Query 039690
Match_columns 216
No_of_seqs 181 out of 674
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 12:14:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039690.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039690hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12428 DUF3675: Protein of u 100.0 1.4E-46 3E-51 300.3 10.3 118 47-167 1-118 (118)
2 KOG1609 Protein involved in mR 99.7 1.3E-19 2.8E-24 158.7 -2.5 185 7-192 95-282 (323)
3 PHA02825 LAP/PHD finger-like p 99.6 1.5E-16 3.2E-21 133.2 4.0 65 6-84 19-83 (162)
4 smart00744 RINGv The RING-vari 99.5 4.3E-15 9.2E-20 102.0 3.8 42 1-42 8-49 (49)
5 PF12906 RINGv: RING-variant d 99.5 9.2E-15 2E-19 99.6 0.3 39 3-41 9-47 (47)
6 PHA02862 5L protein; Provision 99.4 6.1E-14 1.3E-18 116.3 3.5 40 9-48 16-55 (156)
7 COG5183 SSM4 Protein involved 99.4 3.3E-13 7.1E-18 134.9 4.4 59 1-59 21-81 (1175)
8 KOG3053 Uncharacterized conser 99.2 6.8E-12 1.5E-16 112.4 3.0 48 7-54 37-90 (293)
9 PF13639 zf-RING_2: Ring finge 94.2 0.019 4.1E-07 37.5 0.7 22 19-42 23-44 (44)
10 PF12861 zf-Apc11: Anaphase-pr 93.0 0.072 1.6E-06 41.0 2.2 30 19-48 54-84 (85)
11 PF12678 zf-rbx1: RING-H2 zinc 89.2 0.21 4.4E-06 36.5 1.4 22 19-42 52-73 (73)
12 cd00162 RING RING-finger (Real 88.6 0.42 9.1E-06 29.4 2.3 25 19-44 20-44 (45)
13 KOG1493 Anaphase-promoting com 86.4 0.47 1E-05 36.3 1.8 30 18-47 52-82 (84)
14 smart00184 RING Ring finger. E 85.3 1.3 2.8E-05 26.0 3.2 31 5-41 9-39 (39)
15 PF13920 zf-C3HC4_3: Zinc fing 81.7 1.1 2.5E-05 29.8 2.0 36 4-46 12-48 (50)
16 COG5243 HRD1 HRD ubiquitin lig 80.7 1.2 2.7E-05 42.9 2.5 33 19-53 320-352 (491)
17 COG5194 APC11 Component of SCF 79.6 1.4 3.1E-05 34.0 2.1 26 20-47 57-82 (88)
18 smart00504 Ubox Modified RING 79.1 1.7 3.7E-05 29.5 2.2 34 6-46 13-46 (63)
19 COG4420 Predicted membrane pro 79.0 25 0.00054 30.9 9.8 49 115-163 60-110 (191)
20 PF06210 DUF1003: Protein of u 78.5 24 0.00051 28.0 8.8 49 115-163 6-56 (108)
21 PF11793 FANCL_C: FANCL C-term 78.4 0.64 1.4E-05 33.8 -0.1 31 18-48 29-68 (70)
22 KOG4628 Predicted E3 ubiquitin 73.7 2.1 4.6E-05 40.5 2.0 32 9-46 247-278 (348)
23 PLN03208 E3 ubiquitin-protein 71.2 4.4 9.4E-05 35.5 3.2 28 19-46 38-79 (193)
24 PF00097 zf-C3HC4: Zinc finger 70.6 3.7 8E-05 25.8 2.0 23 19-41 19-41 (41)
25 KOG2930 SCF ubiquitin ligase, 64.3 4.8 0.00011 32.4 1.9 26 20-47 84-109 (114)
26 KOG0827 Predicted E3 ubiquitin 57.5 6.8 0.00015 38.1 2.0 23 20-42 29-52 (465)
27 PF05191 ADK_lid: Adenylate ki 57.5 4.7 0.0001 26.1 0.7 18 36-53 2-19 (36)
28 KOG0802 E3 ubiquitin ligase [P 56.6 6.5 0.00014 38.6 1.7 26 18-45 315-340 (543)
29 PF08746 zf-RING-like: RING-li 56.0 6 0.00013 26.3 1.0 21 21-41 23-43 (43)
30 PF14570 zf-RING_4: RING/Ubox 49.8 20 0.00043 24.9 2.8 35 6-46 12-48 (48)
31 PF14634 zf-RING_5: zinc-RING 45.1 22 0.00048 23.0 2.4 32 5-43 13-44 (44)
32 PF00301 Rubredoxin: Rubredoxi 45.1 10 0.00022 26.0 0.7 34 36-70 2-36 (47)
33 smart00782 PhnA_Zn_Ribbon PhnA 43.7 21 0.00046 24.5 2.2 31 32-62 4-35 (47)
34 KOG1734 Predicted RING-contain 43.2 7.1 0.00015 36.4 -0.3 28 20-47 255-282 (328)
35 cd00730 rubredoxin Rubredoxin; 42.4 21 0.00046 24.7 2.0 17 36-52 2-18 (50)
36 KOG0823 Predicted E3 ubiquitin 40.9 17 0.00037 32.8 1.7 38 3-45 56-94 (230)
37 PF13894 zf-C2H2_4: C2H2-type 40.7 11 0.00024 20.2 0.3 11 37-47 2-12 (24)
38 PF09788 Tmemb_55A: Transmembr 40.1 39 0.00085 30.9 3.9 61 107-167 189-249 (256)
39 PF12273 RCR: Chitin synthesis 39.9 34 0.00074 27.2 3.2 32 154-185 7-38 (130)
40 PF05210 Sprouty: Sprouty prot 38.9 19 0.00041 28.9 1.5 24 4-32 53-77 (108)
41 PF09607 BrkDBD: Brinker DNA-b 38.0 21 0.00044 25.8 1.5 21 13-33 23-49 (58)
42 COG2322 Predicted membrane pro 37.3 1.3E+02 0.0027 26.3 6.3 55 114-168 84-143 (177)
43 PF07301 DUF1453: Protein of u 36.5 1.5E+02 0.0032 25.0 6.5 53 115-174 95-147 (148)
44 PF11874 DUF3394: Domain of un 36.4 16 0.00034 31.8 0.8 21 156-176 162-182 (183)
45 PF00096 zf-C2H2: Zinc finger, 35.4 13 0.00029 20.4 0.1 11 37-47 2-12 (23)
46 PF13923 zf-C3HC4_2: Zinc fing 35.1 30 0.00065 21.7 1.8 20 20-41 20-39 (39)
47 PF10571 UPF0547: Uncharacteri 30.5 25 0.00054 21.2 0.7 13 34-46 13-25 (26)
48 PF15227 zf-C3HC4_4: zinc fing 28.9 34 0.00073 22.3 1.2 19 23-41 22-42 (42)
49 TIGR00599 rad18 DNA repair pro 28.2 44 0.00096 32.2 2.4 33 7-46 39-71 (397)
50 COG1983 PspC Putative stress-r 27.7 70 0.0015 23.9 2.9 15 152-166 45-59 (70)
51 COG4846 CcdC Membrane protein 27.4 1.6E+02 0.0035 25.0 5.2 45 115-161 96-140 (163)
52 PF12874 zf-met: Zinc-finger o 26.2 24 0.00052 19.8 0.1 11 37-47 2-12 (25)
53 COG1773 Rubredoxin [Energy pro 25.9 57 0.0012 23.3 2.0 35 35-70 3-38 (55)
54 PF05290 Baculo_IE-1: Baculovi 25.9 85 0.0018 26.4 3.3 44 3-47 90-133 (140)
55 PF13465 zf-H2C2_2: Zinc-finge 25.8 30 0.00065 20.2 0.5 14 33-46 12-25 (26)
56 PF13878 zf-C2H2_3: zinc-finge 25.4 36 0.00077 22.4 0.9 16 34-49 12-27 (41)
57 PF13913 zf-C2HC_2: zinc-finge 25.3 29 0.00063 20.4 0.4 12 36-47 3-14 (25)
58 PF05129 Elf1: Transcription e 24.9 11 0.00024 28.4 -1.9 30 33-69 44-73 (81)
59 cd00924 Cyt_c_Oxidase_Vb Cytoc 24.8 19 0.0004 28.2 -0.7 24 28-51 72-95 (97)
60 smart00451 ZnF_U1 U1-like zinc 24.6 36 0.00079 20.4 0.8 13 34-46 2-14 (35)
61 PF01363 FYVE: FYVE zinc finge 24.0 19 0.00041 25.2 -0.7 20 28-47 2-21 (69)
62 PF04564 U-box: U-box domain; 23.8 59 0.0013 23.3 1.9 27 19-46 24-50 (73)
63 KOG0825 PHD Zn-finger protein 23.4 43 0.00094 35.6 1.4 31 10-47 142-172 (1134)
64 PF13912 zf-C2H2_6: C2H2-type 22.8 30 0.00066 19.7 0.1 12 36-47 2-13 (27)
65 PF05417 Peptidase_C41: Hepati 22.7 30 0.00065 29.2 0.2 63 9-76 23-97 (161)
66 PLN02248 cellulose synthase-li 22.1 3.9E+02 0.0085 29.5 8.1 39 4-47 140-178 (1135)
67 PLN02294 cytochrome c oxidase 21.3 31 0.00068 29.9 -0.0 26 28-53 134-159 (174)
68 PF12907 zf-met2: Zinc-binding 20.7 24 0.00052 23.6 -0.7 13 35-47 1-13 (40)
69 PF14941 OAF: Transcriptional 20.5 31 0.00068 31.2 -0.2 53 5-57 178-236 (240)
70 PRK11877 psaI photosystem I re 20.2 1.3E+02 0.0029 20.0 2.8 32 139-170 4-35 (38)
No 1
>PF12428 DUF3675: Protein of unknown function (DUF3675) ; InterPro: IPR022143 This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with PF00097 from PFAM. There are two completely conserved residues (R and L) that may be functionally important.
