Query psy6706
Match_columns 119
No_of_seqs 107 out of 330
Neff 5.0
Searched_HMMs 46136
Date Sat Aug 17 00:57:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6706.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6706hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3399|consensus 100.0 1.1E-54 2.4E-59 315.1 -2.6 118 1-118 1-119 (122)
2 PF03226 Yippee-Mis18: Yippee 100.0 3.6E-33 7.8E-38 192.3 6.2 89 14-108 2-94 (96)
3 PF11648 RIG-I_C-RD: C-termina 95.9 0.0034 7.4E-08 45.5 1.1 88 14-103 4-93 (123)
4 TIGR00357 methionine-R-sulfoxi 94.7 0.038 8.2E-07 41.2 3.4 67 12-86 38-105 (134)
5 PRK00222 methionine sulfoxide 94.5 0.031 6.8E-07 42.0 2.6 85 12-107 41-125 (142)
6 PF01641 SelR: SelR domain; I 94.3 0.031 6.8E-07 41.0 2.2 71 12-89 35-105 (124)
7 PRK05508 methionine sulfoxide 94.0 0.065 1.4E-06 39.2 3.3 64 12-85 31-94 (119)
8 PRK05550 bifunctional methioni 92.2 0.12 2.6E-06 42.7 2.7 64 12-85 34-97 (283)
9 KOG0856|consensus 90.9 0.33 7.1E-06 36.7 3.6 66 12-85 52-118 (146)
10 PF14976 FAM72: FAM72 protein 90.8 0.49 1.1E-05 35.9 4.5 63 13-87 14-88 (150)
11 PRK14018 trifunctional thiored 90.8 0.26 5.6E-06 43.7 3.5 68 12-86 416-483 (521)
12 COG0229 Conserved domain frequ 85.6 1.4 3E-05 33.2 3.9 65 12-83 40-104 (140)
13 PF09814 HECT_2: HECT-like Ubi 69.4 9 0.0002 31.2 4.5 16 14-29 106-121 (354)
14 TIGR01053 LSD1 zinc finger dom 58.9 8.9 0.00019 21.6 1.9 21 3-23 8-28 (31)
15 PF04828 GFA: Glutathione-depe 47.8 22 0.00048 22.6 2.7 20 64-83 42-61 (92)
16 PRK02935 hypothetical protein; 47.7 13 0.00029 26.9 1.7 24 13-36 85-108 (110)
17 PF06943 zf-LSD1: LSD1 zinc fi 45.2 19 0.00041 19.5 1.7 20 3-22 5-24 (25)
18 PF03811 Zn_Tnp_IS1: InsA N-te 40.7 18 0.00039 21.0 1.2 27 69-95 4-31 (36)
19 PF11023 DUF2614: Protein of u 39.1 13 0.00029 27.1 0.6 24 13-36 84-107 (114)
20 PF13465 zf-H2C2_2: Zinc-finge 34.8 27 0.00058 18.3 1.3 15 10-24 10-24 (26)
21 TIGR02820 formald_GSH S-(hydro 34.6 53 0.0011 25.5 3.4 30 54-84 74-103 (182)
22 PF00096 zf-C2H2: Zinc finger, 31.9 8.5 0.00018 19.0 -1.0 16 15-30 1-16 (23)
23 COG3791 Uncharacterized conser 30.3 37 0.0008 24.5 1.8 22 66-87 65-86 (133)
24 PF13912 zf-C2H2_6: C2H2-type 30.2 7.7 0.00017 19.9 -1.4 18 14-31 1-18 (27)
25 PF14803 Nudix_N_2: Nudix N-te 29.8 28 0.00061 19.9 0.9 14 72-85 2-15 (34)
26 KOG2462|consensus 28.6 18 0.00039 30.1 -0.1 22 10-31 211-232 (279)
27 PF02945 Endonuclease_7: Recom 28.0 8.9 0.00019 26.0 -1.7 16 68-83 50-65 (81)
28 PF13842 Tnp_zf-ribbon_2: DDE_ 27.5 48 0.001 18.5 1.6 15 13-27 15-29 (32)
29 PF10955 DUF2757: Protein of u 27.3 26 0.00057 23.7 0.5 16 14-29 4-19 (76)
30 PF13248 zf-ribbon_3: zinc-rib 26.0 24 0.00052 18.6 0.1 11 70-80 16-26 (26)
31 PRK05417 glutathione-dependent 25.8 65 0.0014 25.1 2.5 38 66-107 89-126 (191)
32 PF10058 DUF2296: Predicted in 25.7 21 0.00046 22.4 -0.2 35 45-84 2-36 (54)
33 TIGR00037 eIF_5A translation i 25.1 1.1E+02 0.0024 22.2 3.5 30 36-65 35-64 (130)
34 smart00132 LIM Zinc-binding do 24.8 29 0.00063 18.4 0.3 13 13-25 26-38 (39)
35 PF00412 LIM: LIM domain; Int 24.4 33 0.00071 20.3 0.5 16 13-28 25-40 (58)
36 PRK11586 napB nitrate reductas 24.3 48 0.001 25.2 1.5 28 12-39 118-145 (149)
37 PF10238 Eapp_C: E2F-associate 24.2 48 0.001 24.7 1.5 26 11-36 26-54 (136)
38 PF13240 zinc_ribbon_2: zinc-r 23.4 29 0.00063 18.1 0.1 10 71-80 14-23 (23)
39 PLN03107 eukaryotic translatio 23.1 1.2E+02 0.0026 22.9 3.5 30 36-65 49-78 (159)
40 smart00661 RPOL9 RNA polymeras 23.1 96 0.0021 18.1 2.4 17 13-29 19-35 (52)
41 PF06397 Desulfoferrod_N: Desu 22.7 48 0.001 19.4 1.0 12 13-24 5-16 (36)
42 PRK00398 rpoP DNA-directed RNA 21.9 53 0.0011 19.3 1.1 14 14-27 3-16 (46)
43 KOG2272|consensus 21.6 64 0.0014 27.1 1.8 32 11-46 134-165 (332)
44 PF10246 MRP-S35: Mitochondria 21.5 26 0.00057 25.2 -0.4 50 44-98 10-65 (104)
45 KOG2324|consensus 21.0 71 0.0015 28.1 2.1 13 79-91 271-283 (457)
46 PRK05978 hypothetical protein; 20.4 50 0.0011 24.9 0.9 24 2-27 42-65 (148)
No 1
>KOG3399|consensus
Probab=100.00 E-value=1.1e-54 Score=315.15 Aligned_cols=118 Identities=48% Similarity=0.842 Sum_probs=115.3
Q ss_pred CcceeeeccCCc-ceEEccCCCCCcCCCCCeeeecccCCCcceEEEeeeccccCCCccceEeccccEEeeeeeeccCCCc
Q psy6706 1 MGRIFLDHIGGS-RLFSCAACDTILTNRRELISTRFTGATGRAFLFHRVVNLNYSDVQDRVMLTGRHMVRDVSCKNCNTK 79 (119)
Q Consensus 1 MGr~f~~yl~~~-~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~H~v~dI~C~~C~~~ 79 (119)
|||+|.++|++. +.|+|++|+||||.++||||++|+|++|+||||++|+||..|+.|+|.|+||+|+|+||+|+.|++.
