Query 034010
Match_columns 106
No_of_seqs 105 out of 331
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 08:47:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034010.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034010hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3399 Predicted Yippee-type 100.0 2.7E-50 5.8E-55 286.6 -2.5 102 3-104 8-110 (122)
2 PF03226 Yippee-Mis18: Yippee 100.0 5.6E-34 1.2E-38 192.2 6.0 88 9-102 2-93 (96)
3 PF11648 RIG-I_C-RD: C-termina 96.2 0.0023 5E-08 45.4 1.4 88 9-98 4-93 (123)
4 TIGR00357 methionine-R-sulfoxi 94.9 0.035 7.5E-07 40.5 3.6 68 7-81 38-105 (134)
5 PRK00222 methionine sulfoxide 94.9 0.027 6E-07 41.4 3.0 69 6-81 40-108 (142)
6 PF01641 SelR: SelR domain; I 94.7 0.037 8E-07 39.8 3.2 72 7-85 35-106 (124)
7 PRK05508 methionine sulfoxide 94.1 0.067 1.4E-06 38.4 3.5 64 7-80 31-94 (119)
8 PRK05550 bifunctional methioni 92.9 0.096 2.1E-06 42.3 2.9 63 7-80 34-97 (283)
9 PRK14018 trifunctional thiored 90.9 0.28 6E-06 42.6 3.7 70 6-82 415-484 (521)
10 PF14976 FAM72: FAM72 protein 88.4 1.2 2.5E-05 33.2 4.8 62 9-82 15-88 (150)
11 KOG0856 Predicted pilin-like t 88.3 0.67 1.5E-05 34.3 3.5 65 7-80 52-118 (146)
12 COG0229 Conserved domain frequ 83.1 2.2 4.7E-05 31.5 4.0 65 7-78 40-104 (140)
13 PF09814 HECT_2: HECT-like Ubi 77.7 4.5 9.8E-05 32.2 4.6 17 9-25 106-122 (354)
14 PF11023 DUF2614: Protein of u 54.5 5.2 0.00011 28.6 0.5 25 8-32 84-108 (114)
15 PF13465 zf-H2C2_2: Zinc-finge 47.5 11 0.00025 19.3 1.0 14 5-18 10-23 (26)
16 KOG2462 C2H2-type Zn-finger pr 46.0 6.3 0.00014 32.0 -0.2 22 5-26 211-232 (279)
17 PRK05417 glutathione-dependent 42.2 27 0.00059 26.7 2.8 35 45-80 74-108 (191)
18 COG3791 Uncharacterized conser 40.4 20 0.00044 25.3 1.7 22 61-82 65-86 (133)
19 PF04828 GFA: Glutathione-depe 40.0 35 0.00076 21.1 2.7 31 48-78 31-61 (92)
20 TIGR02820 formald_GSH S-(hydro 38.0 51 0.0011 25.0 3.7 34 45-79 70-103 (182)
21 PF14803 Nudix_N_2: Nudix N-te 37.9 19 0.00041 20.3 1.0 14 67-80 2-15 (34)
22 PF10955 DUF2757: Protein of u 37.4 13 0.00029 24.7 0.4 16 9-24 4-19 (76)
23 PF03811 Zn_Tnp_IS1: InsA N-te 37.2 22 0.00048 20.2 1.2 27 64-90 4-31 (36)
24 TIGR00037 eIF_5A translation i 37.0 38 0.00081 24.1 2.7 31 31-61 35-65 (130)
25 PRK11586 napB nitrate reductas 33.3 27 0.00058 26.0 1.5 28 7-34 118-145 (149)
26 PF00412 LIM: LIM domain; Int 31.9 23 0.0005 20.5 0.8 15 9-23 26-40 (58)
27 PF02945 Endonuclease_7: Recom 31.2 8.1 0.00018 25.7 -1.4 16 63-78 50-65 (81)
28 smart00132 LIM Zinc-binding do 31.0 20 0.00043 18.7 0.4 13 8-20 26-38 (39)
29 KOG2272 Focal adhesion protein 29.0 32 0.00069 28.3 1.3 33 5-41 133-165 (332)
30 KOG2324 Prolyl-tRNA synthetase 28.8 45 0.00097 28.7 2.2 13 74-86 271-283 (457)
31 PF13912 zf-C2H2_6: C2H2-type 28.7 6 0.00013 20.0 -1.9 18 9-26 1-18 (27)
32 PF11682 DUF3279: Protein of u 28.7 33 0.00073 24.8 1.3 18 8-25 27-44 (128)
33 PF13248 zf-ribbon_3: zinc-rib 28.5 19 0.00042 18.6 0.0 11 65-75 16-26 (26)
34 PF10058 DUF2296: Predicted in 28.1 22 0.00048 21.8 0.3 35 40-79 2-36 (54)
35 PF00096 zf-C2H2: Zinc finger, 28.0 8.2 0.00018 18.6 -1.4 16 10-25 1-16 (23)
36 PF04246 RseC_MucC: Positive r 27.1 86 0.0019 21.7 3.2 45 8-53 15-59 (135)
37 PF10246 MRP-S35: Mitochondria 26.7 41 0.00089 23.7 1.4 45 44-93 15-65 (104)
38 PF06170 DUF983: Protein of un 26.1 29 0.00062 23.2 0.5 23 11-41 10-32 (86)
39 PF13240 zinc_ribbon_2: zinc-r 26.0 23 0.0005 18.1 0.0 10 66-75 14-23 (23)
40 PF03150 CCP_MauG: Di-haem cyt 25.9 17 0.00038 26.5 -0.6 21 4-24 17-37 (159)
41 TIGR03791 TTQ_mauG tryptophan 24.7 47 0.001 26.7 1.6 32 4-35 18-51 (291)
42 PLN03107 eukaryotic translatio 24.4 92 0.002 23.0 3.0 31 31-61 49-79 (159)
43 cd02669 Peptidase_C19M A subfa 24.3 61 0.0013 27.0 2.2 53 4-76 23-77 (440)
44 PF13842 Tnp_zf-ribbon_2: DDE_ 24.2 64 0.0014 17.6 1.6 15 8-22 15-29 (32)
45 PRK00398 rpoP DNA-directed RNA 24.0 43 0.00094 19.2 1.0 14 9-22 3-16 (46)
46 COG3043 NapB Nitrate reductase 23.7 53 0.0011 24.6 1.6 30 6-35 123-152 (155)
47 PF12760 Zn_Tnp_IS1595: Transp 22.8 67 0.0015 18.5 1.7 12 6-17 34-45 (46)
48 cd07973 Spt4 Transcription elo 22.6 39 0.00085 23.2 0.7 22 11-32 22-49 (98)
49 PRK03999 translation initiatio 22.5 1.1E+02 0.0024 21.7 3.0 30 31-60 34-63 (129)
50 TIGR01053 LSD1 zinc finger dom 22.2 63 0.0014 17.7 1.3 17 2-18 12-28 (31)
51 TIGR00319 desulf_FeS4 desulfof 21.0 61 0.0013 17.5 1.2 13 8-20 6-18 (34)
52 PF06397 Desulfoferrod_N: Desu 20.9 53 0.0011 18.8 0.9 12 8-19 5-16 (36)
53 cd00974 DSRD Desulforedoxin (D 20.9 62 0.0014 17.5 1.2 13 8-20 3-15 (34)
54 smart00714 LITAF Possible memb 20.5 52 0.0011 20.3 0.9 11 67-77 54-64 (67)
55 PF14353 CpXC: CpXC protein 20.5 45 0.00098 22.9 0.7 46 40-87 15-60 (128)
No 1
>KOG3399 consensus Predicted Yippee-type zinc-binding protein [General function prediction only]
Probab=100.00 E-value=2.7e-50 Score=286.57 Aligned_cols=102 Identities=45% Similarity=0.919 Sum_probs=97.5
Q ss_pred ccCC-CCEEEcccCCCCcCCCCCceecceeCCCCcEEEeecccccccCcceeeeeecccEEEeeeeeccCCCceeeEEEE
Q 034010 3 EFDG-RPFFSCRNCLNPLAFHHDLISKTFKAQTGQAYMFSNAMNVVLGRKEDKQMITGMYTIAKIYCSNCGQELGWHYLR 81 (106)
Q Consensus 3 ~l~g-~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~h~V~dI~C~~C~~~lGWkY~~ 81 (106)
++.+ ++.|+|++|+||||.++|||||+|+|++|+||||++|+||+.|+.|+|.|+||+|+|+||+|+.|++.|||||+.
