Query 022315
Match_columns 299
No_of_seqs 66 out of 68
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 02:36:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022315.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022315hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00401 ZnF_GATA zinc finge 99.2 4.6E-12 1E-16 90.8 1.7 39 193-231 2-41 (52)
2 PF00320 GATA: GATA zinc finge 99.2 9.4E-13 2E-17 88.3 -2.1 34 197-230 1-35 (36)
3 cd00202 ZnF_GATA Zinc finger D 99.1 1.4E-11 3.1E-16 89.3 0.4 35 196-230 1-36 (54)
4 KOG1601 GATA-4/5/6 transcripti 98.6 1.6E-08 3.4E-13 81.0 2.8 35 194-228 199-234 (340)
5 COG5641 GAT1 GATA Zn-finger-co 93.5 0.037 8E-07 55.8 1.7 38 192-229 156-198 (498)
6 TIGR02098 MJ0042_CXXC MJ0042 f 67.7 2.8 6E-05 27.6 1.0 32 195-226 3-36 (38)
7 smart00653 eIF2B_5 domain pres 61.6 3.8 8.2E-05 33.9 0.9 29 194-224 80-110 (110)
8 PF14803 Nudix_N_2: Nudix N-te 55.7 5.3 0.00011 27.3 0.7 29 195-223 1-30 (34)
9 PF13717 zinc_ribbon_4: zinc-r 52.9 8.6 0.00019 26.0 1.3 31 196-226 4-36 (36)
10 PF01783 Ribosomal_L32p: Ribos 52.1 13 0.00028 27.2 2.2 27 194-230 26-52 (56)
11 PF09297 zf-NADH-PPase: NADH p 50.6 7.4 0.00016 25.2 0.7 29 194-225 3-31 (32)
12 smart00834 CxxC_CXXC_SSSS Puta 50.3 8.5 0.00018 25.0 1.0 33 193-225 4-36 (41)
13 PTZ00405 cytochrome c; Provisi 46.1 9.1 0.0002 31.4 0.8 15 190-204 18-32 (114)
14 TIGR00244 transcriptional regu 45.6 14 0.00031 32.6 1.9 36 196-231 2-44 (147)
15 COG2816 NPY1 NTP pyrophosphohy 42.5 23 0.00049 34.1 2.9 44 182-228 99-142 (279)
16 smart00542 FYRC "FY-rich" doma 41.2 10 0.00022 29.5 0.4 22 21-42 49-70 (86)
17 COG4306 Uncharacterized protei 38.5 12 0.00027 33.3 0.4 25 209-233 62-86 (160)
18 PF13719 zinc_ribbon_5: zinc-r 35.5 21 0.00046 24.1 1.1 31 196-226 4-36 (37)
19 PF11333 DUF3135: Protein of u 33.2 1.2E+02 0.0025 24.3 5.1 48 248-295 7-58 (83)
20 PF04814 HNF-1_N: Hepatocyte n 32.9 19 0.00042 32.7 0.8 24 246-269 104-127 (180)
21 TIGR02159 PA_CoA_Oxy4 phenylac 32.4 17 0.00037 31.2 0.4 33 194-226 105-141 (146)
22 PF11641 Antigen_Bd37: Glycosy 31.8 51 0.0011 31.1 3.3 41 249-293 42-85 (224)
23 PRK00464 nrdR transcriptional 31.2 30 0.00066 30.2 1.7 36 196-231 2-44 (154)
24 PRK05978 hypothetical protein; 30.9 46 0.00099 29.2 2.7 36 192-229 31-66 (148)
25 smart00661 RPOL9 RNA polymeras 30.1 44 0.00096 22.7 2.0 39 195-234 1-39 (52)
26 TIGR00311 aIF-2beta translatio 29.8 23 0.00049 30.3 0.7 31 194-225 97-128 (133)
27 smart00659 RPOLCX RNA polymera 29.7 32 0.00069 24.4 1.3 26 195-224 3-28 (44)
28 PRK05978 hypothetical protein; 29.7 38 0.00083 29.7 2.0 38 161-212 33-70 (148)
29 PRK00420 hypothetical protein; 29.5 1.4E+02 0.0031 25.1 5.3 30 193-227 22-52 (112)
30 PRK00398 rpoP DNA-directed RNA 28.8 30 0.00066 23.8 1.1 29 195-226 4-32 (46)
31 PRK12336 translation initiatio 28.2 29 0.00064 31.0 1.1 34 194-229 98-133 (201)
32 PF11291 DUF3091: Protein of u 28.0 1.3E+02 0.0029 25.1 4.8 39 260-298 7-45 (100)
33 PF05965 FYRC: F/Y rich C-term 27.9 15 0.00032 28.0 -0.7 22 21-42 53-74 (86)
34 PF10167 NEP: Uncharacterised 27.9 66 0.0014 27.2 3.1 28 101-128 10-42 (118)
35 PRK03988 translation initiatio 27.9 25 0.00055 30.2 0.6 31 194-225 102-133 (138)
36 PF07282 OrfB_Zn_ribbon: Putat 27.4 37 0.0008 24.5 1.3 30 194-226 28-57 (69)
37 PF09538 FYDLN_acid: Protein o 26.5 29 0.00063 28.8 0.7 14 213-226 7-20 (108)
38 COG3259 FrhA Coenzyme F420-red 25.9 1.5E+02 0.0032 30.6 5.6 35 80-118 166-200 (441)
39 PRK00241 nudC NADH pyrophospha 25.9 38 0.00082 31.1 1.4 29 195-226 100-128 (256)
40 COG1941 FrhG Coenzyme F420-red 25.6 30 0.00065 33.0 0.7 26 199-225 201-226 (247)
41 COG4077 Uncharacterized protei 25.5 32 0.00069 30.9 0.8 15 15-29 93-107 (156)
42 PF14877 mIF3: Mitochondrial t 25.4 84 0.0018 28.6 3.5 16 259-274 84-99 (181)
43 PF01920 Prefoldin_2: Prefoldi 24.0 1.4E+02 0.0031 22.4 4.0 38 252-289 54-91 (106)
44 PF09723 Zn-ribbon_8: Zinc rib 24.0 37 0.00081 23.3 0.8 31 193-223 4-34 (42)
45 COG1327 Predicted transcriptio 23.7 49 0.0011 29.7 1.7 79 196-274 2-97 (156)
46 PF14787 zf-CCHC_5: GAG-polypr 23.6 47 0.001 23.6 1.2 24 214-237 1-26 (36)
47 PF03604 DNA_RNApol_7kD: DNA d 22.6 62 0.0013 21.9 1.6 25 196-224 2-26 (32)
48 COG5349 Uncharacterized protei 22.3 49 0.0011 28.9 1.3 38 190-229 17-54 (126)
49 COG1381 RecO Recombinational D 21.8 99 0.0021 28.1 3.2 29 194-222 154-182 (251)
50 KOG3507 DNA-directed RNA polym 21.6 37 0.0008 26.6 0.4 29 192-224 18-46 (62)
51 PF12041 DELLA: Transcriptiona 21.5 66 0.0014 25.9 1.8 22 270-292 1-31 (73)
52 PTZ00048 cytochrome c; Provisi 21.5 43 0.00094 27.2 0.8 13 192-204 21-33 (115)
53 PF08889 WbqC: WbqC-like prote 21.2 1E+02 0.0022 27.7 3.1 56 23-120 88-151 (219)
54 PF12172 DUF35_N: Rubredoxin-l 20.9 38 0.00082 22.3 0.3 25 192-223 9-33 (37)
55 PRK15043 transcriptional regul 20.5 2E+02 0.0044 27.0 5.0 53 241-293 57-110 (243)
56 PRK12729 fliE flagellar hook-b 20.3 1.6E+02 0.0034 25.7 4.0 22 107-128 88-115 (127)
57 KOG2773 Apoptosis antagonizing 20.3 1.3E+02 0.0027 31.4 3.9 98 18-130 316-436 (483)
58 PF10752 DUF2533: Protein of u 20.0 2.1E+02 0.0046 23.7 4.4 35 261-295 3-40 (84)
No 1
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.20 E-value=4.6e-12 Score=90.79 Aligned_cols=39 Identities=31% Similarity=0.656 Sum_probs=36.1
Q ss_pred cccccCccccccccC-cCCCCCCccccccccccccCCccc
Q 022315 193 FKKNCAHCHCQNTSQ-LTSPNGPKSLCDGCISSYGKDKDL 231 (299)
Q Consensus 193 ~~r~C~~C~ttkTp~-R~GP~GPKSLCNACGiRyrk~r~~ 231 (299)
..+.|++|++++||+ |.||.|++.||||||++|++....
