Query 030110
Match_columns 183
No_of_seqs 121 out of 615
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 08:40:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030110.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030110hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00270 rpsU 30S ribosomal pr 99.9 1.4E-22 3.1E-27 143.9 7.2 61 89-149 1-61 (64)
2 TIGR00030 S21p ribosomal prote 99.9 1.8E-22 3.9E-27 141.0 6.4 57 90-146 1-57 (58)
3 COG0828 RpsU Ribosomal protein 99.8 2.8E-21 6.2E-26 139.5 7.3 62 89-150 1-62 (67)
4 PF01165 Ribosomal_S21: Riboso 99.6 3.4E-19 7.4E-24 122.3 -9.7 57 90-146 1-57 (57)
5 PF09269 DUF1967: Domain of un 70.0 3.3 7.2E-05 29.5 1.8 23 101-123 30-52 (69)
6 TIGR03595 Obg_CgtA_exten Obg f 69.8 5 0.00011 28.6 2.7 23 101-123 30-52 (69)
7 COG1356 tfx Transcriptional re 47.4 13 0.00027 30.9 1.8 28 89-116 67-94 (143)
8 PF04898 Glu_syn_central: Glut 45.6 21 0.00046 32.3 3.0 46 69-120 218-263 (287)
9 PF14044 NETI: NETI protein 41.0 21 0.00046 25.6 1.9 18 92-109 2-19 (57)
10 PRK13780 phosphocarrier protei 38.8 46 0.001 24.6 3.5 28 88-116 59-86 (88)
11 TIGR03884 sel_bind_Methan sele 38.3 43 0.00094 25.1 3.2 28 88-115 15-42 (74)
12 PF11393 IcmL: Macrophage kill 33.9 41 0.00088 25.6 2.6 28 101-128 52-79 (108)
13 PF06084 Cytomega_TRL10: Cytom 30.8 72 0.0016 26.4 3.7 22 152-173 124-148 (150)
14 PF00352 TBP: Transcription fa 27.4 66 0.0014 23.2 2.7 37 79-115 50-86 (86)
15 PF01877 RNA_binding: RNA bind 27.0 1.3E+02 0.0029 23.2 4.4 33 89-122 47-79 (120)
16 PRK09256 hypothetical protein; 26.6 2.2E+02 0.0049 23.0 5.8 44 89-135 69-116 (138)
17 COG2101 SPT15 TATA-box binding 26.5 50 0.0011 28.6 2.2 39 79-117 147-185 (185)
18 COG2061 ACT-domain-containing 26.2 61 0.0013 27.7 2.6 32 86-117 130-161 (170)
19 PF12010 DUF3502: Domain of un 26.2 29 0.00062 27.2 0.6 29 87-116 87-115 (134)
20 KOG3229 Vacuolar sorting prote 25.5 80 0.0017 28.1 3.3 26 100-125 123-148 (227)
21 KOG2767 Translation initiation 24.7 82 0.0018 30.1 3.4 12 165-176 198-209 (400)
22 smart00878 Biotin_carb_C Bioti 24.7 76 0.0016 24.3 2.7 26 88-114 50-75 (107)
23 PHA03237 envelope glycoprotein 24.4 1E+02 0.0022 29.5 4.0 13 71-83 302-314 (424)
24 KOG3032 Uncharacterized conser 24.4 1.9E+02 0.0041 26.3 5.4 19 98-116 163-181 (264)
25 PF04147 Nop14: Nop14-like fam 23.7 1.2E+02 0.0025 31.0 4.5 44 102-145 780-825 (840)
26 KOG0345 ATP-dependent RNA heli 23.0 27 0.00058 34.5 -0.1 22 101-122 474-495 (567)
27 PHA03346 US22 family homolog; 21.8 97 0.0021 30.4 3.4 14 167-180 433-446 (520)
28 PF06679 DUF1180: Protein of u 21.6 54 0.0012 27.4 1.4 7 166-172 146-152 (163)
29 PF12230 PRP21_like_P: Pre-mRN 21.5 75 0.0016 26.7 2.3 45 103-147 4-50 (229)
30 KOG3671 Actin regulatory prote 21.3 83 0.0018 31.3 2.8 10 166-175 560-569 (569)
31 KOG0709 CREB/ATF family transc 21.1 93 0.002 30.4 3.1 24 100-123 246-269 (472)
32 PLN03014 carbonic anhydrase 21.0 1.1E+02 0.0023 28.8 3.3 19 97-115 80-98 (347)
33 KOG3562 Forkhead/HNF-3-related 20.9 70 0.0015 29.0 2.1 13 166-178 114-126 (277)
No 1
>PRK00270 rpsU 30S ribosomal protein S21; Reviewed
Probab=99.87 E-value=1.4e-22 Score=143.92 Aligned_cols=61 Identities=41% Similarity=0.698 Sum_probs=58.2
Q ss_pred ceEEEecCCCcHHHHHHHHHHHHHhhhhHHHHhhhcccCCchHHHHHHHHHHHHHHHHhhh
Q 030110 89 NVQVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRRRRS 149 (183)
Q Consensus 89 mv~V~V~enE~iE~ALRRFKRkv~keGIL~E~KrRRyYEKPSeKRKRK~~eA~rR~rKrr~ 149 (183)
|++|.|++||+||.|||+|||+|+++|||+|+|+|+||||||++|+|+..+|.+|++++.+
T Consensus 1 M~~V~V~~~e~ie~Alrrfkr~~~k~gil~e~r~r~~yekPs~krkrk~~~a~rr~~k~~~ 61 (64)
T PRK00270 1 MPQVKVRENESIDKALRRFKRKVEKAGILRELRRREFYEKPSEKRKRKKAAARKRRRKKLA 61 (64)
T ss_pred CCeeEeCCCChHHHHHHHHHHHHHHcchHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHh
Confidence 7899999999999999999999999999999999999999999999999999999987543
No 2
>TIGR00030 S21p ribosomal protein S21. This model describes bacterial ribosomal protein S21 and most mitochondrial and chloroplast equivalents.