T Consensus 8 ~l~~~~~~y~C~~C~thla~~~dliSksf~gr~G~AyLf~~vvNv~~ge~e~R~mlTG~h~V~di~C~~C~~~~GWkYe~ 87 (122)
T KOG3399|consen 8 MLEANHRLYSCAHCKTHLARHDDLISKSFRGRTGRAYLFNRVVNVIIGETEQRVMLTGLHTVADIFCVLCGTGLGWKYEH 87 (122)
T ss_pred HhccCCceEeccCCcccccchhhccccccccCCCcchhhhhhhhheechHHHHHHHHhHHhhcchhhhhcCCCcceeeee
Confidence 3454 379999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecccCCceecCeEEEEeeccccc
Q 034010 82 AYDLKQKWKEGNFILEKFKMLKE 104 (106)
Q Consensus 82 A~e~sqkYKEGkfILE~~~i~~~ 104 (106)
|||+||||||||||||+++|.++
T Consensus 88 a~e~sQkyKEGk~ilE~~~i~~~ 110 (122)
T KOG3399|consen 88 AYEKSQKYKEGKFILELAEIFKP 110 (122)
T ss_pred ccCchhhhcCcchHHHHHHhcCC
Confidence 99999999999999999999864
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=100.00 E-value=5.6e-34 Score=192.24 Aligned_cols=88 Identities=43% Similarity=0.836 Sum_probs=84.4
Q ss_pred EEEcccCCCCcCCCCCceecceeCCCCcEEEeecccccccCcceeeeeeccc----EEEeeeeeccCCCceeeEEEEecc
Q 034010 9 FFSCRNCLNPLAFHHDLISKTFKAQTGQAYMFSNAMNVVLGRKEDKQMITGM----YTIAKIYCSNCGQELGWHYLRAYD 84 (106)
Q Consensus 9 ~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~----h~V~dI~C~~C~~~lGWkY~~A~e 84 (106)
+|.|++|++|||++++|+| |+|+.|+||||+ ||..++++++.|+||. |+|+||+|++|++.|||||+.|++
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 7777888899999999 999999999999999999999999
Q ss_pred cCCceecCeEEEEeeccc
Q 034010 85 LKQKWKEGNFILEKFKML 102 (106)
Q Consensus 85 ~sqkYKEGkfILE~~~i~ 102 (106)
+ |+||||+||||++.|.
T Consensus 77 ~-~~~k~g~file~~~i~ 93 (96)
T PF03226_consen 77 E-QKYKEGKFILEKASIS 93 (96)
T ss_pred h-HhhhCCEEEEEhhHEE
Confidence 9 9999999999999885
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=96.21 E-value=0.0023 Score=45.37 Aligned_cols=88 Identities=20% Similarity=0.173 Sum_probs=59.4
Q ss_pred EEEcccCCCCcCCCCCceecceeC--CCCcEEEeecccccccCcceeeeeecccEEEeeeeeccCCCceeeEEEEecccC
Q 034010 9 FFSCRNCLNPLAFHHDLISKTFKA--QTGQAYMFSNAMNVVLGRKEDKQMITGMYTIAKIYCSNCGQELGWHYLRAYDLK 86 (106)
Q Consensus 9 ~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 86 (106)
.+-|++|.+.++..+||-.-.-+. --.+. |...+.+...|.+......+.+....|+|.+|+..+|-.+..---+=
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 578999999999999986642110 01122 33566666666664445668899999999999999998776544444
Q ss_pred CceecCeEEEEe
Q 034010 87 QKWKEGNFILEK 98 (106)
Q Consensus 87 qkYKEGkfILE~ 98 (106)
.-.|.-.|.++.
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 556666666443
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=94.92 E-value=0.035 Score=40.51 Aligned_cols=68 Identities=22% Similarity=0.444 Sum_probs=42.2
Q ss_pred CCEEEcccCCCCcCCCCCceecceeCCCCcEEEeecccccccCcceeeeeecccEEEeeeeeccCCCceeeEEEE
Q 034010 7 RPFFSCRNCLNPLAFHHDLISKTFKAQTGQAYMFSNAMNVVLGRKEDKQMITGMYTIAKIYCSNCGQELGWHYLR 81 (106)
Q Consensus 7 ~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~h~V~dI~C~~C~~~lGWkY~~ 81 (106)
+-+|.|+.|+++|-+.++ -|....|=.-.+..+-.-.+...+|.. -|+.. ..|.|.+|+.+||--...
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----KFDSGCGWPSFYKPISEEVVAYERDES--HGMIR-TEVRCRNCDAHLGHVFDD 105 (134)
T ss_pred CeEEEccCCCCccccccc----hhcCCCCCcCcCcccCCCceEEeecCC--CCcEE-EEEEecCCCCccCcccCC
Confidence 458999999999987764 466666633333443111122333322 24443 579999999999975543
No 5
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=94.86 E-value=0.027 Score=41.41 Aligned_cols=69 Identities=20% Similarity=0.413 Sum_probs=42.9
Q ss_pred CCCEEEcccCCCCcCCCCCceecceeCCCCcEEEeecccccccCcceeeeeecccEEEeeeeeccCCCceeeEEEE
Q 034010 6 GRPFFSCRNCLNPLAFHHDLISKTFKAQTGQAYMFSNAMNVVLGRKEDKQMITGMYTIAKIYCSNCGQELGWHYLR 81 (106)
Q Consensus 6 g~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~h~V~dI~C~~C~~~lGWkY~~ 81 (106)
.+-+|.|+.|+++|=+.++ -|....|=.-.+..+-.-.+...+|+ .-|+.. ..|.|..|+.+||--...
