998653
No 69
>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=46.60 E-value=10 Score=28.59 Aligned_cols=29 Identities=24% Similarity=0.542 Sum_probs=13.5
Q ss_pred eEeeecccccccCceeeCCCCceeechhHH
Q 001377 113 ECMICYDMVKRSAPIWSCSSCFSIFHLSCI 142 (1090)
Q Consensus 113 eC~IC~~~i~~~~~vWsC~~C~~vfHL~Ci 142 (1090)
.|-+|-..+.. ..++.|..|-=+||+.||
T Consensus 2 ~C~~C~~~~~~-~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDG-GWFYRCSECDFDLHEECA 30 (30)
T ss_dssp --TTTS----S---EEE-TTT-----HHHH
T ss_pred cCCcCCCcCCC-CceEECccCCCccChhcC
Confidence 47788888887 889999999999999996
No 70
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=46.46 E-value=11 Score=35.97 Aligned_cols=35 Identities=26% Similarity=0.664 Sum_probs=26.8
Q ss_pred HHHhccCcceEeee--cccccccCceeeCCCCceeec
Q 001377 104 QDKLMKSKVECMIC--YDMVKRSAPIWSCSSCFSIFH 138 (1090)
Q Consensus 104 ~e~l~~~~yeC~IC--~~~i~~~~~vWsC~~C~~vfH 138 (1090)
+|..++..|.|+.| ...-+..--||.|..|-.+|-
T Consensus 29 ie~~q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~A 65 (90)
T PRK03976 29 IEEKMRAKHVCPVCGRPKVKRVGTGIWECRKCGAKFA 65 (90)
T ss_pred HHHHHhcCccCCCCCCCceEEEEEEEEEcCCCCCEEe
Confidence 35567789999999 555555566999999987764
No 71
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=45.45 E-value=12 Score=35.86 Aligned_cols=35 Identities=29% Similarity=0.624 Sum_probs=26.9
Q ss_pred HHHhccCcceEeee--cccccccCceeeCCCCceeec
Q 001377 104 QDKLMKSKVECMIC--YDMVKRSAPIWSCSSCFSIFH 138 (1090)
Q Consensus 104 ~e~l~~~~yeC~IC--~~~i~~~~~vWsC~~C~~vfH 138 (1090)
+|..++..|.|+.| ...-+..--||.|..|-.+|-
T Consensus 28 ie~~q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~A 64 (91)
T TIGR00280 28 IEIQQKAKYVCPFCGKKTVKRGSTGIWTCRKCGAKFA 64 (91)
T ss_pred HHHHHhcCccCCCCCCCceEEEeeEEEEcCCCCCEEe
Confidence 35567789999999 665555566999999987764
No 72
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=45.36 E-value=16 Score=43.52 Aligned_cols=47 Identities=28% Similarity=0.706 Sum_probs=36.7
Q ss_pred CcceEeeecccccccCceeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCcccc
Q 001377 110 SKVECMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQSVQL 174 (1090)
Q Consensus 110 ~~yeC~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~~~~ 174 (1090)
..+.|.||.+.+. .+| =..|.|.|...||+.|... .-.||.|+....
T Consensus 25 ~~l~C~IC~d~~~--~Pv--itpCgH~FCs~CI~~~l~~--------------~~~CP~Cr~~~~ 71 (397)
T TIGR00599 25 TSLRCHICKDFFD--VPV--LTSCSHTFCSLCIRRCLSN--------------QPKCPLCRAEDQ 71 (397)
T ss_pred cccCCCcCchhhh--Ccc--CCCCCCchhHHHHHHHHhC--------------CCCCCCCCCccc
Confidence 5789999999774 344 2479999999999999764 237999998753
No 73
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=44.73 E-value=9.7 Score=28.83 Aligned_cols=30 Identities=23% Similarity=0.660 Sum_probs=26.7
Q ss_pred ceEeeecccccccCceeeCCCCceeechhHH
Q 001377 112 VECMICYDMVKRSAPIWSCSSCFSIFHLSCI 142 (1090)
Q Consensus 112 yeC~IC~~~i~~~~~vWsC~~C~~vfHL~Ci 142 (1090)
|.|-||-.+|.... .++|..|=-++|+.|+
T Consensus 1 ~~C~~C~~~~~~~~-~Y~C~~c~f~lh~~Ca 30 (30)
T PF03107_consen 1 FWCDVCRRKIDGFY-FYHCSECCFTLHVRCA 30 (30)
T ss_pred CCCCCCCCCcCCCE-eEEeCCCCCeEcCccC
Confidence 56899999998888 9999999999999885
No 74
>cd02637 R3H_PARN R3H domain of Poly(A)-specific ribonuclease (PARN). PARN is a poly(A)-specific 3' exonuclease from the RNase D family that, in Xenopus, deadenylates a specific class of maternal mRNAs which results in their translational repression. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.
Probab=44.64 E-value=53 Score=29.57 Aligned_cols=54 Identities=19% Similarity=0.226 Sum_probs=32.7
Q ss_pred HHHHHHHHHhccccCCccccceEecCCCChhhHHHHH-HHHHHcC--CceeecCCC-CCceEEEE
Q 001377 783 VEERCKFLVLGKNRGSTNALKVHVFCPMLKDKRDAVR-LIAERWK--LAVNPAGWE-PKRFIVVH 843 (1090)
Q Consensus 783 vE~~L~~fv~~~~~~~~~~~k~~~f~PM~~~kR~fIH-eLAe~yg--L~S~S~d~E-P~R~VvV~ 843 (1090)
+-+.+.+|+.+. ...+.++|||..+|++|+ .|-..|. |..++...| =.|.+++.
T Consensus 4 v~~~i~~fl~s~-------~~~l~le~cngf~RkLiyq~l~~~~~~~I~ve~~~~ekk~~~i~~~ 61 (65)
T cd02637 4 VIERIEAFLESE-------EDDLELEPCNGFQRKLIYQTLEQKYPKGIHVETLETEKKERLIVIE 61 (65)
T ss_pred HHHHHHHHHhcC-------cccccccccccHHHHHHHHHHHHHccccceeeeeeccccceEEEEe
Confidence 345566676653 344778999999999999 4433443 444444433 33444443
No 75
>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.