Probab=100.00 E-value=1.4e-46 Score=300.34 Aligned_cols=118 Identities=63% Similarity=1.005 Sum_probs=114.0
Q ss_pred cccCCCCCCCCCCCcccccccceeeeCCCCCCCChHHHHHHHHHHhhhhcccccccccCCCCcchHHHHHHHHHHHHHHH
Q 039690 47 PGYTAPPPPPQSEDTTIDISEAWTVSGAPLDLHDPRLVAMAAAERHLLDAEYDEYADTNASGAAFCRSAALILMALLLLR 126 (216)
Q Consensus 47 ~~y~~p~p~~~~~~~~i~~~~~w~i~~~~~d~~~pr~i~~~~~e~~~~~~d~~ey~~~~~~~~~~CRsvaii~m~LLlLR 126 (216)
++||+|||++++.+++|+|+++|++++ +|++|||+++|+++|++|+|+||+||+.+|++|++||||+|||||+|||||
T Consensus 1 PgYTaPp~~~~~~~~~i~ir~~we~~~--~d~~~~~~~a~~~ae~~~l~~~y~e~~~~~~~~a~~CRsvAli~m~LLllR 78 (118)
T PF12428_consen 1 PGYTAPPKKFQPGETAIDIRGNWEISR--RDLRDPRFLAMAAAERQFLESEYDEYAASNTRGAACCRSVALIFMVLLLLR 78 (118)
T ss_pred CCCCCCCCCCCcCccceEecCCccccc--cCccchhhhhhhhhhhhccccccccccccCCCceeHHHHHHHHHHHHHHHH
Confidence 589999999999999999999999555 899999999999999999999999999999999999999999999999999
Q ss_pred HHhhhccCCCCCCchHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 039690 127 HALTLTNSDDGEDDASTFFSLFLLRAAGFLLPCYIMAWAVS 167 (216)
Q Consensus 127 h~l~~~~~~~~e~~~~tlftl~~lRaaGilLP~Yim~~~i~ 167 (216)
|+++++++ |+|+|+|++||+++||++|||||||||+|+|+
T Consensus 79 hal~l~~~-~~~~~s~~lftl~~LRaaGilLP~Yim~rais 118 (118)
T PF12428_consen 79 HALALVTG-GAEDYSFTLFTLLLLRAAGILLPCYIMARAIS 118 (118)
T ss_pred HHHHHhcC-CcccccHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 99999996 99999999999999999999999999999974
No 2
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=99.73 E-value=1.3e-19 Score=158.74 Aligned_cols=185 Identities=31% Similarity=0.296 Sum_probs=147.6
Q ss_pred CccccccccCchhhHHHHHHHHHHHHcCCccccccCcccccccCCCCCCCCCCCcccccccceeeeCCCCCCCChHHHHH
Q 039690 7 NLEVPCSCSGSLKYAHRKCVQRWCNEKGDVTCEICHQPYQPGYTAPPPPPQSEDTTIDISEAWTVSGAPLDLHDPRLVAM 86 (216)
Q Consensus 7 ~li~PC~C~GSlkyvH~~CL~~W~~~k~~~~CEICk~~y~~~y~~p~p~~~~~~~~i~~~~~w~i~~~~~d~~~pr~i~~ 86 (216)
.++.||.|+|+++|||+.|+++|+..|++..||+|++.|.+.++.+++............+.|...+. ...+++..+.+
T Consensus 95 ~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~i 173 (323)
T KOG1609|consen 95 LLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINVGTKLKPLIVISKVRSGALSERTLSGM-ILLKVALLVAI 173 (323)
T ss_pred ccccCccccCcHHHHHHHHHHhhhccccCeeeecccccceecceeecceeehhhhhhHhhhheeeehh-hhhhhhhhhee
Confidence 68999999999999999999999999999999999999999988887777665555555666766664 45667777777
Q ss_pred HHHHHhhhhcccccccccCCCCcchHHHHH-HHHHHHHHHHHHhhhccCCC--CCCchHHHHHHHHHHHhhhHHHHHHHH
Q 039690 87 AAAERHLLDAEYDEYADTNASGAAFCRSAA-LILMALLLLRHALTLTNSDD--GEDDASTFFSLFLLRAAGFLLPCYIMA 163 (216)
Q Consensus 87 ~~~e~~~~~~d~~ey~~~~~~~~~~CRsva-ii~m~LLlLRh~l~~~~~~~--~e~~~~tlftl~~lRaaGilLP~Yim~ 163 (216)
......++...++++....+.++..++..+ +++.++.++++.+....... -..+.++.+.+.++|+.+++++.++++
T Consensus 174 ~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 253 (323)
T KOG1609|consen 174 IVSVLPLLLGLLFELVLGVPSLVVESPLANPLALVALGLLGFKIWIFIILSGYIFILKSLKVKLVLIRAVIFLLLIKVVL 253 (323)
T ss_pred eEEeehhhhhhhHHHhccccccccCCCccCchhheeecceechHHHHHHHHHHHHHHHHHHHHHhHhhhhccchhhhhhh
Confidence 666777888888888888888888888888 88888889999887766521 135667777799999999999999998
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhhhhhhhc
Q 039690 164 WAVSILQRRRQRQEAAALAATEVAFMIQA 192 (216)
Q Consensus 164 ~~i~~iQ~~r~rq~~~~~~a~~~~~~~~~ 192 (216)
+++...|.++.+..+...+...+.+...+
T Consensus 254 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 282 (323)
T KOG1609|consen 254 AAVVILQLLLQRLVGYLLANSLTPLYIVS 282 (323)
T ss_pred hhHHHHHHHHhcceeEEEecccceeeecc
Confidence 77777788888888765555555444444
No 3
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=99.63 E-value=1.5e-16 Score=133.23 Aligned_cols=65 Identities=28% Similarity=0.647 Sum_probs=51.8
Q ss_pred CCccccccccCchhhHHHHHHHHHHHHcCCccccccCcccccccCCCCCCCCCCCcccccccceeeeCCCCCCCChHHH
Q 039690 6 KNLEVPCSCSGSLKYAHRKCVQRWCNEKGDVTCEICHQPYQPGYTAPPPPPQSEDTTIDISEAWTVSGAPLDLHDPRLV 84 (216)
Q Consensus 6 ~~li~PC~C~GSlkyvH~~CL~~W~~~k~~~~CEICk~~y~~~y~~p~p~~~~~~~~i~~~~~w~i~~~~~d~~~pr~i 84 (216)
+++.+||+|+||+||||++||++|++++++..||+|+++|++..... | ...|..+. .|-+++.++
T Consensus 19 ~~~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~~~~k-p-----------l~~W~~~~--~dc~~~~l~ 83 (162)
T PHA02825 19 DVVTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIKKNYK-K-----------CTKWRCSF--RDCHDSAIV 83 (162)
T ss_pred CCccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEEEecC-C-----------CccccccC--cchhhHHHH
Confidence 35779999999999999999999999999999999999999875322 1 23576555 566666544
No 4
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=99.54 E-value=4.3e-15 Score=102.01 Aligned_cols=42 Identities=55% Similarity=1.174 Sum_probs=39.5
Q ss_pred CcccCCCccccccccCchhhHHHHHHHHHHHHcCCccccccC
Q 039690 1 EEDSIKNLEVPCSCSGSLKYAHRKCVQRWCNEKGDVTCEICH 42 (216)
Q Consensus 1 EEd~~~~li~PC~C~GSlkyvH~~CL~~W~~~k~~~~CEICk 42 (216)
+++++++++.||+|+||++|||+.||++|+.++++.+||+|+
T Consensus 8 ~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 8 EGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 367888999999999999999999999999999999999996
No 5
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=99.46 E-value=9.2e-15 Score=99.55 Aligned_cols=39 Identities=49% Similarity=1.178 Sum_probs=31.3
Q ss_pred ccCCCccccccccCchhhHHHHHHHHHHHHcCCcccccc
Q 039690 3 DSIKNLEVPCSCSGSLKYAHRKCVQRWCNEKGDVTCEIC 41 (216)
Q Consensus 3 d~~~~li~PC~C~GSlkyvH~~CL~~W~~~k~~~~CEIC 41 (216)
+++++|++||.|+||++|||++||++|+.++++.+||+|
T Consensus 9 ~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 9 EEDEPLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp SSSS-EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CCCCceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 344479999999999999999999999999999999998
No 6
>PHA02862 5L protein; Provisional
Probab=99.43 E-value=6.1e-14 Score=116.31 Aligned_cols=40 Identities=30% Similarity=0.705 Sum_probs=38.5
Q ss_pred cccccccCchhhHHHHHHHHHHHHcCCccccccCcccccc
Q 039690 9 EVPCSCSGSLKYAHRKCVQRWCNEKGDVTCEICHQPYQPG 48 (216)
Q Consensus 9 i~PC~C~GSlkyvH~~CL~~W~~~k~~~~CEICk~~y~~~ 48 (216)
.+||.|+||+||||++||++|++.+++..||+|+++|.++
T Consensus 16 ~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik 55 (156)
T PHA02862 16 NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIK 55 (156)
T ss_pred cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEE
Confidence 6999999999999999999999999999999999999864
No 7
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=99.37 E-value=3.3e-13 Score=134.85 Aligned_cols=59 Identities=37% Similarity=0.737 Sum_probs=53.7
Q ss_pred CcccCCCccccccccCchhhHHHHHHHHHHHHcCCccccccCccccc--ccCCCCCCCCCC
Q 039690 1 EEDSIKNLEVPCSCSGSLKYAHRKCVQRWCNEKGDVTCEICHQPYQP--GYTAPPPPPQSE 59 (216)
Q Consensus 1 EEd~~~~li~PC~C~GSlkyvH~~CL~~W~~~k~~~~CEICk~~y~~--~y~~p~p~~~~~ 59 (216)
|+-+|+|+.+||+|+||+||+|++||.+|+..+++++|||||++|+. .|...+|.-.|.