T Consensus 1 mgR~F~~~l~~~~~~y~C~~C~thla~~~dliSksf~gr~G~AyLf~~vvNv~~ge~e~R~mlTG~h~V~di~C~~C~~~ 80 (122)
T KOG3399|consen 1 MGRLFEAMLEANHRLYSCAHCKTHLARHDDLISKSFRGRTGRAYLFNRVVNVIIGETEQRVMLTGLHTVADIFCVLCGTG 80 (122)
T ss_pred CcchHHHHhccCCceEeccCCcccccchhhccccccccCCCcchhhhhhhhheechHHHHHHHHhHHhhcchhhhhcCCC
Confidence 999999999985 7999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeeEEEecccCCCeecCeEEEEeeeeeccccccccCCC
Q psy6706 80 LGWVYEFALEETQRYKEGRVILERALVTESDVKILDLGS 118 (119)
Q Consensus 80 lGWkY~~A~e~sqkYKEGkfILE~~~i~~~~~~~~~~~~ 118 (119)
|||||+.|||+||||||||||||+++|.+++||+...++
T Consensus 81 ~GWkYe~a~e~sQkyKEGk~ilE~~~i~~~~g~~~~~~~ 119 (122)
T KOG3399|consen 81 LGWKYEHAYEKSQKYKEGKFILELAEIFKPEGWDLEVGA 119 (122)
T ss_pred cceeeeeccCchhhhcCcchHHHHHHhcCCCCchhhcCC
Confidence 999999999999999999999999999999999988765
No 2
>PF03226 Yippee-Mis18: Yippee zinc-binding/DNA-binding /Mis18, centromere assembly; InterPro: IPR004910 This entry represents the Yippee-like (YPEL) family of putative zinc-binding proteins which is highly conserved among eukaryotes. The first protein in this family to be characterised, the Yippee protein from Drosophila, was identified by yeast interaction trap screen as a protein that physically interacts with moth hemolin []. It was subsequently found to be a member of a highly conserved family of proteins found in diverse eukaryotes including plants, animals and fungi []. Mammals contain five members of this family, YPEL1 to YPEL5, while other organisms tend to contain only two or three members. The mammalian proteins all appear to localise in the nucleus. YPEL1-4 are located in an unknown structure located on or close to the mitotic apparatus in the mitotic phase, whereas in the interphase they are located in the nuclei and nucleoli. In contrast, YPEL5 is localised to the centrosome and nucleus during interphase and at the mitotic spindle during mitosis, suggesting a function distinct from that of YPEL1-4. The localisation of the YPEL proteins suggests a novel, thopugh still unknown, function involved in cell division.
Probab=99.98 E-value=3.6e-33 Score=192.33 Aligned_cols=89 Identities=51% Similarity=0.952 Sum_probs=84.8
Q ss_pred eEEccCCCCCcCCCCCeeeecccCCCcceEEEeeeccccCCCccceEecccc----EEeeeeeeccCCCcceeeEEEecc
Q psy6706 14 LFSCAACDTILTNRRELISTRFTGATGRAFLFHRVVNLNYSDVQDRVMLTGR----HMVRDVSCKNCNTKLGWVYEFALE 89 (119)
Q Consensus 14 ~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~----H~v~dI~C~~C~~~lGWkY~~A~e 89 (119)
+|.|++|++||+++++|+| |+|+.|+||||+ ||..+++++|.|+||. |+|+||+|++|++.|||||++|++
T Consensus 2 vf~C~~C~t~l~ds~~lvs--~~g~~~~a~l~~---~v~~~~~~~~~~~t~~~~~~~~~~~l~C~~C~~~lGwkY~~a~~ 76 (96)
T PF03226_consen 2 VFQCKNCKTILADSNELVS--FHGREGKAYLFN---NVSNGVPVDRELMTGETGGDHTVRDLFCSGCNTILGWKYESAPE 76 (96)
T ss_pred EEECCCCCCCcCCHHHhee--cCCCCccEEEEe---eeeecccccceEEEeeCCCCEEEEEeEcccCChhHCcEEEEcCH
Confidence 7999999999999999999 999999999998 7777888999999999 999999999999999999999999
Q ss_pred cCCCeecCeEEEEeeeeec
Q psy6706 90 ETQRYKEGRVILERALVTE 108 (119)
Q Consensus 90 ~sqkYKEGkfILE~~~i~~ 108 (119)
+ |+||||+||||++.|..
T Consensus 77 ~-~~~k~g~file~~~i~~ 94 (96)
T PF03226_consen 77 E-QKYKEGKFILEKASISS 94 (96)
T ss_pred h-HhhhCCEEEEEhhHEEE
Confidence 9 99999999999998863
No 3
>PF11648 RIG-I_C-RD: C-terminal domain of RIG-I; InterPro: IPR021673 This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependent dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity []. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2RQB_A 3GA3_A 2W4R_D 3EQT_A 2RQA_A 2RMJ_A 3NCU_A 2QFD_C 2QFB_D 3TMI_A ....
Probab=95.89 E-value=0.0034 Score=45.49 Aligned_cols=88 Identities=13% Similarity=0.188 Sum_probs=57.6
Q ss_pred eEEccCCCCCcCCCCCeeeecccC--CCcceEEEeeeccccCCCccceEeccccEEeeeeeeccCCCcceeeEEEecccC
Q psy6706 14 LFSCAACDTILTNRRELISTRFTG--ATGRAFLFHRVVNLNYSDVQDRVMLTGRHMVRDVSCKNCNTKLGWVYEFALEET 91 (119)
Q Consensus 14 ~y~C~~C~thLa~~~~liSk~f~G--~~G~AyLf~~v~Nv~~g~~e~r~m~TG~H~v~dI~C~~C~~~lGWkY~~A~e~s 91 (119)
.+-|++|.+.++..+||-.-.-+. --.++ |...+.+...|.+.....-+.+....|+|.+|+..+|-.+..---+=
T Consensus 4 ~llC~kC~~~~C~~~DIr~ie~~hhv~v~p~--F~~~~~~~~~~~~~~~~~~d~~~~~~I~C~~C~~~wG~~m~yk~~~L 81 (123)
T PF11648_consen 4 KLLCRKCKKFACSGSDIRKIENSHHVVVDPE--FWERYIVRPHPKPLQKSFGDWEPNGKIHCKNCGQDWGIMMKYKGVEL 81 (123)
T ss_dssp EEEETTTTCEEEEGGGEEEETTTEEEE-SHH--HHCTEEEEECSSCTSEEESSSEEEEEEEETSTSBEEEEEEEETTEEE
T ss_pred EEECCCCCceeEchhheEEecCCcEEEcCcc--ceeeEEeccCCccccceecceEeCCEEEcCCCChHhhhheEECCccc
Confidence 488999999999999987652110 00112 22444455555553344557789999999999999998776544444
Q ss_pred CCeecCeEEEEe
Q psy6706 92 QRYKEGRVILER 103 (119)
Q Consensus 92 qkYKEGkfILE~ 103 (119)
.-.|.-.|+++.
