Query psy14241
Match_columns 136
No_of_seqs 103 out of 166
Neff 5.6
Searched_HMMs 46136
Date Fri Aug 16 22:59:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14241.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14241hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3095|consensus 100.0 1.2E-42 2.6E-47 283.9 12.3 130 2-134 110-248 (284)
2 COG5174 TFA2 Transcription ini 100.0 5.3E-36 1.1E-40 240.5 11.0 127 6-134 117-252 (285)
3 PF02186 TFIIE_beta: TFIIE bet 98.6 2.1E-08 4.6E-13 66.6 2.4 25 7-31 40-65 (65)
4 cd07977 TFIIE_beta_winged_heli 98.3 5.4E-07 1.2E-11 61.3 2.4 30 2-32 46-75 (75)
5 PF01316 Arg_repressor: Argini 67.7 19 0.00042 24.0 5.1 51 29-90 17-68 (70)
6 PF08784 RPA_C: Replication pr 66.9 12 0.00027 25.7 4.2 43 34-77 49-99 (102)
7 PHA02943 hypothetical protein; 61.7 9.5 0.00021 29.7 3.1 68 33-107 12-87 (165)
8 cd01396 MeCP2_MBD MeCP2, MBD1, 53.0 14 0.00031 24.9 2.5 33 21-56 27-60 (77)
9 smart00540 LEM in nuclear memb 47.0 19 0.00042 22.0 2.1 19 115-133 13-31 (44)
10 PRK04280 arginine repressor; P 46.8 67 0.0015 24.2 5.6 66 28-106 15-81 (148)
11 COG2425 Uncharacterized protei 45.2 78 0.0017 28.2 6.5 89 4-107 300-391 (437)
12 PRK05066 arginine repressor; P 43.6 85 0.0018 23.9 5.7 52 28-90 20-73 (156)
13 PF02604 PhdYeFM_antitox: Anti 43.5 34 0.00073 21.8 3.1 27 52-78 4-32 (75)
14 KOG0775|consensus 41.9 96 0.0021 26.4 6.2 98 29-129 110-222 (304)
15 PF05005 Ocnus: Janus/Ocnus fa 39.2 25 0.00055 25.4 2.1 18 9-26 1-18 (108)
16 PF06757 Ins_allergen_rp: Inse 38.0 26 0.00056 26.8 2.1 29 97-125 43-74 (179)
17 PF07106 TBPIP: Tat binding pr 37.2 1.3E+02 0.0029 22.4 5.9 64 35-103 4-77 (169)
18 TIGR01552 phd_fam prevent-host 36.2 62 0.0013 19.3 3.3 33 52-85 2-35 (52)
19 PRK15483 type III restriction- 31.8 34 0.00074 33.5 2.3 70 33-108 613-687 (986)
20 cd00122 MBD MeCP2, MBD1, MBD2, 30.7 75 0.0016 20.1 3.1 33 21-56 26-59 (62)
21 smart00054 EFh EF-hand, calciu 29.7 48 0.001 15.5 1.7 24 39-62 4-27 (29)
22 cd02549 Peptidase_C39A A sub-f 28.1 2E+02 0.0044 19.7 5.5 70 32-108 44-134 (141)
23 COG2442 Uncharacterized conser 27.1 43 0.00094 22.8 1.6 47 9-64 7-56 (79)
24 PF04255 DUF433: Protein of un 25.7 66 0.0014 20.0 2.2 23 34-63 21-43 (56)
25 COG4190 Predicted transcriptio 25.4 1.2E+02 0.0027 23.1 3.9 60 35-99 67-135 (144)
26 COG0064 GatB Asp-tRNAAsn/Glu-t 23.9 1.3E+02 0.0029 27.2 4.4 50 74-124 263-318 (483)
27 COG2808 PaiB Transcriptional r 23.0 75 0.0016 25.7 2.5 32 24-59 1-33 (209)
28 PHA02583 11 baseplate wedge su 22.6 98 0.0021 25.2 3.0 32 47-78 33-75 (218)
29 PF04703 FaeA: FaeA-like prote 22.2 2.2E+02 0.0048 18.4 4.2 49 34-86 2-58 (62)
30 PF08006 DUF1700: Protein of u 21.7 84 0.0018 23.7 2.4 34 33-70 2-35 (181)
31 PRK11409 antitoxin YefM; Provi 21.6 1.4E+02 0.003 20.1 3.3 36 52-88 4-41 (83)
32 PF03020 LEM: LEM domain; Int 21.5 18 0.00038 22.2 -1.1 19 115-133 13-31 (43)
33 PF04239 DUF421: Protein of un 21.4 34 0.00073 23.9 0.1 58 8-78 3-63 (99)
34 TIGR00988 hip integration host 20.9 1.9E+02 0.0041 19.3 3.9 34 33-70 2-35 (94)
35 PF13867 SAP30_Sin3_bdg: Sin3 20.4 64 0.0014 20.1 1.3 20 33-56 22-41 (53)
36 PRK01022 hypothetical protein; 20.2 1.1E+02 0.0023 23.8 2.7 36 31-70 3-38 (167)
No 1
>KOG3095|consensus
Probab=100.00 E-value=1.2e-42 Score=283.88 Aligned_cols=130 Identities=38% Similarity=0.732 Sum_probs=117.6
Q ss_pred hhhhhHhhhcCCceEEeeCCeEEeccCCCCCCHHHHHHHHHhcccCCCCceeehhhHhhhhhhHHHHhc----CeEEEEc
Q psy14241 2 KWLSTEALQNNPKIEVIEGNKYIFKPVFKIKDRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKN----EIIYVTR 77 (136)
Q Consensus 2 ~~l~~e~L~~npKI~~~~~~~f~ykp~~~Ik~k~~LL~lL~~~~~~~~~Gi~v~dLkd~~p~~~~~i~~----~~i~V~r 77 (136)
+|+..|+|++||||+|+ .+||+|||+|+|||+++||++|++|+ +.|||+|+||+||||+|.++|++ +.|+|++
T Consensus 110 n~~l~esLkkNpri~~d-~~~FsfKp~y~Ird~~~Ll~llr~~~--~~~GI~v~DL~d~~pNv~~~lk~L~~s~eIl~l~ 186 (284)
T KOG3095|consen 110 NWLLLESLKKNPRIEYD-PRTFSFKPTYNIRDKKQLLKLLRKHD--TLGGILVSDLKDAWPNVDEDLKELEKSGEILVLR 186 (284)
T ss_pred cHHHHHHHhhCCceEec-CceeeccCccccCCHHHHHHHHHhcC--ccCceehHHhhhcccchHHHHHHHhcCCcEEEEe