T Consensus 21 e~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~IY~e~mP~~IPf 81 (1175)
T COG5183 21 EDIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDIYKEDMPQIIPF 81 (1175)
T ss_pred CCCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeeeecccCCCcccce
Confidence 56689999999999999999999999999999999999999999865 588888888775
No 8
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.20 E-value=6.8e-12 Score=112.38 Aligned_cols=48 Identities=33% Similarity=0.842 Sum_probs=42.9
Q ss_pred CccccccccCchhhHHHHHHHHHHHHc------CCccccccCcccccccCCCCC
Q 039690 7 NLEVPCSCSGSLKYAHRKCVQRWCNEK------GDVTCEICHQPYQPGYTAPPP 54 (216)
Q Consensus 7 ~li~PC~C~GSlkyvH~~CL~~W~~~k------~~~~CEICk~~y~~~y~~p~p 54 (216)
.+++||.|+||.||||+.||.+|+++| .+..|.+|+++|.++|+...|
T Consensus 37 ~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv~P~l~~ 90 (293)
T KOG3053|consen 37 AWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIVFPQLGP 90 (293)
T ss_pred hhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchheeeccccCh
Confidence 489999999999999999999999998 368999999999999865443
No 9
>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=94.17 E-value=0.019 Score=37.46 Aligned_cols=22 Identities=27% Similarity=0.979 Sum_probs=18.3
Q ss_pred hhHHHHHHHHHHHHcCCccccccC
Q 039690 19 KYAHRKCVQRWCNEKGDVTCEICH 42 (216)
Q Consensus 19 kyvH~~CL~~W~~~k~~~~CEICk 42 (216)
...|.+|+++|++.+ .+|++|+
T Consensus 23 H~fh~~Ci~~~~~~~--~~CP~CR 44 (44)
T PF13639_consen 23 HVFHRSCIKEWLKRN--NSCPVCR 44 (44)
T ss_dssp EEEEHHHHHHHHHHS--SB-TTTH
T ss_pred CeeCHHHHHHHHHhC--CcCCccC
Confidence 689999999999885 4999985
No 10
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=92.95 E-value=0.072 Score=40.98 Aligned_cols=30 Identities=23% Similarity=0.726 Sum_probs=25.3
Q ss_pred hhHHHHHHHHHHHH-cCCccccccCcccccc
Q 039690 19 KYAHRKCVQRWCNE-KGDVTCEICHQPYQPG 48 (216)
Q Consensus 19 kyvH~~CL~~W~~~-k~~~~CEICk~~y~~~ 48 (216)
.-.|..|+.+|++. +.+..|++|+++|+.+
T Consensus 54 H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~k 84 (85)
T PF12861_consen 54 HNFHMHCILKWLSTQSSKGQCPMCRQPWKFK 84 (85)
T ss_pred cHHHHHHHHHHHccccCCCCCCCcCCeeeeC
Confidence 45899999999986 4678999999998753
No 11
>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=89.21 E-value=0.21 Score=36.54 Aligned_cols=22 Identities=27% Similarity=0.940 Sum_probs=17.2
Q ss_pred hhHHHHHHHHHHHHcCCccccccC
Q 039690 19 KYAHRKCVQRWCNEKGDVTCEICH 42 (216)
Q Consensus 19 kyvH~~CL~~W~~~k~~~~CEICk 42 (216)
..-|..||.+|++.+. +|++|+
T Consensus 52 H~FH~~Ci~~Wl~~~~--~CP~CR 73 (73)
T PF12678_consen 52 HIFHFHCISQWLKQNN--TCPLCR 73 (73)
T ss_dssp EEEEHHHHHHHHTTSS--B-TTSS
T ss_pred CCEEHHHHHHHHhcCC--cCCCCC
Confidence 4589999999996544 999995
No 12
>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=88.63 E-value=0.42 Score=29.37 Aligned_cols=25 Identities=32% Similarity=0.979 Sum_probs=20.8
Q ss_pred hhHHHHHHHHHHHHcCCccccccCcc
Q 039690 19 KYAHRKCVQRWCNEKGDVTCEICHQP 44 (216)
Q Consensus 19 kyvH~~CL~~W~~~k~~~~CEICk~~ 44 (216)
...|..|+.+|++. +...|.+|+..
T Consensus 20 H~~c~~C~~~~~~~-~~~~Cp~C~~~ 44 (45)
T cd00162 20 HVFCRSCIDKWLKS-GKNTCPLCRTP 44 (45)
T ss_pred ChhcHHHHHHHHHh-CcCCCCCCCCc
Confidence 34799999999976 67789999875
No 13
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=86.41 E-value=0.47 Score=36.30 Aligned_cols=30 Identities=30% Similarity=0.744 Sum_probs=25.5
Q ss_pred hhhHHHHHHHHHHHHc-CCccccccCccccc
Q 039690 18 LKYAHRKCVQRWCNEK-GDVTCEICHQPYQP 47 (216)
Q Consensus 18 lkyvH~~CL~~W~~~k-~~~~CEICk~~y~~ 47 (216)
....|..|+.+|++.+ ....|+.|++.|+.
T Consensus 52 ~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~ 82 (84)
T KOG1493|consen 52 LHAFHAHCILKWLNTPTSQGQCPMCRQTWQF 82 (84)
T ss_pred HHHHHHHHHHHHhcCccccccCCcchheeEe
Confidence 3458999999999866 56899999999875
No 14
>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=85.30 E-value=1.3 Score=26.03 Aligned_cols=31 Identities=32% Similarity=0.910 Sum_probs=22.3
Q ss_pred CCCccccccccCchhhHHHHHHHHHHHHcCCcccccc
Q 039690 5 IKNLEVPCSCSGSLKYAHRKCVQRWCNEKGDVTCEIC 41 (216)
Q Consensus 5 ~~~li~PC~C~GSlkyvH~~CL~~W~~~k~~~~CEIC 41 (216)
.+....||.- ..|..|+++|++ ++...|.+|
T Consensus 9 ~~~~~~~C~H-----~~c~~C~~~~~~-~~~~~CP~C 39 (39)
T smart00184 9 KDPVVLPCGH-----TFCRSCIRKWLK-SGNNTCPIC 39 (39)
T ss_pred CCcEEecCCC-----hHHHHHHHHHHH-hCcCCCCCC
Confidence 3445666543 479999999998 566678776
No 15
>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=81.68 E-value=1.1 Score=29.79 Aligned_cols=36 Identities=25% Similarity=0.631 Sum_probs=27.3
Q ss_pred cCCCccccccccCchhh-HHHHHHHHHHHHcCCccccccCcccc
Q 039690 4 SIKNLEVPCSCSGSLKY-AHRKCVQRWCNEKGDVTCEICHQPYQ 46 (216)
Q Consensus 4 ~~~~li~PC~C~GSlky-vH~~CL~~W~~~k~~~~CEICk~~y~ 46 (216)
..+....||. .. +-..|+.+|.+ +...|.+|+++.+
T Consensus 12 ~~~~~~~pCg-----H~~~C~~C~~~~~~--~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 12 PRDVVLLPCG-----HLCFCEECAERLLK--RKKKCPICRQPIE 48 (50)
T ss_dssp BSSEEEETTC-----EEEEEHHHHHHHHH--TTSBBTTTTBB-S
T ss_pred CCceEEeCCC-----ChHHHHHHhHHhcc--cCCCCCcCChhhc
Confidence 3445677875 23 67799999998 8899999998865
No 16
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=80.68 E-value=1.2 Score=42.90 Aligned_cols=33 Identities=27% Similarity=0.729 Sum_probs=24.8
Q ss_pred hhHHHHHHHHHHHHcCCccccccCcccccccCCCC
Q 039690 19 KYAHRKCVQRWCNEKGDVTCEICHQPYQPGYTAPP 53 (216)
Q Consensus 19 kyvH~~CL~~W~~~k~~~~CEICk~~y~~~y~~p~ 53 (216)
+..|-.||+.|+.- ..+|+||+.+.......|-
T Consensus 320 HilHl~CLknW~ER--qQTCPICr~p~ifd~~~~~ 352 (491)
T COG5243 320 HILHLHCLKNWLER--QQTCPICRRPVIFDQSSPT 352 (491)
T ss_pred ceeeHHHHHHHHHh--ccCCCcccCccccccCCCC
Confidence 36899999999964 5689999998655444443
No 17
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=79.55 E-value=1.4 Score=33.97 Aligned_cols=26 Identities=23% Similarity=0.586 Sum_probs=22.5
Q ss_pred hHHHHHHHHHHHHcCCccccccCccccc
Q 039690 20 YAHRKCVQRWCNEKGDVTCEICHQPYQP 47 (216)
Q Consensus 20 yvH~~CL~~W~~~k~~~~CEICk~~y~~ 47 (216)
-.|..|+.+|++. ...|++|+++|+.
