Query 031927
Match_columns 150
No_of_seqs 46 out of 48
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 07:16:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031927.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031927hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG4270 Predicted membrane pro 53.9 19 0.00042 28.7 3.6 49 87-135 44-92 (131)
2 TIGR02831 spo_II_M stage II sp 53.9 23 0.00049 28.7 4.2 63 72-134 33-100 (200)
3 PF11300 DUF3102: Protein of u 47.7 74 0.0016 25.0 6.0 35 49-87 18-52 (130)
4 PF13003 MRL1: Ribosomal prote 40.7 14 0.00029 29.6 0.9 29 76-104 54-82 (133)
5 TIGR03747 conj_TIGR03747 integ 36.7 2E+02 0.0042 24.6 7.3 76 48-137 83-160 (233)
6 PF00317 Ribonuc_red_lgN: Ribo 36.1 17 0.00038 25.2 0.8 38 52-89 24-62 (83)
7 PF04508 Pox_A_type_inc: Viral 34.3 41 0.0009 19.6 2.1 16 54-69 1-16 (23)
8 PLN02453 complex I subunit 28.9 22 0.00048 27.5 0.4 12 78-89 57-68 (105)
9 PF11399 DUF3192: Protein of u 27.5 26 0.00057 26.7 0.6 16 72-87 7-22 (102)
10 PF02909 TetR_C: Tetracyclin r 27.2 1.1E+02 0.0025 21.5 3.9 57 74-130 3-65 (139)
11 PF00758 EPO_TPO: Erythropoiet 25.4 89 0.0019 25.7 3.3 51 58-108 9-75 (165)
12 PF12468 TTSSLRR: Type III sec 24.7 36 0.00077 22.4 0.8 11 77-87 24-34 (46)
13 PF13632 Glyco_trans_2_3: Glyc 24.7 2.9E+02 0.0063 20.3 6.8 43 48-90 92-140 (193)
14 PHA02855 anti-apoptotic membra 24.4 81 0.0018 26.4 3.0 23 101-123 82-104 (180)
15 PF04102 SlyX: SlyX; InterPro 22.9 32 0.0007 23.6 0.3 23 57-79 42-69 (69)
16 PF00134 Cyclin_N: Cyclin, N-t 21.8 2.3E+02 0.005 19.6 4.5 19 63-81 3-21 (127)
17 TIGR00388 glyQ glycyl-tRNA syn 21.4 42 0.0009 30.0 0.8 16 62-77 104-119 (293)
18 PF04547 Anoctamin: Calcium-ac 21.2 2.9E+02 0.0064 24.3 6.0 71 55-138 262-350 (452)
19 cd00733 GlyRS_alpha_core Class 21.1 43 0.00093 29.7 0.8 16 62-77 103-118 (279)
20 PF10680 RRN9: RNA polymerase 21.0 36 0.00078 24.0 0.3 15 71-85 42-56 (71)
21 PF00517 GP41: Retroviral enve 20.9 1.4E+02 0.003 24.5 3.6 24 78-102 102-125 (204)
22 CHL00080 psbM photosystem II p 20.1 1.1E+02 0.0023 19.5 2.2 17 117-133 10-26 (34)
No 1
>COG4270 Predicted membrane protein [Function unknown]
Probab=53.90 E-value=19 Score=28.66 Aligned_cols=49 Identities=20% Similarity=0.270 Sum_probs=44.3
Q ss_pred hhhhhHHHHHHHHHHHHHhhhcCchHHHHHHHHHHHhhchHHHHHHHHH
Q 031927 87 YACYDEFICKLVGFLQTQLMNSRPSFALGMLAVVAMSVPASTFMVILRL 135 (150)
Q Consensus 87 y~~Y~s~Vc~a~g~LQ~~LMntRP~vAlg~~all~lSVP~S~~~v~~~l 135 (150)
-..|.+++.|.+|-+-.++=..|+..+-|+.+|++...|+-.-+..+.+
T Consensus 44 tav~VSG~fEilgglaLlip~~s~~aa~gl~~l~laVfPANiYMa~h~l 92 (131)
T COG4270 44 TAVLVSGIFEILGGLALLIPAPSQAAAWGLIILLLAVFPANIYMAQHKL 92 (131)
T ss_pred hHHHHHHHHHHHhhhhhhcCCcHHHHHhhHHHHHHHHcchHHHHHhhcC
Confidence 3589999999999999888889999999999999999999999888744
No 2
>TIGR02831 spo_II_M stage II sporulation protein M. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This predicted integral membrane protein is designated stage II sporulation protein M.
