Query 026596
Match_columns 236
No_of_seqs 35 out of 37
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 10:04:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026596.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026596hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01342 SAND: SAND domain; I 97.1 8.6E-05 1.9E-09 56.3 -0.6 55 29-96 8-67 (82)
2 smart00258 SAND SAND domain. 95.9 0.0027 5.8E-08 48.3 0.7 56 32-96 3-58 (73)
3 PF07496 zf-CW: CW-type Zinc F 91.9 0.06 1.3E-06 37.2 0.6 47 136-187 1-48 (50)
4 PF07897 DUF1675: Protein of u 44.8 26 0.00055 32.7 3.5 49 32-84 221-273 (284)
5 PF07610 DUF1573: Protein of u 43.9 15 0.00033 24.5 1.5 28 31-60 16-43 (45)
6 smart00134 LU Ly-6 antigen / u 34.3 19 0.0004 25.7 0.8 16 190-205 40-55 (79)
7 PF14205 Cys_rich_KTR: Cystein 34.3 15 0.00033 27.2 0.3 26 136-161 2-27 (55)
8 PF07943 PBP5_C: Penicillin-bi 32.1 49 0.0011 23.6 2.6 23 39-61 58-80 (91)
9 COG4049 Uncharacterized protei 32.1 18 0.00039 27.5 0.4 14 136-149 15-28 (65)
10 PF14901 Jiv90: Cleavage induc 30.1 27 0.00057 28.1 1.1 33 139-171 6-46 (94)
11 PF11101 DUF2884: Protein of u 29.3 53 0.0012 28.8 2.9 21 98-118 36-59 (229)
12 PF12800 Fer4_4: 4Fe-4S bindin 28.6 26 0.00057 19.8 0.6 11 200-210 1-11 (17)
13 PF13333 rve_2: Integrase core 27.7 28 0.0006 23.6 0.7 12 72-83 41-52 (52)
14 PF12760 Zn_Tnp_IS1595: Transp 27.5 31 0.00068 23.1 0.9 18 136-154 17-34 (46)
15 PF04369 Lactococcin: Lactococ 27.5 34 0.00073 25.8 1.1 20 6-25 2-21 (60)
16 PF15389 DUF4612: Domain of un 27.0 27 0.00058 29.0 0.6 25 37-61 1-31 (115)
17 PF09832 DUF2059: Uncharacteri 26.2 28 0.00062 24.0 0.5 13 13-25 16-28 (64)
18 PF03293 Pox_RNA_pol: Poxvirus 25.4 74 0.0016 27.9 3.0 34 30-63 66-102 (160)
19 PF07244 Surf_Ag_VNR: Surface 25.3 34 0.00074 23.3 0.8 22 10-31 10-32 (78)
20 COG0227 RpmB Ribosomal protein 25.2 33 0.00072 26.6 0.8 27 80-106 19-50 (77)
21 PF01927 Mut7-C: Mut7-C RNAse 24.5 36 0.00077 27.6 0.9 13 134-146 120-132 (147)
22 COG1281 Disulfide bond chapero 22.5 21 0.00045 33.4 -0.9 46 32-79 232-284 (286)
23 cd00184 TNF Tumor Necrosis Fac 20.8 87 0.0019 24.6 2.4 21 41-63 32-52 (137)
24 PF00751 DM: DM DNA binding do 20.5 44 0.00096 23.6 0.6 16 216-231 23-38 (47)
25 PF13986 DUF4224: Domain of un 20.3 62 0.0013 22.4 1.3 16 13-28 2-17 (47)
No 1
>PF01342 SAND: SAND domain; InterPro: IPR000770 The SAND domain (named after Sp100, AIRE-1, NucP41/75, DEAF-1) is a conserved ~80 residue region found in a number of nuclear proteins, many of which function in chromatin-dependent transcriptional control. These include proteins linked to various human diseases, such as the Sp100 (Speckled protein 100 kDa), NUDR (Nuclear DEAF-1 related), GMEB (Glucocorticoid Modulatory Element Binding) proteins and AIRE-1 (Autoimmune regulator 1) proteins. Proteins containing the SAND domain have a modular structure; the SAND domain can be associated with a number of other modules, including the bromodomain, the PHD finger and the MYND finger. Because no SAND domain has been found in yeast, it is thought that the SAND domain could be restricted to animal phyla. Many SAND domain-containing proteins, including NUDR, DEAF-1 (Deformed epidermal autoregulatory factor-1) and GMEB, have been shown to bind DNA sequences specifically. The SAND domain has been proposed to mediate the DNA binding activity of these proteins [, ]. The resolution of the 3D structure of the SAND domain from Sp100b has revealed that it consists of a novel alpha/beta fold. The SAND domain adopts a compact fold consisting of a strongly twisted, five-stranded antiparallel beta-sheet with four alpha-helices packing against one side of the beta-sheet. The opposite side of the beta-sheet is solvent exposed. The beta-sheet and alpha-helical parts of the structure form two distinct regions. Multiple hydrophobic residues pack between these regions to form a structural core. A conserved KDWK sequence motif is found within the alpha-helical, positively charged surface patch. The DNA binding surface has been mapped to the alpha-helical region encompassing the KDWK motif [].; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 1OQJ_B 1UFN_A 1H5P_A.