Confidence 69999999999999999 55999999999999999999999985 59999999999999999999998 7777776
Q ss_pred CC--CCceEEEecCCCCCCCCCHHHHHhhhhccCCc-hhh--HHHHhcCCCCCCcChhhhhc
Q psy14241 78 PA--DKRKVMFYNDKSAQLDLDEDFQKLWRSISVDG-MIL--RIRSFYGVDYFSGAGEKAEK 134 (136)
Q Consensus 78 ~~--d~~~vvf~ND~~~~~~vD~efk~lW~~v~vP~-~~d--~~L~~~Glkp~~~~~~~~~~ 134 (136)
+. ++++||||||.+|.+.||+||++|||+|.||+ +.+ ++|+++||+||++..+++.+
T Consensus 187 t~~d~k~kivf~ND~~~~~~VDdEFk~LWr~V~Ip~~~~dle~eL~k~GLkp~~~v~p~~~~ 248 (284)
T KOG3095|consen 187 TPKDDKPKIVFYNDKSCSFSVDDEFKKLWRSVTIPSMELDLEEELQKQGLKPMKDVDPKKAA 248 (284)
T ss_pred ccCCCCCceEEecCCCCCcccCHHHHHHHHhCCCChHHHHHHHHHHHhCCCcccccchHHhh
Confidence 64 68999999999999999999999999999998 445 99999999999954444443
No 2
>COG5174 TFA2 Transcription initiation factor IIE, beta subunit [Transcription]
Probab=100.00 E-value=5.3e-36 Score=240.50 Aligned_cols=127 Identities=19% Similarity=0.363 Sum_probs=119.3
Q ss_pred hHhhhcCCceEEeeC-CeEEeccCCCCCCHHHHHHHHHhcccCCCCceeehhhHhhhhhhHHHHhc----CeEEEEcCC-
Q psy14241 6 TEALQNNPKIEVIEG-NKYIFKPVFKIKDRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKN----EIIYVTRPA- 79 (136)
Q Consensus 6 ~e~L~~npKI~~~~~-~~f~ykp~~~Ik~k~~LL~lL~~~~~~~~~Gi~v~dLkd~~p~~~~~i~~----~~i~V~r~~- 79 (136)
.++|+.+.||.|++. +||.|+|.|+|||.++||++|+. |.++.||++++|+||||+|...|++ ++|+|+|++
T Consensus 117 v~Llkk~~ri~~d~~~~Tf~fkply~irS~~~llk~lrs--q~t~~Gls~k~L~Dgwpnv~~~veeLek~~eIliLrt~k 194 (285)
T COG5174 117 VLLLKKKRRIRIDATHSTFMFKPLYSIRSVEDLLKVLRS--QGTEEGLSMKKLMDGWPNVVPFVEELEKSNEILILRTDK 194 (285)
T ss_pred HHHHhhccCceeccCCceEEeeccccccCHHHHHHHHHh--hcccccccHHHhhcCCCcccHHHHHHhhcCcEEEEeecC
Confidence 357999999999987 79999999999999999999999 5999999999999999999999998 899999974
Q ss_pred CC-ceEEEecCCCCCCCCCHHHHHhhhhccCCchhh--HHHHhcCCCCCCcChhhhhc
Q psy14241 80 DK-RKVMFYNDKSAQLDLDEDFQKLWRSISVDGMIL--RIRSFYGVDYFSGAGEKAEK 134 (136)
Q Consensus 80 d~-~~vvf~ND~~~~~~vD~efk~lW~~v~vP~~~d--~~L~~~Glkp~~~~~~~~~~ 134 (136)
|+ +++||+|+.++.++||+||++||++|.+|...| ++|..+|||||+++|..++.
T Consensus 195 Dg~p~~vW~n~~n~~c~vD~ef~~~W~~V~ip~~~dL~reL~~~GLKptsvdp~t~KR 252 (285)
T COG5174 195 DGSPVVVWNNTQNLECPVDPEFKSLWNQVRIPTYHDLIRELNTAGLKPTSVDPNTKKR 252 (285)
T ss_pred CCCceEEEeCCCCcCCCCCHHHHHHHHhCCCchHHHHHHHHHhcCCCccccCcchhcc
Confidence 64 899999999999999999999999999999998 99999999999999987764
No 3
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This entry represents the beta subunit of the transcription factor TFIIE.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1D8K_A 1D8J_A.
Probab=98.61 E-value=2.1e-08 Score=66.60 Aligned_cols=25 Identities=44% Similarity=0.721 Sum_probs=18.2
Q ss_pred HhhhcCCceEEeeCC-eEEeccCCCC
Q psy14241 7 EALQNNPKIEVIEGN-KYIFKPVFKI 31 (136)
Q Consensus 7 e~L~~npKI~~~~~~-~f~ykp~~~I 31 (136)
+.|++||||+|+|+| +|+|||+|+|
T Consensus 40 ~~Lk~npKI~~d~~~~~f~fkp~ynI 65 (65)
T PF02186_consen 40 QWLKNNPKIEYDPDGNTFSFKPKYNI 65 (65)
T ss_dssp HHHHH-TTEEEE-TT-CEEE--TTT-
T ss_pred HHHHcCCCEEEecCCCEEEeccCCCC
Confidence 567799999999996 9999999997
No 4
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=98.26 E-value=5.4e-07 Score=61.30 Aligned_cols=30 Identities=47% Similarity=0.925 Sum_probs=28.0
Q ss_pred hhhhhHhhhcCCceEEeeCCeEEeccCCCCC
Q psy14241 2 KWLSTEALQNNPKIEVIEGNKYIFKPVFKIK 32 (136)
Q Consensus 2 ~~l~~e~L~~npKI~~~~~~~f~ykp~~~Ik 32 (136)
+||..+++.|||++... +|||+|||+|+||
T Consensus 46 ~~L~~~~~~~n~~~~~~-~~tf~fkP~y~Ir 75 (75)
T cd07977 46 EWLKSEALVNNPKIDPK-DGTFSFKPKYNIR 75 (75)
T ss_pred HHHHhhhhccCceeccC-CCEEEeccCCCCC
Confidence 69999999999999987 7899999999997
No 5
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=67.69 E-value=19 Score=23.95 Aligned_cols=51 Identities=20% Similarity=0.354 Sum_probs=31.1
Q ss_pred CCCCCHHHHHHHHHhcccCCCCceeehhhHhhhhhhHHHHhc-CeEEEEcCCCCceEEEecCC
Q psy14241 29 FKIKDRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKN-EIIYVTRPADKRKVMFYNDK 90 (136)
Q Consensus 29 ~~Ik~k~~LL~lL~~~~~~~~~Gi~v~dLkd~~p~~~~~i~~-~~i~V~r~~d~~~vvf~ND~ 90 (136)
+.|.+.++|+.+|+++ |+.+.. +.+-.||++ +.+=|....++.....+++.