T Consensus 82 P~L~iksfvv~~ 93 (123)
T PF11648_consen 82 PCLKIKSFVVEL 93 (123)
T ss_dssp EEE-GGGEEEEE
T ss_pred cEEEeeeeeeee
Confidence 566677777443
No 4
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=94.69 E-value=0.038 Score=41.16 Aligned_cols=67 Identities=19% Similarity=0.485 Sum_probs=42.0
Q ss_pred cceEEccCCCCCcCCCCCeeeecccCCCcceEEEeee-ccccCCCccceEeccccEEeeeeeeccCCCcceeeEEE
Q psy6706 12 SRLFSCAACDTILTNRRELISTRFTGATGRAFLFHRV-VNLNYSDVQDRVMLTGRHMVRDVSCKNCNTKLGWVYEF 86 (119)
Q Consensus 12 ~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v-~Nv~~g~~e~r~m~TG~H~v~dI~C~~C~~~lGWkY~~ 86 (119)
.-+|.|+.|+++|-++++ -|....|=.-.+..+ -|. +...+|.. -|+.. ..|.|.+|+.+||--...
T Consensus 38 ~G~Y~C~~Cg~pLF~S~~----KfdSg~GWPSF~~~i~~~~-V~~~~D~s--~gm~R-tEv~C~~Cg~HLGHVF~D 105 (134)
T TIGR00357 38 EGIYVDITCGEPLFSSED----KFDSGCGWPSFYKPISEEV-VAYERDES--HGMIR-TEVRCRNCDAHLGHVFDD 105 (134)
T ss_pred CeEEEccCCCCccccccc----hhcCCCCCcCcCcccCCCc-eEEeecCC--CCcEE-EEEEecCCCCccCcccCC
Confidence 468999999999987765 355555544444444 122 22233322 24333 579999999999965543
No 5
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=94.50 E-value=0.031 Score=41.98 Aligned_cols=85 Identities=19% Similarity=0.380 Sum_probs=49.2
Q ss_pred cceEEccCCCCCcCCCCCeeeecccCCCcceEEEeeeccccCCCccceEeccccEEeeeeeeccCCCcceeeEEEecccC
Q psy6706 12 SRLFSCAACDTILTNRRELISTRFTGATGRAFLFHRVVNLNYSDVQDRVMLTGRHMVRDVSCKNCNTKLGWVYEFALEET 91 (119)
Q Consensus 12 ~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~H~v~dI~C~~C~~~lGWkY~~A~e~s 91 (119)
.-+|.|+.|+++|=++++ -|....|=.-.+..+-.-.+...+|+ .-|+. =..|.|..|+.+||-.....- .
T Consensus 41 ~G~Y~C~~Cg~pLF~S~~----Kf~Sg~GWPSF~~~i~~~~V~~~~D~--s~gm~-RtEv~C~~Cg~HLGHVF~DGP--~ 111 (142)
T PRK00222 41 KGIYVCIVCGEPLFSSDT----KFDSGCGWPSFTKPIDEEAIRELRDT--SHGMV-RTEVRCANCDSHLGHVFPDGP--K 111 (142)
T ss_pred CeEEEecCCCchhcCCcc----cccCCCCCcCcCcccCCCceEEeecc--CCCce-EEEEEeCCCCCccCcccCCCC--C
Confidence 568999999999988754 46555665554554421122222222 11222 257999999999997665432 2
Q ss_pred CCeecCeEEEEeeeee
Q psy6706 92 QRYKEGRVILERALVT 107 (119)
Q Consensus 92 qkYKEGkfILE~~~i~ 107 (119)
+. -=+|-|.-+.|.
T Consensus 112 pt--g~RyCINs~sL~ 125 (142)
T PRK00222 112 PT--GLRYCINSASLK 125 (142)
T ss_pred CC--CCEeeeceeeEE
Confidence 21 115555555444
No 6
>PF01641 SelR: SelR domain; InterPro: IPR002579 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A []. The overall structure shows no resemblance to the structures of MsrA (IPR002569 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin. In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0008113 peptide-methionine-(S)-S-oxide reductase activity, 0055114 oxidation-reduction process; PDB: 1L1D_A 3E0O_D 2KZN_A 3HCG_B 3HCH_A 2L1U_A 3MAO_A 2K8D_A 3HCJ_A 3HCI_A ....
Probab=94.29 E-value=0.031 Score=41.03 Aligned_cols=71 Identities=21% Similarity=0.475 Sum_probs=42.5
Q ss_pred cceEEccCCCCCcCCCCCeeeecccCCCcceEEEeeeccccCCCccceEeccccEEeeeeeeccCCCcceeeEEEecc
Q psy6706 12 SRLFSCAACDTILTNRRELISTRFTGATGRAFLFHRVVNLNYSDVQDRVMLTGRHMVRDVSCKNCNTKLGWVYEFALE 89 (119)
Q Consensus 12 ~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~H~v~dI~C~~C~~~lGWkY~~A~e 89 (119)
.-+|.|+.|+++|=+++. -|....|=.-.+..+..-.+...+|.. -|+ .-..|.|.+|+.+||=-......
T Consensus 35 ~G~Y~C~~Cg~pLF~S~~----Kf~Sg~GWPSF~~~i~~~~v~~~~D~s--~g~-~R~Ev~C~~Cg~HLGHVF~DGp~ 105 (124)
T PF01641_consen 35 EGIYVCAVCGTPLFSSDT----KFDSGCGWPSFWQPIPGDAVKEREDFS--HGM-VRTEVRCARCGSHLGHVFDDGPP 105 (124)
T ss_dssp SEEEEETTTS-EEEEGGG----EETSSSSSSEESSCSSTTSEEEEEEEC--TSS-EEEEEEETTTCCEEEEEESTSST
T ss_pred CEEEEcCCCCCccccCcc----cccCCcCCccccCcCChHHEEEecccc--CCc-eEEEEEecCCCCccccEeCCCCC
Confidence 468999999999976653 355555554444443321222222222 133 34579999999999976654443
No 7
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=93.99 E-value=0.065 Score=39.24 Aligned_cols=64 Identities=22% Similarity=0.510 Sum_probs=42.4
Q ss_pred cceEEccCCCCCcCCCCCeeeecccCCCcceEEEeeeccccCCCccceEeccccEEeeeeeeccCCCcceeeEE
Q psy6706 12 SRLFSCAACDTILTNRRELISTRFTGATGRAFLFHRVVNLNYSDVQDRVMLTGRHMVRDVSCKNCNTKLGWVYE 85 (119)
Q Consensus 12 ~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~H~v~dI~C~~C~~~lGWkY~ 85 (119)
.-+|.|+.|+++|=++++ -|....|=.-.+..+-|. +...+|.. | .=..|.|.+|+.+||--..