Probab=97.12 E-value=8.6e-05 Score=56.27 Aligned_cols=55 Identities=36% Similarity=0.746 Sum_probs=36.9
Q ss_pred CceEEEcccccceeecCcceeeEE--e-eCC--eeeEeeecCCCCCCCCCChhhhhhccccccccccccceEE
Q 026596 29 GDYIEVTCGCTSHRYGDAVGRLRV--F-SNG--DLEITCECTPGCNEDKMTPGAFEKHSGRETARKWKNNVWV 96 (236)
Q Consensus 29 edyvEV~CGcTs~rYGD~VGRLri--~-~~G--~~~ItCeC~PgC~~dkltp~aFEkHs~reta~kWkn~vWV 96 (236)
+.-|.|+|| +..|.|-. + ..| +-=|.++ ..-+||.+||+|+|++++.+||..|-|
T Consensus 8 ~~~lpVtCG-------~~~G~L~~~k~~~~g~~~kCI~~~------g~~~TP~eFE~~~G~~~sK~WK~SIr~ 67 (82)
T PF01342_consen 8 DPELPVTCG-------DVKGTLYKKKFVKQGICGKCIQCE------GRWFTPSEFERHGGKGSSKDWKRSIRC 67 (82)
T ss_dssp CSEEEEEET-------TEEEEEEHHHH-TTGTTSS-EEET------TEEE-HHHHHHHHTTCTCS-HHHHSEE
T ss_pred CCeEeeEeC-------CeEEEEEHHHhhcccccCceEeeC------CcEECHHHHHhhcCcccCCCCCccEEE
Confidence 567999996 44555542 2 222 1123222 567999999999999999999999998
No 2
>smart00258 SAND SAND domain.
Probab=95.93 E-value=0.0027 Score=48.32 Aligned_cols=56 Identities=27% Similarity=0.503 Sum_probs=38.3
Q ss_pred EEEcccccceeecCcceeeEEeeCCeeeEeeecCCCCCCCCCChhhhhhccccccccccccceEE
Q 026596 32 IEVTCGCTSHRYGDAVGRLRVFSNGDLEITCECTPGCNEDKMTPGAFEKHSGRETARKWKNNVWV 96 (236)
Q Consensus 32 vEV~CGcTs~rYGD~VGRLri~~~G~~~ItCeC~PgC~~dkltp~aFEkHs~reta~kWkn~vWV 96 (236)
|.|+||- .-|.|-..--++ -|.+-|+-- ...=+||.+||+++|++++.+||..|=+
T Consensus 3 lpV~CG~-------~~g~L~~~kf~~-G~~~kCI~~-~~~~~TP~eFe~~~g~~~~K~WK~sIR~ 58 (73)
T smart00258 3 LPVTCGT-------VKGILYKKKFKC-GISVKCIQY-EDKWFTPKEFEIEGGKGKSKDWKRSIRC 58 (73)
T ss_pred cceeeCC-------eeeeeeHhhhhc-CcccCCccC-CCEEEChHHHHhhcCCcccCCcchheeE
Confidence 5678864 445554333222 355666532 4456899999999999999999998754
No 3
>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.