T Consensus 17 ~~i~sQ~eL~~~L~~~------Gi~vTQ-----aTiSRDLkeL~~vKv~~~~g~~~Y~l~~~~ 68 (70)
T PF01316_consen 17 HEISSQEELVELLEEE------GIEVTQ-----ATISRDLKELGAVKVPDGNGKYRYVLPEET 68 (70)
T ss_dssp S---SHHHHHHHHHHT------T-T--H-----HHHHHHHHHHT-EEEECTTSSEEEE-TTST
T ss_pred CCcCCHHHHHHHHHHc------CCCcch-----hHHHHHHHHcCcEEeeCCCCCEEEEecCcC
Confidence 6789999999999995 777643 567788888 88777754444455555543
No 6
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=66.91 E-value=12 Score=25.65 Aligned_cols=43 Identities=28% Similarity=0.427 Sum_probs=29.7
Q ss_pred HHHHHHHHHhcccCCCCceeehhhHhhh----hhhHHHHhc----CeEEEEc
Q psy14241 34 RKGLLKLLKQHDLKGIGGILLDDVRESL----PHCEKALKN----EIIYVTR 77 (136)
Q Consensus 34 k~~LL~lL~~~~~~~~~Gi~v~dLkd~~----p~~~~~i~~----~~i~V~r 77 (136)
++.+|++|+.. .....||++.+|.... ..+.++|+. +.|+-+-
T Consensus 49 ~~~Vl~~i~~~-~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi 99 (102)
T PF08784_consen 49 QDKVLNFIKQQ-PNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIYSTI 99 (102)
T ss_dssp HHHHHHHHHC-----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEESS
T ss_pred HHHHHHHHHhc-CCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEeccc
Confidence 67899999993 4778999999999987 334455554 7776554
No 7
>PHA02943 hypothetical protein; Provisional
Probab=61.73 E-value=9.5 Score=29.67 Aligned_cols=68 Identities=16% Similarity=0.185 Sum_probs=47.1
Q ss_pred CHHHHHHHHHhcccCCCCceeehhhHh----hhhhhHHHHhc----CeEEEEcCCCCceEEEecCCCCCCCCCHHHHHhh
Q psy14241 33 DRKGLLKLLKQHDLKGIGGILLDDVRE----SLPHCEKALKN----EIIYVTRPADKRKVMFYNDKSAQLDLDEDFQKLW 104 (136)
Q Consensus 33 ~k~~LL~lL~~~~~~~~~Gi~v~dLkd----~~p~~~~~i~~----~~i~V~r~~d~~~vvf~ND~~~~~~vD~efk~lW 104 (136)
-++++|++| + .|+.+.+++.+ ||-.|.-.|.- +.|.=.+ ..+..+.+.||..+..-|++=|+++|
T Consensus 12 R~~eILE~L-k-----~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~-~G~~tyw~l~~day~~~v~~~~Relw 84 (165)
T PHA02943 12 RMIKTLRLL-A-----DGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVE-IGRAAIWCLDEDAYTNLVFEIKRELW 84 (165)
T ss_pred HHHHHHHHH-h-----cCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEe-ecceEEEEEChHHHHHHHHHHHHHHH
Confidence 367889999 4 46787888776 56666655543 5544333 23567777777777777999999999
Q ss_pred hhc
Q psy14241 105 RSI 107 (136)
Q Consensus 105 ~~v 107 (136)
+=|
T Consensus 85 rlv 87 (165)
T PHA02943 85 RLV 87 (165)
T ss_pred HHH
Confidence 865
No 8
>cd01396 MeCP2_MBD MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1.
Probab=53.00 E-value=14 Score=24.89 Aligned_cols=33 Identities=24% Similarity=0.459 Sum_probs=26.3
Q ss_pred CeEEeccC-CCCCCHHHHHHHHHhcccCCCCceeehh
Q psy14241 21 NKYIFKPV-FKIKDRKGLLKLLKQHDLKGIGGILLDD 56 (136)
Q Consensus 21 ~~f~ykp~-~~Ik~k~~LL~lL~~~~~~~~~Gi~v~d 56 (136)
+.|-|-|. ..+||+.+|.++|..+ +.+++.+++
T Consensus 27 DvyY~sP~Gkk~RS~~ev~~yL~~~---~~~~~~~~~ 60 (77)
T cd01396 27 DVYYISPTGKKFRSKVELARYLEKN---GPTSLDLSD 60 (77)
T ss_pred eEEEECCCCCEEECHHHHHHHHHhC---CCCCCcHhH
Confidence 47888888 6899999999999996 355666654
No 9
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=46.96 E-value=19 Score=22.01 Aligned_cols=19 Identities=11% Similarity=-0.060 Sum_probs=16.6
Q ss_pred HHHHhcCCCCCCcChhhhh
Q psy14241 115 RIRSFYGVDYFSGAGEKAE 133 (136)
Q Consensus 115 ~~L~~~Glkp~~~~~~~~~ 133 (136)
++|.++|+.|.+.++..|+
T Consensus 13 ~~L~~~G~~~gPIt~sTR~ 31 (44)
T smart00540 13 AELKQYGLPPGPITDTTRK 31 (44)
T ss_pred HHHHHcCCCCCCcCcchHH
Confidence 7899999999999887764
No 10
>PRK04280 arginine repressor; Provisional
Probab=46.79 E-value=67 Score=24.17 Aligned_cols=66 Identities=14% Similarity=0.254 Sum_probs=42.2
Q ss_pred CCCCCCHHHHHHHHHhcccCCCCceeehhhHhhhhhhHHHHhc-CeEEEEcCCCCceEEEecCCCCCCCCCHHHHHhhhh
Q psy14241 28 VFKIKDRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKN-EIIYVTRPADKRKVMFYNDKSAQLDLDEDFQKLWRS 106 (136)
Q Consensus 28 ~~~Ik~k~~LL~lL~~~~~~~~~Gi~v~dLkd~~p~~~~~i~~-~~i~V~r~~d~~~vvf~ND~~~~~~vD~efk~lW~~ 106 (136)
.+.|.+.++|+++|+++ |+.+.. +.+-.||++ +.+=|.....+-+...+++... ...+-|..+.++
T Consensus 15 ~~~I~tQeeL~~~L~~~------Gi~vTQ-----ATiSRDikeL~lvKv~~~~G~~~Y~lp~~~~~--~~~~~l~~~~~~ 81 (148)
T PRK04280 15 NNEIETQDELVDRLREE------GFNVTQ-----ATVSRDIKELHLVKVPLPDGRYKYSLPADQRF--NPLQKLKRALMD 81 (148)
T ss_pred hCCCCCHHHHHHHHHHc------CCCeeh-----HHHHHHHHHcCCEEeecCCCcEEEeecccccc--chHHHHHHHHHH
Confidence 36899999999999995 777654 567788888 7766665433334555554432 222344444443
No 11
>COG2425 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=45.20 E-value=78 Score=28.23 Aligned_cols=89 Identities=20% Similarity=0.197 Sum_probs=61.8
Q ss_pred hhhHhhhcCCceE---EeeCCeEEeccCCCCCCHHHHHHHHHhcccCCCCceeehhhHhhhhhhHHHHhcCeEEEEcCCC
Q psy14241 4 LSTEALQNNPKIE---VIEGNKYIFKPVFKIKDRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKNEIIYVTRPAD 80 (136)
Q Consensus 4 l~~e~L~~npKI~---~~~~~~f~ykp~~~Ik~k~~LL~lL~~~~~~~~~Gi~v~dLkd~~p~~~~~i~~~~i~V~r~~d 80 (136)
|+.-||+.|-++- |+ +..+.|+....+++-++++++|... -.|| -|+.-+.-.+.+++++... .