Probab=53.90 E-value=23 Score=28.69 Aligned_cols=63 Identities=11% Similarity=0.057 Sum_probs=46.9
Q ss_pred cCCCCcchHHHH---HHHhhhhh--HHHHHHHHHHHHHhhhcCchHHHHHHHHHHHhhchHHHHHHHH
Q 031927 72 NYEPPAEWMEWE---KQYYACYD--EFICKLVGFLQTQLMNSRPSFALGMLAVVAMSVPASTFMVILR 134 (150)
Q Consensus 72 ~ye~P~~WmeWE---K~~y~~Y~--s~Vc~a~g~LQ~~LMntRP~vAlg~~all~lSVP~S~~~v~~~ 134 (150)
|+-.|..++|.. ++++..++ .++...--+.|.++-|.++.+.+-++.+..+++|.-.++++.+
T Consensus 33 ~~~~~~~~~~l~~~~~~f~~~~~~~~~~~~~~~f~~if~nn~~~~~li~~lGl~~~Gip~i~~~l~~n 100 (200)
T TIGR02831 33 NSMSIVQKNDLYFYLSNFFGQLSGGNSASYGDIFRQSLFNNIKYVGLMWILGLSIIGLPIILILDFLK 100 (200)
T ss_pred hcCCHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence 566788888887 66666663 2233345688999999999988888888889999988755444
No 3
>PF11300 DUF3102: Protein of unknown function (DUF3102); InterPro: IPR021451 This entry is represented by Streptococcus phage 7201, Orf2. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=47.75 E-value=74 Score=24.98 Aligned_cols=35 Identities=29% Similarity=0.525 Sum_probs=29.0
Q ss_pred CccccchhHHHHHHHHHHHHhhhcCCCCcchHHHHHHHh
Q 031927 49 GQLVDENMIVLRKRIHEMKVMERNYEPPAEWMEWEKQYY 87 (150)
Q Consensus 49 G~LVDE~MiVLRkRI~Emkm~E~~ye~P~~WmeWEK~~y 87 (150)
|+.+=++||-.=+|..|+|.. .|..+|.+|=|.-+
T Consensus 18 ~~~~l~~~iEIGrrL~eaK~~----l~HGef~~Wle~~~ 52 (130)
T PF11300_consen 18 GQILLESAIEIGRRLKEAKEL----LPHGEFGKWLEEEV 52 (130)
T ss_pred HHHHHHHHHHHHHHHHHHHHh----CCHHHHHHHHHHHc
Confidence 455667899999999999953 68999999999766
No 4
>PF13003 MRL1: Ribosomal protein L1; InterPro: IPR024663 This entry represents a ribosomal protein L1 domain found mainly in chordates.
Probab=40.68 E-value=14 Score=29.56 Aligned_cols=29 Identities=28% Similarity=0.406 Sum_probs=24.0
Q ss_pred CcchHHHHHHHhhhhhHHHHHHHHHHHHH
Q 031927 76 PAEWMEWEKQYYACYDEFICKLVGFLQTQ 104 (150)
Q Consensus 76 P~~WmeWEK~~y~~Y~s~Vc~a~g~LQ~~ 104 (150)
|-.+||||++||+.=--+|-.|+.+|-.|
T Consensus 54 ~y~~~e~~~~lyPr~Iyeve~Ai~mLKkf 82 (133)
T PF13003_consen 54 SYSYMEWEKRLYPRPIYEVEKAIDMLKKF 82 (133)
T ss_pred ccccccccceeccccHHHHHHHHHHHHhc
Confidence 67799999999986666788889888665
No 5
>TIGR03747 conj_TIGR03747 integrating conjugative element membrane protein, PFL_4697 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.