Probab=91.91 E-value=0.06 Score=37.21 Aligned_cols=47 Identities=36% Similarity=0.587 Sum_probs=22.0
Q ss_pred cceeeeccccccccccccChhHHhhhhhhhcCCCcccCCCC-CCccccCcHHH
Q 026596 136 DEFVRCARCNKERRFRLRTKEECLIHHNALADKNWKCSDLP-YDKITCDDEEE 187 (236)
Q Consensus 136 DEFvrCt~CgKeRRFrLrsk~ecr~yHdAl~~~~WtCsd~p-y~kitCdDdEE 187 (236)
|.+|.|.+|+|=|+.....-+.. +.+.+ .|+|++-| ...-+|+..||
T Consensus 1 ~~WVQCd~C~KWR~lp~~~~~~~----~~~~d-~W~C~~n~~~~~~sC~~pee 48 (50)
T PF07496_consen 1 DYWVQCDSCLKWRRLPEEVDPIR----EELPD-PWYCSMNPDPPFNSCDAPEE 48 (50)
T ss_dssp -EEEE-TTT--EEEE-CCHHCTS----CCSST-T--GGGSS-CCC-STTS--S
T ss_pred CeEEECCCCCceeeCChhhCccc----ccCCC-eEEcCCCCCCCCCCCCCccc
Confidence 56899999999999762111100 12233 89999976 23366877665
No 4
>PF07897 DUF1675: Protein of unknown function (DUF1675); InterPro: IPR012463 The members of this family are sequences derived from hypothetical plant proteins of unknown function. One member of this family (Q9SFV5 from SWISSPROT) is annotated as a putative RNA-binding protein, but no evidence was found to support this.
Probab=44.85 E-value=26 Score=32.68 Aligned_cols=49 Identities=27% Similarity=0.575 Sum_probs=34.0
Q ss_pred EEEcccccce--eecC-cceeeEEe-eCCeeeEeeecCCCCCCCCCChhhhhhcccc
Q 026596 32 IEVTCGCTSH--RYGD-AVGRLRVF-SNGDLEITCECTPGCNEDKMTPGAFEKHSGR 84 (236)
Q Consensus 32 vEV~CGcTs~--rYGD-~VGRLri~-~~G~~~ItCeC~PgC~~dkltp~aFEkHs~r 84 (236)
-++.|-.|.- -.|- .-|=|-=| ..+|+-|-|-| +..-|||+.|=||+|.
T Consensus 221 ~~mp~v~t~g~gpng~~i~g~ly~y~~~~~v~i~c~c----hg~~~~~~efv~h~~~ 273 (284)
T PF07897_consen 221 EDMPCVSTTGDGPNGKRIEGFLYKYGKGEEVRIVCVC----HGSFLSPAEFVKHAGG 273 (284)
T ss_pred ccCCceeeccCCCCCceeeEEEEEecCCCeEEEEEEe----cCCCCCHHHHHHhcCC
Confidence 4556655532 1232 23566666 56799999986 6778999999999985
No 5
>PF07610 DUF1573: Protein of unknown function (DUF1573); InterPro: IPR011467 These hypothetical proteins from bacteria, such as Rhodopirellula baltica, Bacteroides thetaiotaomicron and Porphyromonas gingivalis, share a region of conserved sequence towards their N termini.
Probab=43.93 E-value=15 Score=24.52 Aligned_cols=28 Identities=21% Similarity=0.640 Sum_probs=18.5
Q ss_pred eEEEcccccceeecCcceeeEEeeCCeeeE
Q 026596 31 YIEVTCGCTSHRYGDAVGRLRVFSNGDLEI 60 (236)
Q Consensus 31 yvEV~CGcTs~rYGD~VGRLri~~~G~~~I 60 (236)
-|+..||||...|.... |.-..+|++.+
T Consensus 16 ~v~tsCgCt~~~~~~~~--i~PGes~~i~v 43 (45)
T PF07610_consen 16 DVQTSCGCTTAEYSKKP--IAPGESGKIKV 43 (45)
T ss_pred EeeEccCCEEeeCCcce--ECCCCEEEEEE
Confidence 45679999999998843 44444444443
No 6
>smart00134 LU Ly-6 antigen / uPA receptor -like domain. Three-fold repeated domain in urokinase-type plasminogen activator receptor; occurs singly in other GPI-linked cell-surface glycoproteins (Ly-6 family, CD59, thymocyte B cell antigen, Sgp-2). Topology of these domains is similar to that of snake venom neurotoxins.