Probab=44.30 E-value=55 Score=31.26 Aligned_cols=60 Identities=20% Similarity=0.438 Sum_probs=34.8
Q ss_pred EEecCcccchh---hhHHHHhhcCee--eEEEecCCceEEEecChhhHHHHHHhhcCccccccEEE
Q 001377 883 VSFLDLPRESD---ISALVLRFGGEC--ELVWLNDKNALAVFSDPARAATATRRLDHGSVYYGAVV 943 (1090)
Q Consensus 883 v~~~dl~~~~~---i~~~~~~f~g~~--el~wi~d~~~l~vF~~p~~~~~a~~~l~~~~~~~~~~~ 943 (1090)
|.+.+|+...| |..-|++..+.| .+..+-..+|++.|.++.-|+.|..++++-.|| |-.|
T Consensus 5 L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~~~tAilrF~~~~~A~RA~KRmegEdVf-G~kI 69 (90)
T PF11608_consen 5 LYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVSGGTAILRFPNQEFAERAQKRMEGEDVF-GNKI 69 (90)
T ss_dssp EEEES--TTS-HHHHHHHHHHHHHTTT--EEE--TT-EEEEESSHHHHHHHHHHHTT--SS-SS--
T ss_pred EEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEeCCEEEEEeCCHHHHHHHHHhhcccccc-cceE
Confidence 45566765444 333344433333 355566899999999999999999999999999 5544
No 76
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=44.27 E-value=14 Score=35.36 Aligned_cols=34 Identities=32% Similarity=0.627 Sum_probs=25.9
Q ss_pred HHHhccCcceEeee--cccccccC-ceeeCCCCceeec
Q 001377 104 QDKLMKSKVECMIC--YDMVKRSA-PIWSCSSCFSIFH 138 (1090)
Q Consensus 104 ~e~l~~~~yeC~IC--~~~i~~~~-~vWsC~~C~~vfH 138 (1090)
+|..++..|.|+.| .. |+|.. -||.|..|-.+|-
T Consensus 29 ie~~q~a~y~CpfCgk~~-vkR~a~GIW~C~~C~~~~A 65 (90)
T PTZ00255 29 IEISQHAKYFCPFCGKHA-VKRQAVGIWRCKGCKKTVA 65 (90)
T ss_pred HHHHHhCCccCCCCCCCc-eeeeeeEEEEcCCCCCEEe
Confidence 35567789999999 44 55544 6999999987764
No 77
>PF13893 RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....
Probab=43.86 E-value=75 Score=26.50 Aligned_cols=46 Identities=22% Similarity=0.328 Sum_probs=31.5
Q ss_pred HHHHhhcCeeeEEEecC---CceEEEecChhhHHHHHHhhcCccccccEEE
Q 001377 896 ALVLRFGGECELVWLND---KNALAVFSDPARAATATRRLDHGSVYYGAVV 943 (1090)
Q Consensus 896 ~~~~~f~g~~el~wi~d---~~~l~vF~~p~~~~~a~~~l~~~~~~~~~~~ 943 (1090)
.+..+| |+.+-..+.. ..+.+.|.++.-|..|++.|.+.. +.|-.+
T Consensus 3 ~~f~~f-G~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~~-~~g~~l 51 (56)
T PF13893_consen 3 KLFSKF-GEVKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGRQ-FNGRPL 51 (56)
T ss_dssp HHHTTT-S-EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTSE-ETTEEE
T ss_pred HHhCCc-ccEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCE-ECCcEE
Confidence 444567 5665444443 558899999999999999996544 556555
No 78
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=41.11 E-value=11 Score=31.45 Aligned_cols=35 Identities=29% Similarity=0.800 Sum_probs=23.5
Q ss_pred EeeecccccccCc---eeeCCCCceeechhHHHHHhcC
Q 001377 114 CMICYDMVKRSAP---IWSCSSCFSIFHLSCIKKWARA 148 (1090)
Q Consensus 114 C~IC~~~i~~~~~---vWsC~~C~~vfHL~CikkWa~~ 148 (1090)
|-||++.-....+ .=.|..=....|..|+++|...
T Consensus 1 CrIC~~~~~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~ 38 (47)
T PF12906_consen 1 CRICLEGEEEDEPLISPCRCKGSMKYVHRSCLERWIRE 38 (47)
T ss_dssp ETTTTEE-SSSS-EE-SSS-SSCCGSEECCHHHHHHHH
T ss_pred CeEeCCcCCCCCceecccccCCCcchhHHHHHHHHHHh
Confidence 5688887776662 2234444459999999999986
No 79
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.05 E-value=69 Score=39.27 Aligned_cols=72 Identities=22% Similarity=0.361 Sum_probs=46.7
Q ss_pred CCCCCChhHHHHHHHHHhccCcceEeeecccccccCceeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCC
Q 001377 90 LPKDLDLPQLLQEIQDKLMKSKVECMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGC 169 (1090)
Q Consensus 90 ~~~d~~~~~l~~~l~e~l~~~~yeC~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C 169 (1090)
.-.|+|++-....|...+-.-.|.|+||+++----.. ..|-|||=.+||-.....++- ...-+||-|
T Consensus 165 qn~dpD~p~~~e~i~qv~~~t~~~CPICL~~~~~p~~----t~CGHiFC~~CiLqy~~~s~~---------~~~~~CPiC 231 (513)
T KOG2164|consen 165 QNTDPDAPVDWEDIFQVYGSTDMQCPICLEPPSVPVR----TNCGHIFCGPCILQYWNYSAI---------KGPCSCPIC 231 (513)
T ss_pred hccCCccccchHHhhhhhcCcCCcCCcccCCCCcccc----cccCceeeHHHHHHHHhhhcc---------cCCccCCch
Confidence 3345666655555555544449999999987432221 248999999998776665421 224579999
Q ss_pred Ccccc
Q 001377 170 QSVQL 174 (1090)
Q Consensus 170 ~~~~~ 174 (1090)
++...