T Consensus 31 ~G~Y~C~~Cg~pLF~S~~----KfdSg~GWPSF~~~i~~~-v~~~~D~~---~--~RtEv~C~~C~~HLGHVF~ 94 (119)
T PRK05508 31 KGTYVCKQCGAPLYRSED----KFKSGCGWPSFDDEIKGA-VKRIPDAD---G--RRTEIVCANCGGHLGHVFE 94 (119)
T ss_pred CeEEEecCCCCccccccc----cccCCCCCcccCcccccc-eEEEecCC---C--cEEEEEeCCCCCccCcccC
Confidence 468999999999987764 466566654445554332 23333433 2 2467999999999995543
No 8
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=92.23 E-value=0.12 Score=42.67 Aligned_cols=64 Identities=23% Similarity=0.551 Sum_probs=42.7
Q ss_pred cceEEccCCCCCcCCCCCeeeecccCCCcceEEEeeeccccCCCccceEeccccEEeeeeeeccCCCcceeeEE
Q psy6706 12 SRLFSCAACDTILTNRRELISTRFTGATGRAFLFHRVVNLNYSDVQDRVMLTGRHMVRDVSCKNCNTKLGWVYE 85 (119)
Q Consensus 12 ~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~H~v~dI~C~~C~~~lGWkY~ 85 (119)
.-+|.|+.|+++|=++++ -|....|=.-.++.+-|-.. ..++. .|+ =..|.|.+|+.+||--..
T Consensus 34 ~G~y~c~~c~~~LF~s~~----Kf~sg~GWPsF~~~~~~~~~-~~~d~---~~~--R~Ev~c~~c~~HLGHvF~ 97 (283)
T PRK05550 34 KGVYLCRRCGAPLFRSED----KFNSGCGWPSFDDEIPGAVK-RLPDA---DGR--RTEIVCANCGAHLGHVFE 97 (283)
T ss_pred CcEEEcCCCCchhcCChh----hccCCCCCcCcCcccCCccE-EEEcC---CCc--eEEEEecCCCCccCcccC
Confidence 468999999999988654 46556665444665544322 22222 233 478999999999996654
No 9
>KOG0856|consensus
Probab=90.90 E-value=0.33 Score=36.71 Aligned_cols=66 Identities=24% Similarity=0.518 Sum_probs=37.7
Q ss_pred cceEEccCCCCCcCCCCCeeeecccCCCcceEEEeeeccccCCCccceEe-ccccEEeeeeeeccCCCcceeeEE
Q psy6706 12 SRLFSCAACDTILTNRRELISTRFTGATGRAFLFHRVVNLNYSDVQDRVM-LTGRHMVRDVSCKNCNTKLGWVYE 85 (119)
Q Consensus 12 ~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~r~m-~TG~H~v~dI~C~~C~~~lGWkY~ 85 (119)
+-+|.|+.|.++|-.+.- -|....|=--.|+.+- .|....+.. .-|.| =.+|.|..|+.+||--.+
T Consensus 52 ~GvY~C~~C~~pLykS~t----KfdsgcGWPAF~e~i~---~gaI~r~~d~s~~~~-R~Ev~Ca~C~~HLGHVF~ 118 (146)
T KOG0856|consen 52 EGVYVCAGCGTPLYKSTT----KFDSGCGWPAFFEAIG---PGAITRTPDNSRGGR-RTEVSCATCGGHLGHVFK 118 (146)
T ss_pred CceEEEeecCCccccccc----cccCCCCCchhhhccC---CCceeeccccCCCCc-ceEEEEeecCCceeeeec
Confidence 469999999999977643 4554445433333321 111111111 01112 357999999999995543
No 10
>PF14976 FAM72: FAM72 protein
Probab=90.83 E-value=0.49 Score=35.93 Aligned_cols=63 Identities=24% Similarity=0.536 Sum_probs=40.7
Q ss_pred ceEEccCCCCCcCCCCCeeeecccCCCcceEEEeeeccccC----CCccceEecccc--------EEeeeeeeccCCCcc
Q psy6706 13 RLFSCAACDTILTNRRELISTRFTGATGRAFLFHRVVNLNY----SDVQDRVMLTGR--------HMVRDVSCKNCNTKL 80 (119)
Q Consensus 13 ~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~----g~~e~r~m~TG~--------H~v~dI~C~~C~~~l 80 (119)
.+..|+.|.+-|+...- ||.|..+ .|+.+ -||....-.+|. =.++|+-|.+|+..|
T Consensus 14 ~~L~C~~C~~~l~~RgM-----------kAvLLad-t~ieLySTD~~P~~~v~~vg~~y~t~~C~C~~~d~aC~~CGn~v 81 (150)
T PF14976_consen 14 YILCCKFCDQVLCNRGM-----------KAVLLAD-TNIELYSTDIPPTNCVDFVGSCYFTRTCKCKIQDIACLGCGNIV 81 (150)
T ss_pred EEEECCCCCchhccchh-----------hheeecC-CccEEEecCCCCcccccccccceecccCceEeeeeeeecCCCee
Confidence 46889999998876432 4555554 33332 122222223333 389999999999999
Q ss_pred eeeEEEe
Q psy6706 81 GWVYEFA 87 (119)
Q Consensus 81 GWkY~~A 87 (119)
|+.+...
T Consensus 82 GYhV~~P 88 (150)
T PF14976_consen 82 GYHVVVP 88 (150)
T ss_pred eeEEEEE
Confidence 9888764
No 11
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=90.75 E-value=0.26 Score=43.69 Aligned_cols=68 Identities=10% Similarity=0.172 Sum_probs=42.6
Q ss_pred cceEEccCCCCCcCCCCCeeeecccCCCcceEEEeeeccccCCCccceEeccccEEeeeeeeccCCCcceeeEEE
Q psy6706 12 SRLFSCAACDTILTNRRELISTRFTGATGRAFLFHRVVNLNYSDVQDRVMLTGRHMVRDVSCKNCNTKLGWVYEF 86 (119)
Q Consensus 12 ~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~H~v~dI~C~~C~~~lGWkY~~ 86 (119)
+-+|.|+.|+++|=++++ -|....|=.-.+..+-+-.+...+|. .-|++. ..|.|.+|+.+||-....