Probab=34.32 E-value=19 Score=25.68 Aligned_cols=16 Identities=50% Similarity=1.163 Sum_probs=13.7
Q ss_pred hhhhhcCCCCCCCCCC
Q 026596 190 SRRVYRGCIRSPTCKG 205 (236)
Q Consensus 190 S~k~~RGCsrSstC~G 205 (236)
..+++|||+++++|+.
T Consensus 40 ~~~~~rgC~~~~~Cp~ 55 (79)
T smart00134 40 GSVVYKGCATSPICPG 55 (79)
T ss_pred CceEEcCccCCCCCCC
Confidence 4669999999999974
No 7
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=34.31 E-value=15 Score=27.23 Aligned_cols=26 Identities=19% Similarity=0.520 Sum_probs=20.5
Q ss_pred cceeeeccccccccccccChhHHhhh
Q 026596 136 DEFVRCARCNKERRFRLRTKEECLIH 161 (236)
Q Consensus 136 DEFvrCt~CgKeRRFrLrsk~ecr~y 161 (236)
++|+.|..||.-.|-++|.--+.+|+
T Consensus 2 ~~Wi~CP~CgnKTR~kir~DT~LkNf 27 (55)
T PF14205_consen 2 SEWILCPICGNKTRLKIREDTVLKNF 27 (55)
T ss_pred CeEEECCCCCCccceeeecCceeccc
Confidence 68999999999888888765555544
No 8
>PF07943 PBP5_C: Penicillin-binding protein 5, C-terminal domain; InterPro: IPR012907 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry contains proteins that are annotated as penicillin-binding protein 5 and 6. These belong to MEROPS peptidase family S11 (D-Ala-D-Ala carboxypeptidase A family, clan SE). Penicillin-binding protein 5 expressed by Escherichia coli functions as a D-alanyl-D-alanine carboxypeptidase. It is composed of two domains that are oriented at approximately right angles to each other. The N-terminal domain (IPR001967 from INTERPRO) is the catalytic domain. The C-terminal domain, this entry, is organised into a sandwich of two anti-parallel beta-sheets, and has a relatively hydrophobic surface as compared to the N-terminal domain. Its precise function is unknown; it may mediate interactions with other cell wall-synthesising enzymes, thus allowing the protein to be recruited to areas of active cell wall synthesis. It may also function as a linker domain that positions the active site in the catalytic domain closer to the peptidoglycan layer, to allow it to interact with cell wall peptides []. ; GO: 0009002 serine-type D-Ala-D-Ala carboxypeptidase activity, 0006508 proteolysis; PDB: 3A3J_A 3MFD_B 1XP4_D 3MZD_A 1NZU_A 1NJ4_A 1Z6F_A 3MZF_A 1NZO_A 3MZE_A ....