T Consensus 300 l~~~alaenR~~~~~lF~-s~~~~~el~~k~~~~~e~i~fL~~~---f~GG---TD~~~~l~~al~~~k~~~~------~ 366 (437)
T COG2425 300 LMRIALAENRDCYVILFD-SEVIEYELYEKKIDIEELIEFLSYV---FGGG---TDITKALRSALEDLKSREL------F 366 (437)
T ss_pred HHHHHHHhccceEEEEec-ccceeeeecCCccCHHHHHHHHhhh---cCCC---CChHHHHHHHHHHhhcccc------c
Confidence 4566888886644 45 4899999999999999999999996 3566 7899999999999987110 1
Q ss_pred CceEEEecCCCCCCCCCHHHHHhhhhc
Q psy14241 81 KRKVMFYNDKSAQLDLDEDFQKLWRSI 107 (136)
Q Consensus 81 ~~~vvf~ND~~~~~~vD~efk~lW~~v 107 (136)
+.++||.-|.-.. ++++|..-|...
T Consensus 367 ~adiv~ITDg~~~--~~~~~~~~v~e~ 391 (437)
T COG2425 367 KADIVVITDGEDE--RLDDFLRKVKEL 391 (437)
T ss_pred CCCEEEEeccHhh--hhhHHHHHHHHH
Confidence 1334444444443 236666666543
No 12
>PRK05066 arginine repressor; Provisional
Probab=43.59 E-value=85 Score=23.88 Aligned_cols=52 Identities=8% Similarity=0.121 Sum_probs=36.2
Q ss_pred CCCCCCHHHHHHHHHhcccCCCCcee-ehhhHhhhhhhHHHHhc-CeEEEEcCCCCceEEEecCC
Q psy14241 28 VFKIKDRKGLLKLLKQHDLKGIGGIL-LDDVRESLPHCEKALKN-EIIYVTRPADKRKVMFYNDK 90 (136)
Q Consensus 28 ~~~Ik~k~~LL~lL~~~~~~~~~Gi~-v~dLkd~~p~~~~~i~~-~~i~V~r~~d~~~vvf~ND~ 90 (136)
.+.|.+.++|+++|+++ |+. +.. +.+-.+|++ +.+=|.....+-+...+++.
T Consensus 20 ~~~I~tQeeL~~~L~~~------Gi~~vTQ-----ATiSRDikeL~lvKv~~~~G~~~Y~l~~~~ 73 (156)
T PRK05066 20 EEKFGSQGEIVTALQEQ------GFDNINQ-----SKVSRMLTKFGAVRTRNAKMEMVYCLPAEL 73 (156)
T ss_pred hCCCCCHHHHHHHHHHC------CCCeecH-----HHHHHHHHHcCCEEeeCCCCCEEEEeCCCC
Confidence 36899999999999995 777 543 556778888 77666554333455555544
No 13
>PF02604 PhdYeFM_antitox: Antitoxin Phd_YefM, type II toxin-antitoxin system; InterPro: IPR006442 This entry is represented by Bacteriophage P1, prevent-host-death protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family of proteins is characterised by a region of about 55 amino acids toward the N-terminal end of bacterial proteins which are themselves only 85 amino acids, or thereabouts, in length. The best-characterised member is prevent-host-death (phd) of bacteriophage P1, the antidote partner of death-on-curing (doc) (IPR006440 from INTERPRO) in an addiction module. Addiction modules prevent plasmid curing by killing the host cell as the longer-lived killing protein persists while the gene for the shorter-lived antidote is lost. Note, however, that relatively few members of this family appear to be plasmid or phage-encoded. Also, there is little overlap, except for phage P1 itself, of species with this family and with the doc family. ; PDB: 3DBO_A 2ODK_B 3G5O_D 2A6Q_B 3D55_C 3OEI_E 3CTO_C 3K33_D 3KH2_F 3HS2_C ....
Probab=43.52 E-value=34 Score=21.80 Aligned_cols=27 Identities=11% Similarity=0.331 Sum_probs=22.9
Q ss_pred eeehhhHhhhhhhHHHHhc-Ce-EEEEcC
Q psy14241 52 ILLDDVRESLPHCEKALKN-EI-IYVTRP 78 (136)
Q Consensus 52 i~v~dLkd~~p~~~~~i~~-~~-i~V~r~ 78 (136)
+++.|++.....+.+.+.+ +. |+|++.
T Consensus 4 vs~~e~r~~~~~~l~~v~~~~~pv~It~~ 32 (75)
T PF02604_consen 4 VSITEFRNNFSELLDEVEEGEEPVIITKN 32 (75)
T ss_dssp EEHHHHHHTHHHHHHHHHHCT-EEEEEET
T ss_pred ecHHHHHHHHHHHHHHHHcCCCeEEEEEC
Confidence 6889999999999999999 54 888875
No 14
>KOG0775|consensus
Probab=41.90 E-value=96 Score=26.37 Aligned_cols=98 Identities=10% Similarity=0.029 Sum_probs=65.5
Q ss_pred CCCCCHHHHHHHHHhcccCCCCceeehhhHhhhhhhH--HHHhc--------CeEEEEcCCCCceEEEecCCCCCCC---
Q psy14241 29 FKIKDRKGLLKLLKQHDLKGIGGILLDDVRESLPHCE--KALKN--------EIIYVTRPADKRKVMFYNDKSAQLD--- 95 (136)
Q Consensus 29 ~~Ik~k~~LL~lL~~~~~~~~~Gi~v~dLkd~~p~~~--~~i~~--------~~i~V~r~~d~~~vvf~ND~~~~~~--- 95 (136)
|...+-++|..+|..| .+.--.--+|++=|-.+- ++=+. +++-|.|.---+|.+|--+....+-
T Consensus 110 fH~gnf~eLY~iLE~h---~Fs~~~h~~LQ~lWl~AhY~EAek~RGR~LgaV~KYRvRrKfPlPrTIWDGEet~yCFKek 186 (304)
T KOG0775|consen 110 FHSGNFRELYHILENH---KFSPHNHPKLQALWLKAHYKEAEKLRGRPLGAVDKYRVRRKFPLPRTIWDGEETVYCFKEK 186 (304)
T ss_pred HhcccHHHHHHHHHhc---cCChhhhHHHHHHHHHHHHHHHHHhcCCcCCccccceeeccCCCCCccccCceeeeehhHh
Confidence 4567788999999997 477777788999887753 21111 7888877433466666544433211
Q ss_pred CCHHHHHhhhhccCCchhh-HHHHhc-CCCCCCcCh
Q psy14241 96 LDEDFQKLWRSISVDGMIL-RIRSFY-GVDYFSGAG 129 (136)
Q Consensus 96 vD~efk~lW~~v~vP~~~d-~~L~~~-Glkp~~~~~ 129 (136)
--.-+++.+..-+-|+..+ ++|.++ ||++|++..
T Consensus 187 SR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsN 222 (304)
T KOG0775|consen 187 SRSLLREWYLQNPYPSPREKRELAEATGLTITQVSN 222 (304)
T ss_pred hHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhh
Confidence 0112455556668888888 999988 999999853
No 15
>PF05005 Ocnus: Janus/Ocnus family (Ocnus); InterPro: IPR007702 This family is comprised of the Ocnus, Janus-A and Janus-B proteins. These proteins have been found to be testes specific in Drosophila melanogaster [].; PDB: 2OZX_A 2OZW_A 2NMM_C 2AI6_A 2HW4_A.
