Query psy1192
Match_columns 108
No_of_seqs 46 out of 48
Neff 3.2
Searched_HMMs 46136
Date Fri Aug 16 22:19:45 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1192.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1192hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0117|consensus 98.3 8.1E-08 1.8E-12 83.6 -0.2 50 40-99 1-50 (506)
2 PF02885 Glycos_trans_3N: Glyc 84.7 2.4 5.2E-05 26.9 4.3 32 33-65 13-44 (66)
3 PF09851 SHOCT: Short C-termin 68.5 4.9 0.00011 22.7 2.0 25 8-32 6-30 (31)
4 PF02268 TFIIA_gamma_N: Transc 62.6 12 0.00026 23.8 3.1 29 6-50 15-43 (49)
5 cd07372 2A5CPDO_B The beta sub 62.6 5.8 0.00013 32.3 2.1 52 23-74 218-270 (294)
6 KOG3463|consensus 62.4 10 0.00022 28.0 3.1 49 5-70 15-67 (109)
7 PRK00782 hypothetical protein; 62.2 6.4 0.00014 31.1 2.3 36 13-48 173-215 (267)
8 PF08044 DUF1707: Domain of un 61.7 9.9 0.00021 24.0 2.6 34 4-37 9-42 (53)
9 PRK00188 trpD anthranilate pho 58.8 18 0.00039 29.7 4.4 44 5-65 2-45 (339)
10 PF05553 DUF761: Cotton fibre 55.1 11 0.00025 22.7 2.0 27 20-46 1-27 (38)
11 PF04305 DUF455: Protein of un 52.3 30 0.00066 28.0 4.6 75 23-105 166-250 (253)
12 CHL00171 cpcB phycocyanin beta 49.5 29 0.00063 26.7 3.9 53 22-74 103-168 (172)
13 PF10987 DUF2806: Protein of u 48.8 23 0.0005 27.6 3.3 51 1-52 54-104 (219)
14 PF14520 HHH_5: Helix-hairpin- 44.7 47 0.001 20.3 3.7 41 9-49 17-60 (60)
15 PF12767 SAGA-Tad1: Transcript 43.1 20 0.00043 28.1 2.2 40 12-69 35-74 (252)
16 PF15107 FAM216B: FAM216B prot 42.2 17 0.00037 27.0 1.6 20 51-72 34-53 (113)
17 PF08564 CDC37_C: Cdc37 C term 41.7 27 0.00058 24.9 2.5 36 23-59 36-71 (99)
18 smart00567 EZ_HEAT E-Z type HE 40.7 43 0.00093 17.6 2.7 25 26-50 5-29 (30)
19 cd08330 CARD_ASC_NALP1 Caspase 39.2 20 0.00043 24.0 1.5 64 3-72 14-77 (82)
20 TIGR00134 gatE_arch glutamyl-t 39.0 50 0.0011 30.2 4.4 64 2-70 531-601 (620)
21 cd08329 CARD_BIRC2_BIRC3 Caspa 38.9 19 0.0004 24.8 1.3 62 4-71 23-84 (94)
22 PF04120 Iron_permease: Low af 37.6 32 0.00069 25.6 2.4 40 3-42 68-113 (132)
23 CHL00172 cpeB phycoerythrin be 37.1 60 0.0013 25.4 4.0 53 22-74 103-173 (177)
24 cd08324 CARD_NOD1_CARD4 Caspas 36.6 21 0.00045 25.3 1.3 25 2-26 13-37 (85)
25 PF11864 DUF3384: Domain of un 36.3 1.4E+02 0.003 25.4 6.4 64 5-70 378-445 (464)
26 PF08269 Cache_2: Cache domain 35.3 24 0.00052 23.0 1.4 30 8-37 24-53 (95)
27 PRK14965 DNA polymerase III su 34.8 1.4E+02 0.0031 26.4 6.4 62 9-74 220-294 (576)
28 PRK09071 hypothetical protein; 34.4 43 0.00093 27.7 3.0 32 33-65 19-50 (323)
29 cd07370 HPCD The Class III ext 34.3 33 0.00072 27.1 2.2 35 13-47 174-230 (280)
30 PRK07394 hypothetical protein; 33.4 65 0.0014 26.8 3.9 32 33-65 20-51 (342)
31 smart00845 GatB_Yqey GatB doma 32.3 1.2E+02 0.0026 21.8 4.7 13 4-16 59-71 (147)
32 TIGR01245 trpD anthranilate ph 31.9 49 0.0011 27.1 2.9 32 33-65 8-39 (330)
33 PRK06078 pyrimidine-nucleoside 31.3 59 0.0013 28.5 3.4 31 34-65 15-45 (434)
34 PRK13363 protocatechuate 4,5-d 30.4 34 0.00073 28.7 1.8 37 12-48 243-283 (335)
35 PRK06647 DNA polymerase III su 29.3 2E+02 0.0044 25.6 6.4 57 14-74 227-294 (563)
36 cd07951 ED_3B_N_AMMECR1 The N- 28.9 43 0.00094 25.7 2.0 35 13-47 164-212 (256)
37 cd01671 CARD Caspase activatio 28.6 38 0.00082 21.2 1.4 23 4-26 13-35 (80)
38 PF08585 DUF1767: Domain of un 28.5 46 0.00099 21.8 1.8 20 36-55 31-50 (90)
39 PF14866 Toxin_38: Potassium c 28.2 42 0.00091 22.2 1.6 28 40-72 7-34 (56)
40 cd07359 PCA_45_Doxase_B_like S 26.8 44 0.00096 26.0 1.8 31 13-43 178-219 (271)
41 PF01861 DUF43: Protein of unk 26.8 15 0.00033 30.0 -0.8 36 5-42 58-93 (243)
42 PF00619 CARD: Caspase recruit 26.7 43 0.00094 21.1 1.4 22 5-26 17-38 (85)
43 PRK13364 protocatechuate 4,5-d 26.0 40 0.00086 27.4 1.4 27 12-39 183-220 (278)
44 PLN02641 anthranilate phosphor 25.2 1.4E+02 0.003 25.0 4.5 44 4-65 2-45 (343)
45 KOG4114|consensus 25.0 48 0.001 23.0 1.5 28 33-61 39-66 (73)
46 PF01875 Memo: Memo-like prote 25.0 74 0.0016 25.3 2.8 31 24-55 203-233 (276)
47 cd00668 Ile_Leu_Val_MetRS_core 24.7 1.3E+02 0.0029 23.7 4.1 48 2-49 112-176 (312)
48 PF00814 Peptidase_M22: Glycop 24.2 33 0.00073 27.1 0.7 25 2-26 29-53 (268)
49 PF01471 PG_binding_1: Putativ 24.1 92 0.002 18.3 2.5 32 4-35 6-37 (57)
50 TIGR01339 phycocy_beta phycocy 24.0 1.3E+02 0.0029 23.2 3.9 53 22-74 101-166 (170)
51 PF13646 HEAT_2: HEAT repeats; 23.9 1.2E+02 0.0026 18.5 3.0 46 23-68 15-60 (88)
52 PF07128 DUF1380: Protein of u 23.5 1.2E+02 0.0025 23.1 3.4 54 20-75 28-86 (139)
53 PRK08136 glycosyl transferase 23.5 85 0.0018 26.0 2.9 32 33-65 18-49 (317)
54 PRK14955 DNA polymerase III su 23.5 3.3E+02 0.0072 22.5 6.4 54 16-73 242-306 (397)
55 PF02607 B12-binding_2: B12 bi 23.4 1.9E+02 0.0042 17.8 4.4 55 22-76 2-56 (79)
56 COG0142 IspA Geranylgeranyl py 22.6 78 0.0017 25.8 2.5 48 5-52 266-318 (322)
57 PLN02890 geranyl diphosphate s 22.4 1.8E+02 0.0038 25.3 4.7 62 10-72 347-420 (422)
58 PF08930 DUF1912: Domain of un 22.0 31 0.00068 24.4 0.1 21 12-32 25-45 (84)
59 COG2880 Uncharacterized protei 21.7 2.1E+02 0.0046 19.4 4.1 43 7-50 4-65 (67)
60 PRK05820 deoA thymidine phosph 21.3 97 0.0021 27.2 2.9 32 33-65 15-46 (440)
61 COG0547 TrpD Anthranilate phos 21.2 1.8E+02 0.004 24.6 4.5 32 33-65 15-46 (338)
62 PF14779 BBS1: Ciliary BBSome 21.1 2.9E+02 0.0063 22.7 5.5 48 4-55 129-176 (257)
63 cd07320 Extradiol_Dioxygenase_ 21.1 81 0.0018 23.9 2.2 30 13-42 163-209 (260)
64 TIGR02644 Y_phosphoryl pyrimid 21.0 1E+02 0.0022 26.8 3.0 32 33-65 12-43 (405)
65 cd05152 MPH2' Macrolide 2'-Pho 20.9 1.5E+02 0.0034 23.2 3.8 38 7-45 235-274 (276)
66 cd08332 CARD_CASP2 Caspase act 20.8 64 0.0014 21.9 1.4 22 5-26 21-42 (90)
67 PRK14971 DNA polymerase III su 20.8 3.6E+02 0.0078 24.3 6.4 57 14-74 229-296 (614)
68 cd08323 CARD_APAF1 Caspase act 20.5 63 0.0014 22.1 1.4 21 6-26 16-36 (86)
69 cd07981 TAF12 TATA Binding Pro 20.2 1.8E+02 0.0039 18.8 3.4 37 2-43 3-39 (72)
70 TIGR02643 T_phosphoryl thymidi 20.1 1.1E+02 0.0023 27.0 3.0 31 34-65 15-45 (437)
71 PF04051 TRAPP: Transport prot 20.0 62 0.0013 23.4 1.3 17 57-73 109-125 (152)
No 1
>KOG0117|consensus
Probab=98.35 E-value=8.1e-08 Score=83.62 Aligned_cols=50 Identities=48% Similarity=0.610 Sum_probs=41.5
Q ss_pred HHHHHHHHhhcccccccchhHHHHHHHHHHHHHhhccCCCCcccccccCCCCCCHHhhcc
Q psy1192 40 AIAVLNQFLESNLEHVSNKSAFLCGIMKTYRQKSRSGMAGVASTSAVLTLKGPDEEKIKF 99 (108)
Q Consensus 40 Al~vl~qF~eS~L~hV~NKSAFL~gVMKtyRqr~r~g~~g~~~~~~~~l~kGPde~kIK~ 99 (108)
|+++++||++|+|+||+|||||+|+.|++++|++.++..|.++ +|++|++
T Consensus 1 ~~~~~~~~kes~~s~~~~~~a~~~~~~~~~~~~~~~~~~~~~~----------~eaal~a 50 (506)
T KOG0117|consen 1 ASFVLTEFKESDLSHVQEKSAFLDGDNDTSNQREEQGVAGVQS----------EEAALKA 50 (506)
T ss_pred CchHHHHHhhhhhhhhhhhhhhccccCcchhhccccccccccc----------HHHHHHH
Confidence 5789999999999999999999999999999999765443322 6777665
No 2
>PF02885 Glycos_trans_3N: Glycosyl transferase family, helical bundle domain Prosite entry for Thymidine and pyrimidine-nucleoside phosphorylases; InterPro: IPR017459 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. The glycosyl transferase family includes anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase (2.4.2.2 from EC) catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism. This N-terminal domain is found in various family 3 glycosyl transferases, including anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism.; PDB: 2DSJ_B 2ELC_B 2BPQ_A 1ZVW_B 3QR9_B 1V8G_B 2WK5_C 2J0F_C 2WK6_B 1UOU_A ....