Probab=32.07 E-value=49 Score=23.58 Aligned_cols=23 Identities=30% Similarity=0.479 Sum_probs=18.5
Q ss_pred cceeecCcceeeEEeeCCeeeEe
Q 026596 39 TSHRYGDAVGRLRVFSNGDLEIT 61 (236)
Q Consensus 39 Ts~rYGD~VGRLri~~~G~~~It 61 (236)
..-+=|+-||.|.|+.+|++..+
T Consensus 58 aPi~kG~~vG~~~v~~~~~~i~~ 80 (91)
T PF07943_consen 58 APIKKGQVVGTLTVYLDGKLIGE 80 (91)
T ss_dssp SGBGTTSEEEEEEEEETTEEEEE
T ss_pred CcccCCCEEEEEEEEECCEEEEE
Confidence 34567999999999999987544
No 9
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=32.07 E-value=18 Score=27.55 Aligned_cols=14 Identities=50% Similarity=1.103 Sum_probs=12.2
Q ss_pred cceeeecccccccc
Q 026596 136 DEFVRCARCNKERR 149 (236)
Q Consensus 136 DEFvrCt~CgKeRR 149 (236)
.+|++|.+||+-=|
T Consensus 15 E~~lrCPRC~~~FR 28 (65)
T COG4049 15 EEFLRCPRCGMVFR 28 (65)
T ss_pred ceeeeCCchhHHHH
Confidence 58999999999765
No 10
>PF14901 Jiv90: Cleavage inducing molecular chaperone
Probab=30.13 E-value=27 Score=28.09 Aligned_cols=33 Identities=30% Similarity=0.798 Sum_probs=26.2
Q ss_pred eeecccc-ccccccccCh-------hHHhhhhhhhcCCCcc
Q 026596 139 VRCARCN-KERRFRLRTK-------EECLIHHNALADKNWK 171 (236)
Q Consensus 139 vrCt~Cg-KeRRFrLrsk-------~ecr~yHdAl~~~~Wt 171 (236)
++|++|| +-+||..+.. .+|+++|-|-.+.-|-
T Consensus 6 i~C~~C~~~H~r~~t~r~~~~AR~C~~C~~~H~Ak~gDiWa 46 (94)
T PF14901_consen 6 IRCDKCGGKHKRIETDRPPSAARYCQDCKIRHPAKEGDIWA 46 (94)
T ss_pred eechhhCCeeeeEEecCchhhhHhHHHhhhhcccccCCeEE
Confidence 6788885 5677777655 4999999999998885
No 11
>PF11101 DUF2884: Protein of unknown function (DUF2884); InterPro: IPR021307 Some members in this bacterial family of proteins are annotated as YggN which currently has no known function.
Probab=29.31 E-value=53 Score=28.79 Aligned_cols=21 Identities=33% Similarity=0.518 Sum_probs=15.6
Q ss_pred eCCcccccc---hhhHHHHhhhhh
Q 026596 98 ANGEKVPLS---KTVLLKYYNQAS 118 (236)
Q Consensus 98 ~~~~kvpL~---kT~LlkyY~~~~ 118 (236)
|+|++|+|+ +..|..|+....
T Consensus 36 i~G~~v~L~~~Q~q~l~~Y~~~lr 59 (229)
T PF11101_consen 36 INGKKVSLNAEQQQALQQYQQGLR 59 (229)
T ss_pred ECCEEccCCHHHHHHHHHHHHHHH
Confidence 488889887 567888887543
No 12
>PF12800 Fer4_4: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding; PDB: 1BD6_A 1BQX_A 1BWE_A 1BC6_A.
Probab=28.62 E-value=26 Score=19.76 Aligned_cols=11 Identities=55% Similarity=1.301 Sum_probs=7.0
Q ss_pred CCCCCCCCcee
Q 026596 200 SPTCKGCTSCV 210 (236)
Q Consensus 200 SstC~GCstCv 210 (236)
|..|.||..|+
T Consensus 1 ~~~C~~C~~C~ 11 (17)
T PF12800_consen 1 QERCIGCGSCV 11 (17)
T ss_dssp -CCCTTSSSST
T ss_pred CCcCCCCchHH
Confidence 35677777765
No 13
>PF13333 rve_2: Integrase core domain
Probab=27.74 E-value=28 Score=23.65 Aligned_cols=12 Identities=8% Similarity=0.243 Sum_probs=10.3
Q ss_pred CCChhhhhhccc
Q 026596 72 KMTPGAFEKHSG 83 (236)
Q Consensus 72 kltp~aFEkHs~ 83 (236)
.|||.+|++|+.
