Query 040196
Match_columns 83
No_of_seqs 106 out of 141
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 06:03:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040196.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040196hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3404 G10 protein/predicted 100.0 6.9E-47 1.5E-51 270.9 5.7 75 1-75 1-116 (145)
2 PF01125 G10: G10 protein; In 100.0 2.5E-46 5.4E-51 268.0 5.5 75 1-75 1-117 (145)
3 COG5132 BUD31 Cell cycle contr 100.0 2.8E-39 6.2E-44 231.4 5.3 75 1-75 1-116 (146)
4 PF14077 WD40_alt: Alternative 88.6 0.53 1.1E-05 29.0 2.7 23 16-39 21-43 (48)
5 PF08513 LisH: LisH; InterPro 73.3 4.9 0.00011 21.1 2.5 19 28-46 2-20 (27)
6 smart00667 LisH Lissencephaly 70.0 7.2 0.00016 19.4 2.7 20 27-46 4-23 (34)
7 PF14553 YqbF: YqbF, hypotheti 68.6 2.4 5.3E-05 25.4 0.8 16 28-43 20-35 (43)
8 PRK11798 ClpXP protease specif 64.0 4 8.7E-05 29.5 1.3 16 28-43 10-25 (138)
9 PF06163 DUF977: Bacterial pro 58.3 5.9 0.00013 28.5 1.3 32 41-82 80-111 (127)
10 PF10730 DUF2521: Protein of u 58.3 18 0.00039 26.6 3.8 33 26-58 92-137 (147)
11 smart00151 SWIB SWI complex, B 51.7 17 0.00036 22.7 2.5 29 18-46 7-42 (77)
12 cd08808 CARD_CARD11_CARMA1 Cas 51.5 19 0.00041 24.4 2.8 32 15-46 2-34 (86)
13 COG2969 SspB Stringent starvat 50.3 10 0.00023 28.2 1.5 14 29-42 12-25 (155)
14 PF12401 DUF3662: Protein of u 48.2 9.6 0.00021 25.8 1.0 32 12-43 61-92 (116)
15 PF08271 TF_Zn_Ribbon: TFIIB z 44.9 6 0.00013 22.2 -0.3 22 61-82 3-27 (43)
16 COG3433 Aryl carrier domain [S 41.7 8.6 0.00019 25.5 0.0 12 46-57 36-47 (74)
17 PF02201 SWIB: SWIB/MDM2 domai 40.1 40 0.00088 20.9 2.9 29 18-46 7-42 (76)
18 KOG3222 Inosine triphosphate p 39.4 29 0.00062 26.7 2.5 39 7-45 141-195 (195)
19 KOG1753 40S ribosomal protein 39.1 36 0.00077 25.1 2.8 18 26-45 84-101 (145)
20 cd08806 CARD_CARD14_CARMA2 Cas 38.4 32 0.00069 23.3 2.3 32 15-46 2-34 (86)
21 PF08343 RNR_N: Ribonucleotide 38.0 29 0.00063 22.7 2.0 21 32-52 46-66 (82)
22 PF12644 DUF3782: Protein of u 36.2 62 0.0013 19.0 3.2 39 10-51 24-64 (64)
23 PF12257 DUF3608: Protein of u 35.0 23 0.00049 28.1 1.4 11 45-55 103-113 (281)
24 PF09812 MRP-L28: Mitochondria 34.1 31 0.00066 24.9 1.8 22 17-39 100-121 (157)
25 PF13878 zf-C2H2_3: zinc-finge 34.0 16 0.00035 20.8 0.3 15 68-82 7-21 (41)
26 PF03449 GreA_GreB_N: Transcri 33.0 34 0.00074 21.7 1.8 23 11-33 7-33 (74)
27 PF11848 DUF3368: Domain of un 32.9 37 0.00081 19.6 1.8 24 17-40 20-46 (48)
28 PRK14134 recX recombination re 32.8 68 0.0015 24.7 3.7 16 28-43 253-268 (283)
29 COG5418 Predicted secreted pro 31.3 6.3 0.00014 29.5 -2.1 25 11-35 41-71 (164)
30 PF14394 DUF4423: Domain of un 31.1 33 0.00071 24.6 1.6 21 11-31 130-150 (171)
31 PF08866 DUF1831: Putative ami 30.8 23 0.00049 24.9 0.7 24 26-50 89-112 (112)
32 cd08785 CARD_CARD9-like Caspas 30.7 96 0.0021 20.3 3.6 35 15-49 2-37 (86)
33 PF13495 Phage_int_SAM_4: Phag 29.4 40 0.00087 19.9 1.6 14 31-44 72-85 (85)
34 PF08811 DUF1800: Protein of u 29.2 95 0.0021 25.3 4.1 59 10-69 243-313 (462)
35 PF12029 DUF3516: Domain of un 29.0 69 0.0015 27.5 3.3 19 7-25 26-45 (461)
36 KOG4019 Calcineurin-mediated s 28.8 18 0.00039 27.7 -0.1 12 10-21 115-126 (193)
37 PRK10304 ferritin; Provisional 27.9 78 0.0017 22.5 3.1 46 9-55 74-145 (165)
38 KOG2404 Fumarate reductase, fl 27.2 81 0.0018 27.0 3.4 44 2-45 126-171 (477)
39 PF07261 DnaB_2: Replication i 25.8 87 0.0019 18.4 2.6 48 9-57 12-66 (77)
40 PF01199 Ribosomal_L34e: Ribos 25.7 28 0.00061 23.6 0.4 17 66-82 70-86 (94)
41 PRK06342 transcription elongat 25.7 43 0.00094 24.1 1.4 20 11-30 32-51 (160)
42 COG0782 Uncharacterized conser 25.6 74 0.0016 22.5 2.6 25 12-36 3-31 (151)
43 PF00104 Hormone_recep: Ligand 24.9 2E+02 0.0044 18.8 4.4 28 17-44 143-171 (203)
44 PF05982 DUF897: Domain of unk 24.9 50 0.0011 26.9 1.8 42 11-56 194-236 (327)
45 smart00430 HOLI Ligand binding 24.8 1.4E+02 0.0031 18.7 3.6 22 20-41 121-142 (163)
46 PF13718 GNAT_acetyltr_2: GNAT 24.6 28 0.0006 26.1 0.3 31 44-77 159-189 (196)
47 KOG0995 Centromere-associated 24.5 57 0.0012 28.7 2.1 21 26-46 72-92 (581)
48 PF06945 DUF1289: Protein of u 24.2 31 0.00068 20.4 0.4 20 64-83 4-23 (51)
49 PF14529 Exo_endo_phos_2: Endo 24.2 1.5E+02 0.0032 18.0 3.5 20 28-47 54-73 (119)
50 TIGR01446 DnaD_dom DnaD and ph 23.6 1.2E+02 0.0026 17.9 3.0 45 12-57 15-66 (73)
51 PF10929 DUF2811: Protein of u 23.5 2E+02 0.0044 18.1 4.1 32 17-48 9-49 (57)
52 COG2001 Uncharacterized protei 23.2 48 0.001 24.1 1.3 17 9-25 45-61 (146)
53 PF14754 IFR3_antag: Papain-li 23.1 35 0.00075 26.5 0.5 12 72-83 36-47 (249)
54 PF02696 UPF0061: Uncharacteri 22.9 1E+02 0.0022 26.1 3.2 30 27-56 198-250 (487)
55 PRK01885 greB transcription el 22.8 62 0.0013 23.0 1.8 16 10-25 7-22 (157)
56 PF08711 Med26: TFIIS helical 22.8 27 0.00059 20.0 -0.1 11 44-54 41-51 (53)
57 PF02268 TFIIA_gamma_N: Transc 22.6 1.2E+02 0.0027 18.3 2.8 7 19-25 16-22 (49)
58 TIGR00423 radical SAM domain p 22.5 1.2E+02 0.0026 23.0 3.3 47 13-59 66-121 (309)
59 PF13606 Ank_3: Ankyrin repeat 22.1 39 0.00085 17.5 0.5 16 30-46 14-29 (30)
60 cd00197 VHS_ENTH_ANTH VHS, ENT 21.4 2.3E+02 0.0051 18.0 4.4 9 33-41 60-68 (115)
61 PRK00029 hypothetical protein; 21.3 1E+02 0.0022 26.1 3.0 30 27-56 197-245 (487)
62 PF12174 RST: RCD1-SRO-TAF4 (R 21.3 83 0.0018 20.0 1.9 41 9-49 21-62 (70)
63 PF12941 HCV_NS5a_C: HCV NS5a 21.3 32 0.00068 27.3 0.0 21 44-64 117-137 (244)
64 TIGR01461 greB transcription e 21.3 69 0.0015 22.7 1.7 16 10-25 5-20 (156)
65 PF04422 FrhB_FdhB_N: Coenzyme 20.8 75 0.0016 20.0 1.7 22 29-50 22-43 (82)
66 PF05693 Glycogen_syn: Glycoge 20.7 1.5E+02 0.0032 26.4 3.9 30 16-45 357-386 (633)
67 PRK11667 hypothetical protein; 20.4 47 0.001 24.8 0.7 15 32-46 77-91 (163)
68 PF08727 P3A: Poliovirus 3A pr 20.4 75 0.0016 20.1 1.6 31 10-45 14-44 (57)
69 PF00269 SASP: Small, acid-sol 20.3 1.3E+02 0.0028 18.5 2.6 17 18-34 8-24 (61)
No 1
>KOG3404 consensus G10 protein/predicted nuclear transcription regulator [Transcription]
Probab=100.00 E-value=6.9e-47 Score=270.93 Aligned_cols=75 Identities=61% Similarity=1.120 Sum_probs=73.7
Q ss_pred CCCCCCCCCCCCCchhhhHHHHHHH-----------------------------------------HHHHHHHHHHHHHh
Q 040196 1 MPKVKTNRVQNPEGWELIEPTLREL-----------------------------------------QKEISMELYEFCLD 39 (83)
Q Consensus 1 MPkir~~~k~pPeG~e~IeptL~e~-----------------------------------------~k~ISreLYe~~l~ 39 (83)
|||||++||+||+|||+|||||++| |++||+|||+||++
T Consensus 1 mpkv~~~rk~~Pdg~e~IeptL~e~e~kmReae~~~~~~~~~~E~lwpIfqlhHQrsRYiYdlyykR~~IS~eLY~~~l~ 80 (145)
T KOG3404|consen 1 MPKVKRSRKPPPDGWELIEPTLEEFEAKMREAETEPHEGKRKTESLWPIFQLHHQRSRYIYDLYYKRKAISRELYDYCLK 80 (145)
T ss_pred CCccCcCCCCCCcchhhhhhhHHHHHHHHHHhhcCcccCCCcchhhhhHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999 99999999999999
Q ss_pred hchhhHHHHHccCccchhhhhhccccccCCCCcchh
Q 040196 40 QGYAVRNLIAKGKQPGYERLCCLRCMQPHDHNFQMH 75 (83)
