Query 021489
Match_columns 311
No_of_seqs 95 out of 97
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 03:22:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021489.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021489hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07800 DUF1644: Protein of u 100.0 2.5E-92 5.5E-97 613.1 12.6 157 28-184 1-162 (162)
2 KOG4172 Predicted E3 ubiquitin 97.1 8.7E-05 1.9E-09 57.0 -0.5 22 26-48 5-26 (62)
3 PF13920 zf-C3HC4_3: Zinc fing 96.9 0.00098 2.1E-08 46.8 3.2 49 28-114 1-49 (50)
4 PLN03208 E3 ubiquitin-protein 96.8 0.0015 3.3E-08 59.5 4.3 76 20-118 9-84 (193)
5 PHA02929 N1R/p28-like protein; 95.1 0.016 3.5E-07 54.1 2.8 47 28-113 173-227 (238)
6 KOG2164 Predicted E3 ubiquitin 94.2 0.064 1.4E-06 55.2 4.8 83 29-164 186-274 (513)
7 cd00162 RING RING-finger (Real 93.9 0.066 1.4E-06 34.2 2.9 33 31-75 1-33 (45)
8 COG5574 PEX10 RING-finger-cont 92.6 0.066 1.4E-06 51.4 1.9 21 28-48 214-234 (271)
9 PHA02926 zinc finger-like prot 92.1 0.13 2.7E-06 48.8 3.0 13 28-40 169-181 (242)
10 PF13639 zf-RING_2: Ring finge 91.9 0.077 1.7E-06 36.2 1.1 32 31-75 2-36 (44)
11 PF13909 zf-H2C2_5: C2H2-type 91.3 0.1 2.3E-06 31.6 1.1 21 135-155 4-24 (24)
12 TIGR00599 rad18 DNA repair pro 90.7 0.13 2.8E-06 51.4 1.7 20 28-47 25-44 (397)
13 KOG4265 Predicted E3 ubiquitin 84.8 0.66 1.4E-05 46.1 2.5 33 29-73 290-322 (349)
14 KOG0823 Predicted E3 ubiquitin 84.6 0.89 1.9E-05 43.0 3.1 58 26-119 44-101 (230)
15 KOG3002 Zn finger protein [Gen 84.4 0.88 1.9E-05 43.9 3.1 29 128-156 135-165 (299)
16 PF12678 zf-rbx1: RING-H2 zinc 83.9 0.47 1E-05 36.3 0.9 44 29-74 19-64 (73)
17 PF13923 zf-C3HC4_2: Zinc fing 83.7 0.49 1.1E-05 31.7 0.8 32 32-75 1-32 (39)
18 KOG0804 Cytoplasmic Zn-finger 82.3 0.45 9.8E-06 48.9 0.2 37 28-73 174-210 (493)
19 PF03145 Sina: Seven in absent 81.8 0.4 8.6E-06 42.0 -0.3 29 128-156 43-73 (198)
20 PF15227 zf-C3HC4_4: zinc fing 80.9 0.78 1.7E-05 32.0 1.0 17 32-48 1-17 (42)
21 smart00184 RING Ring finger. E 77.4 1.5 3.2E-05 26.8 1.4 30 32-74 1-30 (39)
22 smart00744 RINGv The RING-vari 72.6 4.7 0.0001 29.0 3.1 37 31-77 1-41 (49)
23 PF11793 FANCL_C: FANCL C-term 72.5 2.5 5.4E-05 32.3 1.8 64 29-113 2-66 (70)
24 KOG0825 PHD Zn-finger protein 67.3 2.2 4.7E-05 47.0 0.6 41 22-71 208-248 (1134)
25 COG5540 RING-finger-containing 66.7 4.1 8.8E-05 40.7 2.3 48 28-113 322-372 (374)
26 KOG1001 Helicase-like transcri 62.7 4.4 9.4E-05 43.1 1.8 47 30-114 455-501 (674)
27 KOG0802 E3 ubiquitin ligase [P 60.8 4.8 0.0001 41.0 1.6 43 20-75 279-329 (543)
28 smart00504 Ubox Modified RING 60.4 5 0.00011 28.3 1.2 19 29-47 1-19 (63)
29 PF00097 zf-C3HC4: Zinc finger 59.0 4.5 9.7E-05 26.7 0.8 31 32-75 1-32 (41)
30 KOG4692 Predicted E3 ubiquitin 57.6 4.1 9E-05 41.5 0.6 23 26-48 419-441 (489)
31 TIGR00570 cdk7 CDK-activating 55.1 11 0.00023 37.2 2.8 36 28-73 2-39 (309)
32 PF12861 zf-Apc11: Anaphase-pr 55.1 12 0.00026 30.7 2.7 10 102-111 71-80 (85)
33 COG2835 Uncharacterized conser 53.5 5.3 0.00011 31.1 0.4 9 103-111 9-17 (60)
34 KOG2177 Predicted E3 ubiquitin 53.0 3.8 8.3E-05 33.9 -0.4 21 28-48 12-32 (386)
35 KOG0320 Predicted E3 ubiquitin 52.5 6 0.00013 36.6 0.7 62 13-112 116-177 (187)
36 PRK11827 hypothetical protein; 48.3 7.6 0.00016 29.9 0.6 12 102-113 8-19 (60)
37 KOG4275 Predicted E3 ubiquitin 45.8 8.5 0.00018 38.3 0.6 20 29-48 300-319 (350)
38 PF13445 zf-RING_UBOX: RING-ty 42.2 12 0.00025 26.7 0.7 16 32-47 1-19 (43)
39 PF10614 CsgF: Type VIII secre 41.1 85 0.0018 27.9 6.0 65 142-206 39-116 (142)
40 KOG1785 Tyrosine kinase negati 40.9 9.6 0.00021 39.5 0.2 15 103-117 406-420 (563)
41 PF13894 zf-C2H2_4: C2H2-type 38.2 23 0.00051 20.0 1.5 18 137-154 6-24 (24)
42 KOG1006 Mitogen-activated prot 38.2 13 0.00027 37.3 0.5 12 48-59 224-235 (361)
43 PHA02862 5L protein; Provision 36.3 44 0.00095 30.4 3.5 62 29-125 2-65 (156)
44 KOG0824 Predicted E3 ubiquitin 35.8 25 0.00054 35.0 2.1 57 29-123 7-63 (324)
45 KOG4029 Transcription factor H 35.0 27 0.00059 31.7 2.1 48 118-168 106-154 (228)
46 PF15060 PPDFL: Differentiatio 33.4 20 0.00044 30.9 1.0 15 218-232 50-64 (110)
47 PF11396 DUF2874: Protein of u 32.1 25 0.00054 24.9 1.1 40 181-222 11-60 (61)
48 PRK04028 glutamyl-tRNA(Gln) am 28.3 21 0.00047 38.0 0.3 13 28-40 78-92 (630)
49 PRK10050 curli assembly protei 27.9 1.9E+02 0.004 25.9 6.0 63 142-204 37-105 (138)
50 KOG1039 Predicted E3 ubiquitin 26.6 33 0.00071 34.2 1.2 130 28-189 160-316 (344)
51 PF14634 zf-RING_5: zinc-RING 23.6 43 0.00094 23.0 1.0 17 31-47 1-20 (44)
52 KOG0754 Mitochondrial oxodicar 23.0 44 0.00096 32.9 1.3 35 25-80 67-101 (294)
53 PF04216 FdhE: Protein involve 22.4 34 0.00074 32.0 0.5 40 24-65 167-209 (290)
54 PF00653 BIR: Inhibitor of Apo 21.0 20 0.00043 26.8 -1.2 31 100-130 34-65 (70)
55 smart00734 ZnF_Rad18 Rad18-lik 20.9 39 0.00085 21.7 0.4 8 30-37 2-9 (26)
No 1
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=100.00 E-value=2.5e-92 Score=613.09 Aligned_cols=157 Identities=57% Similarity=1.092 Sum_probs=142.8
Q ss_pred ccccccccccCCCceeeeecccCCCCCcccccCCCCCccchHHHHHHhhCCCCCCCCccCC----ccCC-CCccCCCCCC
Q 021489 28 DDVTCPICLDFPHNGVLLLCSSYEKGCRPFVCDTDHLHSNCLDRFKNAYGVSPPSTSEVNS----AANT-QPMVSEDSCR 102 (311)
Q Consensus 28 edvtCpICME~PHNAVLLlCSSh~KGCRPYMCdTS~RHSNCLDQFkka~~~~~~s~s~~~~----~~~~-~~~~~~~~~~ 102 (311)
|||+||||||||||||||+||||+|||||||||||||||||||||||||+++.++++.+.. +.++ ....+..+++
T Consensus 1 ed~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (162)
T PF07800_consen 1 EDVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQPE 80 (162)
T ss_pred CCccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCccccccccccccc
Confidence 7999999999999999999999999999999999999999999999999987754433222 1111 1233457889
Q ss_pred ccCccccccccCEEEcchhHHhhccccCcCcccCccccccHHHHHHhhhhhCCCCCCCCCCchhHHHHHHhhhhhhhhhH
Q 021489 103 PACPLCRGEVTGWVVADKVRDYLNEKKRCCEEDQCTFAGTYLELRKHAQLEHPHSRPSKIDPARQLDWENFQQSSEIIDV 182 (311)
Q Consensus 103 L~CPLCRGeVkGWtVVe~AR~~LN~K~RsC~~e~CsF~GtY~eLrKHar~~HP~arP~eVDP~rq~~W~~lE~ere~~Dv 182 (311)
|+||||||+|+|||||++||+|||+|+|+||+|+|+|+|||.|||||||.+||++||++|||+||++|++||+|+|++||
T Consensus 81 L~CPLCRG~V~GWtvve~AR~~LN~K~RsC~~e~C~F~GtY~eLrKHar~~HP~~rP~~vDP~rq~~W~~le~~re~~D~ 160 (162)