Probab=39.20 E-value=25 Score=25.43 Aligned_cols=18 Identities=11% Similarity=0.396 Sum_probs=14.9
Q ss_pred hhcCCceEEeeCCeEEec
Q psy14241 9 LQNNPKIEVIEGNKYIFK 26 (136)
Q Consensus 9 L~~npKI~~~~~~~f~yk 26 (136)
|.+-|.|..+|.|+|.|-
T Consensus 1 L~~vP~V~id~~G~fKYv 18 (108)
T PF05005_consen 1 LEKVPDVDIDPEGVFKYV 18 (108)
T ss_dssp CTTS-SEEEESSSEEEEE
T ss_pred CCCCCeEEecCCceEEEE
Confidence 567899999999999997
No 16
>PF06757 Ins_allergen_rp: Insect allergen related repeat, nitrile-specifier detoxification; InterPro: IPR010629 This entry represents several insect specific allergen repeats. These repeats are commonly found in various proteins from cockroaches, fruit flies and mosquitos. It has been suggested that the repeat sequences have evolved by duplication of an ancestral amino acid domain, which may have arisen from the mitochondrial energy transfer proteins []. This family exemplifies a case of novel gene evolution. The case in point is the arms-race between plants and their infective insective herbivores in the area of the glucosinolate-myrosinase system. Brassicas have developed the glucosinolate-myrosinase system as chemical defence mechanism against the insects, and consequently the insects have adapted to produce a detoxifying molecule, nitrile-specifier protein (NSP). NSP is present in the Pieris rapae (Cabbage white butterfly). NSP is structurally different from and has no amino acid homology to any known detoxifying enzymes, and it appears to have arisen by a process of domain and gene duplication of a sequence of unknown function that is widespread in insect species and referred to as insect-allergen-repeat protein. Thus this family is found either as a single domain or as a multiple repeat-domain [].
Probab=38.01 E-value=26 Score=26.75 Aligned_cols=29 Identities=17% Similarity=0.517 Sum_probs=22.4
Q ss_pred CHHHHHhhhhc-cCCchhh--HHHHhcCCCCC
Q psy14241 97 DEDFQKLWRSI-SVDGMIL--RIRSFYGVDYF 125 (136)
Q Consensus 97 D~efk~lW~~v-~vP~~~d--~~L~~~Glkp~ 125 (136)
.++|+++|+.+ .+|+..+ .-|+++|+...
T Consensus 43 s~~f~~l~~~l~~~pE~~~l~~yL~~~gldv~ 74 (179)
T PF06757_consen 43 SSEFKQLWQQLEALPEVKALLDYLESAGLDVY 74 (179)
T ss_pred ChHHHHHHHHHHcCHHHHHHHHHHHHCCCCHH
Confidence 45899999997 7787777 78888877543
No 17
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=37.16 E-value=1.3e+02 Score=22.42 Aligned_cols=64 Identities=22% Similarity=0.330 Sum_probs=38.5
Q ss_pred HHHHHHHHhcccCCCCceeehhhHhhhhh------hHHHHhc----CeEEEEcCCCCceEEEecCCCCCCCCCHHHHHh
Q psy14241 35 KGLLKLLKQHDLKGIGGILLDDVRESLPH------CEKALKN----EIIYVTRPADKRKVMFYNDKSAQLDLDEDFQKL 103 (136)
Q Consensus 35 ~~LL~lL~~~~~~~~~Gi~v~dLkd~~p~------~~~~i~~----~~i~V~r~~d~~~vvf~ND~~~~~~vD~efk~l 103 (136)
+.+|.+|+++ -.--++-||-+..-+ +.++++. +.|... .-.|-+|+|+|...+...=.+|+..|
T Consensus 4 ~~Il~y~~~q----NRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~K-~~GKqkiY~~~Q~~~~~~s~eel~~l 77 (169)
T PF07106_consen 4 DAILEYMKEQ----NRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVEK-EYGKQKIYFANQDELEVPSPEELAEL 77 (169)
T ss_pred HHHHHHHHHc----CCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeeee-eecceEEEeeCccccCCCCchhHHHH
Confidence 5688899986 234455666666533 4455555 665554 44677999999776653333344433
No 18
>TIGR01552 phd_fam prevent-host-death family protein. This model recognizes a region of about 55 amino acids toward the N-terminal end of bacterial proteins of about 85 amino acids in length. The best-characterized member is prevent-host-death (phd) of bacteriophage P1, the antidote partner of death-on-curing (doc) (TIGR01550) in an addiction module. Addiction modules prevent plasmid curing by killing the host cell as the longer-lived killing protein persists while the gene for the shorter-lived antidote is lost. Note, however, that relatively few members of this family appear to be plasmid or phage-encoded. Also, there is little overlap, except for phage P1 itself, of species with this family and with the doc family.
Probab=36.16 E-value=62 Score=19.26 Aligned_cols=33 Identities=15% Similarity=0.318 Sum_probs=24.4
Q ss_pred eeehhhHhhhhhhHHHHhc-CeEEEEcCCCCceEE
Q psy14241 52 ILLDDVRESLPHCEKALKN-EIIYVTRPADKRKVM 85 (136)
Q Consensus 52 i~v~dLkd~~p~~~~~i~~-~~i~V~r~~d~~~vv 85 (136)
+++.+++.-...+.+.+.. +.|+|+|. +++.++
T Consensus 2 v~~te~r~~~~~~l~~v~~~~pv~It~~-g~~~av 35 (52)
T TIGR01552 2 VSLSEAKNKLGELLKRVRDGEPVTITKR-GRPVAV 35 (52)
T ss_pred cCHHHHHHHHHHHHHHHHCCCCEEEEEC-CcceEE
Confidence 5678899889998888887 57888875 344443
No 19
>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional
Probab=31.85 E-value=34 Score=33.47 Aligned_cols=70 Identities=16% Similarity=0.245 Sum_probs=43.0
Q ss_pred CHHHHHHHHHhcccCCCCcee----ehhhHhhhhhhHHHHhc-CeEEEEcCCCCceEEEecCCCCCCCCCHHHHHhhhhc
Q psy14241 33 DRKGLLKLLKQHDLKGIGGIL----LDDVRESLPHCEKALKN-EIIYVTRPADKRKVMFYNDKSAQLDLDEDFQKLWRSI 107 (136)
Q Consensus 33 ~k~~LL~lL~~~~~~~~~Gi~----v~dLkd~~p~~~~~i~~-~~i~V~r~~d~~~vvf~ND~~~~~~vD~efk~lW~~v 107 (136)
..++|...|.....-...|.. -.+|+++||...+.+-. +.+.+.+. ++++.|-.|-..+ +||+.||..|
T Consensus 613 ~~~~l~~~L~~~~~Id~~~~~~~~~~~~l~~~~pe~~~~~l~~~k~~~~n~-~~~~~vk~rk~~~-----~eFk~LWe~I 686 (986)
T PRK15483 613 TELRLLEDLDDKKIIDRSNNFKEDGFDWLLEAYPELFQTGLRKGKVRDNKP-ASKLTVKLRKENY-----EELKSLWEQI 686 (986)
T ss_pred cHHHHHHHHHHcCccCccCcccHhHHHHHHhhCcHHHHHHhhcCCccccCC-CcCceeecchHHH-----HHHHHHHHHh
Confidence 667888888765333333432 35677788887664433 66554443 3444554444333 8999999997
Q ss_pred c
Q psy14241 108 S 108 (136)
Q Consensus 108 ~ 108 (136)
.