Q Consensus 40 ~~yaD~~LIaKWKK~GYE~LCCl~CIq~~d~nfgt~ 75 (83)
|+|||++|||||||+|||+||||||||++|+||||+
T Consensus 81 ~~yaD~~LiakWkk~GYE~LCClRCIq~~dsn~Gt~ 116 (145)
T KOG3404|consen 81 EKYADKNLIAKWKKQGYENLCCLRCIQTRDSNFGTT 116 (145)
T ss_pred cccchHHHHHHHhhcCccceeeeeeccccccCCCce
Confidence 999999999999999999999999999999999965
No 2
>PF01125 G10: G10 protein; InterPro: IPR001748 A Xenopus protein known as G10 [] has been found to be highly conserved in a wide range of eukaryotic species. The function of G10 is still unknown. G10 is a protein of about 17 to 18 kDa (143 to 157 residues) which is hydrophilic and whose C-terminal half is rich in cysteines and could be involved in metal-binding.; GO: 0005634 nucleus
Probab=100.00 E-value=2.5e-46 Score=267.98 Aligned_cols=75 Identities=59% Similarity=1.026 Sum_probs=71.9
Q ss_pred CCCCCCCC-CCCCCchhhhHHHHHHH-----------------------------------------HHHHHHHHHHHHH
Q 040196 1 MPKVKTNR-VQNPEGWELIEPTLREL-----------------------------------------QKEISMELYEFCL 38 (83)
Q Consensus 1 MPkir~~~-k~pPeG~e~IeptL~e~-----------------------------------------~k~ISreLYe~~l 38 (83)
||+||+++ ++||+|||+|||||++| +|+||+|||||||
T Consensus 1 MPkir~~~~k~pP~G~~~Ie~tL~e~~~kmr~ae~~~~~~k~k~e~lWpI~rI~hqrSRYIydlyYk~k~ISkeLY~~ll 80 (145)
T PF01125_consen 1 MPKIRTSRKKPPPEGFEKIEPTLEEFEQKMREAENEPHEGKRKNESLWPIFRIHHQRSRYIYDLYYKRKAISKELYDWLL 80 (145)
T ss_pred CCCcccCCCCCCCCchHHHHHHHHHHHHHHHHHhhCCCcCCCCCccccceeeecchhhhHHHHHHHHhhhccHHHHHHHH
Confidence 99999865 99999999999999999 8899999999999
Q ss_pred hhchhhHHHHHccCccchhhhhhccccccCCCCcchh
Q 040196 39 DQGYAVRNLIAKGKQPGYERLCCLRCMQPHDHNFQMH 75 (83)
Q Consensus 39 ~~~yaD~~LIaKWKK~GYE~LCCl~CIq~~d~nfgt~ 75 (83)
+|+|||++|||||||+|||+||||+|||++|+|||||
T Consensus 81 ~~~yaD~~LIaKWKk~GYE~LCCl~Ciq~~~~n~g~t 117 (145)
T PF01125_consen 81 KEKYADANLIAKWKKPGYEKLCCLRCIQTRDTNFGTT 117 (145)
T ss_pred HcCCcCHHHHHHhccccHHHHHHHHHhccccccCCCc
Confidence 9999999999999999999999999999999999843
No 3
>COG5132 BUD31 Cell cycle control protein, G10 family [Transcription / Cell division and chromosome partitioning]
Probab=100.00 E-value=2.8e-39 Score=231.44 Aligned_cols=75 Identities=44% Similarity=0.826 Sum_probs=72.6
Q ss_pred CCCCCCCC-CCCCCchhhhHHHHHHH----------------------------------------HHHHHHHHHHHHHh
Q 040196 1 MPKVKTNR-VQNPEGWELIEPTLREL----------------------------------------QKEISMELYEFCLD 39 (83)
Q Consensus 1 MPkir~~~-k~pPeG~e~IeptL~e~----------------------------------------~k~ISreLYe~~l~ 39 (83)
||+|+++| |+||+|||+|+|||++| |++||.+||+||++
T Consensus 1 MPRi~t~rskp~PdgFeki~ptL~~fe~~mRqaen~~~~~sk~E~lwpIfQLHHQRSRYIY~LyyKR~aISt~LY~wL~k 80 (146)
T COG5132 1 MPRIPTNRSKPAPDGFEKIRPTLEKFEAEMRQAENAPLAPSKPENLWPIFQLHHQRSRYIYNLYYKRGAISTKLYGWLSK 80 (146)
T ss_pred CCcCccCCCCCCCcchhhhcchHHHHHHHHHHHhcCCCCCCChHHhhHHHHHHHhhhHHHHHHHhhhhhHHHHHHHHHHH
Confidence 99999988 77899999999999999 89999999999999
Q ss_pred hchhhHHHHHccCccchhhhhhccccccCCCCcchh
Q 040196 40 QGYAVRNLIAKGKQPGYERLCCLRCMQPHDHNFQMH 75 (83)
Q Consensus 40 ~~yaD~~LIaKWKK~GYE~LCCl~CIq~~d~nfgt~ 75 (83)
|+|||.+|||||+|.|||+||||||||+.+++||++
T Consensus 81 ~~yaD~~LiakW~k~GYEkLCCLRCIQ~~esk~Gst 116 (146)
T COG5132 81 NRYADHELIAKWDKVGYEKLCCLRCIQPIESKHGST 116 (146)
T ss_pred hcccchhHhhhhcccchhhhhhHhhcCcccccCCCE
Confidence 999999999999999999999999999999999954
No 4
>PF14077 WD40_alt: Alternative WD40 repeat motif
Probab=88.63 E-value=0.53 Score=29.04 Aligned_cols=23 Identities=30% Similarity=0.602 Sum_probs=17.9
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHh
Q 040196 16 ELIEPTLRELQKEISMELYEFCLD 39 (83)
Q Consensus 16 e~IeptL~e~~k~ISreLYe~~l~ 39 (83)
..+|+.+..||| |+|+||||.-+
T Consensus 21 ~eLEeEV~~LrK-INrdLfdFSt~ 43 (48)
T PF14077_consen 21 SELEEEVRTLRK-INRDLFDFSTR 43 (48)
T ss_pred HHHHHHHHHHHH-HhHHHHhhhhh
Confidence 456777777787 99999999643
No 5
>PF08513 LisH: LisH; InterPro: IPR013720 The LisH motif is found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerization motif, and that other structural elements are likely to play an important role in dimerisation [, , ]. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex []. ; PDB: 2XTE_L 2XTC_B 2XTD_A 1UUJ_B.
Probab=73.28 E-value=4.9 Score=21.08 Aligned_cols=19 Identities=21% Similarity=0.653 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHhhchhhHH
Q 040196 28 EISMELYEFCLDQGYAVRN 46 (83)
Q Consensus 28 ~ISreLYe~~l~~~yaD~~ 46 (83)
.|..=+|+||+++||.+..
T Consensus 2 ~Ln~lI~~YL~~~Gy~~tA 20 (27)
T PF08513_consen 2 ELNQLIYDYLVENGYKETA 20 (27)
T ss_dssp HHHHHHHHHHHHCT-HHHH
T ss_pred HHHHHHHHHHHHCCcHHHH
Confidence 3566689999999998864
No 6
>smart00667 LisH Lissencephaly type-1-like homology motif. Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.
Probab=70.01 E-value=7.2 Score=19.36 Aligned_cols=20 Identities=25% Similarity=0.489 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHhhchhhHH
Q 040196 27 KEISMELYEFCLDQGYAVRN 46 (83)
Q Consensus 27 k~ISreLYe~~l~~~yaD~~ 46 (83)
+.+.+=+++|++++||.+..
T Consensus 4 ~~l~~lI~~yL~~~g~~~ta 23 (34)
T smart00667 4 SELNRLILEYLLRNGYEETA 23 (34)
T ss_pred HHHHHHHHHHHHHcCHHHHH
Confidence 45667799999999998765
No 7
>PF14553 YqbF: YqbF, hypothetical protein domain; PDB: 2HJQ_A.
Probab=68.55 E-value=2.4 Score=25.39 Aligned_cols=16 Identities=19% Similarity=0.538 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHhhchh
Q 040196 28 EISMELYEFCLDQGYA 43 (83)
Q Consensus 28 ~ISreLYe~~l~~~ya 43 (83)
.||+++|+||.++++-
T Consensus 20 ~V~kk~y~YL~~ne~F 35 (43)
T PF14553_consen 20 KVSKKIYNYLNDNEFF 35 (43)
T ss_dssp EE-HHHHHHHHHSTTE
T ss_pred ehhHHHHHHHhcCCcE
Confidence 4799999999998864
No 8
>PRK11798 ClpXP protease specificity-enhancing factor; Provisional
Probab=63.97 E-value=4 Score=29.55 Aligned_cols=16 Identities=31% Similarity=0.596 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHhhchh
Q 040196 28 EISMELYEFCLDQGYA 43 (83)
Q Consensus 28 ~ISreLYe~~l~~~ya 43 (83)
-+=|.|||||++||+-
T Consensus 10 YLlRA~yeW~~Dn~~T 25 (138)
T PRK11798 10 YLLRALYEWIVDNGLT 25 (138)
T ss_pred HHHHHHHHHHhhCCCC
Confidence 3568899999999873
No 9
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=58.27 E-value=5.9 Score=28.47 Aligned_cols=32 Identities=28% Similarity=0.351 Sum_probs=24.6
Q ss_pred chhhHHHHHccCccchhhhhhccccccCCCCcchhhhhhhhc
Q 040196 41 GYAVRNLIAKGKQPGYERLCCLRCMQPHDHNFQMHECAECLR 82 (83)
Q Consensus 41 ~yaD~~LIaKWKK~GYE~LCCl~CIq~~d~nfgt~~c~~~~~ 82 (83)
+.+|+.|| |+.|-+| |+.-|-.. +.+|.||-+
T Consensus 80 ~~~~~~~~--~~~pdg~-------~rry~~~~-n~ic~ecr~ 111 (127)
T PF06163_consen 80 KLVDPDLI--WKLPDGE-------IRRYDRRQ-NIICRECRK 111 (127)
T ss_pred hhccchhh--hhCCCcc-------cccccccc-chhHHHHhh
Confidence 45899998 8889888 56666655 679999964
No 10
>PF10730 DUF2521: Protein of unknown function (DUF2521); InterPro: IPR019667 This entry represents a protein of unknown function specific to Bacillus.