T PF07800_consen 81 LACPLCRGEVKGWTVVEPARRFLNAKKRSCSQESCSFSGTYSELRKHARSEHPSARPSEVDPQRQRDWERLEREREYGDV 160 (162)
T ss_pred ccCccccCceeceEEchHHHHHhccCCccCcccccccccCHHHHHHHHHhhCCCCCCccCCHHHHHHHHHHHHhhhhhcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HH
Q 021489 183 LS 184 (311)
Q Consensus 183 iS 184 (311)
||
T Consensus 161 iS 162 (162)
T PF07800_consen 161 IS 162 (162)
T ss_pred cC
Confidence 97
No 2
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.12 E-value=8.7e-05 Score=57.04 Aligned_cols=22 Identities=36% Similarity=1.034 Sum_probs=19.2
Q ss_pred CCccccccccccCCCceeeeecc
Q 021489 26 NWDDVTCPICLDFPHNGVLLLCS 48 (311)
Q Consensus 26 eWedvtCpICME~PHNAVLLlCS 48 (311)
+|. .-|-||||+|-|.||..|-
T Consensus 5 ~~~-dECTICye~pvdsVlYtCG 26 (62)
T KOG4172|consen 5 QWS-DECTICYEHPVDSVLYTCG 26 (62)
T ss_pred ccc-cceeeeccCcchHHHHHcc
Confidence 787 7899999999999997663
No 3
>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=96.90 E-value=0.00098 Score=46.79 Aligned_cols=49 Identities=35% Similarity=0.925 Sum_probs=33.8
Q ss_pred ccccccccccCCCceeeeecccCCCCCcccccCCCCCccchHHHHHHhhCCCCCCCCccCCccCCCCccCCCCCCccCcc
Q 021489 28 DDVTCPICLDFPHNGVLLLCSSYEKGCRPFVCDTDHLHSNCLDRFKNAYGVSPPSTSEVNSAANTQPMVSEDSCRPACPL 107 (311)
Q Consensus 28 edvtCpICME~PHNAVLLlCSSh~KGCRPYMCdTS~RHSNCLDQFkka~~~~~~s~s~~~~~~~~~~~~~~~~~~L~CPL 107 (311)
|+..|+||++.|.++|++-|. |- .+| ..|++++.+. ...||+
T Consensus 1 ~~~~C~iC~~~~~~~~~~pCg-H~-----~~C------~~C~~~~~~~--------------------------~~~CP~ 42 (50)
T PF13920_consen 1 EDEECPICFENPRDVVLLPCG-HL-----CFC------EECAERLLKR--------------------------KKKCPI 42 (50)
T ss_dssp -HSB-TTTSSSBSSEEEETTC-EE-----EEE------HHHHHHHHHT--------------------------TSBBTT
T ss_pred CcCCCccCCccCCceEEeCCC-Ch-----HHH------HHHhHHhccc--------------------------CCCCCc
Confidence 577899999999999999763 11 122 3677777761 167999
Q ss_pred ccccccC
Q 021489 108 CRGEVTG 114 (311)
Q Consensus 108 CRGeVkG 114 (311)
||.+|..
T Consensus 43 Cr~~i~~ 49 (50)
T PF13920_consen 43 CRQPIES 49 (50)
T ss_dssp TTBB-SE
T ss_pred CChhhcC
Confidence 9999863
No 4
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=96.78 E-value=0.0015 Score=59.48 Aligned_cols=76 Identities=25% Similarity=0.464 Sum_probs=47.7
Q ss_pred ccccccCCccccccccccCCCceeeeecccCCCCCcccccCCCCCccchHHHHHHhhCCCCCCCCccCCccCCCCccCCC
Q 021489 20 DVQLNTNWDDVTCPICLDFPHNGVLLLCSSYEKGCRPFVCDTDHLHSNCLDRFKNAYGVSPPSTSEVNSAANTQPMVSED 99 (311)
Q Consensus 20 d~~l~keWedvtCpICME~PHNAVLLlCSSh~KGCRPYMCdTS~RHSNCLDQFkka~~~~~~s~s~~~~~~~~~~~~~~~ 99 (311)
|..+...=++..||||+|...++|++.|- | .- ...|+.++-.+...+... .. .....
T Consensus 9 ~~~~~~~~~~~~CpICld~~~dPVvT~CG-H-~F-----------C~~CI~~wl~~s~~s~~~-----~~-----~~~~~ 65 (193)
T PLN03208 9 DTTLVDSGGDFDCNICLDQVRDPVVTLCG-H-LF-----------CWPCIHKWTYASNNSRQR-----VD-----QYDHK 65 (193)
T ss_pred cceeccCCCccCCccCCCcCCCcEEcCCC-c-hh-----------HHHHHHHHHHhccccccc-----cc-----ccccc
Confidence 45555555789999999999999998773 1 22 246888876553221110 00 00012
Q ss_pred CCCccCccccccccCEEEc
Q 021489 100 SCRPACPLCRGEVTGWVVA 118 (311)
Q Consensus 100 ~~~L~CPLCRGeVkGWtVV 118 (311)
...+.||+||.+|.-=+++
T Consensus 66 k~~~~CPvCR~~Is~~~Lv 84 (193)
T PLN03208 66 REPPKCPVCKSDVSEATLV 84 (193)
T ss_pred CCCCcCCCCCCcCChhcEE
Confidence 4568999999999765443
No 5
>PHA02929 N1R/p28-like protein; Provisional
Probab=95.07 E-value=0.016 Score=54.09 Aligned_cols=47 Identities=30% Similarity=0.788 Sum_probs=31.6
Q ss_pred ccccccccccCCCc--------eeeeecccCCCCCcccccCCCCCccchHHHHHHhhCCCCCCCCccCCccCCCCccCCC
Q 021489 28 DDVTCPICLDFPHN--------GVLLLCSSYEKGCRPFVCDTDHLHSNCLDRFKNAYGVSPPSTSEVNSAANTQPMVSED 99 (311)
Q Consensus 28 edvtCpICME~PHN--------AVLLlCSSh~KGCRPYMCdTS~RHSNCLDQFkka~~~~~~s~s~~~~~~~~~~~~~~~ 99 (311)
++..||||||.-.+ +||+.|- - .-|..|+.++.+.
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~------------H-~FC~~CI~~Wl~~------------------------ 215 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCN------------H-VFCIECIDIWKKE------------------------ 215 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCC------------C-cccHHHHHHHHhc------------------------
Confidence 46899999997433 4666552 1 2356788887642
Q ss_pred CCCccCcccccccc
Q 021489 100 SCRPACPLCRGEVT 113 (311)
Q Consensus 100 ~~~L~CPLCRGeVk 113 (311)
...||+||..+.
T Consensus 216 --~~tCPlCR~~~~ 227 (238)
T PHA02929 216 --KNTCPVCRTPFI 227 (238)
T ss_pred --CCCCCCCCCEee
Confidence 136999999876
No 6
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.17 E-value=0.064 Score=55.19 Aligned_cols=83 Identities=30% Similarity=0.543 Sum_probs=56.4
Q ss_pred cccccccccCCCceeeeecccCCCCCcccccCCCCCccchHHHHHHhhCCCCCCCCccCCccCCCCccCCCCCCccCccc
Q 021489 29 DVTCPICLDFPHNGVLLLCSSYEKGCRPFVCDTDHLHSNCLDRFKNAYGVSPPSTSEVNSAANTQPMVSEDSCRPACPLC 108 (311)
Q Consensus 29 dvtCpICME~PHNAVLLlCSSh~KGCRPYMCdTS~RHSNCLDQFkka~~~~~~s~s~~~~~~~~~~~~~~~~~~L~CPLC 108 (311)
+..||||+|.|==||+-.|-- -| | =+||=||-..-.. ..--.||||
T Consensus 186 ~~~CPICL~~~~~p~~t~CGH------iF-C------~~CiLqy~~~s~~---------------------~~~~~CPiC 231 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRTNCGH------IF-C------GPCILQYWNYSAI---------------------KGPCSCPIC 231 (513)
T ss_pred CCcCCcccCCCCcccccccCc------ee-e------HHHHHHHHhhhcc---------------------cCCccCCch
Confidence 999999999999999988731 12 1 2699999876421 122579999
Q ss_pred cccccC--E-EEc-chhHHhhccccCcCcccCccccccHHHHHHhhhhhC--CCCCCCCCCc
Q 021489 109 RGEVTG--W-VVA-DKVRDYLNEKKRCCEEDQCTFAGTYLELRKHAQLEH--PHSRPSKIDP 164 (311)
Q Consensus 109 RGeVkG--W-tVV-e~AR~~LN~K~RsC~~e~CsF~GtY~eLrKHar~~H--P~arP~eVDP 164 (311)
|-.|.= = +|. +.- +.=.+|+-|++-.- +.-|+-..||
T Consensus 232 ~s~I~~kdl~pv~~e~~-------------------qkke~l~~~~~~ng~~~~~r~F~~d~ 274 (513)
T KOG2164|consen 232 RSTITLKDLLPVFIEDD-------------------QKKEELKLHQDPNGIPDYNRRFSGDP 274 (513)
T ss_pred hhhccccceeeeeeccc-------------------cccHHHHHHhcccCCCccccceecCc
Confidence 988765 1 111 111 34455888887664 7777777887
No 7
>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=93.90 E-value=0.066 Score=34.18 Aligned_cols=33 Identities=33% Similarity=0.786 Sum_probs=22.3
Q ss_pred cccccccCCCceeeeecccCCCCCcccccCCCCCccchHHHHHHh
Q 021489 31 TCPICLDFPHNGVLLLCSSYEKGCRPFVCDTDHLHSNCLDRFKNA 75 (311)
Q Consensus 31 tCpICME~PHNAVLLlCSSh~KGCRPYMCdTS~RHSNCLDQFkka 75 (311)
.|+||++...+.+.+. + |+-.| |..|++++.+.