T Consensus 687 n 687 (986)
T PRK15483 687 N 687 (986)
T ss_pred h
Confidence 4
No 20
>cd00122 MBD MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family.
Probab=30.69 E-value=75 Score=20.10 Aligned_cols=33 Identities=18% Similarity=0.504 Sum_probs=24.9
Q ss_pred CeEEeccC-CCCCCHHHHHHHHHhcccCCCCceeehh
Q psy14241 21 NKYIFKPV-FKIKDRKGLLKLLKQHDLKGIGGILLDD 56 (136)
Q Consensus 21 ~~f~ykp~-~~Ik~k~~LL~lL~~~~~~~~~Gi~v~d 56 (136)
+.|-|-|. -.+||+.++-++|..+ +..++.+++
T Consensus 26 dv~Y~sP~Gk~~Rs~~ev~~yL~~~---~~~~l~~~~ 59 (62)
T cd00122 26 DVYYYSPCGKKLRSKPEVARYLEKT---GPSSLDLEN 59 (62)
T ss_pred eEEEECCCCceecCHHHHHHHHHhC---CCCCCcHHH
Confidence 36777777 6899999999999995 355665543
No 21
>smart00054 EFh EF-hand, calcium binding motif. EF-hands are calcium-binding motifs that occur at least in pairs. Links between disease states and genes encoding EF-hands, particularly the S100 subclass, are emerging. Each motif consists of a 12 residue loop flanked on either side by a 12 residue alpha-helix. EF-hands undergo a conformational change unpon binding calcium ions.
Probab=29.71 E-value=48 Score=15.48 Aligned_cols=24 Identities=21% Similarity=0.398 Sum_probs=14.7
Q ss_pred HHHHhcccCCCCceeehhhHhhhh
Q psy14241 39 KLLKQHDLKGIGGILLDDVRESLP 62 (136)
Q Consensus 39 ~lL~~~~~~~~~Gi~v~dLkd~~p 62 (136)
.+++..+..+.|.|+..++...+.
T Consensus 4 ~~f~~~d~~~~g~i~~~e~~~~~~ 27 (29)
T smart00054 4 EAFRLFDKDGDGKIDFEEFKDLLK 27 (29)
T ss_pred HHHHHHCCCCCCcEeHHHHHHHHH
Confidence 334444445566788888877654
No 22
>cd02549 Peptidase_C39A A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are
Probab=28.06 E-value=2e+02 Score=19.72 Aligned_cols=70 Identities=16% Similarity=0.311 Sum_probs=39.5
Q ss_pred CCHHHHHHH-HHhcccCCCCceeehhhHhhhhhhHHHHhcC-----------------eEEEEcCCCCceEEEecCCCCC
Q psy14241 32 KDRKGLLKL-LKQHDLKGIGGILLDDVRESLPHCEKALKNE-----------------IIYVTRPADKRKVMFYNDKSAQ 93 (136)
Q Consensus 32 k~k~~LL~l-L~~~~~~~~~Gi~v~dLkd~~p~~~~~i~~~-----------------~i~V~r~~d~~~vvf~ND~~~~ 93 (136)
.+..+|++. ++++ |+..+.+..++. +.+.++.+ ..+|+..-+....++.+||...
T Consensus 44 ~~~~~l~~~~a~~~------G~~~~~~~~~~~-~~~~l~~~~Pvi~~~~~~~~~~~~gH~vVv~g~~~~~~~~i~DP~~~ 116 (141)
T cd02549 44 TYPKPIVSAAARKY------GLVVRPLTGLLA-LLRQLAAGHPVIVSVNLGVSITPSGHAMVVIGYDRKGNVYVNDPGGG 116 (141)
T ss_pred cCHHHHHHHHHhhC------CCcEEECCCHHH-HHHHHHCCCeEEEEEecCcccCCCCeEEEEEEEcCCCCEEEECCCCC
Confidence 667889999 8775 555555544444 44555551 2222222231344667787653
Q ss_pred C--CCC-HHHHHhhhhcc
Q psy14241 94 L--DLD-EDFQKLWRSIS 108 (136)
Q Consensus 94 ~--~vD-~efk~lW~~v~ 108 (136)
. .++ ++|.++|.+-.
T Consensus 117 ~~~~~~~~~f~~~w~~~~ 134 (141)
T cd02549 117 RRLVVSFDEFEKAWKRMG 134 (141)
T ss_pred cCEEEeHHHHHHHHHHcC
Confidence 2 343 48999997643
No 23
>COG2442 Uncharacterized conserved protein [Function unknown]
Probab=27.06 E-value=43 Score=22.81 Aligned_cols=47 Identities=17% Similarity=0.248 Sum_probs=32.8
Q ss_pred hhcCCceEEeeC---CeEEeccCCCCCCHHHHHHHHHhcccCCCCceeehhhHhhhhhh
Q psy14241 9 LQNNPKIEVIEG---NKYIFKPVFKIKDRKGLLKLLKQHDLKGIGGILLDDVRESLPHC 64 (136)
Q Consensus 9 L~~npKI~~~~~---~~f~ykp~~~Ik~k~~LL~lL~~~~~~~~~Gi~v~dLkd~~p~~ 64 (136)
....+.|.++|+ |+=+++=.= | .-..+|..|+. |++.+||.+-||++
T Consensus 7 ~~~~~~I~~~P~i~gGkP~I~GtR-I-~V~~Il~~l~~-------G~s~eeil~dyp~L 56 (79)
T COG2442 7 QKLLNRIVITPGICGGKPCIRGTR-I-PVWDILEMLAA-------GESIEEILADYPDL 56 (79)
T ss_pred ccccCeeEeCCcccCCcceEeCce-e-cHHHHHHHHHC-------CCCHHHHHHhCCCC
Confidence 345568888877 555554331 1 35677887775 99999999999964
No 24
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=25.73 E-value=66 Score=19.98 Aligned_cols=23 Identities=26% Similarity=0.510 Sum_probs=16.2
Q ss_pred HHHHHHHHHhcccCCCCceeehhhHhhhhh
Q psy14241 34 RKGLLKLLKQHDLKGIGGILLDDVRESLPH 63 (136)
Q Consensus 34 k~~LL~lL~~~~~~~~~Gi~v~dLkd~~p~ 63 (136)
-..++.++. .|.+.+++.+.||+
T Consensus 21 v~~i~~~~~-------~G~s~eeI~~~yp~ 43 (56)
T PF04255_consen 21 VRDILDLLA-------AGESPEEIAEDYPS 43 (56)
T ss_dssp HHHHHHHHH-------TT--HHHHHHHSTT
T ss_pred HHHHHHHHH-------cCCCHHHHHHHCCC
Confidence 356666663 49999999999996
No 25
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=25.37 E-value=1.2e+02 Score=23.08 Aligned_cols=60 Identities=20% Similarity=0.440 Sum_probs=40.7
Q ss_pred HHHHHHHHhcccCCCCceeehhhHh----hhhhhHHHHhc----CeEEEEcC-CCCceEEEecCCCCCCCCCHH
Q psy14241 35 KGLLKLLKQHDLKGIGGILLDDVRE----SLPHCEKALKN----EIIYVTRP-ADKRKVMFYNDKSAQLDLDED 99 (136)