T Consensus 232 ~s~I~ 236 (513)
T KOG2164|consen 232 RSTIT 236 (513)
T ss_pred hhhcc
Confidence 87643
No 80
>smart00362 RRM_2 RNA recognition motif.
Probab=39.47 E-value=1.2e+02 Score=24.88 Aligned_cols=52 Identities=23% Similarity=0.254 Sum_probs=35.4
Q ss_pred chhhhHHHHhhcCeeeEEEecC-----CceEEEecChhhHHHHHHhhcCccccccEEE
Q 001377 891 ESDISALVLRFGGECELVWLND-----KNALAVFSDPARAATATRRLDHGSVYYGAVV 943 (1090)
Q Consensus 891 ~~~i~~~~~~f~g~~el~wi~d-----~~~l~vF~~p~~~~~a~~~l~~~~~~~~~~~ 943 (1090)
..+|..++.+|+.--.+..+.+ ..+.+.|.++..|+.|++.|+... +.|..+
T Consensus 13 ~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~-~~~~~i 69 (72)
T smart00362 13 EEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTK-LGGRPL 69 (72)
T ss_pred HHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcE-ECCEEE
Confidence 4567777777764334545544 468899999999999999887633 345433
No 81
>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=37.71 E-value=36 Score=29.15 Aligned_cols=44 Identities=18% Similarity=0.292 Sum_probs=33.9
Q ss_pred ceEeeecccccccCceeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCccc
Q 001377 112 VECMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQSVQ 173 (1090)
Q Consensus 112 yeC~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~~~ 173 (1090)
+.|.||.+.++. +|=. .|-+||...||.+|.+. .-.||-|+...
T Consensus 2 ~~Cpi~~~~~~~--Pv~~--~~G~v~~~~~i~~~~~~--------------~~~cP~~~~~~ 45 (63)
T smart00504 2 FLCPISLEVMKD--PVIL--PSGQTYERRAIEKWLLS--------------HGTDPVTGQPL 45 (63)
T ss_pred cCCcCCCCcCCC--CEEC--CCCCEEeHHHHHHHHHH--------------CCCCCCCcCCC
Confidence 579999998764 5543 56799999999999975 23688887664
No 82
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=36.74 E-value=92 Score=26.28 Aligned_cols=46 Identities=20% Similarity=0.305 Sum_probs=31.4
Q ss_pred cchhhhHHHHhhcCeeeEEEec-C------CceEEEecChhhHHHHHHhhcCcc
Q 001377 890 RESDISALVLRFGGECELVWLN-D------KNALAVFSDPARAATATRRLDHGS 936 (1090)
Q Consensus 890 ~~~~i~~~~~~f~g~~el~wi~-d------~~~l~vF~~p~~~~~a~~~l~~~~ 936 (1090)
.+.+|..+..+|| ..+..++. + .-+.+.|.++..|+.|++.|++..
T Consensus 11 t~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~ 63 (70)
T PF00076_consen 11 TEEELRDFFSQFG-KIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKK 63 (70)
T ss_dssp SHHHHHHHHHTTS-TEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEE
T ss_pred CHHHHHHHHHHhh-hcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCE
Confidence 3456667766675 44333333 2 227799999999999999998843
No 83
>cd07135 ALDH_F14-YMR110C Saccharomyces cerevisiae aldehyde dehydrogenase family 14 and related proteins. Aldehyde dehydrogenase family 14 (ALDH14), isolated mainly from the mitochondrial outer membrane of Saccharomyces cerevisiae (YMR110C) and most closely related to the plant and animal ALDHs and fatty ALDHs family 3 members, and similar fungal sequences, are present in this CD.
Probab=36.17 E-value=2e+02 Score=34.81 Aligned_cols=129 Identities=15% Similarity=0.145 Sum_probs=62.1
Q ss_pred hHHHHHHHHHHHHHhccccCCccccceEecCCC-ChhhHHHHHHHHHHcCCceeecCCCCCceEEEEeCCCCCCCccccc
Q 001377 778 KWVLSVEERCKFLVLGKNRGSTNALKVHVFCPM-LKDKRDAVRLIAERWKLAVNPAGWEPKRFIVVHVTPKSKPPPRVIG 856 (1090)
Q Consensus 778 ~~~~~vE~~L~~fv~~~~~~~~~~~k~~~f~PM-~~~kR~fIHeLAe~ygL~S~S~d~EP~R~VvV~kt~~Sk~P~~lLs 856 (1090)
.|++++.+.+..+..+.. ...-.+-|| ++.++.-|.++.+..|-.-. +|.... .....+++-+|.