Probab=84.67 E-value=2.4 Score=26.93 Aligned_cols=32 Identities=22% Similarity=0.425 Sum_probs=23.4
Q ss_pred hcCChHHHHHHHHHHhhcccccccchhHHHHHH
Q psy1192 33 KEYPSEGAIAVLNQFLESNLEHVSNKSAFLCGI 65 (108)
Q Consensus 33 kef~~e~Al~vl~qF~eS~L~hV~NKSAFL~gV 65 (108)
+.++.++|..+++.+.+-+.+-+ ..+||||++
T Consensus 13 ~~Ls~~e~~~~~~~i~~g~~s~~-qiaAfL~al 44 (66)
T PF02885_consen 13 EDLSREEAKAAFDAILDGEVSDA-QIAAFLMAL 44 (66)
T ss_dssp ----HHHHHHHHHHHHTTSS-HH-HHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHcCCCCHH-HHHHHHHHH
Confidence 56778889999999998888877 689999986
No 3
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=68.54 E-value=4.9 Score=22.71 Aligned_cols=25 Identities=8% Similarity=0.094 Sum_probs=20.5
Q ss_pred HHHHHHhcCCCCCcccchHHHHHHh
Q psy1192 8 IIFLSHNFPGKLLHKDLDDRALDAL 32 (108)
Q Consensus 8 ~~l~~iy~sG~l~~~DLDeRAidaL 32 (108)
..|.++|+.|.++.++...+--..|
T Consensus 6 ~~L~~l~~~G~IseeEy~~~k~~ll 30 (31)
T PF09851_consen 6 EKLKELYDKGEISEEEYEQKKARLL 30 (31)
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHHh
Confidence 4688999999999999987765544
No 4
>PF02268 TFIIA_gamma_N: Transcription initiation factor IIA, gamma subunit, helical domain; InterPro: IPR015872 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the alpha-helical domain found at the N-terminal of the gamma subunit of transcription factor TFIIA.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=62.61 E-value=12 Score=23.79 Aligned_cols=29 Identities=28% Similarity=0.211 Sum_probs=21.8
Q ss_pred HHHHHHHHhcCCCCCcccchHHHHHHhhcCChHHHHHHHHHHhhc
Q psy1192 6 IQIIFLSHNFPGKLLHKDLDDRALDALKEYPSEGAIAVLNQFLES 50 (108)
Q Consensus 6 iq~~l~~iy~sG~l~~~DLDeRAidaLkef~~e~Al~vl~qF~eS 50 (108)
.+..|++++..|.++| +-|..||++|..|
T Consensus 15 L~dtLDeli~~~~I~p----------------~La~kVL~~FDks 43 (49)
T PF02268_consen 15 LTDTLDELIQEGKITP----------------QLAMKVLEQFDKS 43 (49)
T ss_dssp HHHHHHHHHHTTSS-H----------------HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCCH----------------HHHHHHHHHHHHH
Confidence 5677889999888876 4688888888765
No 5
>cd07372 2A5CPDO_B The beta subunit of the Class III extradiol dioxygenase, 2-amino-5-chlorophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol. 2-amino-5-chlorophenol 1,6-dioxygenase (2A5CPDO), catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol, which is an intermediate during p-chloronitrobenzene degradation. This enzyme is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. The active 2A5CPDO enzyme is probably a heterotetramer, composed of two alpha and two beta subunits. The alpha and beta subunits share significant sequence similarity and may have evolved by gene duplication. This model describes the beta subunit, which contains a putative metal binding site with two conserved histidines; these residues are equivalent to two out of three Fe(II) bindin
Probab=62.57 E-value=5.8 Score=32.25 Aligned_cols=52 Identities=15% Similarity=0.295 Sum_probs=38.3
Q ss_pred cchHHHHHHhhcCChHHHHHHHHHHhhcccccccchh-HHHHHHHHHHHHHhh
Q psy1192 23 DLDDRALDALKEYPSEGAIAVLNQFLESNLEHVSNKS-AFLCGIMKTYRQKSR 74 (108)
Q Consensus 23 DLDeRAidaLkef~~e~Al~vl~qF~eS~L~hV~NKS-AFL~gVMKtyRqr~r 74 (108)
++|.|.++.|++=+.+..+....+|.+.---.-.=++ .+++|.|.-+..+.+
T Consensus 218 ~fD~~vl~~l~~gd~~~l~~~~~~~~~~A~ge~g~~~~~~~~ga~~~~~~~~~ 270 (294)
T cd07372 218 QWDMRMIELMRQGRMKEVFRLLPQFIEEAFAEVKSGAFTWMHAAMQYPELAAE 270 (294)
T ss_pred HHHHHHHHHHHcCCHHHHHhcCHHHHHHhccccchHHHHHHHHhhcCCCcCce
Confidence 6799999999999999999999999876621111234 789999955444433
No 6
>KOG3463|consensus
Probab=62.39 E-value=10 Score=28.01 Aligned_cols=49 Identities=33% Similarity=0.320 Sum_probs=36.3
Q ss_pred hHHHHHHHHhcCCCCCcccchHHHHHHhhcCChHHHHHHHHHHhhccc----ccccchhHHHHHHHHHHH
Q psy1192 5 NIQIIFLSHNFPGKLLHKDLDDRALDALKEYPSEGAIAVLNQFLESNL----EHVSNKSAFLCGIMKTYR 70 (108)
Q Consensus 5 ~iq~~l~~iy~sG~l~~~DLDeRAidaLkef~~e~Al~vl~qF~eS~L----~hV~NKSAFL~gVMKtyR 70 (108)
..|..||++...|.|+|+ .|..||.||..|-- .+|.||--|= |=+.|||
T Consensus 15 ~L~~tLDe~v~~g~itp~----------------la~~VL~~FDKSi~~al~~~vk~kmsfk-g~L~tYr 67 (109)
T KOG3463|consen 15 ALQKTLDELVSDGVITPS----------------LAKKVLEQFDKSINEALNDKVKNKMSFK-GKLDTYR 67 (109)
T ss_pred HHHHHHHHHHHcCCCCHH----------------HHHHHHHHHHHHHHHHHHHhcccceeee-eccceee
Confidence 478999999999999874 57788888876632 3566766665 7777776
No 7
>PRK00782 hypothetical protein; Provisional
Probab=62.24 E-value=6.4 Score=31.13 Aligned_cols=36 Identities=14% Similarity=0.169 Sum_probs=30.5
Q ss_pred HhcCCCCCc-------ccchHHHHHHhhcCChHHHHHHHHHHh
Q psy1192 13 HNFPGKLLH-------KDLDDRALDALKEYPSEGAIAVLNQFL 48 (108)
Q Consensus 13 iy~sG~l~~-------~DLDeRAidaLkef~~e~Al~vl~qF~ 48 (108)
+.-||+++| .++|.++++.+.+.+.++-...+++..
T Consensus 173 iIaSsDlSH~~~~~~a~~~D~~~i~~I~~~d~~~l~~~~~~~~ 215 (267)
T PRK00782 173 VIASSDFTHYEPAERAKEKDMILIEAILDLDVDGFYDEIYRMN 215 (267)
T ss_pred EEEeCCCcCcCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHhcC
Confidence 567899999 789999999999999998877766544
No 8
>PF08044 DUF1707: Domain of unknown function (DUF1707); InterPro: IPR012551 This domain is found in a variety of actinomycetales proteins. All of the proteins containing this domain are hypothetical and probably membrane bound or associated. Currently, it is unclear to the function of this domain.
Probab=61.75 E-value=9.9 Score=24.00 Aligned_cols=34 Identities=18% Similarity=0.159 Sum_probs=28.1
Q ss_pred hhHHHHHHHHhcCCCCCcccchHHHHHHhhcCCh
Q psy1192 4 ENIQIIFLSHNFPGKLLHKDLDDRALDALKEYPS 37 (108)
Q Consensus 4 ~~iq~~l~~iy~sG~l~~~DLDeRAidaLkef~~ 37 (108)
+....+|..-|..|.|+++++|+|.-.++.--..
T Consensus 9 ~~~~~~L~~a~a~GrL~~~Ef~~R~~~a~~A~t~ 42 (53)
T PF08044_consen 9 ERAVDLLRAAFAEGRLSLDEFDERLDAAYAARTR 42 (53)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCcH
Confidence 4567789999999999999999999877765443
No 9
>PRK00188 trpD anthranilate phosphoribosyltransferase; Provisional
Probab=58.84 E-value=18 Score=29.66 Aligned_cols=44 Identities=11% Similarity=0.205 Sum_probs=35.2
Q ss_pred hHHHHHHHHhcCCCCCcccchHHHHHHhhcCChHHHHHHHHHHhhcccccccchhHHHHHH
Q psy1192 5 NIQIIFLSHNFPGKLLHKDLDDRALDALKEYPSEGAIAVLNQFLESNLEHVSNKSAFLCGI 65 (108)
Q Consensus 5 ~iq~~l~~iy~sG~l~~~DLDeRAidaLkef~~e~Al~vl~qF~eS~L~hV~NKSAFL~gV 65 (108)
+|..+|.+|+.. +.++.++|..++.++.+.+.+-+ ..+||||.+
T Consensus 2 ~~~~~i~~l~~g----------------~~Lt~~Ea~~~~~~il~g~~~~~-q~~AfL~al 45 (339)
T PRK00188 2 TMKELLEKLVEG----------------EDLSEEEAEELMDAIMSGEATPA-QIAAFLTAL 45 (339)
T ss_pred CHHHHHHHHhCC----------------CCCCHHHHHHHHHHHHcCCCCHH-HHHHHHHHH
Confidence 356667777652 67888999999999999988888 689999876
No 10
>PF05553 DUF761: Cotton fibre expressed protein; InterPro: IPR008480 This family consists of several plant proteins of unknown function. Three of the sequences from Gossypium hirsutum (Upland cotton) in this family are described as G. hirsutum fibre expressed proteins []. The remaining sequences, found in Arabidopsis thaliana, are uncharacterised.
Probab=55.12 E-value=11 Score=22.74 Aligned_cols=27 Identities=11% Similarity=0.214 Sum_probs=21.3
Q ss_pred CcccchHHHHHHhhcCChHHHHHHHHH
Q psy1192 20 LHKDLDDRALDALKEYPSEGAIAVLNQ 46 (108)
Q Consensus 20 ~~~DLDeRAidaLkef~~e~Al~vl~q 46 (108)
+.+|||.||=+|++.|...--+.-++.
T Consensus 1 ~~~evd~rAe~FI~~f~~qlrlqr~~S 27 (38)
T PF05553_consen 1 SDDEVDRRAEEFIAKFREQLRLQRQES 27 (38)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457999999999999998866655543
No 11
>PF04305 DUF455: Protein of unknown function (DUF455); InterPro: IPR007402 This is a family of uncharacterised proteins.
Probab=52.30 E-value=30 Score=27.97 Aligned_cols=75 Identities=23% Similarity=0.375 Sum_probs=57.7
Q ss_pred cchHHHHHHhhcCChHHHHHHHHHHhhcccccccchhHHHHHHHH--------HHHHHhhccCCCCcccccccCCCCC--
Q psy1192 23 DLDDRALDALKEYPSEGAIAVLNQFLESNLEHVSNKSAFLCGIMK--------TYRQKSRSGMAGVASTSAVLTLKGP-- 92 (108)
Q Consensus 23 DLDeRAidaLkef~~e~Al~vl~qF~eS~L~hV~NKSAFL~gVMK--------tyRqr~r~g~~g~~~~~~~~l~kGP-- 92 (108)
|+-.+.++-|+++....+..+|+.+-.=+..||..=..++.-+.+ +|++-++.-.. ...+||
T Consensus 166 D~~p~~~~k~~~~gD~~sa~iL~~I~~DEi~HV~~G~rWf~~~c~~~~~~p~~~f~~lv~~~~~--------~~~k~pfN 237 (253)
T PF04305_consen 166 DVTPFIIEKFRSAGDEESAAILEIILRDEIGHVAIGNRWFRYLCEQRGLDPWETFRELVRQYFR--------GKLKGPFN 237 (253)
T ss_pred CCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhccccHHHHHHHHHHHhCC--------CCCCCCCC
Confidence 677888999999999999999999999999999887776554443 58888874211 224778
Q ss_pred CHHhhcccCCCCC
Q psy1192 93 DEEKIKFGSGSDF 105 (108)
Q Consensus 93 de~kIK~~~~~~~ 105 (108)
.++-.++|...+|
T Consensus 238 ~eaR~~AGfs~~~ 250 (253)
T PF04305_consen 238 EEARLKAGFSEEE 250 (253)
T ss_pred HHHHHHcCCCHHH
Confidence 7888888876543
No 12
>CHL00171 cpcB phycocyanin beta subunit; Reviewed
Probab=49.46 E-value=29 Score=26.69 Aligned_cols=53 Identities=23% Similarity=0.408 Sum_probs=43.8
Q ss_pred ccchHHHHHHhhc------CChHHHHHHHHHHhhcccccccchhH-------HHHHHHHHHHHHhh
Q psy1192 22 KDLDDRALDALKE------YPSEGAIAVLNQFLESNLEHVSNKSA-------FLCGIMKTYRQKSR 74 (108)
Q Consensus 22 ~DLDeRAidaLke------f~~e~Al~vl~qF~eS~L~hV~NKSA-------FL~gVMKtyRqr~r 74 (108)
+=||||.+.-||| +|.......|+..++.-+..+.|++. =||+-+-+|=|+.-
T Consensus 103 ~~L~e~~L~GlrE~Y~~lgvP~~~~i~al~~mk~~al~~~~~~~~~~~g~c~~l~~e~~~yFd~~~ 168 (172)
T CHL00171 103 SVLDDRCLNGLRETYQALGVPGSSVAVAVQKMKEAAVSLANDSSGVTVGDCSALISELASYFDRAA 168 (172)
T ss_pred hHHhHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHHHHHhcCccCCCCcchHHHHHHHHhHHHHHH
Confidence 3489999988887 67777888999999999999988776 67888888888754
No 13
>PF10987 DUF2806: Protein of unknown function (DUF2806); InterPro: IPR021254 This bacterial family of proteins has no known function.
Probab=48.82 E-value=23 Score=27.65 Aligned_cols=51 Identities=16% Similarity=0.075 Sum_probs=43.2
Q ss_pred CchhhHHHHHHHHhcCCCCCcccchHHHHHHhhcCChHHHHHHHHHHhhccc
Q psy1192 1 IHLENIQIIFLSHNFPGKLLHKDLDDRALDALKEYPSEGAIAVLNQFLESNL 52 (108)
Q Consensus 1 ~~~~~iq~~l~~iy~sG~l~~~DLDeRAidaLkef~~e~Al~vl~qF~eS~L 52 (108)
||.+++|.+--+|...-...|...==|+++.|+.++-++|. +++++..--.