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCC
Confidence 467999999999999 999999999999999999998764
No 2
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=99.19 E-value=9.4e-13 Score=88.30 Aligned_cols=34 Identities=35% Similarity=0.754 Sum_probs=27.4
Q ss_pred cCccccccccC-cCCCCCCccccccccccccCCcc
Q 022315 197 CAHCHCQNTSQ-LTSPNGPKSLCDGCISSYGKDKD 230 (299)
Q Consensus 197 C~~C~ttkTp~-R~GP~GPKSLCNACGiRyrk~r~ 230 (299)
|++|+|++||+ |.||.|+.+||||||++|+|.+.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~~ 35 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYGK 35 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHSS
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhCC
Confidence 89999999999 99999999999999999998763
No 3
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=99.11 E-value=1.4e-11 Score=89.31 Aligned_cols=35 Identities=26% Similarity=0.589 Sum_probs=33.1
Q ss_pred ccCccccccccC-cCCCCCCccccccccccccCCcc
Q 022315 196 NCAHCHCQNTSQ-LTSPNGPKSLCDGCISSYGKDKD 230 (299)
Q Consensus 196 ~C~~C~ttkTp~-R~GP~GPKSLCNACGiRyrk~r~ 230 (299)
.|++|++++||+ |.||.|+..||||||++|++...
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~ 36 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGV 36 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcCC
Confidence 599999999999 99999999999999999999873
No 4
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.64 E-value=1.6e-08 Score=81.03 Aligned_cols=35 Identities=37% Similarity=0.817 Sum_probs=34.0
Q ss_pred ccccCccccccccC-cCCCCCCccccccccccccCC
Q 022315 194 KKNCAHCHCQNTSQ-LTSPNGPKSLCDGCISSYGKD 228 (299)
Q Consensus 194 ~r~C~~C~ttkTp~-R~GP~GPKSLCNACGiRyrk~ 228 (299)
.+.|.+|.+++||+ |.||.||+++|||||++|++.
T Consensus 199 ~~~c~~~~~~~t~~~r~~~~g~~~~cnacgl~~k~~ 234 (340)
T KOG1601|consen 199 LRQCSNCGTTKTPLWRRGPEGPKSLCNACGLRYKKG 234 (340)
T ss_pred CcccCCCCCCCCcceecCCCCCccccccchhhhhhc
Confidence 58999999999999 999999999999999999998
No 5
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=93.48 E-value=0.037 Score=55.78 Aligned_cols=38 Identities=18% Similarity=0.380 Sum_probs=32.1
Q ss_pred ccccccCccccccccC-cCCCCC----CccccccccccccCCc
Q 022315 192 NFKKNCAHCHCQNTSQ-LTSPNG----PKSLCDGCISSYGKDK 229 (299)
Q Consensus 192 ~~~r~C~~C~ttkTp~-R~GP~G----PKSLCNACGiRyrk~r 229 (299)
+....|..|.|+.||+ |-+..+ +-.||||||+-|.--.
T Consensus 156 ~~~~vc~Nc~t~stPlwrR~~~~~s~~~n~lcnaCgl~~klhg 198 (498)
T COG5641 156 NQPHVCSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLKLHG 198 (498)
T ss_pred cccchhccccccCCccccccccccccCCccccccccccccccC
Confidence 3445999999999999 888887 8899999999887543
No 6
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=67.71 E-value=2.8 Score=27.56 Aligned_cols=32 Identities=22% Similarity=0.424 Sum_probs=24.9
Q ss_pred cccCccccccccC--cCCCCCCcccccccccccc
Q 022315 195 KNCAHCHCQNTSQ--LTSPNGPKSLCDGCISSYG 226 (299)
Q Consensus 195 r~C~~C~ttkTp~--R~GP~GPKSLCNACGiRyr 226 (299)
-.|.+|+++..-. ..++.|++-.|.-||-.|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 3699999977655 5667788899999997763
No 7
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=61.57 E-value=3.8 Score=33.88 Aligned_cols=29 Identities=24% Similarity=0.432 Sum_probs=21.9
Q ss_pred ccccCccccccccC-cCCCCCCccc-ccccccc
Q 022315 194 KKNCAHCHCQNTSQ-LTSPNGPKSL-CDGCISS 224 (299)
Q Consensus 194 ~r~C~~C~ttkTp~-R~GP~GPKSL-CNACGiR 224 (299)
--.|..|+...|-+ +. .+--.| |+|||-+
T Consensus 80 yVlC~~C~spdT~l~k~--~r~~~l~C~aCGa~ 110 (110)
T smart00653 80 YVLCPECGSPDTELIKE--NRLFFLKCEACGAR 110 (110)
T ss_pred cEECCCCCCCCcEEEEe--CCeEEEEccccCCC
Confidence 35799999999999 66 333333 9999964
No 8
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=55.68 E-value=5.3 Score=27.29 Aligned_cols=29 Identities=17% Similarity=0.405 Sum_probs=16.7
Q ss_pred cccCccccccccC-cCCCCCCccccccccc
Q 022315 195 KNCAHCHCQNTSQ-LTSPNGPKSLCDGCIS 223 (299)
Q Consensus 195 r~C~~C~ttkTp~-R~GP~GPKSLCNACGi 223 (299)
|.|.+|++.-+.. ..|-.=++-.|.+||.
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred CccccccChhhhhcCCCCCccceECCCCCC
Confidence 4699999875554 5677778999999984
No 9
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=52.90 E-value=8.6 Score=26.02 Aligned_cols=31 Identities=23% Similarity=0.583 Sum_probs=25.1
Q ss_pred ccCccccccccC--cCCCCCCcccccccccccc
Q 022315 196 NCAHCHCQNTSQ--LTSPNGPKSLCDGCISSYG 226 (299)
Q Consensus 196 ~C~~C~ttkTp~--R~GP~GPKSLCNACGiRyr 226 (299)
.|.+|++.-.-. ...|.|=+-.|-.||-.|+
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEeC
Confidence 588999886544 6778888999999998774
No 10
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 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 [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=52.08 E-value=13 Score=27.19 Aligned_cols=27 Identities=26% Similarity=0.642 Sum_probs=20.0
Q ss_pred ccccCccccccccCcCCCCCCccccccccccccCCcc
Q 022315 194 KKNCAHCHCQNTSQLTSPNGPKSLCDGCISSYGKDKD 230 (299)
Q Consensus 194 ~r~C~~C~ttkTp~R~GP~GPKSLCNACGiRyrk~r~ 230 (299)
.-.|.+|+..+ =|..+|.+|| |-++|.