T Consensus 40 ~~G~Y~C~~Cg~pLF~S~~----Kf~Sg~GWPSF~~~i~~~~V~~~~D~--s~gm~R-tEv~C~~Cg~HLGHVF~D 108 (142)
T PRK00222 40 EKGIYVCIVCGEPLFSSDT----KFDSGCGWPSFTKPIDEEAIRELRDT--SHGMVR-TEVRCANCDSHLGHVFPD 108 (142)
T ss_pred CCeEEEecCCCchhcCCcc----cccCCCCCcCcCcccCCCceEEeecc--CCCceE-EEEEeCCCCCccCcccCC
Confidence 3458999999999987743 46666774443444322222222332 123322 579999999999986644
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=94.70 E-value=0.037 Score=39.81 Aligned_cols=72 Identities=21% Similarity=0.414 Sum_probs=44.2
Q ss_pred CCEEEcccCCCCcCCCCCceecceeCCCCcEEEeecccccccCcceeeeeecccEEEeeeeeccCCCceeeEEEEeccc
Q 034010 7 RPFFSCRNCLNPLAFHHDLISKTFKAQTGQAYMFSNAMNVVLGRKEDKQMITGMYTIAKIYCSNCGQELGWHYLRAYDL 85 (106)
Q Consensus 7 ~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~h~V~dI~C~~C~~~lGWkY~~A~e~ 85 (106)
+-+|.|+.|+++|=+.+ .-|....|=.-.+..+..-.+...+|.. -|+. -..|.|.+|+.+||=-......+
T Consensus 35 ~G~Y~C~~Cg~pLF~S~----~Kf~Sg~GWPSF~~~i~~~~v~~~~D~s--~g~~-R~Ev~C~~Cg~HLGHVF~DGp~~ 106 (124)
T PF01641_consen 35 EGIYVCAVCGTPLFSSD----TKFDSGCGWPSFWQPIPGDAVKEREDFS--HGMV-RTEVRCARCGSHLGHVFDDGPPP 106 (124)
T ss_dssp SEEEEETTTS-EEEEGG----GEETSSSSSSEESSCSSTTSEEEEEEEC--TSSE-EEEEEETTTCCEEEEEESTSSTT
T ss_pred CEEEEcCCCCCccccCc----ccccCCcCCccccCcCChHHEEEecccc--CCce-EEEEEecCCCCccccEeCCCCCC
Confidence 45899999999987654 3477677733334443332233333322 2444 45689999999999866655443
No 7
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=94.13 E-value=0.067 Score=38.38 Aligned_cols=64 Identities=28% Similarity=0.550 Sum_probs=42.2
Q ss_pred CCEEEcccCCCCcCCCCCceecceeCCCCcEEEeecccccccCcceeeeeecccEEEeeeeeccCCCceeeEEE
Q 034010 7 RPFFSCRNCLNPLAFHHDLISKTFKAQTGQAYMFSNAMNVVLGRKEDKQMITGMYTIAKIYCSNCGQELGWHYL 80 (106)
Q Consensus 7 ~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~h~V~dI~C~~C~~~lGWkY~ 80 (106)
+-+|.|+.|+++|=+.++ -|....|=.-.+..+-|. +...+|.. | .-..|.|+.|+.+||--..
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 458999999999987754 477777733334444332 33333433 2 2467999999999997543
No 8
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=92.88 E-value=0.096 Score=42.26 Aligned_cols=63 Identities=30% Similarity=0.600 Sum_probs=42.3
Q ss_pred CCEEEcccCCCCcCCCCCceecceeCCCC-cEEEeecccccccCcceeeeeecccEEEeeeeeccCCCceeeEEE
Q 034010 7 RPFFSCRNCLNPLAFHHDLISKTFKAQTG-QAYMFSNAMNVVLGRKEDKQMITGMYTIAKIYCSNCGQELGWHYL 80 (106)
Q Consensus 7 ~~~y~C~~C~thLa~~~~liSk~f~G~~G-~AyLf~~v~Nv~~g~~e~r~m~TG~h~V~dI~C~~C~~~lGWkY~ 80 (106)
+-+|.|+.|+++|=++++ -|....| ++| +..+-|-.. ..++.. |+ -..|.|..|+++||--..
T Consensus 34 ~G~y~c~~c~~~LF~s~~----Kf~sg~GWPsF-~~~~~~~~~-~~~d~~---~~--R~Ev~c~~c~~HLGHvF~ 97 (283)
T PRK05550 34 KGVYLCRRCGAPLFRSED----KFNSGCGWPSF-DDEIPGAVK-RLPDAD---GR--RTEIVCANCGAHLGHVFE 97 (283)
T ss_pred CcEEEcCCCCchhcCChh----hccCCCCCcCc-CcccCCccE-EEEcCC---Cc--eEEEEecCCCCccCcccC
Confidence 458999999999987653 4666777 454 555544322 222222 33 478999999999998554
No 9
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=90.92 E-value=0.28 Score=42.55 Aligned_cols=70 Identities=11% Similarity=0.096 Sum_probs=43.8
Q ss_pred CCCEEEcccCCCCcCCCCCceecceeCCCCcEEEeecccccccCcceeeeeecccEEEeeeeeccCCCceeeEEEEe
Q 034010 6 GRPFFSCRNCLNPLAFHHDLISKTFKAQTGQAYMFSNAMNVVLGRKEDKQMITGMYTIAKIYCSNCGQELGWHYLRA 82 (106)
Q Consensus 6 g~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~h~V~dI~C~~C~~~lGWkY~~A 82 (106)
.+-+|.|+.|+++|=+++ .-|....|=.-.+..+-+-.+...+|. .-|++. ..|.|+.|+.+||--....
T Consensus 415 ~~G~y~c~~c~~pLf~s~----~Kf~sg~GWPsF~~~i~~~~v~~~~d~--s~g~~R-~Ev~c~~c~~HLGHvf~dg 484 (521)
T PRK14018 415 KPGIYVDVVSGEPLFSSA----DKYDSGCGWPSFTRPIDAKVVTEHDDF--SYNMRR-TEVRSRAADSHLGHVFPDG 484 (521)
T ss_pred CCEEEEecCCCCccccCc----ccccCCCCCcccCcccCcCceEEeecc--CCCceE-EEEEECCCCCcCCcccCCC
Confidence 345899999999998775 347666773333333322222223332 224443 4799999999999866543
No 10
>PF14976 FAM72: FAM72 protein
Probab=88.36 E-value=1.2 Score=33.22 Aligned_cols=62 Identities=23% Similarity=0.437 Sum_probs=39.0
Q ss_pred EEEcccCCCCcCCCCCceecceeCCCCcEEEeeccccccc----Ccceeeeeeccc--------EEEeeeeeccCCCcee
Q 034010 9 FFSCRNCLNPLAFHHDLISKTFKAQTGQAYMFSNAMNVVL----GRKEDKQMITGM--------YTIAKIYCSNCGQELG 76 (106)
Q Consensus 9 ~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~----g~~e~r~m~TG~--------h~V~dI~C~~C~~~lG 76 (106)
+..|++|.+-|+... =||.|..+ .|+.. -||....-.+|. =.++|+-|..|+..||
T Consensus 15 ~L~C~~C~~~l~~Rg-----------MkAvLLad-t~ieLySTD~~P~~~v~~vg~~y~t~~C~C~~~d~aC~~CGn~vG 82 (150)
T PF14976_consen 15 ILCCKFCDQVLCNRG-----------MKAVLLAD-TNIELYSTDIPPTNCVDFVGSCYFTRTCKCKIQDIACLGCGNIVG 82 (150)
T ss_pred EEECCCCCchhccch-----------hhheeecC-CccEEEecCCCCcccccccccceecccCceEeeeeeeecCCCeee
Confidence 468999998876532 25655554 33332 122222223333 3699999999999999
Q ss_pred eEEEEe
Q 034010 77 WHYLRA 82 (106)
Q Consensus 77 WkY~~A 82 (106)
+.++..