T Consensus 54 isn~~mQ~LWakILa~Ei~~PGs~SlrtL~~Lk~mt~~eA~-lf~k~~~~~~ 104 (219)
T PF10987_consen 54 ISNEEMQELWAKILAGEIKNPGSFSLRTLQTLKQMTKKEAQ-LFQKACSFAC 104 (219)
T ss_pred cCcHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHhCCHHHHH-HHHHHHHHhe
Confidence 78999999999999888888899999999999999999985 5666654333
No 14
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=44.71 E-value=47 Score=20.34 Aligned_cols=41 Identities=17% Similarity=0.062 Sum_probs=31.0
Q ss_pred HHHHHhcCCCCCcccc---hHHHHHHhhcCChHHHHHHHHHHhh
Q psy1192 9 IFLSHNFPGKLLHKDL---DDRALDALKEYPSEGAIAVLNQFLE 49 (108)
Q Consensus 9 ~l~~iy~sG~l~~~DL---DeRAidaLkef~~e~Al~vl~qF~e 49 (108)
+...|++.|.-+.+|| |...+..+.-+.+..|..++.++++
T Consensus 17 ~a~~L~~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~~ 60 (60)
T PF14520_consen 17 RAEKLYEAGIKTLEDLANADPEELAEIPGIGEKTAEKIIEAARE 60 (60)
T ss_dssp HHHHHHHTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHHHH
T ss_pred HHHHHHhcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHHhC
Confidence 4567888888877765 5556777788889999888888764
No 15
>PF12767 SAGA-Tad1: Transcriptional regulator of RNA polII, SAGA, subunit; InterPro: IPR024738 The yeast Spt-Ada-Gcn5-Acetyl (SAGA) transferase complex is a multifunctional coactivator involved in multiple cellular processes [], including regulation of transcription by RNA polymerase II [, ]. It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA []. This entry represents Ada1 (known as Tada1 in higher eukaryotes), one of the subunits that constitute the SAGA core. It also functions as a component of the SALSA and SLIK complexes. ; GO: 0070461 SAGA-type complex
Probab=43.10 E-value=20 Score=28.06 Aligned_cols=40 Identities=20% Similarity=0.290 Sum_probs=31.7
Q ss_pred HHhcCCCCCcccchHHHHHHhhcCChHHHHHHHHHHhhcccccccchhHHHHHHHHHH
Q psy1192 12 SHNFPGKLLHKDLDDRALDALKEYPSEGAIAVLNQFLESNLEHVSNKSAFLCGIMKTY 69 (108)
Q Consensus 12 ~iy~sG~l~~~DLDeRAidaLkef~~e~Al~vl~qF~eS~L~hV~NKSAFL~gVMKty 69 (108)
..|-+|+++.+|+|..|..+| + .+. |+=..+|+.+|+.+=
T Consensus 35 ~~fl~~klsk~Efd~~~~~~L---~-------------~~~--~~LHN~li~sIl~na 74 (252)
T PF12767_consen 35 KRFLSGKLSKEEFDKECRRIL---G-------------REN--VHLHNQLILSILKNA 74 (252)
T ss_pred HHHHHhccCHHHHHHHHHHHh---C-------------hhH--HHHHHHHHHHHHHHH
Confidence 668899999999999999999 1 122 444567999999887
No 16
>PF15107 FAM216B: FAM216B protein family
Probab=42.17 E-value=17 Score=26.95 Aligned_cols=20 Identities=25% Similarity=0.516 Sum_probs=14.3
Q ss_pred ccccccchhHHHHHHHHHHHHH
Q psy1192 51 NLEHVSNKSAFLCGIMKTYRQK 72 (108)
Q Consensus 51 ~L~hV~NKSAFL~gVMKtyRqr 72 (108)
||.-- -..|||||||-|--+
T Consensus 34 DLT~G--QkrYl~SI~kIYns~ 53 (113)
T PF15107_consen 34 DLTQG--QKRYLYSIAKIYNSR 53 (113)
T ss_pred hhhhh--hhHHHHHHHHHhCcH
Confidence 55544 357999999998543
No 17
>PF08564 CDC37_C: Cdc37 C terminal domain; InterPro: IPR013873 Cdc37 is a protein required for the activity of numerous eukaryotic protein kinases. This entry corresponds to the C-terminal domain whose function is unclear. It is found C-terminal to the Hsp90 chaperone (heat shock protein 90) binding domain IPR013874 from INTERPRO and the N-terminal kinase binding domain of Cdc37 IPR013855 from INTERPRO []. ; PDB: 1US7_B.
Probab=41.74 E-value=27 Score=24.91 Aligned_cols=36 Identities=25% Similarity=0.244 Sum_probs=23.3
Q ss_pred cchHHHHHHhhcCChHHHHHHHHHHhhcccccccchh
Q psy1192 23 DLDDRALDALKEYPSEGAIAVLNQFLESNLEHVSNKS 59 (108)
Q Consensus 23 DLDeRAidaLkef~~e~Al~vl~qF~eS~L~hV~NKS 59 (108)
||| ..-..|..+|++.|..+++.|.+|.|-++...-
T Consensus 36 ~ld-~vnkVl~~M~veeAE~~v~~~~esGi~~~~~~~ 71 (99)
T PF08564_consen 36 DLD-EVNKVLGKMPVEEAEYHVERCIESGIWSPEAGI 71 (99)
T ss_dssp -----HHHHHT--SSSHHHHHHHHHHHTTSS--TT--
T ss_pred CHH-HHHHHHHhCCHHHHHHHHHHHHhCCccccccCc
Confidence 443 355788899999999999999999999986543
No 18
>smart00567 EZ_HEAT E-Z type HEAT repeats. Present in subunits of cyanobacterial phycocyanin lyase, and other proteins. Probable scaffolding role.
Probab=40.65 E-value=43 Score=17.61 Aligned_cols=25 Identities=32% Similarity=0.276 Sum_probs=20.1
Q ss_pred HHHHHHhhcCChHHHHHHHHHHhhc
Q psy1192 26 DRALDALKEYPSEGAIAVLNQFLES 50 (108)
Q Consensus 26 eRAidaLkef~~e~Al~vl~qF~eS 50 (108)
-+|..+|..+..+.|...|.+..+.
T Consensus 5 ~~aa~aLg~~~~~~a~~~L~~~l~d 29 (30)
T smart00567 5 HEAAFALGQLGDEEAVPALIKALED 29 (30)
T ss_pred HHHHHHHHHcCCHhHHHHHHHHhcC
Confidence 3688889999888899988887653
No 19
>cd08330 CARD_ASC_NALP1 Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins. Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They se
Probab=39.21 E-value=20 Score=23.98 Aligned_cols=64 Identities=11% Similarity=0.015 Sum_probs=39.9
Q ss_pred hhhHHHHHHHHhcCCCCCcccchHHHHHHhhcCChHHHHHHHHHHhhcccccccchhHHHHHHHHHHHHH
Q psy1192 3 LENIQIIFLSHNFPGKLLHKDLDDRALDALKEYPSEGAIAVLNQFLESNLEHVSNKSAFLCGIMKTYRQK 72 (108)
Q Consensus 3 ~~~iq~~l~~iy~sG~l~~~DLDeRAidaLkef~~e~Al~vl~qF~eS~L~hV~NKSAFL~gVMKtyRqr 72 (108)
..++.-+|+.|++.|.++.++.|+ |.+ +.=+-+.|-..+.= ..-.|-..+..|.-.+..++..-
T Consensus 14 v~~v~~ilD~L~~~~Vit~e~~~~--I~a-~~T~~~kar~Lld~---l~~kG~~A~~~F~~~L~e~~p~L 77 (82)
T cd08330 14 VTNVDPILDKLHGKKVITQEQYSE--VRA-EKTNQEKMRKLFSF---VRSWGASCKDIFYQILREEEPYL 77 (82)
T ss_pred HhhHHHHHHHHHHCCCCCHHHHHH--HHc-CCCcHHHHHHHHHH---HHccCHHHHHHHHHHHHHhChHH
Confidence 347888999999999999887664 222 22334444443332 22256677777777776565543
No 20
>TIGR00134 gatE_arch glutamyl-tRNA(Gln) amidotransferase, subunit E. The Archaea have an Asp-tRNA(Asn) amidotransferase instead of an Asp--tRNA ligase, but the genes have not been identified. It is likely that this protein replaces gatB in Asp-tRNA(Asn) amidotransferase but that both enzymes share gatA.
Probab=39.02 E-value=50 Score=30.17 Aligned_cols=64 Identities=23% Similarity=0.265 Sum_probs=37.9
Q ss_pred chhhHHHHHHHHhcCCCCCcccchHHHHHH--hhcCChHHHHHHHHHHhhcccccccch----hHHHHH-HHHHHH
Q psy1192 2 HLENIQIIFLSHNFPGKLLHKDLDDRALDA--LKEYPSEGAIAVLNQFLESNLEHVSNK----SAFLCG-IMKTYR 70 (108)
Q Consensus 2 ~~~~iq~~l~~iy~sG~l~~~DLDeRAida--Lkef~~e~Al~vl~qF~eS~L~hV~NK----SAFL~g-VMKtyR 70 (108)
-.+.+..+|..+++++. ++++ .++- |+.++.++-..++++....|-.-|... -.|||| |||.++
T Consensus 531 s~~~~k~vl~~~~~~~~-~~~~----iiee~gL~qlsdeel~~iV~evI~en~~~V~~~~~k~~G~lmGqVMk~tk 601 (620)
T TIGR00134 531 AKEGLREILKCMCDEPL-AAED----AARKLKLKLLAEEEIESIIQEIIEENLDMISERGEGAMGPLMGQAMGRLR 601 (620)
T ss_pred cHHHHHHHHHHHHhCCC-CHHH----HHHHcCCcCCCHHHHHHHHHHHHHhChHhhhccCHhHHHHHHHHHHHHhc
Confidence 34567778888888775 3322 3322 466677777788888877764444332 246665 455543
No 21
>cd08329 CARD_BIRC2_BIRC3 Caspase activation and recruitment domain found in Baculoviral IAP repeat-containing proteins, BIRC2 (c-IAP1) and BIRC3 (c-IAP2). Caspase activation and recruitment domain (CARD) similar to those found in Baculoviral IAP repeat (BIR)-containing protein 2 (BIRC2) or cellular Inhibitor of Apoptosis Protein 1 (c-IAP1), and BIRC3 (or c-IAP2). IAPs are anti-apoptotic proteins that contain at least one BIR domain. Most IAPs also contain a C-terminal RING domain. In addition, both BIRC2 and BIRC3 contain a CARD. BIRC2 and BIRC3, through their binding with TRAF (TNF receptor-associated factor) 2, are recruited to TNFR-1/2 signaling complexes, where they regulate caspase-8 activity. They also play important roles in pro-survival NF-kB signaling pathways. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interac
Probab=38.86 E-value=19 Score=24.83 Aligned_cols=62 Identities=13% Similarity=0.061 Sum_probs=38.0
Q ss_pred hhHHHHHHHHhcCCCCCcccchHHHHHHhhcCChHHHHHHHHHHhhcccccccchhHHHHHHHHHHHH
Q psy1192 4 ENIQIIFLSHNFPGKLLHKDLDDRALDALKEYPSEGAIAVLNQFLESNLEHVSNKSAFLCGIMKTYRQ 71 (108)
Q Consensus 4 ~~iq~~l~~iy~sG~l~~~DLDeRAidaLkef~~e~Al~vl~qF~eS~L~hV~NKSAFL~gVMKtyRq 71 (108)
.++.-+|+.||+.|.++.++.|+= .+ +..+.+.|-..|.-.. -.|-+-.+.|+-.+..++..
T Consensus 23 ~~v~~ilD~Ll~~~Vlt~ee~e~I--~~-~~t~~~qAr~Lld~l~---~KG~~A~~~F~~~L~e~~~~ 84 (94)
T cd08329 23 TSVLPILDSLLSANVITEQEYDVI--KQ-KTQTPLQARELIDTVL---VKGNAAAEVFRNCLKKNDPV 84 (94)
T ss_pred hhhHHHHHHHHHcCCCCHHHHHHH--Hc-CCChHHHHHHHHHHHH---hhhHHHHHHHHHHHHhcCHh
Confidence 356779999999999999988642 22 3334566666655443 23444455566555444433
No 22
>PF04120 Iron_permease: Low affinity iron permease ; InterPro: IPR007251 Although originally identified as a low-affinity iron(II) permease [, ], Fet4 has since been shown to import several other transition metal ions, including copper [, ] and zinc []. Copper, cobalt, and cadmium inhibit Fet4 [, ]. Fet4 is an integral protein of the plasma membrane [, ]. FET4 is not essential, not even in fet3 fet4 double mutants []. Over expression of FET4 improves growth under alkaline conditions []. Transcription of FET4 is induced by Aft1 in response to low levels of iron [, , ] or by Zap1 in response to low zinc [, ], but not in response to low copper []. When the high-affinity iron permease component Fet3 is deleted, FET4 is induced by the addition of copper, zinc, cobalt, or manganese []. It is also induced under anaerobic conditions [, , ] and repressed by Rox1 in aerobic conditions [, ]. Rox1 attenuates the activation of FET4 by Aft1 or Zap1 []. ; GO: 0055085 transmembrane transport
Probab=37.56 E-value=32 Score=25.63 Aligned_cols=40 Identities=13% Similarity=0.033 Sum_probs=30.6
Q ss_pred hhhHHHHHHHHhcC------CCCCcccchHHHHHHhhcCChHHHHH
Q psy1192 3 LENIQIIFLSHNFP------GKLLHKDLDDRALDALKEYPSEGAIA 42 (108)
Q Consensus 3 ~~~iq~~l~~iy~s------G~l~~~DLDeRAidaLkef~~e~Al~ 42 (108)
...+|..|++|... ..+.-||+||.-++.++..=++.|..