T Consensus 1 ~C~iC~~~~~~~~~~~------~-----C~H~~-c~~C~~~~~~~ 33 (45)
T cd00162 1 ECPICLEEFREPVVLL------P-----CGHVF-CRSCIDKWLKS 33 (45)
T ss_pred CCCcCchhhhCceEec------C-----CCChh-cHHHHHHHHHh
Confidence 5999999986666554 1 33332 67899887654
No 8
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.59 E-value=0.066 Score=51.38 Aligned_cols=21 Identities=29% Similarity=0.607 Sum_probs=18.3
Q ss_pred ccccccccccCCCceeeeecc
Q 021489 28 DDVTCPICLDFPHNGVLLLCS 48 (311)
Q Consensus 28 edvtCpICME~PHNAVLLlCS 48 (311)
-|-.|+||||.||+++-+.|.
T Consensus 214 ~d~kC~lC~e~~~~ps~t~Cg 234 (271)
T COG5574 214 ADYKCFLCLEEPEVPSCTPCG 234 (271)
T ss_pred cccceeeeecccCCccccccc
Confidence 466799999999999988875
No 9
>PHA02926 zinc finger-like protein; Provisional
Probab=92.07 E-value=0.13 Score=48.82 Aligned_cols=13 Identities=23% Similarity=0.657 Sum_probs=10.7
Q ss_pred ccccccccccCCC
Q 021489 28 DDVTCPICLDFPH 40 (311)
Q Consensus 28 edvtCpICME~PH 40 (311)
++..|+||||.-+
T Consensus 169 kE~eCgICmE~I~ 181 (242)
T PHA02926 169 KEKECGICYEVVY 181 (242)
T ss_pred CCCCCccCccccc
Confidence 5689999999744
No 10
>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=91.92 E-value=0.077 Score=36.18 Aligned_cols=32 Identities=31% Similarity=0.729 Sum_probs=22.7
Q ss_pred cccccccCC---CceeeeecccCCCCCcccccCCCCCccchHHHHHHh
Q 021489 31 TCPICLDFP---HNGVLLLCSSYEKGCRPFVCDTDHLHSNCLDRFKNA 75 (311)
Q Consensus 31 tCpICME~P---HNAVLLlCSSh~KGCRPYMCdTS~RHSNCLDQFkka 75 (311)
.||||||.- ...|.|.| + -.=|..|+.++-+.
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C------------~-H~fh~~Ci~~~~~~ 36 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPC------------G-HVFHRSCIKEWLKR 36 (44)
T ss_dssp CETTTTCBHHTTSCEEEETT------------S-EEEEHHHHHHHHHH
T ss_pred CCcCCChhhcCCCeEEEccC------------C-CeeCHHHHHHHHHh
Confidence 699999864 45666655 2 23478999999865
No 11
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=91.30 E-value=0.1 Score=31.63 Aligned_cols=21 Identities=24% Similarity=0.703 Sum_probs=18.3
Q ss_pred cCccccccHHHHHHhhhhhCC
Q 021489 135 DQCTFAGTYLELRKHAQLEHP 155 (311)
Q Consensus 135 e~CsF~GtY~eLrKHar~~HP 155 (311)
.-|+|+.+..+|.+|++..||
T Consensus 4 ~~C~y~t~~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 4 PHCSYSTSKSNLKRHLKRHHP 24 (24)
T ss_dssp SSSS-EESHHHHHHHHHHHHS
T ss_pred CCCCCcCCHHHHHHHHHhhCc
Confidence 459999999999999999997
No 12
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=90.71 E-value=0.13 Score=51.38 Aligned_cols=20 Identities=40% Similarity=0.765 Sum_probs=16.9
Q ss_pred ccccccccccCCCceeeeec
Q 021489 28 DDVTCPICLDFPHNGVLLLC 47 (311)
Q Consensus 28 edvtCpICME~PHNAVLLlC 47 (311)
+..+||||++...+.|++-|
T Consensus 25 ~~l~C~IC~d~~~~PvitpC 44 (397)
T TIGR00599 25 TSLRCHICKDFFDVPVLTSC 44 (397)
T ss_pred cccCCCcCchhhhCccCCCC
Confidence 35799999999999998754
No 13
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.85 E-value=0.66 Score=46.06 Aligned_cols=33 Identities=30% Similarity=0.709 Sum_probs=26.2
Q ss_pred cccccccccCCCceeeeecccCCCCCcccccCCCCCccchHHHHH
Q 021489 29 DVTCPICLDFPHNGVLLLCSSYEKGCRPFVCDTDHLHSNCLDRFK 73 (311)
Q Consensus 29 dvtCpICME~PHNAVLLlCSSh~KGCRPYMCdTS~RHSNCLDQFk 73 (311)
.-.|.|||.-|-|.|||-|- .||= =|+|-|+++
T Consensus 290 gkeCVIClse~rdt~vLPCR--------HLCL----Cs~Ca~~Lr 322 (349)
T KOG4265|consen 290 GKECVICLSESRDTVVLPCR--------HLCL----CSGCAKSLR 322 (349)
T ss_pred CCeeEEEecCCcceEEecch--------hheh----hHhHHHHHH
Confidence 56799999999999999773 2331 278999998
No 14
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.62 E-value=0.89 Score=42.98 Aligned_cols=58 Identities=31% Similarity=0.634 Sum_probs=42.8
Q ss_pred CCccccccccccCCCceeeeecccCCCCCcccccCCCCCccchHHHHHHhhCCCCCCCCccCCccCCCCccCCCCCCccC
Q 021489 26 NWDDVTCPICLDFPHNGVLLLCSSYEKGCRPFVCDTDHLHSNCLDRFKNAYGVSPPSTSEVNSAANTQPMVSEDSCRPAC 105 (311)
Q Consensus 26 eWedvtCpICME~PHNAVLLlCSSh~KGCRPYMCdTS~RHSNCLDQFkka~~~~~~s~s~~~~~~~~~~~~~~~~~~L~C 105 (311)
+=-.-.|-||+|-++.+||-+|-- -=|=| ||=|+-..+. ..-.|
T Consensus 44 ~~~~FdCNICLd~akdPVvTlCGH--LFCWp-----------ClyqWl~~~~-----------------------~~~~c 87 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKDPVVTLCGH--LFCWP-----------CLYQWLQTRP-----------------------NSKEC 87 (230)
T ss_pred CCCceeeeeeccccCCCEEeeccc--ceehH-----------HHHHHHhhcC-----------------------CCeeC
Confidence 334567999999999999999841 12433 7878765533 12458
Q ss_pred ccccccccCEEEcc
Q 021489 106 PLCRGEVTGWVVAD 119 (311)
Q Consensus 106 PLCRGeVkGWtVVe 119 (311)
|-|+++|..=|||-
T Consensus 88 PVCK~~Vs~~~vvP 101 (230)
T KOG0823|consen 88 PVCKAEVSIDTVVP 101 (230)
T ss_pred CccccccccceEEe
Confidence 99999999999984
No 15
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=84.42 E-value=0.88 Score=43.91 Aligned_cols=29 Identities=24% Similarity=0.602 Sum_probs=26.6
Q ss_pred ccCcCccc--CccccccHHHHHHhhhhhCCC
Q 021489 128 KKRCCEED--QCTFAGTYLELRKHAQLEHPH 156 (311)
Q Consensus 128 K~RsC~~e--~CsF~GtY~eLrKHar~~HP~ 156 (311)
.+=+|.+- .|.|.|.|++|..|.+..|+.
T Consensus 135 ~~~~CP~p~~~C~~~G~~~~l~~H~~~~hk~ 165 (299)
T KOG3002|consen 135 RPCSCPVPGAECKYTGSYKDLYAHLNDTHKS 165 (299)
T ss_pred CCcCCCCCcccCCccCcHHHHHHHHHhhChh
Confidence 56688888 999999999999999999987
No 16
>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=83.93 E-value=0.47 Score=36.34 Aligned_cols=44 Identities=20% Similarity=0.508 Sum_probs=29.3
Q ss_pred cccccccccCCCceeeeecccCCCCCcccc--cCCCCCccchHHHHHH
Q 021489 29 DVTCPICLDFPHNGVLLLCSSYEKGCRPFV--CDTDHLHSNCLDRFKN 74 (311)
Q Consensus 29 dvtCpICME~PHNAVLLlCSSh~KGCRPYM--CdTS~RHSNCLDQFkk 74 (311)
+-.|+||++.-+.... -|..-...|-.-+ |+-.| |.-|+.|+-+
T Consensus 19 ~d~C~IC~~~l~~~~~-~~~~~~~~~~i~~~~C~H~F-H~~Ci~~Wl~ 64 (73)
T PF12678_consen 19 DDNCAICREPLEDPCP-ECQAPQDECPIVWGPCGHIF-HFHCISQWLK 64 (73)
T ss_dssp CSBETTTTSBTTSTTC-CHHHCTTTS-EEEETTSEEE-EHHHHHHHHT
T ss_pred CCcccccChhhhChhh-hhcCCccccceEecccCCCE-EHHHHHHHHh
Confidence 4459999999866553 5655556665543 76555 7789988864
No 17
>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=83.75 E-value=0.49 Score=31.68 Aligned_cols=32 Identities=25% Similarity=0.668 Sum_probs=20.2
Q ss_pred ccccccCCCceeeeecccCCCCCcccccCCCCCccchHHHHHHh
Q 021489 32 CPICLDFPHNGVLLLCSSYEKGCRPFVCDTDHLHSNCLDRFKNA 75 (311)
Q Consensus 32 CpICME~PHNAVLLlCSSh~KGCRPYMCdTS~RHSNCLDQFkka 75 (311)
||||++.+-|+|.++.- +-+| ...|+.++.+.