Probab=58.27 E-value=18 Score=26.58 Aligned_cols=33 Identities=30% Similarity=0.515 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHHhhc-------------hhhHHHHHccCccchhh
Q 040196 26 QKEISMELYEFCLDQG-------------YAVRNLIAKGKQPGYER 58 (83)
Q Consensus 26 ~k~ISreLYe~~l~~~-------------yaD~~LIaKWKK~GYE~ 58 (83)
.+.++.+||+|++.-+ |+-...|.-|-+.||++
T Consensus 92 e~~l~~~L~~~l~~W~~~~~~~~~~esly~ac~~fI~~WW~EGf~~ 137 (147)
T PF10730_consen 92 EKQLIDTLYNFLCYWGHIGEEDFDQESLYYACEQFIDSWWKEGFEK 137 (147)
T ss_pred HHHHHHHHHHHHHHhhhhcccchhhhHHHHHHHHHHHHHHHHHHHH
Confidence 6778999999999855 45567899999999985
No 11
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=51.73 E-value=17 Score=22.74 Aligned_cols=29 Identities=21% Similarity=0.437 Sum_probs=24.3
Q ss_pred hHHHHHHH-------HHHHHHHHHHHHHhhchhhHH
Q 040196 18 IEPTLREL-------QKEISMELYEFCLDQGYAVRN 46 (83)
Q Consensus 18 IeptL~e~-------~k~ISreLYe~~l~~~yaD~~ 46 (83)
+.|.|.+| +..|..-|++|.-.+++.|++
T Consensus 7 ls~~L~~~lg~~~~tr~ev~~~lw~YIk~n~L~d~~ 42 (77)
T smart00151 7 LSPELAKVLGAPEMTRTEIIKRLWEYIKEHNLQDPQ 42 (77)
T ss_pred CCHHHHHHhCCCcCcHHHHHHHHHHHHHHhcccCCc
Confidence 45667777 888999999999999999864
No 12
>cd08808 CARD_CARD11_CARMA1 Caspase activation and recruitment domain of CARD11-like proteins. Caspase activation and recruitment domain (CARD) similar to that found in CARD11, also known as caspase recruitment domain-containing membrane-associated guanylate kinase protein 1 (CARMA1). CARMA1, together with BCL10 (B-cell lymphoma 10) and Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1), form the L-CBM signalosome (CBM complex in lymphoid immune cells) which mediates activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. CARMA1 associates with BCL10 via a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by as
Probab=51.49 E-value=19 Score=24.40 Aligned_cols=32 Identities=19% Similarity=0.197 Sum_probs=27.5
Q ss_pred hhhhHHHHHHHHHHHHHH-HHHHHHhhchhhHH
Q 040196 15 WELIEPTLRELQKEISME-LYEFCLDQGYAVRN 46 (83)
Q Consensus 15 ~e~IeptL~e~~k~ISre-LYe~~l~~~yaD~~ 46 (83)
|+.||..-.++.+.|..+ |-.||.++|..|..
T Consensus 2 w~~~e~~R~~L~~~l~p~~v~pYLrQ~~Il~~~ 34 (86)
T cd08808 2 WENVECNRHMLSRYINPAKLTPYLRQCKVIDEQ 34 (86)
T ss_pred hHHHHHHHHHHHHHhhHhhccHHHHHcCCCChh
Confidence 899999988888888775 99999999998764
No 13
>COG2969 SspB Stringent starvation protein B [General function prediction only]
Probab=50.28 E-value=10 Score=28.16 Aligned_cols=14 Identities=36% Similarity=0.593 Sum_probs=12.2
Q ss_pred HHHHHHHHHHhhch
Q 040196 29 ISMELYEFCLDQGY 42 (83)
Q Consensus 29 ISreLYe~~l~~~y 42 (83)
+-|.|||||+++++
T Consensus 12 LlRA~yeWl~DN~~ 25 (155)
T COG2969 12 LLRALYEWLLDNQL 25 (155)
T ss_pred HHHHHHHHHhcCCC
Confidence 56789999999986
No 14
>PF12401 DUF3662: Protein of unknown function (DUF2662) ; InterPro: IPR022128 This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with PF00498 from PFAM. ; PDB: 2LC0_A.
Probab=48.17 E-value=9.6 Score=25.84 Aligned_cols=32 Identities=34% Similarity=0.541 Sum_probs=25.7
Q ss_pred CCchhhhHHHHHHHHHHHHHHHHHHHHhhchh
Q 040196 12 PEGWELIEPTLRELQKEISMELYEFCLDQGYA 43 (83)
Q Consensus 12 PeG~e~IeptL~e~~k~ISreLYe~~l~~~ya 43 (83)
|+.|+.+.+..+.|..+++..|.++.-+|||.
T Consensus 61 ~~D~~~l~~~~~~l~~el~~~l~~~a~~qgy~ 92 (116)
T PF12401_consen 61 PEDYERLSPWGDRLARELADYLAEHAREQGYT 92 (116)
T ss_dssp HHHHHHH-S-SHHHHHHHHHHHHHHHHHHT-B
T ss_pred HHHHHHHhhhHHHHHHHHHHHHHHHHHHCCCe
Confidence 67888999988888999999999999999985
No 15
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=44.89 E-value=6 Score=22.25 Aligned_cols=22 Identities=23% Similarity=0.449 Sum_probs=14.8
Q ss_pred hccccccC---CCCcchhhhhhhhc
Q 040196 61 CLRCMQPH---DHNFQMHECAECLR 82 (83)
Q Consensus 61 Cl~CIq~~---d~nfgt~~c~~~~~ 82 (83)
|..|-.+. |..-|..+|.+|..
T Consensus 3 Cp~Cg~~~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 3 CPNCGSKEIVFDPERGELVCPNCGL 27 (43)
T ss_dssp BTTTSSSEEEEETTTTEEEETTT-B
T ss_pred CcCCcCCceEEcCCCCeEECCCCCC
Confidence 45565543 66678899999963
No 16
>COG3433 Aryl carrier domain [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=41.71 E-value=8.6 Score=25.49 Aligned_cols=12 Identities=17% Similarity=0.434 Sum_probs=10.1
Q ss_pred HHHHccCccchh
Q 040196 46 NLIAKGKQPGYE 57 (83)
Q Consensus 46 ~LIaKWKK~GYE 57 (83)
.|.++|||.|++
T Consensus 36 ~L~~~wR~~G~~ 47 (74)
T COG3433 36 ALLERWRKRGAD 47 (74)
T ss_pred HHHHHHHHcCCc
Confidence 467899999986
No 17
>PF02201 SWIB: SWIB/MDM2 domain; InterPro: IPR003121 The SWI/SNF family of complexes, which are conserved from yeast to humans, are ATP-dependent chromatin-remodelling proteins that facilitate transcription activation []. The mammalian complexes are made up of 9-12 proteins called BAFs (BRG1-associated factors). The BAF60 family have at least three members: BAF60a, which is ubiquitous, BAF60b and BAF60c, which are expressed in muscle and pancreatic tissues, respectively. BAF60b is present in alternative forms of the SWI/SNF complex, including complex B (SWIB), which lacks BAF60a. The SWIB domain is a conserved region found within the BAF60b proteins [], and can be found fused to the C terminus of DNA topoisomerase in Chlamydia. MDM2 is an oncoprotein that acts as a cellular inhibitor of the p53 tumour suppressor by binding to the transactivation domain of p53 and suppressing its ability to activate transcription []. p53 acts in response to DNA damage, inducing cell cycle arrest and apoptosis. Inactivation of p53 is a common occurrence in neoplastic transformations. The core of MDM2 folds into an open bundle of four helices, which is capped by two small 3-stranded beta-sheets. It consists of a duplication of two structural repeats. MDM2 has a deep hydrophobic cleft on which the p53 alpha-helix binds; p53 residues involved in transactivation are buried deep within the cleft of MDM2, thereby concealing the p53 transactivation domain. The SWIB and MDM2 domains are homologous and share a common fold.; GO: 0005515 protein binding; PDB: 1V31_A 3FE7_A 3JZQ_B 3EQY_B 2VYR_A 3JZO_A 3DAB_E 3LBJ_E 3FEA_A 3FDO_A ....
Probab=40.10 E-value=40 Score=20.94 Aligned_cols=29 Identities=17% Similarity=0.439 Sum_probs=24.1
Q ss_pred hHHHHHHH-------HHHHHHHHHHHHHhhchhhHH
Q 040196 18 IEPTLREL-------QKEISMELYEFCLDQGYAVRN 46 (83)
Q Consensus 18 IeptL~e~-------~k~ISreLYe~~l~~~yaD~~ 46 (83)
+.|.|.++ |.+|-+.|++|.-.+++.|++
T Consensus 7 ls~~L~~~lg~~~~sr~~v~~~lw~YIk~~~L~dp~ 42 (76)
T PF02201_consen 7 LSPELAEFLGEDELSRSEVVKRLWQYIKENNLQDPK 42 (76)
T ss_dssp HHHHHHHHTT-SCEEHHHHHHHHHHHHHHTTSBESS
T ss_pred CCHHHHHHhCCCCCCHHHHHHHHHHHHHHhcCCCcc
Confidence 45667777 888999999999999998864
No 18
>KOG3222 consensus Inosine triphosphate pyrophosphatase [Nucleotide transport and metabolism]
Probab=39.41 E-value=29 Score=26.71 Aligned_cols=39 Identities=26% Similarity=0.365 Sum_probs=28.0
Q ss_pred CCCCCCCchhhh------HHHHHHH----------HHHHHHHHHHHHHhhchhhH
Q 040196 7 NRVQNPEGWELI------EPTLREL----------QKEISMELYEFCLDQGYAVR 45 (83)
Q Consensus 7 ~~k~pPeG~e~I------eptL~e~----------~k~ISreLYe~~l~~~yaD~ 45 (83)
+|-+-+.|||.| +.|..|+ |-.-+..|=+|+-++|+.|+
T Consensus 141 ~rG~~~fGwd~iFqP~g~~~tyaEMpk~ekN~iSHRy~A~~klk~yl~~~g~~~~ 195 (195)
T KOG3222|consen 141 PRGPTDFGWDPIFQPDGYEQTYAEMPKDEKNAISHRYRALAKLKEYLAENGVLDA 195 (195)
T ss_pred CCCCCCCCCCcccCCCccccchhhCChhHhhhhhHHHHHHHHHHHHHHhcCcccC
Confidence 345668999987 5577777 33334578899999988774
No 19
>KOG1753 consensus 40S ribosomal protein S16 [Translation, ribosomal structure and biogenesis]
Probab=39.11 E-value=36 Score=25.12 Aligned_cols=18 Identities=22% Similarity=0.394 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHhhchhhH
Q 040196 26 QKEISMELYEFCLDQGYAVR 45 (83)
Q Consensus 26 ~k~ISreLYe~~l~~~yaD~ 45 (83)
+.+||+.|+.|. ++|+|.