T Consensus 68 ~~al~~KLdeLi~~~~~a~n~li~iE~l~~~el~~~~~~~~~~~~~ 113 (132)
T PF04120_consen 68 TKALQAKLDELIRAVKEARNELIDIEDLTEEELEEIRKRYERLAEQ 113 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCcccCCHHHHHHHHHHHHHHHHH
Confidence 45788999999876 56888899999888887765555443
No 23
>CHL00172 cpeB phycoerythrin beta subunit; Provisional
Probab=37.12 E-value=60 Score=25.39 Aligned_cols=53 Identities=23% Similarity=0.401 Sum_probs=43.0
Q ss_pred ccchHHHHHHhhc------CChHHHHHHHHHHhhcccccccchhH------------HHHHHHHHHHHHhh
Q psy1192 22 KDLDDRALDALKE------YPSEGAIAVLNQFLESNLEHVSNKSA------------FLCGIMKTYRQKSR 74 (108)
Q Consensus 22 ~DLDeRAidaLke------f~~e~Al~vl~qF~eS~L~hV~NKSA------------FL~gVMKtyRqr~r 74 (108)
+=||||++.=||| +|.......++..|+.-+.+|+|... -||+-+-+|=|+.-
T Consensus 103 ~~lde~~L~GlrE~Y~sLgVP~~~~~~~~~~mk~aa~~~~~~~~~~~~~~~~~gdc~~l~sei~~yFD~~~ 173 (177)
T CHL00172 103 SVLEDRCLNGLKETYIALGVPANSSARAVSIMKASAVAFINNTASQRKMSTAQGDCSALASEVASYFDRVT 173 (177)
T ss_pred cchhHHHHHHHHHHHHHHCCCchHHHHHHHHHHHHHHHHhcCCCcccccCCCcccHHHHHHHHHhHHHHHH
Confidence 4489999999997 67777888899999999999988666 67777788877754
No 24
>cd08324 CARD_NOD1_CARD4 Caspase activation and recruitment domain similar to that found in NOD1. Caspase activation and recruitment domain (CARD) found in human NOD1 (CARD4) and similar proteins. NOD1 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD1, as well as NOD2, the N-terminal effector domain is a CARD. Nod1-CARD has been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form hom
Probab=36.56 E-value=21 Score=25.27 Aligned_cols=25 Identities=16% Similarity=0.081 Sum_probs=21.7
Q ss_pred chhhHHHHHHHHhcCCCCCcccchH
Q psy1192 2 HLENIQIIFLSHNFPGKLLHKDLDD 26 (108)
Q Consensus 2 ~~~~iq~~l~~iy~sG~l~~~DLDe 26 (108)
|.-|+|=+||.||+.|.++.||-|.
T Consensus 13 rI~~v~plLD~Ll~n~~it~E~y~~ 37 (85)
T cd08324 13 HIRNTQCLVDNLLKNDYFSTEDAEI 37 (85)
T ss_pred HHHhhHHHHHHHhccCCccHHHHHH
Confidence 3468899999999999999999773
No 25
>PF11864 DUF3384: Domain of unknown function (DUF3384); InterPro: IPR024584 This entry represents the N-terminal domain of tuberin which is functionally uncharacterised.
Probab=36.29 E-value=1.4e+02 Score=25.40 Aligned_cols=64 Identities=17% Similarity=0.073 Sum_probs=47.6
Q ss_pred hHHHHHHHHhcCCCCC--cccchHHHHHHhhcCChHHHHHHHHHHhhcccccccch--hHHHHHHHHHHH
Q psy1192 5 NIQIIFLSHNFPGKLL--HKDLDDRALDALKEYPSEGAIAVLNQFLESNLEHVSNK--SAFLCGIMKTYR 70 (108)
Q Consensus 5 ~iq~~l~~iy~sG~l~--~~DLDeRAidaLkef~~e~Al~vl~qF~eS~L~hV~NK--SAFL~gVMKtyR 70 (108)
.|-..++++|+++.+. .+++=+=-.+.....|+..|+.+| |.+..+-+-.|= -..+.-+|.+|=
T Consensus 378 ~l~~~ie~L~~~~~~~g~~~~~~~f~~~~~~~lp~s~~~~vl--~~~~~~~~Ps~~~W~~n~~~ll~~F~ 445 (464)
T PF11864_consen 378 SLLSSIESLYEQHDFNGPKDKLFNFFERVHSYLPDSSALLVL--FYEERSCSPSNPDWLDNLQKLLDRFY 445 (464)
T ss_pred HHHHHHHHHHhCCCcCccHHHHHHHHHHHhccCCHHHHHHHH--HHHhcccCCCChHHHHHHHHHHHHHh
Confidence 3455678999998776 555555566666788999999999 888888777665 455667777776
No 26
>PF08269 Cache_2: Cache domain; InterPro: IPR013163 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins, including the animal dihydropyridine-sensitive voltage-gated Ca2+ channel; alpha-2delta subunit, and various bacterial chemotaxis receptors. The name Cache comes from CAlcium channels and CHEmotaxis receptors. This domain consists of an N-terminal part with three predicted strands and an alpha-helix, and a C-terminal part with a strand dyad followed by a relatively unstructured region. The N-terminal portion of the (unpermuted) Cache domain contains three predicted strands that could form a sheet analogous to that present in the core of the PAS domain structure. Cache domains are particularly widespread in bacteria, with Vibrio cholerae. The animal calcium channel alpha-2delta subunits might have acquired a part of their extracellular domains from a bacterial source []. The Cache domain appears to have arisen from the GAF-PAS fold despite their divergent functions []. This entry is composed of the type 2 Cache domain.; PDB: 2QHK_A 4EXO_A.
Probab=35.34 E-value=24 Score=22.96 Aligned_cols=30 Identities=20% Similarity=0.308 Sum_probs=16.7
Q ss_pred HHHHHHhcCCCCCcccchHHHHHHhhcCCh
Q psy1192 8 IIFLSHNFPGKLLHKDLDDRALDALKEYPS 37 (108)
Q Consensus 8 ~~l~~iy~sG~l~~~DLDeRAidaLkef~~ 37 (108)
..+.+.++.|.++.++--++|+++|+.+..
T Consensus 24 ~~~~~~~~~g~ls~eea~~~a~~~l~~~r~ 53 (95)
T PF08269_consen 24 ESYYAQAQAGKLSEEEAQQQAREALRALRY 53 (95)
T ss_dssp HHHHHC-STT-----TTHHHHHHHHHH--S
T ss_pred HHHHHHHhcCCccHHHHHHHHHHHHhcccc
Confidence 344566778999999999999999965543
No 27
>PRK14965 DNA polymerase III subunits gamma and tau; Provisional
Probab=34.76 E-value=1.4e+02 Score=26.36 Aligned_cols=62 Identities=10% Similarity=0.039 Sum_probs=44.3
Q ss_pred HHHHH--hcCCCCCcccchH-----------HHHHHhhcCChHHHHHHHHHHhhcccccccchhHHHHHHHHHHHHHhh
Q psy1192 9 IFLSH--NFPGKLLHKDLDD-----------RALDALKEYPSEGAIAVLNQFLESNLEHVSNKSAFLCGIMKTYRQKSR 74 (108)
Q Consensus 9 ~l~~i--y~sG~l~~~DLDe-----------RAidaLkef~~e~Al~vl~qF~eS~L~hV~NKSAFL~gVMKtyRqr~r 74 (108)
.|+++ |..+.++.+|+++ ..++++..-+...|+.+++++.+. |. +=..||-.+++.||+-..
T Consensus 220 ~Ldqliay~g~~It~edV~~llG~~~~~~l~~ll~al~~~d~~~al~~l~~l~~~---G~-~~~~~l~~Ll~~~RdLl~ 294 (576)
T PRK14965 220 TLDQVLAFCGDAVGDDDVAELLGVVDRRLLLDISAAVFGRDTRALLEIVERVDEF---GY-NMRQFCQELIDHLRNLVV 294 (576)
T ss_pred HHHHHHHhccCCCCHHHHHHHhCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CC-CHHHHHHHHHHHHHHHHH
Confidence 34444 5556777777654 456677788899999999888753 33 245789999999999854
No 28
>PRK09071 hypothetical protein; Validated
Probab=34.43 E-value=43 Score=27.75 Aligned_cols=32 Identities=22% Similarity=0.309 Sum_probs=27.6
Q ss_pred hcCChHHHHHHHHHHhhcccccccchhHHHHHH
Q psy1192 33 KEYPSEGAIAVLNQFLESNLEHVSNKSAFLCGI 65 (108)
Q Consensus 33 kef~~e~Al~vl~qF~eS~L~hV~NKSAFL~gV 65 (108)
+.++.++|..+++++.+-+.+-+ ..+||||++
T Consensus 19 ~~Lt~eEa~~~~~~il~g~~~~~-q~aAfL~al 50 (323)
T PRK09071 19 RSLTREEARQAMGMILDGEVEDD-QLGAFLMLL 50 (323)
T ss_pred CCCCHHHHHHHHHHHHcCCCCHH-HHHHHHHHH
Confidence 36778999999999999998888 689999875
No 29
>cd07370 HPCD The Class III extradiol dioxygenase, homoprotocatechuate 2,3-dioxygenase, catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate. 3,4-dihydroxyphenylacetate (homoprotocatechuate) 2,3-dioxygenase (HPCD) catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate (hpca), a central intermediate in the bacterial degradation of aromatic compounds. The enzyme incorporates both atoms of molecular oxygen into hpca, resulting in aromatic ring-opening to yield alpha-hydroxy-delta-carboxymethyl cis-muconic semialdehyde. HPCD is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon.
Probab=34.29 E-value=33 Score=27.13 Aligned_cols=35 Identities=26% Similarity=0.338 Sum_probs=27.5
Q ss_pred HhcCCCCCcc----------------------cchHHHHHHhhcCChHHHHHHHHHH
Q psy1192 13 HNFPGKLLHK----------------------DLDDRALDALKEYPSEGAIAVLNQF 47 (108)
Q Consensus 13 iy~sG~l~~~----------------------DLDeRAidaLkef~~e~Al~vl~qF 47 (108)
|+-||.++|- +.|++++++|++.+.+..+....++
T Consensus 174 iIaSG~lsH~l~~~~~~~~~~~~~~~~~p~~~~fD~~~~~~i~~gD~~~L~~~~~~~ 230 (280)
T cd07370 174 LLASGSLSHRFWPNRELEAHEDPFTISSPFNRQVDLRVLELWKEGRHAEFLDMLPDY 230 (280)
T ss_pred EEEeccccccCccCCCccccccccccCChhHHHHHHHHHHHHHcCCHHHHHHhCHHH
Confidence 6678888883 7999999999999988765554433
No 30
>PRK07394 hypothetical protein; Provisional
Probab=33.42 E-value=65 Score=26.81 Aligned_cols=32 Identities=25% Similarity=0.258 Sum_probs=27.1
Q ss_pred hcCChHHHHHHHHHHhhcccccccchhHHHHHH
Q psy1192 33 KEYPSEGAIAVLNQFLESNLEHVSNKSAFLCGI 65 (108)
Q Consensus 33 kef~~e~Al~vl~qF~eS~L~hV~NKSAFL~gV 65 (108)
+.++.++|..++.++.+-+.+-+ ...|||+++
T Consensus 20 ~~Lt~eea~~~~~~il~g~~~~~-q~aAfL~al 51 (342)
T PRK07394 20 KDLTREEAADALKLMLLGEATPA-QIGAFLIAH 51 (342)
T ss_pred CCcCHHHHHHHHHHHHcCCCCHH-HHHHHHHHH
Confidence 45678999999999999888887 788999875
No 31
>smart00845 GatB_Yqey GatB domain. This domain is found in GatB and proteins related to bacterial Yqey. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB which transamidates Glu-tRNA to Gln-tRNA. The function of this domain is uncertain. It does however suggest that Yqey and its relatives have a role in tRNA metabolism.
Probab=32.35 E-value=1.2e+02 Score=21.77 Aligned_cols=13 Identities=0% Similarity=-0.240 Sum_probs=7.1
Q ss_pred hhHHHHHHHHhcC
Q psy1192 4 ENIQIIFLSHNFP 16 (108)
Q Consensus 4 ~~iq~~l~~iy~s 16 (108)
..++.+|..++++
T Consensus 59 ~~ak~vl~~~~~~ 71 (147)
T smart00845 59 KIAKEVLEELLES 71 (147)
T ss_pred HHHHHHHHHHHHc
Confidence 4455556655554
No 32
>TIGR01245 trpD anthranilate phosphoribosyltransferase. In many widely different species, including E. coli, Thermotoga maritima, and Archaeoglobus fulgidus, this enzymatic domain (anthranilate phosphoribosyltransferase) is found C-terminal to glutamine amidotransferase; the fusion protein is designated anthranilate synthase component II (EC 4.1.3.27)
Probab=31.86 E-value=49 Score=27.07 Aligned_cols=32 Identities=13% Similarity=0.302 Sum_probs=27.8
Q ss_pred hcCChHHHHHHHHHHhhcccccccchhHHHHHH
Q psy1192 33 KEYPSEGAIAVLNQFLESNLEHVSNKSAFLCGI 65 (108)
Q Consensus 33 kef~~e~Al~vl~qF~eS~L~hV~NKSAFL~gV 65 (108)
+.++.++|..++..+.+-+..-+ ...||||++
T Consensus 8 ~~Lt~eEa~~~~~~il~g~~~~~-q~~AfL~al 39 (330)
T TIGR01245 8 KDLSRDEAEQLMKEIMSGEASPA-QIAAILAAL 39 (330)
T ss_pred CCcCHHHHHHHHHHHHcCCCCHH-HHHHHHHHH
Confidence 57888999999999999888877 789999977
No 33
>PRK06078 pyrimidine-nucleoside phosphorylase; Reviewed
Probab=31.25 E-value=59 Score=28.48 Aligned_cols=31 Identities=16% Similarity=0.221 Sum_probs=27.2
Q ss_pred cCChHHHHHHHHHHhhcccccccchhHHHHHH
Q psy1192 34 EYPSEGAIAVLNQFLESNLEHVSNKSAFLCGI 65 (108)
Q Consensus 34 ef~~e~Al~vl~qF~eS~L~hV~NKSAFL~gV 65 (108)
+++.+++.++++.+.+-++.-. ..+||||++
T Consensus 15 ~Lt~eE~~~~~~~i~~g~~~d~-qiaAfL~Al 45 (434)
T PRK06078 15 ELTTEEINFFIEGYTNGTIPDY-QMSALAMAI 45 (434)
T ss_pred CCCHHHHHHHHHHHHcCCCCHH-HHHHHHHHH
Confidence 5788889999999998888877 789999998
No 34
>PRK13363 protocatechuate 4,5-dioxygenase subunit beta; Provisional
Probab=30.40 E-value=34 Score=28.68 Aligned_cols=37 Identities=22% Similarity=0.231 Sum_probs=29.9
Q ss_pred HHhcCCCCCcc----cchHHHHHHhhcCChHHHHHHHHHHh
Q psy1192 12 SHNFPGKLLHK----DLDDRALDALKEYPSEGAIAVLNQFL 48 (108)
Q Consensus 12 ~iy~sG~l~~~----DLDeRAidaLkef~~e~Al~vl~qF~ 48 (108)
-|+-||.++|- ++|.+++++|.+.+.+..+..-.++.