Probab=36.65 E-value=2e+02 Score=24.58 Aligned_cols=76 Identities=12% Similarity=0.256 Sum_probs=46.7
Q ss_pred CCccccchhHHHHHHHHHHHHh-hh-cCCCCcchHHHHHHHhhhhhHHHHHHHHHHHHHhhhcCchHHHHHHHHHHHhhc
Q 031927 48 RGQLVDENMIVLRKRIHEMKVM-ER-NYEPPAEWMEWEKQYYACYDEFICKLVGFLQTQLMNSRPSFALGMLAVVAMSVP 125 (150)
Q Consensus 48 gG~LVDE~MiVLRkRI~Emkm~-E~-~ye~P~~WmeWEK~~y~~Y~s~Vc~a~g~LQ~~LMntRP~vAlg~~all~lSVP 125 (150)
.--.||-|+. +-|++.... ++ ..+ .+-..|-+.+|...++-.-.++=.+|.++++ ++++++++|
T Consensus 83 ~~lFV~TG~~---~~l~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~yl~a~~~~~~~f~iR---------L~IL~~~lP 148 (233)
T TIGR03747 83 DWLFVKSGLL---DWIQDETTVAAAGGRG--RSLRYWAAWLYVYARDYLLAAVYVTLVFLVR---------LVILVLAIP 148 (233)
T ss_pred HHHHHHhhHH---HHHHhhhccccccchh--hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHH
Confidence 3456777775 334443321 11 111 4566677777766666666677777777776 678888889
Q ss_pred hHHHHHHHHHHH
Q 031927 126 ASTFMVILRLLE 137 (150)
Q Consensus 126 ~S~~~v~~~l~~ 137 (150)
.-..+++.-+++
T Consensus 149 lfll~~~~glvD 160 (233)
T TIGR03747 149 LFLLAAFVGLVD 160 (233)
T ss_pred HHHHHHHHHHHH
Confidence 877777666543
No 6
>PF00317 Ribonuc_red_lgN: Ribonucleotide reductase, all-alpha domain; InterPro: IPR013509 Ribonucleotide reductase (1.17.4.1 from EC) [, ] catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs divide into three classes on the basis of their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, bacteriophage and viruses, use a diiron-tyrosyl radical, Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in anaerobic bacteria and bacteriophage, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. Ribonucleotide reductase is an oligomeric enzyme composed of a large subunit (700 to 1000 residues) and a small subunit (300 to 400 residues) - class II RNRs are less complex, using the small molecule B12 in place of the small chain []. The reduction of ribonucleotides to deoxyribonucleotides involves the transfer of free radicals, the function of each metallocofactor is to generate an active site thiyl radical. This thiyl radical then initiates the nucleotide reduction process by hydrogen atom abstraction from the ribonucleotide []. The radical-based reaction involves five cysteines: two of these are located at adjacent anti-parallel strands in a new type of ten-stranded alpha/beta-barrel; two others reside at the carboxyl end in a flexible arm; and the fifth, in a loop in the centre of the barrel, is positioned to initiate the radical reaction []. There are several regions of similarity in the sequence of the large chain of prokaryotes, eukaryotes and viruses spread across 3 domains: an N-terminal domain common to the mammalian and bacterial enzymes; a C-terminal domain common to the mammalian and viral ribonucleotide reductases; and a central domain common to all three [].; GO: 0004748 ribonucleoside-diphosphate reductase activity, 0005524 ATP binding, 0006260 DNA replication, 0055114 oxidation-reduction process; PDB: 1PEM_A 2BQ1_E 1PEU_A 1PEQ_A 1PEO_A 1XJN_A 1XJK_A 3O0O_B 1XJF_A 3O0Q_A ....
Probab=36.14 E-value=17 Score=25.18 Aligned_cols=38 Identities=24% Similarity=0.423 Sum_probs=26.0
Q ss_pred ccchhHHHHHHHHHHHH-hhhcCCCCcchHHHHHHHhhh
Q 031927 52 VDENMIVLRKRIHEMKV-MERNYEPPAEWMEWEKQYYAC 89 (150)
Q Consensus 52 VDE~MiVLRkRI~Emkm-~E~~ye~P~~WmeWEK~~y~~ 89 (150)
+.|.---+=+||--.=+ +|..|+.+.+|++|+++||..
T Consensus 24 ~~Etpq~~~~RVA~~la~~e~~y~~~~~~~~~~~~fy~~ 62 (83)
T PF00317_consen 24 VIETPQEMFMRVAMALASAEPKYDDAEDRMEWAEEFYDL 62 (83)
T ss_dssp B--SHHHHHHHHHHHHHTCCGG-THCCTHHHHHHHHHHH
T ss_pred EeeCHHHHHHHHHHHHHHHcccccccCCHHHHHHHHHHH
Confidence 67766666666654444 477788899999999999953
No 7
>PF04508 Pox_A_type_inc: Viral A-type inclusion protein repeat ; InterPro: IPR007596 The repeat is found in the A-type inclusion protein of the Poxvirus family [].; GO: 0016032 viral reproduction
Probab=34.30 E-value=41 Score=19.57 Aligned_cols=16 Identities=31% Similarity=0.470 Sum_probs=12.5
Q ss_pred chhHHHHHHHHHHHHh
Q 031927 54 ENMIVLRKRIHEMKVM 69 (150)
Q Consensus 54 E~MiVLRkRI~Emkm~ 69 (150)
+.|--||.||.+++.+
T Consensus 1 ~E~~rlr~rI~dLer~ 16 (23)
T PF04508_consen 1 REMNRLRNRISDLERQ 16 (23)
T ss_pred ChHHHHHHHHHHHHHH
Confidence 3577899999998753
No 8
>PLN02453 complex I subunit
Probab=28.86 E-value=22 Score=27.47 Aligned_cols=12 Identities=33% Similarity=1.044 Sum_probs=10.1
Q ss_pred chHHHHHHHhhh
Q 031927 78 EWMEWEKQYYAC 89 (150)
Q Consensus 78 ~WmeWEK~~y~~ 89 (150)
.|.+||..||..