T Consensus 84 rqa~~kalvayy--qkyvDE 101 (145)
T KOG1753|consen 84 RQAIAKALVAYY--QKYVDE 101 (145)
T ss_pred HHHhhHHHHHHH--HHHHHH
Confidence 889999999887 457775
No 20
>cd08806 CARD_CARD14_CARMA2 Caspase activation and recruitment domain of CARD14-like proteins. Caspase activation and recruitment domain (CARD) similar to that found in CARD14, also known as BIMP2 or CARMA2 (caspase recruitment domain-containing membrane-associated guanylate kinase protein 2). CARD14 has been identified as a novel member of the MAGUK (membrane-associated guanylate kinase) family that functions as upstream activators of BCL10 (B-cell lymphoma 10) and NF-kB signaling. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways
Probab=38.42 E-value=32 Score=23.31 Aligned_cols=32 Identities=16% Similarity=0.264 Sum_probs=26.7
Q ss_pred hhhhHHHHHHHHHHHHHH-HHHHHHhhchhhHH
Q 040196 15 WELIEPTLRELQKEISME-LYEFCLDQGYAVRN 46 (83)
Q Consensus 15 ~e~IeptL~e~~k~ISre-LYe~~l~~~yaD~~ 46 (83)
|+.||..-.++.+.|... |-.||.++|..|..
T Consensus 2 w~~le~~R~~L~~~l~p~~l~pYLrQ~~IL~~~ 34 (86)
T cd08806 2 WEMMEDHRHRIVRGIRPSRLTPYLRQAKVLDQL 34 (86)
T ss_pred hHHHHHHHHHHHHhhcHhhccHHHHHcCCCChh
Confidence 888888888887778775 99999999988764
No 21
>PF08343 RNR_N: Ribonucleotide reductase N-terminal; InterPro: IPR013554 This domain is found at the N terminus of bacterial ribonucleoside-diphosphate reductases (ribonucleotide reductases, RNRs) which catalyse the formation of deoxyribonucleotides []. It occurs together with the RNR all-alpha domain (IPR013509 from INTERPRO) and the RNR barrel domain (IPR000788 from INTERPRO). ; GO: 0004748 ribonucleoside-diphosphate reductase activity, 0006260 DNA replication, 0055114 oxidation-reduction process, 0005971 ribonucleoside-diphosphate reductase complex; PDB: 1PEM_A 2BQ1_E 1PEU_A 1PEQ_A 1PEO_A.
Probab=38.01 E-value=29 Score=22.70 Aligned_cols=21 Identities=14% Similarity=0.381 Sum_probs=16.3
Q ss_pred HHHHHHHhhchhhHHHHHccC
Q 040196 32 ELYEFCLDQGYAVRNLIAKGK 52 (83)
Q Consensus 32 eLYe~~l~~~yaD~~LIaKWK 52 (83)
|=.+||+++||-|+.++.+-.
T Consensus 46 Erl~yLv~~~YYe~~~l~~Ys 66 (82)
T PF08343_consen 46 ERLDYLVENDYYEKEVLDKYS 66 (82)
T ss_dssp HHHHHHHHTTSB-HHHHTTS-
T ss_pred HHHHHHHHcCcHHHHHHHhCC
Confidence 456899999999999998653
No 22
>PF12644 DUF3782: Protein of unknown function (DUF3782); InterPro: IPR024271 This functionally uncharacterised family of proteins is found in bacteria and archaea. Proteins in this family are typically between 91 and 186 amino acids in length.
Probab=36.22 E-value=62 Score=19.04 Aligned_cols=39 Identities=15% Similarity=0.057 Sum_probs=24.2
Q ss_pred CCCCchhhhHHHHHHH--HHHHHHHHHHHHHhhchhhHHHHHcc
Q 040196 10 QNPEGWELIEPTLREL--QKEISMELYEFCLDQGYAVRNLIAKG 51 (83)
Q Consensus 10 ~pPeG~e~IeptL~e~--~k~ISreLYe~~l~~~yaD~~LIaKW 51 (83)
-+++.+..|+..++.+ +-.+ .=+..-++|+.|--.+++|
T Consensus 24 lt~e~~~~l~~~~~al~~~~~~---~~e~afr~G~~d~l~~~~~ 64 (64)
T PF12644_consen 24 LTKEDKKRLEEYIDALGARWGL---ESEEAFRQGFRDGLRLLGY 64 (64)
T ss_pred cCHHHHHHHHHHHHHHHHHhHH---HHHHHHHHHHHHHHHHhCc
Confidence 4567777777777666 2111 2234456788888777776
No 23
>PF12257 DUF3608: Protein of unknown function (DUF3608); InterPro: IPR022046 This domain family is found in eukaryotes, and is approximately 280 amino acids in length. The family is found in association with PF00610 from PFAM.
Probab=35.00 E-value=23 Score=28.07 Aligned_cols=11 Identities=36% Similarity=0.386 Sum_probs=9.4
Q ss_pred HHHHHccCccc
Q 040196 45 RNLIAKGKQPG 55 (83)
Q Consensus 45 ~~LIaKWKK~G 55 (83)
++|.+|||+.|
T Consensus 103 ~~lf~kWk~~~ 113 (281)
T PF12257_consen 103 PELFKKWKEIG 113 (281)
T ss_pred HHHHHHHhhcC
Confidence 56999999987
No 24
>PF09812 MRP-L28: Mitochondrial ribosomal protein L28; InterPro: IPR019192 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Members of this family are components of the mitochondrial large ribosomal subunit. Mature mitochondrial ribosomes consist of a small (37S) and a large (54S) subunit. The 37S subunit contains at least 33 different proteins and 1 molecule of RNA (15S). The 54S subunit contains at least 45 different proteins and 1 molecule of RNA (21S) [, ].
Probab=34.10 E-value=31 Score=24.91 Aligned_cols=22 Identities=32% Similarity=0.383 Sum_probs=13.7
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHh
Q 040196 17 LIEPTLRELQKEISMELYEFCLD 39 (83)
Q Consensus 17 ~IeptL~e~~k~ISreLYe~~l~ 39 (83)
-+...|++|+. +|.+||+--+.
T Consensus 100 sq~~AleeLr~-~S~eLY~aA~~ 121 (157)
T PF09812_consen 100 SQQKALEELRL-ESPELYQAAIQ 121 (157)
T ss_pred HHHHHHHHHHh-CCHHHHHHHhc
Confidence 34445555554 88889886654
No 25
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=34.00 E-value=16 Score=20.83 Aligned_cols=15 Identities=20% Similarity=0.512 Sum_probs=11.4
Q ss_pred CCCCcchhhhhhhhc
Q 040196 68 HDHNFQMHECAECLR 82 (83)
Q Consensus 68 ~d~nfgt~~c~~~~~ 82 (83)
+...||.++|++|.-
T Consensus 7 gq~~~~~~~C~~CgM 21 (41)
T PF13878_consen 7 GQKSFGATTCPTCGM 21 (41)
T ss_pred CCCccCCcCCCCCCC
Confidence 345689999999963
No 26
>PF03449 GreA_GreB_N: Transcription elongation factor, N-terminal; InterPro: IPR022691 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A 2ETN_C 2P4V_B.
Probab=33.00 E-value=34 Score=21.71 Aligned_cols=23 Identities=39% Similarity=0.745 Sum_probs=17.8
Q ss_pred CCCchhhhHHHHHHH----HHHHHHHH
Q 040196 11 NPEGWELIEPTLREL----QKEISMEL 33 (83)
Q Consensus 11 pPeG~e~IeptL~e~----~k~ISreL 33 (83)
.|+||+.+...|+.| +.+|++++
T Consensus 7 T~~g~~~L~~EL~~L~~~~rpe~~~~i 33 (74)
T PF03449_consen 7 TPEGYEKLQAELEHLKNVERPEIAEEI 33 (74)
T ss_dssp EHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHhhhHHHHHHH
Confidence 489999999999998 34555554
No 27
>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.
Probab=32.94 E-value=37 Score=19.59 Aligned_cols=24 Identities=38% Similarity=0.454 Sum_probs=19.2
Q ss_pred hhHHHHHHHHH---HHHHHHHHHHHhh
Q 040196 17 LIEPTLRELQK---EISMELYEFCLDQ 40 (83)
Q Consensus 17 ~IeptL~e~~k---~ISreLYe~~l~~ 40 (83)
.++|.|++++. -||.+||+..++.
T Consensus 20 ~~~~~l~~l~~~g~~is~~l~~~~L~~ 46 (48)
T PF11848_consen 20 EVKPLLDRLQQAGFRISPKLIEEILRR 46 (48)
T ss_pred hHHHHHHHHHHcCcccCHHHHHHHHHH
Confidence 68888999844 4899999988863
No 28
>PRK14134 recX recombination regulator RecX; Provisional
Probab=32.80 E-value=68 Score=24.71 Aligned_cols=16 Identities=31% Similarity=0.611 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHhhchh
Q 040196 28 EISMELYEFCLDQGYA 43 (83)
Q Consensus 28 ~ISreLYe~~l~~~ya 43 (83)
.+.+.||.||++.||-
T Consensus 253 k~~~Kl~~~L~rkGf~ 268 (283)
T PRK14134 253 KIYRRLSNYLLRRGYS 268 (283)
T ss_pred HHHHHHHHHHHhCCCC
Confidence 3667888899988874
No 29
>COG5418 Predicted secreted protein [Function unknown]
Probab=31.27 E-value=6.3 Score=29.51 Aligned_cols=25 Identities=28% Similarity=0.849 Sum_probs=14.6
Q ss_pred CCCchhhhH---HHHHHH---HHHHHHHHHH
Q 040196 11 NPEGWELIE---PTLREL---QKEISMELYE 35 (83)
Q Consensus 11 pPeG~e~Ie---ptL~e~---~k~ISreLYe 35 (83)
-|+||..|. |.++=| |..||||.||
T Consensus 41 npk~~~IiqlPCPE~~yLg~~R~~~tke~~d 71 (164)
T COG5418 41 NPKDWNIIQLPCPEFEYLGWPRPPMTKEVFD 71 (164)
T ss_pred CCCCCceEeccCchHHhhCCCCCCcCHHHhc
Confidence 377777775 333333 6667776665
No 30
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=31.09 E-value=33 Score=24.61 Aligned_cols=21 Identities=33% Similarity=0.545 Sum_probs=18.3
Q ss_pred CCCchhhhHHHHHHHHHHHHH
Q 040196 11 NPEGWELIEPTLRELQKEISM 31 (83)
Q Consensus 11 pPeG~e~IeptL~e~~k~ISr 31 (83)
-+++|++|...|++||+.|..