T Consensus 243 lIIaSGdLSH~l~~~efD~~~l~~l~~~D~~~L~~~~~~~~ 283 (335)
T PRK13363 243 AVIASGGLSHFVIDEELDRLIIDAIRAKDFAALASLDEAIL 283 (335)
T ss_pred EEEEeCccccCCcHHHHHHHHHHHHHcCCHHHHHccCHHHH
Confidence 36789999998 99999999999999887666554444
No 35
>PRK06647 DNA polymerase III subunits gamma and tau; Validated
Probab=29.34 E-value=2e+02 Score=25.58 Aligned_cols=57 Identities=12% Similarity=0.184 Sum_probs=43.8
Q ss_pred hcCCCCCcccchH-----------HHHHHhhcCChHHHHHHHHHHhhcccccccchhHHHHHHHHHHHHHhh
Q psy1192 14 NFPGKLLHKDLDD-----------RALDALKEYPSEGAIAVLNQFLESNLEHVSNKSAFLCGIMKTYRQKSR 74 (108)
Q Consensus 14 y~sG~l~~~DLDe-----------RAidaLkef~~e~Al~vl~qF~eS~L~hV~NKSAFL~gVMKtyRqr~r 74 (108)
|..|.++.+++.+ ..++++.+=+.+.|+.++..+..+. . +-.++|-.+++-||+-..
T Consensus 227 ~~~~~It~e~V~~llg~~~~~~if~LidaI~~~D~~~al~~l~~Ll~~G---~-d~~~iL~~Ll~~fRdLL~ 294 (563)
T PRK06647 227 FSDSDITLEQIRSKMGLTGDEFLEKLASSILNEDAKELLCVLDSVFLSG---V-SVEQFLLDCIEFFRELLF 294 (563)
T ss_pred hcCCCCCHHHHHHHhCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC---C-CHHHHHHHHHHHHHHHHH
Confidence 5567788777766 4567777888999999998887643 3 345899999999999864
No 36
>cd07951 ED_3B_N_AMMECR1 The N-terminal domain, an extradiol dioxygenase class III subunit B-like domain, of unknown proteins containing a C-terminal AMMECR1 domain. This subfamily is composed of uncharacterized proteins containing an N-terminal domain with similarity to the catalytic B subunit of class III extradiol dioxygenases and a C-terminal AMMECR1-like domain. This model represents the N-terminal domain. Class III extradiol dioxygenases use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon, however, proteins in this subfamily do not contain a potential metal binding site and may not exhibit class III extradiol dioxygenase-like activity. The AMMECR1 protein was proposed to be a regulatory factor that is potentially involved in the development of AMME contiguous gene deletion syndrome.
Probab=28.94 E-value=43 Score=25.67 Aligned_cols=35 Identities=20% Similarity=0.284 Sum_probs=27.4
Q ss_pred HhcCCCCCcc--------------cchHHHHHHhhcCChHHHHHHHHHH
Q psy1192 13 HNFPGKLLHK--------------DLDDRALDALKEYPSEGAIAVLNQF 47 (108)
Q Consensus 13 iy~sG~l~~~--------------DLDeRAidaLkef~~e~Al~vl~qF 47 (108)
|.-||.++|. +.|.+++++|.+.+.+..++...++
T Consensus 164 ii~SgdlsH~l~~~~p~~~~~~a~~~D~~~~~~l~~~D~~~L~~~~~~~ 212 (256)
T cd07951 164 LIASGDLSHRLTEDAPGGYDPRGPEFDAAIAEALAKGDVDALLALDPEL 212 (256)
T ss_pred EEEecccccccCCCCCCCCCcchHHHHHHHHHHHHcCCHHHHHhcCHHH
Confidence 5567888883 8999999999999998666655444
No 37
>cd01671 CARD Caspase activation and recruitment domain: a protein-protein interaction domain. Caspase activation and recruitment domains (CARDs) are death domains (DDs) found associated with caspases. Caspases are aspartate-specific cysteine proteases with functions in apoptosis, immune signaling, inflammation, and host-defense mechanisms. In addition to caspases, proteins containing CARDs include adaptor proteins such as RAIDD, CARD9, and RIG-I-like helicases, which can form mutliprotein complexes and play important roles in mediating the signals to induce immune and inflammatory responses. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=28.63 E-value=38 Score=21.19 Aligned_cols=23 Identities=9% Similarity=0.118 Sum_probs=19.8
Q ss_pred hhHHHHHHHHhcCCCCCcccchH
Q psy1192 4 ENIQIIFLSHNFPGKLLHKDLDD 26 (108)
Q Consensus 4 ~~iq~~l~~iy~sG~l~~~DLDe 26 (108)
.++..+|+.+++.|.++.+|.++
T Consensus 13 ~~~~~il~~L~~~~vlt~~e~~~ 35 (80)
T cd01671 13 LDVEDVLDHLLSDGVLTEEEYEK 35 (80)
T ss_pred ccHHHHHHHHHHcCCCCHHHHHH
Confidence 46778999999999999998865
No 38
>PF08585 DUF1767: Domain of unknown function (DUF1767); InterPro: IPR013894 This domain is present in eukaryotic proteins of unknown function, and is sometimes found to the N terminus of ubiquitin-binding and nucleic acid-binding domains. ; PDB: 3NBI_A.
Probab=28.45 E-value=46 Score=21.83 Aligned_cols=20 Identities=35% Similarity=0.316 Sum_probs=15.6
Q ss_pred ChHHHHHHHHHHhhcccccc
Q psy1192 36 PSEGAIAVLNQFLESNLEHV 55 (108)
Q Consensus 36 ~~e~Al~vl~qF~eS~L~hV 55 (108)
...-+..|++||..|||.-+
T Consensus 31 ~~~~~~~v~~~~L~sDL~~~ 50 (90)
T PF08585_consen 31 LEELAEEVYEQLLNSDLRDS 50 (90)
T ss_dssp HHHHHHHHHHHHHTS-HHHH
T ss_pred HHHHHHHHHHHHHHchhhhc
Confidence 45567899999999999876
No 39
>PF14866 Toxin_38: Potassium channel toxin
Probab=28.21 E-value=42 Score=22.15 Aligned_cols=28 Identities=21% Similarity=0.400 Sum_probs=21.0
Q ss_pred HHHHHHHHhhcccccccchhHHHHHHHHHHHHH
Q psy1192 40 AIAVLNQFLESNLEHVSNKSAFLCGIMKTYRQK 72 (108)
Q Consensus 40 Al~vl~qF~eS~L~hV~NKSAFL~gVMKtyRqr 72 (108)
|..|....++ +.+||.|.|-+|..|=..
T Consensus 7 ~k~~~~K~k~-----l~~kse~~Cp~i~~~Ce~ 34 (56)
T PF14866_consen 7 AKAVVHKVKA-----LTAKSEYGCPAIEGWCED 34 (56)
T ss_pred HHHHHHHHHh-----hhcccccCchhHHhHHHH
Confidence 4555555555 899999999999887544
No 40
>cd07359 PCA_45_Doxase_B_like Subunit B of the Class III Extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, and simlar enzymes. This subfamily of class III extradiol dioxygenases consists of a number of proteins with known enzymatic activities: Protocatechuate (PCA) 4,5-dioxygenase (LigAB), 2,3-dihydroxyphenylpropionate 1,2-dioxygenase (MhpB), 3-O-Methylgallate Dioxygenase, 2-aminophenol 1,6-dioxygenase, as well as proteins without any known enzymatic activity. These proteins play essential roles in the degradation of aromatic compounds by catalyzing the incorporation of both atoms of molecular oxygen into their preferred substrates. As members of the Class III extradiol dioxygenase family, the enzymes use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like class III enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model repres
Probab=26.80 E-value=44 Score=25.96 Aligned_cols=31 Identities=26% Similarity=0.203 Sum_probs=25.6
Q ss_pred HhcCCCCCcc-----------cchHHHHHHhhcCChHHHHHH
Q psy1192 13 HNFPGKLLHK-----------DLDDRALDALKEYPSEGAIAV 43 (108)
Q Consensus 13 iy~sG~l~~~-----------DLDeRAidaLkef~~e~Al~v 43 (108)
|+-||.++|- ++|..++++|.+-+.+..+..
T Consensus 178 iIaSGdlSH~l~~~~~g~~~~~fD~~~~~~l~~~d~~~l~~~ 219 (271)
T cd07359 178 VLGTGGLSHWPGGPRHGEINEEFDREFLDLLERGDLEALLKA 219 (271)
T ss_pred EEecCcccCCCCCccccccCHHHHHHHHHHHHhCCHHHHHhc
Confidence 6778999986 999999999999987754444
No 41
>PF01861 DUF43: Protein of unknown function DUF43; InterPro: IPR002723 This family of prokaryotic proteins have not been characterised. All the members are 350-400 amino acids long.; PDB: 2QM3_A.
Probab=26.75 E-value=15 Score=29.96 Aligned_cols=36 Identities=19% Similarity=0.430 Sum_probs=21.8
Q ss_pred hHHHHHHHHhcCCCCCcccchHHHHHHhhcCChHHHHH
Q psy1192 5 NIQIIFLSHNFPGKLLHKDLDDRALDALKEYPSEGAIA 42 (108)
Q Consensus 5 ~iq~~l~~iy~sG~l~~~DLDeRAidaLkef~~e~Al~ 42 (108)
||+.-|-.+ ...++=-|+|||.+++++++..+..+.
T Consensus 58 SlA~al~~~--~~~I~VvDiDeRll~fI~~~a~~~gl~ 93 (243)
T PF01861_consen 58 SLALALTGL--PKRITVVDIDERLLDFINRVAEEEGLP 93 (243)
T ss_dssp HHHHHHHT----SEEEEE-S-HHHHHHHHHHHHHHT--
T ss_pred HHHHHhhCC--CCeEEEEEcCHHHHHHHHHHHHHcCCc
Confidence 455554333 345777899999999999887776554
No 42
>PF00619 CARD: Caspase recruitment domain; InterPro: IPR001315 The caspase recruitment domain domain (CARD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. CARD is related in sequence and structure to the death domain (DD, see IPR000488 from INTERPRO) and the death effector domain (DED, see IPR001875 from INTERPRO), which work in similar pathways and show similar interaction properties []. The CARD domain typically associates with other CARD-containing proteins, forming either dimers or trimers. CARD domains can be found in isolation, or in combination with other domains. Domains associated with CARD include: NACHT (IPR007111 from INTERPRO) (in Nal1 and Bir1), NB-ARC (IPR002182 from INTERPRO) (in Apaf-1), pyrin/dapin domains (IPR004020 from INTERPRO) (in Nal1), leucine-rich repeats () (in Nal1), WD repeats (IPR001680 from INTERPRO) (in Apaf1), Src homology domains (IPR001452 from INTERPRO), PDZ (IPR001478 from INTERPRO), RING, kinase and DD domains []. CARD-containing proteins are involved in apoptosis through their regulation of caspases that contain CARDs in their N-terminal pro-domains, including human caspases 1, 2, 9, 11 and 12 []. CARD-containing proteins are also involved in inflammation through their regulation of NF-kappaB []. The mechanisms by which CARDs activate caspases and NF-kappaB involve the assembly of multi-protein complexes, which can facilitate dimerisation or serve as scaffolds on which proteases and kinases are assembled and activated.; GO: 0005515 protein binding, 0042981 regulation of apoptosis, 0005622 intracellular; PDB: 2NSN_A 2NZ7_B 2DBD_A 4E9M_C 2B1W_A 3YGS_P 2KN6_A 3CRD_A 1DGN_A 3KAT_A ....
Probab=26.74 E-value=43 Score=21.09 Aligned_cols=22 Identities=14% Similarity=0.193 Sum_probs=19.2
Q ss_pred hHHHHHHHHhcCCCCCcccchH
Q psy1192 5 NIQIIFLSHNFPGKLLHKDLDD 26 (108)
Q Consensus 5 ~iq~~l~~iy~sG~l~~~DLDe 26 (108)
++..+|+.|++.|.++.+|.++
T Consensus 17 ~~~~ild~L~~~~vlt~~e~e~ 38 (85)
T PF00619_consen 17 DLDDILDHLLSRGVLTEEEYEE 38 (85)
T ss_dssp HHHHHHHHHHHTTSSSHHHHHH
T ss_pred cHHHHHHHHHHCCCCCHHHHHH
Confidence 5778999999999999998764
No 43
>PRK13364 protocatechuate 4,5-dioxygenase subunit beta; Provisional
Probab=26.00 E-value=40 Score=27.36 Aligned_cols=27 Identities=30% Similarity=0.295 Sum_probs=22.9
Q ss_pred HHhcCCCCCcc-----------cchHHHHHHhhcCChHH
Q psy1192 12 SHNFPGKLLHK-----------DLDDRALDALKEYPSEG 39 (108)
Q Consensus 12 ~iy~sG~l~~~-----------DLDeRAidaLkef~~e~ 39 (108)
-|+-||.++|. +.|.+.+|+|++ +.+.