T Consensus 57 kwEdWE~p~Y~~ 68 (105)
T PLN02453 57 KWEDWELPCYIT 68 (105)
T ss_pred ccccchhhHHHH
Confidence 599999999943
No 9
>PF11399 DUF3192: Protein of unknown function (DUF3192); InterPro: IPR021534 Some members in this family of proteins are annotated as lipoproteins however this cannot be confirmed.
Probab=27.47 E-value=26 Score=26.68 Aligned_cols=16 Identities=31% Similarity=0.979 Sum_probs=13.3
Q ss_pred cCCCCcchHHHHHHHh
Q 031927 72 NYEPPAEWMEWEKQYY 87 (150)
Q Consensus 72 ~ye~P~~WmeWEK~~y 87 (150)
.|++-++||.||++-.
T Consensus 7 ~~~~~~~~~~W~drq~ 22 (102)
T PF11399_consen 7 VYDDDPDWMDWEDRQA 22 (102)
T ss_pred EcCCCcccCCHHHHHH
Confidence 3678889999999875
No 10
>PF02909 TetR_C: Tetracyclin repressor, C-terminal all-alpha domain; InterPro: IPR004111 The antibiotic tetracycline has a broad spectrum of activity, acting to inhibit bacterial protein synthesis by binding to the 30S ribosomal subunit, which prevents the association of the aminoacyl-tRNA to the ribosomal acceptor A site. Tetracycline binding is reversible, therefore diluting out the antibiotic can reverse its effects. Tetracycline resistance genes are often located on mobile elements, such as plasmids, transposons and/or conjugative transposons, which can sometimes be transferred between bacterial species. In certain cases, tetracycline can enhance the transfer of these elements, thereby promoting resistance amongst a bacterial colony. There are three types of tetracycline resistance: tetracycline efflux, ribosomal protection, and tetracycline modification [, ]: Tetracycline efflux proteins belong to the major facilitator superfamily. Efflux proteins are membrane-associated proteins that recognise and export tetracycline from the cell. They are found in both Gram-positive and Gram-negative bacteria []. There are at least 22 different tetracycline efflux proteins, grouped according to sequence similarity: Group 1 are Tet(A), Tet(B), Tet(C), Tet(D), Tet(E), Tet(G), Tet(H), Tet(J), Tet(Z) and Tet(30); Group 2 are Tet(K) and Tet(L); Group 3 are Otr(B) and Tcr(3); Group 4 is TetA(P); Group 5 is Tet(V). In addition, there are the efflux proteins Tet(31), Tet(33), Tet(V), Tet(Y), Tet(34), and Tet(35). Ribosomal protection proteins are cytoplasmic proteins that display homology with the elongation factors EF-Tu and EF-G. Protection proteins bind the ribosome, causing an alteration in ribosomal conformation that prevents tetracycline from binding. There are at least ten ribosomal protection proteins: Tet(M), Tet(O), Tet(S), Tet(W), Tet(32), Tet(36), Tet(Q), Tet(T), Otr(A), and TetB(P). Both Tet(M) and Tet(O) have ribosome-dependent GTPase activity, the hydrolysis of GTP providing the energy for the ribosomal conformational changes. Tetracycline modification proteins include the enzymes Tet(37) and Tet(X), both of which inactivate tetracycline. In addition, there are the tetracycline resistance proteins Tet(U) and Otr(C). The expression of several of these tet genes is controlled by a family of tetracycline transcriptional regulators known as TetR. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity []. The TetR proteins identified in over 115 genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. This entry represents the C-terminal domain found in the tetracycline transcriptional repressor TetR, which binds to the Tet(A) gene to repress its expression in the absence of tetracycline []. Tet(A) is a membrane-associated efflux protein that exports tetracycline from the cell before it can attach to ribosomes and inhibit polypeptide chain growth. TetR occurs as a homodimer and uses two helix-turn-helix (HTH) motifs to bind tandem DNA operators, thereby blocking the expression of the associated genes, TetA and TetR. The structure of the class D TetR repressor protein [] involves 10 alpha-helices, with connecting turns and loops. The three N-terminal helices constitute the DNA-binding HTH domain, which has an inverse orientation compared with HTH motifs in other DNA-binding proteins. The core of the protein, formed by helices 5-10, is responsible for dimerisation and contains, for each monomer, a binding pocket that accommodates tetracycline in the presence of a divalent cation.; GO: 0045892 negative regulation of transcription, DNA-dependent; PDB: 2Y30_B 3ZQL_C 2Y31_B 2Y2Z_A 2VPR_A 3B6A_A 3B6C_A 2OPT_A 2NS7_B 2NS8_C ....
