Query 027756
Match_columns 219
No_of_seqs 275 out of 1046
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 14:42:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027756.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027756hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06200 tify: tify domain; I 99.7 1.6E-16 3.5E-21 102.1 5.2 35 11-45 2-36 (36)
2 cd00202 ZnF_GATA Zinc finger D 99.6 2E-16 4.3E-21 110.1 3.6 44 140-185 1-44 (54)
3 smart00401 ZnF_GATA zinc finge 99.6 1.2E-15 2.6E-20 105.3 3.5 45 138-184 3-48 (52)
4 PF00320 GATA: GATA zinc finge 99.5 1.2E-15 2.7E-20 97.8 1.1 36 141-178 1-36 (36)
5 PF06203 CCT: CCT motif; Inte 99.5 8.3E-15 1.8E-19 98.4 2.4 44 65-108 1-44 (45)
6 KOG1601 GATA-4/5/6 transcripti 98.7 8.8E-09 1.9E-13 86.8 3.3 46 138-185 199-244 (340)
7 PF09425 CCT_2: Divergent CCT 98.6 2.3E-08 5E-13 60.3 1.6 26 62-88 1-26 (27)
8 COG5641 GAT1 GATA Zn-finger-co 98.4 1.5E-07 3.2E-12 90.8 3.0 59 132-192 152-215 (498)
9 KOG3554 Histone deacetylase co 92.6 0.3 6.6E-06 47.6 6.4 56 138-195 386-449 (693)
10 COG5641 GAT1 GATA Zn-finger-co 91.6 0.093 2E-06 51.3 1.7 52 134-186 293-344 (498)
11 PF13619 KTSC: KTSC domain 82.8 2.1 4.6E-05 29.8 3.8 37 5-41 6-43 (60)
12 PF14803 Nudix_N_2: Nudix N-te 81.0 0.5 1.1E-05 30.0 0.0 30 139-170 1-30 (34)
13 KOG1601 GATA-4/5/6 transcripti 78.4 0.59 1.3E-05 39.1 -0.3 41 62-102 290-330 (340)
14 PF02701 zf-Dof: Dof domain, z 66.0 7 0.00015 28.2 2.8 47 136-184 3-52 (63)
15 PF01783 Ribosomal_L32p: Ribos 65.4 1.8 4E-05 30.0 -0.2 26 137-174 25-50 (56)
16 PF06677 Auto_anti-p27: Sjogre 64.5 2.8 6.2E-05 27.6 0.6 25 138-169 17-41 (41)
17 PF04810 zf-Sec23_Sec24: Sec23 64.5 2.9 6.2E-05 27.0 0.6 31 138-170 2-32 (40)
18 COG3952 Predicted membrane pro 59.5 2.4 5.2E-05 33.7 -0.6 21 152-174 75-95 (113)
19 PF13717 zinc_ribbon_4: zinc-r 58.6 3 6.5E-05 26.4 -0.1 33 139-172 3-35 (36)
20 KOG1561 CCAAT-binding factor, 58.1 7.2 0.00016 36.1 2.2 30 85-114 217-249 (307)
21 PF01412 ArfGap: Putative GTPa 57.6 8.9 0.00019 30.0 2.4 38 136-177 11-48 (116)
22 PRK03988 translation initiatio 56.4 3.7 8.1E-05 33.7 0.0 30 139-171 103-132 (138)
23 TIGR00311 aIF-2beta translatio 55.0 4.1 8.9E-05 33.2 0.1 30 139-171 98-127 (133)
24 KOG3740 Uncharacterized conser 53.6 5 0.00011 40.5 0.4 37 137-175 461-500 (706)
25 PRK05978 hypothetical protein; 53.2 5.8 0.00013 33.0 0.7 34 138-176 33-66 (148)
26 smart00653 eIF2B_5 domain pres 52.3 4.9 0.00011 31.7 0.1 29 139-170 81-109 (110)
27 PF06689 zf-C4_ClpX: ClpX C4-t 51.5 7.2 0.00016 25.3 0.8 32 139-171 2-33 (41)
28 PF09889 DUF2116: Uncharacteri 51.4 7.8 0.00017 27.5 1.0 30 137-176 2-32 (59)
29 COG1645 Uncharacterized Zn-fin 50.8 5.9 0.00013 32.4 0.4 27 138-172 28-54 (131)
30 PRK00420 hypothetical protein; 49.3 7.9 0.00017 30.8 0.8 30 138-174 23-52 (112)
31 PRK12336 translation initiatio 48.6 5.8 0.00013 34.3 -0.0 33 139-174 99-131 (201)