T Consensus 183 ~iIaSG~LSH~l~~~p~G~~~~~fD~~~l~~l~~-d~~~ 220 (278)
T PRK13364 183 VVIGTGGLSHQLDGERAGFINKDFDLQCMDSLVS-DPEW 220 (278)
T ss_pred EEEEeCccccCCCCCCcccCCHHHHHHHHHHHHh-CHHH
Confidence 36678888888 999999999998 8774
No 44
>PLN02641 anthranilate phosphoribosyltransferase
Probab=25.19 E-value=1.4e+02 Score=25.04 Aligned_cols=44 Identities=23% Similarity=0.230 Sum_probs=29.8
Q ss_pred hhHHHHHHHHhcCCCCCcccchHHHHHHhhcCChHHHHHHHHHHhhcccccccchhHHHHHH
Q psy1192 4 ENIQIIFLSHNFPGKLLHKDLDDRALDALKEYPSEGAIAVLNQFLESNLEHVSNKSAFLCGI 65 (108)
Q Consensus 4 ~~iq~~l~~iy~sG~l~~~DLDeRAidaLkef~~e~Al~vl~qF~eS~L~hV~NKSAFL~gV 65 (108)
++|+..|.+|..-. .++.|+|..++..+.+- ..-+ ...||||++
T Consensus 2 ~~~~~~l~~l~~g~----------------~Lt~eEa~~~~~~il~~-~~~~-qigAfL~al 45 (343)
T PLN02641 2 ASFRQLIESLIQGT----------------DLTEEEAEAALDFLLDD-ADEA-QISAFLVLL 45 (343)
T ss_pred ccHHHHHHHHhCCC----------------CCCHHHHHHHHHHHHcC-CCHH-HHHHHHHHH
Confidence 46777777776544 56677777777777763 5555 677888765
No 45
>KOG4114|consensus
Probab=25.04 E-value=48 Score=22.99 Aligned_cols=28 Identities=32% Similarity=0.595 Sum_probs=22.0
Q ss_pred hcCChHHHHHHHHHHhhcccccccchhHH
Q psy1192 33 KEYPSEGAIAVLNQFLESNLEHVSNKSAF 61 (108)
Q Consensus 33 kef~~e~Al~vl~qF~eS~L~hV~NKSAF 61 (108)
+++|++ -.++++-|.++.-+=|-+++.|
T Consensus 39 ~~vPee-C~al~~af~dCKRslvDmrkRf 66 (73)
T KOG4114|consen 39 KDVPEE-CIALMKAFLDCKRSLVDMRKRF 66 (73)
T ss_pred ccCcHH-HHHHHHHHHHHHHHHHHHHHHH
Confidence 668877 8999999999988777665544
No 46
>PF01875 Memo: Memo-like protein; InterPro: IPR002737 This entry contains proteins from all branches of life. The molecular function of these proteins are unknown, but Memo (mediator of ErbB2-driven cell motility) a human protein is included in this family []. It has been suggested that Memo controls cell migration by relaying extracellular chemotactic signals to the microtubule cytoskeleton [].; PDB: 3BD0_C 3BCZ_C.
Probab=24.99 E-value=74 Score=25.28 Aligned_cols=31 Identities=23% Similarity=0.270 Sum_probs=22.4
Q ss_pred chHHHHHHhhcCChHHHHHHHHHHhhcccccc
Q psy1192 24 LDDRALDALKEYPSEGAIAVLNQFLESNLEHV 55 (108)
Q Consensus 24 LDeRAidaLkef~~e~Al~vl~qF~eS~L~hV 55 (108)
+|.++|+.+.+++.++....+++-+.+ .=|.
T Consensus 203 ~D~~~i~~i~~~d~~~~~~~~~~~~~t-~CG~ 233 (276)
T PF01875_consen 203 LDREAIEAIEALDPEGFYEYLKETNNT-ACGR 233 (276)
T ss_dssp HHHHHHHHHHTT-HHHHHHHHHHH-----TTH
T ss_pred HHHHHHHHHHccCHHHHHHHHHHcCCc-eech
Confidence 499999999999999999888887666 4443
No 47
>cd00668 Ile_Leu_Val_MetRS_core catalytic core domain of isoleucyl, leucyl, valyl and methioninyl tRNA synthetases. Catalytic core domain of isoleucyl, leucyl, valyl and methioninyl tRNA synthetases. These class I enzymes are all monomers. However, in some species, MetRS functions as a homodimer, as a result of an additional C-terminal domain. These enzymes aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. Enzymes in this subfamily share an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids. MetRS has a significantly shorter insertion, which lacks the editing function.
Probab=24.68 E-value=1.3e+02 Score=23.71 Aligned_cols=48 Identities=19% Similarity=0.293 Sum_probs=31.4
Q ss_pred chhhHHHHHHHHhcCCCCCc---------------ccchHHHHHHhhcCC--hHHHHHHHHHHhh
Q psy1192 2 HLENIQIIFLSHNFPGKLLH---------------KDLDDRALDALKEYP--SEGAIAVLNQFLE 49 (108)
Q Consensus 2 ~~~~iq~~l~~iy~sG~l~~---------------~DLDeRAidaLkef~--~e~Al~vl~qF~e 49 (108)
|.+.++..+.+|++.|.+-. .++-+++++.++..+ .+..+..+.++.+
T Consensus 112 ~~~~v~~~f~~L~~~G~iY~~~~~v~~~~~~f~~~~~l~~~~~~~~~~~~~~p~~~~~~~~~~l~ 176 (312)
T cd00668 112 YSKAVELIFSRLYEKGLIYRGTHPVRITEQWFFDMPKFKEKLLKALRRGKIVPEHVKNRMEAWLE 176 (312)
T ss_pred HHHHHHHHHHHHHHCCCEEeecceeEeeeeEEEEcHHHHHHHHHHHhcCCcCChHHHHHHHHHHh
Confidence 56788999999999999776 345566666666543 1234444444444
No 48
>PF00814 Peptidase_M22: Glycoprotease family; InterPro: IPR000905 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M22 (clan MK). The type example being O-sialoglycoprotein endopeptidase (3.4.24.57 from EC) from Pasteurella haemolytica (Mannheimia haemolytica). O-Sialoglycoprotein endopeptidase is secreted by the bacterium P. haemolytica, and digests only proteins that are heavily sialylated, in particular those with sialylated serine and threonine residues []. Substrate proteins include glycophorin A and leukocyte surface antigens CD34, CD43, CD44 and CD45 [, ]. Removal of glycosylation, by treatment with neuraminidase, completely negates susceptibility to O-sialoglycoprotein endopeptidase digestion [, ]. Sequence similarity searches have revealed other members of the M22 family, from yeast, Mycobacterium, Haemophilus influenzae and the cyanobacterium Synechocystis []. The zinc-binding and catalytic residues of this family have not been determined, although the motif HMEGH may be a zinc-binding region [].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2A6A_A 2GEL_G 2GEM_B 1OKJ_B 3ENO_A 3EN9_B 2VWB_B 3ENH_B 2IVO_D 2IVP_A ....
Probab=24.23 E-value=33 Score=27.05 Aligned_cols=25 Identities=20% Similarity=0.189 Sum_probs=16.5
Q ss_pred chhhHHHHHHHHhcCCCCCcccchH
Q psy1192 2 HLENIQIIFLSHNFPGKLLHKDLDD 26 (108)
Q Consensus 2 ~~~~iq~~l~~iy~sG~l~~~DLDe 26 (108)
|+++|...++++.+.-.++.+|||-
T Consensus 29 H~~~L~~~i~~~l~~~~~~~~did~ 53 (268)
T PF00814_consen 29 HSENLPPLIEELLKEAGISLSDIDA 53 (268)
T ss_dssp HHHHHHHHHHHHHHHHTS-GGGESE
T ss_pred HHHHHHHHHHHHHHHcCCCHHHCCE
Confidence 6677777777777766677777663
No 49
>PF01471 PG_binding_1: Putative peptidoglycan binding domain; InterPro: IPR002477 This entry represents peptidoglycan binding domain (PGBD), as well as related domains that share the same structure. PGBD may have a general peptidoglycan binding function, has a core structure consisting of a closed, three-helical bundle with a left-handed twist. It is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation [, , ]. Examples are: Muramoyl-pentapeptide carboxypeptidase (3.4.17.8 from EC) N-acetylmuramoyl-L-alanine amidase cwlA precursor (cell wall hydrolase, autolysin, 3.5.1.28 from EC) Autolytic lysozyme (1,4-beta-N-acetylmuramidase, autolysin, 3.2.1.17 from EC) Membrane-bound lytic murein transglycosylase B Zinc-containing D-alanyl-D-alanine-cleaving carboxypeptidase, VanX []. Many of the proteins having this domain are as yet uncharacterised. However, some are known to belong to MEROPS peptidase family M15 (clan MD), subfamily M15A metallopeptidases. A number of the proteins belonging to subfamily M15A are non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. Eukaryotic enzymes can contain structurally similar PGBD-like domains. Matrix metalloproteinases (MMP), which catalyse extracellular matrix degradation, have N-terminal domains that resemble PGBD. Examples are gelatinase A (MMP-2), which degrades type IV collagen [], stromelysin-1 (MMP-3), which plays a role in arthritis and tumour invasion [, ], and gelatinase B (MMP-9) secreted by neutrophils as part of the innate immune defence mechanism []. Several MMPs are implicated in cancer progression, since degradation of the extracellular matrix is an essential step in the cascade of metastasis [].; GO: 0008152 metabolic process; PDB: 1L6J_A 3BKH_A 3BKV_A 1GXD_A 1EAK_D 1CK7_A 1SLM_A 1LBU_A 1SU3_B.
Probab=24.14 E-value=92 Score=18.30 Aligned_cols=32 Identities=13% Similarity=0.162 Sum_probs=16.1
Q ss_pred hhHHHHHHHHhcCCCCCcccchHHHHHHhhcC
Q psy1192 4 ENIQIIFLSHNFPGKLLHKDLDDRALDALKEY 35 (108)
Q Consensus 4 ~~iq~~l~~iy~sG~l~~~DLDeRAidaLkef 35 (108)
..+|..|..+.-...-.....|+...+|++.|
T Consensus 6 ~~lq~~L~~~gy~~~~~~g~~~~~t~~Av~~f 37 (57)
T PF01471_consen 6 KALQQYLNRLGYYPGPVDGIFDPETREAVKAF 37 (57)
T ss_dssp HHHHHHHHHTTTT-SSTTSBSHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCCCCCCCcCHHHHHHHHHH
Confidence 34666666653331223355666666555544
No 50
>TIGR01339 phycocy_beta phycocyanin, beta subunit. This model excludes the closely related phycoerythrocyanin beta subunit.
Probab=23.95 E-value=1.3e+02 Score=23.17 Aligned_cols=53 Identities=25% Similarity=0.406 Sum_probs=39.5
Q ss_pred ccchHHHHHHhhc------CChHHHHHHHHHHhhcccccccchhH-------HHHHHHHHHHHHhh
Q psy1192 22 KDLDDRALDALKE------YPSEGAIAVLNQFLESNLEHVSNKSA-------FLCGIMKTYRQKSR 74 (108)
Q Consensus 22 ~DLDeRAidaLke------f~~e~Al~vl~qF~eS~L~hV~NKSA-------FL~gVMKtyRqr~r 74 (108)
+=||||.+.-||| +|.......|+..++.-++.+++... =||+.+-+|=|+.-
T Consensus 101 ~~ld~~gl~GLrE~Y~aLgVP~~~~v~al~~mK~~~~~~~~~~~~~~~g~c~~l~sei~~yFD~~~ 166 (170)
T TIGR01339 101 SVLEDRCLNGLRETYLALGTPGSSVAAGVQKMKDAALAIVNDTAGITSGDCSSLMAEIATYFDRAA 166 (170)
T ss_pred chhhHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHHHHHhccccCCCCcchHHHHHHHHhHHHHHH
Confidence 3489999988886 56667777899999988888876433 46677777777653
No 51
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=23.90 E-value=1.2e+02 Score=18.48 Aligned_cols=46 Identities=24% Similarity=0.210 Sum_probs=36.9
Q ss_pred cchHHHHHHhhcCChHHHHHHHHHHhhcccccccchhHHHHHHHHH
Q psy1192 23 DLDDRALDALKEYPSEGAIAVLNQFLESNLEHVSNKSAFLCGIMKT 68 (108)
Q Consensus 23 DLDeRAidaLkef~~e~Al~vl~qF~eS~L~hV~NKSAFL~gVMKt 68 (108)
.+-..|+.+|.++..+.+...|-+..+++=..|+...++-.|-|.+
T Consensus 15 ~vr~~a~~~L~~~~~~~~~~~L~~~l~d~~~~vr~~a~~aL~~i~~ 60 (88)
T PF13646_consen 15 QVRAEAARALGELGDPEAIPALIELLKDEDPMVRRAAARALGRIGD 60 (88)
T ss_dssp HHHHHHHHHHHCCTHHHHHHHHHHHHTSSSHHHHHHHHHHHHCCHH
T ss_pred HHHHHHHHHHHHcCCHhHHHHHHHHHcCCCHHHHHHHHHHHHHhCC
Confidence 4556788888899988899888888888888888888887777654
No 52
>PF07128 DUF1380: Protein of unknown function (DUF1380); InterPro: IPR009811 This family consists of several hypothetical bacterial proteins of around 140 residues in length. Members of this family seem to be specific to Enterobacteria. The function of this family is unknown.