T Consensus 416 ~G~y~c~~c~~pLf~s~~----Kf~sg~GWPsF~~~i~~~~v~~~~d~--s~g~~R-~Ev~c~~c~~HLGHvf~d 483 (521)
T PRK14018 416 PGIYVDVVSGEPLFSSAD----KYDSGCGWPSFTRPIDAKVVTEHDDF--SYNMRR-TEVRSRAADSHLGHVFPD 483 (521)
T ss_pred CEEEEecCCCCccccCcc----cccCCCCCcccCcccCcCceEEeecc--CCCceE-EEEEECCCCCcCCcccCC
Confidence 568999999999988753 45555555444444322222222232 123433 479999999999966644
No 12
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=85.56 E-value=1.4 Score=33.21 Aligned_cols=65 Identities=23% Similarity=0.469 Sum_probs=38.9
Q ss_pred cceEEccCCCCCcCCCCCeeeecccCCCcceEEEeeeccccCCCccceEeccccEEeeeeeeccCCCcceee
Q psy6706 12 SRLFSCAACDTILTNRRELISTRFTGATGRAFLFHRVVNLNYSDVQDRVMLTGRHMVRDVSCKNCNTKLGWV 83 (119)
Q Consensus 12 ~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~H~v~dI~C~~C~~~lGWk 83 (119)
.-+|.|+.|+.+|=.+++= |....|=--.+.-+..-.+...+|+ .-|++. ..|.|.+|+++||--
T Consensus 40 ~GiY~c~~cg~pLF~S~~K----fdSgcGWPSF~~pi~~~~I~~~~D~--S~gM~R-tEVrc~~c~sHLGHV 104 (140)
T COG0229 40 KGIYVCIVCGEPLFSSEDK----FDSGCGWPSFTKPISPDAITYKEDR--SHGMVR-TEVRCANCDSHLGHV 104 (140)
T ss_pred CceEEeecCCCcccccccc----ccCCCCCccccccCCcccceEeecc--CCCcEE-EEEEecCCCCccccc
Confidence 4689999999999877653 4434443323333322222233332 223333 469999999999943
No 13
>PF09814 HECT_2: HECT-like Ubiquitin-conjugating enzyme (E2)-binding; InterPro: IPR019193 This entry consists of E3 ubiquitin-protein ligases which accept ubiquitin from specific E2 ubiquitin-conjugating enzymes, and transfer it to substrates, generally promoting their degradation by the proteasome [].
Probab=69.35 E-value=9 Score=31.16 Aligned_cols=16 Identities=25% Similarity=0.592 Sum_probs=13.2
Q ss_pred eEEccCCCCCcCCCCC
Q psy6706 14 LFSCAACDTILTNRRE 29 (119)
Q Consensus 14 ~y~C~~C~thLa~~~~ 29 (119)
.+.|++|++.|.....
T Consensus 106 ~~~C~~C~~~li~~~~ 121 (354)
T PF09814_consen 106 SLCCRNCKNPLIPSRN 121 (354)
T ss_pred EEECCCCCCcccCccc
Confidence 7999999999976543
No 14
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=58.85 E-value=8.9 Score=21.64 Aligned_cols=21 Identities=33% Similarity=0.593 Sum_probs=16.0
Q ss_pred ceeeeccCCcceEEccCCCCC
Q psy6706 3 RIFLDHIGGSRLFSCAACDTI 23 (119)
Q Consensus 3 r~f~~yl~~~~~y~C~~C~th 23 (119)
|+-+.|+.|-+.++|+.|++.
T Consensus 8 ~t~L~yP~gA~~vrCs~C~~v 28 (31)
T TIGR01053 8 RTLLMYPRGASSVRCALCQTV 28 (31)
T ss_pred CcEeecCCCCCeEECCCCCeE
Confidence 345678888888999998764
No 15
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=47.84 E-value=22 Score=22.58 Aligned_cols=20 Identities=20% Similarity=0.233 Sum_probs=14.0
Q ss_pred ccEEeeeeeeccCCCcceee
Q psy6706 64 GRHMVRDVSCKNCNTKLGWV 83 (119)
Q Consensus 64 G~H~v~dI~C~~C~~~lGWk 83 (119)
....+.-.+|.+|++.|.+.
T Consensus 42 s~~~~~r~FC~~CGs~l~~~ 61 (92)
T PF04828_consen 42 SGKGVERYFCPTCGSPLFSE 61 (92)
T ss_dssp TTSSCEEEEETTT--EEEEE
T ss_pred CCCcCcCcccCCCCCeeecc
Confidence 44556669999999999976
No 16
>PRK02935 hypothetical protein; Provisional
Probab=47.68 E-value=13 Score=26.90 Aligned_cols=24 Identities=33% Similarity=0.577 Sum_probs=20.4
Q ss_pred ceEEccCCCCCcCCCCCeeeeccc
Q psy6706 13 RLFSCAACDTILTNRRELISTRFT 36 (119)
Q Consensus 13 ~~y~C~~C~thLa~~~~liSk~f~ 36 (119)
++..|-+|++||+...++--|.|+
T Consensus 85 rvD~CM~C~~PLTLd~~legkefd 108 (110)
T PRK02935 85 RVDACMHCNQPLTLDRSLEGKEFD 108 (110)
T ss_pred ceeecCcCCCcCCcCccccccCcC
Confidence 788999999999998888766664
No 17
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=45.18 E-value=19 Score=19.53 Aligned_cols=20 Identities=35% Similarity=0.579 Sum_probs=15.8
Q ss_pred ceeeeccCCcceEEccCCCC
Q psy6706 3 RIFLDHIGGSRLFSCAACDT 22 (119)
Q Consensus 3 r~f~~yl~~~~~y~C~~C~t 22 (119)
|..+.|..|-+.-.|+.|++
T Consensus 5 r~~L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 5 RTLLMYPRGAPSVRCACCHT 24 (25)
T ss_pred CceEEcCCCCCCeECCccCc
Confidence 45677888878889999876
No 18
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=40.70 E-value=18 Score=21.01 Aligned_cols=27 Identities=26% Similarity=0.366 Sum_probs=22.0
Q ss_pred eeeeeccCCCcc-eeeEEEecccCCCee
Q psy6706 69 RDVSCKNCNTKL-GWVYEFALEETQRYK 95 (119)
Q Consensus 69 ~dI~C~~C~~~l-GWkY~~A~e~sqkYK 95 (119)
-||.|..|.+.- --|.-+.-.-.|+|.
T Consensus 4 i~v~CP~C~s~~~v~k~G~~~~G~qryr 31 (36)
T PF03811_consen 4 IDVHCPRCQSTEGVKKNGKSPSGHQRYR 31 (36)
T ss_pred EeeeCCCCCCCCcceeCCCCCCCCEeEe
Confidence 378999999998 777777777778774
No 19
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=39.07 E-value=13 Score=27.08 Aligned_cols=24 Identities=29% Similarity=0.475 Sum_probs=20.6
Q ss_pred ceEEccCCCCCcCCCCCeeeeccc
Q psy6706 13 RLFSCAACDTILTNRRELISTRFT 36 (119)
Q Consensus 13 ~~y~C~~C~thLa~~~~liSk~f~ 36 (119)
+...|-+|++||+...++--|.|+
T Consensus 84 r~D~CM~C~~pLTLd~~legkef~ 107 (114)
T PF11023_consen 84 RVDACMHCKEPLTLDPSLEGKEFD 107 (114)
T ss_pred hhhccCcCCCcCccCchhhcchhh
Confidence 567999999999999988877775
No 20
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=34.83 E-value=27 Score=18.26 Aligned_cols=15 Identities=20% Similarity=0.729 Sum_probs=11.5
Q ss_pred CCcceEEccCCCCCc
Q psy6706 10 GGSRLFSCAACDTIL 24 (119)
Q Consensus 10 ~~~~~y~C~~C~thL 24 (119)
.+++.|.|..|..-+
T Consensus 10 ~~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 10 TGEKPYKCPYCGKSF 24 (26)
T ss_dssp SSSSSEEESSSSEEE
T ss_pred CCCCCCCCCCCcCee
Confidence 457889999998543
No 21
>TIGR02820 formald_GSH S-(hydroxymethyl)glutathione synthase. The formation of S-(hydroxymethyl)glutathione synthase from glutathione and formaldehyde occurs naturally, but this enzyme speeds its formation in some species as part of a pathway of formaldehyde detoxification.