T Consensus 1 C~iC~~~~~~~~~~~~C-----------GH~f-C~~C~~~~~~~ 32 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPC-----------GHSF-CKECIEKYLEK 32 (39)
T ss_dssp ETTTTSB-SSEEEECTT-----------SEEE-EHHHHHHHHHC
T ss_pred CCCCCCcccCcCEECCC-----------CCch-hHHHHHHHHHC
Confidence 89999999999544422 2222 24677777665
No 18
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=82.27 E-value=0.45 Score=48.89 Aligned_cols=37 Identities=27% Similarity=0.634 Sum_probs=28.1
Q ss_pred ccccccccccCCCceeeeecccCCCCCcccccCCCCCccchHHHHH
Q 021489 28 DDVTCPICLDFPHNGVLLLCSSYEKGCRPFVCDTDHLHSNCLDRFK 73 (311)
Q Consensus 28 edvtCpICME~PHNAVLLlCSSh~KGCRPYMCdTS~RHSNCLDQFk 73 (311)
|--|||||+|.=-..| .|=+|-+|+-||+|+ ||.++.
T Consensus 174 ELPTCpVCLERMD~s~--------~gi~t~~c~Hsfh~~-cl~~w~ 210 (493)
T KOG0804|consen 174 ELPTCPVCLERMDSST--------TGILTILCNHSFHCS-CLMKWW 210 (493)
T ss_pred cCCCcchhHhhcCccc--------cceeeeecccccchH-HHhhcc
Confidence 6789999999755433 477899999999765 776553
No 19
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=81.78 E-value=0.4 Score=41.98 Aligned_cols=29 Identities=28% Similarity=0.579 Sum_probs=21.7
Q ss_pred ccCcCcc--cCccccccHHHHHHhhhhhCCC
Q 021489 128 KKRCCEE--DQCTFAGTYLELRKHAQLEHPH 156 (311)
Q Consensus 128 K~RsC~~--e~CsF~GtY~eLrKHar~~HP~ 156 (311)
++-.|+. .+|.|.|++.+|.+|.+..|+.
T Consensus 43 ~p~~CP~~~~~C~~~G~~~~l~~Hl~~~H~~ 73 (198)
T PF03145_consen 43 RPCSCPFPGSGCDWQGSYKELLDHLRDKHSW 73 (198)
T ss_dssp SEEE-SSSSTT---EEECCCHHHHHHHHTTT
T ss_pred cCCcCCCCCCCccccCCHHHHHHHHHHHCCC
Confidence 4556777 8999999999999999999964
No 20
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=80.95 E-value=0.78 Score=31.96 Aligned_cols=17 Identities=53% Similarity=1.128 Sum_probs=13.9
Q ss_pred ccccccCCCceeeeecc
Q 021489 32 CPICLDFPHNGVLLLCS 48 (311)
Q Consensus 32 CpICME~PHNAVLLlCS 48 (311)
||||++.-++.|.|.|.
T Consensus 1 CpiC~~~~~~Pv~l~CG 17 (42)
T PF15227_consen 1 CPICLDLFKDPVSLPCG 17 (42)
T ss_dssp ETTTTSB-SSEEE-SSS
T ss_pred CCccchhhCCccccCCc
Confidence 89999999999999883
No 21
>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=77.40 E-value=1.5 Score=26.77 Aligned_cols=30 Identities=30% Similarity=0.835 Sum_probs=22.6
Q ss_pred ccccccCCCceeeeecccCCCCCcccccCCCCCccchHHHHHH
Q 021489 32 CPICLDFPHNGVLLLCSSYEKGCRPFVCDTDHLHSNCLDRFKN 74 (311)
Q Consensus 32 CpICME~PHNAVLLlCSSh~KGCRPYMCdTS~RHSNCLDQFkk 74 (311)
|+||++...+.++|.|. -. -+.+|++++.+
T Consensus 1 C~iC~~~~~~~~~~~C~------------H~-~c~~C~~~~~~ 30 (39)
T smart00184 1 CPICLEELKDPVVLPCG------------HT-FCRSCIRKWLK 30 (39)
T ss_pred CCcCccCCCCcEEecCC------------Ch-HHHHHHHHHHH
Confidence 89999999999988642 22 15678888766
No 22
>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=72.61 E-value=4.7 Score=29.04 Aligned_cols=37 Identities=32% Similarity=0.740 Sum_probs=25.9
Q ss_pred ccccccc--CCCceeeeecccCCCCCcccccCC--CCCccchHHHHHHhhC
Q 021489 31 TCPICLD--FPHNGVLLLCSSYEKGCRPFVCDT--DHLHSNCLDRFKNAYG 77 (311)
Q Consensus 31 tCpICME--~PHNAVLLlCSSh~KGCRPYMCdT--S~RHSNCLDQFkka~~ 77 (311)
.|-||++ .+-|..++-| .|-- .|-|..||+++.....
T Consensus 1 ~CrIC~~~~~~~~~l~~PC----------~C~G~~~~vH~~Cl~~W~~~~~ 41 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPC----------RCKGSLKYVHQECLERWINESG 41 (49)
T ss_pred CccCCCCCCCCCCeeEecc----------ccCCchhHHHHHHHHHHHHHcC
Confidence 4889997 5555555444 3543 5889999999987643
No 23
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=72.50 E-value=2.5 Score=32.35 Aligned_cols=64 Identities=22% Similarity=0.491 Sum_probs=26.1
Q ss_pred cccccccccCCC-ceeeeecccCCCCCcccccCCCCCccchHHHHHHhhCCCCCCCCccCCccCCCCccCCCCCCccCcc
Q 021489 29 DVTCPICLDFPH-NGVLLLCSSYEKGCRPFVCDTDHLHSNCLDRFKNAYGVSPPSTSEVNSAANTQPMVSEDSCRPACPL 107 (311)
Q Consensus 29 dvtCpICME~PH-NAVLLlCSSh~KGCRPYMCdTS~RHSNCLDQFkka~~~~~~s~s~~~~~~~~~~~~~~~~~~L~CPL 107 (311)
+..|+||++.=| +.=+ -.+.|..=.|.-. -|..||-++=.+..+...+ -....-.||.
T Consensus 2 ~~~C~IC~~~~~~~~~~-----p~~~C~n~~C~~~-fH~~CL~~wf~~~~~~~~~---------------~~~~~G~CP~ 60 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEI-----PDVVCPNPSCGKK-FHLLCLSEWFLSLEKSRQS---------------FIPIFGECPY 60 (70)
T ss_dssp --S-SSS--SS-TT----------B--S-TT-----B-SGGGHHHHHHHHSSS-T---------------TT--EEE-TT
T ss_pred CCCCCcCCcEecCCCCc-----CceEcCCcccCCH-HHHHHHHHHHHHcccCCee---------------ecccccCCcC
Confidence 467999998754 2111 1245655566544 4889998877664432210 0234467999
Q ss_pred cccccc
Q 021489 108 CRGEVT 113 (311)
Q Consensus 108 CRGeVk 113 (311)
|+.+|+
T Consensus 61 C~~~i~ 66 (70)
T PF11793_consen 61 CSSPIS 66 (70)
T ss_dssp T-SEEE
T ss_pred CCCeee
Confidence 998874
No 24
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=67.34 E-value=2.2 Score=47.03 Aligned_cols=41 Identities=37% Similarity=0.688 Sum_probs=33.7
Q ss_pred ccccCCccccccccccCCCceeeeecccCCCCCcccccCCCCCccchHHH
Q 021489 22 QLNTNWDDVTCPICLDFPHNGVLLLCSSYEKGCRPFVCDTDHLHSNCLDR 71 (311)
Q Consensus 22 ~l~keWedvtCpICME~PHNAVLLlCSSh~KGCRPYMCdTS~RHSNCLDQ 71 (311)
.+.-+=|.+.|.||--+=|--|||||-+ |+--|-|+-|||=
T Consensus 208 ~~~~~~E~~~C~IC~~~DpEdVLLLCDs---------CN~~~YH~YCLDP 248 (1134)
T KOG0825|consen 208 ISGLSQEEVKCDICTVHDPEDVLLLCDS---------CNKVYYHVYCLDP 248 (1134)
T ss_pred ccCcccccccceeeccCChHHhheeecc---------cccceeeccccCc
Confidence 3444558899999999999999999986 6666788889874
No 25
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=66.66 E-value=4.1 Score=40.73 Aligned_cols=48 Identities=33% Similarity=0.872 Sum_probs=35.3
Q ss_pred ccccccccccCCCceeeeecccCCCCCcccc---cCCCCCccchHHHHHHhhCCCCCCCCccCCccCCCCccCCCCCCcc
Q 021489 28 DDVTCPICLDFPHNGVLLLCSSYEKGCRPFV---CDTDHLHSNCLDRFKNAYGVSPPSTSEVNSAANTQPMVSEDSCRPA 104 (311)
Q Consensus 28 edvtCpICME~PHNAVLLlCSSh~KGCRPYM---CdTS~RHSNCLDQFkka~~~~~~s~s~~~~~~~~~~~~~~~~~~L~ 104 (311)
.+|-|.|||+- +-||=| || |+--| |--|+|.+-.-|. ++
T Consensus 322 ~GveCaICms~-----------fiK~d~-~~vlPC~H~F-H~~Cv~kW~~~y~-------------------------~~ 363 (374)
T COG5540 322 KGVECAICMSN-----------FIKNDR-LRVLPCDHRF-HVGCVDKWLLGYS-------------------------NK 363 (374)
T ss_pred CCceEEEEhhh-----------hcccce-EEEeccCcee-chhHHHHHHhhhc-------------------------cc
Confidence 45889999974 336655 54 77655 5669998877665 78
Q ss_pred Ccccccccc
Q 021489 105 CPLCRGEVT 113 (311)
Q Consensus 105 CPLCRGeVk 113 (311)
||.||-+|.