Probab=27.23 E-value=1.1e+02 Score=21.52 Aligned_cols=57 Identities=12% Similarity=0.193 Sum_probs=33.5
Q ss_pred CCCcchHHHHHHHhhhhhHHHHHHHHHHHHHhhhcC--c-hHH---HHHHHHHHHhhchHHHH
Q 031927 74 EPPAEWMEWEKQYYACYDEFICKLVGFLQTQLMNSR--P-SFA---LGMLAVVAMSVPASTFM 130 (150)
Q Consensus 74 e~P~~WmeWEK~~y~~Y~s~Vc~a~g~LQ~~LMntR--P-~vA---lg~~all~lSVP~S~~~ 130 (150)
+|+.+|-+|=+.+..+|.+-..+-=++.+..+.+.. | .+. -.+-+|.-.++|..-.+
T Consensus 3 ~~~~~W~~~l~~~a~~~r~~~~~hP~~~~~~~~~~~~~p~~l~~~e~~l~~L~~aG~~~~~a~ 65 (139)
T PF02909_consen 3 DPGDDWRERLRALARAYRAALLRHPWLAELLLARPPPGPNALRLMEAMLRALRDAGFSPEEAA 65 (139)
T ss_dssp CTTSEHHHHHHHHHHHHHHHHHTSTTHHHHHHTSSCTSHHHHHHHHHHHHHHHHTTEEHHHHH
T ss_pred cCCCCHHHHHHHHHHHHHHHHHHCcCHHHHHHhcCCCChhHHHHHHHHHHHHHHcCcCHHHHH
Confidence 466789999999999888776665455544444322 2 122 23344555566654433
No 11
>PF00758 EPO_TPO: Erythropoietin/thrombopoietin; InterPro: IPR001323 Erythropoietin, a plasma glycoprotein, is the primary physiological mediator of erythropoiesis []. It is involved in the regulation of the level of peripheral erythrocytes by stimulating the differentiation of erythroid progenitor cells, found in the spleen and bone marrow, into mature erythrocytes []. It is primarily produced in adult kidneys and foetal liver, acting by attachment to specific binding sites on erythroid progenitor cells, stimulating their differentiation []. Severe kidney dysfunction causes reduction in the plasma levels of erythropoietin, resulting in chronic anaemia - injection of purified erythropoietin into the blood stream can help to relieve this type of anaemia. Levels of erythropoietin in plasma fluctuate with varying oxygen tension of the blood, but androgens and prostaglandins also modulate the levels to some extent []. Erythropoietin glycoprotein sequences are well conserved, a consequence of which is that the hormones are cross-reactive among mammals, i.e. that from one species, say human, can stimulate erythropoiesis in other species, say mouse or rat []. Thrombopoeitin (TPO), a glycoprotein, is the mammalian0 hormone which functions as a megakaryocytic lineage specific growth and differentiation factor affecting the proliferation and maturation from their committed progenitor cells acting at a late stage of megakaryocyte development. It acts as a circulating regulator of platelet numbers.; GO: 0005179 hormone activity, 0005576 extracellular region; PDB: 1EER_A 1CN4_C 1BUY_A 1V7N_Z 1V7M_X.
Probab=25.44 E-value=89 Score=25.73 Aligned_cols=51 Identities=22% Similarity=0.318 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHhhhcC----------------CCCcchHHHHHHHhhhhhHHHHHHHHHHHHHhhhc
Q 031927 58 VLRKRIHEMKVMERNY----------------EPPAEWMEWEKQYYACYDEFICKLVGFLQTQLMNS 108 (150)
Q Consensus 58 VLRkRI~Emkm~E~~y----------------e~P~~WmeWEK~~y~~Y~s~Vc~a~g~LQ~~LMnt 108 (150)
||.|=|+|.|.+|.-- ..--+.-+|||+--..=..+|-..+.+|+--++..