T Consensus 130 s~~~~~ki~~~i~~fRk~i~~ 150 (171)
T PF14394_consen 130 SREDYEKIKKEIREFRKKIIA 150 (171)
T ss_pred CHHHHHHHHHHHHHHHHHHHH
Confidence 368999999999999988874
No 31
>PF08866 DUF1831: Putative amino acid metabolism; InterPro: IPR014965 These short proteins are functionally uncharacterised. ; PDB: 2IAY_A.
Probab=30.76 E-value=23 Score=24.89 Aligned_cols=24 Identities=25% Similarity=0.414 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHhhchhhHHHHHc
Q 040196 26 QKEISMELYEFCLDQGYAVRNLIAK 50 (83)
Q Consensus 26 ~k~ISreLYe~~l~~~yaD~~LIaK 50 (83)
+.++..|.|.|+++ +++|++.+.|
T Consensus 89 ~~~~~ve~~~Fi~d-~lveR~Vl~k 112 (112)
T PF08866_consen 89 DNAELVEKYYFIMD-DLVERGVLEK 112 (112)
T ss_dssp --HHHHHHHHHHHH-HHHHTTSEE-
T ss_pred ccHHHHHHHHHHHH-HHHhcccccC
Confidence 67899999999998 7888876543
No 32
>cd08785 CARD_CARD9-like Caspase activation and recruitment domain of CARD9 and related proteins. Caspase activation and recruitment domain (CARD) found in CARD9, CARD14 (CARMA2), CARD10 (CARMA3), CARD11 (CARMA1) and BCL10. BCL10 (B-cell lymphoma 10), together with Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1), are integral components of the CBM signalosome. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells), and with CARD11 to form L-CBM (CBM complex in lymphoid immune cells), which mediates activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. BCL10/Malt1 also associates with CARD10, which is more widely expressed and is not restricted to hematopoietic cells, to play a role in GPCR-induced NF-kB activation. CARD14 has also been shown to associate with BCL10. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inf
Probab=30.70 E-value=96 Score=20.32 Aligned_cols=35 Identities=17% Similarity=0.115 Sum_probs=22.5
Q ss_pred hhhhHHHHHHH-HHHHHHHHHHHHHhhchhhHHHHH
Q 040196 15 WELIEPTLREL-QKEISMELYEFCLDQGYAVRNLIA 49 (83)
Q Consensus 15 ~e~IeptL~e~-~k~ISreLYe~~l~~~yaD~~LIa 49 (83)
||.++.-=..| +...-.++++||+..|..|.+=+.
T Consensus 2 ~~~L~~~R~~L~~~l~~~~l~d~L~q~~VLt~~d~E 37 (86)
T cd08785 2 WEALEGMRHRLTRKINPSRLTPYLRQCKVLDEQDEE 37 (86)
T ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHhcCCCCHHHHH
Confidence 55555544444 333334599999999998877543
No 33
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=29.36 E-value=40 Score=19.88 Aligned_cols=14 Identities=21% Similarity=0.695 Sum_probs=7.3
Q ss_pred HHHHHHHHhhchhh
Q 040196 31 MELYEFCLDQGYAV 44 (83)
Q Consensus 31 reLYe~~l~~~yaD 44 (83)
+-+|+|+++++|.|
T Consensus 72 ~~ff~~~~~~~~~~ 85 (85)
T PF13495_consen 72 RSFFRWLLERGYEQ 85 (85)
T ss_dssp HHHHHCTSS-----
T ss_pred HHHHHHHHcCCCCC
Confidence 45899999888875
No 34
>PF08811 DUF1800: Protein of unknown function (DUF1800); InterPro: IPR014917 This is an entry of large bacterial proteins of unknown function.
Probab=29.16 E-value=95 Score=25.35 Aligned_cols=59 Identities=15% Similarity=0.128 Sum_probs=42.9
Q ss_pred CCCC--chhhhHHHHHHH------HHHHHHHHHHHHHhhchhhHHHHHc----cCccchhhhhhccccccCC
Q 040196 10 QNPE--GWELIEPTLREL------QKEISMELYEFCLDQGYAVRNLIAK----GKQPGYERLCCLRCMQPHD 69 (83)
Q Consensus 10 ~pPe--G~e~IeptL~e~------~k~ISreLYe~~l~~~yaD~~LIaK----WKK~GYE~LCCl~CIq~~d 69 (83)
.-|. |-+.++..|+.+ -+-|++.||.+++-.. .++++|+. |++.+|+--=-++-|-+.+
T Consensus 243 t~~~~~g~~~~~~~ld~L~~hP~tA~fia~kL~~~fv~d~-P~~~~V~~la~~f~~~~gdl~~vl~all~s~ 313 (462)
T PF08811_consen 243 TIPAAGGNDDGDDVLDILAEHPATARFIARKLIRRFVADN-PPPAYVARLAAAFRDNDGDLKAVLRALLTSP 313 (462)
T ss_pred cCCCCCchHHHHHHHHHHHcCCchHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHcCCCcHHHHHHHHHCCH
Confidence 3455 999999999999 6679999999999866 67777654 7777766544444444433
No 35
>PF12029 DUF3516: Domain of unknown function (DUF3516); InterPro: IPR021904 This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is typically between 460 to 473 amino acids in length. This domain is found associated with PF00270 from PFAM, PF00271 from PFAM.
Probab=28.99 E-value=69 Score=27.46 Aligned_cols=19 Identities=37% Similarity=0.515 Sum_probs=13.6
Q ss_pred CCCCCCCchhh-hHHHHHHH
Q 040196 7 NRVQNPEGWEL-IEPTLREL 25 (83)
Q Consensus 7 ~~k~pPeG~e~-IeptL~e~ 25 (83)
.+|+|||||=- =|.|.+.|
T Consensus 26 ~rkk~PeG~V~W~e~TF~rL 45 (461)
T PF12029_consen 26 VRKKPPEGFVSWSEKTFERL 45 (461)
T ss_pred cCCCCCCCccCCCHHHHHHH
Confidence 34899999843 36677777
No 36
>KOG4019 consensus Calcineurin-mediated signaling pathway inhibitor DSCR1 [Signal transduction mechanisms; General function prediction only]
Probab=28.76 E-value=18 Score=27.72 Aligned_cols=12 Identities=50% Similarity=0.960 Sum_probs=9.9
Q ss_pred CCCCchhhhHHH
Q 040196 10 QNPEGWELIEPT 21 (83)
Q Consensus 10 ~pPeG~e~Iept 21 (83)
-||-||+.||+.
T Consensus 115 SPPvgWe~~eda 126 (193)
T KOG4019|consen 115 SPPVGWEPIEDA 126 (193)
T ss_pred CCCCCCcccccC
Confidence 478999999863
No 37
>PRK10304 ferritin; Provisional
Probab=27.92 E-value=78 Score=22.48 Aligned_cols=46 Identities=11% Similarity=0.174 Sum_probs=30.2
Q ss_pred CCCCCchhhhHHHHHHH---------------------HHHHHHHHHHHHHhh-----chhhHHHHHccCccc
Q 040196 9 VQNPEGWELIEPTLREL---------------------QKEISMELYEFCLDQ-----GYAVRNLIAKGKQPG 55 (83)
Q Consensus 9 k~pPeG~e~IeptL~e~---------------------~k~ISreLYe~~l~~-----~yaD~~LIaKWKK~G 55 (83)
..||.-|+.+++.++.- +...|+.+.+|.+++ ..++ .|+.+.+.-|
T Consensus 74 ~~p~~~~~s~~e~~~~~l~~E~~vt~~i~~l~~~A~~~~D~~t~~fl~~fl~EQveEe~~~~-~l~~~l~~~~ 145 (165)
T PRK10304 74 ESPFAEYSSLDELFQETYKHEQLITQKINELAHAAMTNQDYPTFNFLQWYVSEQHEEEKLFK-SIIDKLSLAG 145 (165)
T ss_pred CCCccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHHH-HHHHHHHhhC
Confidence 34778888888877765 334567778888876 2333 3667666554
No 38
>KOG2404 consensus Fumarate reductase, flavoprotein subunit [Energy production and conversion]
Probab=27.16 E-value=81 Score=27.01 Aligned_cols=44 Identities=23% Similarity=0.346 Sum_probs=31.1
Q ss_pred CCCCCCCCCCCCchhhhHHHHHHHHHHHHH--HHHHHHHhhchhhH
Q 040196 2 PKVKTNRVQNPEGWELIEPTLRELQKEISM--ELYEFCLDQGYAVR 45 (83)
Q Consensus 2 Pkir~~~k~pPeG~e~IeptL~e~~k~ISr--eLYe~~l~~~yaD~ 45 (83)
||--++..|-|+|||.+..--+.++|.-|. |+..-++..+.+|-
T Consensus 126 pRTHr~s~plppgfei~~~L~~~l~k~as~~pe~~ki~~nskvv~i 171 (477)
T KOG2404|consen 126 PRTHRSSGPLPPGFEIVKALSTRLKKKASENPELVKILLNSKVVDI 171 (477)
T ss_pred CcccccCCCCCCchHHHHHHHHHHHHhhhcChHHHhhhhcceeeee
Confidence 554444467799999998877777665443 78888877776663
No 39
>PF07261 DnaB_2: Replication initiation and membrane attachment; InterPro: IPR006343 This entry represents a domain found in several bacterial replication initiation and membrane attachment proteins, DnaB and DnaD. The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA []. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria []. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and Plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication []. This domain tends to be found towards the C terminus of DnaB and DnaD proteins and is alpha helical in nature.; PDB: 2I5U_A 2ZC2_A.
Probab=25.83 E-value=87 Score=18.37 Aligned_cols=48 Identities=23% Similarity=0.388 Sum_probs=30.3
Q ss_pred CCCCCchhhhHHHHH--HHHHHHHHHHHHHHHhhc-----hhhHHHHHccCccchh
Q 040196 9 VQNPEGWELIEPTLR--ELQKEISMELYEFCLDQG-----YAVRNLIAKGKQPGYE 57 (83)
Q Consensus 9 k~pPeG~e~IeptL~--e~~k~ISreLYe~~l~~~-----yaD~~LIaKWKK~GYE 57 (83)
.+.|--.+.|+..++ .|...+=.+++++++.++ |+++ .+..|++.|-.