T Consensus 263 ~f~~~l~~~~~~~~~g~p------~~~~~~gpli~~~~~~~i~~~v~~ag~~v~-~gg~~~-------~~g~~~~Ptvl~ 328 (436)
T cd07135 263 EFVEELKKVLDEFYPGGA------NASPDYTRIVNPRHFNRLKSLLDTTKGKVV-IGGEMD-------EATRFIPPTIVS 328 (436)
T ss_pred HHHHHHHHHHHHhcCCCC------CCCCCcCCCCCHHHHHHHHHHHHhcCCeEE-ECCCcC-------CCCCEEccEEEe
Confidence 356666667766654321 111235676 66777777766655432111 111110 011223333332
Q ss_pred cccccccCCCCCCCcCcccccCCceEEEecCcccchhhhHHHHhhcCeeeEEEecCCceEEEec-ChhhHHHHHHhhcCc
Q 001377 857 VKGATTVNAPHAPVFDPLVDMDPRLVVSFLDLPRESDISALVLRFGGECELVWLNDKNALAVFS-DPARAATATRRLDHG 935 (1090)
Q Consensus 857 ~~~~~~~~~~~~~~fna~v~~d~~~~v~~~dl~~~~~i~~~~~~f~g~~el~wi~d~~~l~vF~-~p~~~~~a~~~l~~~ 935 (1090)
... ........|.|-|++ .++.++|++-...+..-. +| .-...||+ |+.++....++|+.|
T Consensus 329 ~~~-~~~~~~~~E~FgPvl-----~v~~~~~~deai~~an~~-~~-----------gL~~~v~t~d~~~a~~~~~~l~~g 390 (436)
T cd07135 329 DVS-WDDSLMSEELFGPVL-----PIIKVDDLDEAIKVINSR-DT-----------PLALYIFTDDKSEIDHILTRTRSG 390 (436)
T ss_pred cCC-CccHHHhccccCCce-----EEEecCCHHHHHHHHhCC-CC-----------CceEEEEcCCHHHHHHHHhcCCcC
Confidence 211 111112345677664 345666652222211110 11 12345666 778888999999998
Q ss_pred ccc
Q 001377 936 SVY 938 (1090)
Q Consensus 936 ~~~ 938 (1090)
.+|
T Consensus 391 ~v~ 393 (436)
T cd07135 391 GVV 393 (436)
T ss_pred eEE
Confidence 888
No 84
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=32.42 E-value=32 Score=30.01 Aligned_cols=32 Identities=25% Similarity=0.601 Sum_probs=29.6
Q ss_pred cceEeeecccccccCceeeCCCCceeechhHH
Q 001377 111 KVECMICYDMVKRSAPIWSCSSCFSIFHLSCI 142 (1090)
Q Consensus 111 ~yeC~IC~~~i~~~~~vWsC~~C~~vfHL~Ci 142 (1090)
..-|.+|-..|+..++|=.|..|-+++|..|-
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 35699999999999999999999999999995
No 85
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=31.47 E-value=29 Score=33.05 Aligned_cols=32 Identities=25% Similarity=0.611 Sum_probs=23.7
Q ss_pred HhccCcceEeeeccccccc--CceeeCCCCceee
Q 001377 106 KLMKSKVECMICYDMVKRS--APIWSCSSCFSIF 137 (1090)
Q Consensus 106 ~l~~~~yeC~IC~~~i~~~--~~vWsC~~C~~vf 137 (1090)
.-+...|+|+.|-...-++ .-||.|..|-.+|
T Consensus 30 ~~~~~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 30 AQQRAKHVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred HHHhcCCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 3456799999998775333 3499999987765
No 86
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=30.53 E-value=2.9e+02 Score=28.35 Aligned_cols=53 Identities=17% Similarity=0.286 Sum_probs=35.5
Q ss_pred cchhhhHHHHhhcCeeeEEEecCC-------ceEEEecChhhHHHHHHhhcCccccccEEE
Q 001377 890 RESDISALVLRFGGECELVWLNDK-------NALAVFSDPARAATATRRLDHGSVYYGAVV 943 (1090)
Q Consensus 890 ~~~~i~~~~~~f~g~~el~wi~d~-------~~l~vF~~p~~~~~a~~~l~~~~~~~~~~~ 943 (1090)
.+.+|..+...|+.--.+..+.|. -+.+.|.++.-|+.||+.|+.. .+.|-.+
T Consensus 47 te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~-~i~Gr~l 106 (144)
T PLN03134 47 DDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGK-ELNGRHI 106 (144)
T ss_pred CHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCC-EECCEEE
Confidence 456777777677522233333332 2778999999999999999755 4556666
No 87
>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=30.50 E-value=43 Score=38.78 Aligned_cols=11 Identities=0% Similarity=0.141 Sum_probs=6.0
Q ss_pred HHHHhhhCCCC
Q 001377 742 RVLADAFEITT 752 (1090)
Q Consensus 742 ~~LA~Al~I~~ 752 (1090)
++++..||-..
T Consensus 76 krv~~i~Nk~e 86 (309)
T TIGR00570 76 KRVLKIYNKRE 86 (309)
T ss_pred HHHHHHHccch
Confidence 44556666543
No 88
>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
Probab=30.02 E-value=2.4e+02 Score=23.17 Aligned_cols=52 Identities=25% Similarity=0.304 Sum_probs=34.5
Q ss_pred chhhhHHHHhhcCeeeEEEecC------CceEEEecChhhHHHHHHhhcCccccccEEE
Q 001377 891 ESDISALVLRFGGECELVWLND------KNALAVFSDPARAATATRRLDHGSVYYGAVV 943 (1090)
Q Consensus 891 ~~~i~~~~~~f~g~~el~wi~d------~~~l~vF~~p~~~~~a~~~l~~~~~~~~~~~ 943 (1090)
+.+|..++.+|+.-..+..+.+ ..+.+.|.++..|..|++.++... +.|..+
T Consensus 13 ~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~-~~~~~~ 70 (74)
T cd00590 13 EEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKE-LGGRPL 70 (74)
T ss_pred HHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCe-ECCeEE
Confidence 4566677766743223333333 357788999999999999988865 445444
No 89
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=28.63 E-value=1.3e+02 Score=32.35 Aligned_cols=36 Identities=33% Similarity=0.513 Sum_probs=31.0
Q ss_pred CeeeEEEec---CCceEEEecChhhHHHHHHhhcCcccc
Q 001377 903 GECELVWLN---DKNALAVFSDPARAATATRRLDHGSVY 938 (1090)
Q Consensus 903 g~~el~wi~---d~~~l~vF~~p~~~~~a~~~l~~~~~~ 938 (1090)
|....+||. -.-|.+.|.||-.|+.|.+.|+.-..-
T Consensus 35 G~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~c 73 (195)
T KOG0107|consen 35 GPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDIC 73 (195)
T ss_pred CcceeEEEeecCCCceEEeccCcccHHHHHhhcCCcccc
Confidence 688899998 355788999999999999999987766
No 90
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.67 E-value=61 Score=38.14 Aligned_cols=66 Identities=26% Similarity=0.513 Sum_probs=43.9
Q ss_pred cCcceEeeecccccccCc-ee---eCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCccccCCCCCcee
Q 001377 109 KSKVECMICYDMVKRSAP-IW---SCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQSVQLTSSKEIRY 182 (1090)
Q Consensus 109 ~~~yeC~IC~~~i~~~~~-vW---sC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~~~~~~~~p~~y 182 (1090)
...-+|-||.+.|.-... += .=.+|-+.|=|+||++|-..-.. .....--||-|+....-. +|..|
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~-------~~~~sksCP~CRv~s~~v-~pS~~ 228 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQF-------ESKTSKSCPFCRVPSSFV-NPSSF 228 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhcc-------ccccccCCCcccCccccc-cccce
Confidence 467899999999865541 11 11368999999999999843211 113367899999875432 45555
No 91
>smart00360 RRM RNA recognition motif.