T Consensus 364 CPvCrt~iP 372 (374)
T COG5540 364 CPVCRTAIP 372 (374)
T ss_pred CCccCCCCC
Confidence 999998873
No 26
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=62.75 E-value=4.4 Score=43.13 Aligned_cols=47 Identities=30% Similarity=0.648 Sum_probs=37.7
Q ss_pred ccccccccCCCceeeeecccCCCCCcccccCCCCCccchHHHHHHhhCCCCCCCCccCCccCCCCccCCCCCCccCcccc
Q 021489 30 VTCPICLDFPHNGVLLLCSSYEKGCRPFVCDTDHLHSNCLDRFKNAYGVSPPSTSEVNSAANTQPMVSEDSCRPACPLCR 109 (311)
Q Consensus 30 vtCpICME~PHNAVLLlCSSh~KGCRPYMCdTS~RHSNCLDQFkka~~~~~~s~s~~~~~~~~~~~~~~~~~~L~CPLCR 109 (311)
..|+||+| |=.+|+-.|. |..|.+.++++-..+. ...||+||
T Consensus 455 ~~c~ic~~-~~~~~it~c~----------------h~~c~~c~~~~i~~~~---------------------~~~~~~cr 496 (674)
T KOG1001|consen 455 HWCHICCD-LDSFFITRCG----------------HDFCVECLKKSIQQSE---------------------NAPCPLCR 496 (674)
T ss_pred cccccccc-cccceeeccc----------------chHHHHHHHhcccccc---------------------CCCCcHHH
Confidence 69999999 8888888774 8999999999865222 12899999
Q ss_pred ccccC
Q 021489 110 GEVTG 114 (311)
Q Consensus 110 GeVkG 114 (311)
+.+.-
T Consensus 497 ~~l~~ 501 (674)
T KOG1001|consen 497 NVLKE 501 (674)
T ss_pred HHHHH
Confidence 98854
No 27
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=60.77 E-value=4.8 Score=40.97 Aligned_cols=43 Identities=28% Similarity=0.511 Sum_probs=32.2
Q ss_pred ccccccCC---ccccccccccCCCc-----eeeeecccCCCCCcccccCCCCCccchHHHHHHh
Q 021489 20 DVQLNTNW---DDVTCPICLDFPHN-----GVLLLCSSYEKGCRPFVCDTDHLHSNCLDRFKNA 75 (311)
Q Consensus 20 d~~l~keW---edvtCpICME~PHN-----AVLLlCSSh~KGCRPYMCdTS~RHSNCLDQFkka 75 (311)
+..++++= .+.+|+||+|.=|+ +-+|.|+. -.|..||-+.-+.
T Consensus 279 ~~~~~~~~~~~~~~~C~IC~e~l~~~~~~~~~rL~C~H-------------ifh~~CL~~W~er 329 (543)
T KOG0802|consen 279 GATLEERGLALSDELCIICLEELHSGHNITPKRLPCGH-------------IFHDSCLRSWFER 329 (543)
T ss_pred ccChHHhhhhhcCCeeeeechhhccccccccceeeccc-------------chHHHHHHHHHHH
Confidence 44444432 48899999998777 78888874 4689999887766
No 28
>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=60.39 E-value=5 Score=28.35 Aligned_cols=19 Identities=32% Similarity=0.672 Sum_probs=16.0
Q ss_pred cccccccccCCCceeeeec
Q 021489 29 DVTCPICLDFPHNGVLLLC 47 (311)
Q Consensus 29 dvtCpICME~PHNAVLLlC 47 (311)
+..||||++..-|.|++.|
T Consensus 1 ~~~Cpi~~~~~~~Pv~~~~ 19 (63)
T smart00504 1 EFLCPISLEVMKDPVILPS 19 (63)
T ss_pred CcCCcCCCCcCCCCEECCC
Confidence 3579999999999998755
No 29
>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=59.01 E-value=4.5 Score=26.74 Aligned_cols=31 Identities=39% Similarity=0.918 Sum_probs=22.0
Q ss_pred ccccccCCCcee-eeecccCCCCCcccccCCCCCccchHHHHHHh
Q 021489 32 CPICLDFPHNGV-LLLCSSYEKGCRPFVCDTDHLHSNCLDRFKNA 75 (311)
Q Consensus 32 CpICME~PHNAV-LLlCSSh~KGCRPYMCdTS~RHSNCLDQFkka 75 (311)
||||++.+-+.+ +|.|- =-.| ..|+.++.+.
T Consensus 1 C~iC~~~~~~~~~~~~C~-------H~fC------~~C~~~~~~~ 32 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCG-------HSFC------RDCLRKWLEN 32 (41)
T ss_dssp ETTTSSBCSSEEEETTTS-------EEEE------HHHHHHHHHH
T ss_pred CCcCCccccCCCEEecCC-------Ccch------HHHHHHHHHh
Confidence 899999999999 66542 2222 4677777776
No 30
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=57.63 E-value=4.1 Score=41.52 Aligned_cols=23 Identities=43% Similarity=0.829 Sum_probs=21.3
Q ss_pred CCccccccccccCCCceeeeecc
Q 021489 26 NWDDVTCPICLDFPHNGVLLLCS 48 (311)
Q Consensus 26 eWedvtCpICME~PHNAVLLlCS 48 (311)
+=||-.||||--+|-|||.--|+
T Consensus 419 ~sEd~lCpICyA~pi~Avf~PC~ 441 (489)
T KOG4692|consen 419 DSEDNLCPICYAGPINAVFAPCS 441 (489)
T ss_pred CcccccCcceecccchhhccCCC
Confidence 45899999999999999999997
No 31
>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=55.06 E-value=11 Score=37.18 Aligned_cols=36 Identities=28% Similarity=0.722 Sum_probs=20.9
Q ss_pred cccccccccc--CCCceeeeecccCCCCCcccccCCCCCccchHHHHH
Q 021489 28 DDVTCPICLD--FPHNGVLLLCSSYEKGCRPFVCDTDHLHSNCLDRFK 73 (311)
Q Consensus 28 edvtCpICME--~PHNAVLLlCSSh~KGCRPYMCdTS~RHSNCLDQFk 73 (311)
++-.||||+. +..+...|+=+ .|-==|| .+|++++-
T Consensus 2 d~~~CP~Ck~~~y~np~~kl~i~----~CGH~~C------~sCv~~l~ 39 (309)
T TIGR00570 2 DDQGCPRCKTTKYRNPSLKLMVN----VCGHTLC------ESCVDLLF 39 (309)
T ss_pred CCCCCCcCCCCCccCcccccccC----CCCCccc------HHHHHHHh
Confidence 4578999999 45555333211 2333334 26999973
No 32
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=55.05 E-value=12 Score=30.74 Aligned_cols=10 Identities=40% Similarity=1.248 Sum_probs=8.1
Q ss_pred CccCcccccc
Q 021489 102 RPACPLCRGE 111 (311)
Q Consensus 102 ~L~CPLCRGe 111 (311)
+-.||+||.+
T Consensus 71 ~~~CPmCR~~ 80 (85)
T PF12861_consen 71 KGQCPMCRQP 80 (85)
T ss_pred CCCCCCcCCe
Confidence 3589999975
No 33
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=53.52 E-value=5.3 Score=31.08 Aligned_cols=9 Identities=56% Similarity=1.527 Sum_probs=8.6
Q ss_pred ccCcccccc
Q 021489 103 PACPLCRGE 111 (311)
Q Consensus 103 L~CPLCRGe 111 (311)
|+||+|+|.
T Consensus 9 LaCP~~kg~ 17 (60)
T COG2835 9 LACPVCKGP 17 (60)
T ss_pred eeccCcCCc
Confidence 899999998
No 34
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.95 E-value=3.8 Score=33.86 Aligned_cols=21 Identities=48% Similarity=1.160 Sum_probs=16.4
Q ss_pred ccccccccccCCCceeeeecc
Q 021489 28 DDVTCPICLDFPHNGVLLLCS 48 (311)
Q Consensus 28 edvtCpICME~PHNAVLLlCS 48 (311)
+.++||||+|.=-..++|-|-
T Consensus 12 ~~~~C~iC~~~~~~p~~l~C~ 32 (386)
T KOG2177|consen 12 EELTCPICLEYFREPVLLPCG 32 (386)
T ss_pred ccccChhhHHHhhcCcccccc
Confidence 789999999976666777553
No 35
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.45 E-value=6 Score=36.63 Aligned_cols=62 Identities=24% Similarity=0.410 Sum_probs=34.9
Q ss_pred ccccCccccccccCCccccccccccCCCceeeeecccCCCCCcccccCCCCCccchHHHHHHhhCCCCCCCCccCCccCC
Q 021489 13 LIACDMEDVQLNTNWDDVTCPICLDFPHNGVLLLCSSYEKGCRPFVCDTDHLHSNCLDRFKNAYGVSPPSTSEVNSAANT 92 (311)
Q Consensus 13 ~~~~~~ed~~l~keWedvtCpICME~PHNAVLLlCSSh~KGCRPYMCdTS~RHSNCLDQFkka~~~~~~s~s~~~~~~~~ 92 (311)
+..++-.++.+.++ .-+.|||||+.=-.-|. ---+|--=|+++..+.+-
T Consensus 116 p~~~~k~v~~~~~~-~~~~CPiCl~~~sek~~-------------------vsTkCGHvFC~~Cik~al----------- 164 (187)
T KOG0320|consen 116 PNRRDKDVDPLRKE-GTYKCPICLDSVSEKVP-------------------VSTKCGHVFCSQCIKDAL----------- 164 (187)
T ss_pred CCcccccccccccc-cccCCCceecchhhccc-------------------cccccchhHHHHHHHHHH-----------
Confidence 33444423333333 44899999985333332 123666677777765431
Q ss_pred CCccCCCCCCccCccccccc
Q 021489 93 QPMVSEDSCRPACPLCRGEV 112 (311)
Q Consensus 93 ~~~~~~~~~~L~CPLCRGeV 112 (311)
...-.||+||-+|
T Consensus 165 -------k~~~~CP~C~kkI 177 (187)
T KOG0320|consen 165 -------KNTNKCPTCRKKI 177 (187)
T ss_pred -------HhCCCCCCccccc
Confidence 1236799999755
No 36
>PRK11827 hypothetical protein; Provisional
Probab=48.31 E-value=7.6 Score=29.93 Aligned_cols=12 Identities=42% Similarity=1.005 Sum_probs=10.3
Q ss_pred CccCcccccccc
Q 021489 102 RPACPLCRGEVT 113 (311)
Q Consensus 102 ~L~CPLCRGeVk 113 (311)
-|+||+|.|++.