T Consensus 57 aFH~HCI~rWL~T--k~~CPld~q~w~~ 82 (88)
T COG5194 57 AFHDHCIYRWLDT--KGVCPLDRQTWVL 82 (88)
T ss_pred HHHHHHHHHHHhh--CCCCCCCCceeEE
Confidence 4799999999988 4589999999875
No 18
>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=79.09 E-value=1.7 Score=29.52 Aligned_cols=34 Identities=21% Similarity=0.445 Sum_probs=25.9
Q ss_pred CCccccccccCchhhHHHHHHHHHHHHcCCccccccCcccc
Q 039690 6 KNLEVPCSCSGSLKYAHRKCVQRWCNEKGDVTCEICHQPYQ 46 (216)
Q Consensus 6 ~~li~PC~C~GSlkyvH~~CL~~W~~~k~~~~CEICk~~y~ 46 (216)
++...|| | +..-+.|+.+|++. +.+|++|+..+.
T Consensus 13 ~Pv~~~~---G--~v~~~~~i~~~~~~--~~~cP~~~~~~~ 46 (63)
T smart00504 13 DPVILPS---G--QTYERRAIEKWLLS--HGTDPVTGQPLT 46 (63)
T ss_pred CCEECCC---C--CEEeHHHHHHHHHH--CCCCCCCcCCCC
Confidence 3555655 3 56789999999977 568999998774
No 19
>COG4420 Predicted membrane protein [Function unknown]
Probab=79.03 E-value=25 Score=30.92 Aligned_cols=49 Identities=24% Similarity=0.221 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHHHhhhccCC--CCCCchHHHHHHHHHHHhhhHHHHHHHH
Q 039690 115 AALILMALLLLRHALTLTNSD--DGEDDASTFFSLFLLRAAGFLLPCYIMA 163 (216)
Q Consensus 115 vaii~m~LLlLRh~l~~~~~~--~~e~~~~tlftl~~lRaaGilLP~Yim~ 163 (216)
+.+.|.++|++|-.+.+.... .-|.|+|.++.|++-=.|.|--|+..|.
T Consensus 60 fil~~~~~ll~Wi~lNl~~~~~~~wDpyPFi~LnLllS~~AaiqAp~IlmS 110 (191)
T COG4420 60 FILTFTLLLLLWIVLNLFLVPGLAWDPYPFILLNLLLSTLAAIQAPLILMS 110 (191)
T ss_pred HHHHHHHHHHHHHHHHHhhhcCCcCCCccHHHHHHHHHHHHHHHHhHHHHH
Confidence 667788889999888776653 2389999999999888888888885554
No 20
>PF06210 DUF1003: Protein of unknown function (DUF1003); InterPro: IPR010406 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=78.53 E-value=24 Score=28.04 Aligned_cols=49 Identities=16% Similarity=0.208 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHHhhhccCC--CCCCchHHHHHHHHHHHhhhHHHHHHHH
Q 039690 115 AALILMALLLLRHALTLTNSD--DGEDDASTFFSLFLLRAAGFLLPCYIMA 163 (216)
Q Consensus 115 vaii~m~LLlLRh~l~~~~~~--~~e~~~~tlftl~~lRaaGilLP~Yim~ 163 (216)
..+++++++++|-.+.+.... .-|-|||.++++++-=.|.++-|+..|.
T Consensus 6 Fi~~~~~~~~~Wi~~N~~~~~~~~fDpyPFilLnl~lS~~Aa~~ap~Ilms 56 (108)
T PF06210_consen 6 FIIIFTVFLAVWILLNILAPPRPAFDPYPFILLNLVLSLEAAYQAPLILMS 56 (108)
T ss_pred HHHHHHHHHHHHHHHHhhccccCCCCCccHHHHHHHHHHHHHHHHHHHHHH
Confidence 456677777888777776653 2388999999998887888888875443
No 21
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=78.37 E-value=0.64 Score=33.84 Aligned_cols=31 Identities=23% Similarity=0.381 Sum_probs=18.8
Q ss_pred hhhHHHHHHHHHHHHc--C-------CccccccCcccccc
Q 039690 18 LKYAHRKCVQRWCNEK--G-------DVTCEICHQPYQPG 48 (216)
Q Consensus 18 lkyvH~~CL~~W~~~k--~-------~~~CEICk~~y~~~ 48 (216)
-+..|..||.+|+... + ...|+.|+.+.+..
T Consensus 29 ~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~~ 68 (70)
T PF11793_consen 29 GKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISWS 68 (70)
T ss_dssp ---B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEGG
T ss_pred CCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeEe
Confidence 5678999999999753 1 34699999887653
No 22
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=73.66 E-value=2.1 Score=40.50 Aligned_cols=32 Identities=25% Similarity=0.795 Sum_probs=25.7
Q ss_pred cccccccCchhhHHHHHHHHHHHHcCCccccccCcccc
Q 039690 9 EVPCSCSGSLKYAHRKCVQRWCNEKGDVTCEICHQPYQ 46 (216)
Q Consensus 9 i~PC~C~GSlkyvH~~CL~~W~~~k~~~~CEICk~~y~ 46 (216)
+-||+ +--|..|+..|+... ...|++||+.-.
T Consensus 247 iLPC~-----H~FH~~CIDpWL~~~-r~~CPvCK~di~ 278 (348)
T KOG4628|consen 247 ILPCS-----HKFHVNCIDPWLTQT-RTFCPVCKRDIR 278 (348)
T ss_pred EecCC-----CchhhccchhhHhhc-CccCCCCCCcCC
Confidence 56775 468999999999887 667999999543
No 23
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=71.23 E-value=4.4 Score=35.51 Aligned_cols=28 Identities=14% Similarity=0.595 Sum_probs=21.7
Q ss_pred hhHHHHHHHHHHHH--------------cCCccccccCcccc
Q 039690 19 KYAHRKCVQRWCNE--------------KGDVTCEICHQPYQ 46 (216)
Q Consensus 19 kyvH~~CL~~W~~~--------------k~~~~CEICk~~y~ 46 (216)
+.....|+.+|+.. ++...|.+|+....
T Consensus 38 H~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is 79 (193)
T PLN03208 38 HLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVS 79 (193)
T ss_pred chhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCC
Confidence 45678999999863 24578999999873
No 24
>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=70.58 E-value=3.7 Score=25.83 Aligned_cols=23 Identities=30% Similarity=0.989 Sum_probs=19.9
Q ss_pred hhHHHHHHHHHHHHcCCcccccc
Q 039690 19 KYAHRKCVQRWCNEKGDVTCEIC 41 (216)
Q Consensus 19 kyvH~~CL~~W~~~k~~~~CEIC 41 (216)
.....+|+.+|++.++...|.+|
T Consensus 19 H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 19 HSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp EEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CcchHHHHHHHHHhcCCccCCcC
Confidence 34789999999998888889987
No 25
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=64.29 E-value=4.8 Score=32.43 Aligned_cols=26 Identities=19% Similarity=0.525 Sum_probs=21.7
Q ss_pred hHHHHHHHHHHHHcCCccccccCccccc
Q 039690 20 YAHRKCVQRWCNEKGDVTCEICHQPYQP 47 (216)
Q Consensus 20 yvH~~CL~~W~~~k~~~~CEICk~~y~~ 47 (216)
-.|..|+.+|++. ...|++|+++...
T Consensus 84 aFH~hCisrWlkt--r~vCPLdn~eW~~ 109 (114)
T KOG2930|consen 84 AFHFHCISRWLKT--RNVCPLDNKEWVF 109 (114)
T ss_pred HHHHHHHHHHHhh--cCcCCCcCcceeE
Confidence 3799999999966 5689999998765
No 26
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=57.51 E-value=6.8 Score=38.07 Aligned_cols=23 Identities=26% Similarity=0.853 Sum_probs=19.7
Q ss_pred hHHHHHHHHHHHHc-CCccccccC
Q 039690 20 YAHRKCVQRWCNEK-GDVTCEICH 42 (216)
Q Consensus 20 yvH~~CL~~W~~~k-~~~~CEICk 42 (216)
..|..||.+|+..- .++.|+||+
T Consensus 29 ifh~~cl~qwfe~~Ps~R~cpic~ 52 (465)
T KOG0827|consen 29 IFHTTCLTQWFEGDPSNRGCPICQ 52 (465)
T ss_pred HHHHHHHHHHHccCCccCCCCcee
Confidence 58999999999765 448999999
No 27
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=57.51 E-value=4.7 Score=26.05 Aligned_cols=18 Identities=22% Similarity=0.626 Sum_probs=13.9
Q ss_pred ccccccCcccccccCCCC
Q 039690 36 VTCEICHQPYQPGYTAPP 53 (216)
Q Consensus 36 ~~CEICk~~y~~~y~~p~ 53 (216)
+.|+.|+..|...|.+|.