T Consensus 26 l~~c~~cg~~~--------~~H~vc~~cG--~y~~r~ 52 (56)
T PF01783_consen 26 LVKCPNCGEPK--------LPHRVCPSCG--YYKGRQ 52 (56)
T ss_dssp EEESSSSSSEE--------STTSBCTTTB--BSSSSS
T ss_pred eeeeccCCCEe--------cccEeeCCCC--eECCEE
Confidence 45688888655 4778999998 666654
No 11
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=50.64 E-value=7.4 Score=25.24 Aligned_cols=29 Identities=21% Similarity=0.554 Sum_probs=17.6
Q ss_pred ccccCccccccccCcCCCCCCccccccccccc
Q 022315 194 KKNCAHCHCQNTSQLTSPNGPKSLCDGCISSY 225 (299)
Q Consensus 194 ~r~C~~C~ttkTp~R~GP~GPKSLCNACGiRy 225 (299)
-|.|+.|++...+ -+.|-.-.|.+||.++
T Consensus 3 ~rfC~~CG~~t~~---~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 3 HRFCGRCGAPTKP---APGGWARRCPSCGHEH 31 (32)
T ss_dssp TSB-TTT--BEEE----SSSS-EEESSSS-EE
T ss_pred CcccCcCCccccC---CCCcCEeECCCCcCEe
Confidence 4679999887744 4557889999999764
No 12
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=50.29 E-value=8.5 Score=25.05 Aligned_cols=33 Identities=15% Similarity=0.414 Sum_probs=23.0
Q ss_pred cccccCccccccccCcCCCCCCccccccccccc
Q 022315 193 FKKNCAHCHCQNTSQLTSPNGPKSLCDGCISSY 225 (299)
Q Consensus 193 ~~r~C~~C~ttkTp~R~GP~GPKSLCNACGiRy 225 (299)
..-.|.+|+..-+.......++..-|..||...
T Consensus 4 Y~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKISDDPLATCPECGGDV 36 (41)
T ss_pred EEEEcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence 345799999876655332337888899999843
No 13
>PTZ00405 cytochrome c; Provisional
Probab=46.14 E-value=9.1 Score=31.37 Aligned_cols=15 Identities=33% Similarity=0.576 Sum_probs=10.9
Q ss_pred hhccccccCcccccc
Q 022315 190 MSNFKKNCAHCHCQN 204 (299)
Q Consensus 190 ~~~~~r~C~~C~ttk 204 (299)
...|.+.|+-||+..
T Consensus 18 ~~lF~~~C~aCH~~~ 32 (114)
T PTZ00405 18 EKLFKGRAAQCHTAT 32 (114)
T ss_pred HHHHHhhhHhhCCCC
Confidence 344666799999854
No 14
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=45.65 E-value=14 Score=32.59 Aligned_cols=36 Identities=19% Similarity=0.445 Sum_probs=28.3
Q ss_pred ccCccccccccC---cCCCCC----CccccccccccccCCccc
Q 022315 196 NCAHCHCQNTSQ---LTSPNG----PKSLCDGCISSYGKDKDL 231 (299)
Q Consensus 196 ~C~~C~ttkTp~---R~GP~G----PKSLCNACGiRyrk~r~~ 231 (299)
.|..|+...|-. |....| -.--|.+||.||----+.
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErv 44 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERA 44 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeec
Confidence 699999988876 777777 446899999999765543
No 15
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=42.47 E-value=23 Score=34.06 Aligned_cols=44 Identities=16% Similarity=0.246 Sum_probs=31.6
Q ss_pred hHHhHHhhhhccccccCccccccccCcCCCCCCccccccccccccCC
Q 022315 182 DAALSEKEMSNFKKNCAHCHCQNTSQLTSPNGPKSLCDGCISSYGKD 228 (299)
Q Consensus 182 d~a~s~~~~~~~~r~C~~C~ttkTp~R~GP~GPKSLCNACGiRyrk~ 228 (299)
..|.+=-+.....|.|.+|++...|. ..|=+-.|+.||.++--.
T Consensus 99 ~~a~~l~~w~~~~RFCg~CG~~~~~~---~~g~~~~C~~cg~~~fPR 142 (279)
T COG2816 99 ARAVQLLEWYRSHRFCGRCGTKTYPR---EGGWARVCPKCGHEHFPR 142 (279)
T ss_pred HHHHHHHHHHhhCcCCCCCCCcCccc---cCceeeeCCCCCCccCCC
Confidence 33444444555689999999988665 456789999999987443
No 16
>smart00542 FYRC "FY-rich" domain, C-terminal region. is sometimes closely juxtaposed with the N-terminal region (FYRN), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.
Probab=41.22 E-value=10 Score=29.52 Aligned_cols=22 Identities=27% Similarity=0.487 Sum_probs=20.3
Q ss_pred CCCcccchHHHHHHHhhcCCCC
Q 022315 21 GPDYFGFYTCEIMELLSQDEDP 42 (299)
Q Consensus 21 GPD~FgyY~~eV~eLLSQdEd~ 42 (299)
|||+|||=...|..|+.|...+
T Consensus 49 G~~mFGls~p~V~~lie~Lpga 70 (86)
T smart00542 49 GEDMFGLSSPAVVKLIEQLPGV 70 (86)
T ss_pred cHHHhCCCcHHHHHHHHhCCCc
Confidence 9999999999999999887766
No 17
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.48 E-value=12 Score=33.31 Aligned_cols=25 Identities=20% Similarity=0.356 Sum_probs=19.7
Q ss_pred CCCCCCccccccccccccCCccccc
Q 022315 209 TSPNGPKSLCDGCISSYGKDKDLHS 233 (299)
Q Consensus 209 ~GP~GPKSLCNACGiRyrk~r~~~l 233 (299)
+|---|-|.|+.||.||--..+...
T Consensus 62 g~dye~psfchncgs~fpwterkia 86 (160)
T COG4306 62 GGDYEPPSFCHNCGSRFPWTERKIA 86 (160)
T ss_pred CCCCCCcchhhcCCCCCCcHHHHHh
Confidence 4666799999999999987665443
No 18
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=35.54 E-value=21 Score=24.06 Aligned_cols=31 Identities=19% Similarity=0.492 Sum_probs=22.9
Q ss_pred ccCccccccccC--cCCCCCCcccccccccccc
Q 022315 196 NCAHCHCQNTSQ--LTSPNGPKSLCDGCISSYG 226 (299)
Q Consensus 196 ~C~~C~ttkTp~--R~GP~GPKSLCNACGiRyr 226 (299)
.|.+|++.---. +.++.|=+--|-.|+-.|.
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 588888875433 6677777888888887764
No 19
>PF11333 DUF3135: Protein of unknown function (DUF3135); InterPro: IPR021482 This family of proteins with unkown function appears to be restricted to Proteobacteria.
Probab=33.21 E-value=1.2e+02 Score=24.28 Aligned_cols=48 Identities=25% Similarity=0.490 Sum_probs=37.5
Q ss_pred cchhhhhccCchHHHHHHHHhHHHHHHH-HhHHHHHHHHH---HHHHHhhcc
Q 022315 248 DDLQFLLESDSSEVEETVKKYSDELFAT-LGHMEQKLEEL---LNTVVSRCR 295 (299)
Q Consensus 248 dd~k~lle~d~s~vee~vkkysdel~~t-lg~meq~le~l---ld~v~~~cr 295 (299)
|+++-|-++|+...|+.-++-.+++... =..|..+|..+ +|-++.+|.
T Consensus 7 D~L~~LA~~dPe~fe~lr~~~~ee~I~~a~~~~q~rL~~lQ~~Id~~~~~~k 58 (83)
T PF11333_consen 7 DELKELAQNDPEAFEQLRQELIEEMIESAPEEMQPRLRALQFHIDMQRSRCK 58 (83)
T ss_pred HHHHHHHHhCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHcC
Confidence 7889999999999988888888877665 45677777776 466677764
No 20
>PF04814 HNF-1_N: Hepatocyte nuclear factor 1 (HNF-1), N terminus; InterPro: IPR006899 This domain consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerisation sequence [] and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3) [].; GO: 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2GYP_B 1IC8_B 2H8R_B 1G2Y_D 1F93_H 1G39_D 1G2Z_B 1JB6_B.