Probab=99.87 E-value=1.8e-22 Score=140.98 Aligned_cols=57 Identities=37% Similarity=0.694 Sum_probs=54.7
Q ss_pred eEEEecCCCcHHHHHHHHHHHHHhhhhHHHHhhhcccCCchHHHHHHHHHHHHHHHH
Q 030110 90 VQVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRR 146 (183)
Q Consensus 90 v~V~V~enE~iE~ALRRFKRkv~keGIL~E~KrRRyYEKPSeKRKRK~~eA~rR~rK 146 (183)
++|.|++||+||+|||+|||+|+++|||+|||+|+||||||++|+|+.++|++|+++
T Consensus 1 ~~V~V~~~e~ie~alrrfkr~~~~~gil~e~r~r~~yeKPs~krkrk~~~a~rr~~k 57 (58)
T TIGR00030 1 PTVKVKEGESIDSALRRFKRKLEKEGILRELKKRRYYEKPSERRRRKEKAAAKRIRK 57 (58)
T ss_pred CeeEeCCCCcHHHHHHHHHHHHHHcchHHHHHHHHhhcCHHHHHHHHHHHHHHHHhc
Confidence 579999999999999999999999999999999999999999999999999998865
No 3
>COG0828 RpsU Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]
Probab=99.85 E-value=2.8e-21 Score=139.45 Aligned_cols=62 Identities=40% Similarity=0.667 Sum_probs=58.5
Q ss_pred ceEEEecCCCcHHHHHHHHHHHHHhhhhHHHHhhhcccCCchHHHHHHHHHHHHHHHHhhhc
Q 030110 89 NVQVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRRRRSQ 150 (183)
Q Consensus 89 mv~V~V~enE~iE~ALRRFKRkv~keGIL~E~KrRRyYEKPSeKRKRK~~eA~rR~rKrr~~ 150 (183)
|++|.|++||+||.|||+|||+|+++|||+|+|+|+|||+|+++++||..+|.+|..|+..+
T Consensus 1 M~~v~V~ene~~d~ALrrFKr~~~k~gil~e~k~r~~yEkPs~krkrK~a~a~kr~~k~~~k 62 (67)
T COG0828 1 MPQVKVRENEPLDKALRRFKRKVEKEGILREMKEREFYEKPSEKRKRKKAAARKRKFKRLRK 62 (67)
T ss_pred CCeeeecCCChHHHHHHHHHHHHHHHHHHHHHHHHHhccCchHHHHHHHHHHHHHHHHHHHH
Confidence 78999999999999999999999999999999999999999999999999999998776543
No 4
>PF01165 Ribosomal_S21: Ribosomal protein S21; InterPro: IPR001911 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 [, ]. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryote ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S21 contains 55-70 amino acid residues, and has only been found in eubacteria to date, though it has been reported that plant chloroplasts and mammalian mitochondria contain ribosomal subunit protein S21. Experimental evidence has revealed that S21 is well exposed on the surface of the Escherichia coli ribosome [], and is one of the 'split proteins': these are a discrete group that are selectively removed from 30S subunits under low salt conditions and are required for the formation of activated 30S reconstitution intermediate (RI*) particles.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2VHO_U 3J18_U 2AVY_U 3OFO_U 3OFP_U 2WWL_U 3J0X_X 3IZV_Y 3ORA_U 3IZW_Y ....