Probab=27.07 E-value=1.9e+02 Score=23.54 Aligned_cols=53 Identities=21% Similarity=0.268 Sum_probs=33.5
Q ss_pred cchhhhHHHHhhcCeeeEEEecC-------CceEEEecChhhHHHHHHhhcCccccccEEE
Q 001377 890 RESDISALVLRFGGECELVWLND-------KNALAVFSDPARAATATRRLDHGSVYYGAVV 943 (1090)
Q Consensus 890 ~~~~i~~~~~~f~g~~el~wi~d-------~~~l~vF~~p~~~~~a~~~l~~~~~~~~~~~ 943 (1090)
.+.+|..++..||.-..+.-+.+ ..+.+.|.++..|..|++.|++.. +.|..+
T Consensus 9 ~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~-~~~~~~ 68 (71)
T smart00360 9 TEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKE-LDGRPL 68 (71)
T ss_pred CHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCe-eCCcEE
Confidence 44567777767763222322223 257788999999999999888433 345443
No 92
>KOG0558 consensus Dihydrolipoamide transacylase (alpha-keto acid dehydrogenase E2 subunit) [Energy production and conversion]
Probab=26.59 E-value=62 Score=37.88 Aligned_cols=232 Identities=16% Similarity=0.122 Sum_probs=124.2
Q ss_pred HHHHHHHHHhhhCCCCCCccccCcCCcchhHHHHHHHHhChhHHHHHHHHHHHHHhcccc--CCccccceEecCCCChhh
Q 001377 737 KLERKRVLADAFEITTPNLDALHFGESAVTELLADLYRRDPKWVLSVEERCKFLVLGKNR--GSTNALKVHVFCPMLKDK 814 (1090)
Q Consensus 737 k~~R~~~LA~Al~I~~p~~~~~~f~e~~yse~Ll~~~~~~~~~~~~vE~~L~~fv~~~~~--~~~~~~k~~~f~PM~~~k 814 (1090)
..---|+||..++|+-......--.-...-|.+|.|.-+.+.|+..=--.+...+-.... ++......-.-.|+.-.+
T Consensus 173 aTPaVRrlA~e~~idla~v~gtGKdGRvLKeDvL~fl~q~pg~~~~~~~~~~a~~~~~~ps~~a~~~~~~Dkt~plrGf~ 252 (474)
T KOG0558|consen 173 ATPAVRRLAKENGIDLAEVTGTGKDGRVLKEDVLRFLGQVPGFVTDPSPSEHAVIPGPSPSTKASSNLEADKTVPLRGFS 252 (474)
T ss_pred cCHHHHHHHHHhCCceEeeeccCCCCcchHHHHHHHhccCCCCccCCCCceeecCCCCCCcccccCcccccceeechhHH
Confidence 344668999999998543222110011256788888888887765333222222222211 111112223346888999
Q ss_pred HHHHHHHHHHcCCceeecCCCCCceEEEE--------eC----CCCCCCccccc------ccccc-------ccCCCCCC
Q 001377 815 RDAVRLIAERWKLAVNPAGWEPKRFIVVH--------VT----PKSKPPPRVIG------VKGAT-------TVNAPHAP 869 (1090)
Q Consensus 815 R~fIHeLAe~ygL~S~S~d~EP~R~VvV~--------kt----~~Sk~P~~lLs------~~~~~-------~~~~~~~~ 869 (1090)
|++|.-+-+..+|--+.|-.|-+---+|. .+ ..|.+|-.+-+ ..+.+ ..+.+...
T Consensus 253 rAMvKtMt~alkiPHF~y~dEIn~~sLvklr~elk~~a~e~~IKltfmPf~iKaaSlaL~kyP~vNss~d~~~e~ii~K~ 332 (474)
T KOG0558|consen 253 RAMVKTMTEALKIPHFGYVDEINCDSLVKLRQELKENAKERGIKLTFMPFFIKAASLALLKYPIVNSSFDEESENIILKG 332 (474)
T ss_pred HHHHHHHHHHhcCCccccccccChHHHHHHHHHHhhhhhhcCceeeehHHHHHHHHHHHhhCccccchhhhhhhhhhhhc
Confidence 99999999999999999888843221111 11 12344433211 11110 00111112
Q ss_pred CcCcccccCCceEEEecCc---------ccchhhhHHHHh-----------hcCeeeEEEec--CCce-EEEecChhhHH
Q 001377 870 VFDPLVDMDPRLVVSFLDL---------PRESDISALVLR-----------FGGECELVWLN--DKNA-LAVFSDPARAA 926 (1090)
Q Consensus 870 ~fna~v~~d~~~~v~~~dl---------~~~~~i~~~~~~-----------f~g~~el~wi~--d~~~-l~vF~~p~~~~ 926 (1090)
..|--|-||...||...++ +.+-+|.+|+.. .+|-|.|.-|. ..+. .-+..-|.-|-
T Consensus 333 sHNIgvAmdT~~GLvVPNiKN~q~~si~eIakeLnrLq~~g~~~qls~~D~t~GTftLSNIG~IGGtf~~P~i~~PeVAI 412 (474)
T KOG0558|consen 333 SHNIGVAMDTEQGLVVPNIKNVQSLSIFEIAKELNRLQELGANGQLSPEDLTGGTFTLSNIGAIGGTFASPVIMPPEVAI 412 (474)
T ss_pred ccceeEEecCCCceeccCccccchhhHHHHHHHHHHHHHhhhcCCcChhhccCceEEeeecccccccccCcccccchhhh
Confidence 2455566777777777666 234455565532 34778887777 3441 11222344444
Q ss_pred HHHH-------hhcCccccccEEEEeCCCCCccccccCCCCcccccccccccccCCccch
Q 001377 927 TATR-------RLDHGSVYYGAVVVQNVGAPSTANAWGGPGTVKEVGAALSSQRGNPWKK 979 (1090)
Q Consensus 927 ~a~~-------~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 979 (1090)
-||- --+.+++|+.-|+..+ |-.+--+-||++-+ -=.|-||.