T Consensus 12 ~~s~~e~~~l~~~~~~~~~~~~~v~~ai~~~~~~~~~~~~Yi~~-Il~~W~~~gi~ 66 (77)
T PF07261_consen 12 PPSPSEIEKLEKWIDDYGFSPEVVNEAIEYALENNKRSFNYIEK-ILNNWKQKGIK 66 (77)
T ss_dssp S--HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCT--SHHHHHH-HHHHHHHCT--
T ss_pred CCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCCHHHHHH-HHHHHHHcCCC
Confidence 344555667777777 666667777888888644 5553 34459888854
No 40
>PF01199 Ribosomal_L34e: Ribosomal protein L34e; InterPro: IPR008195 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaebacterial ribosomal proteins belong to the L34e family. These include, vertebrate L34, mosquito L31 [], plant L34 [], yeast putative ribosomal protein YIL052c and archaebacterial L34e.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_i 3IZS_i 4A19_L 4A1D_L 4A18_L 4A1B_L.
Probab=25.72 E-value=28 Score=23.56 Aligned_cols=17 Identities=18% Similarity=0.548 Sum_probs=11.5
Q ss_pred ccCCCCcchhhhhhhhc
Q 040196 66 QPHDHNFQMHECAECLR 82 (83)
Q Consensus 66 q~~d~nfgt~~c~~~~~ 82 (83)
-+-+-.||.+.|+.|++
T Consensus 70 k~vsRaYGG~lc~~cvr 86 (94)
T PF01199_consen 70 KTVSRAYGGSLCHKCVR 86 (94)
T ss_dssp H--CCTSSSS-HHHHHH
T ss_pred CCCCCCCCccchHHHHH
Confidence 34456799999999986
No 41
>PRK06342 transcription elongation factor regulatory protein; Validated
Probab=25.68 E-value=43 Score=24.06 Aligned_cols=20 Identities=15% Similarity=0.270 Sum_probs=16.7
Q ss_pred CCCchhhhHHHHHHHHHHHH
Q 040196 11 NPEGWELIEPTLRELQKEIS 30 (83)
Q Consensus 11 pPeG~e~IeptL~e~~k~IS 30 (83)
.|+||+.++..|+.|+.+|+
T Consensus 32 T~~G~~~L~~El~~L~~~i~ 51 (160)
T PRK06342 32 TEAGLKALEDQLAQARAAYE 51 (160)
T ss_pred CHHHHHHHHHHHHHHHHHHH
Confidence 48999999999999965553
No 42
>COG0782 Uncharacterized conserved protein, YhbC family [Function unknown]
Probab=25.62 E-value=74 Score=22.50 Aligned_cols=25 Identities=28% Similarity=0.409 Sum_probs=20.6
Q ss_pred CCchhhhHHHHHHH----HHHHHHHHHHH
Q 040196 12 PEGWELIEPTLREL----QKEISMELYEF 36 (83)
Q Consensus 12 PeG~e~IeptL~e~----~k~ISreLYe~ 36 (83)
++||+.+++-|+.+ +.+|++++.+.
T Consensus 3 ~~g~~~l~~el~~l~~~~rp~i~~~i~~a 31 (151)
T COG0782 3 DEGFRKLKEELEYLKPVERPEIVEEIADA 31 (151)
T ss_pred chHHHHHHHHHHHhhhccchHHHHHHHHH
Confidence 68999999999999 55788776654
No 43
>PF00104 Hormone_recep: Ligand-binding domain of nuclear hormone receptor; InterPro: IPR000536 Steroid or nuclear hormone receptors constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences (IPR001628 from INTERPRO), connected via a linker region to a C-terminal ligand-binding domain. In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The ligand-binding domain acts in response to ligand binding, which caused a conformational change in the receptor to induce a response, thereby acting as a molecular switch to turn on transcriptional activity []. For example, after binding of the glucocorticoid receptor to the corticosteroid ligand, the receptor is induced to perform functions ranging from nuclear translocation, oligomerisation, cofactor/kinase/transcription factor association, and DNA binding []. The ligand-binding domain is a flexible unit, where the binding of a ligand stabilises its conformation, which in turn favours coactivator binding to modify receptor activity []; the coactivator can bind to the activator function 2 (AF2) site at the C-terminal end of the ligand-binding domain []. The binding of different ligands can alter the conformation of the ligand-binding domain, which ultimately affects the DNA-binding specificity of the DNA-binding domain. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components. This entry represents the C-terminal ligand-binding domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0003707 steroid hormone receptor activity, 0006355 regulation of transcription, DNA-dependent, 0043401 steroid hormone mediated signaling pathway, 0005634 nucleus; PDB: 3IXP_D 1R20_D 2R40_D 1R1K_D 1PDU_B 1OSH_A 3GD2_A 3DCT_A 3OMK_C 3FLI_A ....
Probab=24.94 E-value=2e+02 Score=18.81 Aligned_cols=28 Identities=18% Similarity=0.203 Sum_probs=20.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHH-Hhhchhh
Q 040196 17 LIEPTLRELQKEISMELYEFC-LDQGYAV 44 (83)
Q Consensus 17 ~IeptL~e~~k~ISreLYe~~-l~~~yaD 44 (83)
.....++++|..|.++|.+|+ -..+..|
T Consensus 143 ~~~~~~~~~r~~~~~~L~~y~~~~~~~~~ 171 (203)
T PF00104_consen 143 ETREIVEELRDRIIQALHSYYNQSKGPED 171 (203)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHHHHHSTTT
T ss_pred chhHHHHHHHHHHHHHHHHHHhccCCCcc
Confidence 444567788999999999999 4445554
No 44
>PF05982 DUF897: Domain of unknown function (DUF897) ; InterPro: IPR010293 This is a family of bacterial proteins with unknown function
Probab=24.92 E-value=50 Score=26.93 Aligned_cols=42 Identities=29% Similarity=0.481 Sum_probs=33.8
Q ss_pred CCCchhhhHHHHHHH-HHHHHHHHHHHHHhhchhhHHHHHccCccch
Q 040196 11 NPEGWELIEPTLREL-QKEISMELYEFCLDQGYAVRNLIAKGKQPGY 56 (83)
Q Consensus 11 pPeG~e~IeptL~e~-~k~ISreLYe~~l~~~yaD~~LIaKWKK~GY 56 (83)
-|+|++.|+|...++ +-. |-=|+|+.|..-..=+..+||.|.
T Consensus 194 g~~g~~~i~pf~~~lF~G~----L~lFLLeMGl~A~~rL~~l~~~g~ 236 (327)
T PF05982_consen 194 GPEGVESIKPFFVDLFKGV----LCLFLLEMGLVAARRLRDLRKVGW 236 (327)
T ss_pred CccchhhccchhhccHHHH----HHHHHHHhhHHHHHhhHHHHhhhH
Confidence 378888888887666 333 556899999999999999999885
No 45
>smart00430 HOLI Ligand binding domain of hormone receptors.
Probab=24.83 E-value=1.4e+02 Score=18.70 Aligned_cols=22 Identities=23% Similarity=0.389 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhc
Q 040196 20 PTLRELQKEISMELYEFCLDQG 41 (83)
Q Consensus 20 ptL~e~~k~ISreLYe~~l~~~ 41 (83)
.+++++++.+...|..|+..++
T Consensus 121 ~~~~~~~~~~~~~L~~y~~~~~ 142 (163)
T smart00430 121 EILEKLQEKLANALHDYYLKNY 142 (163)
T ss_pred HHHHHHHHHHHHHHHHHHHHcC
Confidence 5677779999999999997754
No 46
>PF13718 GNAT_acetyltr_2: GNAT acetyltransferase 2; PDB: 2ZPA_B.
Probab=24.56 E-value=28 Score=26.06 Aligned_cols=31 Identities=13% Similarity=0.128 Sum_probs=18.5
Q ss_pred hHHHHHccCccchhhhhhccccccCCCCcchhhh
Q 040196 44 VRNLIAKGKQPGYERLCCLRCMQPHDHNFQMHEC 77 (83)
Q Consensus 44 D~~LIaKWKK~GYE~LCCl~CIq~~d~nfgt~~c 77 (83)
..+|+.-|+|.||..+ +.-|+.|...|...|
T Consensus 159 t~~Ll~FW~k~gf~pv---~l~~~~n~~SGe~S~ 189 (196)
T PF13718_consen 159 TPELLKFWQKNGFVPV---YLGQTRNEASGEHSA 189 (196)
T ss_dssp -HHHHHHHHCTT-EEE---EE-SS--TTT---EE
T ss_pred CHHHHHHHHHCCcEEE---EEecCcccccCceee
Confidence 5899999999999864 666777776665544
No 47
>KOG0995 consensus Centromere-associated protein HEC1 [Cell cycle control, cell division, chromosome partitioning]
Probab=24.51 E-value=57 Score=28.69 Aligned_cols=21 Identities=14% Similarity=0.472 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHhhchhhHH
Q 040196 26 QKEISMELYEFCLDQGYAVRN 46 (83)
Q Consensus 26 ~k~ISreLYe~~l~~~yaD~~ 46 (83)
+.++-+.+|+||+.+||.++-
T Consensus 72 ~s~c~~~I~~fL~engf~~~i 92 (581)
T KOG0995|consen 72 RSQCIRQIYNFLVENGFSHPI 92 (581)
T ss_pred HHHHHHHHHHHHHHcCCCCCh
Confidence 778899999999999999653
No 48
>PF06945 DUF1289: Protein of unknown function (DUF1289); InterPro: IPR010710 This family consists of a number of hypothetical bacterial proteins. The aligned region spans around 56 residues and contains 4 highly conserved cysteine residues towards the N terminus. The function of this family is unknown.
Probab=24.16 E-value=31 Score=20.36 Aligned_cols=20 Identities=25% Similarity=0.421 Sum_probs=15.0
Q ss_pred ccccCCCCcchhhhhhhhcC
Q 040196 64 CMQPHDHNFQMHECAECLRT 83 (83)
Q Consensus 64 CIq~~d~nfgt~~c~~~~~~ 83 (83)
||..=..+.++.+|-.|+||
T Consensus 4 Ci~vC~~d~~~~~C~GC~RT 23 (51)
T PF06945_consen 4 CIGVCKLDPSDGVCRGCGRT 23 (51)
T ss_pred CccccccCCCCCccCCCCCc
Confidence 44444566788999999997
No 49
>PF14529 Exo_endo_phos_2: Endonuclease-reverse transcriptase ; PDB: 2EI9_A 1WDU_B.
Probab=24.15 E-value=1.5e+02 Score=17.99 Aligned_cols=20 Identities=10% Similarity=0.027 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHhhchhhHHH
Q 040196 28 EISMELYEFCLDQGYAVRNL 47 (83)
Q Consensus 28 ~ISreLYe~~l~~~yaD~~L 47 (83)
.-.++|.+|+...++++.+.