T Consensus 8 ILaCP~ckg~L~ 19 (60)
T PRK11827 8 IIACPVCNGKLW 19 (60)
T ss_pred heECCCCCCcCe
Confidence 389999999875
No 37
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.82 E-value=8.5 Score=38.33 Aligned_cols=20 Identities=40% Similarity=0.929 Sum_probs=18.3
Q ss_pred cccccccccCCCceeeeecc
Q 021489 29 DVTCPICLDFPHNGVLLLCS 48 (311)
Q Consensus 29 dvtCpICME~PHNAVLLlCS 48 (311)
+-.|-|||+-|-..|||-|-
T Consensus 300 ~~LC~ICmDaP~DCvfLeCG 319 (350)
T KOG4275|consen 300 RRLCAICMDAPRDCVFLECG 319 (350)
T ss_pred HHHHHHHhcCCcceEEeecC
Confidence 66799999999999999983
No 38
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=42.18 E-value=12 Score=26.68 Aligned_cols=16 Identities=50% Similarity=1.267 Sum_probs=7.5
Q ss_pred ccccccC--CCc-eeeeec
Q 021489 32 CPICLDF--PHN-GVLLLC 47 (311)
Q Consensus 32 CpICME~--PHN-AVLLlC 47 (311)
||||.|+ +.| +|+|.|
T Consensus 1 CpIc~e~~~~~n~P~~L~C 19 (43)
T PF13445_consen 1 CPICKEFSTEENPPMVLPC 19 (43)
T ss_dssp -TTT----TTSS-EEE-SS
T ss_pred CCccccccCCCCCCEEEeC
Confidence 8999994 222 688876
No 39
>PF10614 CsgF: Type VIII secretion system (T8SS), CsgF protein; InterPro: IPR018893 Fimbriae are cell-surface protein polymers, of e.g. Escherichia coli and Salmonella spp, that mediate interactions important for host and environmental persistence, development of biofilms, motility, colonisation and invasion of cells, and conjugation. Four general assembly pathways for different fimbriae have been proposed, one of which is extracellular nucleation-precipitation (ENP), that differs from the others in that fibre-growth occurs extracellularly. Thin aggregative fimbriae (Tafi) are the only fimbriae dependent on the ENP pathway. Tafi were first identified in Salmonella spp. and the controlling operon termed agf; however subsequent isolation of the homologous operon in E. coli led to its being called csg. Tafi are known as curli because, in the absence of extracellular polysaccharides, their morphology appears curled; however, when expressed with such polysaccharides their morphology appears as a tangled amorphous matrix []. CsgF is one of three putative curli assembly factors appearing to act as a nucleator protein. Unlike eukaryotic amyloid formation, curli biogenesis is a productive pathway requiring a specific assembly machinery [].
Probab=41.05 E-value=85 Score=27.90 Aligned_cols=65 Identities=22% Similarity=0.172 Sum_probs=43.4
Q ss_pred cHHHHHHhhhhhCCCCCCCCCC------chhHHHHHHhhhhhhhhhHHHHhhcc-------CCCceeecceeeecCCC
Q 021489 142 TYLELRKHAQLEHPHSRPSKID------PARQLDWENFQQSSEIIDVLSTIHSE-------VPRGVVLGDYVIEYGDD 206 (311)
Q Consensus 142 tY~eLrKHar~~HP~arP~eVD------P~rq~~W~~lE~ere~~DviStI~S~-------~PgavV~GDYVIE~gdd 206 (311)
+|.-|-..|..--....|..-| +.-..+...--+.+=+..|.+-|... -||.+.+|||.||.-+.
T Consensus 39 Ngs~LL~~A~AQN~~~dp~~~~~~~~~~~S~l~~F~~sLqsqlls~l~~~i~~~~fGe~~~~~Gt~~~gdf~I~i~~~ 116 (142)
T PF10614_consen 39 NGSWLLSSAQAQNDFKDPSAEDDFSTSSLSALDRFTQSLQSQLLSQLSRDITQGIFGEDPQKPGTFTTGDFTIEIVNS 116 (142)
T ss_pred cHHHHhhhhhhcCCcCCCccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCCceEEECCEEEEEEeC
Confidence 4667778888777777777753 22333343333445566666666655 79999999999996544
No 40
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=40.89 E-value=9.6 Score=39.53 Aligned_cols=15 Identities=40% Similarity=0.931 Sum_probs=13.4
Q ss_pred ccCccccccccCEEE
Q 021489 103 PACPLCRGEVTGWVV 117 (311)
Q Consensus 103 L~CPLCRGeVkGWtV 117 (311)
-.||.||-|||||.-
T Consensus 406 q~CPFCRcEIKGte~ 420 (563)
T KOG1785|consen 406 QTCPFCRCEIKGTEP 420 (563)
T ss_pred CCCCceeeEeccccc
Confidence 579999999999983
No 41
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=38.21 E-value=23 Score=19.96 Aligned_cols=18 Identities=33% Similarity=0.560 Sum_probs=13.2
Q ss_pred cccc-ccHHHHHHhhhhhC
Q 021489 137 CTFA-GTYLELRKHAQLEH 154 (311)
Q Consensus 137 CsF~-GtY~eLrKHar~~H 154 (311)
|.+. .++.+|++|++..|
T Consensus 6 C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 6 CGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp TS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCcHHHHHHHHHhhC
Confidence 4443 57889999999877
No 42
>KOG1006 consensus Mitogen-activated protein kinase (MAPK) kinase MKK4 [Signal transduction mechanisms]
Probab=38.18 E-value=13 Score=37.27 Aligned_cols=12 Identities=33% Similarity=1.121 Sum_probs=10.1
Q ss_pred ccCCCCCccccc
Q 021489 48 SSYEKGCRPFVC 59 (311)
Q Consensus 48 SSh~KGCRPYMC 59 (311)
-+++-||||||=
T Consensus 224 kT~daGCrpYmA 235 (361)
T KOG1006|consen 224 KTVDAGCRPYMA 235 (361)
T ss_pred hhhccCCccccC
Confidence 368899999995
No 43
>PHA02862 5L protein; Provisional
Probab=36.30 E-value=44 Score=30.39 Aligned_cols=62 Identities=19% Similarity=0.352 Sum_probs=42.3
Q ss_pred cccccccccCCCceeeeecccCCCCCcccccCCC--CCccchHHHHHHhhCCCCCCCCccCCccCCCCccCCCCCCccCc
Q 021489 29 DVTCPICLDFPHNGVLLLCSSYEKGCRPFVCDTD--HLHSNCLDRFKNAYGVSPPSTSEVNSAANTQPMVSEDSCRPACP 106 (311)
Q Consensus 29 dvtCpICME~PHNAVLLlCSSh~KGCRPYMCdTS--~RHSNCLDQFkka~~~~~~s~s~~~~~~~~~~~~~~~~~~L~CP 106 (311)
+..|-||.+.=... =+|=-|.-+ +-|..||.|.-+. +.+-.||
T Consensus 2 ~diCWIC~~~~~e~-----------~~PC~C~GS~K~VHq~CL~~WIn~------------------------S~k~~Ce 46 (156)
T PHA02862 2 SDICWICNDVCDER-----------NNFCGCNEEYKVVHIKCMQLWINY------------------------SKKKECN 46 (156)
T ss_pred CCEEEEecCcCCCC-----------cccccccCcchhHHHHHHHHHHhc------------------------CCCcCcc
Confidence 35788998863222 156677544 6699999999943 1235799
Q ss_pred cccccccCEEEcchhHHhh
Q 021489 107 LCRGEVTGWVVADKVRDYL 125 (311)
Q Consensus 107 LCRGeVkGWtVVe~AR~~L 125 (311)
||+.+-.==+.-.|-|++.