T Consensus 9 vl~k~I~EAkdae~~~~~C~e~c~L~~~v~vP~t~vnf~~Wk~k~~~~ka~EV~~gL~LL~eav~~~ 75 (165)
T PF00758_consen 9 VLNKYIREAKDAENAMSQCSEGCSLSEPVTVPDTDVNFYEWKKKNVQEKAQEVWQGLWLLSEAVLRA 75 (165)
T ss_dssp HHHHHHHHHHHHHHHHCCSTSSTEESCEEEEE-TTB-CHHHCCS-HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhcCCCcCCCCCceecCceeeeHHHHHHhhhHHHHHHHHHHHHHHHHHHHHH
Confidence 6889999999998722 12347889999988777777766666665554443
No 12
>PF12468 TTSSLRR: Type III secretion system leucine rich repeat protein ; PDB: 3CVR_A 3G06_A 1JL5_A 1G9U_A.
Probab=24.68 E-value=36 Score=22.41 Aligned_cols=11 Identities=45% Similarity=0.969 Sum_probs=8.5
Q ss_pred cchHHHHHHHh
Q 031927 77 AEWMEWEKQYY 87 (150)
Q Consensus 77 ~~WmeWEK~~y 87 (150)
+.|.||||.-=
T Consensus 24 aiWseW~~~ap 34 (46)
T PF12468_consen 24 AIWSEWERNAP 34 (46)
T ss_dssp HHHHHHHHTS-
T ss_pred HHHHHHHHcCC
Confidence 67999999754
No 13
>PF13632 Glyco_trans_2_3: Glycosyl transferase family group 2
Probab=24.68 E-value=2.9e+02 Score=20.33 Aligned_cols=43 Identities=16% Similarity=0.047 Sum_probs=24.4
Q ss_pred CCccccchhHHHHH------HHHHHHHhhhcCCCCcchHHHHHHHhhhh
Q 031927 48 RGQLVDENMIVLRK------RIHEMKVMERNYEPPAEWMEWEKQYYACY 90 (150)
Q Consensus 48 gG~LVDE~MiVLRk------RI~Emkm~E~~ye~P~~WmeWEK~~y~~Y 90 (150)
++..+-|++..-.+ ||.-...++...+.|.+|.+|=||-..-+
T Consensus 92 ~~~~~~ED~~l~~~l~~~G~~~~~~~~~~~~~~~p~t~~~~~~Qr~RW~ 140 (193)
T PF13632_consen 92 DPFSIGEDMDLGFRLRRAGYRIVYVPDAIVYTEAPPTFRAFIRQRRRWA 140 (193)
T ss_pred ccccccchHHHHHHHHHCCCEEEEecccceeeeCCCCHHHHHHHHHHHH
Confidence 46777788764321 11111112234467999999988877533
No 14
>PHA02855 anti-apoptotic membrane protein; Provisional
Probab=24.43 E-value=81 Score=26.42 Aligned_cols=23 Identities=22% Similarity=0.521 Sum_probs=18.9
Q ss_pred HHHHhhhcCchHHHHHHHHHHHh
Q 031927 101 LQTQLMNSRPSFALGMLAVVAMS 123 (150)
Q Consensus 101 LQ~~LMntRP~vAlg~~all~lS 123 (150)
..+++-..||||-++.++|+++-
T Consensus 82 ie~L~~D~rPSVKLA~iSLlSiI 104 (180)
T PHA02855 82 IESLNNDNRPSVKLAIISLISMI 104 (180)
T ss_pred HHHHHhcCCchhHHHHHHHHHHH
Confidence 45667889999999999998753
No 15
>PF04102 SlyX: SlyX; InterPro: IPR007236 The SlyX protein has no known function. It is short, less than 80 amino acids, and its gene is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C terminus. The protein may be a coiled-coil structure.; PDB: 3EFG_A.