Probab=34.59 E-value=53 Score=25.51 Aligned_cols=30 Identities=17% Similarity=0.239 Sum_probs=17.9
Q ss_pred CCccceEeccccEEeeeeeeccCCCcceeeE
Q psy6706 54 SDVQDRVMLTGRHMVRDVSCKNCNTKLGWVY 84 (119)
Q Consensus 54 g~~e~r~m~TG~H~v~dI~C~~C~~~lGWkY 84 (119)
|.........|.+.. --||..|++.|-+..
T Consensus 74 G~~~l~~Y~ss~~~~-R~FC~~CGS~L~~~~ 103 (182)
T TIGR02820 74 NGDKLKVVDASATIQ-RHACKGCGTHMYGRI 103 (182)
T ss_pred CCcceEEEeCCCCEE-eecCCCCCCcccccc
Confidence 443333233344444 449999999996554
No 22
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=31.92 E-value=8.5 Score=19.00 Aligned_cols=16 Identities=19% Similarity=0.789 Sum_probs=12.3
Q ss_pred EEccCCCCCcCCCCCe
Q psy6706 15 FSCAACDTILTNRREL 30 (119)
Q Consensus 15 y~C~~C~thLa~~~~l 30 (119)
|.|..|+..+...++|
T Consensus 1 y~C~~C~~~f~~~~~l 16 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNL 16 (23)
T ss_dssp EEETTTTEEESSHHHH
T ss_pred CCCCCCCCccCCHHHH
Confidence 7899999887776554
No 23
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=30.30 E-value=37 Score=24.46 Aligned_cols=22 Identities=18% Similarity=0.246 Sum_probs=16.7
Q ss_pred EEeeeeeeccCCCcceeeEEEe
Q psy6706 66 HMVRDVSCKNCNTKLGWVYEFA 87 (119)
Q Consensus 66 H~v~dI~C~~C~~~lGWkY~~A 87 (119)
+.+.-.+|..|+++|-|+....
T Consensus 65 ~~~~r~FC~~CGs~l~~~~~~~ 86 (133)
T COG3791 65 GSAGRGFCPTCGSPLFWRGPDE 86 (133)
T ss_pred CCCCCeecccCCCceEEecCCC
Confidence 3444449999999999997654
No 24
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=30.19 E-value=7.7 Score=19.94 Aligned_cols=18 Identities=22% Similarity=0.571 Sum_probs=13.5
Q ss_pred eEEccCCCCCcCCCCCee
Q psy6706 14 LFSCAACDTILTNRRELI 31 (119)
Q Consensus 14 ~y~C~~C~thLa~~~~li 31 (119)
+|.|..|+.-+.+.+.++
T Consensus 1 ~~~C~~C~~~F~~~~~l~ 18 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALR 18 (27)
T ss_dssp SEEETTTTEEESSHHHHH
T ss_pred CCCCCccCCccCChhHHH
Confidence 588999998877665554
No 25
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=29.84 E-value=28 Score=19.93 Aligned_cols=14 Identities=21% Similarity=0.415 Sum_probs=7.2
Q ss_pred eeccCCCcceeeEE
Q psy6706 72 SCKNCNTKLGWVYE 85 (119)
Q Consensus 72 ~C~~C~~~lGWkY~ 85 (119)
||..|++.|-++..
T Consensus 2 fC~~CG~~l~~~ip 15 (34)
T PF14803_consen 2 FCPQCGGPLERRIP 15 (34)
T ss_dssp B-TTT--B-EEE--
T ss_pred ccccccChhhhhcC
Confidence 79999999988875
No 26
>KOG2462|consensus
Probab=28.56 E-value=18 Score=30.10 Aligned_cols=22 Identities=32% Similarity=0.742 Sum_probs=19.1
Q ss_pred CCcceEEccCCCCCcCCCCCee
Q psy6706 10 GGSRLFSCAACDTILTNRRELI 31 (119)
Q Consensus 10 ~~~~~y~C~~C~thLa~~~~li 31 (119)
.|++.|.|.+|+.-+|..+.|-
T Consensus 211 TGEKPF~C~hC~kAFADRSNLR 232 (279)
T KOG2462|consen 211 TGEKPFSCPHCGKAFADRSNLR 232 (279)
T ss_pred cCCCCccCCcccchhcchHHHH
Confidence 5789999999999999887764
No 27
>PF02945 Endonuclease_7: Recombination endonuclease VII; InterPro: IPR004211 This family of proteins which includes Bacteriophage T4 endonuclease VII, Mycobacteriophage D29 gene 59, and other as yet uncharacterised proteins. The T4 endonuclease VII (Endo VII) recognises a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches. The structure of this enzyme has been resolved and it was found that the monomers form an elongated, intertwined molecular dimer that exibits extreme domain swapping. Two pairs of antiparallel helices which form a novel 'four-helix cross' motif are the major dimerisation elements [].; PDB: 3GOX_A 3FC3_A 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=28.02 E-value=8.9 Score=26.01 Aligned_cols=16 Identities=56% Similarity=1.059 Sum_probs=14.9
Q ss_pred eeeeeeccCCCcceee
Q psy6706 68 VRDVSCKNCNTKLGWV 83 (119)
Q Consensus 68 v~dI~C~~C~~~lGWk 83 (119)
||-+-|..|++.||+-
T Consensus 50 vRGlLC~~CN~~lG~~ 65 (81)
T PF02945_consen 50 VRGLLCRSCNTALGKV 65 (81)
T ss_dssp EEEEEEHHHHHHHHHC
T ss_pred chhhhhhHHhhhhccc
Confidence 9999999999999975
No 28
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=27.50 E-value=48 Score=18.53 Aligned_cols=15 Identities=27% Similarity=0.640 Sum_probs=12.6
Q ss_pred ceEEccCCCCCcCCC
Q psy6706 13 RLFSCAACDTILTNR 27 (119)
Q Consensus 13 ~~y~C~~C~thLa~~ 27 (119)
..|.|..|..+|...