T Consensus 41 ~lsP~eyr~~~l 52 (52)
T PF13333_consen 41 GLSPVEYRNQYL 52 (52)
T ss_pred CcCHHHHHHhhC
Confidence 699999999863
No 14
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=27.49 E-value=31 Score=23.10 Aligned_cols=18 Identities=44% Similarity=1.126 Sum_probs=14.6
Q ss_pred cceeeeccccccccccccC
Q 026596 136 DEFVRCARCNKERRFRLRT 154 (236)
Q Consensus 136 DEFvrCt~CgKeRRFrLrs 154 (236)
|.|+ |..||...-++|++
T Consensus 17 ~g~~-CP~Cg~~~~~~~~~ 34 (46)
T PF12760_consen 17 DGFV-CPHCGSTKHYRLKT 34 (46)
T ss_pred CCCC-CCCCCCeeeEEeCC
Confidence 4566 99999988888877
No 15
>PF04369 Lactococcin: Lactococcin-like family; InterPro: IPR007464 Bacteriocins are produced by bacteria to inhibit the growth of similar or closely related bacterial strains. The class II bacteriocins are small heat-stable proteins for which disulphide bonds are the only modification to the peptide. Lactococcin A and B are class-IId bacteriocins (one-peptide non-pediocin-like bacteriocin) [, ].; GO: 0042742 defense response to bacterium, 0005576 extracellular region
Probab=27.48 E-value=34 Score=25.79 Aligned_cols=20 Identities=40% Similarity=0.557 Sum_probs=14.9
Q ss_pred cccccccccChHhHhhhhcc
Q 026596 6 EKESVLMMFSDEELREISGV 25 (236)
Q Consensus 6 ~~~~g~~LF~eEELr~i~gv 25 (236)
++..-....|+|||.+|.|=
T Consensus 2 ~~~~nf~~~sdeeL~~i~GG 21 (60)
T PF04369_consen 2 ENQLNFNILSDEELSKINGG 21 (60)
T ss_pred cccccceecCHHHHhhccCC
Confidence 44444567899999999874
No 16
>PF15389 DUF4612: Domain of unknown function (DUF4612)
Probab=26.95 E-value=27 Score=29.02 Aligned_cols=25 Identities=48% Similarity=0.624 Sum_probs=23.0
Q ss_pred cccceeecCcc------eeeEEeeCCeeeEe
Q 026596 37 GCTSHRYGDAV------GRLRVFSNGDLEIT 61 (236)
Q Consensus 37 GcTs~rYGD~V------GRLri~~~G~~~It 61 (236)
||||.+-++|| |+.+.+++|++++.
T Consensus 1 GC~sak~~~~v~~~e~~~~~k~~sn~D~~~d 31 (115)
T PF15389_consen 1 GCTSAKQVSAVPNDEEGGNGKAHSNGDLFSD 31 (115)
T ss_pred CccccccccccCcchhhcccccccccccccc
Confidence 89999999998 89999999999876
No 17
>PF09832 DUF2059: Uncharacterized protein conserved in bacteria (DUF2059); InterPro: IPR018637 This entry contains proteins that have no known function. ; PDB: 2X3O_B 3OAO_A.
Probab=26.18 E-value=28 Score=24.01 Aligned_cols=13 Identities=38% Similarity=0.598 Sum_probs=10.6
Q ss_pred ccChHhHhhhhcc
Q 026596 13 MFSDEELREISGV 25 (236)
Q Consensus 13 LF~eEELr~i~gv 25 (236)
-|+++||+.|..|
T Consensus 16 ~ft~~El~~i~~F 28 (64)
T PF09832_consen 16 HFTEEELDAILAF 28 (64)
T ss_dssp HS-HHHHHHHHHH
T ss_pred HCCHHHHHHHHHH
Confidence 6999999999876
No 18
>PF03293 Pox_RNA_pol: Poxvirus DNA-directed RNA polymerase, 18 kD subunit; InterPro: IPR004973 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The Poxvirus DNA-directed RNA polymerase (2.7.7.6 from EC) catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. The enzyme consists of at least eight subunits, this is the 18 kDa subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0019083 viral transcription
Probab=25.38 E-value=74 Score=27.91 Aligned_cols=34 Identities=29% Similarity=0.659 Sum_probs=28.5
Q ss_pred ceEEEcccccceee--cCcc-eeeEEeeCCeeeEeee
Q 026596 30 DYIEVTCGCTSHRY--GDAV-GRLRVFSNGDLEITCE 63 (236)
Q Consensus 30 dyvEV~CGcTs~rY--GD~V-GRLri~~~G~~~ItCe 63 (236)