T Consensus 47 LCkteY~Ik~~yKpf~kW~ 65 (156)
T PHA02862 47 LCKTKYNIKKTYVSFKKWN 65 (156)
T ss_pred CCCCeEEEEEccccHHHhh
Confidence 9999876444556777774
No 44
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.75 E-value=25 Score=35.05 Aligned_cols=57 Identities=23% Similarity=0.442 Sum_probs=38.3
Q ss_pred cccccccccCCCceeeeecccCCCCCcccccCCCCCccchHHHHHHhhCCCCCCCCccCCccCCCCccCCCCCCccCccc
Q 021489 29 DVTCPICLDFPHNGVLLLCSSYEKGCRPFVCDTDHLHSNCLDRFKNAYGVSPPSTSEVNSAANTQPMVSEDSCRPACPLC 108 (311)
Q Consensus 29 dvtCpICME~PHNAVLLlCSSh~KGCRPYMCdTS~RHSNCLDQFkka~~~~~~s~s~~~~~~~~~~~~~~~~~~L~CPLC 108 (311)
+.-|+||.--|---|-|-|- |--|.---|.+|- ..++.||+|
T Consensus 7 ~~eC~IC~nt~n~Pv~l~C~----------------HkFCyiCiKGsy~----------------------ndk~~CavC 48 (324)
T KOG0824|consen 7 KKECLICYNTGNCPVNLYCF----------------HKFCYICIKGSYK----------------------NDKKTCAVC 48 (324)
T ss_pred CCcceeeeccCCcCcccccc----------------chhhhhhhcchhh----------------------cCCCCCcee
Confidence 45799998766656777662 3334433444433 456789999
Q ss_pred cccccCEEEcchhHH
Q 021489 109 RGEVTGWVVADKVRD 123 (311)
Q Consensus 109 RGeVkGWtVVe~AR~ 123 (311)
|++|-.-...+|--+
T Consensus 49 R~pids~i~~~psl~ 63 (324)
T KOG0824|consen 49 RFPIDSTIDFEPSLK 63 (324)
T ss_pred cCCCCcchhcchhhh
Confidence 999988887777655
No 45
>KOG4029 consensus Transcription factor HAND2/Transcription factor TAL1/TAL2/LYL1 [Transcription]
Probab=34.98 E-value=27 Score=31.66 Aligned_cols=48 Identities=21% Similarity=0.264 Sum_probs=39.8
Q ss_pred cchhHHhhccccCcCcccCccccccHHHHHHhhhhhCC-CCCCCCCCchhHH
Q 021489 118 ADKVRDYLNEKKRCCEEDQCTFAGTYLELRKHAQLEHP-HSRPSKIDPARQL 168 (311)
Q Consensus 118 Ve~AR~~LN~K~RsC~~e~CsF~GtY~eLrKHar~~HP-~arP~eVDP~rq~ 168 (311)
....|...|++ +-+--..+..-|.+||+|+=.+++ ..|-++||..|..
T Consensus 106 ~~~~~~~~n~R---ER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A 154 (228)
T KOG4029|consen 106 TSAQRQARNAR---ERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLA 154 (228)
T ss_pred hhhhhhhhhhh---hhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHH
Confidence 34567778877 444555999999999999999999 9999999998865
No 46
>PF15060 PPDFL: Differentiation and proliferation regulator
Probab=33.39 E-value=20 Score=30.86 Aligned_cols=15 Identities=33% Similarity=0.882 Sum_probs=12.0
Q ss_pred CCCCcceeeehhhhc
Q 021489 218 DEGNWWTSCILYQVF 232 (311)
Q Consensus 218 ~~g~w~Ts~~l~~~f 232 (311)
+.|.||.+|||-+-.
T Consensus 50 d~g~WW~sfFF~k~~ 64 (110)
T PF15060_consen 50 DPGHWWASFFFGKST 64 (110)
T ss_pred CCCcceEEeEecccc
Confidence 569999999987643
No 47
>PF11396 DUF2874: Protein of unknown function (DUF2874); InterPro: IPR021533 This bacterial family of proteins are probable periplasmic proteins with unknown function. There are between one and four copies of this domain per sequence. ; PDB: 3DUE_A 3U1W_B 3DB7_A 4DSD_A 3ELG_A.
Probab=32.14 E-value=25 Score=24.92 Aligned_cols=40 Identities=28% Similarity=0.550 Sum_probs=24.0
Q ss_pred hHHHHhhccCCCceee----------cceeeecCCCCCCCCCCCCCCCCCCc
Q 021489 181 DVLSTIHSEVPRGVVL----------GDYVIEYGDDETGDEFEDFPGDEGNW 222 (311)
Q Consensus 181 DviStI~S~~PgavV~----------GDYVIE~gdd~~~d~~e~~~~~~g~w 222 (311)
-|..+|.+.+||+.|. +-|.|+.. -++++.+..=..+|+|
T Consensus 11 ~v~~~i~~~yp~~~i~~v~~~~~~~~~~Y~v~l~--~~~~~~~v~fd~~G~~ 60 (61)
T PF11396_consen 11 AVKNAIKKNYPGAKIKEVEKETDPGGKYYEVELK--KGGNEYEVYFDANGNW 60 (61)
T ss_dssp HHHHHHHHHSTTSEEEEEEEEEETTEEEEEEEET--ETTTSEEEEEETTS-E
T ss_pred HHHHHHHHHCCCCeEEEEEEEEcCCCCEEEEEEE--EeCCeEEEEEcCCCCC
Confidence 4678899999999887 55666655 2233333333345665
No 48
>PRK04028 glutamyl-tRNA(Gln) amidotransferase subunit E; Validated
Probab=28.30 E-value=21 Score=37.99 Aligned_cols=13 Identities=46% Similarity=0.820 Sum_probs=11.3
Q ss_pred cccccccccc--CCC
Q 021489 28 DDVTCPICLD--FPH 40 (311)
Q Consensus 28 edvtCpICME--~PH 40 (311)
.+.+|||||. +||
T Consensus 78 n~~~c~v~~~~~~P~ 92 (630)
T PRK04028 78 NDTTCLVEADEEPPH 92 (630)
T ss_pred CCCcCccccCCCCCC
Confidence 3789999999 698
No 49
>PRK10050 curli assembly protein CsgF; Provisional
Probab=27.89 E-value=1.9e+02 Score=25.90 Aligned_cols=63 Identities=24% Similarity=0.265 Sum_probs=38.6
Q ss_pred cHHHHHHhhhhhCCCCCCCCCCc---hhH---HHHHHhhhhhhhhhHHHHhhccCCCceeecceeeecC
Q 021489 142 TYLELRKHAQLEHPHSRPSKIDP---ARQ---LDWENFQQSSEIIDVLSTIHSEVPRGVVLGDYVIEYG 204 (311)
Q Consensus 142 tY~eLrKHar~~HP~arP~eVDP---~rq---~~W~~lE~ere~~DviStI~S~~PgavV~GDYVIE~g 204 (311)
||.-|-..|..-.-...|...|. .-+ .....=-+.+=+.-+.+.|...-||-+.+|||-||.-
T Consensus 37 N~s~Ll~~A~AQN~~~dp~~~~~~~~~~~sald~F~~sLqs~Lls~L~~~i~~G~~G~~~tgd~~i~i~ 105 (138)
T PRK10050 37 NGAFLLNSAQAQNSYKDPSYNDDFGIETPSALDNFTQAIQSQILGGLLSNINTGKPGRMVTNDYIVDIA 105 (138)
T ss_pred cHHHHHHHhhhcccccCCcccccccccchhHHHHHHHHHHHHHHHHHHhhccCCCCceEEECCEEEEEE
Confidence 35667777766665666655553 222 2222222334455666666667799999999999954
No 50
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.59 E-value=33 Score=34.17 Aligned_cols=130 Identities=21% Similarity=0.389 Sum_probs=70.7
Q ss_pred ccccccccccC----CC----ceeeeecccCCCCCcccccCCCCCccchHHHHHHhhCCCCCCCCccCCccCCCCccCCC
Q 021489 28 DDVTCPICLDF----PH----NGVLLLCSSYEKGCRPFVCDTDHLHSNCLDRFKNAYGVSPPSTSEVNSAANTQPMVSED 99 (311)
Q Consensus 28 edvtCpICME~----PH----NAVLLlCSSh~KGCRPYMCdTS~RHSNCLDQFkka~~~~~~s~s~~~~~~~~~~~~~~~ 99 (311)
++..|-||||- +| +++|+.| --.+|-.=+|..+|..|| . .
T Consensus 160 ~~k~CGICme~i~ek~~~~~rfgilpnC-------~H~~Cl~Cir~wr~~~q~------~-------------------~ 207 (344)
T KOG1039|consen 160 SEKECGICMETINEKAASERRFGILPNC-------NHSFCLNCIRKWRQATQF------E-------------------S 207 (344)
T ss_pred ccccceehhhhccccchhhhhcccCCCc-------chhhhhcHhHhhhhhhcc------c-------------------c
Confidence 47899999984 21 3344444 344555444444444444 1 1
Q ss_pred CCCccCcccccccc------CEEEcchh-----HHhhcc-ccCcCc-----ccCccc--cccHHHHHHhhhhhCCCCCCC
Q 021489 100 SCRPACPLCRGEVT------GWVVADKV-----RDYLNE-KKRCCE-----EDQCTF--AGTYLELRKHAQLEHPHSRPS 160 (311)
Q Consensus 100 ~~~L~CPLCRGeVk------GWtVVe~A-----R~~LN~-K~RsC~-----~e~CsF--~GtY~eLrKHar~~HP~arP~ 160 (311)
.+.-.||.||...+ .|.+-++. .+|.++ +.+-|. .-.|-| .-.|+.+--++...-|...+.
T Consensus 208 ~~sksCP~CRv~s~~v~pS~~Wv~t~~~k~~li~e~~~~~s~~~c~yf~~~~g~cPf~s~~~y~h~~~~~~~~~~~~~~~ 287 (344)
T KOG1039|consen 208 KTSKSCPFCRVPSSFVNPSSFWVETKEEKQKLIEEYEAEMSAKDCKYFSQGLGSCPFGSKCFYKHLLPSGASTDPGRQYS 287 (344)
T ss_pred ccccCCCcccCccccccccceeeeecccccccHHHHHHHhhccchhhhcCCCCCCCCCCccccccccccccccccCCCCc
Confidence 23467999998754 48876442 222221 122221 122333 223555556666666655555
Q ss_pred CCCchhHHHHHHhhhhhhhhhHHHHhhcc
Q 021489 161 KIDPARQLDWENFQQSSEIIDVLSTIHSE 189 (311)
Q Consensus 161 eVDP~rq~~W~~lE~ere~~DviStI~S~ 189 (311)
..=|..+-.|...+.+-+..+.++-..+.