Probab=32.94 E-value=19 Score=32.68 Aligned_cols=24 Identities=25% Similarity=0.385 Sum_probs=20.6
Q ss_pred cccchhhhhccCchHHHHHHHHhH
Q 022315 246 VDDDLQFLLESDSSEVEETVKKYS 269 (299)
Q Consensus 246 v~dd~k~lle~d~s~vee~vkkys 269 (299)
..+.|.-||..|+..|+|+||.|-
T Consensus 104 ~~~~Ve~llr~D~~~VkeeIK~fl 127 (180)
T PF04814_consen 104 QRAEVEELLRRDPWRVKEEIKAFL 127 (180)
T ss_dssp HHHHHHHCTTS-HHHHHHHHHHHH
T ss_pred hHHHHHHHHhhCHHHHHHHHHHHH
Confidence 457888999999999999999994
No 21
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=32.43 E-value=17 Score=31.22 Aligned_cols=33 Identities=24% Similarity=0.673 Sum_probs=26.9
Q ss_pred ccccCccccccccC--cCCCCCCccc--ccccccccc
Q 022315 194 KKNCAHCHCQNTSQ--LTSPNGPKSL--CDGCISSYG 226 (299)
Q Consensus 194 ~r~C~~C~ttkTp~--R~GP~GPKSL--CNACGiRyr 226 (299)
.-.|.+|+.++|-+ +-|++-=|+| |++|.--|-
T Consensus 105 ~~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~epf~ 141 (146)
T TIGR02159 105 SVQCPRCGSADTTITSIFGPTACKALYRCRACKEPFE 141 (146)
T ss_pred CCcCCCCCCCCcEeecCCCChhhHHHhhhhhhCCcHh
Confidence 46899999999998 8888876765 899976653
No 22
>PF11641 Antigen_Bd37: Glycosylphosphatidylinositol-anchored merozoite surface protein; InterPro: IPR021669 This family of proteins represents the core region of Bd37, a surface antigen of B.divergens which is GPI-anchored at the surface of the merozoite. The structure of the protein consists of mainly alpha folds and has three sub domains []. ; PDB: 2JO7_A.
Probab=31.81 E-value=51 Score=31.08 Aligned_cols=41 Identities=29% Similarity=0.562 Sum_probs=26.9
Q ss_pred chhhhhccCchHHHH---HHHHhHHHHHHHHhHHHHHHHHHHHHHHhh
Q 022315 249 DLQFLLESDSSEVEE---TVKKYSDELFATLGHMEQKLEELLNTVVSR 293 (299)
Q Consensus 249 d~k~lle~d~s~vee---~vkkysdel~~tlg~meq~le~lld~v~~~ 293 (299)
|-..||.-|+..|++ .||+|- .++|-+-+..|+-||+.|..
T Consensus 42 dtDlLlkVD~~~V~kAG~kVK~YL----esiGI~G~sVEe~LD~LM~k 85 (224)
T PF11641_consen 42 DTDLLLKVDQAKVKKAGEKVKAYL----ESIGITGDSVEESLDNLMTK 85 (224)
T ss_dssp HHHTTT---HHHHHHHHHHHHHHH----HHHH--S--HHHHHHHHHHH
T ss_pred ccchhhccCHHHHHHHHHHHHHHH----HHhcCCCCcHHHHHHHHHHH
Confidence 445789999999985 688884 57788888999999998864
No 23
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=31.25 E-value=30 Score=30.21 Aligned_cols=36 Identities=17% Similarity=0.435 Sum_probs=24.0
Q ss_pred ccCccccccccC---cCCCCC----CccccccccccccCCccc
Q 022315 196 NCAHCHCQNTSQ---LTSPNG----PKSLCDGCISSYGKDKDL 231 (299)
Q Consensus 196 ~C~~C~ttkTp~---R~GP~G----PKSLCNACGiRyrk~r~~ 231 (299)
.|.+|+...|-. |.=+.| -.--|+.||-+|.---.+
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~ 44 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERV 44 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEec
Confidence 699999877665 333334 125699999999654433
No 24
>PRK05978 hypothetical protein; Provisional
Probab=30.95 E-value=46 Score=29.20 Aligned_cols=36 Identities=17% Similarity=0.484 Sum_probs=25.0
Q ss_pred ccccccCccccccccCcCCCCCCccccccccccccCCc
Q 022315 192 NFKKNCAHCHCQNTSQLTSPNGPKSLCDGCISSYGKDK 229 (299)
Q Consensus 192 ~~~r~C~~C~ttkTp~R~GP~GPKSLCNACGiRyrk~r 229 (299)
+...+|.+|+--+ +-.|..-...-|.+||.+|...|
T Consensus 31 Gl~grCP~CG~G~--LF~g~Lkv~~~C~~CG~~~~~~~ 66 (148)
T PRK05978 31 GFRGRCPACGEGK--LFRAFLKPVDHCAACGEDFTHHR 66 (148)
T ss_pred HHcCcCCCCCCCc--ccccccccCCCccccCCccccCC
Confidence 6677788887544 32355567778888888887665
No 25
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=30.09 E-value=44 Score=22.71 Aligned_cols=39 Identities=13% Similarity=0.247 Sum_probs=25.6
Q ss_pred cccCccccccccCcCCCCCCccccccccccccCCcccccc
Q 022315 195 KNCAHCHCQNTSQLTSPNGPKSLCDGCISSYGKDKDLHSD 234 (299)
Q Consensus 195 r~C~~C~ttkTp~R~GP~GPKSLCNACGiRyrk~r~~~l~ 234 (299)
+.|.+|+..-.+. .+.....--|..||-.++...+....
T Consensus 1 ~FCp~Cg~~l~~~-~~~~~~~~vC~~Cg~~~~~~~~~~~~ 39 (52)
T smart00661 1 KFCPKCGNMLIPK-EGKEKRRFVCRKCGYEEPIEQKYVYK 39 (52)
T ss_pred CCCCCCCCccccc-cCCCCCEEECCcCCCeEECCCcEEEE
Confidence 4699998855443 22223577899999888776553443
No 26
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=29.81 E-value=23 Score=30.29 Aligned_cols=31 Identities=16% Similarity=0.285 Sum_probs=22.7
Q ss_pred ccccCccccccccC-cCCCCCCccccccccccc
Q 022315 194 KKNCAHCHCQNTSQ-LTSPNGPKSLCDGCISSY 225 (299)
Q Consensus 194 ~r~C~~C~ttkTp~-R~GP~GPKSLCNACGiRy 225 (299)
--.|..|+...|-+ +.+- -----|+|||-+.