Probab=99.63 E-value=3.4e-19 Score=122.30 Aligned_cols=57 Identities=40% Similarity=0.704 Sum_probs=50.9
Q ss_pred eEEEecCCCcHHHHHHHHHHHHHhhhhHHHHhhhcccCCchHHHHHHHHHHHHHHHH
Q 030110 90 VQVVVDENEPEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKRKTREAAKRNRR 146 (183)
Q Consensus 90 v~V~V~enE~iE~ALRRFKRkv~keGIL~E~KrRRyYEKPSeKRKRK~~eA~rR~rK 146 (183)
|+|.|++||++|.||++|+++|+++||++|+|+++|||||+++|+++..++.+|..|
T Consensus 1 v~V~V~~~~~~e~Alrr~~r~~~~~gi~~~~r~r~~yekps~kRkrk~~~~~rr~~k 57 (57)
T PF01165_consen 1 VTVKVRDGEDVERALRRFKRKVRRNGILKELRKRRFYEKPSEKRKRKRSERWRRRFK 57 (57)
T ss_dssp ---EEESSSSSSSSSGTTCCTSSTTHHHTTTSSSB-SSSCCCCTTHCCCCCTHHHHH
T ss_pred CeeecCCCCCHHHHHHHHHHHHHHcChHHHHHHHHhcCCHHHHHHHHHHHHHHHHhC
Confidence 589999999999999999999999999999999999999999999999999888764
No 5
>PF09269 DUF1967: Domain of unknown function (DUF1967); InterPro: IPR015349 The Obg family comprises a group of ancient P-loop small G proteins (GTPases) belonging to the TRAFAC (for translation factors) class and can be subdivided into several distinct protein subfamilies []. OBG GTPases have been found in both prokaryotes and eukaryotes []. The structure of the OBG GTPase from Thermus thermophilus has been determined []. This entry represents a C-terminal domain found in certain OBG GTPases. This domain contains a four-stranded beta sheet and three alpha helices flanked by an additional beta strand. It is predominantly found in the bacterial GTP-binding protein Obg, and is functionally uncharacterised. ; GO: 0000166 nucleotide binding; PDB: 1UDX_A.
Probab=70.04 E-value=3.3 Score=29.47 Aligned_cols=23 Identities=30% Similarity=0.577 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHhhhhHHHHhhh
Q 030110 101 ERLLNRFRREVMRAGVIQECKRR 123 (183)
Q Consensus 101 E~ALRRFKRkv~keGIL~E~KrR 123 (183)
+.+++||.+.+.+-||.+++|+.
T Consensus 30 ~e~~~rf~~~L~~~Gv~~~L~~~ 52 (69)
T PF09269_consen 30 EESLRRFQRKLKKMGVEKALRKA 52 (69)
T ss_dssp GGGHHHHHHHHHHTTHHHHHHTT
T ss_pred HHHHHHHHHHHHHCCHHHHHHHc
Confidence 46789999999999999999975
No 6
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=69.82 E-value=5 Score=28.59 Aligned_cols=23 Identities=26% Similarity=0.505 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHhhhhHHHHhhh
Q 030110 101 ERLLNRFRREVMRAGVIQECKRR 123 (183)
Q Consensus 101 E~ALRRFKRkv~keGIL~E~KrR 123 (183)
+.|++||.+.+.+.||.+.+++.
T Consensus 30 ~e~~~~f~~~L~~~Gv~~~L~~~ 52 (69)
T TIGR03595 30 DENLRRFARKLKKLGVEDALRKA 52 (69)
T ss_pred HHHHHHHHHHHHHCCHHHHHHHc
Confidence 57899999999999999999875
No 7
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=47.38 E-value=13 Score=30.92 Aligned_cols=28 Identities=25% Similarity=0.408 Sum_probs=26.3
Q ss_pred ceEEEecCCCcHHHHHHHHHHHHHhhhh
Q 030110 89 NVQVVVDENEPEERLLNRFRREVMRAGV 116 (183)
Q Consensus 89 mv~V~V~enE~iE~ALRRFKRkv~keGI 116 (183)
.++|.|+.||.++....++=++-+.+||
T Consensus 67 pv~i~v~aGe~~dei~e~l~k~adeagi 94 (143)
T COG1356 67 PVSITVKAGEDIDEIPERLFKEADEAGI 94 (143)
T ss_pred CeEEEecCCCcHHHHHHHHHHhcccccc
Confidence 4899999999999999999999999997
No 8
>PF04898 Glu_syn_central: Glutamate synthase central domain; InterPro: IPR006982 Glutamate synthase (GltS)1 is a key enzyme in the early stages of the assimilation of ammonia in bacteria, yeasts, and plants. In bacteria, L-glutamate is involved in osmoregulation, is the precursor for other amino acids, and can be the precursor for haem biosynthesis. In plants, GltS is especially essential in the reassimilation of ammonia released by photorespiration. On the basis of the amino acid sequence and the nature of the electron donor, three different classes of GltS can de defined as follows: 1) ferredoxin-dependent GltS (Fd-GltS), 2) NADPH-dependent GltS (NADPH-GltS), and 3) NADH-dependent GltS (properties of the three classes have been reviewed extensively []). The enzyme is a complex iron-sulphur flavoprotein catalysing the reductive transfer of the amido nitrogen from L-glutamine to 2-oxoglutarate to form two molecules of L-glutamate via intramolecular channelling of ammonia from the amidotransferase domain to the FMN-binding domain. Reaction of amidotransferase domain: L-glutamine + H2O = L-glutamate + NH3 Reactions of FMN-binding domain: 2-oxoglutarate + NH3 = 2-iminoglutarate + H2O 2e + FMNox = FMNred 2-iminoglutarate + FMNred = L-glutamate + FMNox The central domain of glutamate synthase connects the N-terminal amidotransferase domain with the FMN-binding domain and has an alpha/beta overall topology [].; GO: 0015930 glutamate synthase activity, 0006807 nitrogen compound metabolic process, 0055114 oxidation-reduction process; PDB: 1EA0_A 2VDC_E 1OFE_A 1LLW_A 1OFD_A 1LLZ_A 1LM1_A.