T Consensus 15 T~~~C~~C~v~lC~~ 29 (32)
T PF13842_consen 15 TRYMCSKCDVPLCVE 29 (32)
T ss_pred eEEEccCCCCcccCC
Confidence 579999999988764
No 29
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=27.26 E-value=26 Score=23.73 Aligned_cols=16 Identities=19% Similarity=0.478 Sum_probs=13.5
Q ss_pred eEEccCCCCCcCCCCC
Q psy6706 14 LFSCAACDTILTNRRE 29 (119)
Q Consensus 14 ~y~C~~C~thLa~~~~ 29 (119)
.|.|++|++.+..-+.
T Consensus 4 ~Y~CRHCg~~IG~i~~ 19 (76)
T PF10955_consen 4 HYYCRHCGTKIGTIDA 19 (76)
T ss_pred EEEecCCCCEEEEeec
Confidence 4999999999987655
No 30
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=26.04 E-value=24 Score=18.64 Aligned_cols=11 Identities=45% Similarity=0.896 Sum_probs=6.7
Q ss_pred eeeeccCCCcc
Q psy6706 70 DVSCKNCNTKL 80 (119)
Q Consensus 70 dI~C~~C~~~l 80 (119)
+-+|..|++.|
T Consensus 16 ~~fC~~CG~~L 26 (26)
T PF13248_consen 16 AKFCPNCGAKL 26 (26)
T ss_pred cccChhhCCCC
Confidence 45667666654
No 31
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=25.77 E-value=65 Score=25.15 Aligned_cols=38 Identities=16% Similarity=0.175 Sum_probs=23.6
Q ss_pred EEeeeeeeccCCCcceeeEEEecccCCCeecCeEEEEeeeee
Q psy6706 66 HMVRDVSCKNCNTKLGWVYEFALEETQRYKEGRVILERALVT 107 (119)
Q Consensus 66 H~v~dI~C~~C~~~lGWkY~~A~e~sqkYKEGkfILE~~~i~ 107 (119)
..+.--+|..|++.|-+.++..-.. -.|..+|-...+-
T Consensus 89 ~~i~R~FC~~CGS~L~~~~e~~~~~----~pgl~fV~~gllD 126 (191)
T PRK05417 89 ATIQRHACKECGVHMYGRIENKDHP----FYGLDFVHTELSQ 126 (191)
T ss_pred CCeEeeeCCCCCCccccccccccCC----CCCeEEEehhhcC
Confidence 3355559999999998887622101 1366666555543
No 32
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=25.68 E-value=21 Score=22.39 Aligned_cols=35 Identities=17% Similarity=0.347 Sum_probs=24.7
Q ss_pred EeeeccccCCCccceEeccccEEeeeeeeccCCCcceeeE
Q psy6706 45 FHRVVNLNYSDVQDRVMLTGRHMVRDVSCKNCNTKLGWVY 84 (119)
Q Consensus 45 f~~v~Nv~~g~~e~r~m~TG~H~v~dI~C~~C~~~lGWkY 84 (119)
|++++.+..|..+ |+...---+-|.+|..+=|---
T Consensus 2 ~Dki~d~L~G~d~-----~~~~~r~aLIC~~C~~hNGla~ 36 (54)
T PF10058_consen 2 FDKILDVLLGDDP-----TSPSNRYALICSKCFSHNGLAP 36 (54)
T ss_pred hHHHHHHHhCCCC-----ccccCceeEECcccchhhcccc
Confidence 4567777777766 4554445566999999998654
No 33
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=25.07 E-value=1.1e+02 Score=22.16 Aligned_cols=30 Identities=13% Similarity=0.028 Sum_probs=25.4
Q ss_pred cCCCcceEEEeeeccccCCCccceEecccc
Q psy6706 36 TGATGRAFLFHRVVNLNYSDVQDRVMLTGR 65 (119)
Q Consensus 36 ~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~ 65 (119)
.|+||.|+.--.+.|+..|..-+..+.++-
T Consensus 35 pGkhG~A~vr~k~knl~tG~~~e~~f~s~~ 64 (130)
T TIGR00037 35 PGKHGHAKARVVAIGIFTGKKLEFVSPSTS 64 (130)
T ss_pred CCCCCcEEEEEEEEECCCCCEEEEEECCCC
Confidence 689999999999999999998877666554
No 34
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=24.79 E-value=29 Score=18.41 Aligned_cols=13 Identities=31% Similarity=0.774 Sum_probs=10.8
Q ss_pred ceEEccCCCCCcC
Q psy6706 13 RLFSCAACDTILT 25 (119)
Q Consensus 13 ~~y~C~~C~thLa 25 (119)
.-|.|..|+..|+
T Consensus 26 ~Cf~C~~C~~~L~ 38 (39)
T smart00132 26 ECFKCSKCGKPLG 38 (39)
T ss_pred cCCCCcccCCcCc
Confidence 4489999999886
No 35
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=24.36 E-value=33 Score=20.25 Aligned_cols=16 Identities=25% Similarity=0.681 Sum_probs=13.6
Q ss_pred ceEEccCCCCCcCCCC
Q psy6706 13 RLFSCAACDTILTNRR 28 (119)
Q Consensus 13 ~~y~C~~C~thLa~~~ 28 (119)
.-|.|..|+.+|...+
T Consensus 25 ~Cf~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 25 ECFKCSKCGKPLNDGD 40 (58)
T ss_dssp TTSBETTTTCBTTTSS
T ss_pred cccccCCCCCccCCCe
Confidence 4589999999998776
No 36
>PRK11586 napB nitrate reductase cytochrome C550 subunit; Provisional
Probab=24.28 E-value=48 Score=25.25 Aligned_cols=28 Identities=18% Similarity=0.479 Sum_probs=24.2
Q ss_pred cceEEccCCCCCcCCCCCeeeecccCCC
Q psy6706 12 SRLFSCAACDTILTNRRELISTRFTGAT 39 (119)
Q Consensus 12 ~~~y~C~~C~thLa~~~~liSk~f~G~~ 39 (119)
.+.|-|..|+++=+...-|+.-.|....
T Consensus 118 prRYfCtQCHVPQada~PLV~N~F~~~~ 145 (149)
T PRK11586 118 PRRYFCLQCHVPQADTAPIVGNTFTPSK 145 (149)
T ss_pred ccceeeccccCccccCccCCCCCccchh
Confidence 4779999999999999999999887543
No 37
>PF10238 Eapp_C: E2F-associated phosphoprotein; InterPro: IPR019370 This entry represents E2F binding proteins. E2F transcription factors play an essential role in cell proliferation and apoptosis and their activity is frequently deregulated in human cancers. E2F activity is regulated by a variety of mechanisms, frequently mediated by proteins binding to individual members or a subgroup of the family. E2F-associated phosphoprotein (EAPP)interacts with a subset of E2F factors and influences E2F-dependent promoter activity. EAPP is present throughout the cell cycle but disappears during mitosis [].