T Consensus 413 gAlGrie~vPrFnkk~~V~~a~IM~Vs---------wsADHRViDGaTma--rFsn~WK~ 461 (474)
T KOG0558|consen 413 GALGRIEKVPRFNKKGEVYPASIMMVS---------WSADHRVIDGATMA--RFSNQWKE 461 (474)
T ss_pred hhccccccccccCCCCCEEEeEEEEEE---------eecCceeeccHHHH--HHHHHHHH
Confidence 4443 3468899988888433 55555566666554 24467764
No 93
>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=26.33 E-value=58 Score=26.88 Aligned_cols=41 Identities=34% Similarity=0.869 Sum_probs=20.8
Q ss_pred EeeecccccccCceeeCC--CCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCC
Q 001377 114 CMICYDMVKRSAPIWSCS--SCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGC 169 (1090)
Q Consensus 114 C~IC~~~i~~~~~vWsC~--~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C 169 (1090)
|.+|-+-|..-+ -|+ .|-.-||..|++++.+... .. +||+|
T Consensus 1 C~~C~~iv~~G~---~C~~~~C~~r~H~~C~~~y~r~~~-----------~~-~CP~C 43 (43)
T PF08746_consen 1 CEACKEIVTQGQ---RCSNRDCNVRLHDDCFKKYFRHRS-----------NP-KCPNC 43 (43)
T ss_dssp -TTT-SB-SSSE---E-SS--S--EE-HHHHHHHTTT-S-----------S--B-TTT
T ss_pred CcccchhHeeec---cCCCCccCchHHHHHHHHHHhcCC-----------CC-CCcCC
Confidence 344444444333 366 5888999999999998642 12 89987
No 94
>cd07133 ALDH_CALDH_CalB Coniferyl aldehyde dehydrogenase-like. Coniferyl aldehyde dehydrogenase (CALDH, EC=1.2.1.68) of Pseudomonas sp. strain HR199 (CalB) which catalyzes the NAD+-dependent oxidation of coniferyl aldehyde to ferulic acid, and similar sequences, are present in this CD.
Probab=26.28 E-value=5.2e+02 Score=31.19 Aligned_cols=24 Identities=38% Similarity=0.450 Sum_probs=19.8
Q ss_pred eEEEec-ChhhHHHHHHhhcCcccc
Q 001377 915 ALAVFS-DPARAATATRRLDHGSVY 938 (1090)
Q Consensus 915 ~l~vF~-~p~~~~~a~~~l~~~~~~ 938 (1090)
...||+ |.+++....++|+.|.+|
T Consensus 367 ~~~v~t~d~~~a~~~~~~l~~G~v~ 391 (434)
T cd07133 367 ALYYFGEDKAEQDRVLRRTHSGGVT 391 (434)
T ss_pred eEEEECCCHHHHHHHHHhCCcceEE
Confidence 346888 677888899999999888
No 95
>PLN02203 aldehyde dehydrogenase
Probab=25.87 E-value=3.6e+02 Score=33.24 Aligned_cols=24 Identities=21% Similarity=0.236 Sum_probs=19.3
Q ss_pred eEEEec-ChhhHHHHHHhhcCcccc
Q 001377 915 ALAVFS-DPARAATATRRLDHGSVY 938 (1090)
Q Consensus 915 ~l~vF~-~p~~~~~a~~~l~~~~~~ 938 (1090)
..+||+ |..++...++.|+.|.+|
T Consensus 375 ~a~vft~d~~~a~~~~~~l~~G~V~ 399 (484)
T PLN02203 375 AIYAFTNNEKLKRRILSETSSGSVT 399 (484)
T ss_pred eEEEEcCCHHHHHHHHHhCCcceEE
Confidence 457788 666788899999998888
No 96
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=25.67 E-value=1.7e+02 Score=38.24 Aligned_cols=45 Identities=20% Similarity=0.165 Sum_probs=28.9
Q ss_pred eEEE--ecCCceEEEecChhhHHHHHHhhcCccccccEEEE-eCCCCC
Q 001377 906 ELVW--LNDKNALAVFSDPARAATATRRLDHGSVYYGAVVV-QNVGAP 950 (1090)
Q Consensus 906 el~w--i~d~~~l~vF~~p~~~~~a~~~l~~~~~~~~~~~~-~~~~~~ 950 (1090)
.|+| ++-+..++||--+.-.+..+-...-|+...|.+++ +.+.-.