T Consensus 2 r~C~~Cg~~Yh~~~~pP~ 19 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPK 19 (36)
T ss_dssp EEETTTTEEEETTTB--S
T ss_pred cCcCCCCCccccccCCCC
Confidence 579999999999887653
No 28
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.63 E-value=6.5 Score=38.63 Aligned_cols=26 Identities=23% Similarity=0.653 Sum_probs=22.1
Q ss_pred hhhHHHHHHHHHHHHcCCccccccCccc
Q 039690 18 LKYAHRKCVQRWCNEKGDVTCEICHQPY 45 (216)
Q Consensus 18 lkyvH~~CL~~W~~~k~~~~CEICk~~y 45 (216)
.+..|..||++|++. ..+|.+|+..+
T Consensus 315 ~Hifh~~CL~~W~er--~qtCP~CR~~~ 340 (543)
T KOG0802|consen 315 GHIFHDSCLRSWFER--QQTCPTCRTVL 340 (543)
T ss_pred ccchHHHHHHHHHHH--hCcCCcchhhh
Confidence 456899999999977 77999999954
No 29
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=55.97 E-value=6 Score=26.31 Aligned_cols=21 Identities=19% Similarity=0.763 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHHcCCcccccc
Q 039690 21 AHRKCVQRWCNEKGDVTCEIC 41 (216)
Q Consensus 21 vH~~CL~~W~~~k~~~~CEIC 41 (216)
.|..|++.++..+.+..|+.|
T Consensus 23 ~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 23 LHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp E-HHHHHHHTTT-SS-B-TTT
T ss_pred HHHHHHHHHHhcCCCCCCcCC
Confidence 899999999988877789877
No 30
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=49.79 E-value=20 Score=24.87 Aligned_cols=35 Identities=23% Similarity=0.579 Sum_probs=17.1
Q ss_pred CCccccccccCchhhHHHHHHHHHHHHc--CCccccccCcccc
Q 039690 6 KNLEVPCSCSGSLKYAHRKCVQRWCNEK--GDVTCEICHQPYQ 46 (216)
Q Consensus 6 ~~li~PC~C~GSlkyvH~~CL~~W~~~k--~~~~CEICk~~y~ 46 (216)
+.-..||.|. ++-|+.=|.+-+ .+..|.=|+.+|+
T Consensus 12 d~~~~PC~Cg------f~IC~~C~~~i~~~~~g~CPgCr~~Y~ 48 (48)
T PF14570_consen 12 DKDFYPCECG------FQICRFCYHDILENEGGRCPGCREPYK 48 (48)
T ss_dssp CTT--SSTTS----------HHHHHHHTTSS-SB-TTT--B--
T ss_pred CCccccCcCC------CcHHHHHHHHHHhccCCCCCCCCCCCC
Confidence 3446899994 456776676655 5899999999985
No 31
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=45.14 E-value=22 Score=23.02 Aligned_cols=32 Identities=22% Similarity=0.482 Sum_probs=24.4
Q ss_pred CCCccccccccCchhhHHHHHHHHHHHHcCCccccccCc
Q 039690 5 IKNLEVPCSCSGSLKYAHRKCVQRWCNEKGDVTCEICHQ 43 (216)
Q Consensus 5 ~~~li~PC~C~GSlkyvH~~CL~~W~~~k~~~~CEICk~ 43 (216)
..+++.+| -.....+|++++. +....|.+|++
T Consensus 13 ~~~~l~~C-----gH~~C~~C~~~~~--~~~~~CP~C~k 44 (44)
T PF14634_consen 13 RRPRLTSC-----GHIFCEKCLKKLK--GKSVKCPICRK 44 (44)
T ss_pred CCeEEccc-----CCHHHHHHHHhhc--CCCCCCcCCCC
Confidence 34566776 3467889999888 78899999985
No 32
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=45.07 E-value=10 Score=26.00 Aligned_cols=34 Identities=24% Similarity=0.608 Sum_probs=18.3
Q ss_pred ccccccCcccccccCCCCCCCCCCCccc-cccccee
Q 039690 36 VTCEICHQPYQPGYTAPPPPPQSEDTTI-DISEAWT 70 (216)
Q Consensus 36 ~~CEICk~~y~~~y~~p~p~~~~~~~~i-~~~~~w~ 70 (216)
..|.+|++.|......|.-...+ .|.. ++-++|.
T Consensus 2 y~C~~CgyvYd~~~Gd~~~~i~p-Gt~F~~Lp~~w~ 36 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPENGIPP-GTPFEDLPDDWV 36 (47)
T ss_dssp EEETTTSBEEETTTBBGGGTB-T-T--GGGS-TT-B
T ss_pred cCCCCCCEEEcCCcCCcccCcCC-CCCHHHCCCCCc
Confidence 47999999999877654332222 2222 4455664
No 33
>smart00782 PhnA_Zn_Ribbon PhnA Zinc-Ribbon. This protein family includes an uncharacterised member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterised phosphonoacetate hydrolase designated PhnA.
Probab=43.74 E-value=21 Score=24.45 Aligned_cols=31 Identities=23% Similarity=0.568 Sum_probs=18.8
Q ss_pred HcCCccccccCccccc-ccCCCCCCCCCCCcc
Q 039690 32 EKGDVTCEICHQPYQP-GYTAPPPPPQSEDTT 62 (216)
Q Consensus 32 ~k~~~~CEICk~~y~~-~y~~p~p~~~~~~~~ 62 (216)
.+...+||+|+..-.. .|..||-+-.+.+..
T Consensus 4 ~Rs~~kCELC~a~~~L~vy~Vpp~~~~~~d~~ 35 (47)
T smart00782 4 ARCESKCELCGSDSPLVVYAVPPSSDVTADNS 35 (47)
T ss_pred HHcCCcccCcCCCCCceEEecCCCCCCCccce
Confidence 3456789999987663 466665443333333
No 34
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=43.21 E-value=7.1 Score=36.36 Aligned_cols=28 Identities=25% Similarity=0.668 Sum_probs=24.7
Q ss_pred hHHHHHHHHHHHHcCCccccccCccccc
Q 039690 20 YAHRKCVQRWCNEKGDVTCEICHQPYQP 47 (216)
Q Consensus 20 yvH~~CL~~W~~~k~~~~CEICk~~y~~ 47 (216)
--|+.|++-||-..++.+|+-||.+-..
T Consensus 255 vFHEfCIrGWcivGKkqtCPYCKekVdl 282 (328)
T KOG1734|consen 255 VFHEFCIRGWCIVGKKQTCPYCKEKVDL 282 (328)
T ss_pred chHHHhhhhheeecCCCCCchHHHHhhH
Confidence 4799999999999999999999987543
No 35
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=42.41 E-value=21 Score=24.66 Aligned_cols=17 Identities=35% Similarity=0.800 Sum_probs=13.8
Q ss_pred ccccccCcccccccCCC
Q 039690 36 VTCEICHQPYQPGYTAP 52 (216)
Q Consensus 36 ~~CEICk~~y~~~y~~p 52 (216)
..|.+|++.|......|
T Consensus 2 y~C~~CgyiYd~~~Gd~ 18 (50)
T cd00730 2 YECRICGYIYDPAEGDP 18 (50)
T ss_pred cCCCCCCeEECCCCCCc
Confidence 47999999999876654
No 36
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.93 E-value=17 Score=32.77 Aligned_cols=38 Identities=13% Similarity=0.446 Sum_probs=25.4
Q ss_pred ccCCCccccccccCchhhHHHHHHHHHHHHc-CCccccccCccc
Q 039690 3 DSIKNLEVPCSCSGSLKYAHRKCVQRWCNEK-GDVTCEICHQPY 45 (216)
Q Consensus 3 d~~~~li~PC~C~GSlkyvH~~CL~~W~~~k-~~~~CEICk~~y 45 (216)
...++.++.|. - .-==-||-+|+..+ +...|.+||.+-
T Consensus 56 ~akdPVvTlCG---H--LFCWpClyqWl~~~~~~~~cPVCK~~V 94 (230)
T KOG0823|consen 56 LAKDPVVTLCG---H--LFCWPCLYQWLQTRPNSKECPVCKAEV 94 (230)
T ss_pred ccCCCEEeecc---c--ceehHHHHHHHhhcCCCeeCCcccccc
Confidence 34556666664 0 11136999999876 566779999876
No 37
>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=40.66 E-value=11 Score=20.22 Aligned_cols=11 Identities=27% Similarity=1.029 Sum_probs=7.2
Q ss_pred cccccCccccc
Q 039690 37 TCEICHQPYQP 47 (216)
Q Consensus 37 ~CEICk~~y~~ 47 (216)
.|++|+..|..
T Consensus 2 ~C~~C~~~~~~ 12 (24)
T PF13894_consen 2 QCPICGKSFRS 12 (24)
T ss_dssp E-SSTS-EESS
T ss_pred CCcCCCCcCCc
Confidence 69999998864
No 38
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=40.07 E-value=39 Score=30.94 Aligned_cols=61 Identities=20% Similarity=0.242 Sum_probs=41.1
Q ss_pred CCcchHHHHHHHHHHHHHHHHHhhhccCCCCCCchHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 039690 107 SGAAFCRSAALILMALLLLRHALTLTNSDDGEDDASTFFSLFLLRAAGFLLPCYIMAWAVS 167 (216)
Q Consensus 107 ~~~~~CRsvaii~m~LLlLRh~l~~~~~~~~e~~~~tlftl~~lRaaGilLP~Yim~~~i~ 167 (216)
-|..|.|.-+|+|.+|-++=-++.+....++-+++...-.++++=+..||+=++.++|++.
T Consensus 189 VG~~faRkR~i~f~llgllfliiaigltvGT~~~A~~~~giY~~wv~~~l~a~~~~~rs~y 249 (256)
T PF09788_consen 189 VGPRFARKRAIIFFLLGLLFLIIAIGLTVGTWTYAKTYGGIYVSWVGLFLIALICLIRSIY 249 (256)
T ss_pred ccchHhhhHHHHHHHHHHHHHHHHHHHhhhhHHHHhhcCcEeHHHHHHHHHHHHHHHHhhe
Confidence 3667889888888877666555555554456666666545555666667777888888763
No 39
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=39.92 E-value=34 Score=27.20 Aligned_cols=32 Identities=16% Similarity=0.269 Sum_probs=13.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 039690 154 GFLLPCYIMAWAVSILQRRRQRQEAAALAATE 185 (216)
Q Consensus 154 GilLP~Yim~~~i~~iQ~~r~rq~~~~~~a~~ 185 (216)
+|++.+.|++-.+..+-|||+|....-+.-|.