T Consensus 83 YhV~~P 88 (150)
T PF14976_consen 83 YHVVVP 88 (150)
T ss_pred eEEEEE
Confidence 988754
No 11
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=88.26 E-value=0.67 Score=34.32 Aligned_cols=65 Identities=23% Similarity=0.486 Sum_probs=39.3
Q ss_pred CCEEEcccCCCCcCCCCCceecceeCCCC-cEEEeecccccccCcceeeee-ecccEEEeeeeeccCCCceeeEEE
Q 034010 7 RPFFSCRNCLNPLAFHHDLISKTFKAQTG-QAYMFSNAMNVVLGRKEDKQM-ITGMYTIAKIYCSNCGQELGWHYL 80 (106)
Q Consensus 7 ~~~y~C~~C~thLa~~~~liSk~f~G~~G-~AyLf~~v~Nv~~g~~e~r~m-~TG~h~V~dI~C~~C~~~lGWkY~ 80 (106)
+-+|.|..|.++|-... .-|....| +|| |+.+ + .|....+.. .-|.+ =.+|.|..|+.+||--.+
T Consensus 52 ~GvY~C~~C~~pLykS~----tKfdsgcGWPAF-~e~i-~--~gaI~r~~d~s~~~~-R~Ev~Ca~C~~HLGHVF~ 118 (146)
T KOG0856|consen 52 EGVYVCAGCGTPLYKST----TKFDSGCGWPAF-FEAI-G--PGAITRTPDNSRGGR-RTEVSCATCGGHLGHVFK 118 (146)
T ss_pred CceEEEeecCCcccccc----ccccCCCCCchh-hhcc-C--CCceeeccccCCCCc-ceEEEEeecCCceeeeec
Confidence 46999999999997754 35766666 454 3322 1 222111111 11122 357899999999997544
No 12
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=83.09 E-value=2.2 Score=31.49 Aligned_cols=65 Identities=26% Similarity=0.492 Sum_probs=41.5
Q ss_pred CCEEEcccCCCCcCCCCCceecceeCCCCcEEEeecccccccCcceeeeeecccEEEeeeeeccCCCceeeE
Q 034010 7 RPFFSCRNCLNPLAFHHDLISKTFKAQTGQAYMFSNAMNVVLGRKEDKQMITGMYTIAKIYCSNCGQELGWH 78 (106)
Q Consensus 7 ~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~h~V~dI~C~~C~~~lGWk 78 (106)
+-+|.|+.|+.+|=++++ -|....|=--.+..+.+-.+...+|+ .-|++. ..|.|.+|+++||--
T Consensus 40 ~GiY~c~~cg~pLF~S~~----KfdSgcGWPSF~~pi~~~~I~~~~D~--S~gM~R-tEVrc~~c~sHLGHV 104 (140)
T COG0229 40 KGIYVCIVCGEPLFSSED----KFDSGCGWPSFTKPISPDAITYKEDR--SHGMVR-TEVRCANCDSHLGHV 104 (140)
T ss_pred CceEEeecCCCccccccc----cccCCCCCccccccCCcccceEeecc--CCCcEE-EEEEecCCCCccccc
Confidence 459999999999977654 46666663222344333333334443 335544 368999999999963
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=77.69 E-value=4.5 Score=32.17 Aligned_cols=17 Identities=41% Similarity=0.864 Sum_probs=13.8
Q ss_pred EEEcccCCCCcCCCCCc
Q 034010 9 FFSCRNCLNPLAFHHDL 25 (106)
Q Consensus 9 ~y~C~~C~thLa~~~~l 25 (106)
.+.|++|++.|.....+
T Consensus 106 ~~~C~~C~~~li~~~~~ 122 (354)
T PF09814_consen 106 SLCCRNCKNPLIPSRNF 122 (354)
T ss_pred EEECCCCCCcccCcccc
Confidence 69999999999766543
No 14
>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=54.46 E-value=5.2 Score=28.61 Aligned_cols=25 Identities=28% Similarity=0.579 Sum_probs=21.6
Q ss_pred CEEEcccCCCCcCCCCCceecceeC
Q 034010 8 PFFSCRNCLNPLAFHHDLISKTFKA 32 (106)
Q Consensus 8 ~~y~C~~C~thLa~~~~liSk~f~G 32 (106)
|...|-+|++||+...++--|.|+-
T Consensus 84 r~D~CM~C~~pLTLd~~legkef~~ 108 (114)
T PF11023_consen 84 RVDACMHCKEPLTLDPSLEGKEFDE 108 (114)
T ss_pred hhhccCcCCCcCccCchhhcchhhH
Confidence 5679999999999999998887763
No 15
>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=47.47 E-value=11 Score=19.34 Aligned_cols=14 Identities=21% Similarity=0.603 Sum_probs=11.1
Q ss_pred CCCCEEEcccCCCC
Q 034010 5 DGRPFFSCRNCLNP 18 (106)
Q Consensus 5 ~g~~~y~C~~C~th 18 (106)
.|++.|.|..|..-
T Consensus 10 ~~~k~~~C~~C~k~ 23 (26)
T PF13465_consen 10 TGEKPYKCPYCGKS 23 (26)
T ss_dssp SSSSSEEESSSSEE
T ss_pred CCCCCCCCCCCcCe
Confidence 36789999999753
No 16
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=46.01 E-value=6.3 Score=32.05 Aligned_cols=22 Identities=32% Similarity=0.544 Sum_probs=19.3
Q ss_pred CCCCEEEcccCCCCcCCCCCce
Q 034010 5 DGRPFFSCRNCLNPLAFHHDLI 26 (106)
Q Consensus 5 ~g~~~y~C~~C~thLa~~~~li 26 (106)
-|+++|+|.+|+.-+|..+.|-
T Consensus 211 TGEKPF~C~hC~kAFADRSNLR 232 (279)
T KOG2462|consen 211 TGEKPFSCPHCGKAFADRSNLR 232 (279)
T ss_pred cCCCCccCCcccchhcchHHHH
Confidence 4889999999999999888775
No 17
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=42.21 E-value=27 Score=26.68 Aligned_cols=35 Identities=20% Similarity=0.239 Sum_probs=21.2
Q ss_pred ccccCcceeeeeecccEEEeeeeeccCCCceeeEEE
Q 034010 45 NVVLGRKEDKQMITGMYTIAKIYCSNCGQELGWHYL 80 (106)
Q Consensus 45 Nv~~g~~e~r~m~TG~h~V~dI~C~~C~~~lGWkY~ 80 (106)
.+..|+...+...+|. .+.--||..|++.|-+..+
T Consensus 74 ~it~g~~~l~~y~ss~-~i~R~FC~~CGS~L~~~~e 108 (191)
T PRK05417 74 TVTANGDKLKVVDESA-TIQRHACKECGVHMYGRIE 108 (191)
T ss_pred EEEeCCcceEEEeCCC-CeEeeeCCCCCCccccccc
Confidence 3433544333333333 3455599999999988776
No 18
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=40.45 E-value=20 Score=25.26 Aligned_cols=22 Identities=23% Similarity=0.572 Sum_probs=16.5
Q ss_pred EEEeeeeeccCCCceeeEEEEe
Q 034010 61 YTIAKIYCSNCGQELGWHYLRA 82 (106)
Q Consensus 61 h~V~dI~C~~C~~~lGWkY~~A 82 (106)
..+.-.||..|+++|-|+....