32 COG5349 Uncharacterized protei 46.5 7.9 0.00017 31.5 0.4 34 138-176 21-54 (126)
33 PF08271 TF_Zn_Ribbon: TFIIB z 44.0 8.5 0.00018 24.9 0.2 29 140-173 2-30 (43)
34 TIGR02098 MJ0042_CXXC MJ0042 f 43.3 5.3 0.00011 24.9 -0.8 33 139-172 3-35 (38)
35 PF01873 eIF-5_eIF-2B: Domain 42.2 9.1 0.0002 30.8 0.2 29 139-170 94-122 (125)
36 PF09297 zf-NADH-PPase: NADH p 41.9 6.3 0.00014 24.0 -0.6 28 138-171 3-30 (32)
37 KOG1598 Transcription initiati 41.0 13 0.00029 36.7 1.2 35 139-178 1-35 (521)
38 PRK05342 clpX ATP-dependent pr 40.3 21 0.00046 34.1 2.4 30 137-168 8-37 (412)
39 PRK12286 rpmF 50S ribosomal pr 39.9 12 0.00027 26.2 0.6 25 136-171 25-49 (57)
40 smart00521 CBF CCAAT-Binding t 39.7 36 0.00077 24.5 2.9 21 86-106 40-61 (62)
41 PF12773 DZR: Double zinc ribb 38.9 19 0.00042 23.5 1.4 30 135-171 9-38 (50)
42 TIGR00416 sms DNA repair prote 37.8 13 0.00029 35.7 0.6 26 136-171 5-30 (454)
43 PRK00423 tfb transcription ini 37.6 22 0.00047 32.5 1.9 25 132-156 24-53 (310)
44 PRK11788 tetratricopeptide rep 37.2 15 0.00033 32.7 0.9 26 136-171 352-377 (389)
45 PF13248 zf-ribbon_3: zinc-rib 37.0 21 0.00045 20.8 1.2 22 139-170 3-24 (26)
46 smart00778 Prim_Zn_Ribbon Zinc 36.9 20 0.00043 23.1 1.1 30 138-169 3-32 (37)
47 PRK14892 putative transcriptio 35.2 12 0.00026 29.1 -0.1 36 137-175 20-55 (99)
48 COG5347 GTPase-activating prot 35.0 21 0.00046 33.2 1.5 39 135-177 17-55 (319)
49 TIGR03573 WbuX N-acetyl sugar 35.0 24 0.00052 32.6 1.8 32 139-174 2-33 (343)
50 PF07282 OrfB_Zn_ribbon: Putat 33.7 21 0.00045 24.9 0.9 28 139-172 29-56 (69)
51 PRK11823 DNA repair protein Ra 33.7 16 0.00035 35.1 0.4 27 136-172 5-31 (446)
52 COG2816 NPY1 NTP pyrophosphohy 32.3 18 0.00039 33.1 0.5 37 132-174 105-141 (279)
53 TIGR03655 anti_R_Lar restricti 32.2 21 0.00045 24.1 0.7 29 139-171 2-35 (53)
54 COG3529 Predicted nucleic-acid 29.5 13 0.00028 26.8 -0.7 33 138-173 10-43 (66)
55 PHA00626 hypothetical protein 29.3 20 0.00043 25.5 0.2 31 140-175 2-36 (59)
56 smart00105 ArfGap Putative GTP 29.1 46 0.001 25.8 2.3 38 137-178 2-39 (112)
57 PF12553 DUF3742: Protein of u 28.7 21 0.00046 24.8 0.2 12 151-162 33-44 (54)
58 TIGR00515 accD acetyl-CoA carb 28.4 7.9 0.00017 35.3 -2.5 32 138-174 26-57 (285)
59 smart00834 CxxC_CXXC_SSSS Puta 27.4 25 0.00054 21.8 0.4 29 139-170 6-34 (41)
60 PF00130 C1_1: Phorbol esters/ 26.9 18 0.00038 23.9 -0.4 32 137-175 10-41 (53)
61 smart00661 RPOL9 RNA polymeras 26.8 32 0.00069 22.5 0.8 31 140-174 2-32 (52)
62 PRK00241 nudC NADH pyrophospha 25.9 22 0.00047 31.7 -0.1 36 133-174 94-129 (256)
63 PF02007 MtrH: Tetrahydrometha 25.7 70 0.0015 29.6 3.1 26 18-43 27-56 (296)
64 TIGR01031 rpmF_bact ribosomal 25.5 26 0.00056 24.3 0.2 24 136-170 24-47 (55)
65 cd01121 Sms Sms (bacterial rad 25.3 26 0.00057 32.9 0.3 22 140-171 2-23 (372)
66 KOG0706 Predicted GTPase-activ 24.8 34 0.00074 33.3 1.0 40 135-178 20-59 (454)