T Consensus 97 yVlC~~C~sPdT~l~k~~r-~~~l~C~ACGa~~ 128 (133)
T TIGR00311 97 YVICRECNRPDTRIIKEGR-VSLLKCEACGAKA 128 (133)
T ss_pred eEECCCCCCCCcEEEEeCC-eEEEecccCCCCC
Confidence 35799999999999 6432 1234799999764
No 27
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=29.71 E-value=32 Score=24.44 Aligned_cols=26 Identities=19% Similarity=0.386 Sum_probs=19.5
Q ss_pred cccCccccccccCcCCCCCCcccccccccc
Q 022315 195 KNCAHCHCQNTSQLTSPNGPKSLCDGCISS 224 (299)
Q Consensus 195 r~C~~C~ttkTp~R~GP~GPKSLCNACGiR 224 (299)
-.|.+|+...+.. .+..--|..||-|
T Consensus 3 Y~C~~Cg~~~~~~----~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK----SKDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC----CCCceECCCCCce
Confidence 3699999987655 3445679999977
No 28
>PRK05978 hypothetical protein; Provisional
Probab=29.65 E-value=38 Score=29.68 Aligned_cols=38 Identities=18% Similarity=0.266 Sum_probs=30.0
Q ss_pred ccCCCCccCCccccCCCcchhhHHhHHhhhhccccccCccccccccCcCCCC
Q 022315 161 SLKHGSCREGSVSNGIDSKSLDAALSEKEMSNFKKNCAHCHCQNTSQLTSPN 212 (299)
Q Consensus 161 ~~~~gs~r~g~~~~~~~s~pld~a~s~~~~~~~~r~C~~C~ttkTp~R~GP~ 212 (299)
+-+|-.|.+|+.|.+ --.....|++|+..-+..|.+--
T Consensus 33 ~grCP~CG~G~LF~g--------------~Lkv~~~C~~CG~~~~~~~a~Dg 70 (148)
T PRK05978 33 RGRCPACGEGKLFRA--------------FLKPVDHCAACGEDFTHHRADDL 70 (148)
T ss_pred cCcCCCCCCCccccc--------------ccccCCCccccCCccccCCcccc
Confidence 457999999999975 33456789999999888876653
No 29
>PRK00420 hypothetical protein; Validated
Probab=29.50 E-value=1.4e+02 Score=25.14 Aligned_cols=30 Identities=20% Similarity=0.361 Sum_probs=20.5
Q ss_pred cccccCccccccccC-cCCCCCCccccccccccccC
Q 022315 193 FKKNCAHCHCQNTSQ-LTSPNGPKSLCDGCISSYGK 227 (299)
Q Consensus 193 ~~r~C~~C~ttkTp~-R~GP~GPKSLCNACGiRyrk 227 (299)
....|..|+ +|+ |. ..| +..|.+||..+--
T Consensus 22 l~~~CP~Cg---~pLf~l-k~g-~~~Cp~Cg~~~~v 52 (112)
T PRK00420 22 LSKHCPVCG---LPLFEL-KDG-EVVCPVHGKVYIV 52 (112)
T ss_pred ccCCCCCCC---Ccceec-CCC-ceECCCCCCeeee
Confidence 346888888 455 32 334 7899999986643
No 30
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=28.84 E-value=30 Score=23.79 Aligned_cols=29 Identities=21% Similarity=0.305 Sum_probs=19.9
Q ss_pred cccCccccccccCcCCCCCCcccccccccccc
Q 022315 195 KNCAHCHCQNTSQLTSPNGPKSLCDGCISSYG 226 (299)
Q Consensus 195 r~C~~C~ttkTp~R~GP~GPKSLCNACGiRyr 226 (299)
-.|..|++.-+-. |..-...|.-||-++-
T Consensus 4 y~C~~CG~~~~~~---~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVELD---EYGTGVRCPYCGYRIL 32 (46)
T ss_pred EECCCCCCEEEEC---CCCCceECCCCCCeEE
Confidence 4699999876443 2222678999998764
No 31
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=28.24 E-value=29 Score=30.95 Aligned_cols=34 Identities=21% Similarity=0.302 Sum_probs=24.5
Q ss_pred ccccCccccccccC-cCCCCCC-ccccccccccccCCc
Q 022315 194 KKNCAHCHCQNTSQ-LTSPNGP-KSLCDGCISSYGKDK 229 (299)
Q Consensus 194 ~r~C~~C~ttkTp~-R~GP~GP-KSLCNACGiRyrk~r 229 (299)
--.|..|+...|-+ +.+ +- ---|+|||-+.-=+.
T Consensus 98 yV~C~~C~~pdT~l~k~~--~~~~l~C~aCGa~~~v~~ 133 (201)
T PRK12336 98 YVICSECGLPDTRLVKED--RVLMLRCDACGAHRPVKK 133 (201)
T ss_pred eEECCCCCCCCcEEEEcC--CeEEEEcccCCCCccccc
Confidence 35799999999999 653 22 236999998765443
No 32
>PF11291 DUF3091: Protein of unknown function (DUF3091); InterPro: IPR021442 This eukaryotic family of proteins has no known function.
Probab=27.98 E-value=1.3e+02 Score=25.09 Aligned_cols=39 Identities=21% Similarity=0.433 Sum_probs=34.0
Q ss_pred HHHHHHHHhHHHHHHHHhHHHHHHHHHHHHHHhhcccCC
Q 022315 260 EVEETVKKYSDELFATLGHMEQKLEELLNTVVSRCRSFG 298 (299)
Q Consensus 260 ~vee~vkkysdel~~tlg~meq~le~lld~v~~~cr~mt 298 (299)
+++.--.+||.+.+..|..-.+.|+++.|+.-+.=.+||
T Consensus 7 EI~rdY~n~s~~v~E~l~~~~~~Lkq~f~~~qS~~~~mT 45 (100)
T PF11291_consen 7 EIRRDYPNFSEEVFEKLNRCSVKLKQYFDKLQSKKENMT 45 (100)
T ss_pred HHHHHhhhchHHHHHHHHHHHHHHHHHHHHHHhcccCcc
Confidence 566667789999999999999999999999988777776
No 33
>PF05965 FYRC: F/Y rich C-terminus; InterPro: IPR003889 The "FY-rich" domain C-terminal region is sometimes closely juxtaposed with the N-terminal region (IPR003888 from INTERPRO), but sometimes is far distant. It is of unknown function, but occurs frequently in chromatin-associated proteins like trithorax and its homologues.; GO: 0005634 nucleus; PDB: 2WZO_A.
Probab=27.93 E-value=15 Score=27.99 Aligned_cols=22 Identities=23% Similarity=0.507 Sum_probs=19.6
Q ss_pred CCCcccchHHHHHHHhhcCCCC
Q 022315 21 GPDYFGFYTCEIMELLSQDEDP 42 (299)
Q Consensus 21 GPD~FgyY~~eV~eLLSQdEd~ 42 (299)
||++|||=...|..||.|-...
T Consensus 53 G~~~FGls~p~V~~lie~Lp~a 74 (86)
T PF05965_consen 53 GPEMFGLSNPAVQRLIESLPGA 74 (86)
T ss_dssp HHHHHSTTSHHHHHHHTTSTTG
T ss_pred HhHhcCCCCHHHHHHHHhCCCc
Confidence 9999999999999999776555
No 34
>PF10167 NEP: Uncharacterised conserved protein; InterPro: IPR019320 This entry represents the uncharacterised protein family UPF0402. It contains a characteristic NEP sequence motif. Their function is not known.
Probab=27.87 E-value=66 Score=27.23 Aligned_cols=28 Identities=25% Similarity=0.523 Sum_probs=20.9
Q ss_pred hhhcchhHHhhh-----hHHHHHHHHHHHhhhc
Q 022315 101 VFDLAPEVDEML-----DPVIAMCQLQSQVRNR 128 (299)
Q Consensus 101 v~~Lt~EVdEml-----dpV~amcqLqSqlrnk 128 (299)
|.-.+..+.||+ +|-+|+++||.|+|..
T Consensus 10 ~~~~~~~~se~i~~~ANEPSlgLYrlQeHvrks 42 (118)
T PF10167_consen 10 VKKVTERISENIHIVANEPSLGLYRLQEHVRKS 42 (118)
T ss_pred HHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHH
Confidence 344455555555 6889999999999987
No 35
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=27.85 E-value=25 Score=30.19 Aligned_cols=31 Identities=16% Similarity=0.249 Sum_probs=22.7
Q ss_pred ccccCccccccccC-cCCCCCCccccccccccc
Q 022315 194 KKNCAHCHCQNTSQ-LTSPNGPKSLCDGCISSY 225 (299)
Q Consensus 194 ~r~C~~C~ttkTp~-R~GP~GPKSLCNACGiRy 225 (299)
--.|..|+...|-+ +.+ .--.--|+|||-+.