T Consensus 65 ~~~~r~FC~~CGs~l~~~~~~~ 86 (133)
T COG3791 65 GSAGRGFCPTCGSPLFWRGPDE 86 (133)
T ss_pred CCCCCeecccCCCceEEecCCC
Confidence 3344449999999999986554
No 19
>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=39.99 E-value=35 Score=21.11 Aligned_cols=31 Identities=19% Similarity=0.356 Sum_probs=16.6
Q ss_pred cCcceeeeeecccEEEeeeeeccCCCceeeE
Q 034010 48 LGRKEDKQMITGMYTIAKIYCSNCGQELGWH 78 (106)
Q Consensus 48 ~g~~e~r~m~TG~h~V~dI~C~~C~~~lGWk 78 (106)
.|+..-+........+.-.+|.+|++.|.+.
T Consensus 31 ~g~~~l~~y~~s~~~~~r~FC~~CGs~l~~~ 61 (92)
T PF04828_consen 31 SGSENLKEYQFSGKGVERYFCPTCGSPLFSE 61 (92)
T ss_dssp E-GGGEEEC--TTSSCEEEEETTT--EEEEE
T ss_pred eccccceEEEeCCCcCcCcccCCCCCeeecc
Confidence 4544444344233445558999999999976
No 20
>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=38.05 E-value=51 Score=25.04 Aligned_cols=34 Identities=15% Similarity=0.153 Sum_probs=20.0
Q ss_pred ccccCcceeeeeecccEEEeeeeeccCCCceeeEE
Q 034010 45 NVVLGRKEDKQMITGMYTIAKIYCSNCGQELGWHY 79 (106)
Q Consensus 45 Nv~~g~~e~r~m~TG~h~V~dI~C~~C~~~lGWkY 79 (106)
.+..|+........|.+..+ -||..|++.|-+..
T Consensus 70 ~i~~G~~~l~~Y~ss~~~~R-~FC~~CGS~L~~~~ 103 (182)
T TIGR02820 70 TVTANGDKLKVVDASATIQR-HACKGCGTHMYGRI 103 (182)
T ss_pred EEecCCcceEEEeCCCCEEe-ecCCCCCCcccccc
Confidence 34345444333334545444 49999999996654
No 21
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=37.87 E-value=19 Score=20.25 Aligned_cols=14 Identities=29% Similarity=0.797 Sum_probs=7.3
Q ss_pred eeccCCCceeeEEE
Q 034010 67 YCSNCGQELGWHYL 80 (106)
Q Consensus 67 ~C~~C~~~lGWkY~ 80 (106)
||..|++.|-++..
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 89999999988876
No 22
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=37.44 E-value=13 Score=24.68 Aligned_cols=16 Identities=19% Similarity=0.553 Sum_probs=13.6
Q ss_pred EEEcccCCCCcCCCCC
Q 034010 9 FFSCRNCLNPLAFHHD 24 (106)
Q Consensus 9 ~y~C~~C~thLa~~~~ 24 (106)
.|.|+||++.+..-+.
T Consensus 4 ~Y~CRHCg~~IG~i~~ 19 (76)
T PF10955_consen 4 HYYCRHCGTKIGTIDA 19 (76)
T ss_pred EEEecCCCCEEEEeec
Confidence 4999999999987665
No 23
>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=37.25 E-value=22 Score=20.19 Aligned_cols=27 Identities=11% Similarity=0.226 Sum_probs=21.5
Q ss_pred eeeeeccCCCce-eeEEEEecccCCcee
Q 034010 64 AKIYCSNCGQEL-GWHYLRAYDLKQKWK 90 (106)
Q Consensus 64 ~dI~C~~C~~~l-GWkY~~A~e~sqkYK 90 (106)
-||.|..|.+.- --|.-+...-.|+|.
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 478999999988 777777777777774
No 24
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=36.99 E-value=38 Score=24.11 Aligned_cols=31 Identities=16% Similarity=0.108 Sum_probs=25.9
Q ss_pred eCCCCcEEEeecccccccCcceeeeeecccE
Q 034010 31 KAQTGQAYMFSNAMNVVLGRKEDKQMITGMY 61 (106)
Q Consensus 31 ~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~h 61 (106)
.|+||.|+.--.+.|+..|..-+..+.++--
T Consensus 35 pGkhG~A~vr~k~knl~tG~~~e~~f~s~~~ 65 (130)
T TIGR00037 35 PGKHGHAKARVVAIGIFTGKKLEFVSPSTSK 65 (130)
T ss_pred CCCCCcEEEEEEEEECCCCCEEEEEECCCCE
Confidence 6889999999999999999988777665543
No 25
>PRK11586 napB nitrate reductase cytochrome C550 subunit; Provisional
Probab=33.34 E-value=27 Score=26.05 Aligned_cols=28 Identities=21% Similarity=0.407 Sum_probs=24.6
Q ss_pred CCEEEcccCCCCcCCCCCceecceeCCC
Q 034010 7 RPFFSCRNCLNPLAFHHDLISKTFKAQT 34 (106)
Q Consensus 7 ~~~y~C~~C~thLa~~~~liSk~f~G~~ 34 (106)
++.|-|..|+++=+...-||.-.|....
T Consensus 118 prRYfCtQCHVPQada~PLV~N~F~~~~ 145 (149)
T PRK11586 118 PRRYFCLQCHVPQADTAPIVGNTFTPSK 145 (149)
T ss_pred ccceeeccccCccccCccCCCCCccchh
Confidence 5789999999999999999999997544
No 26
>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=31.88 E-value=23 Score=20.48 Aligned_cols=15 Identities=33% Similarity=0.713 Sum_probs=11.3
Q ss_pred EEEcccCCCCcCCCC
Q 034010 9 FFSCRNCLNPLAFHH 23 (106)
Q Consensus 9 ~y~C~~C~thLa~~~ 23 (106)
-|.|..|+.+|...+
T Consensus 26 Cf~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 26 CFKCSKCGKPLNDGD 40 (58)
T ss_dssp TSBETTTTCBTTTSS
T ss_pred ccccCCCCCccCCCe
Confidence 468888888887665
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=31.25 E-value=8.1 Score=25.65 Aligned_cols=16 Identities=25% Similarity=0.696 Sum_probs=14.8
Q ss_pred EeeeeeccCCCceeeE
Q 034010 63 IAKIYCSNCGQELGWH 78 (106)
Q Consensus 63 V~dI~C~~C~~~lGWk 78 (106)
||-+-|..|++.+|+-
T Consensus 50 vRGlLC~~CN~~lG~~ 65 (81)
T PF02945_consen 50 VRGLLCRSCNTALGKV 65 (81)
T ss_dssp EEEEEEHHHHHHHHHC
T ss_pred chhhhhhHHhhhhccc
Confidence 9999999999999974
No 28
>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=31.03 E-value=20 Score=18.67 Aligned_cols=13 Identities=38% Similarity=0.971 Sum_probs=10.6
Q ss_pred CEEEcccCCCCcC
Q 034010 8 PFFSCRNCLNPLA 20 (106)
Q Consensus 8 ~~y~C~~C~thLa 20 (106)
.-|.|..|+..|+
T Consensus 26 ~Cf~C~~C~~~L~ 38 (39)
T smart00132 26 ECFKCSKCGKPLG 38 (39)
T ss_pred cCCCCcccCCcCc
Confidence 3488999999886
No 29
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=29.02 E-value=32 Score=28.27 Aligned_cols=33 Identities=27% Similarity=0.616 Sum_probs=24.8
Q ss_pred CCCCEEEcccCCCCcCCCCCceecceeCCCCcEEEee
Q 034010 5 DGRPFFSCRNCLNPLAFHHDLISKTFKAQTGQAYMFS 41 (106)
Q Consensus 5 ~g~~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~ 41 (106)
.|.-.|.|-.|+.|+-. +.| .|+|..--+|.|+
T Consensus 133 ~~~g~YvC~KCh~~iD~-~~l---~fr~d~yH~yHFk 165 (332)
T KOG2272|consen 133 KGRGRYVCQKCHAHIDE-QPL---TFRGDPYHPYHFK 165 (332)
T ss_pred cccceeehhhhhhhccc-ccc---cccCCCCCcccee
Confidence 34458999999999877 333 3778877888887
No 30
>KOG2324 consensus Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=28.80 E-value=45 Score=28.75 Aligned_cols=13 Identities=31% Similarity=0.457 Sum_probs=10.2
Q ss_pred ceeeEEEEecccC
Q 034010 74 ELGWHYLRAYDLK 86 (106)
Q Consensus 74 ~lGWkY~~A~e~s 86 (106)
.||=||-+++...