Probab=45.56 E-value=21 Score=32.25 Aligned_cols=46 Identities=17% Similarity=0.338 Sum_probs=31.0
Q ss_pred hhhhccchhhhhhhcccCccceEEEecCCCcHHHHHHHHHHHHHhhhhHHHH
Q 030110 69 ASVICPSLAYANTLFFKSAYNVQVVVDENEPEERLLNRFRREVMRAGVIQEC 120 (183)
Q Consensus 69 ~sv~~p~la~sn~l~fk~~~mv~V~V~enE~iE~ALRRFKRkv~keGIL~E~ 120 (183)
.+++||.|+|.-+........+. +-+.+.|++++++.+.+ ||++-+
T Consensus 218 A~AV~PYla~e~~~~~~~~~~~~-----~~~~~~~~~ny~~a~~k-GllKim 263 (287)
T PF04898_consen 218 ADAVNPYLAYETIRELAERGELP-----ELSPEEAIKNYRKALEK-GLLKIM 263 (287)
T ss_dssp -SEEEEHCCHHHHHHCCCCCCCC-----T--HHHHHHHHHHHHHH-HHHHHH
T ss_pred HhhhcHHHHHHHHHHHHhcCCCC-----CCCHHHHHHHHHHHHHH-HHHHHH
Confidence 46789999998876644332222 55789999999998875 666644
No 9
>PF14044 NETI: NETI protein
Probab=41.02 E-value=21 Score=25.57 Aligned_cols=18 Identities=33% Similarity=0.492 Sum_probs=15.6
Q ss_pred EEecCCCcHHHHHHHHHH
Q 030110 92 VVVDENEPEERLLNRFRR 109 (183)
Q Consensus 92 V~V~enE~iE~ALRRFKR 109 (183)
..|.|||+|+..|-|+++
T Consensus 2 FeV~enETI~~CL~RM~~ 19 (57)
T PF14044_consen 2 FEVEENETISDCLARMKK 19 (57)
T ss_pred eeccCCCcHHHHHHHHHH
Confidence 468999999999999764
No 10
>PRK13780 phosphocarrier protein HPr; Provisional
Probab=38.81 E-value=46 Score=24.55 Aligned_cols=28 Identities=7% Similarity=0.264 Sum_probs=22.6
Q ss_pred cceEEEecCCCcHHHHHHHHHHHHHhhhh
Q 030110 88 YNVQVVVDENEPEERLLNRFRREVMRAGV 116 (183)
Q Consensus 88 ~mv~V~V~enE~iE~ALRRFKRkv~keGI 116 (183)
..+.|.+ +|++.+.||..+...+.++|+
T Consensus 59 ~~v~i~a-~G~De~~Al~~l~~~l~~~~l 86 (88)
T PRK13780 59 ADITISA-EGADAADAIAAIEETMKKEGL 86 (88)
T ss_pred CEEEEEE-eCcCHHHHHHHHHHHHHhccc
Confidence 4555555 888999999999999988765
No 11
>TIGR03884 sel_bind_Methan selenium-binding protein. This model describes a homopentameric selenium-binding protein with a suggested role in selenium transport and delivery to selenophosphate synthase, the SelD protein. This protein family is closely related to pfam01906, but is shorter because of several deleted regions. It is restricted to the archaeal genus Methanococcus.
Probab=38.30 E-value=43 Score=25.10 Aligned_cols=28 Identities=21% Similarity=0.500 Sum_probs=23.4
Q ss_pred cceEEEecCCCcHHHHHHHHHHHHHhhh
Q 030110 88 YNVQVVVDENEPEERLLNRFRREVMRAG 115 (183)
Q Consensus 88 ~mv~V~V~enE~iE~ALRRFKRkv~keG 115 (183)
|-+.|+...++++|.||+++.....+-|
T Consensus 15 ~yl~iv~~~~~d~d~Al~eM~e~A~~lG 42 (74)
T TIGR03884 15 YYLGIVSTESDNVDEIVENLREKVKAKG 42 (74)
T ss_pred EEEEEEEEecCCHHHHHHHHHHHHHHcC
Confidence 5677888899999999999998877644
No 12
>PF11393 IcmL: Macrophage killing protein with similarity to conjugation protein; InterPro: IPR021055 IcmL contains two amphipathic beta-sheet regions, required for the pore-forming ability which may be related to the transfer of this protein into a host cell membrane []. The icmL gene shows significant similarity to plasmid genes involved in conjugation however IcmL is thought to be required for macrophage killing. It is unknown whether conjugation plays a role in macrophage killing [].