T Consensus 7 iii~~i~l~~~~~~~~~rRR~r~G~~P~~gt~ 38 (130)
T PF12273_consen 7 IIIVAILLFLFLFYCHNRRRRRRGLQPIYGTR 38 (130)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCCCcCCce
Confidence 34444544544344344444444333333343
No 40
>PF05210 Sprouty: Sprouty protein (Spry); InterPro: IPR007875 Sprouty (Spry) and Spred (Sprouty related EVH1 domain) proteins have been identified as inhibitors of the Ras/mitogen-activated protein kinase (MAPK) cascade, a pathway crucial for developmental processes initiated by activation of various receptor tyrosine kinases [1,2]. These proteins share a conserved, C-terminal cysteine-rich region, the SPR domain. This domain has been defined as a novel cytosol to membrane translocation domain [, , , ]. It has been found to be a PtdIns(4,5)P2-binding domain that targets the proteins to a cellular localization that maximizes their inhibitory potential [, ]. It also mediates homodimer formation of these proteins [, ]. The SPR domain can occur in association with the WH1 domain (see IPR000697 from INTERPRO) (located in the N-terminal part of the proteins) in the Spred proteins.; GO: 0007275 multicellular organismal development, 0009966 regulation of signal transduction, 0016020 membrane
Probab=38.88 E-value=19 Score=28.92 Aligned_cols=24 Identities=29% Similarity=0.796 Sum_probs=17.9
Q ss_pred cCCCc-cccccccCchhhHHHHHHHHHHHH
Q 039690 4 SIKNL-EVPCSCSGSLKYAHRKCVQRWCNE 32 (216)
Q Consensus 4 ~~~~l-i~PC~C~GSlkyvH~~CL~~W~~~ 32 (216)
++++. .+||+|.. +.+|..||.--
T Consensus 53 ~e~d~ad~PCSC~~-----~~~c~~RW~~L 77 (108)
T PF05210_consen 53 DEGDCADHPCSCDT-----PSRCCARWLAL 77 (108)
T ss_pred CCcccCCCccccCC-----ccchHHHHHHH
Confidence 33444 56999987 88999999753
No 41
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=38.05 E-value=21 Score=25.79 Aligned_cols=21 Identities=24% Similarity=0.863 Sum_probs=13.8
Q ss_pred cccCchh-----h-HHHHHHHHHHHHc
Q 039690 13 SCSGSLK-----Y-AHRKCVQRWCNEK 33 (216)
Q Consensus 13 ~C~GSlk-----y-vH~~CL~~W~~~k 33 (216)
.|+|+.+ | |++.|+++|++.+
T Consensus 23 nc~~~~RAaarkf~V~r~~Vr~W~kqe 49 (58)
T PF09607_consen 23 NCKGNQRAAARKFNVSRRQVRKWRKQE 49 (58)
T ss_dssp TTTT-HHHHHHHTTS-HHHHHHHHTTH
T ss_pred chhhhHHHHHHHhCccHHHHHHHHHHH
Confidence 4665443 3 7999999999654
No 42
>COG2322 Predicted membrane protein [Function unknown]
Probab=37.28 E-value=1.3e+02 Score=26.30 Aligned_cols=55 Identities=24% Similarity=0.231 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHHHHHhhhccCCCC-----CCchHHHHHHHHHHHhhhHHHHHHHHHHHHH
Q 039690 114 SAALILMALLLLRHALTLTNSDDG-----EDDASTFFSLFLLRAAGFLLPCYIMAWAVSI 168 (216)
Q Consensus 114 svaii~m~LLlLRh~l~~~~~~~~-----e~~~~tlftl~~lRaaGilLP~Yim~~~i~~ 168 (216)
..+++|+++-+-||-+.-.+..++ ..|-|-+++=..|-++++-|-.|.++++++-
T Consensus 84 ~l~l~FlvlYltr~~l~~~t~f~~~G~~k~~Y~~iL~~Hi~LA~i~vPLal~al~~a~~~ 143 (177)
T COG2322 84 TLALVFLVLYLTRHGLGGETAFGGTGIYKGIYFFILITHIILAAINVPLALYALILAWKG 143 (177)
T ss_pred HHHHHHHHHHHHHHhccccccCCCCeeeehHHHHHHHHHHHHHHHhhhHHHHHHHHHhcc
Confidence 367889999999998888772222 2466667777788999999999999999874
No 43
>PF07301 DUF1453: Protein of unknown function (DUF1453); InterPro: IPR009916 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown. Members of this family seem to be found exclusively in the Order Bacillales.
Probab=36.52 E-value=1.5e+02 Score=25.04 Aligned_cols=53 Identities=28% Similarity=0.488 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHHhhhccCCCCCCchHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHH
Q 039690 115 AALILMALLLLRHALTLTNSDDGEDDASTFFSLFLLRAAGFLLPCYIMAWAVSILQRRRQ 174 (216)
Q Consensus 115 vaii~m~LLlLRh~l~~~~~~~~e~~~~tlftl~~lRaaGilLP~Yim~~~i~~iQ~~r~ 174 (216)
..+++..||++|-.+-...+ + .-++-.+-.+|++=|-| ||+-|-++...+-|+
T Consensus 95 F~~ili~LlviR~~l~~~l~-~-~i~~~~~~~mFf~lAfg-----mIvpWRiamy~kyrk 147 (148)
T PF07301_consen 95 FIFILIGLLVIRIVLKSYLS-G-SIDPGQLSGMFFLLAFG-----MIVPWRIAMYIKYRK 147 (148)
T ss_pred HHHHHHHHHHHHHHHHHHHH-c-cCCHHHHHHHHHHHHHH-----HHHHHHHHHHHHHhc
Confidence 66778889999999988887 3 23333444455554544 555577777766653
No 44
>PF11874 DUF3394: Domain of unknown function (DUF3394); InterPro: IPR021814 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 190 amino acids in length. This domain is found associated with PF06808 from PFAM.
Probab=36.41 E-value=16 Score=31.75 Aligned_cols=21 Identities=38% Similarity=0.656 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 039690 156 LLPCYIMAWAVSILQRRRQRQ 176 (216)
Q Consensus 156 lLP~Yim~~~i~~iQ~~r~rq 176 (216)
.+|-.+++-.|..+||||+++
T Consensus 162 yiPAlLLL~lv~~lQrRR~~~ 182 (183)
T PF11874_consen 162 YIPALLLLGLVAWLQRRRRRK 182 (183)
T ss_pred eHHHHHHHHHHHHHhhhhccC
Confidence 357777777888999999864
No 45
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=35.36 E-value=13 Score=20.40 Aligned_cols=11 Identities=27% Similarity=0.993 Sum_probs=9.3
Q ss_pred cccccCccccc
Q 039690 37 TCEICHQPYQP 47 (216)
Q Consensus 37 ~CEICk~~y~~ 47 (216)
.|++|+..|..
T Consensus 2 ~C~~C~~~f~~ 12 (23)
T PF00096_consen 2 KCPICGKSFSS 12 (23)
T ss_dssp EETTTTEEESS
T ss_pred CCCCCCCccCC
Confidence 69999999875
No 46
>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=35.11 E-value=30 Score=21.69 Aligned_cols=20 Identities=15% Similarity=0.803 Sum_probs=15.4
Q ss_pred hHHHHHHHHHHHHcCCcccccc
Q 039690 20 YAHRKCVQRWCNEKGDVTCEIC 41 (216)
Q Consensus 20 yvH~~CL~~W~~~k~~~~CEIC 41 (216)
.....|+.+|++. +.+|.+|
T Consensus 20 ~fC~~C~~~~~~~--~~~CP~C 39 (39)
T PF13923_consen 20 SFCKECIEKYLEK--NPKCPVC 39 (39)
T ss_dssp EEEHHHHHHHHHC--TSB-TTT
T ss_pred chhHHHHHHHHHC--cCCCcCC
Confidence 4688999999977 3788877
No 47
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=30.46 E-value=25 Score=21.22 Aligned_cols=13 Identities=15% Similarity=0.501 Sum_probs=11.0
Q ss_pred CCccccccCcccc
Q 039690 34 GDVTCEICHQPYQ 46 (216)
Q Consensus 34 ~~~~CEICk~~y~ 46 (216)
....|+.|++.|.
T Consensus 13 ~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 13 SAKFCPHCGYDFE 25 (26)
T ss_pred hcCcCCCCCCCCc
Confidence 5678999999985
No 48
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=28.89 E-value=34 Score=22.34 Aligned_cols=19 Identities=32% Similarity=0.850 Sum_probs=12.4
Q ss_pred HHHHHHHHHHcCC--cccccc
Q 039690 23 RKCVQRWCNEKGD--VTCEIC 41 (216)
Q Consensus 23 ~~CL~~W~~~k~~--~~CEIC 41 (216)
+.||.+|.++++. ..|.+|
T Consensus 22 ~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 22 RSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp HHHHHHHHCCSSSST---SSS
T ss_pred HHHHHHHHHccCCcCCCCcCC
Confidence 5899999976644 588877
No 49
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.16 E-value=44 Score=32.23 Aligned_cols=33 Identities=21% Similarity=0.506 Sum_probs=23.7
Q ss_pred CccccccccCchhhHHHHHHHHHHHHcCCccccccCcccc
Q 039690 7 NLEVPCSCSGSLKYAHRKCVQRWCNEKGDVTCEICHQPYQ 46 (216)
Q Consensus 7 ~li~PC~C~GSlkyvH~~CL~~W~~~k~~~~CEICk~~y~ 46 (216)
+.+.||. +.....|+.+|+..+ ..|.+|+..+.