67 TIGR00244 transcriptional regu 24.7 30 0.00065 28.9 0.5 39 139-177 1-43 (147)
68 KOG0712 Molecular chaperone (D 24.6 38 0.00083 31.8 1.3 36 138-173 143-181 (337)
69 PF10083 DUF2321: Uncharacteri 24.6 33 0.00071 29.0 0.7 36 137-172 38-78 (158)
70 PF02045 CBFB_NFYA: CCAAT-bind 23.6 57 0.0012 23.2 1.7 18 87-104 40-58 (58)
71 COG2331 Uncharacterized protei 23.3 27 0.00058 26.3 -0.0 35 138-175 12-46 (82)
72 COG1962 MtrH Tetrahydromethano 22.8 82 0.0018 29.0 2.9 26 18-43 35-64 (313)
73 PF10777 YlaC: Inner membrane 22.8 2.4E+02 0.0053 23.8 5.5 48 16-79 95-142 (155)
74 PRK00423 tfb transcription ini 22.6 39 0.00084 30.8 0.9 34 137-175 10-43 (310)
75 COG4260 Membrane protease subu 22.4 46 0.001 31.0 1.3 31 136-171 313-343 (345)
76 PRK00979 tetrahydromethanopter 22.3 92 0.002 29.0 3.2 26 18-43 32-61 (308)
77 PRK01110 rpmF 50S ribosomal pr 22.1 33 0.00072 24.2 0.2 23 138-172 27-49 (60)
78 PRK14047 putative methyltransf 21.8 99 0.0021 28.8 3.3 26 18-43 32-61 (310)
79 PF12156 ATPase-cat_bd: Putati 21.6 60 0.0013 24.3 1.6 35 139-173 1-37 (88)
80 PF15321 ATAD4: ATPase family 21.6 22 0.00048 27.0 -0.8 12 70-81 69-80 (84)
81 TIGR01114 mtrH N5-methyltetrah 21.5 1E+02 0.0022 28.8 3.4 26 18-43 32-61 (314)
82 PF09723 Zn-ribbon_8: Zinc rib 21.4 36 0.00079 22.0 0.3 29 139-170 6-34 (42)
83 COG1096 Predicted RNA-binding 20.9 36 0.00079 29.5 0.3 27 138-172 149-175 (188)
84 PLN00162 transport protein sec 20.8 41 0.00089 34.7 0.7 33 137-171 52-84 (761)
No 1
>PF06200 tify: tify domain; InterPro: IPR010399 The tify domain is a 36-amino acid domain only found among Embryophyta (land plants). It has been named after the most conserved amino acid pattern (TIF[F/Y]XG) it contains, but was previously known as the Zim domain. As the use of uppercase characters (TIFY) might imply that the domain is fully conserved across proteins, a lowercase lettering has been chosen in an attempt to highlight the reality of its natural variability. Based on the domain architecture, tify domain containing proteins can be classified into two groups. Group I is formed by proteins possessing a CCT (CONSTANS, CO-like, and TOC1) domain and a GATA-type zinc finger in addition to the tify domain. Group II contains proteins characterised by the tify domain but lacking a GATA-type zinc finger. Tify domain containing proteins might be involved in developmental processes and some of them have features that are characteristic for transcription factors: a nuclear localisation and the presence of a putative DNA-binding domain []. Some proteins known to contain a tify domain include: Arabidopsis thaliana Zinc-finger protein expressed in Inflorescence Meristem (ZIM), a putative transcription factor involved in inflorescence and flower development [, ]. A. thaliana ZIM-like proteins (ZML) []. A. thaliana PEAPOD1 and PEAPOD2 (PPD1 and PPD2) [].