Probab=33.87 E-value=41 Score=25.58 Aligned_cols=28 Identities=18% Similarity=0.449 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHhhhhHHHHhhhcccCC
Q 030110 101 ERLLNRFRREVMRAGVIQECKRRRFFET 128 (183)
Q Consensus 101 E~ALRRFKRkv~keGIL~E~KrRRyYEK 128 (183)
+.+...|...+++.|+|+.+|.++....
T Consensus 52 ~~g~~~f~~aL~~Sg~l~~ik~~~l~~~ 79 (108)
T PF11393_consen 52 DEGWNSFQKALQKSGILDAIKDKRLNLS 79 (108)
T ss_pred HHHHHHHHHHHHHCCCHHHHHhcceEEe
Confidence 4566779999999999999999987654
No 13
>PF06084 Cytomega_TRL10: Cytomegalovirus TRL10 protein; InterPro: IPR009284 This family consists of several Cytomegalovirus TRL10 proteins. TRL10 represents a structural component of the virus particle and like the other HCMV envelope glycoproteins, is present in a disulphide-linked complex [].
Probab=30.81 E-value=72 Score=26.38 Aligned_cols=22 Identities=32% Similarity=0.442 Sum_probs=9.8
Q ss_pred CCCCCCcCC---CCCCCCCCCCCCC
Q 030110 152 RGPVQNRQE---ATPTKKDDDDEDN 173 (183)
Q Consensus 152 r~~~~~k~e---~~~~~~~ddd~Dn 173 (183)
|...|+..+ ....+.||||+||
T Consensus 124 rp~rq~d~~p~~~~~~~dd~e~ed~ 148 (150)
T PF06084_consen 124 RPCRQNDNSPPIEPNGTDDEEDEDD 148 (150)
T ss_pred CcccccCCCCcccCCCCCccccccc
Confidence 444454443 1233344555555
No 14
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=27.38 E-value=66 Score=23.16 Aligned_cols=37 Identities=19% Similarity=0.263 Sum_probs=28.7
Q ss_pred hhhhcccCccceEEEecCCCcHHHHHHHHHHHHHhhh
Q 030110 79 ANTLFFKSAYNVQVVVDENEPEERLLNRFRREVMRAG 115 (183)
Q Consensus 79 sn~l~fk~~~mv~V~V~enE~iE~ALRRFKRkv~keG 115 (183)
+-++.|.++.++-+-.+.-|.++.|++++-+.+++-|
T Consensus 50 ~t~~IF~sGki~itGaks~~~~~~a~~~i~~~L~~~~ 86 (86)
T PF00352_consen 50 ATVLIFSSGKIVITGAKSEEEAKKAIEKILPILQKLG 86 (86)
T ss_dssp EEEEEETTSEEEEEEESSHHHHHHHHHHHHHHHHHTT
T ss_pred EEEEEEcCCEEEEEecCCHHHHHHHHHHHHHHHHHcC
Confidence 4456677777777777788889999999999888765
No 15
>PF01877 RNA_binding: RNA binding; InterPro: IPR002739 The proteins in this entry are functionally uncharacterised.; PDB: 2WNY_B 2NWU_A 2NRQ_A 2OGK_A 3D7A_B 3C9G_B 2PZZ_D.
Probab=26.95 E-value=1.3e+02 Score=23.25 Aligned_cols=33 Identities=6% Similarity=0.222 Sum_probs=23.9
Q ss_pred ceEEEecCCCcHHHHHHHHHHHHHhhhhHHHHhh
Q 030110 89 NVQVVVDENEPEERLLNRFRREVMRAGVIQECKR 122 (183)
Q Consensus 89 mv~V~V~enE~iE~ALRRFKRkv~keGIL~E~Kr 122 (183)
++.+.+.. +.....|++|...+....|+..+|.