T Consensus 271 ~LG~kYS~~lna~ 283 (457)
T KOG2324|consen 271 LLGTKYSKPLNAK 283 (457)
T ss_pred EeccccccccCce
Confidence 6888888887765
No 31
>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=28.71 E-value=6 Score=19.96 Aligned_cols=18 Identities=22% Similarity=0.427 Sum_probs=13.2
Q ss_pred EEEcccCCCCcCCCCCce
Q 034010 9 FFSCRNCLNPLAFHHDLI 26 (106)
Q Consensus 9 ~y~C~~C~thLa~~~~li 26 (106)
+|.|..|+.-+.+.+.++
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 488999988777665544
No 32
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=28.69 E-value=33 Score=24.78 Aligned_cols=18 Identities=28% Similarity=0.724 Sum_probs=15.2
Q ss_pred CEEEcccCCCCcCCCCCc
Q 034010 8 PFFSCRNCLNPLAFHHDL 25 (106)
Q Consensus 8 ~~y~C~~C~thLa~~~~l 25 (106)
+.|.|.+|+.+|..+.+-
T Consensus 27 ~~~tC~~Cg~~L~lh~~~ 44 (128)
T PF11682_consen 27 DHWTCHSCGCPLILHPGT 44 (128)
T ss_pred CeEEEecCCceEEEecCC
Confidence 679999999999888543
No 33
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=28.46 E-value=19 Score=18.61 Aligned_cols=11 Identities=45% Similarity=1.253 Sum_probs=6.5
Q ss_pred eeeeccCCCce
Q 034010 65 KIYCSNCGQEL 75 (106)
Q Consensus 65 dI~C~~C~~~l 75 (106)
+-||..|++.|
T Consensus 16 ~~fC~~CG~~L 26 (26)
T PF13248_consen 16 AKFCPNCGAKL 26 (26)
T ss_pred cccChhhCCCC
Confidence 44666666543
No 34
>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=28.05 E-value=22 Score=21.81 Aligned_cols=35 Identities=26% Similarity=0.426 Sum_probs=24.2
Q ss_pred eecccccccCcceeeeeecccEEEeeeeeccCCCceeeEE
Q 034010 40 FSNAMNVVLGRKEDKQMITGMYTIAKIYCSNCGQELGWHY 79 (106)
Q Consensus 40 f~~v~Nv~~g~~e~r~m~TG~h~V~dI~C~~C~~~lGWkY 79 (106)
|++++.+..|..+ |+...---+-|.+|.++=|---
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 5678888888776 3333333456999999998743
No 35
>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=27.96 E-value=8.2 Score=18.65 Aligned_cols=16 Identities=19% Similarity=0.588 Sum_probs=11.9
Q ss_pred EEcccCCCCcCCCCCc
Q 034010 10 FSCRNCLNPLAFHHDL 25 (106)
Q Consensus 10 y~C~~C~thLa~~~~l 25 (106)
|.|..|+..++..++|
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 7899998877766554
No 36
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=27.10 E-value=86 Score=21.70 Aligned_cols=45 Identities=16% Similarity=0.338 Sum_probs=33.5
Q ss_pred CEEEcccCCCCcCCCCCceecceeCCCCcEEEeecccccccCccee
Q 034010 8 PFFSCRNCLNPLAFHHDLISKTFKAQTGQAYMFSNAMNVVLGRKED 53 (106)
Q Consensus 8 ~~y~C~~C~thLa~~~~liSk~f~G~~G~AyLf~~v~Nv~~g~~e~ 53 (106)
+.=.|.+|+..=.-...++++.+.++. .-+...+-.|+..|+..+
T Consensus 15 r~saC~~C~~~~~Cg~~~~~~~~~~~~-~~~~~~~~~~~~~GD~V~ 59 (135)
T PF04246_consen 15 RSSACGSCSASGGCGTGLLAKLFSGKP-ITFRAPNPIGAKVGDRVE 59 (135)
T ss_pred cCCcCcccCCCCCCCcchhhhhcCCCc-EEEEecCCCCCCCCCEEE
Confidence 334699998776677778888888877 666667777888887654
No 37
>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=26.67 E-value=41 Score=23.66 Aligned_cols=45 Identities=20% Similarity=0.228 Sum_probs=28.6
Q ss_pred cccccCcceeeeeeccc--EEEeeeeeccCCCceeeEEE----EecccCCceecCe
Q 034010 44 MNVVLGRKEDKQMITGM--YTIAKIYCSNCGQELGWHYL----RAYDLKQKWKEGN 93 (106)
Q Consensus 44 ~Nv~~g~~e~r~m~TG~--h~V~dI~C~~C~~~lGWkY~----~A~e~sqkYKEGk 93 (106)
-=+..|+++++. ++|. |+|.|- =---+|||.. +.-.++++|..|-
T Consensus 15 ~fi~lG~~~gk~-V~G~I~hvv~dd----LYIDfG~KFhcVc~rp~~~~~~y~~G~ 65 (104)
T PF10246_consen 15 PFIQLGDPEGKI-VIGKIFHVVDDD----LYIDFGGKFHCVCKRPAVNGEKYVRGS 65 (104)
T ss_pred hhhhcCCccCCE-EEEEEEEEecCc----eEEEeCCceeEEEecccccccccccCC
Confidence 334578888775 6676 777652 1123588864 3345778899984
No 38
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=26.13 E-value=29 Score=23.22 Aligned_cols=23 Identities=26% Similarity=0.517 Sum_probs=18.0
Q ss_pred EcccCCCCcCCCCCceecceeCCCCcEEEee
Q 034010 11 SCRNCLNPLAFHHDLISKTFKAQTGQAYMFS 41 (106)
Q Consensus 11 ~C~~C~thLa~~~~liSk~f~G~~G~AyLf~ 41 (106)
.|.+|+.+++..+ ...|+||+.-
T Consensus 10 ~C~~CG~d~~~~~--------adDgPA~fvi 32 (86)
T PF06170_consen 10 RCPHCGLDYSHAR--------ADDGPAYFVI 32 (86)
T ss_pred cccccCCccccCC--------cCccchhHHH
Confidence 6999999998776 4567887654
No 39
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=26.01 E-value=23 Score=18.08 Aligned_cols=10 Identities=50% Similarity=1.341 Sum_probs=5.7
Q ss_pred eeeccCCCce
Q 034010 66 IYCSNCGQEL 75 (106)
Q Consensus 66 I~C~~C~~~l 75 (106)
.+|..|++.|
T Consensus 14 ~fC~~CG~~l 23 (23)
T PF13240_consen 14 KFCPNCGTPL 23 (23)
T ss_pred cchhhhCCcC
Confidence 3566666543
No 40
>PF03150 CCP_MauG: Di-haem cytochrome c peroxidase; InterPro: IPR004852 This is a group of distinct cytochrome c peroxidases (CCPs) that contain two haem groups. Similar to other cytochrome c peroxidases, they reduce hydrogen peroxide to water using c-type haem as an oxidizable substrate. However, since they possess two, instead of one, haem prosthetic groups, bacterial CCPs reduce hydrogen peroxide without the need to generate semi-stable free radicals. The two haem groups have significantly different redox potentials. The high potential (+320 mV) haem feeds electrons from electron shuttle proteins to the low potential (-330 mV) haem, where peroxide is reduced (indeed, the low potential site is known as the peroxidatic site) []. The CCP protein itself is structured into two domains, each containing one c-type haem group, with a calcium-binding site at the domain interface. This family also includes MauG proteins, whose similarity to di-haem CCP was previously recognised [].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1IQC_A 2VHD_B 1EB7_A 3RN0_A 3SVW_B 3RMZ_A 3SJL_B 3PXW_A 3SLE_B 3PXS_A ....