T Consensus 54 ~~~~~l~~~~~~~~l~~~~~ 73 (119)
T PF14529_consen 54 RRGEQLLDWLDSHNLVDLNP 73 (119)
T ss_dssp HHHHHHHHHHHHCTEEE---
T ss_pred hhHHHHHHHhhhceeeeeec
Confidence 67889999999999997754
No 50
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=23.60 E-value=1.2e+02 Score=17.91 Aligned_cols=45 Identities=22% Similarity=0.183 Sum_probs=28.9
Q ss_pred CCchhhhHHHHHHH--HHHHHHHHHHHHHhh-----chhhHHHHHccCccchh
Q 040196 12 PEGWELIEPTLREL--QKEISMELYEFCLDQ-----GYAVRNLIAKGKQPGYE 57 (83)
Q Consensus 12 PeG~e~IeptL~e~--~k~ISreLYe~~l~~-----~yaD~~LIaKWKK~GYE 57 (83)
|--.+.|..-++++ .-.+=.+++++++++ +|+++=| ..|++.|-.
T Consensus 15 ~~e~~~i~~~~~~~~~~~evI~~ai~~a~~~~~~~~~Yi~~Il-~~W~~~gi~ 66 (73)
T TIGR01446 15 PFEMEDLKYWLDEFGNSPELIKEALKEAVSNNKANYKYIDAIL-NNWKNNGIK 66 (73)
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCHHHHHHHH-HHHHHcCCC
Confidence 45566677777775 235556777778754 4666444 459998864
No 51
>PF10929 DUF2811: Protein of unknown function (DUF2811); InterPro: IPR021231 This is a bacterial family of uncharacterised proteins.
Probab=23.47 E-value=2e+02 Score=18.08 Aligned_cols=32 Identities=16% Similarity=0.306 Sum_probs=24.5
Q ss_pred hhHHHHHHH---------HHHHHHHHHHHHHhhchhhHHHH
Q 040196 17 LIEPTLREL---------QKEISMELYEFCLDQGYAVRNLI 48 (83)
Q Consensus 17 ~IeptL~e~---------~k~ISreLYe~~l~~~yaD~~LI 48 (83)
.+-..|..| .+.++-.|=-||+.+|.-|+.+-
T Consensus 9 ~L~~~m~~fie~hP~WDQ~Rl~~aALa~FL~QnG~~~r~~~ 49 (57)
T PF10929_consen 9 DLHQAMKDFIETHPNWDQYRLFQAALAGFLLQNGCQDRAVT 49 (57)
T ss_pred HHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCchhHHHH
Confidence 445566666 77888889999999998887653
No 52
>COG2001 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.24 E-value=48 Score=24.07 Aligned_cols=17 Identities=35% Similarity=0.532 Sum_probs=15.2
Q ss_pred CCCCCchhhhHHHHHHH
Q 040196 9 VQNPEGWELIEPTLREL 25 (83)
Q Consensus 9 k~pPeG~e~IeptL~e~ 25 (83)
.-|++.||.++..|..+
T Consensus 45 vyp~~ewe~~~~kl~~l 61 (146)
T COG2001 45 VYPLAEWERLEEKLSAL 61 (146)
T ss_pred ecCHHHHHHHHHHHHcC
Confidence 35889999999999998
No 53
>PF14754 IFR3_antag: Papain-like auto-proteinase
Probab=23.06 E-value=35 Score=26.51 Aligned_cols=12 Identities=42% Similarity=0.683 Sum_probs=10.1
Q ss_pred cchhhhhhhhcC
Q 040196 72 FQMHECAECLRT 83 (83)
Q Consensus 72 fgt~~c~~~~~~ 83 (83)
-|++.||||.|.
T Consensus 36 dgstlcaecfrg 47 (249)
T PF14754_consen 36 DGSTLCAECFRG 47 (249)
T ss_pred cCccHHHHHhcc
Confidence 589999999873
No 54
>PF02696 UPF0061: Uncharacterized ACR, YdiU/UPF0061 family; InterPro: IPR003846 The proteins in this entry are functionally uncharacterised.
Probab=22.90 E-value=1e+02 Score=26.12 Aligned_cols=30 Identities=20% Similarity=0.380 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHhhchhh-----------------------HHHHHccCccch
Q 040196 27 KEISMELYEFCLDQGYAV-----------------------RNLIAKGKQPGY 56 (83)
Q Consensus 27 k~ISreLYe~~l~~~yaD-----------------------~~LIaKWKK~GY 56 (83)
...-+.|-||+++.-|.+ +.|||+|---||
T Consensus 198 ~~~l~~L~dy~i~~~~pe~~~~~~~~~~~y~~~~~~v~~rtA~lvA~Wq~vGF 250 (487)
T PF02696_consen 198 PEGLRQLADYVIKRHYPEIQGHLADDEDPYLALLREVVERTAELVAQWQAVGF 250 (487)
T ss_pred HHHHHHHHHHHHHHhCCcccccccccccHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 344567788888776652 579999999998
No 55
>PRK01885 greB transcription elongation factor GreB; Reviewed
Probab=22.85 E-value=62 Score=22.99 Aligned_cols=16 Identities=25% Similarity=0.387 Sum_probs=14.5
Q ss_pred CCCCchhhhHHHHHHH
Q 040196 10 QNPEGWELIEPTLREL 25 (83)
Q Consensus 10 ~pPeG~e~IeptL~e~ 25 (83)
-.|+|++.++..|+.|
T Consensus 7 lT~~g~~~L~~EL~~L 22 (157)
T PRK01885 7 ITREGYARLKQELDYL 22 (157)
T ss_pred cCHHHHHHHHHHHHHH
Confidence 4589999999999999
No 56
>PF08711 Med26: TFIIS helical bundle-like domain; InterPro: IPR017923 Transcription factor IIS (TFIIS) is a transcription elongation factor that increases the overall transcription rate of RNA polymerase II by reactivating transcription elongation complexes that have arrested transcription. The three structural domains of TFIIS are conserved from yeast to human. The 80 or so N-terminal residues form a protein interaction domain containing a conserved motif, which has been called the LW motif because of the invariant leucine and tryptophan residues it contains. Although the N-terminal domain is not needed for transcriptional activity, a similar sequence has been identified in other transcription factors and proteins that are predominantly nuclear localized [, ]: MED26 (also known as CRSP70 and ARC70), a subunit of the Mediator complex, which is required for the activity of the enhancer-binding protein Sp1. Elongin A, a subunit of a transcription elongation factor previously known as SIII. It increases the rate of transcription by suppressing transient pausing of the elongation complex. PPP1R10, a nuclear regulatory subunit of protein phosphatase 1 that was previously known as p99, FB19 or PNUTS. PIBP, a small hypothetical protein that could be a phosphoinositide binding protein. IWS1, which is thought to function in both transcription initiation and elongation. The TFIIS N-terminal domain is a compact four-helix bundle. The hydrophobic core residues of helices 2, 3, and 4 are well conserved among TFIIS domains, although helix 1 is less conserved []. ; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 1EO0_A 3OAK_A 3NFQ_B 3O8Z_A 1WJT_A 2XPL_A 2XPO_A 2XPP_A 2XPN_A.
Probab=22.78 E-value=27 Score=19.99 Aligned_cols=11 Identities=36% Similarity=0.383 Sum_probs=8.3
Q ss_pred hHHHHHccCcc
Q 040196 44 VRNLIAKGKQP 54 (83)
Q Consensus 44 D~~LIaKWKK~ 54 (83)
-.+||.+||+.
T Consensus 41 A~~Li~~Wk~~ 51 (53)
T PF08711_consen 41 AKELIKKWKRI 51 (53)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHhHh
Confidence 46799999863
No 57
>PF02268 TFIIA_gamma_N: Transcription initiation factor IIA, gamma subunit, helical domain; InterPro: IPR015872 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the alpha-helical domain found at the N-terminal of the gamma subunit of transcription factor TFIIA.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=22.59 E-value=1.2e+02 Score=18.31 Aligned_cols=7 Identities=57% Similarity=0.620 Sum_probs=3.5
Q ss_pred HHHHHHH
Q 040196 19 EPTLREL 25 (83)
Q Consensus 19 eptL~e~ 25 (83)
.++|+|+
T Consensus 16 ~dtLDel 22 (49)
T PF02268_consen 16 TDTLDEL 22 (49)
T ss_dssp HHHHHHH
T ss_pred HHHHHHH
Confidence 3445555
No 58
>TIGR00423 radical SAM domain protein, CofH subfamily. This protein family includes the CofH protein of coenzyme F(420) biosynthesis from Methanocaldococcus jannaschii, but appears to hit genomes more broadly than just the subset that make coenzyme F(420), so that narrower group is being built as a separate family.
Probab=22.50 E-value=1.2e+02 Score=22.95 Aligned_cols=47 Identities=21% Similarity=0.442 Sum_probs=32.5
Q ss_pred CchhhhHHHHHHHHHH--------HHH-HHHHHHHhhchhhHHHHHccCccchhhh
Q 040196 13 EGWELIEPTLRELQKE--------ISM-ELYEFCLDQGYAVRNLIAKGKQPGYERL 59 (83)
Q Consensus 13 eG~e~IeptL~e~~k~--------ISr-eLYe~~l~~~yaD~~LIaKWKK~GYE~L 59 (83)
..++.++..++.+++. +|+ |++-++-..|..+.+++++||+.|-..+
T Consensus 66 ~~~~~~~~i~~~Ik~~~~~i~~~~~s~~e~~~~~~~~g~~~~e~l~~LkeAGl~~i 121 (309)
T TIGR00423 66 LDIEYYEELFRAIKQEFPDVHIHAFSPMEVYFLAKNEGLSIEEVLKRLKKAGLDSM 121 (309)
T ss_pred CCHHHHHHHHHHHHHHCCCceEEecCHHHHHHHHHHcCCCHHHHHHHHHHcCCCcC
Confidence 4566667766666543 232 4555556678889999999999996655
No 59
>PF13606 Ank_3: Ankyrin repeat
Probab=22.14 E-value=39 Score=17.48 Aligned_cols=16 Identities=31% Similarity=0.611 Sum_probs=11.5
Q ss_pred HHHHHHHHHhhchhhHH
Q 040196 30 SMELYEFCLDQGYAVRN 46 (83)
Q Consensus 30 SreLYe~~l~~~yaD~~ 46 (83)
+.|+-+|||+.| +|.|
T Consensus 14 ~~e~v~~Ll~~g-advn 29 (30)
T PF13606_consen 14 NIEIVKYLLEHG-ADVN 29 (30)
T ss_pred CHHHHHHHHHcC-CCCC
Confidence 357889999877 6643
No 60
>cd00197 VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membra
Probab=21.36 E-value=2.3e+02 Score=18.05 Aligned_cols=9 Identities=33% Similarity=0.933 Sum_probs=6.3
Q ss_pred HHHHHHhhc
Q 040196 33 LYEFCLDQG 41 (83)
Q Consensus 33 LYe~~l~~~ 41 (83)
|-|+|+++|
T Consensus 60 lLe~lvkN~ 68 (115)
T cd00197 60 LLEYCVKNC 68 (115)
T ss_pred HHHHHHHHc
Confidence 667777765
No 61
>PRK00029 hypothetical protein; Validated
Probab=21.33 E-value=1e+02 Score=26.15 Aligned_cols=30 Identities=23% Similarity=0.455 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHhhchhh-------------------HHHHHccCccch
Q 040196 27 KEISMELYEFCLDQGYAV-------------------RNLIAKGKQPGY 56 (83)
Q Consensus 27 k~ISreLYe~~l~~~yaD-------------------~~LIaKWKK~GY 56 (83)
...-+.|-||+|+.-|-| +.|||+|-.-||
T Consensus 197 ~~~l~~L~dy~I~~hyP~~~~~~~~y~~~~~~Vv~rtA~lvA~Wq~vGF 245 (487)
T PRK00029 197 PELLRQLADYVIARHYPELADAEDPYLALFAEVVERTARLIAQWQAVGF 245 (487)
T ss_pred HHHHHHHHHHHHHHHCccccccccHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 345566777777766532 579999999998
No 62
>PF12174 RST: RCD1-SRO-TAF4 (RST) plant domain; InterPro: IPR022003 This domain is found in many plant proteins including SROs and RCD1s; it is required for interaction with multiple plant transcription factors.