T Consensus 47 ~l~~~i~~-~~~~~~l~~l~~~l~~~~i~d~~~~ 79 (120)
T PF01877_consen 47 ILEVRIEG-KEALKSLKKLHELLRDQEILDTARS 79 (120)
T ss_dssp EEEEEEEE-CHHHHHHHHHHHHHHHTTHHHHHHH
T ss_pred EEEEEEec-ccHHHHHHHHHHHHhhhhhhhHHHH
Confidence 34444533 3678999999999999988766553
No 16
>PRK09256 hypothetical protein; Provisional
Probab=26.56 E-value=2.2e+02 Score=22.96 Aligned_cols=44 Identities=16% Similarity=0.096 Sum_probs=29.5
Q ss_pred ceEEEecCCC----cHHHHHHHHHHHHHhhhhHHHHhhhcccCCchHHHHH
Q 030110 89 NVQVVVDENE----PEERLLNRFRREVMRAGVIQECKRRRFFETKQDEKKR 135 (183)
Q Consensus 89 mv~V~V~enE----~iE~ALRRFKRkv~keGIL~E~KrRRyYEKPSeKRKR 135 (183)
.+.|.+.+.- |.+.||.+|..++..+.... ++|--.+|+..-++
T Consensus 69 ~l~i~~~~~RSQ~~Nr~~al~kL~~~i~~~~~~p---~~r~~tk~~~~~~~ 116 (138)
T PRK09256 69 VIVIKAQEFRSQERNREDALERLVALIREALKPP---KKRRATKPTRGSKE 116 (138)
T ss_pred cEEEEECCcCCHHHHHHHHHHHHHHHHHHHhhcc---ccccCCcccHHHHH
Confidence 4666666543 78999999999999876643 23344677654443
No 17
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=26.54 E-value=50 Score=28.55 Aligned_cols=39 Identities=18% Similarity=0.267 Sum_probs=33.5
Q ss_pred hhhhcccCccceEEEecCCCcHHHHHHHHHHHHHhhhhH
Q 030110 79 ANTLFFKSAYNVQVVVDENEPEERLLNRFRREVMRAGVI 117 (183)
Q Consensus 79 sn~l~fk~~~mv~V~V~enE~iE~ALRRFKRkv~keGIL 117 (183)
.-+|-|.+..||-.=.+.-|.+++|++.++.+++.-|++
T Consensus 147 VV~LiF~SGK~ViTGaK~~ed~~~Av~~i~~~L~elgll 185 (185)
T COG2101 147 VVLLLFGSGKLVITGAKSEEDAEQAVEKIQSRLEELGLL 185 (185)
T ss_pred EEEEEecCCcEEEecCCCHHHHHHHHHHHHHHHHHhccC
Confidence 457788888888888888899999999999999987764
No 18
>COG2061 ACT-domain-containing protein, predicted allosteric regulator of homoserine dehydrogenase [Amino acid transport and metabolism]
Probab=26.24 E-value=61 Score=27.69 Aligned_cols=32 Identities=16% Similarity=0.327 Sum_probs=26.6
Q ss_pred CccceEEEecCCCcHHHHHHHHHHHHHhhhhH
Q 030110 86 SAYNVQVVVDENEPEERLLNRFRREVMRAGVI 117 (183)
Q Consensus 86 ~~~mv~V~V~enE~iE~ALRRFKRkv~keGIL 117 (183)
+.-++++.+-+.|.++.|+++|+-.+++-++|
T Consensus 130 SsA~iti~a~~~e~l~ea~~~l~ev~~eK~Ll 161 (170)
T COG2061 130 SSARITIIAVGKEKLDEALRRLKEVAMEKDLL 161 (170)
T ss_pred cceeEEEEEcChhHHHHHHHHHHHHHhhcCcE
Confidence 34578888888899999999999998876654
No 19
>PF12010 DUF3502: Domain of unknown function (DUF3502); InterPro: IPR022627 This domain is about 140 amino acids in length and is functionally uncharacterised. It is found in bacteria C-terminal to PF01547 from PFAM.
Probab=26.21 E-value=29 Score=27.19 Aligned_cols=29 Identities=21% Similarity=0.331 Sum_probs=20.8
Q ss_pred ccceEEEecCCCcHHHHHHHHHHHHHhhhh
Q 030110 87 AYNVQVVVDENEPEERLLNRFRREVMRAGV 116 (183)
Q Consensus 87 ~~mv~V~V~enE~iE~ALRRFKRkv~keGI 116 (183)
.|...+..+--+ .|.+|..|+.+|..+||
T Consensus 87 ~Y~~~L~~G~vd-~e~~~~~~~~kLk~AGi 115 (134)
T PF12010_consen 87 EYYPPLETGLVD-PEEALPEFNEKLKAAGI 115 (134)
T ss_pred HHHHHHHccCCC-HHHHHHHHHHHHHHhCh
Confidence 343333333334 89999999999999994
No 20
>KOG3229 consensus Vacuolar sorting protein VPS24 [Intracellular trafficking, secretion, and vesicular transport]
Probab=25.50 E-value=80 Score=28.12 Aligned_cols=26 Identities=23% Similarity=0.460 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHhhhhHHHHhhhcc
Q 030110 100 EERLLNRFRREVMRAGVIQECKRRRF 125 (183)
Q Consensus 100 iE~ALRRFKRkv~keGIL~E~KrRRy 125 (183)
+-..+|-|-+++.|+|||.|+..-.+
T Consensus 123 l~~TMrelSkEmmKaGIIEEmvdet~ 148 (227)
T KOG3229|consen 123 LAATMRELSKEMMKAGIIEEMVDETM 148 (227)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55679999999999999999987554
No 21
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=24.74 E-value=82 Score=30.09 Aligned_cols=12 Identities=33% Similarity=1.113 Sum_probs=7.8
Q ss_pred CCCCCCCCCCCC
Q 030110 165 KKDDDDEDNWEL 176 (183)
Q Consensus 165 ~~~ddd~DnWel 176 (183)
+..|||||.|..