Probab=25.86 E-value=17 Score=26.49 Aligned_cols=21 Identities=29% Similarity=0.540 Sum_probs=12.6
Q ss_pred cCCCCEEEcccCCCCcCCCCC
Q 034010 4 FDGRPFFSCRNCLNPLAFHHD 24 (106)
Q Consensus 4 l~g~~~y~C~~C~thLa~~~~ 24 (106)
|++....+|+.||.+=....+
T Consensus 17 LS~~~~~SCasCH~~~~~~td 37 (159)
T PF03150_consen 17 LSGDGTVSCASCHDPEHGFTD 37 (159)
T ss_dssp GSTTSS--HHHHS-TTTTTS-
T ss_pred cCCCcCcCchhhCCCcccCCc
Confidence 677889999999987533333
No 41
>TIGR03791 TTQ_mauG tryptophan tryptophylquinone biosynthesis enzyme MauG. Members of this protein family are the tryptophan tryptophylquinone biosynthesis (TTQ) enzyme MauG, as found in Methylobacterium extorquens and related species. This protein is required to complete the maturation of the TTQ cofactor in the methylamine dehydrogenase light (beta) chain.
Probab=24.74 E-value=47 Score=26.66 Aligned_cols=32 Identities=19% Similarity=0.263 Sum_probs=22.1
Q ss_pred cCCCCEEEcccCCCCcCCCCC--ceecceeCCCC
Q 034010 4 FDGRPFFSCRNCLNPLAFHHD--LISKTFKAQTG 35 (106)
Q Consensus 4 l~g~~~y~C~~C~thLa~~~~--liSk~f~G~~G 35 (106)
|++....+|+.|+.+-.-..+ .+|.+..|+.|
T Consensus 18 LS~~~~~SCasCH~p~~~~~d~~~~s~G~~g~~~ 51 (291)
T TIGR03791 18 LSRDGSMSCATCHNPGLGWSDGLILALGADGVEH 51 (291)
T ss_pred cCCCCCcCchhcCCccccCCCCcccccCCCCCCC
Confidence 778889999999998554333 35655555444
No 42
>PLN03107 eukaryotic translation initiation factor 5A; Provisional
Probab=24.36 E-value=92 Score=23.03 Aligned_cols=31 Identities=16% Similarity=0.239 Sum_probs=26.4
Q ss_pred eCCCCcEEEeecccccccCcceeeeeecccE
Q 034010 31 KAQTGQAYMFSNAMNVVLGRKEDKQMITGMY 61 (106)
Q Consensus 31 ~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~h 61 (106)
.|+||.|+.--.+.|+..|...+....++--
T Consensus 49 pGKHG~A~vr~k~knl~TG~k~e~~f~s~~~ 79 (159)
T PLN03107 49 TGKHGHAKCHFVAIDIFTGKKLEDIVPSSHN 79 (159)
T ss_pred CCCCCcEEEEEEEEECCCCCEEEEEecCCCE
Confidence 7999999999999999999998877766553
No 43
>cd02669 Peptidase_C19M A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=24.31 E-value=61 Score=27.00 Aligned_cols=53 Identities=25% Similarity=0.313 Sum_probs=31.2
Q ss_pred cCCCCEEEcccCCCCcCCCCCceecceeCCCCc--EEEeecccccccCcceeeeeecccEEEeeeeeccCCCcee
Q 034010 4 FDGRPFFSCRNCLNPLAFHHDLISKTFKAQTGQ--AYMFSNAMNVVLGRKEDKQMITGMYTIAKIYCSNCGQELG 76 (106)
Q Consensus 4 l~g~~~y~C~~C~thLa~~~~liSk~f~G~~G~--AyLf~~v~Nv~~g~~e~r~m~TG~h~V~dI~C~~C~~~lG 76 (106)
+..+.+|.|-.|+ +-|.|+.|. ||.-..-.|-.+ --.+.| .++||-.|+..|.
T Consensus 23 ~~~~n~~~CL~cg-----------~~~~g~~~~~ha~~H~~~~~H~~----~v~l~t-----~~~yc~~~~~~v~ 77 (440)
T cd02669 23 LSNLNVYACLVCG-----------KYFQGRGKGSHAYTHSLEDNHHV----FLNLET-----LKFYCLPDNYEII 77 (440)
T ss_pred CCCCcEEEEcccC-----------CeecCCCCCcHHHHHhhccCCCE----EEECCC-----CCEEEeCCCCEEe
Confidence 4556789999998 677777554 444322111111 111122 7899999988765
No 44
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=24.17 E-value=64 Score=17.64 Aligned_cols=15 Identities=27% Similarity=0.680 Sum_probs=12.4
Q ss_pred CEEEcccCCCCcCCC
Q 034010 8 PFFSCRNCLNPLAFH 22 (106)
Q Consensus 8 ~~y~C~~C~thLa~~ 22 (106)
..|.|..|..+|...
T Consensus 15 T~~~C~~C~v~lC~~ 29 (32)
T PF13842_consen 15 TRYMCSKCDVPLCVE 29 (32)
T ss_pred eEEEccCCCCcccCC
Confidence 579999999888754
No 45
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=23.97 E-value=43 Score=19.23 Aligned_cols=14 Identities=14% Similarity=0.562 Sum_probs=9.8
Q ss_pred EEEcccCCCCcCCC
Q 034010 9 FFSCRNCLNPLAFH 22 (106)
Q Consensus 9 ~y~C~~C~thLa~~ 22 (106)
.|.|.+|++.+...