T Consensus 102 yVlC~~C~spdT~l~k~~-r~~~l~C~ACGa~~ 133 (138)
T PRK03988 102 YVICPECGSPDTKLIKEG-RIWVLKCEACGAET 133 (138)
T ss_pred cEECCCCCCCCcEEEEcC-CeEEEEcccCCCCC
Confidence 35799999999999 642 12345699999764
No 36
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=27.41 E-value=37 Score=24.49 Aligned_cols=30 Identities=20% Similarity=0.465 Sum_probs=21.3
Q ss_pred ccccCccccccccCcCCCCCCcccccccccccc
Q 022315 194 KKNCAHCHCQNTSQLTSPNGPKSLCDGCISSYG 226 (299)
Q Consensus 194 ~r~C~~C~ttkTp~R~GP~GPKSLCNACGiRyr 226 (299)
-+.|..|+... ...+.+-.-.|..||..+-
T Consensus 28 Sq~C~~CG~~~---~~~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 28 SQTCPRCGHRN---KKRRSGRVFTCPNCGFEMD 57 (69)
T ss_pred ccCccCccccc---ccccccceEEcCCCCCEEC
Confidence 45688888776 3356667778888987753
No 37
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=26.49 E-value=29 Score=28.78 Aligned_cols=14 Identities=29% Similarity=0.688 Sum_probs=8.7
Q ss_pred CCcccccccccccc
Q 022315 213 GPKSLCDGCISSYG 226 (299)
Q Consensus 213 GPKSLCNACGiRyr 226 (299)
|=|-.|..||.||-
T Consensus 7 GtKR~Cp~CG~kFY 20 (108)
T PF09538_consen 7 GTKRTCPSCGAKFY 20 (108)
T ss_pred CCcccCCCCcchhc
Confidence 55666666666664
No 38
>COG3259 FrhA Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion]
Probab=25.93 E-value=1.5e+02 Score=30.58 Aligned_cols=35 Identities=9% Similarity=0.194 Sum_probs=26.0
Q ss_pred ccCcccchhHHHHHHHHHHHhhhhcchhHHhhhhHHHHH
Q 022315 80 SIGAGFTDFKKERLRSLLRQGVFDLAPEVDEMLDPVIAM 118 (299)
Q Consensus 80 ~iGaglSDfkkErLksLLrQ~v~~Lt~EVdEmldpV~am 118 (299)
+++--+|+-.+++|..++||.+.. ++++++.+..+
T Consensus 166 G~~~~lsee~~~~l~~~ake~~~l----A~~~~e~~~~l 200 (441)
T COG3259 166 GVAKNLSEEAREKLLDRAKEALEL----ADRTVELFKEL 200 (441)
T ss_pred ccCCCCCHHHHHHHHHHHHHHHHH----HHHHHHHHHHH
Confidence 567779999999999999998743 45555555444
No 39
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=25.87 E-value=38 Score=31.06 Aligned_cols=29 Identities=24% Similarity=0.423 Sum_probs=14.2
Q ss_pred cccCccccccccCcCCCCCCcccccccccccc
Q 022315 195 KNCAHCHCQNTSQLTSPNGPKSLCDGCISSYG 226 (299)
Q Consensus 195 r~C~~C~ttkTp~R~GP~GPKSLCNACGiRyr 226 (299)
|.|.+|++...+ ...|-+-.|.+||.++-
T Consensus 100 ~fC~~CG~~~~~---~~~~~~~~C~~c~~~~y 128 (256)
T PRK00241 100 RFCGYCGHPMHP---SKTEWAMLCPHCRERYY 128 (256)
T ss_pred ccccccCCCCee---cCCceeEECCCCCCEEC
Confidence 456666554322 23344455666665443
No 40
>COG1941 FrhG Coenzyme F420-reducing hydrogenase, gamma subunit [Energy production and conversion]
Probab=25.62 E-value=30 Score=32.98 Aligned_cols=26 Identities=15% Similarity=0.335 Sum_probs=20.6
Q ss_pred ccccccccCcCCCCCCccccccccccc
Q 022315 199 HCHCQNTSQLTSPNGPKSLCDGCISSY 225 (299)
Q Consensus 199 ~C~ttkTp~R~GP~GPKSLCNACGiRy 225 (299)
.|-+..-|.| ||.||...|+.||.-|
T Consensus 201 ~CP~~ai~c~-Gc~g~~~~~~~~Ga~~ 226 (247)
T COG1941 201 SCPSRAIPCR-GCRGNIPRCIKCGACF 226 (247)
T ss_pred cCCccCCccc-CCcCCcccchhhhHHH
Confidence 4555566668 7999999999999665
No 41
>COG4077 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.46 E-value=32 Score=30.87 Aligned_cols=15 Identities=47% Similarity=0.642 Sum_probs=12.2
Q ss_pred cccCCCCCCcccchH
Q 022315 15 GQLGPIGPDYFGFYT 29 (299)
Q Consensus 15 ~r~g~~GPD~FgyY~ 29 (299)
..-++|+||.|||-+
T Consensus 93 ~te~~i~~d~~GfeR 107 (156)
T COG4077 93 LTENPIYPDTFGFER 107 (156)
T ss_pred hhcCCCccCcchHHH
Confidence 445899999999965
No 42
>PF14877 mIF3: Mitochondrial translation initiation factor
Probab=25.44 E-value=84 Score=28.62 Aligned_cols=16 Identities=56% Similarity=0.764 Sum_probs=13.8
Q ss_pred hHHHHHHHHhHHHHHH
Q 022315 259 SEVEETVKKYSDELFA 274 (299)
Q Consensus 259 s~vee~vkkysdel~~ 274 (299)
..|.+++|.|||+|-.
T Consensus 84 v~~~~alk~YSd~LAk 99 (181)
T PF14877_consen 84 VEVREALKQYSDELAK 99 (181)
T ss_pred ecHHHHHHHHHHHHHH
Confidence 4689999999999864
No 43
>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.
Probab=24.00 E-value=1.4e+02 Score=22.40 Aligned_cols=38 Identities=18% Similarity=0.323 Sum_probs=28.8
Q ss_pred hhhccCchHHHHHHHHhHHHHHHHHhHHHHHHHHHHHH
Q 022315 252 FLLESDSSEVEETVKKYSDELFATLGHMEQKLEELLNT 289 (299)
Q Consensus 252 ~lle~d~s~vee~vkkysdel~~tlg~meq~le~lld~ 289 (299)
.|++.|..++.+.+++..+.+-..+..++.+++.+-..
T Consensus 54 ~fv~~~~~~~~~~L~~~~~~~~~~i~~l~~~~~~l~~~ 91 (106)
T PF01920_consen 54 MFVKQDKEEAIEELEERIEKLEKEIKKLEKQLKYLEKK 91 (106)
T ss_dssp EEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36677888888888888888888887777777766554
No 44
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=23.96 E-value=37 Score=23.33 Aligned_cols=31 Identities=16% Similarity=0.380 Sum_probs=21.5
Q ss_pred cccccCccccccccCcCCCCCCccccccccc
Q 022315 193 FKKNCAHCHCQNTSQLTSPNGPKSLCDGCIS 223 (299)
Q Consensus 193 ~~r~C~~C~ttkTp~R~GP~GPKSLCNACGi 223 (299)
..-+|..|+.+-.-.+..-..+...|.+||-
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEEEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 4457899997665553333377888999987
No 45
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=23.67 E-value=49 Score=29.75 Aligned_cols=79 Identities=19% Similarity=0.304 Sum_probs=45.3
Q ss_pred ccCccccccccC---cCCCCCC----ccccccccccccCCcccccc-----CccC-ccccCCc-cccchhhhhcc---Cc
Q 022315 196 NCAHCHCQNTSQ---LTSPNGP----KSLCDGCISSYGKDKDLHSD-----SNIG-ADKENGE-VDDDLQFLLES---DS 258 (299)
Q Consensus 196 ~C~~C~ttkTp~---R~GP~GP----KSLCNACGiRyrk~r~~~l~-----~~~g-~~k~~gE-v~dd~k~lle~---d~ 258 (299)
.|..|+...|-. |.-..|- .--|..||-||--=-+..+- .+-| -+.=+.+ +...+..-++. +.