T Consensus 39 PvitpCg-----H~FCs~CI~~~l~~~--~~CP~Cr~~~~ 71 (397)
T TIGR00599 39 PVLTSCS-----HTFCSLCIRRCLSNQ--PKCPLCRAEDQ 71 (397)
T ss_pred ccCCCCC-----CchhHHHHHHHHhCC--CCCCCCCCccc
Confidence 4455553 345678999999764 48999999874
No 50
>COG1983 PspC Putative stress-responsive transcriptional regulator [Transcription / Signal transduction mechanisms]
Probab=27.70 E-value=70 Score=23.85 Aligned_cols=15 Identities=33% Similarity=0.541 Sum_probs=11.5
Q ss_pred HhhhHHHHHHHHHHH
Q 039690 152 AAGFLLPCYIMAWAV 166 (216)
Q Consensus 152 aaGilLP~Yim~~~i 166 (216)
..|+.++.||++|.|
T Consensus 45 ~~~~~ii~Yiia~~i 59 (70)
T COG1983 45 LTGFGIIAYIIAALI 59 (70)
T ss_pred chhHHHHHHHHHHHH
Confidence 346678899999865
No 51
>COG4846 CcdC Membrane protein involved in cytochrome C biogenesis [Posttranslational modification, protein turnover, chaperones]
Probab=27.40 E-value=1.6e+02 Score=25.00 Aligned_cols=45 Identities=27% Similarity=0.456 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHHHhhhccCCCCCCchHHHHHHHHHHHhhhHHHHHH
Q 039690 115 AALILMALLLLRHALTLTNSDDGEDDASTFFSLFLLRAAGFLLPCYI 161 (216)
Q Consensus 115 vaii~m~LLlLRh~l~~~~~~~~e~~~~tlftl~~lRaaGilLP~Yi 161 (216)
...|++-||++|-++-+..+ +. -+.=.+-.+|++=|-|.++|-=+
T Consensus 96 F~~ILigLLiiRi~~K~~is-~s-id~geLsGMF~ilAf~MIvPWRi 140 (163)
T COG4846 96 FPVILIGLLIIRIVMKYIIS-GS-IDVGELSGMFWILAFGMIVPWRI 140 (163)
T ss_pred chhHHHHHHHHHHHHHHHHc-CC-ccHHHhhhHHHHHHHHhhhHHHH
Confidence 46788999999999999987 33 33345666778888888888543
No 52
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=26.16 E-value=24 Score=19.76 Aligned_cols=11 Identities=27% Similarity=1.108 Sum_probs=9.0
Q ss_pred cccccCccccc
Q 039690 37 TCEICHQPYQP 47 (216)
Q Consensus 37 ~CEICk~~y~~ 47 (216)
.|++|+..|..
T Consensus 2 ~C~~C~~~f~s 12 (25)
T PF12874_consen 2 YCDICNKSFSS 12 (25)
T ss_dssp EETTTTEEESS
T ss_pred CCCCCCCCcCC
Confidence 69999988864
No 53
>COG1773 Rubredoxin [Energy production and conversion]
Probab=25.93 E-value=57 Score=23.29 Aligned_cols=35 Identities=23% Similarity=0.558 Sum_probs=22.6
Q ss_pred CccccccCcccccccCCCCCCCCCCCccc-cccccee
Q 039690 35 DVTCEICHQPYQPGYTAPPPPPQSEDTTI-DISEAWT 70 (216)
Q Consensus 35 ~~~CEICk~~y~~~y~~p~p~~~~~~~~i-~~~~~w~ 70 (216)
...|.+|++.|...-..|.-.. +..|.. ++-++|.
T Consensus 3 ~~~C~~CG~vYd~e~Gdp~~gi-~pgT~fedlPd~w~ 38 (55)
T COG1773 3 RWRCSVCGYVYDPEKGDPRCGI-APGTPFEDLPDDWV 38 (55)
T ss_pred ceEecCCceEeccccCCccCCC-CCCCchhhCCCccC
Confidence 4689999999998765443333 334543 4556675
No 54
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=25.87 E-value=85 Score=26.38 Aligned_cols=44 Identities=14% Similarity=0.355 Sum_probs=34.6
Q ss_pred ccCCCccccccccCchhhHHHHHHHHHHHHcCCccccccCccccc
Q 039690 3 DSIKNLEVPCSCSGSLKYAHRKCVQRWCNEKGDVTCEICHQPYQP 47 (216)
Q Consensus 3 d~~~~li~PC~C~GSlkyvH~~CL~~W~~~k~~~~CEICk~~y~~ 47 (216)
..|..+..|=.|.|. +.---=|.+-|-..+-.-.|++||+.|+.
T Consensus 90 S~ee~FLKPneCCgY-~iCn~Cya~LWK~~~~ypvCPvCkTSFKs 133 (140)
T PF05290_consen 90 SAEERFLKPNECCGY-SICNACYANLWKFCNLYPVCPVCKTSFKS 133 (140)
T ss_pred cchhhcCCcccccch-HHHHHHHHHHHHHcccCCCCCcccccccc
Confidence 346678889899883 34455567889888889999999999985
No 55
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=25.82 E-value=30 Score=20.24 Aligned_cols=14 Identities=14% Similarity=0.619 Sum_probs=11.6
Q ss_pred cCCccccccCcccc
Q 039690 33 KGDVTCEICHQPYQ 46 (216)
Q Consensus 33 k~~~~CEICk~~y~ 46 (216)
...-.|++|++.|.
T Consensus 12 ~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 12 EKPYKCPYCGKSFS 25 (26)
T ss_dssp SSSEEESSSSEEES
T ss_pred CCCCCCCCCcCeeC
Confidence 45789999999885
No 56
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=25.44 E-value=36 Score=22.36 Aligned_cols=16 Identities=44% Similarity=0.964 Sum_probs=13.2
Q ss_pred CCccccccCccccccc
Q 039690 34 GDVTCEICHQPYQPGY 49 (216)
Q Consensus 34 ~~~~CEICk~~y~~~y 49 (216)
+.++|..|+-.|.++.
T Consensus 12 ~~~~C~~CgM~Y~~~~ 27 (41)
T PF13878_consen 12 GATTCPTCGMLYSPGS 27 (41)
T ss_pred CCcCCCCCCCEECCCC
Confidence 5789999999998653
No 57
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=25.34 E-value=29 Score=20.43 Aligned_cols=12 Identities=42% Similarity=1.190 Sum_probs=10.2
Q ss_pred ccccccCccccc
Q 039690 36 VTCEICHQPYQP 47 (216)
Q Consensus 36 ~~CEICk~~y~~ 47 (216)
..|++|+..|..
T Consensus 3 ~~C~~CgR~F~~ 14 (25)
T PF13913_consen 3 VPCPICGRKFNP 14 (25)
T ss_pred CcCCCCCCEECH
Confidence 579999999964
No 58
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=24.88 E-value=11 Score=28.37 Aligned_cols=30 Identities=23% Similarity=0.669 Sum_probs=17.7
Q ss_pred cCCccccccCcccccccCCCCCCCCCCCcccccccce
Q 039690 33 KGDVTCEICHQPYQPGYTAPPPPPQSEDTTIDISEAW 69 (216)
Q Consensus 33 k~~~~CEICk~~y~~~y~~p~p~~~~~~~~i~~~~~w 69 (216)
.+...|.+|+..|++.++ +....+|+-..|
T Consensus 44 ~~~~~C~~Cg~~~~~~i~-------~L~epiDVY~~w 73 (81)
T PF05129_consen 44 IGILSCRVCGESFQTKIN-------PLSEPIDVYSEW 73 (81)
T ss_dssp EEEEEESSS--EEEEE---------SS--TTHHHHHH
T ss_pred EEEEEecCCCCeEEEccC-------ccCcccchhHHH
Confidence 367899999999988653 345566666666
No 59
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=24.85 E-value=19 Score=28.24 Aligned_cols=24 Identities=13% Similarity=0.346 Sum_probs=18.7
Q ss_pred HHHHHcCCccccccCcccccccCC
Q 039690 28 RWCNEKGDVTCEICHQPYQPGYTA 51 (216)
Q Consensus 28 ~W~~~k~~~~CEICk~~y~~~y~~ 51 (216)
.|+.+.....|+.|++-|+.++-.
T Consensus 72 ~~l~~g~~~rC~eCG~~fkL~~v~ 95 (97)
T cd00924 72 MWLEKGKPKRCPECGHVFKLVDVG 95 (97)
T ss_pred EEEeCCCceeCCCCCcEEEEEECC
Confidence 455566789999999999987643
No 60
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=24.56 E-value=36 Score=20.37 Aligned_cols=13 Identities=23% Similarity=0.943 Sum_probs=10.5
Q ss_pred CCccccccCcccc
Q 039690 34 GDVTCEICHQPYQ 46 (216)
Q Consensus 34 ~~~~CEICk~~y~ 46 (216)
+...|++|+..|.