--|-|+|--|-+.| ||-| |.|-|..+-...|.|-
T Consensus 66 ivv~VPC~vtykyYk~GDvV~GtLnIedESni~V~Cg 102 (160)
T PF03293_consen 66 IVVKVPCNVTYKYYKVGDVVRGTLNIEDESNITVQCG 102 (160)
T ss_pred EEEEeeeEEEEEEEeeCCEEEEEEEecccCceEEEcC
Confidence 35778999999877 9987 8999999988888774
No 19
>PF07244 Surf_Ag_VNR: Surface antigen variable number repeat; InterPro: IPR010827 This motif is found primarily in bacterial surface antigens, normally as variable number repeats at the N terminus. The C terminus of these proteins is normally represented by IPR000184 from INTERPRO. There may also be a relationship to haemolysin activator HlyB (IPR005565 from INTERPRO). The alignment centres on a -GY- or -GF- motif. Some members of this family are found in the mitochondria. It is predicted to have a mixed alpha/beta secondary structure.; GO: 0019867 outer membrane; PDB: 2X8X_X 3MC8_A 3OG5_A 3MC9_B 2QCZ_B 3EFC_A 3Q6B_A 2QDF_A 2V9H_A.
Probab=25.34 E-value=34 Score=23.25 Aligned_cols=22 Identities=45% Similarity=0.578 Sum_probs=17.3
Q ss_pred cc-cccChHhHhhhhcceecCce
Q 026596 10 VL-MMFSDEELREISGVKRGGDY 31 (236)
Q Consensus 10 g~-~LF~eEELr~i~gvk~Gedy 31 (236)
|. ..|++++|+..++++.|+-|
T Consensus 10 Gn~~~~~~~~l~~~l~~~~G~~~ 32 (78)
T PF07244_consen 10 GNLKKFSDEELRRELGLKPGDPF 32 (78)
T ss_dssp SE-SSSHHHHHHHCHSS-TTSBE
T ss_pred cCceEeCHHHHHhhcCCCCCCEe
Confidence 53 68999999998899999765
No 20
>COG0227 RpmB Ribosomal protein L28 [Translation, ribosomal structure and biogenesis]
Probab=25.16 E-value=33 Score=26.64 Aligned_cols=27 Identities=30% Similarity=0.597 Sum_probs=22.1
Q ss_pred hccccccccccccce-----EEEeCCcccccc
Q 026596 80 KHSGRETARKWKNNV-----WVIANGEKVPLS 106 (236)
Q Consensus 80 kHs~reta~kWkn~v-----WV~~~~~kvpL~ 106 (236)
.||.+-|.++|.-|+ |+.++|..+-|+
T Consensus 19 Shs~~kTkRr~~pNlq~~~~~~~~~g~~~~l~ 50 (77)
T COG0227 19 SHSHNKTKRRFLPNLQKVRFWSLSDGRFKRLR 50 (77)
T ss_pred cccccccceeecCccEEEEEEEccCCcEEEEE
Confidence 599999999999885 788888776664
No 21
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=24.53 E-value=36 Score=27.58 Aligned_cols=13 Identities=54% Similarity=1.055 Sum_probs=11.1
Q ss_pred cccceeeeccccc
Q 026596 134 HRDEFVRCARCNK 146 (236)
Q Consensus 134 HRDEFvrCt~CgK 146 (236)
+-++|-+|++|||
T Consensus 120 ~~~~f~~C~~C~k 132 (147)
T PF01927_consen 120 TYDEFWRCPGCGK 132 (147)
T ss_pred cCCeEEECCCCCC
Confidence 4477999999998
No 22
>COG1281 Disulfide bond chaperones of the HSP33 family [Posttranslational modification, protein turnover, chaperones]
Probab=22.50 E-value=21 Score=33.35 Aligned_cols=46 Identities=26% Similarity=0.504 Sum_probs=30.1
Q ss_pred EEEcccccceeecCcceeeE-------EeeCCeeeEeeecCCCCCCCCCChhhhh
Q 026596 32 IEVTCGCTSHRYGDAVGRLR-------VFSNGDLEITCECTPGCNEDKMTPGAFE 79 (236)
Q Consensus 32 vEV~CGcTs~rYGD~VGRLr-------i~~~G~~~ItCeC~PgC~~dkltp~aFE 79 (236)
|+.-|.|+--|.+++.=.|- |..+|..+|+|+.|-. .-.+++..+|
T Consensus 232 v~f~C~CSrEr~~~aL~~lg~eEi~~m~eedg~iev~C~FC~~--~Y~f~~~ei~ 284 (286)
T COG1281 232 VEFRCSCSRERVAAALLSLGKEELEDMLEEDGGIEVTCEFCGT--KYLFDEEEIE 284 (286)
T ss_pred ceEEcCCCHHHHHHHHHhcCHHHHHHHHhcCCCeEEEeeccCC--EEecCHHHHh
Confidence 77788888888887765542 3446788888887754 2334444443
No 23
>cd00184 TNF Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding.