Probab=23.53 E-value=1.2e+02 Score=23.14 Aligned_cols=54 Identities=20% Similarity=0.193 Sum_probs=38.6
Q ss_pred CcccchHHHHHHhhcCChHHHHHHHHHHhhccc-----ccccchhHHHHHHHHHHHHHhhc
Q psy1192 20 LHKDLDDRALDALKEYPSEGAIAVLNQFLESNL-----EHVSNKSAFLCGIMKTYRQKSRS 75 (108)
Q Consensus 20 ~~~DLDeRAidaLkef~~e~Al~vl~qF~eS~L-----~hV~NKSAFL~gVMKtyRqr~r~ 75 (108)
+++|+=+-|-.+==+++.++|-.||++..+... .||++ .+++.+|+.-|...|+
T Consensus 28 T~eDV~~~a~gme~~lTd~E~~aVL~~I~~~~~~~~~~~GVs~--~~V~el~~~~r~~~R~ 86 (139)
T PF07128_consen 28 TREDVRALADGMEYNLTDDEARAVLARIGDIPEDQRHEEGVSS--GTVMELIREVRRAARQ 86 (139)
T ss_pred cHHHHHHHHhcCCCCCCHHHHHHHHHHHhcCccccchhccccH--HHHHHHHHHHHhcCCc
Confidence 556654444433345689999999999999766 56654 8899999998855553
No 53
>PRK08136 glycosyl transferase family protein; Provisional
Probab=23.51 E-value=85 Score=26.03 Aligned_cols=32 Identities=16% Similarity=0.333 Sum_probs=26.9
Q ss_pred hcCChHHHHHHHHHHhhcccccccchhHHHHHH
Q psy1192 33 KEYPSEGAIAVLNQFLESNLEHVSNKSAFLCGI 65 (108)
Q Consensus 33 kef~~e~Al~vl~qF~eS~L~hV~NKSAFL~gV 65 (108)
+.++.++|..++.++.+-+.+-+ ...|||+.+
T Consensus 18 ~~Lt~eEA~~~~~~il~g~~~~~-qi~AfL~al 49 (317)
T PRK08136 18 RDLDRDTARALYGAMLDGRVPDL-ELGAILIAL 49 (317)
T ss_pred CCcCHHHHHHHHHHHHcCCCCHH-HHHHHHHHH
Confidence 56788999999999998888777 688998864
No 54
>PRK14955 DNA polymerase III subunits gamma and tau; Provisional
Probab=23.46 E-value=3.3e+02 Score=22.54 Aligned_cols=54 Identities=13% Similarity=0.220 Sum_probs=39.2
Q ss_pred CCCCCcccchH-----------HHHHHhhcCChHHHHHHHHHHhhcccccccchhHHHHHHHHHHHHHh
Q psy1192 16 PGKLLHKDLDD-----------RALDALKEYPSEGAIAVLNQFLESNLEHVSNKSAFLCGIMKTYRQKS 73 (108)
Q Consensus 16 sG~l~~~DLDe-----------RAidaLkef~~e~Al~vl~qF~eS~L~hV~NKSAFL~gVMKtyRqr~ 73 (108)
.+.++.+|+++ ..+|++-+=+.+.|+.+++++.+..-..+ ..|--+.+-||+-.
T Consensus 242 ~~~It~~~v~~~v~~~~~~~vf~l~~ai~~~~~~~al~~~~~l~~~~~~~~----~iL~ll~~~~R~ll 306 (397)
T PRK14955 242 EGSIRYDKVAELLNYIDDEHFFAVTDAVADGDAVAMLDVAQFVIRNGYDEQ----DFLEKLIEHLRNFL 306 (397)
T ss_pred CCccCHHHHHHHHCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHH----HHHHHHHHHHHHHH
Confidence 34677777764 45778888888899999988875443332 46778889999964
No 55
>PF02607 B12-binding_2: B12 binding domain; InterPro: IPR003759 Cobalamin-dependent methionine synthase (2.1.1.13 from EC) is a large modular protein that catalyses methyl transfer from methyltetrahydrofolate (CH3-H4folate) to homocysteine. During the catalytic cycle, it supports three distinct methyl transfer reactions, each involving the cobalamin (vitamin B12) cofactor and a substrate bound to its own functional unit []. The cobalamin cofactor plays an essential role in this reaction, accepting the methyl group from CH3-H4folate to form methylcob(III)alamin, and in turn donating the methyl group to homocysteine to generate methionine and cob(I)alamin. Methionine synthase is a large enzyme composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and CH3-H4folate, the third module binds the cobalamin cofactor and the C-terminal module binds S-adenosylmethionine. The cobalamin-binding module is composed of two structurally distinct domains: a 4-helical bundle cap domain (residues 651-740 in the Escherichia coli enzyme) and an alpha/beta B12-binding domain (residues 741-896) (IPR006158 from INTERPRO). The 4-helical bundle forms a cap over the alpha/beta domain, which acts to shield the methyl ligand of cobalamin from solvent []. Furthermore, in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO). The alpha/beta domain is a common cobalamin-binding motif, whereas the 4-helical bundle domain with its methyl cap is a distinctive feature of methionine synthases. This entry represents the 4-helical bundle cap domain. This domain is also present in other shorter proteins that bind to B12, and is always found N terminus to the alpha/beta B12-binding domain.; GO: 0008705 methionine synthase activity, 0031419 cobalamin binding, 0046872 metal ion binding, 0009086 methionine biosynthetic process; PDB: 3EZX_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 2I2X_P.
Probab=23.40 E-value=1.9e+02 Score=17.85 Aligned_cols=55 Identities=25% Similarity=0.218 Sum_probs=35.3
Q ss_pred ccchHHHHHHhhcCChHHHHHHHHHHhhcccccccchhHHHHHHHHHHHHHhhcc
Q psy1192 22 KDLDDRALDALKEYPSEGAIAVLNQFLESNLEHVSNKSAFLCGIMKTYRQKSRSG 76 (108)
Q Consensus 22 ~DLDeRAidaLkef~~e~Al~vl~qF~eS~L~hV~NKSAFL~gVMKtyRqr~r~g 76 (108)
+++-++..+++-+++.+.+...+++..+....-..==-..|+-+|+.-=++..+|
T Consensus 2 ~~~~~~l~~al~~~d~~~~~~~~~~~l~~g~~~~~i~~~~l~p~m~~iG~~w~~~ 56 (79)
T PF02607_consen 2 EELIERLLDALLAGDEEEAEALLEEALAQGYPPEDIIEEILMPAMEEIGELWEEG 56 (79)
T ss_dssp HHHHHHHHHHHHTT-CCHHHHHHHHHHHCSSSTTHHHHHTHHHHHHHHHHHHHTT
T ss_pred hHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHhCC
Confidence 3566788999999999999999999887632211111223556666665665543
No 56
>COG0142 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]
Probab=22.63 E-value=78 Score=25.77 Aligned_cols=48 Identities=17% Similarity=0.194 Sum_probs=36.7
Q ss_pred hHHHHHHHHhcCCCCCc-----ccchHHHHHHhhcCChHHHHHHHHHHhhccc
Q psy1192 5 NIQIIFLSHNFPGKLLH-----KDLDDRALDALKEYPSEGAIAVLNQFLESNL 52 (108)
Q Consensus 5 ~iq~~l~~iy~sG~l~~-----~DLDeRAidaLkef~~e~Al~vl~qF~eS~L 52 (108)
.+....+-+.++|-+.. .++-+.|++.|+.+|...+..+|.++.+.-.
T Consensus 266 ~~~~~~~~~~~~g~~~~~~~~a~~~~~~a~~~L~~l~~~~~~~~L~~la~~i~ 318 (322)
T COG0142 266 EVEEALELLRKSGAIEYAKNLAKTYVEKAKEALEKLPDSEAKEALLELADFII 318 (322)
T ss_pred HHHHHHHHHHHcchHHHHHHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHH
Confidence 35566667777777776 7888999999999996678888888776544
No 57
>PLN02890 geranyl diphosphate synthase
Probab=22.39 E-value=1.8e+02 Score=25.30 Aligned_cols=62 Identities=18% Similarity=0.087 Sum_probs=31.0
Q ss_pred HHHHhcCCCCCcccchHHHHHHhhcCCh------------HHHHHHHHHHhhcccccccchhHHHHHHHHHHHHH
Q psy1192 10 FLSHNFPGKLLHKDLDDRALDALKEYPS------------EGAIAVLNQFLESNLEHVSNKSAFLCGIMKTYRQK 72 (108)
Q Consensus 10 l~~iy~sG~l~~~DLDeRAidaLkef~~------------e~Al~vl~qF~eS~L~hV~NKSAFL~gVMKtyRqr 72 (108)
+..++..+..+++|+| ++++.+++-+. +.|+..|+.|-+++-..|.--...|..+....-+|
T Consensus 347 l~~~l~~~~~~~~~v~-~~~~~i~~~gaie~a~~la~~~~~~A~~~L~~lp~s~~~~~~~~r~~L~~L~~~vi~R 420 (422)
T PLN02890 347 LREVVDRGFDNPANVD-IALEYLGKSRGIQRTRELAREHANLAAAAIESLPETDDEDVLTSRRALIDLTERVITR 420 (422)
T ss_pred HHHHHhcccCCHHHHH-HHHHHHHHcCHHHHHHHHHHHHHHHHHHHHHhCCCCccccchHHHHHHHHHHHHHHhc
Confidence 4456666766666666 44555555432 33555555555444333322234455555444333
No 58
>PF08930 DUF1912: Domain of unknown function (DUF1912); InterPro: IPR015026 This protein has no known function. It is found in various Streptococcal proteins. ; PDB: 1Z0P_A.
Probab=22.04 E-value=31 Score=24.40 Aligned_cols=21 Identities=33% Similarity=0.339 Sum_probs=11.6
Q ss_pred HHhcCCCCCcccchHHHHHHh
Q psy1192 12 SHNFPGKLLHKDLDDRALDAL 32 (108)
Q Consensus 12 ~iy~sG~l~~~DLDeRAidaL 32 (108)
.+-++-+|..+|=||||-||.
T Consensus 25 Am~~s~kv~eeD~derAkdA~ 45 (84)
T PF08930_consen 25 AMKESQKVAEEDGDERAKDAY 45 (84)
T ss_dssp HHHHHHHH------HHHHHHH
T ss_pred HHHHHHHHHHHcccHHHHHHH
Confidence 445677888999999999985
No 59
>COG2880 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.66 E-value=2.1e+02 Score=19.38 Aligned_cols=43 Identities=19% Similarity=0.108 Sum_probs=28.9
Q ss_pred HHHHHHHhcCCCCCc-------------------ccchHHHHHHhhcCChHHHHHHHHHHhhc
Q psy1192 7 QIIFLSHNFPGKLLH-------------------KDLDDRALDALKEYPSEGAIAVLNQFLES 50 (108)
Q Consensus 7 q~~l~~iy~sG~l~~-------------------~DLDeRAidaLkef~~e~Al~vl~qF~eS 50 (108)
-++...+|+.|.+.| +++.++....++... +....++.+|-++
T Consensus 4 ~kIIEaiYEnGVfKPLqkv~LkEGekv~i~i~~~e~~~~~lk~~~k~~~-e~~~e~l~e~e~e 65 (67)
T COG2880 4 PKIIEAIYENGVLKPLKKVDLKEGEKVKIVIRVKEKIYEILKGSLKEIK-EILEEILEEIEDE 65 (67)
T ss_pred HHHHHHHHhcccccccccccCCCCCEEEEEEechHHHHHHHHHHHhhhh-HHHHHHHHHHHhh
Confidence 467788899997654 555566666666555 5677777777654
No 60
>PRK05820 deoA thymidine phosphorylase; Reviewed
Probab=21.26 E-value=97 Score=27.21 Aligned_cols=32 Identities=9% Similarity=0.122 Sum_probs=27.8
Q ss_pred hcCChHHHHHHHHHHhhcccccccchhHHHHHH
Q psy1192 33 KEYPSEGAIAVLNQFLESNLEHVSNKSAFLCGI 65 (108)
Q Consensus 33 kef~~e~Al~vl~qF~eS~L~hV~NKSAFL~gV 65 (108)
++++.++|.++++.+.+-+..-. ..+||||.+
T Consensus 15 ~~Lt~eE~~~~~~~i~~G~~~d~-QiaAfLmAl 46 (440)
T PRK05820 15 GALSDEEIDWFIDGYTDGTVSDG-QIAALAMAI 46 (440)
T ss_pred CCCCHHHHHHHHHHHHcCCCCHH-HHHHHHHHH
Confidence 46788889999999999888888 789999987
No 61
>COG0547 TrpD Anthranilate phosphoribosyltransferase [Amino acid transport and metabolism]
Probab=21.21 E-value=1.8e+02 Score=24.61 Aligned_cols=32 Identities=19% Similarity=0.329 Sum_probs=27.5
Q ss_pred hcCChHHHHHHHHHHhhcccccccchhHHHHHH
Q psy1192 33 KEYPSEGAIAVLNQFLESNLEHVSNKSAFLCGI 65 (108)
Q Consensus 33 kef~~e~Al~vl~qF~eS~L~hV~NKSAFL~gV 65 (108)
+.++.++|..+++...+-+.+-+ ...||||.+
T Consensus 15 ~~L~~~eA~~l~~~il~g~~~~~-qi~A~L~Al 46 (338)
T COG0547 15 RDLDREEARELFKAILSGEASPA-QIGAFLTAL 46 (338)
T ss_pred CCCCHHHHHHHHHHHhcCCCCHH-HHHHHHHHH
Confidence 67888999999999999999988 678888753
No 62
>PF14779 BBS1: Ciliary BBSome complex subunit 1
Probab=21.09 E-value=2.9e+02 Score=22.70 Aligned_cols=48 Identities=21% Similarity=0.261 Sum_probs=28.4
Q ss_pred hhHHHHHHHHhcCCCCCcccchHHHHHHhhcCChHHHHHHHHHHhhcccccc
Q psy1192 4 ENIQIIFLSHNFPGKLLHKDLDDRALDALKEYPSEGAIAVLNQFLESNLEHV 55 (108)
Q Consensus 4 ~~iq~~l~~iy~sG~l~~~DLDeRAidaLkef~~e~Al~vl~qF~eS~L~hV 55 (108)
+.....|.+|-+ .++..|=.|.+++| .++.++-.+.+++++++-|.+-
T Consensus 129 ~~l~~~L~~lr~---~~~~~LS~rSl~~L-~l~~ee~~~fi~~~k~~pl~~~ 176 (257)
T PF14779_consen 129 ETLKEMLESLRD---IAGVKLSPRSLRFL-QLDPEEREAFIERYKDSPLKRQ 176 (257)
T ss_pred HHHHHHHHHHhh---ccCCccCHHHHHHH-CCCHHHHHHHHHHHhcCCcccC
Confidence 334444444333 45566677777777 4466666666777776666554
No 63
>cd07320 Extradiol_Dioxygenase_3B_like Subunit B of Class III Extradiol ring-cleavage dioxygenases. Dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. Two major groups of dioxygenases have been identified according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be further divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two-domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B. This model represents the catalytic subunit B of extradiol dioxygenase class
Probab=21.08 E-value=81 Score=23.95 Aligned_cols=30 Identities=23% Similarity=0.300 Sum_probs=24.3
Q ss_pred HhcCCCCCcc-----------------cchHHHHHHhhcCChHHHHH
Q psy1192 13 HNFPGKLLHK-----------------DLDDRALDALKEYPSEGAIA 42 (108)
Q Consensus 13 iy~sG~l~~~-----------------DLDeRAidaLkef~~e~Al~ 42 (108)
|+-||.++|- +.|+.++++|.+.+.+.-+.