T Consensus 2 ~~~~C~~C~~~~~ 14 (35)
T smart00451 2 GGFYCKLCNVTFT 14 (35)
T ss_pred cCeEccccCCccC
Confidence 4567999999886
No 61
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=24.03 E-value=19 Score=25.17 Aligned_cols=20 Identities=20% Similarity=0.710 Sum_probs=12.0
Q ss_pred HHHHHcCCccccccCccccc
Q 039690 28 RWCNEKGDVTCEICHQPYQP 47 (216)
Q Consensus 28 ~W~~~k~~~~CEICk~~y~~ 47 (216)
.|...+....|.+|+..|.+
T Consensus 2 ~W~~d~~~~~C~~C~~~F~~ 21 (69)
T PF01363_consen 2 HWVPDSEASNCMICGKKFSL 21 (69)
T ss_dssp -SSSGGG-SB-TTT--B-BS
T ss_pred CcCCCCCCCcCcCcCCcCCC
Confidence 68888889999999999964
No 62
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=23.84 E-value=59 Score=23.30 Aligned_cols=27 Identities=22% Similarity=0.428 Sum_probs=19.3
Q ss_pred hhHHHHHHHHHHHHcCCccccccCcccc
Q 039690 19 KYAHRKCVQRWCNEKGDVTCEICHQPYQ 46 (216)
Q Consensus 19 kyvH~~CL~~W~~~k~~~~CEICk~~y~ 46 (216)
+..=+.|+++|++. +..+|.+|+....
T Consensus 24 ~tyer~~I~~~l~~-~~~~~P~t~~~l~ 50 (73)
T PF04564_consen 24 HTYERSAIERWLEQ-NGGTDPFTRQPLS 50 (73)
T ss_dssp EEEEHHHHHHHHCT-TSSB-TTT-SB-S
T ss_pred CEEcHHHHHHHHHc-CCCCCCCCCCcCC
Confidence 45678999999977 7788999976654
No 63
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=23.37 E-value=43 Score=35.59 Aligned_cols=31 Identities=19% Similarity=0.462 Sum_probs=25.1
Q ss_pred ccccccCchhhHHHHHHHHHHHHcCCccccccCccccc
Q 039690 10 VPCSCSGSLKYAHRKCVQRWCNEKGDVTCEICHQPYQP 47 (216)
Q Consensus 10 ~PC~C~GSlkyvH~~CL~~W~~~k~~~~CEICk~~y~~ 47 (216)
.+|.| |.|..|+..|.+ ...+|.+|..+|--
T Consensus 142 k~c~H-----~FC~~Ci~sWsR--~aqTCPiDR~EF~~ 172 (1134)
T KOG0825|consen 142 KHTAH-----YFCEECVGSWSR--CAQTCPVDRGEFGE 172 (1134)
T ss_pred ccccc-----ccHHHHhhhhhh--hcccCchhhhhhhe
Confidence 56666 899999999984 45689999999953
No 64
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=22.80 E-value=30 Score=19.70 Aligned_cols=12 Identities=17% Similarity=0.802 Sum_probs=9.6
Q ss_pred ccccccCccccc
Q 039690 36 VTCEICHQPYQP 47 (216)
Q Consensus 36 ~~CEICk~~y~~ 47 (216)
..|++|+..|..
T Consensus 2 ~~C~~C~~~F~~ 13 (27)
T PF13912_consen 2 FECDECGKTFSS 13 (27)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCccCCccCC
Confidence 369999999864
No 65
>PF05417 Peptidase_C41: Hepatitis E cysteine protease; InterPro: IPR008748 This entry represents the cysteine proteinase of hepatitis E virus, which is a papain-like protease that cleaves the viral polyprotein encoded by ORF1 of the hepatitis E virus (Porcine hemagglutinating encephalomyelitis virus) [, , ].; GO: 0016032 viral reproduction, 0019082 viral protein processing
Probab=22.73 E-value=30 Score=29.19 Aligned_cols=63 Identities=33% Similarity=0.728 Sum_probs=36.6
Q ss_pred cccccccCchhhHHHH--HHHHHHHHc--------CCccccccCc--ccccccCCCCCCCCCCCcccccccceeeeCCCC
Q 039690 9 EVPCSCSGSLKYAHRK--CVQRWCNEK--------GDVTCEICHQ--PYQPGYTAPPPPPQSEDTTIDISEAWTVSGAPL 76 (216)
Q Consensus 9 i~PC~C~GSlkyvH~~--CL~~W~~~k--------~~~~CEICk~--~y~~~y~~p~p~~~~~~~~i~~~~~w~i~~~~~ 76 (216)
..||.|..-++-+-++ |+++|+... ....=+.|+. .|.- ....| ..+...+++|+..++|+++
T Consensus 23 ~~~CrCr~~~r~~~~k~CCfmrwLgQeCtCFl~p~eg~~gd~g~Dneayeg-sdVDp----AE~a~~~iSGsYiV~G~~L 97 (161)
T PF05417_consen 23 SVPCRCRSFLRKAAKKFCCFMRWLGQECTCFLQPVEGLVGDQGHDNEAYEG-SDVDP----AEEATVDISGSYIVTGSQL 97 (161)
T ss_pred ccccccHHHHHHHhhCceehhhhhcccceEEccchhhhhcccccccccccC-CcCCC----CCcceEeeeeeEEEchHHH
Confidence 5799999999987776 799999642 0111122221 1221 11111 1233567888888888754
No 66
>PLN02248 cellulose synthase-like protein
Probab=22.12 E-value=3.9e+02 Score=29.50 Aligned_cols=39 Identities=23% Similarity=0.486 Sum_probs=28.1
Q ss_pred cCCCccccccccCchhhHHHHHHHHHHHHcCCccccccCccccc
Q 039690 4 SIKNLEVPCSCSGSLKYAHRKCVQRWCNEKGDVTCEICHQPYQP 47 (216)
Q Consensus 4 ~~~~li~PC~C~GSlkyvH~~CL~~W~~~k~~~~CEICk~~y~~ 47 (216)
+.+.-+.||.|.= -+-++|...-++. ...|.=||..|+.
T Consensus 140 ~~~~~~~~~~~~~---~~~~~~~~~~~~~--~~~~~~~~~~~~~ 178 (1135)
T PLN02248 140 ERGEDLLPCECGF---KICRDCYIDAVKS--GGICPGCKEPYKV 178 (1135)
T ss_pred cccccCCcccccc---hhHHhHhhhhhhc--CCCCCCCcccccc
Confidence 3455578999952 3567776665554 6699999999965
No 67
>PLN02294 cytochrome c oxidase subunit Vb
Probab=21.33 E-value=31 Score=29.88 Aligned_cols=26 Identities=19% Similarity=0.563 Sum_probs=20.1
Q ss_pred HHHHHcCCccccccCcccccccCCCC
Q 039690 28 RWCNEKGDVTCEICHQPYQPGYTAPP 53 (216)
Q Consensus 28 ~W~~~k~~~~CEICk~~y~~~y~~p~ 53 (216)
.|+.+.....|..|++.|+.+|--|.
T Consensus 134 f~L~kGkp~RCpeCG~~fkL~~vG~~ 159 (174)
T PLN02294 134 FWLEKGKSFECPVCTQYFELEVVGPG 159 (174)
T ss_pred EEecCCCceeCCCCCCEEEEEEeCCC
Confidence 45666667889999999999875543
No 68
>PF12907 zf-met2: Zinc-binding
Probab=20.66 E-value=24 Score=23.57 Aligned_cols=13 Identities=31% Similarity=1.030 Sum_probs=10.2
Q ss_pred CccccccCccccc
Q 039690 35 DVTCEICHQPYQP 47 (216)
Q Consensus 35 ~~~CEICk~~y~~ 47 (216)
+..|.||++.|-.
T Consensus 1 ~i~C~iC~qtF~~ 13 (40)
T PF12907_consen 1 NIICKICRQTFMQ 13 (40)
T ss_pred CcCcHHhhHHHHh
Confidence 4689999998853
No 69
>PF14941 OAF: Transcriptional regulator, Out at first
Probab=20.45 E-value=31 Score=31.22 Aligned_cols=53 Identities=26% Similarity=0.524 Sum_probs=42.0
Q ss_pred CCCccccccccCchhhHHHHHHHHHHHHcC----Cccccc--cCcccccccCCCCCCCC
Q 039690 5 IKNLEVPCSCSGSLKYAHRKCVQRWCNEKG----DVTCEI--CHQPYQPGYTAPPPPPQ 57 (216)
Q Consensus 5 ~~~li~PC~C~GSlkyvH~~CL~~W~~~k~----~~~CEI--Ck~~y~~~y~~p~p~~~ 57 (216)
.+++-.||-|+=++-.-+.-|.-++|+.|+ +-+|-| |+.-|...|-.|.+...
T Consensus 178 ~~d~w~PC~C~l~lci~WYPCgLKYCkgkd~k~ssYrCGIKTC~Kc~~f~yYV~qKqlC 236 (240)
T PF14941_consen 178 TSDSWKPCICRLELCIEWYPCGLKYCKGKDQKPSSYRCGIKTCQKCYQFDYYVPQKQLC 236 (240)
T ss_pred cCCCCCceeeeecceeeeEccchhhccCCCCCCCccccccccccccccceeecChhhcc
Confidence 456678999999999999999999998775 556654 77778888877765543
No 70
>PRK11877 psaI photosystem I reaction center subunit VIII; Reviewed
Probab=20.19 E-value=1.3e+02 Score=19.98 Aligned_cols=32 Identities=16% Similarity=0.380 Sum_probs=24.3
Q ss_pred CchHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Q 039690 139 DDASTFFSLFLLRAAGFLLPCYIMAWAVSILQ 170 (216)
Q Consensus 139 ~~~~tlftl~~lRaaGilLP~Yim~~~i~~iQ 170 (216)
+|+.+.+--++.=.+|++.|...|+-...-||
T Consensus 4 ~~aas~LPsI~VPlVGlvfPai~Mallf~yIe 35 (38)
T PRK11877 4 DFAASWLPWIFVPLVGWVFPAVFMVLLGRYIT 35 (38)
T ss_pred hHhHHhCchHHHHHHHHHHHHHHHHHHHHHhc
Confidence 56666776777888999999999886655454
Done!