Q Consensus 35 ~~LL~lL~~~~~~~~~Gi~v~dLkd----~~p~~~~~i~~----~~i~V~r~-~d~~~vvf~ND~~~~~~vD~e 99 (136)
-+||+++..+ +--|+.||.+ .++++-..+.. +.|..-++ +++.-.+||.+--++++.|.+
T Consensus 67 leLl~~Ia~~-----~P~Si~ElAe~vgRdv~nvhr~Ls~l~~~GlI~fe~~gq~k~P~~~y~~l~I~lpf~~~ 135 (144)
T COG4190 67 LELLELIAQE-----EPASINELAELVGRDVKNVHRTLSTLADLGLIFFEEDGQRKQPVVWYDELVIDLPFDPE 135 (144)
T ss_pred HHHHHHHHhc-----CcccHHHHHHHhCcchHHHHHHHHHHHhcCeEEEecCCcccCceeeccccEEeeecCcc
Confidence 3567777774 5678888887 47788877776 77666664 235577888776666666543
No 26
>COG0064 GatB Asp-tRNAAsn/Glu-tRNAGln amidotransferase B subunit (PET112 homolog) [Translation, ribosomal structure and biogenesis]
Probab=23.87 E-value=1.3e+02 Score=27.22 Aligned_cols=50 Identities=12% Similarity=0.265 Sum_probs=35.4
Q ss_pred EEEcCCC-CceEEEecCCCCC-CCCCHHHHHhhhhccCCchhh----HHHHhcCCCC
Q psy14241 74 YVTRPAD-KRKVMFYNDKSAQ-LDLDEDFQKLWRSISVDGMIL----RIRSFYGVDY 124 (136)
Q Consensus 74 ~V~r~~d-~~~vvf~ND~~~~-~~vD~efk~lW~~v~vP~~~d----~~L~~~Glkp 124 (136)
+..|++. ....-|+.||.+. +.+++++.+-++ -.+|+..+ +...++|++.
T Consensus 263 ~~mR~KE~a~DYRYfpePDl~p~~is~~~i~~~~-~~lPelP~~~~~r~~~~~gls~ 318 (483)
T COG0064 263 VSMRSKEEAEDYRYFPEPDLPPLEISDEWIEEVR-ATLPELPDEKRERYIKEYGLSE 318 (483)
T ss_pred eeccccccccccccCCCCCcCCccCCHHHHHHHH-HhCCCCCHHHHHHHHHHcCCCH
Confidence 3334432 3477788899885 789999999988 55775444 6667889875
No 27
>COG2808 PaiB Transcriptional regulator [Transcription]
Probab=23.01 E-value=75 Score=25.69 Aligned_cols=32 Identities=25% Similarity=0.393 Sum_probs=24.4
Q ss_pred EeccC-CCCCCHHHHHHHHHhcccCCCCceeehhhHh
Q psy14241 24 IFKPV-FKIKDRKGLLKLLKQHDLKGIGGILLDDVRE 59 (136)
Q Consensus 24 ~ykp~-~~Ik~k~~LL~lL~~~~~~~~~Gi~v~dLkd 59 (136)
+|-|+ |.+.+.+.|+.|++.| +=|+.|.--.+
T Consensus 1 MYiP~~F~~~d~~~L~a~ir~~----pfgtlvt~~~~ 33 (209)
T COG2808 1 MYIPPHFREEDPEVLHALIRAH----PFGTLVTSGGG 33 (209)
T ss_pred CCCCcccccCCHHHHHHHHHhC----CceEEEeccCC
Confidence 47888 6999999999999998 45555554433
No 28
>PHA02583 11 baseplate wedge subunit and tail pin; Provisional
Probab=22.56 E-value=98 Score=25.21 Aligned_cols=32 Identities=22% Similarity=0.503 Sum_probs=26.9
Q ss_pred CCCCceeehhhHhh--hhhhHHHHhc---------CeEEEEcC
Q psy14241 47 KGIGGILLDDVRES--LPHCEKALKN---------EIIYVTRP 78 (136)
Q Consensus 47 ~~~~Gi~v~dLkd~--~p~~~~~i~~---------~~i~V~r~ 78 (136)
+.-||..++++++| ||+|..+|.. +-|++.+.
T Consensus 33 r~IGg~tidq~~kGv~~pNVQSAIdDl~~~a~lpVg~Vii~t~ 75 (218)
T PHA02583 33 RPIGGPTIDQLQKGVYYPNVQSAIDDLATLAELPVGGVIITTE 75 (218)
T ss_pred CcCCCCCHHHHhhcCcCccHHHHHHHHHHhhcCccccEEEecc
Confidence 45899999999998 7999999987 66777654
No 29
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=22.18 E-value=2.2e+02 Score=18.38 Aligned_cols=49 Identities=10% Similarity=0.217 Sum_probs=29.4
Q ss_pred HHHHHHHHHhcccCCCCceeehhhHhhhhh----hHHH---Hhc-CeEEEEcCCCCceEEE
Q psy14241 34 RKGLLKLLKQHDLKGIGGILLDDVRESLPH----CEKA---LKN-EIIYVTRPADKRKVMF 86 (136)
Q Consensus 34 k~~LL~lL~~~~~~~~~Gi~v~dLkd~~p~----~~~~---i~~-~~i~V~r~~d~~~vvf 86 (136)
|+++|++|+.+ .++++-.|+.|..-= +..- ++. ++|--.+...+...+|
T Consensus 2 ke~Il~~i~~~----~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~rG~~~~W 58 (62)
T PF04703_consen 2 KEKILEYIKEQ----NGPLKTREIADALGLSIYQARYYLEKLEKEGKVERSPVRRGKSTYW 58 (62)
T ss_dssp HHCHHHHHHHH----TS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-SSSSS-EE
T ss_pred cHHHHHHHHHc----CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCCCcceee
Confidence 67899999995 578999999997642 2222 333 7765544322333455
No 30
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=21.67 E-value=84 Score=23.73 Aligned_cols=34 Identities=15% Similarity=0.251 Sum_probs=28.8
Q ss_pred CHHHHHHHHHhcccCCCCceeehhhHhhhhhhHHHHhc
Q psy14241 33 DRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKN 70 (136)
Q Consensus 33 ~k~~LL~lL~~~~~~~~~Gi~v~dLkd~~p~~~~~i~~ 70 (136)
||++-|+.|+++ ..+++-+|..|....+++.+++
T Consensus 2 ~k~efL~~L~~~----L~~lp~~e~~e~l~~Y~e~f~d 35 (181)
T PF08006_consen 2 NKNEFLNELEKY----LKKLPEEEREEILEYYEEYFDD 35 (181)
T ss_pred CHHHHHHHHHHH----HHcCCHHHHHHHHHHHHHHHHH
Confidence 688889999997 7789999999888888887775
No 31
>PRK11409 antitoxin YefM; Provisional
Probab=21.58 E-value=1.4e+02 Score=20.13 Aligned_cols=36 Identities=17% Similarity=0.249 Sum_probs=26.3
Q ss_pred eeehhhHhhhhhhHHHHhc--CeEEEEcCCCCceEEEec
Q psy14241 52 ILLDDVRESLPHCEKALKN--EIIYVTRPADKRKVMFYN 88 (136)
Q Consensus 52 i~v~dLkd~~p~~~~~i~~--~~i~V~r~~d~~~vvf~N 88 (136)
+++.+.+..+..+.+.+.+ +-|+|+|. +++.+|--.