T Consensus 288 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 316 (344)
T KOG1039|consen 288 PRRPSNLNTYTNILETTLTLRSLERNLSS 316 (344)
T ss_pred ccccccCcchhhcccceeehhhhhhhhhh
Confidence 66667777777776666666666554443
No 51
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=23.56 E-value=43 Score=22.95 Aligned_cols=17 Identities=29% Similarity=0.657 Sum_probs=12.3
Q ss_pred cccccccCC---Cceeeeec
Q 021489 31 TCPICLDFP---HNGVLLLC 47 (311)
Q Consensus 31 tCpICME~P---HNAVLLlC 47 (311)
.|+||.+.. +.++||.|
T Consensus 1 ~C~~C~~~~~~~~~~~l~~C 20 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSC 20 (44)
T ss_pred CCcCcCccccCCCCeEEccc
Confidence 389999988 45666655
No 52
>KOG0754 consensus Mitochondrial oxodicarboxylate carrier protein [Energy production and conversion]
Probab=23.02 E-value=44 Score=32.88 Aligned_cols=35 Identities=14% Similarity=0.387 Sum_probs=29.8
Q ss_pred cCCccccccccccCCCceeeeecccCCCCCcccccCCCCCccchHHHHHHhhCCCC
Q 021489 25 TNWDDVTCPICLDFPHNGVLLLCSSYEKGCRPFVCDTDHLHSNCLDRFKNAYGVSP 80 (311)
Q Consensus 25 keWedvtCpICME~PHNAVLLlCSSh~KGCRPYMCdTS~RHSNCLDQFkka~~~~~ 80 (311)
.-|+...=|||||-|-.|+=.+ |.||||+.+.-.+
T Consensus 67 ~lykGI~pPIl~EtPKRa~KF~---------------------~~eq~K~~F~~~~ 101 (294)
T KOG0754|consen 67 SLYKGILPPILMETPKRATKFL---------------------TNEQYKKLFQFGN 101 (294)
T ss_pred hhhccCCCHHhhhcchhhhhhc---------------------cHHHHHHHhcCCC
Confidence 4699999999999999998654 5799999998654
No 53
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=22.43 E-value=34 Score=31.97 Aligned_cols=40 Identities=25% Similarity=0.445 Sum_probs=18.0
Q ss_pred ccCCccccccccccCCCceeeeecccCCCC---CcccccCCCCCc
Q 021489 24 NTNWDDVTCPICLDFPHNGVLLLCSSYEKG---CRPFVCDTDHLH 65 (311)
Q Consensus 24 ~keWedvtCpICME~PHNAVLLlCSSh~KG---CRPYMCdTS~RH 65 (311)
...|..-.||||-..|.=+||.-=-. .| ..--+|+|..++
T Consensus 167 ~~~w~~g~CPvCGs~P~~s~l~~~~~--~G~R~L~Cs~C~t~W~~ 209 (290)
T PF04216_consen 167 PEGWQRGYCPVCGSPPVLSVLRGGER--EGKRYLHCSLCGTEWRF 209 (290)
T ss_dssp ---TT-SS-TTT---EEEEEEE--------EEEEEETTT--EEE-
T ss_pred cCCccCCcCCCCCCcCceEEEecCCC--CccEEEEcCCCCCeeee
Confidence 46899999999999999999864322 13 233467777654
No 54
>PF00653 BIR: Inhibitor of Apoptosis domain; InterPro: IPR001370 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The baculovirus inhibitor of apoptosis protein repeat (BIR) is a domain of tandem repeats separated by a variable length linker that seems to confer cell death-preventing activity [, ]. The BIR domains characterise the Inhibitor of Apoptosis (IAP) family of proteins (MEROPS proteinase inhibitor family I32, clan IV) that suppress apoptosis by interacting with and inhibiting the enzymatic activity of both initiator and effector caspases (MEROPS peptidase family C14, IPR002398 from INTERPRO). Several distinct mammalian IAPs including XIAP, c-IAP1, c-IAP2, and ML-IAP, have been identified, and they all exhibit antiapoptotic activity in cell culture. The functional unit in each IAP protein is the baculoviral IAP repeat (BIR), which contains approximately 80 amino acids folded around a zinc atom. Most mammalian IAPs have more than one BIR domain, with the different BIR domains performing distinct functions. For example, in XIAP, the third BIR domain (BIR3) potently inhibits the catalytic activity of caspase-9, whereas the linker sequences immediately preceding the second BIR domain (BIR2) selectively targets caspase-3 or -7. The first-recognised members of family MEROPS inhibitor family I32 were viral proteins that inhibited the apoptosis of infected cells: Cp-IAP from Cydia pomonella granulosis virus (CpGV) [] and Op-IAP from Orgyia pseudotsugata multicapsid polyhedrosis virus(OpMNPV) []. The discovery of homologous proteins in mammals followed soon after with the recognition that mutations in the gene for neuronal apoptosis inhibitory protein (NIAP) underlie spinal muscular atrophy []. The inhibitors in family I32 all possess one or more 80-residue domains known as BIR (baculovirus inhibitor repeat) domains and have accordingly been termed 'BIR-containing' or 'BIRC' proteins as well as IAP proteins. The mechanism of inhibition of caspases by the IAP proteins is complex, and reactive site residues cannot yet be identified with any confidence. Despite the conservation of the BIR or IAP (inhibitor of apoptosis) domains throughout the family it seems clear that other parts of the molecules also make essential contributions to inhibitory activity. Homologs of most components in the mammalian apoptotic pathway have been identified in fruit flies. The Drosophila Apaf-1, known as Dapaf-1, HAC-1 or Dark, shares significant sequence similarity with its mammalian counterpart, and is critically important for the activation of the Drosophila initiator caspase Dronc. Dronc, in turn, cleaves and activates the effector caspase DrICE. The Drosophila IAP, DIAP1, binds to and in-activates both DrICE and Dronc through its BIR1 and BIR2 domains. During apoptosis, the anti-death function of DIAP1 is countered by at least four pro-apoptotic proteins, Reaper, Hid, Grim, and sickle, through direct physical interactions. These four proteins represent the functional homologs of the mammalian protein Smac, and they all share a conserved IAP-binding motif at their N termini. The three proteins Reaper, Hid, and Grim are collectively referred to as the RHG proteins [, ]. Both XIAP and DIAP1 contain a RING domain at their C termini, and can act as an E3 ubiquitin ligase. Indeed, both XIAP and DIAP1 have been shown to promote self-ubiquitination and degradation as well as to negatively regulate the target caspases. Nonetheless, important differences exist between XIAP and DIAP1. The primary function of XIAP is thought to inhibit the catalytic activities of caspases; to what extent the ubiquitinating activity of XIAP contributes to its function remains unclear. For DIAP1, however, the ubiquitinating activity appears to be essential for its function. Recently a Drosophila p53 protein has been identified that mediates apoptosis via a novel pathway involving the activation of the Reaper gene and subsequent inhibition of the inhibitors of apoptosis (IAPs). CIAP1, a major mammalian homologue of Drosophila IAPs, is irreversibly inhibited (cleaved) during p53-dependent apoptosis and this cleavage is mediated by a serine protease. Serine protease inhibitors that block CIAP1 cleavage inhibit p53-dependent apoptosis. Furthermore, activation of the p53 protein increases the transcription of the HTRA2 gene, which encodes a serine protease that interacts with CIAP1 and potentiates apoptosis. Therefore mammalian p53 protein activates apoptosis through a novel pathway functionally similar to that in Drosophila, which involves HTRA2 and subsequent inhibition of CIAP1 by cleavage [].; GO: 0005622 intracellular; PDB: 3HL5_B 3UW5_A 3CM7_A 1G3F_A 1G73_C 3G76_G 3CM2_C 2VSL_A 2OPZ_B 3CLX_A ....
Probab=20.98 E-value=20 Score=26.76 Aligned_cols=31 Identities=19% Similarity=0.325 Sum_probs=24.2
Q ss_pred CCCccCccccccccCEEEc-chhHHhhccccC
Q 021489 100 SCRPACPLCRGEVTGWVVA-DKVRDYLNEKKR 130 (311)
Q Consensus 100 ~~~L~CPLCRGeVkGWtVV-e~AR~~LN~K~R 130 (311)
.....|..|...|.+|... +|..+|.+..+.
T Consensus 34 ~d~v~C~~C~~~l~~w~~~Ddp~~~H~~~sp~ 65 (70)
T PF00653_consen 34 GDRVRCFYCGLELDNWEPNDDPWEEHKRHSPN 65 (70)
T ss_dssp TTEEEETTTTEEEES-STT--HHHHHHHHSTT
T ss_pred CCEEEEeccCCEEeCCCCCCCHHHHHHHHCcC
Confidence 4579999999999999965 688888887773
No 55
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=20.86 E-value=39 Score=21.75 Aligned_cols=8 Identities=50% Similarity=1.613 Sum_probs=5.7
Q ss_pred cccccccc
Q 021489 30 VTCPICLD 37 (311)
Q Consensus 30 vtCpICME 37 (311)
|.||||-.
T Consensus 2 v~CPiC~~ 9 (26)
T smart00734 2 VQCPVCFR 9 (26)
T ss_pred CcCCCCcC
Confidence 57888854
Done!