T Consensus 998 vLqw~~l~csa~lvvkkh~~~q~~~~~~dr~gs~k~G~lKirEe~srl 1045 (1186)
T KOG1117|consen 998 VLQWSSLACSAYLVVKKHLTAQAIKHCSDRLGSIKEGILKIREEPSRL 1045 (1186)
T ss_pred HHhhhccCCcceEEeehhhhHhhhchhhhcccCcccceEEeccCcccc
Confidence 4888 55777777776554333332255678999999986 444443
No 97
>PTZ00381 aldehyde dehydrogenase family protein; Provisional
Probab=25.41 E-value=4e+02 Score=32.91 Aligned_cols=25 Identities=24% Similarity=0.247 Sum_probs=19.7
Q ss_pred ceEEEec-ChhhHHHHHHhhcCcccc
Q 001377 914 NALAVFS-DPARAATATRRLDHGSVY 938 (1090)
Q Consensus 914 ~~l~vF~-~p~~~~~a~~~l~~~~~~ 938 (1090)
-+.+||+ |.+.+...+++++.|.++
T Consensus 369 La~~vft~d~~~~~~~~~~~~sG~v~ 394 (493)
T PTZ00381 369 LALYYFGEDKRHKELVLENTSSGAVV 394 (493)
T ss_pred ceEEEECCCHHHHHHHHHhCCcceEE
Confidence 4678998 566677888999988877
No 98
>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=24.67 E-value=31 Score=32.58 Aligned_cols=32 Identities=25% Similarity=0.472 Sum_probs=23.7
Q ss_pred cceEeeecccccccCceeeCCCCceeechhHHHH
Q 001377 111 KVECMICYDMVKRSAPIWSCSSCFSIFHLSCIKK 144 (1090)
Q Consensus 111 ~yeC~IC~~~i~~~~~vWsC~~C~~vfHL~Cikk 144 (1090)
.-.|.||-..|..+.=++. +. -+|||+.|+++
T Consensus 78 ~~~C~vC~k~l~~~~f~~~-p~-~~v~H~~C~~r 109 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVF-PC-GHVVHYSCIKR 109 (109)
T ss_pred CCCccCcCCcCCCceEEEe-CC-CeEEecccccC
Confidence 4569999999988444444 33 39999999864
No 99
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
Probab=24.27 E-value=80 Score=29.76 Aligned_cols=37 Identities=8% Similarity=0.228 Sum_probs=28.2
Q ss_pred CeeeEEEecCCceEEEecChhhHHHHHHhhc-Cccccc
Q 001377 903 GECELVWLNDKNALAVFSDPARAATATRRLD-HGSVYY 939 (1090)
Q Consensus 903 g~~el~wi~d~~~l~vF~~p~~~~~a~~~l~-~~~~~~ 939 (1090)
-.|.|.|++|++=-+.-+..+..+||+|-.+ +|++++
T Consensus 38 ~~f~lKYlDde~e~v~lssd~eLeE~~rl~~~~~~~l~ 75 (81)
T cd06396 38 NDIQIKYVDEENEEVSVNSQGEYEEALKSAVRQGNLLQ 75 (81)
T ss_pred CcceeEEEcCCCCEEEEEchhhHHHHHHHHHhCCCEEE
Confidence 3889999998776667778999999999544 444543
No 100
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=24.11 E-value=47 Score=42.22 Aligned_cols=37 Identities=32% Similarity=0.752 Sum_probs=33.1
Q ss_pred cceEeeecccccccCceeeCCCCceeechhHHHHHhcCC
Q 001377 111 KVECMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWARAP 149 (1090)
Q Consensus 111 ~yeC~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~~~ 149 (1090)
++.|.||.-.|++.+-| |..|-+|.|-+|.+.|.+.+
T Consensus 1028 ~~~C~~C~l~V~gss~~--Cg~C~Hv~H~sc~~eWf~~g 1064 (1081)
T KOG0309|consen 1028 TFQCAICHLAVRGSSNF--CGTCGHVGHTSCMMEWFRTG 1064 (1081)
T ss_pred eeeeeeEeeEeeccchh--hccccccccHHHHHHHHhcC
Confidence 56799999999988865 99999999999999999975
No 101
>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells. PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi,
Probab=23.95 E-value=91 Score=29.57 Aligned_cols=40 Identities=13% Similarity=0.179 Sum_probs=30.9
Q ss_pred CeeeEEEecCCceEEEecChhhHHHHHHhhcCccccccEEE
Q 001377 903 GECELVWLNDKNALAVFSDPARAATATRRLDHGSVYYGAVV 943 (1090)
Q Consensus 903 g~~el~wi~d~~~l~vF~~p~~~~~a~~~l~~~~~~~~~~~ 943 (1090)
+.|.+.|++|+.=...|.+..-..+|+|.+...--. ++.+
T Consensus 39 q~ft~kw~DEEGDp~tiSS~~EL~EA~rl~~~n~~~-~l~i 78 (83)
T cd06404 39 QPFTLKWIDEEGDPCTISSQMELEEAFRLYELNKDS-ELNI 78 (83)
T ss_pred CcEEEEEECCCCCceeecCHHHHHHHHHHHHhcCcc-cEEE
Confidence 689999999765568899999999999977654444 4444
No 102
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=22.94 E-value=47 Score=31.85 Aligned_cols=33 Identities=36% Similarity=0.718 Sum_probs=23.4
Q ss_pred HHhccCcceEeeeccc-ccccC-ceeeCCCCceee
Q 001377 105 DKLMKSKVECMICYDM-VKRSA-PIWSCSSCFSIF 137 (1090)
Q Consensus 105 e~l~~~~yeC~IC~~~-i~~~~-~vWsC~~C~~vf 137 (1090)
|..++..|.|++|-.. |+|.+ -||.|..|-.+|
T Consensus 29 e~~q~~ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 29 EISQHAKYTCPFCGKTSVKRVATGIWKCKKCGKKF 63 (90)
T ss_dssp HHHHHS-BEESSSSSSEEEEEETTEEEETTTTEEE
T ss_pred HHHHhCCCcCCCCCCceeEEeeeEEeecCCCCCEE
Confidence 4456789999999765 44433 499999998766
No 103
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=22.54 E-value=2.9e+02 Score=23.67 Aligned_cols=54 Identities=26% Similarity=0.406 Sum_probs=34.5
Q ss_pred ecCcccc---hhhhHHHHhhcCee-eEEEecC------CceEEEecChhhHHHHHHhhcCcccccc