Probab=22.89 E-value=32 Score=23.56 Aligned_cols=23 Identities=30% Similarity=0.582 Sum_probs=3.5
Q ss_pred HHHHHHHHHHHHh-----hhcCCCCcch
Q 031927 57 IVLRKRIHEMKVM-----ERNYEPPAEW 79 (150)
Q Consensus 57 iVLRkRI~Emkm~-----E~~ye~P~~W 79 (150)
-.|+.||++++.. ....+||.||
T Consensus 42 ~~L~~rl~~~~~~~~~~~~~~~~~PPHY 69 (69)
T PF04102_consen 42 RLLRERLRELEDPSGSADPPEEEPPPHY 69 (69)
T ss_dssp HHHHHT----------------------
T ss_pred HHHHHHHHHhccccCCCCCCCCCCcCCC
Confidence 3466666666622 2244677775
No 16
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=21.76 E-value=2.3e+02 Score=19.60 Aligned_cols=19 Identities=21% Similarity=0.487 Sum_probs=12.9
Q ss_pred HHHHHHhhhcCCCCcchHH
Q 031927 63 IHEMKVMERNYEPPAEWME 81 (150)
Q Consensus 63 I~Emkm~E~~ye~P~~Wme 81 (150)
++.++..|..+.+|.++.+
T Consensus 3 ~~~~~~~e~~~~~~~~~~~ 21 (127)
T PF00134_consen 3 FRYLLEKELKYKPNPDYLE 21 (127)
T ss_dssp HHHHHHHHHHTTCCTTHGT
T ss_pred HHHHHHHHHHHCcCccccc
Confidence 3566777888777666654
No 17
>TIGR00388 glyQ glycyl-tRNA synthetase, tetrameric type, alpha subunit. This tetrameric form of glycyl-tRNA synthetase (2 alpha, 2 beta) is found in the majority of completed eubacterial genomes, with the two genes fused in a few species. A substantially different homodimeric form (not recognized by this model) replaces this form in the Archaea, animals, yeasts, and some eubacteria.
Probab=21.42 E-value=42 Score=29.98 Aligned_cols=16 Identities=31% Similarity=0.725 Sum_probs=14.6
Q ss_pred HHHHHHHhhhcCCCCc
Q 031927 62 RIHEMKVMERNYEPPA 77 (150)
Q Consensus 62 RI~Emkm~E~~ye~P~ 77 (150)
.-|++|.+|.|||-|+
T Consensus 104 ~~hDIRFVEDnWEsPT 119 (293)
T TIGR00388 104 TEHDIRFVEDNWENPT 119 (293)
T ss_pred cccCeeEeecCCCCCc
Confidence 6799999999999986
No 18
>PF04547 Anoctamin: Calcium-activated chloride channel; InterPro: IPR007632 This family contains the anoctamin/TMEM16 proteins which are thought to be calcium-dependent chloride channel [].
Probab=21.17 E-value=2.9e+02 Score=24.34 Aligned_cols=71 Identities=21% Similarity=0.441 Sum_probs=45.0
Q ss_pred hhHHHHHHHHHHHHhhhc-----------CCCCcchHHHHHHHh-hhhh-----HHHHHHHHHHHHHhhhcCchHHHHHH
Q 031927 55 NMIVLRKRIHEMKVMERN-----------YEPPAEWMEWEKQYY-ACYD-----EFICKLVGFLQTQLMNSRPSFALGML 117 (150)
Q Consensus 55 ~MiVLRkRI~Emkm~E~~-----------ye~P~~WmeWEK~~y-~~Y~-----s~Vc~a~g~LQ~~LMntRP~vAlg~~ 117 (150)
-.+-+.++.++.|..+.. .+....=..||+++. +.|+ .|..|.+ +=.|.+
T Consensus 262 ~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~l~~y~~~g~~~dY~emv-------------iQFGyv 328 (452)
T PF04547_consen 262 VLPYLKKRYRRKKIRKKQRKKQQDERQENEEENQFLQQWEKEYELPPYDPDGLFDDYLEMV-------------IQFGYV 328 (452)
T ss_pred HHHHHHHHHHHHHHHhhhhhcccccccccccccchHHHHHHHhcCCCCCcCCchHHHHHHH-------------HHHHHH
Confidence 344566777776543331 223456678999887 5777 4444433 347899
Q ss_pred HHHHHhhchHHHHHH-HHHHHH
Q 031927 118 AVVAMSVPASTFMVI-LRLLEV 138 (150)
Q Consensus 118 all~lSVP~S~~~v~-~~l~~~ 138 (150)
.+.+.+-|...++.+ .+.+|+
T Consensus 329 ~lF~~afPlapl~allnN~~ei 350 (452)
T PF04547_consen 329 TLFSAAFPLAPLFALLNNIVEI 350 (452)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999887544 444544
No 19
>cd00733 GlyRS_alpha_core Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the attachment of glycine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. This alignment contains only sequences from the GlyRS form which heterotetramerizes. The homodimer form of GlyRS is in a different family of class II aaRS. Class II assignment is based upon structure and the presence of three characteristic sequence motifs.