Probab=21.32 E-value=83 Score=19.97 Aligned_cols=41 Identities=24% Similarity=0.209 Sum_probs=30.8
Q ss_pred CCCCCchhhhHHHHHHH-HHHHHHHHHHHHHhhchhhHHHHH
Q 040196 9 VQNPEGWELIEPTLREL-QKEISMELYEFCLDQGYAVRNLIA 49 (83)
Q Consensus 9 k~pPeG~e~IeptL~e~-~k~ISreLYe~~l~~~yaD~~LIa 49 (83)
.-||+--+.|...-++| ++.||||-+---+++=..|.-|++
T Consensus 21 ~l~~~~~~~l~~~Y~~~k~~kIsR~~fvr~lR~IVGD~lL~s 62 (70)
T PF12174_consen 21 HLPPSKMDLLQKHYEEFKKKKISREEFVRKLRQIVGDQLLRS 62 (70)
T ss_pred HCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Confidence 45777788888888888 778999877667776666776664
No 63
>PF12941 HCV_NS5a_C: HCV NS5a protein C-terminal region; InterPro: IPR024350 This entry represents the C-terminal region of the Hepatitus C virus, NS5a protein. The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the dsRNA dependent (interferon inducible) kinase PKR [, ].; PDB: 3M5O_C.
Probab=21.29 E-value=32 Score=27.28 Aligned_cols=21 Identities=29% Similarity=0.447 Sum_probs=0.0
Q ss_pred hHHHHHccCccchhhhhhccc
Q 040196 44 VRNLIAKGKQPGYERLCCLRC 64 (83)
Q Consensus 44 D~~LIaKWKK~GYE~LCCl~C 64 (83)
+.-||.-||+++|+.-=-.-|
T Consensus 117 NPPLlE~WK~PDY~PPvVhGC 137 (244)
T PF12941_consen 117 NPPLLETWKRPDYEPPVVHGC 137 (244)
T ss_dssp ---------------------
T ss_pred CCCccccccCCCCCCCcccCC
Confidence 467999999999997644444
No 64
>TIGR01461 greB transcription elongation factor GreB. The GreA and GreB transcription elongation factors enable to continuation of RNA transcription past template-encoded arresting sites. Among the Proteobacteria, distinct clades of GreA and GreB are found. GreB differs functionally in that it releases larger oligonucleotides. This model describes proteobacterial GreB.
Probab=21.27 E-value=69 Score=22.73 Aligned_cols=16 Identities=38% Similarity=0.652 Sum_probs=14.6
Q ss_pred CCCCchhhhHHHHHHH
Q 040196 10 QNPEGWELIEPTLREL 25 (83)
Q Consensus 10 ~pPeG~e~IeptL~e~ 25 (83)
-.|+|++.++..|+.|
T Consensus 5 lT~~G~~~L~~El~~L 20 (156)
T TIGR01461 5 ITPEGYEKLKQELNYL 20 (156)
T ss_pred cCHHHHHHHHHHHHHH
Confidence 4589999999999999
No 65
>PF04422 FrhB_FdhB_N: Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term; InterPro: IPR007516 Coenzyme F420 hydrogenase (1.12.99.1 from EC) reduces the low-potential two-electron acceptor coenzyme F420. This entry contains the N termini of F420 hydrogenase and dehydrogenase beta subunits [, ]. The N terminus of Methanobacterium formicicum formate dehydrogenase beta chain (1.2.1.2 from EC, P06130 from SWISSPROT) is also represented in this entry []. This region is often found in association with the 4Fe-4S binding domain, fer4 (IPR001450 from INTERPRO), and the C terminus IPR007525 from INTERPRO.
Probab=20.82 E-value=75 Score=19.99 Aligned_cols=22 Identities=14% Similarity=0.312 Sum_probs=18.1
Q ss_pred HHHHHHHHHHhhchhhHHHHHc
Q 040196 29 ISMELYEFCLDQGYAVRNLIAK 50 (83)
Q Consensus 29 ISreLYe~~l~~~yaD~~LIaK 50 (83)
|-..|..|+|++|++|.-+...
T Consensus 22 ~vTaLl~~lLe~g~Vd~vv~~~ 43 (82)
T PF04422_consen 22 VVTALLAYLLESGLVDGVVVVG 43 (82)
T ss_pred HHHHHHHHHHHcCCceEEEEEe
Confidence 4457999999999999877665
No 66
>PF05693 Glycogen_syn: Glycogen synthase; InterPro: IPR008631 This family consists of the eukaryotic glycogen synthase proteins GYS1, GYS2 and GYS3. Glycogen synthase (GS) is the enzyme responsible for the synthesis of -1,4-linked glucose chains in glycogen. It is the rate limiting enzyme in the synthesis of the polysaccharide, and its activity is highly regulated through phosphorylation at multiple sites and also by allosteric effectors, mainly glucose 6-phosphate (G6P) [].; GO: 0004373 glycogen (starch) synthase activity, 0005978 glycogen biosynthetic process; PDB: 3NB0_C 3RT1_C 3RSZ_D 3O3C_B 3NAZ_B 3NCH_D.
Probab=20.73 E-value=1.5e+02 Score=26.41 Aligned_cols=30 Identities=27% Similarity=0.447 Sum_probs=25.1
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHhhchhhH
Q 040196 16 ELIEPTLRELQKEISMELYEFCLDQGYAVR 45 (83)
Q Consensus 16 e~IeptL~e~~k~ISreLYe~~l~~~yaD~ 45 (83)
..+.+|+++.++.|.+.||+-|++-.+-|.
T Consensus 357 ~~l~~t~~~i~~~~g~~~~~~~~~~~~p~~ 386 (633)
T PF05693_consen 357 KQLRDTVDEIQEKIGKRLFESCLSGRLPDL 386 (633)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHSSS-SH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCCCCh
Confidence 467899999999999999999999766654
No 67
>PRK11667 hypothetical protein; Provisional
Probab=20.39 E-value=47 Score=24.81 Aligned_cols=15 Identities=13% Similarity=0.583 Sum_probs=12.8
Q ss_pred HHHHHHHhhchhhHH
Q 040196 32 ELYEFCLDQGYAVRN 46 (83)
Q Consensus 32 eLYe~~l~~~yaD~~ 46 (83)
-+.+||++++|+..+
T Consensus 77 GiLqyCvknNyl~~~ 91 (163)
T PRK11667 77 GILQYCAKNNYLSAT 91 (163)
T ss_pred HHHHHHHHhccccCc
Confidence 378999999998775
No 68
>PF08727 P3A: Poliovirus 3A protein like; InterPro: IPR014838 The 3A protein is found in positive-strand RNA viruses. It is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0017111 nucleoside-triphosphatase activity; PDB: 1NG7_A.
Probab=20.37 E-value=75 Score=20.10 Aligned_cols=31 Identities=29% Similarity=0.444 Sum_probs=16.1
Q ss_pred CCCCchhhhHHHHHHHHHHHHHHHHHHHHhhchhhH
Q 040196 10 QNPEGWELIEPTLRELQKEISMELYEFCLDQGYAVR 45 (83)
Q Consensus 10 ~pPeG~e~IeptL~e~~k~ISreLYe~~l~~~yaD~ 45 (83)
.||+++ |.+-| +-.=|.|+-+||-+||++=+
T Consensus 14 ~P~P~~--I~DLL---~SV~~~eV~~YC~~~GWIip 44 (57)
T PF08727_consen 14 TPPPPA--IADLL---RSVDSPEVREYCEEQGWIIP 44 (57)
T ss_dssp --SS-T--THHHH---HHH--HHHHHHHHHHT--TT
T ss_pred CCCCHH--HHHHH---HhcCCHHHHHHHHHCCcccc
Confidence 344443 44444 34457789999999998744
No 69
>PF00269 SASP: Small, acid-soluble spore proteins, alpha/beta type; InterPro: IPR001448 Small, acid-soluble spore proteins (SASP or ASSP) are proteins bound to the spore DNA of bacteria of the genera Bacillus, Thermoactynomycetes, and Clostridium [, ]. They are double-stranded DNA-binding proteins that cause DNA to change to an A-like conformation. They protect the DNA backbone from chemical and enzymatic cleavage and are thus involved in dormant spore's high resistance to UV light. SASP are degraded in the first minutes of spore germination and provide amino acids for both new protein synthesis and metabolism. There are two distinct families of SASP: the alpha/beta type and the gamma- type. Alpha/beta SASP are small proteins of about sixty to seventy amino acid residues that are generally coded by a multigene family. The N terminus of alpha/beta SASP contains the site which is cleaved by a SASP- specific protease that acts during germination while the C terminus and is probably involved in DNA-binding.; GO: 0003690 double-stranded DNA binding, 0006265 DNA topological change; PDB: 2Z3X_B.
Probab=20.28 E-value=1.3e+02 Score=18.52 Aligned_cols=17 Identities=35% Similarity=0.382 Sum_probs=14.4
Q ss_pred hHHHHHHHHHHHHHHHH
Q 040196 18 IEPTLRELQKEISMELY 34 (83)
Q Consensus 18 IeptL~e~~k~ISreLY 34 (83)
-+..|++|+-+|++||=
T Consensus 8 a~~~Ld~lK~EiA~ElG 24 (61)
T PF00269_consen 8 AREALDQLKYEIAKELG 24 (61)
T ss_dssp GHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHhC
Confidence 46789999999999984
Done!