Probab=24.23 E-value=48 Score=24.66 Aligned_cols=26 Identities=23% Similarity=0.428 Sum_probs=19.8
Q ss_pred CcceEEccCCCCCcCCCCC---eeeeccc
Q psy6706 11 GSRLFSCAACDTILTNRRE---LISTRFT 36 (119)
Q Consensus 11 ~~~~y~C~~C~thLa~~~~---liSk~f~ 36 (119)
+..+.+|..|-|.|+...+ ....+|+
T Consensus 26 sDavLsCp~Cft~lc~dcQrHe~y~~QYR 54 (136)
T PF10238_consen 26 SDAVLSCPACFTTLCLDCQRHEKYKNQYR 54 (136)
T ss_pred CCceEeCccccceeeecccccchhcceee
Confidence 3578999999999997666 5555664
No 38
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=23.40 E-value=29 Score=18.07 Aligned_cols=10 Identities=50% Similarity=0.933 Sum_probs=5.9
Q ss_pred eeeccCCCcc
Q psy6706 71 VSCKNCNTKL 80 (119)
Q Consensus 71 I~C~~C~~~l 80 (119)
.+|..|++.|
T Consensus 14 ~fC~~CG~~l 23 (23)
T PF13240_consen 14 KFCPNCGTPL 23 (23)
T ss_pred cchhhhCCcC
Confidence 4566666654
No 39
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=23.12 E-value=1.2e+02 Score=22.90 Aligned_cols=30 Identities=13% Similarity=0.214 Sum_probs=26.0
Q ss_pred cCCCcceEEEeeeccccCCCccceEecccc
Q psy6706 36 TGATGRAFLFHRVVNLNYSDVQDRVMLTGR 65 (119)
Q Consensus 36 ~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~ 65 (119)
.|+||.|+.--.+.|+..|...+....++-
T Consensus 49 pGKHG~A~vr~k~knl~TG~k~e~~f~s~~ 78 (159)
T PLN03107 49 TGKHGHAKCHFVAIDIFTGKKLEDIVPSSH 78 (159)
T ss_pred CCCCCcEEEEEEEEECCCCCEEEEEecCCC
Confidence 799999999999999999999887776654
No 40
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=23.12 E-value=96 Score=18.08 Aligned_cols=17 Identities=24% Similarity=0.464 Sum_probs=12.7
Q ss_pred ceEEccCCCCCcCCCCC
Q psy6706 13 RLFSCAACDTILTNRRE 29 (119)
Q Consensus 13 ~~y~C~~C~thLa~~~~ 29 (119)
..|.|..|+-+......
T Consensus 19 ~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 19 RRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CEEECCcCCCeEECCCc
Confidence 47999999987665554
No 41
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=22.68 E-value=48 Score=19.36 Aligned_cols=12 Identities=25% Similarity=1.005 Sum_probs=7.4
Q ss_pred ceEEccCCCCCc
Q psy6706 13 RLFSCAACDTIL 24 (119)
Q Consensus 13 ~~y~C~~C~thL 24 (119)
.+|.|.+|++-+
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 689999999765
No 42
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=21.86 E-value=53 Score=19.27 Aligned_cols=14 Identities=21% Similarity=0.544 Sum_probs=9.9
Q ss_pred eEEccCCCCCcCCC
Q psy6706 14 LFSCAACDTILTNR 27 (119)
Q Consensus 14 ~y~C~~C~thLa~~ 27 (119)
.|.|.+|++.+...
T Consensus 3 ~y~C~~CG~~~~~~ 16 (46)
T PRK00398 3 EYKCARCGREVELD 16 (46)
T ss_pred EEECCCCCCEEEEC
Confidence 58888888766543
No 43
>KOG2272|consensus
Probab=21.60 E-value=64 Score=27.09 Aligned_cols=32 Identities=22% Similarity=0.599 Sum_probs=20.7
Q ss_pred CcceEEccCCCCCcCCCCCeeeecccCCCcceEEEe
Q psy6706 11 GSRLFSCAACDTILTNRRELISTRFTGATGRAFLFH 46 (119)
Q Consensus 11 ~~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~ 46 (119)
+..+|.|..|+.|+-. +.|+ |+|..=-+|.|+
T Consensus 134 ~~g~YvC~KCh~~iD~-~~l~---fr~d~yH~yHFk 165 (332)
T KOG2272|consen 134 GRGRYVCQKCHAHIDE-QPLT---FRGDPYHPYHFK 165 (332)
T ss_pred ccceeehhhhhhhccc-cccc---ccCCCCCcccee
Confidence 3447888888888876 3332 555555566676
No 44
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=21.48 E-value=26 Score=25.17 Aligned_cols=50 Identities=18% Similarity=0.363 Sum_probs=31.2
Q ss_pred EEeeeccccCCCccceEecccc--EEeeeeeeccCCCcceeeEE----EecccCCCeecCe
Q psy6706 44 LFHRVVNLNYSDVQDRVMLTGR--HMVRDVSCKNCNTKLGWVYE----FALEETQRYKEGR 98 (119)
Q Consensus 44 Lf~~v~Nv~~g~~e~r~m~TG~--H~v~dI~C~~C~~~lGWkY~----~A~e~sqkYKEGk 98 (119)
|+++--=+..|+++++. ++|. |+|.|-- ---.|||.. +.-.++++|..|-
T Consensus 10 lLR~S~fi~lG~~~gk~-V~G~I~hvv~ddL----YIDfG~KFhcVc~rp~~~~~~y~~G~ 65 (104)
T PF10246_consen 10 LLRNSPFIQLGDPEGKI-VIGKIFHVVDDDL----YIDFGGKFHCVCKRPAVNGEKYVRGS 65 (104)
T ss_pred HhcCChhhhcCCccCCE-EEEEEEEEecCce----EEEeCCceeEEEecccccccccccCC
Confidence 33433345578888876 5675 8887621 124688864 3345778899984
No 45
>KOG2324|consensus
Probab=21.02 E-value=71 Score=28.12 Aligned_cols=13 Identities=31% Similarity=0.343 Sum_probs=10.5
Q ss_pred cceeeEEEecccC
Q psy6706 79 KLGWVYEFALEET 91 (119)
Q Consensus 79 ~lGWkY~~A~e~s 91 (119)
.||=||-+++...
T Consensus 271 ~LG~kYS~~lna~ 283 (457)
T KOG2324|consen 271 LLGTKYSKPLNAK 283 (457)
T ss_pred EeccccccccCce
Confidence 6899998888655
No 46
>PRK05978 hypothetical protein; Provisional
Probab=20.39 E-value=50 Score=24.89 Aligned_cols=24 Identities=29% Similarity=0.611 Sum_probs=19.4
Q ss_pred cceeeeccCCcceEEccCCCCCcCCC
Q psy6706 2 GRIFLDHIGGSRLFSCAACDTILTNR 27 (119)
Q Consensus 2 Gr~f~~yl~~~~~y~C~~C~thLa~~ 27 (119)
|++|..||.= .=.|.+|+.++...
T Consensus 42 G~LF~g~Lkv--~~~C~~CG~~~~~~ 65 (148)
T PRK05978 42 GKLFRAFLKP--VDHCAACGEDFTHH 65 (148)
T ss_pred Cccccccccc--CCCccccCCccccC
Confidence 7889999873 35799999998765
Done!