Probab=21.09 E-value=43 Score=29.71 Aligned_cols=16 Identities=31% Similarity=0.812 Sum_probs=14.4
Q ss_pred HHHHHHHhhhcCCCCc
Q 031927 62 RIHEMKVMERNYEPPA 77 (150)
Q Consensus 62 RI~Emkm~E~~ye~P~ 77 (150)
.-|++|.+|.|||-|+
T Consensus 103 ~~hDIRFVEDnWEsPT 118 (279)
T cd00733 103 KEHDIRFVEDNWESPT 118 (279)
T ss_pred cccCeeEeecCCCCCc
Confidence 6699999999999986
No 20
>PF10680 RRN9: RNA polymerase I specific transcription initiation factor; InterPro: IPR019622 This entry represents the RNA polymerase I-specific transcription initiation factor RRN9. Initiation of transcription of ribosomal DNA (rDNA) in yeast involves an interaction of upstream activation factor (UAF) with the upstream element of the promoter, to form a stable UAF-template complex. UAF, together with the TATA-binding transcription initiation factor protein (TBP), then recruits an essential core factor to the promoter, to form a stable pre-initiation complex []. This Rrn9 domain, which seems to be constrained to fungi, is the two highly conserved regions of proteins which form one of the subunits of UAF and appears to be the region responsible for the interaction with TBP. The family includes the Schizosaccharomyces pombe (Fission yeast) Arc1 protein, Q10204 from SWISSPROT, which is found to be essential for the accumulation of condensin at kinetochores [].
Probab=21.02 E-value=36 Score=24.01 Aligned_cols=15 Identities=27% Similarity=0.981 Sum_probs=11.5
Q ss_pred hcCCCCcchHHHHHH
Q 031927 71 RNYEPPAEWMEWEKQ 85 (150)
Q Consensus 71 ~~ye~P~~WmeWEK~ 85 (150)
..+.||..|+.|=..
T Consensus 42 ~~~~P~~~WTAWPl~ 56 (71)
T PF10680_consen 42 NPWAPPKNWTAWPLP 56 (71)
T ss_pred cccCCCCCcccCCCC
Confidence 456799999999543
No 21
>PF00517 GP41: Retroviral envelope protein; InterPro: IPR000328 This entry represents envelope proteins from a variety of retroviruses. It includes the GP41 subunit of the envelope protein complex from Human immunodeficiency virus (HIV) and Simian-Human immunodeficiency virus (SIV), which mediate membrane fusion during viral entry []. It has a core composed of a six-helix bundle and is folded by its trimeric N- and C-terminal heptad-repeats (NHR and CHR) []. Derivatives of this protein prevent HIV-1 from entering cell lines and primary human CD4+ cells in vitro [], making it an attractive subject of gene therapy studies against HIV and related retroviruses. The entry also represents envelop proteins from Bovine immunodeficiency virus, Feline immunodeficiency virus and Equine infectious anemia virus (EIAV) [, ], as well as the Gp36 protein from Mouse mammary tumor virus (MMTV) and Human endogenous retrovirus (HERV).; GO: 0005198 structural molecule activity, 0019031 viral envelope; PDB: 2EZO_B 2EZQ_B 2EZR_A 2JNR_B 1F23_D 2EZP_A 1JEK_A 2Q7C_A 2Q5U_A 2Q3I_A ....
Probab=20.88 E-value=1.4e+02 Score=24.47 Aligned_cols=24 Identities=33% Similarity=0.610 Sum_probs=16.2
Q ss_pred chHHHHHHHhhhhhHHHHHHHHHHH
Q 031927 78 EWMEWEKQYYACYDEFICKLVGFLQ 102 (150)
Q Consensus 78 ~WmeWEK~~y~~Y~s~Vc~a~g~LQ 102 (150)
.|++|||+.- +|...+.+...-.|
T Consensus 102 Tw~~W~~~i~-~~~~~i~~ll~~a~ 125 (204)
T PF00517_consen 102 TWQQWEKEIS-NYTGNIYNLLEEAQ 125 (204)
T ss_dssp HHHHHHHHHH-HHHHHHHHHHHHHH
T ss_pred hHHHHHHHhc-ccHHHHHHHHHHHH
Confidence 6888999876 66666665544444
No 22
>CHL00080 psbM photosystem II protein M
Probab=20.07 E-value=1.1e+02 Score=19.52 Aligned_cols=17 Identities=18% Similarity=0.428 Sum_probs=12.7
Q ss_pred HHHHHHhhchHHHHHHH
Q 031927 117 LAVVAMSVPASTFMVIL 133 (150)
Q Consensus 117 ~all~lSVP~S~~~v~~ 133 (150)
+.++.++||++.++++.
T Consensus 10 At~LFi~iPt~FLlily 26 (34)
T CHL00080 10 ATALFILVPTAFLLIIY 26 (34)
T ss_pred HHHHHHHHHHHHHHHhh
Confidence 45677889998877653
Done!