T Consensus 198 t~e~~DDddW~~ 209 (400)
T KOG2767|consen 198 TAEEDDDDDWAV 209 (400)
T ss_pred cccccccccccc
Confidence 344677777975
No 22
>smart00878 Biotin_carb_C Biotin carboxylase C-terminal domain. Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyses the first committed step in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference are in this C-terminal domain.
Probab=24.74 E-value=76 Score=24.32 Aligned_cols=26 Identities=23% Similarity=0.387 Sum_probs=21.9
Q ss_pred cceEEEecCCCcHHHHHHHHHHHHHhh
Q 030110 88 YNVQVVVDENEPEERLLNRFRREVMRA 114 (183)
Q Consensus 88 ~mv~V~V~enE~iE~ALRRFKRkv~ke 114 (183)
+.++|+|. |++-+.|++|+++.|...
T Consensus 50 mlAKliv~-g~~R~~A~~rl~~aL~e~ 75 (107)
T smart00878 50 MIAKLIVH-GETREEAIARLRRALDEF 75 (107)
T ss_pred hceEEEEE-cCCHHHHHHHHHHHHHhC
Confidence 45788886 888999999999999874
No 23
>PHA03237 envelope glycoprotein M; Provisional
Probab=24.43 E-value=1e+02 Score=29.54 Aligned_cols=13 Identities=15% Similarity=0.427 Sum_probs=8.7
Q ss_pred hhccchhhhhhhc
Q 030110 71 VICPSLAYANTLF 83 (183)
Q Consensus 71 v~~p~la~sn~l~ 83 (183)
.+.|.+.|.|.++
T Consensus 302 l~~p~~~Y~~~f~ 314 (424)
T PHA03237 302 LAVTTHDYFNRFY 314 (424)
T ss_pred HHHHHHHHHHHhH
Confidence 4557777777664
No 24
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.35 E-value=1.9e+02 Score=26.34 Aligned_cols=19 Identities=16% Similarity=0.232 Sum_probs=14.9
Q ss_pred CcHHHHHHHHHHHHHhhhh
Q 030110 98 EPEERLLNRFRREVMRAGV 116 (183)
Q Consensus 98 E~iE~ALRRFKRkv~keGI 116 (183)
-.+|.-+.||++.+..+..
T Consensus 163 ~~~d~Ey~rfqkeI~~~~t 181 (264)
T KOG3032|consen 163 PDIDDEYKRFQKEIQDDLT 181 (264)
T ss_pred hhHHHHHHHHHHHHHHHHH
Confidence 3588889999999877553
No 25
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=23.73 E-value=1.2e+02 Score=31.00 Aligned_cols=44 Identities=16% Similarity=0.463 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHh--hhhHHHHhhhcccCCchHHHHHHHHHHHHHHH
Q 030110 102 RLLNRFRREVMR--AGVIQECKRRRFFETKQDEKKRKTREAAKRNR 145 (183)
Q Consensus 102 ~ALRRFKRkv~k--eGIL~E~KrRRyYEKPSeKRKRK~~eA~rR~r 145 (183)
.-++++|+++-| -|-|+|||+--.|.-=-..+.+++..+.|+.+
T Consensus 780 ~E~~KLk~q~KkErKGA~RELRKD~~FlAr~k~ke~~~~D~er~~K 825 (840)
T PF04147_consen 780 AELRKLKAQLKKERKGAMRELRKDNRFLAREKLKEKKEKDAERKEK 825 (840)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 448999999976 59999999999998766555555555554443
No 26
>KOG0345 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=23.01 E-value=27 Score=34.55 Aligned_cols=22 Identities=23% Similarity=0.157 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHhhhhHHHHhh
Q 030110 101 ERLLNRFRREVMRAGVIQECKR 122 (183)
Q Consensus 101 E~ALRRFKRkv~keGIL~E~Kr 122 (183)
|-.++.=+|+-++.-.|++.+.
T Consensus 474 ~ikykdkkrEk~Rq~~l~~~~~ 495 (567)
T KOG0345|consen 474 EIKYKDKKREKQRQQKLKVRKE 495 (567)
T ss_pred hhcccchHHHHHHHHHHHHHHH
Confidence 4567777777777777777666
No 27
>PHA03346 US22 family homolog; Provisional
Probab=21.76 E-value=97 Score=30.35 Aligned_cols=14 Identities=50% Similarity=0.871 Sum_probs=10.1
Q ss_pred CCCCCCCCCCCCCC
Q 030110 167 DDDDEDNWELPEGD 180 (183)
Q Consensus 167 ~ddd~DnWelp~~d 180 (183)
+|||||+||.-+.|
T Consensus 433 ~~~~d~~~~~~~~~ 446 (520)
T PHA03346 433 DDEDDDDWEDLGFD 446 (520)
T ss_pred ccccccccccCCcc
Confidence 57889999765543
No 28
>PF06679 DUF1180: Protein of unknown function (DUF1180); InterPro: IPR009565 This entry consists of several hypothetical eukaryotic proteins thought to be membrane proteins. Their function is unknown.