T Consensus 4 i~~s~~R~~l~~~l~~v~~~~epv~ITr~-g~~~~Vl~S 41 (83)
T PRK11409 4 ISYSEARQNLSATMMKAVEDHAPILITRQ-NGEACVLMS 41 (83)
T ss_pred EcHHHHHHHHHHHHHHHhccCCcEEEEeC-CCCCEEEEe
Confidence 5778889999998877776 66888886 355665443
No 32
>PF03020 LEM: LEM domain; InterPro: IPR003887 The LEM domain is found in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin []. Defects in the emerin gene are a cause of Emery-Dreifuss muscular dystrophy, an X-linked disorder characterised by early contractures, muscle wasting, weakness and cardiomyopathy.; GO: 0005635 nuclear envelope; PDB: 2ODG_C 2ODC_I 1JEI_A 1H9F_A 1GJJ_A.
Probab=21.52 E-value=18 Score=22.16 Aligned_cols=19 Identities=11% Similarity=-0.165 Sum_probs=10.1
Q ss_pred HHHHhcCCCCCCcChhhhh
Q psy14241 115 RIRSFYGVDYFSGAGEKAE 133 (136)
Q Consensus 115 ~~L~~~Glkp~~~~~~~~~ 133 (136)
.+|.++|+.|.+.++..|+
T Consensus 13 ~~L~~~G~~~GPIt~tTR~ 31 (43)
T PF03020_consen 13 EELREYGEPPGPITPTTRK 31 (43)
T ss_dssp HCCCCCT-S-----CCCHH
T ss_pred HHHHHcCCCCCCCCcccHH
Confidence 7888999999888876653
No 33
>PF04239 DUF421: Protein of unknown function (DUF421); InterPro: IPR007353 This family of uncharacterised proteins is known as YDFR family; PDB: 3C6F_D.
Probab=21.35 E-value=34 Score=23.89 Aligned_cols=58 Identities=22% Similarity=0.319 Sum_probs=30.5
Q ss_pred hhhcCCceEEeeCCeEEeccCC-CCCCHHHHHHHHHhcccCCCCce-eehhhHhhhhhhHHHHhc-CeEEEEcC
Q psy14241 8 ALQNNPKIEVIEGNKYIFKPVF-KIKDRKGLLKLLKQHDLKGIGGI-LLDDVRESLPHCEKALKN-EIIYVTRP 78 (136)
Q Consensus 8 ~L~~npKI~~~~~~~f~ykp~~-~Ik~k~~LL~lL~~~~~~~~~Gi-~v~dLkd~~p~~~~~i~~-~~i~V~r~ 78 (136)
.|...|.+-+. +|.|.+...- .==+.++|+..|+++ |+ +++|+.-++ ++. |.|-|.+.
T Consensus 3 l~~g~p~~Li~-dG~i~~~~l~~~~it~~dl~~~LR~~------gi~~l~dV~~a~------lE~~G~lsv~~k 63 (99)
T PF04239_consen 3 LLEGKPTVLIR-DGKIDEDNLRRARITEEDLLSALREQ------GIESLSDVKAAV------LEPNGQLSVIKK 63 (99)
T ss_dssp ------EEEEE-TTEE-HHHHHHTT--HHHHHHHHHHT------T--SGGGEEEEE------E-TTS-EEEEE-
T ss_pred cccCCcEEEEE-CCEECHHHHhHcCCCHHHHHHHHHhh------CCCCHHHcCEEE------ECCCCCEEEEEc
Confidence 45667777777 8999998773 233889999999985 54 565554332 222 66665554
No 34
>TIGR00988 hip integration host factor, beta subunit. This protein forms a site-specific DNA-binding heterodimer with the homologous integration host factor alpha subunit. It is closely related to the DNA-binding protein HU.
Probab=20.91 E-value=1.9e+02 Score=19.34 Aligned_cols=34 Identities=9% Similarity=0.213 Sum_probs=26.6
Q ss_pred CHHHHHHHHHhcccCCCCceeehhhHhhhhhhHHHHhc
Q psy14241 33 DRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKN 70 (136)
Q Consensus 33 ~k~~LL~lL~~~~~~~~~Gi~v~dLkd~~p~~~~~i~~ 70 (136)
++++|++.+.++ ..|++-.+.+..+-...+.|.+
T Consensus 2 ~k~eli~~i~~~----~~~~s~~~v~~vv~~~~~~i~~ 35 (94)
T TIGR00988 2 TKSELIERIATQ----QSHLPAKDVEDAVKTMLEHMAS 35 (94)
T ss_pred CHHHHHHHHHHH----cCCCCHHHHHHHHHHHHHHHHH
Confidence 688999999874 3578888888888877777765
No 35
>PF13867 SAP30_Sin3_bdg: Sin3 binding region of histone deacetylase complex subunit SAP30; PDB: 2LD7_A.
Probab=20.44 E-value=64 Score=20.06 Aligned_cols=20 Identities=15% Similarity=0.411 Sum_probs=13.6
Q ss_pred CHHHHHHHHHhcccCCCCceeehh
Q psy14241 33 DRKGLLKLLKQHDLKGIGGILLDD 56 (136)
Q Consensus 33 ~k~~LL~lL~~~~~~~~~Gi~v~d 56 (136)
+|++|..-+++| +..++++|
T Consensus 22 sK~qLa~~V~kH----F~s~~v~E 41 (53)
T PF13867_consen 22 SKEQLANAVRKH----FNSQPVDE 41 (53)
T ss_dssp -HHHHHHHHHHH----HTT----H
T ss_pred CHHHHHHHHHHH----HhcCCCCH
Confidence 899999999999 77888776
No 36
>PRK01022 hypothetical protein; Provisional
Probab=20.18 E-value=1.1e+02 Score=23.76 Aligned_cols=36 Identities=19% Similarity=0.098 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHhcccCCCCceeehhhHhhhhhhHHHHhc
Q psy14241 31 IKDRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKALKN 70 (136)
Q Consensus 31 Ik~k~~LL~lL~~~~~~~~~Gi~v~dLkd~~p~~~~~i~~ 70 (136)
+.++.+|++.|++. ...+|+.||+..=.-.+.+++.
T Consensus 3 ~m~~~eL~~~Lke~----~~~~si~Dl~~~~~~l~~~~~~ 38 (167)
T PRK01022 3 AMTKGELGEKLKEE----ALEYSIYDLMKARVFLEKDIKY 38 (167)
T ss_pred ccCHHHHHHHHHHH----HhcCCHHHHHHHHHHHHHHHHh
Confidence 56899999999997 8899999999888777777763
Done!