Probab=20.81 E-value=87 Score=24.64 Aligned_cols=21 Identities=24% Similarity=0.232 Sum_probs=18.4
Q ss_pred eeecCcceeeEEeeCCeeeEeee
Q 026596 41 HRYGDAVGRLRVFSNGDLEITCE 63 (236)
Q Consensus 41 ~rYGD~VGRLri~~~G~~~ItCe 63 (236)
-+|=| |+|.|..+|.|+|.+.
T Consensus 32 ~~~~~--g~L~V~~~GlY~VYsQ 52 (137)
T cd00184 32 LELQN--GELVVPQDGLYYIYSQ 52 (137)
T ss_pred eEEEC--CEEEecCCcEEEEEEE
Confidence 56666 9999999999999986
No 24
>PF00751 DM: DM DNA binding domain; InterPro: IPR001275 This domain was first discovered in the doublesex proteins of Drosophila melanogaster and is also seen in proteins from Caenorhabditis elegans []. In D. melanogaster the doublesex gene controls somatic sexual differentiation by producing alternatively spliced mRNAs encoding related sex-specific polypeptides []. These proteins are believed to function as transcription factors on downstream sex-determination genes, especially on neuroblast differentiation and yolk protein genes transcription [, ]. The DM domain binds DNA as a dimer, allowing the recognition of pseudopalindromic sequences [, , ]. The NMR analysis of the DSX DM domain [] revealed a novel zinc module containing 'intertwined' CCHC and HCCC zinc-binding sites. The recognition of the DNA requires the carboxy-terminal basic tail which contacts the minor groove of the target sequence.; GO: 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0007548 sex differentiation, 0005634 nucleus; PDB: 1LPV_A.
Probab=20.48 E-value=44 Score=23.61 Aligned_cols=16 Identities=38% Similarity=1.121 Sum_probs=10.9
Q ss_pred eeeeccCCchhhhhhh
Q 026596 216 ICRFSDCSCQTCIDFT 231 (236)
Q Consensus 216 ~CRF~DC~CQtC~Df~ 231 (236)
.|+|.+|.|..|.-+.
T Consensus 23 ~C~~~~C~C~kC~li~ 38 (47)
T PF00751_consen 23 YCPFRDCQCDKCALIA 38 (47)
T ss_dssp G-TTTT--SHHHHHHH
T ss_pred ccCcCCCcCCCCcCcH
Confidence 4899999999998664
No 25
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=20.30 E-value=62 Score=22.44 Aligned_cols=16 Identities=50% Similarity=0.879 Sum_probs=13.5
Q ss_pred ccChHhHhhhhcceec
Q 026596 13 MFSDEELREISGVKRG 28 (236)
Q Consensus 13 LF~eEELr~i~gvk~G 28 (236)
+.++|||.+|-|.|+-
T Consensus 2 fLT~~El~elTG~k~~ 17 (47)
T PF13986_consen 2 FLTDEELQELTGYKRP 17 (47)
T ss_pred CCCHHHHHHHHCCCCH
Confidence 6789999999998853
Done!