T Consensus 163 iI~SGdlsH~~~~~~~~~~~~~~~~~~efD~~~~~~l~~~d~~~l~~ 209 (260)
T cd07320 163 VVASGDLSHQLQGDRPSSQSGYYPIAEEFDKYVIDNLEELDPVEFKN 209 (260)
T ss_pred EEEeCccccCCCCCCcccccCcCcchHHHHHHHHHHHHcCCHHHHhh
Confidence 5668888884 88999999999999886444
No 64
>TIGR02644 Y_phosphoryl pyrimidine-nucleoside phosphorylase. In general, members of this protein family are designated pyrimidine-nucleoside phosphorylase, enzyme family EC 2.4.2.2, as in Bacillus subtilis, and more narrowly as the enzyme family EC 2.4.2.4, thymidine phosphorylase (alternate name: pyrimidine phosphorylase), as in Escherichia coli. The set of proteins encompassed by this model is designated subfamily rather than equivalog for this reason; the protein name from this model should be used when TIGR02643 does not score above trusted cutoff.
Probab=20.95 E-value=1e+02 Score=26.78 Aligned_cols=32 Identities=22% Similarity=0.304 Sum_probs=27.3
Q ss_pred hcCChHHHHHHHHHHhhcccccccchhHHHHHH
Q psy1192 33 KEYPSEGAIAVLNQFLESNLEHVSNKSAFLCGI 65 (108)
Q Consensus 33 kef~~e~Al~vl~qF~eS~L~hV~NKSAFL~gV 65 (108)
++++.++|.++++.+.+-+..-+ ..+||||.+
T Consensus 12 ~~Lt~eE~~~~~~~i~~G~~~d~-QiaAfLmAl 43 (405)
T TIGR02644 12 KKLSDEEINFFINGYTNGEIPDY-QMSALLMAI 43 (405)
T ss_pred CCCCHHHHHHHHHHHHcCCCCHH-HHHHHHHHH
Confidence 36788889999999988888877 689999987
No 65
>cd05152 MPH2' Macrolide 2'-Phosphotransferase (MPH2'). MPH2' is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). MPH2' catalyzes the transfer of the gamma-phosphoryl group from ATP to the 2'-hydroxyl of macrolide antibiotics such as erythromycin, clarithromycin, and azithromycin, among others. Macrolides penetrate the bacterial cell and bind to ribosomes, where it interrupts protein elongation, leading ultimately to the demise of the bacterium. Phosphorylation of macrolides leads to their inactivation. Based on substrate specificity and amino acid sequence, MPH2' is divided into types I and II, encoded by mphA and mphB genes, respectively. MPH2'I inactivates 14-membered ring macrolides while MPH2'II inactivates both 14- and 16-membered ring macrolides. Enzymatic inactivation of macrolides has been reported
Probab=20.94 E-value=1.5e+02 Score=23.19 Aligned_cols=38 Identities=18% Similarity=0.341 Sum_probs=31.4
Q ss_pred HHHHHHHhcC--CCCCcccchHHHHHHhhcCChHHHHHHHH
Q psy1192 7 QIIFLSHNFP--GKLLHKDLDDRALDALKEYPSEGAIAVLN 45 (108)
Q Consensus 7 q~~l~~iy~s--G~l~~~DLDeRAidaLkef~~e~Al~vl~ 45 (108)
...|-+-|.. |... .+++.+++.-|--+|+|.|+++|.
T Consensus 235 ~~~~~~~Y~~~~g~~~-~~~~~~~~~~~~~~~~~~~~~~~~ 274 (276)
T cd05152 235 LERLIDAYEAAGGRVW-PRMKEHIIELLAAYPVEIALFALD 274 (276)
T ss_pred HHHHHHHHHHcCCCCC-chHHHHHHHHHhccHHHHHHHHHh
Confidence 4556677776 6666 699999999999999999999875
No 66
>cd08332 CARD_CASP2 Caspase activation and recruitment domain of Caspase-2. Caspase activation and recruitment domain (CARD) similar to that found in caspase-2. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Caspase-2 (also known as ICH1, NEDD2, or CASP2) is one of the most evolutionarily conserved caspases, and plays a role in apoptosis, DNA damage response, cell cycle regulation, and tumor suppression. It is localized in the nucleus and exhibits properties of both an initiator and an effector caspase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and
Probab=20.77 E-value=64 Score=21.89 Aligned_cols=22 Identities=5% Similarity=-0.023 Sum_probs=18.0
Q ss_pred hHHHHHHHHhcCCCCCcccchH
Q psy1192 5 NIQIIFLSHNFPGKLLHKDLDD 26 (108)
Q Consensus 5 ~iq~~l~~iy~sG~l~~~DLDe 26 (108)
+...+++.||+.|.+++++.++
T Consensus 21 ~~~~v~~~L~~~gvlt~~~~~~ 42 (90)
T cd08332 21 VLDELLIHLLQKDILTDSMAES 42 (90)
T ss_pred CHHHHHHHHHHcCCCCHHHHHH
Confidence 4566899999999999987654
No 67
>PRK14971 DNA polymerase III subunits gamma and tau; Provisional
Probab=20.76 E-value=3.6e+02 Score=24.28 Aligned_cols=57 Identities=18% Similarity=0.298 Sum_probs=40.1
Q ss_pred hcCCCCCcccchH-----------HHHHHhhcCChHHHHHHHHHHhhcccccccchhHHHHHHHHHHHHHhh
Q psy1192 14 NFPGKLLHKDLDD-----------RALDALKEYPSEGAIAVLNQFLESNLEHVSNKSAFLCGIMKTYRQKSR 74 (108)
Q Consensus 14 y~sG~l~~~DLDe-----------RAidaLkef~~e~Al~vl~qF~eS~L~hV~NKSAFL~gVMKtyRqr~r 74 (108)
|..+.++.+++++ +.+|++.+=+...|+.+++++........ .+|..+.+-|||-..
T Consensus 229 y~~~~It~~~V~~~l~~~~~~~iF~L~dai~~~~~~~al~ll~~Ll~~g~~~~----~iL~~L~~~fRdlL~ 296 (614)
T PRK14971 229 FTGGNITYKSVIENLNILDYDYYFRLTDALLAGKVSDSLLLFDEILNKGFDGS----HFITGLASHFRDLLV 296 (614)
T ss_pred hccCCccHHHHHHHhCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHH----HHHHHHHHHHHHHHH
Confidence 5554566666654 34567777788888888888775544443 589999999999865
No 68
>cd08323 CARD_APAF1 Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1. Caspase activation and recruitment domain (CARD) similar to that found in apoptotic protease-activating factor 1 (APAF-1), which is an activator of caspase-9. APAF-1 contains WD-40 repeats, a CARD, and an ATPase domain. Upon stimulation, APAF-1, together with caspase-9, forms the heptameric 'apoptosome', which leads to the processing and activation of caspase-9, starting a caspase cascade which leads to apoptosis. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effect
Probab=20.54 E-value=63 Score=22.09 Aligned_cols=21 Identities=14% Similarity=0.034 Sum_probs=17.7
Q ss_pred HHHHHHHHhcCCCCCcccchH
Q psy1192 6 IQIIFLSHNFPGKLLHKDLDD 26 (108)
Q Consensus 6 iq~~l~~iy~sG~l~~~DLDe 26 (108)
.+.+++.||+.|.++.+|.|+
T Consensus 16 v~~ild~L~~~gvlt~~~~e~ 36 (86)
T cd08323 16 TSYIMDHMISDGVLTLDEEEK 36 (86)
T ss_pred HHHHHHHHHhcCCCCHHHHHH
Confidence 456899999999999998774
No 69
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=20.16 E-value=1.8e+02 Score=18.81 Aligned_cols=37 Identities=16% Similarity=0.100 Sum_probs=21.3
Q ss_pred chhhHHHHHHHHhcCCCCCcccchHHHHHHhhcCChHHHHHH
Q psy1192 2 HLENIQIIFLSHNFPGKLLHKDLDDRALDALKEYPSEGAIAV 43 (108)
Q Consensus 2 ~~~~iq~~l~~iy~sG~l~~~DLDeRAidaLkef~~e~Al~v 43 (108)
+-.+++..+-++... +-+|+-|.++|.++-++=+..|
T Consensus 3 ~k~~l~~lv~~id~~-----~~~~~da~~~l~~~~e~fv~~v 39 (72)
T cd07981 3 TKRKLQELLKEIDPR-----EQLDPDVEELLLEIADDFVDDV 39 (72)
T ss_pred cHHHHHHHHHhhCCC-----CCcCHHHHHHHHHHHHHHHHHH
Confidence 446677666666432 5566666666665555443333
No 70
>TIGR02643 T_phosphoryl thymidine phosphorylase. Thymidine phosphorylase (alternate name: pyrimidine phosphorylase), EC 2.4.2.4, is the designation for the enzyme of E. coli and other Proteobacteria involved in (deoxy)nucleotide degradation. It often occurs in an operon with a deoxyribose-phosphate aldolase, phosphopentomutase and a purine nucleoside phosphorylase. In many other lineages, the corresponding enzyme is designated pyrimidine-nucleoside phosphorylase (EC 2.4.2.2); the naming convention imposed by this model represents standard literature practice.
Probab=20.07 E-value=1.1e+02 Score=27.04 Aligned_cols=31 Identities=10% Similarity=0.191 Sum_probs=27.0
Q ss_pred cCChHHHHHHHHHHhhcccccccchhHHHHHH
Q psy1192 34 EYPSEGAIAVLNQFLESNLEHVSNKSAFLCGI 65 (108)
Q Consensus 34 ef~~e~Al~vl~qF~eS~L~hV~NKSAFL~gV 65 (108)
+++.+++.++++.+.+-+..-. ..+||||.+
T Consensus 15 ~Lt~eE~~~~i~~i~~g~i~d~-QiaAfLmAl 45 (437)
T TIGR02643 15 SLSDAEIAQFINGITDGSVSEG-QIAAFAMAV 45 (437)
T ss_pred CCCHHHHHHHHHHHHcCCCCHH-HHHHHHHHH
Confidence 6788899999999998888877 689999987
No 71
>PF04051 TRAPP: Transport protein particle (TRAPP) component; InterPro: IPR007194 TRAPP plays a key role in the targeting and/or fusion of ER-to-Golgi transport vesicles with their acceptor compartment. TRAPP is a large multimeric protein that contains at least 10 subunits. This family contains many TRAPP family proteins. The Bet3 subunit is one of the better characterised TRAPP proteins and has a dimeric structure [] with hydrophobic channels. The channel entrances are located on a putative membrane-interacting surface that is distinctively flat, wide and decorated with positively charged residues. Bet3 is proposed to localise TRAPP to the Golgi [].; PDB: 2J3R_A 1WC9_A 2J3T_A 2PWN_A 2J3W_E 1WC8_A 3CUE_N 2C0J_B 3KXC_A 2CFH_A ....
Probab=20.04 E-value=62 Score=23.38 Aligned_cols=17 Identities=35% Similarity=0.554 Sum_probs=14.2
Q ss_pred chhHHHHHHHHHHHHHh
Q psy1192 57 NKSAFLCGIMKTYRQKS 73 (108)
Q Consensus 57 NKSAFL~gVMKtyRqr~ 73 (108)
+-++|.|||||-.=+..
T Consensus 109 ~~~~f~~GiIrGaL~~l 125 (152)
T PF04051_consen 109 NYLAFPCGIIRGALESL 125 (152)
T ss_dssp HTTHHHHHHHHHHHHHT
T ss_pred chhhhHHHHHHHHHHHC
Confidence 78999999999776654
Done!