T Consensus 3 ~y~C~~CG~~~~~~ 16 (46)
T PRK00398 3 EYKCARCGREVELD 16 (46)
T ss_pred EEECCCCCCEEEEC
Confidence 57888888766543
No 46
>COG3043 NapB Nitrate reductase cytochrome c-type subunit [Energy production and conversion]
Probab=23.70 E-value=53 Score=24.64 Aligned_cols=30 Identities=30% Similarity=0.489 Sum_probs=25.4
Q ss_pred CCCEEEcccCCCCcCCCCCceecceeCCCC
Q 034010 6 GRPFFSCRNCLNPLAFHHDLISKTFKAQTG 35 (106)
Q Consensus 6 g~~~y~C~~C~thLa~~~~liSk~f~G~~G 35 (106)
.+|.|-|..|+.+=|...-|+--.|.--.|
T Consensus 123 SPRRYFClQCHVPQaD~kPlV~N~F~p~~~ 152 (155)
T COG3043 123 SPRRYFCLQCHVPQADVKPLVGNTFKPMKG 152 (155)
T ss_pred CccceeeeecccccccccccCCCCcccchh
Confidence 378899999999999999999988875443
No 47
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=22.82 E-value=67 Score=18.49 Aligned_cols=12 Identities=25% Similarity=0.769 Sum_probs=7.0
Q ss_pred CCCEEEcccCCC
Q 034010 6 GRPFFSCRNCLN 17 (106)
Q Consensus 6 g~~~y~C~~C~t 17 (106)
+...|.|+.|+.
T Consensus 34 ~~~~~~C~~C~~ 45 (46)
T PF12760_consen 34 TRGRYRCKACRK 45 (46)
T ss_pred CCCeEECCCCCC
Confidence 345666666654
No 48
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=22.57 E-value=39 Score=23.24 Aligned_cols=22 Identities=27% Similarity=0.549 Sum_probs=13.7
Q ss_pred EcccCCCCcCCCCC------ceecceeC
Q 034010 11 SCRNCLNPLAFHHD------LISKTFKA 32 (106)
Q Consensus 11 ~C~~C~thLa~~~~------liSk~f~G 32 (106)
.|.+|...|...++ -.|.+|.|
T Consensus 22 gCpnC~~~l~~~g~~~~v~~~tT~~f~G 49 (98)
T cd07973 22 GCPNCEGYLDMKGNHERVYDCTSPNFEG 49 (98)
T ss_pred CCCCCcchhccCCCccccccccCCCcce
Confidence 68899766544443 35666765
No 49
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=22.54 E-value=1.1e+02 Score=21.71 Aligned_cols=30 Identities=17% Similarity=0.104 Sum_probs=24.3
Q ss_pred eCCCCcEEEeecccccccCcceeeeeeccc
Q 034010 31 KAQTGQAYMFSNAMNVVLGRKEDKQMITGM 60 (106)
Q Consensus 31 ~G~~G~AyLf~~v~Nv~~g~~e~r~m~TG~ 60 (106)
.|+||.|+.--.+.|+..|...+....++-
T Consensus 34 pGkhg~a~vr~k~knL~tG~~~e~~~~s~d 63 (129)
T PRK03999 34 PGKHGSAKARIVAIGIFDGQKRSLVQPVDA 63 (129)
T ss_pred CCCCCcEEEEEEEEECCCCCEEEEEecCCC
Confidence 688899999899999999987766666554
No 50
>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=22.15 E-value=63 Score=17.74 Aligned_cols=17 Identities=18% Similarity=0.247 Sum_probs=13.6
Q ss_pred cccCCCCEEEcccCCCC
Q 034010 2 AEFDGRPFFSCRNCLNP 18 (106)
Q Consensus 2 ~~l~g~~~y~C~~C~th 18 (106)
.|..|-+.+.|+.|++.
T Consensus 12 ~yP~gA~~vrCs~C~~v 28 (31)
T TIGR01053 12 MYPRGASSVRCALCQTV 28 (31)
T ss_pred ecCCCCCeEECCCCCeE
Confidence 46678888999999874
No 51
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=21.02 E-value=61 Score=17.48 Aligned_cols=13 Identities=23% Similarity=0.639 Sum_probs=10.6
Q ss_pred CEEEcccCCCCcC
Q 034010 8 PFFSCRNCLNPLA 20 (106)
Q Consensus 8 ~~y~C~~C~thLa 20 (106)
.+|.|.+|++-+.
T Consensus 6 ~~ykC~~Cgniv~ 18 (34)
T TIGR00319 6 QVYKCEVCGNIVE 18 (34)
T ss_pred cEEEcCCCCcEEE
Confidence 5899999998663
No 52
>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=20.91 E-value=53 Score=18.79 Aligned_cols=12 Identities=33% Similarity=0.969 Sum_probs=7.2
Q ss_pred CEEEcccCCCCc
Q 034010 8 PFFSCRNCLNPL 19 (106)
Q Consensus 8 ~~y~C~~C~thL 19 (106)
.+|.|.+|++-+
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 589999998754
No 53
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=20.91 E-value=62 Score=17.49 Aligned_cols=13 Identities=23% Similarity=0.616 Sum_probs=10.4
Q ss_pred CEEEcccCCCCcC
Q 034010 8 PFFSCRNCLNPLA 20 (106)
Q Consensus 8 ~~y~C~~C~thLa 20 (106)
.+|.|.+|++-+.
T Consensus 3 ~~ykC~~CGniv~ 15 (34)
T cd00974 3 EVYKCEICGNIVE 15 (34)
T ss_pred cEEEcCCCCcEEE
Confidence 5899999988663
No 54
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=20.49 E-value=52 Score=20.30 Aligned_cols=11 Identities=64% Similarity=1.350 Sum_probs=9.8
Q ss_pred eeccCCCceee
Q 034010 67 YCSNCGQELGW 77 (106)
Q Consensus 67 ~C~~C~~~lGW 77 (106)
+|.+|+..||-
T Consensus 54 ~Cp~C~~~lg~ 64 (67)
T smart00714 54 YCPNCGAFLGT 64 (67)
T ss_pred ECCCCCCEeEE
Confidence 69999999985
No 55
>PF14353 CpXC: CpXC protein
Probab=20.45 E-value=45 Score=22.86 Aligned_cols=46 Identities=15% Similarity=0.354 Sum_probs=29.7
Q ss_pred eecccccccCcceeeeeecccEEEeeeeeccCCCceeeEEEEecccCC
Q 034010 40 FSNAMNVVLGRKEDKQMITGMYTIAKIYCSNCGQELGWHYLRAYDLKQ 87 (106)
Q Consensus 40 f~~v~Nv~~g~~e~r~m~TG~h~V~dI~C~~C~~~lGWkY~~A~e~sq 87 (106)
+-..+|+...|.-...+++|.- -...|.+|+...---|.--|.+-+
T Consensus 15 v~~~I~~~~~p~l~e~il~g~l--~~~~CP~Cg~~~~~~~p~lY~D~~ 60 (128)
T PF14353_consen 15 VWTSINADEDPELKEKILDGSL--FSFTCPSCGHKFRLEYPLLYHDPE 60 (128)
T ss_pred EEeEEcCcCCHHHHHHHHcCCc--CEEECCCCCCceecCCCEEEEcCC
Confidence 4467888877765555667763 334799999977655554444433
Done!