Q 001377 885 FLDLPRE---SDISALVLRFGGEC-ELVWLND------KNALAVFSDPARAATATRRLDHGSVYYG 940 (1090)
Q Consensus 885 ~~dl~~~---~~i~~~~~~f~g~~-el~wi~d------~~~l~vF~~p~~~~~a~~~l~~~~~~~~ 940 (1090)
+.+|+.. .+|..++.+| |.. .+..+.+ ..|.+-|.++..|.+||+.+. +..+.|
T Consensus 3 i~nlp~~~~~~~l~~~f~~~-g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~-~~~~~g 66 (70)
T PF14259_consen 3 ISNLPPSTTEEDLRNFFSRF-GPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLN-GKEIDG 66 (70)
T ss_dssp EESSTTT--HHHHHHHCTTS-SBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHT-TEEETT
T ss_pred EeCCCCCCCHHHHHHHHHhc-CCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCC-CcEECC
Confidence 4455433 3455555455 333 4555554 448899999999999999986 444444
No 104
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=21.63 E-value=66 Score=26.61 Aligned_cols=34 Identities=24% Similarity=0.674 Sum_probs=19.6
Q ss_pred Eeeecccccc-cCceeeCCCCceeechhHHHHHhcCC
Q 001377 114 CMICYDMVKR-SAPIWSCSSCFSIFHLSCIKKWARAP 149 (1090)
Q Consensus 114 C~IC~~~i~~-~~~vWsC~~C~~vfHL~CikkWa~~~ 149 (1090)
|.||.+.... +-+++- .|-++|=..||++|++++
T Consensus 1 CpIc~e~~~~~n~P~~L--~CGH~~c~~cl~~l~~~~ 35 (43)
T PF13445_consen 1 CPICKEFSTEENPPMVL--PCGHVFCKDCLQKLSKKS 35 (43)
T ss_dssp -TTT----TTSS-EEE---SSS-EEEHHHHHHHHHH-
T ss_pred CCccccccCCCCCCEEE--eCccHHHHHHHHHHHhcC
Confidence 7888882221 224663 499999999999999964
No 105
>PRK11241 gabD succinate-semialdehyde dehydrogenase I; Provisional
Probab=21.24 E-value=4.4e+02 Score=32.41 Aligned_cols=131 Identities=17% Similarity=0.168 Sum_probs=65.2
Q ss_pred hHHHHHHHHHHHHHhccccCCccccceEecCCC-ChhhHHHHHHHHHHc---CCceeecCCCCCceEEEEeCCCCCCCcc
Q 001377 778 KWVLSVEERCKFLVLGKNRGSTNALKVHVFCPM-LKDKRDAVRLIAERW---KLAVNPAGWEPKRFIVVHVTPKSKPPPR 853 (1090)
Q Consensus 778 ~~~~~vE~~L~~fv~~~~~~~~~~~k~~~f~PM-~~~kR~fIHeLAe~y---gL~S~S~d~EP~R~VvV~kt~~Sk~P~~ 853 (1090)
.|++++.+.++.|..+.- . .....+-|| ++.++.-|..+.+.. |-.-..-| ++.. ..+.+..|.
T Consensus 304 ~f~~~l~~~~~~l~~G~p----~-~~~~~~Gpli~~~~~~~v~~~i~~a~~~Ga~vl~GG-~~~~-----~~g~f~~Pt- 371 (482)
T PRK11241 304 RFAEKLQQAVSKLHIGDG----L-EKGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGG-KAHE-----LGGNFFQPT- 371 (482)
T ss_pred HHHHHHHHHHhhCCCCCC----C-CCCCCcCCCCCHHHHHHHHHHHHHHHhCCCEEEecC-CCCC-----CCCeEEeeE-
Confidence 455555555555433211 0 112235676 667788788665544 43222222 2110 012222333
Q ss_pred ccccccccccCCCCCCCcCcccccCCceEEEecCcccchhhhHHHHhhcCeeeEEEecCCceEEEec-ChhhHHHHHHhh
Q 001377 854 VIGVKGATTVNAPHAPVFDPLVDMDPRLVVSFLDLPRESDISALVLRFGGECELVWLNDKNALAVFS-DPARAATATRRL 932 (1090)
Q Consensus 854 lLs~~~~~~~~~~~~~~fna~v~~d~~~~v~~~dl~~~~~i~~~~~~f~g~~el~wi~d~~~l~vF~-~p~~~~~a~~~l 932 (1090)
+|.... ........|.|-|++ .++.++|++-...+.--. +|+ | ..+||+ |..++....++|
T Consensus 372 vl~~v~-~~~~i~~eE~FGPVl-----~v~~~~~~~eai~~aN~s-~~G----L-------~a~Vft~d~~~a~~~~~~l 433 (482)
T PRK11241 372 ILVDVP-ANAKVAKEETFGPLA-----PLFRFKDEADVIAQANDT-EFG----L-------AAYFYARDLSRVFRVGEAL 433 (482)
T ss_pred EEECCC-CCChhhhCcCcCCEE-----EEEEeCCHHHHHHHhhCC-CCC----c-------eEEEEcCCHHHHHHHHHHc
Confidence 333211 111222346677775 356777773322222111 343 1 357887 577888899999
Q ss_pred cCcccc
Q 001377 933 DHGSVY 938 (1090)
Q Consensus 933 ~~~~~~ 938 (1090)
+.|.+|
T Consensus 434 ~~G~v~ 439 (482)
T PRK11241 434 EYGIVG 439 (482)
T ss_pred CccEEE
Confidence 998888
No 106
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=20.70 E-value=50 Score=39.08 Aligned_cols=52 Identities=21% Similarity=0.544 Sum_probs=41.3
Q ss_pred cceEeeecccccccCceeeCCCCceeechhHHHHHhcCCCCcchhhhccCCCCCCCCCCCcccc
Q 001377 111 KVECMICYDMVKRSAPIWSCSSCFSIFHLSCIKKWARAPTSADLSAERSQGFNWRCPGCQSVQL 174 (1090)
Q Consensus 111 ~yeC~IC~~~i~~~~~vWsC~~C~~vfHL~CikkWa~~~~s~~~~~~~~~~~~WrCP~C~~~~~ 174 (1090)
..-|-.|-+.|+-...------|-+|||+.|.+....+- ..--||+|+....
T Consensus 365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n------------~~rsCP~CrklrS 416 (518)
T KOG1941|consen 365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENN------------GTRSCPNCRKLRS 416 (518)
T ss_pred hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhC------------CCCCCccHHHHHh
Confidence 355899999998887766667899999999999888543 2567999996543
Done!