Probab=21.55 E-value=54 Score=27.44 Aligned_cols=7 Identities=71% Similarity=1.251 Sum_probs=3.1
Q ss_pred CCCCCCC
Q 030110 166 KDDDDED 172 (183)
Q Consensus 166 ~~ddd~D 172 (183)
.||||||
T Consensus 146 ~ddedeD 152 (163)
T PF06679_consen 146 EDDEDED 152 (163)
T ss_pred CCccccc
Confidence 3444444
No 29
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=21.54 E-value=75 Score=26.68 Aligned_cols=45 Identities=24% Similarity=0.587 Sum_probs=27.9
Q ss_pred HHHHHHHHHH--hhhhHHHHhhhcccCCchHHHHHHHHHHHHHHHHh
Q 030110 103 LLNRFRREVM--RAGVIQECKRRRFFETKQDEKKRKTREAAKRNRRR 147 (183)
Q Consensus 103 ALRRFKRkv~--keGIL~E~KrRRyYEKPSeKRKRK~~eA~rR~rKr 147 (183)
.+..|++... +--||..|+.|--|++=.++++++..+...+.|..
T Consensus 4 ~~~~L~~~~~~~k~~iL~r~~~Raew~k~~~~~k~k~e~~~e~eri~ 50 (229)
T PF12230_consen 4 ILEKLKKDSSDNKQEILERCKQRAEWEKYQEEEKKKEEEEEEKERIA 50 (229)
T ss_dssp ------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccccccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhchh
Confidence 4566777733 33599999999999999988887777666666554
No 30
>KOG3671 consensus Actin regulatory protein (Wiskott-Aldrich syndrome protein) [Signal transduction mechanisms; Cytoskeleton]
Probab=21.35 E-value=83 Score=31.28 Aligned_cols=10 Identities=40% Similarity=1.355 Sum_probs=7.1
Q ss_pred CCCCCCCCCC
Q 030110 166 KDDDDEDNWE 175 (183)
Q Consensus 166 ~~ddd~DnWe 175 (183)
++||+||.||
T Consensus 560 e~d~~ddeWd 569 (569)
T KOG3671|consen 560 EDDENDDEWD 569 (569)
T ss_pred ccccccccCC
Confidence 5566677897
No 31
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=21.11 E-value=93 Score=30.36 Aligned_cols=24 Identities=42% Similarity=0.693 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHhhhhHHHHhhh
Q 030110 100 EERLLNRFRREVMRAGVIQECKRR 123 (183)
Q Consensus 100 iE~ALRRFKRkv~keGIL~E~KrR 123 (183)
.|++|||.||++.+--+-+|-|||
T Consensus 246 EEriLKrvRRKIrNK~SAQESRrk 269 (472)
T KOG0709|consen 246 EERILKRVRRKIRNKRSAQESRRK 269 (472)
T ss_pred HHHHHHHHHHHHHhhhhhHHHHHh
Confidence 488888888888887777776654
No 32
>PLN03014 carbonic anhydrase
Probab=21.04 E-value=1.1e+02 Score=28.79 Aligned_cols=19 Identities=5% Similarity=0.261 Sum_probs=14.8
Q ss_pred CCcHHHHHHHHHHHHHhhh
Q 030110 97 NEPEERLLNRFRREVMRAG 115 (183)
Q Consensus 97 nE~iE~ALRRFKRkv~keG 115 (183)
+++.|.|+.+|++.+...+
T Consensus 80 ~~~~~~~~~~~~~~~~~~~ 98 (347)
T PLN03014 80 TEAYDEAIEALKKLLIEKE 98 (347)
T ss_pred hhhHHHHHHHHHhhccccc
Confidence 3578999999999776543
No 33
>KOG3562 consensus Forkhead/HNF-3-related transcription factor [Transcription]
Probab=20.85 E-value=70 Score=28.99 Aligned_cols=13 Identities=46% Similarity=0.693 Sum_probs=10.6
Q ss_pred CCCCCCCCCCCCC
Q 030110 166 KDDDDEDNWELPE 178 (183)
Q Consensus 166 ~~ddd~DnWelp~ 178 (183)
-+|+|++||+||.
T Consensus 114 ~~d~d~~n~~l~a 126 (277)
T KOG3562|consen 114 SDDKDPSNTHLPA 126 (277)
T ss_pred ccccCcccccccc
Confidence 3678899999985
Done!