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~~~~VvKkdg~Re~F~r~Kl~~gl~~A~~KRpVs~ 81 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELRPLIVVKKDGRREPFDREKLRRGLIRACEKRPVSS 81 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeeccceEECcCCCcCCCCHHHHHHHHHHHHhcCCCCH
Confidence 699999988877 7777773 45799999999766543332 1112 1111111 33444444554 23
Q ss_pred hHHHHHHHHhHHHHHH
Q 022315 259 SEVEETVKKYSDELFA 274 (299)
Q Consensus 259 s~vee~vkkysdel~~ 274 (299)
..+|++|..--.+|.+
T Consensus 82 e~ie~~v~~ie~~Lr~ 97 (156)
T COG1327 82 EQIEEAVSHIERQLRS 97 (156)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 4556666555555544
No 46
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=23.60 E-value=47 Score=23.59 Aligned_cols=24 Identities=21% Similarity=0.457 Sum_probs=13.1
Q ss_pred CccccccccccccCCcc--ccccCcc
Q 022315 214 PKSLCDGCISSYGKDKD--LHSDSNI 237 (299)
Q Consensus 214 PKSLCNACGiRyrk~r~--~~l~~~~ 237 (299)
|.+||.-||..|.-.++ .-.|.++
T Consensus 1 ~~~~CprC~kg~Hwa~~C~sk~d~~G 26 (36)
T PF14787_consen 1 PPGLCPRCGKGFHWASECRSKTDVDG 26 (36)
T ss_dssp ---C-TTTSSSCS-TTT---TCCCCC
T ss_pred CCccCcccCCCcchhhhhhhhhcccC
Confidence 57899999999988774 4444433
No 47
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=22.56 E-value=62 Score=21.90 Aligned_cols=25 Identities=20% Similarity=0.469 Sum_probs=16.7
Q ss_pred ccCccccccccCcCCCCCCcccccccccc
Q 022315 196 NCAHCHCQNTSQLTSPNGPKSLCDGCISS 224 (299)
Q Consensus 196 ~C~~C~ttkTp~R~GP~GPKSLCNACGiR 224 (299)
.|++|+.... . . .+..--|..||-|
T Consensus 2 ~C~~Cg~~~~-~--~-~~~~irC~~CG~R 26 (32)
T PF03604_consen 2 ICGECGAEVE-L--K-PGDPIRCPECGHR 26 (32)
T ss_dssp BESSSSSSE--B--S-TSSTSSBSSSS-S
T ss_pred CCCcCCCeeE-c--C-CCCcEECCcCCCe
Confidence 5899998885 2 2 2344689999977
No 48
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.27 E-value=49 Score=28.94 Aligned_cols=38 Identities=16% Similarity=0.366 Sum_probs=27.5
Q ss_pred hhccccccCccccccccCcCCCCCCccccccccccccCCc
Q 022315 190 MSNFKKNCAHCHCQNTSQLTSPNGPKSLCDGCISSYGKDK 229 (299)
Q Consensus 190 ~~~~~r~C~~C~ttkTp~R~GP~GPKSLCNACGiRyrk~r 229 (299)
+.+..-+|.+|.--+- =.|=.=|.--|.|||-.|...+
T Consensus 17 ~~Gl~grCP~CGeGrL--F~gFLK~~p~C~aCG~dyg~~~ 54 (126)
T COG5349 17 KRGLRGRCPRCGEGRL--FRGFLKVVPACEACGLDYGFAD 54 (126)
T ss_pred HHHhcCCCCCCCCchh--hhhhcccCchhhhccccccCCc
Confidence 4567889999987652 2234445667999999998776
No 49
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=21.79 E-value=99 Score=28.13 Aligned_cols=29 Identities=28% Similarity=0.557 Sum_probs=25.6
Q ss_pred ccccCccccccccCcCCCCCCcccccccc
Q 022315 194 KKNCAHCHCQNTSQLTSPNGPKSLCDGCI 222 (299)
Q Consensus 194 ~r~C~~C~ttkTp~R~GP~GPKSLCNACG 222 (299)
-..|++|+++..|.-.-|..+..+|-.|.
T Consensus 154 l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 154 LTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred hHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 45799999999888888999999999987
No 50
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=21.61 E-value=37 Score=26.63 Aligned_cols=29 Identities=21% Similarity=0.338 Sum_probs=22.7
Q ss_pred ccccccCccccccccCcCCCCCCcccccccccc
Q 022315 192 NFKKNCAHCHCQNTSQLTSPNGPKSLCDGCISS 224 (299)
Q Consensus 192 ~~~r~C~~C~ttkTp~R~GP~GPKSLCNACGiR 224 (299)
-..-.|++|+.-+|-.|+-+ --|--||-|
T Consensus 18 ~miYiCgdC~~en~lk~~D~----irCReCG~R 46 (62)
T KOG3507|consen 18 TMIYICGDCGQENTLKRGDV----IRCRECGYR 46 (62)
T ss_pred cEEEEeccccccccccCCCc----EehhhcchH
Confidence 34678999999998776544 469999977
No 51
>PF12041 DELLA: Transcriptional regulator DELLA protein N terminal; InterPro: IPR021914 Gibberellins are plant hormones which have great impact on growth signalling. DELLA proteins are transcriptional regulators of growth related proteins which are downregulated when gibberellins bind to their receptor GID1. GID1 forms a complex with DELLA proteins and signals them towards 26S proteasome. The N-terminal of DELLA proteins contains conserved DELLA and VHYNP motifs which are important for GID1 binding and proteolysis of the DELLA proteins [].; PDB: 2ZSH_B 2ZSI_B.
Probab=21.55 E-value=66 Score=25.86 Aligned_cols=22 Identities=55% Similarity=0.821 Sum_probs=14.2
Q ss_pred HHHHHHHh---------HHHHHHHHHHHHHHh
Q 022315 270 DELFATLG---------HMEQKLEELLNTVVS 292 (299)
Q Consensus 270 del~~tlg---------~meq~le~lld~v~~ 292 (299)
|||+|-|| ++-||||+| .+||.
T Consensus 1 DellA~lGYkVrsSdmadVAQkLEqL-E~vmg 31 (73)
T PF12041_consen 1 DELLAVLGYKVRSSDMADVAQKLEQL-EMVMG 31 (73)
T ss_dssp -HHHHTTT-B-BGGGHHHHHHHHHHH-HHHHT
T ss_pred CchhhhhcccccchHHHHHHHHHHHH-HHHHc
Confidence 56666655 477888885 56664
No 52
>PTZ00048 cytochrome c; Provisional
Probab=21.52 E-value=43 Score=27.23 Aligned_cols=13 Identities=54% Similarity=1.065 Sum_probs=10.3
Q ss_pred ccccccCcccccc
Q 022315 192 NFKKNCAHCHCQN 204 (299)
Q Consensus 192 ~~~r~C~~C~ttk 204 (299)
.+.+.|+.||+..
T Consensus 21 ~f~~~C~~CH~~~ 33 (115)
T PTZ00048 21 LFKAKCAQCHTIN 33 (115)
T ss_pred HHHhhhhhcCCCc
Confidence 4667899999865
No 53
>PF08889 WbqC: WbqC-like protein family; InterPro: IPR014985 This family of proteins are functionally uncharacterised. However, it is found in an O-antigen gene cluster in Escherichia coli [] and other bacteria [] suggesting a role in O-antigen production. It has been suggested that wbnG may code for a glycine transferase [].
Probab=21.19 E-value=1e+02 Score=27.72 Aligned_cols=56 Identities=21% Similarity=0.302 Sum_probs=38.6
Q ss_pred CcccchHHHHHHHhhcCCCCCCCCcccchhhccccCCCCCCccccCCCCCcccccccccCcccchhHHHHHHHHHHH---
Q 022315 23 DYFGFYTCEIMELLSQDEDPLPSTSRTSELTRKKCSGVRGKDTIDTSGRGTVSSFSNSIGAGFTDFKKERLRSLLRQ--- 99 (299)
Q Consensus 23 D~FgyY~~eV~eLLSQdEd~lp~ssq~sel~~~k~~~~r~~~~v~~s~~~sgs~~S~~iGaglSDfkkErLksLLrQ--- 99 (299)
-||.+|...|+.++.++.+. |+||-.+-|..+++.
T Consensus 88 P~f~~~~~~ie~~~~~~~~~------------------------------------------L~dln~~~l~~i~~~Lgi 125 (219)
T PF08889_consen 88 PYFEEYEPLIEPLYEKPYDN------------------------------------------LADLNEASLEWICDYLGI 125 (219)
T ss_pred CCHHHHHHHHHHHHhCCccc------------------------------------------HHHHHHHHHHHHHHHhCC
Confidence 48999999999999766555 566666555555542
Q ss_pred -hhhhcchhHHh----hhhHHHHHHH
Q 022315 100 -GVFDLAPEVDE----MLDPVIAMCQ 120 (299)
Q Consensus 100 -~v~~Lt~EVdE----mldpV~amcq 120 (299)
.-+..++|.+. -.+.|++||+
T Consensus 126 ~~~i~~sS~l~~~~~~~~~~vi~i~~ 151 (219)
T PF08889_consen 126 DTPIVRSSELNLPEGKKSERVIDICK 151 (219)
T ss_pred CCeEEeccccccCCCCchHHHHHHHH
Confidence 23455666665 6778888873
No 54
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=20.92 E-value=38 Score=22.30 Aligned_cols=25 Identities=24% Similarity=0.632 Sum_probs=14.3
Q ss_pred ccccccCccccccccCcCCCCCCccccccccc
Q 022315 192 NFKKNCAHCHCQNTSQLTSPNGPKSLCDGCIS 223 (299)
Q Consensus 192 ~~~r~C~~C~ttkTp~R~GP~GPKSLCNACGi 223 (299)
-...+|.+|++.--| |+..|.+||.
T Consensus 9 l~~~rC~~Cg~~~~p-------Pr~~Cp~C~s 33 (37)
T PF12172_consen 9 LLGQRCRDCGRVQFP-------PRPVCPHCGS 33 (37)
T ss_dssp EEEEE-TTT--EEES---------SEETTTT-
T ss_pred EEEEEcCCCCCEecC-------CCcCCCCcCc
Confidence 456789999988755 5567888874
No 55
>PRK15043 transcriptional regulator MirA; Provisional
Probab=20.49 E-value=2e+02 Score=26.97 Aligned_cols=53 Identities=15% Similarity=0.235 Sum_probs=40.6
Q ss_pred ccCCccccchhhhhccCchHHHHHHHHhHHHHHHHHhH-HHHHHHHHHHHHHhh
Q 022315 241 KENGEVDDDLQFLLESDSSEVEETVKKYSDELFATLGH-MEQKLEELLNTVVSR 293 (299)
Q Consensus 241 k~~gEv~dd~k~lle~d~s~vee~vkkysdel~~tlg~-meq~le~lld~v~~~ 293 (299)
++.|=...+++.||..+.....+..+.+.++|...|.. -+++|+.+|+.++..
T Consensus 57 ~~~G~~i~eIk~ll~~~~~~~~~~~~~~~~~ll~al~~~d~~~l~~~l~~a~~~ 110 (243)
T PRK15043 57 IDNGVQVSKVKMLLSNENVDVQNGWRDQQETLLTYLQSGNLHSLRTWIKERGQD 110 (243)
T ss_pred HHcCCCHHHHHHHHhccchhhHHHHHHHHHHHHHHHHHhCHHHHHHHHHHHHHH
Confidence 44666677899999888777777788888888776654 478899999887653
No 56
>PRK12729 fliE flagellar hook-basal body protein FliE; Provisional
Probab=20.34 E-value=1.6e+02 Score=25.67 Aligned_cols=22 Identities=14% Similarity=0.167 Sum_probs=14.3
Q ss_pred hHHhhhhHHHHH------HHHHHHhhhc
Q 022315 107 EVDEMLDPVIAM------CQLQSQVRNR 128 (299)
Q Consensus 107 EVdEmldpV~am------cqLqSqlrnk 128 (299)
+.+.+-|-++|| +|+.=|||||
T Consensus 88 ~~vdLhdVMIA~qKAslSlql~vQVRNK 115 (127)
T PRK12729 88 NSVDAHDVMIASEKARVALTFTKTIADG 115 (127)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555555554 3666699998
No 57
>KOG2773 consensus Apoptosis antagonizing transcription factor/protein transport protein [Transcription; Intracellular trafficking, secretion, and vesicular transport]
Probab=20.32 E-value=1.3e+02 Score=31.40 Aligned_cols=98 Identities=26% Similarity=0.322 Sum_probs=60.6
Q ss_pred CCCCCCcccchHH-----HHHHHhhcCCCCCCCCccc----------------chhhccccCCCCCCccccCCCCCcccc
Q 022315 18 GPIGPDYFGFYTC-----EIMELLSQDEDPLPSTSRT----------------SELTRKKCSGVRGKDTIDTSGRGTVSS 76 (299)
Q Consensus 18 g~~GPD~FgyY~~-----eV~eLLSQdEd~lp~ssq~----------------sel~~~k~~~~r~~~~v~~s~~~sgs~ 76 (299)
|.+||-.+.|-.- ||+..|.--|++ --.||+ ...|.|+-++.|+++-+.-+-+ .-.
T Consensus 316 g~a~~~~~kf~~~~~i~~Qi~~~l~d~erl-~~rtq~~r~~~~v~~~~pe~a~~~vpen~~~~p~~~na~~~~ld--pei 392 (483)
T KOG2773|consen 316 GGAAPKCKKFLIPFSINFQIEHFLDDPERL-VKRTQTMRRKFSVLARFPENAQKPVPENKPGEPRGKNASPESLD--PEI 392 (483)
T ss_pred ccccccchhhhccchHHHHHHHHhhCHHHH-HHHhhhccccccccccCcchhccCCcccCCCCCCCccccccccC--ccc
Confidence 6678877777664 777777443332 223333 4568899888888877666543 111
Q ss_pred cccccCcccchhHHHHHHHHHH--HhhhhcchhHHhhhhHHHHHHHHHHHhhhccC
Q 022315 77 FSNSIGAGFTDFKKERLRSLLR--QGVFDLAPEVDEMLDPVIAMCQLQSQVRNRKC 130 (299)
Q Consensus 77 ~S~~iGaglSDfkkErLksLLr--Q~v~~Lt~EVdEmldpV~amcqLqSqlrnkk~ 130 (299)
|= =+||=+--||-||- -+..+-++++.-|.. -| .+|.+ +||+
T Consensus 393 fD------D~DFY~qLLkelIe~k~s~~dns~~~A~~~~---~~-~~qk~--~Kkk 436 (483)
T KOG2773|consen 393 FD------DSDFYQQLLKELIEAKNSMSDNSSDGADMTQ---YM-ELQKQ--NKKK 436 (483)
T ss_pred cC------cHHHHHHHHHHHHHHhhccCCcchhhHHHHH---HH-HHHHH--HHHh
Confidence 21 37898888888887 555555666655552 22 57777 6644
No 58
>PF10752 DUF2533: Protein of unknown function (DUF2533) ; InterPro: IPR019688 This entry represents proteins with unknown function, and appear to be restricted to Bacillus spp.
Probab=20.01 E-value=2.1e+02 Score=23.65 Aligned_cols=35 Identities=23% Similarity=0.412 Sum_probs=26.1
Q ss_pred HHHHHHHhH---HHHHHHHhHHHHHHHHHHHHHHhhcc
Q 022315 261 VEETVKKYS---DELFATLGHMEQKLEELLNTVVSRCR 295 (299)
Q Consensus 261 vee~vkkys---del~~tlg~meq~le~lld~v~~~cr 295 (299)
|-+.+..+| .+...+.-.+|||-|..+|.+|..|+
T Consensus 3 VH~aItaH~~Kq~~~~k~F~~Le~~RE~aIeeav~~c~ 40 (84)
T PF10752_consen 3 VHKAITAHSQKQHAIIKQFLQLEQQREAAIEEAVSLCK 40 (84)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444444 34556667899999999999999997
Done!