Probab=99.65 E-value=1.6e-16 Score=102.06 Aligned_cols=35 Identities=43% Similarity=0.653 Sum_probs=32.5
Q ss_pred cCCCCceEEEeccEEEEecCCCHHHHHHHHHHhcC
Q 027756 11 ERIGDQLTLSFQGQVYVFDSVSPEKVQAVLLLLGG 45 (219)
Q Consensus 11 ~~~~~qLTifY~G~v~Vfd~v~~~ka~~im~la~~ 45 (219)
.++++||||||+|+|+|||+||+|||++||++|+.
T Consensus 2 ~~~~~qLTIfY~G~V~Vfd~v~~~Ka~~im~lA~r 36 (36)
T PF06200_consen 2 SPETAQLTIFYGGQVCVFDDVPPDKAQEIMLLASR 36 (36)
T ss_pred CCCCCcEEEEECCEEEEeCCCCHHHHHHHHHHhcC
Confidence 46789999999999999999999999999999973
No 2
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=99.63 E-value=2e-16 Score=110.07 Aligned_cols=44 Identities=55% Similarity=1.175 Sum_probs=41.1
Q ss_pred cccccccccCCCCccccCCCCCcccchhhhHHHHhcCCCCCCccCC
Q 027756 140 VCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKGTLRDLSKAA 185 (219)
Q Consensus 140 ~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~~~~~~r~~~~~~ 185 (219)
.|+||++ ++||+||+||+|..+|||||||||++++..||+....
T Consensus 1 ~C~~C~~--~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~rp~~~~~ 44 (54)
T cd00202 1 ACSNCGT--TTTPLWRRGPSGGSTLCNACGLYWKKHGVMRPLSKRK 44 (54)
T ss_pred CCCCCCC--CCCcccccCCCCcchHHHHHHHHHHhcCCCCCcccCc
Confidence 4999999 8899999999888999999999999999999998864
No 3
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.58 E-value=1.2e-15 Score=105.25 Aligned_cols=45 Identities=51% Similarity=1.032 Sum_probs=40.6
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHHHhcCCC-CCCccC
Q 027756 138 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKGTL-RDLSKA 184 (219)
Q Consensus 138 ~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~~~~~~-r~~~~~ 184 (219)
...|+||++ +.||+||+||.|..+|||||||||++++.+ +|....
T Consensus 3 ~~~C~~C~~--~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~~rp~~~~ 48 (52)
T smart00401 3 GRSCSNCGT--TETPLWRRGPSGNKTLCNACGLYYKKHGGLKRPLSLK 48 (52)
T ss_pred CCCcCCCCC--CCCCccccCCCCCCcEeecccHHHHHcCCCCCccccc
Confidence 568999999 789999999999989999999999999998 776554
No 4
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=99.54 E-value=1.2e-15 Score=97.77 Aligned_cols=36 Identities=56% Similarity=1.214 Sum_probs=28.5
Q ss_pred ccccccccCCCCccccCCCCCcccchhhhHHHHhcCCC
Q 027756 141 CRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKGTL 178 (219)
Q Consensus 141 C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~~~~~~ 178 (219)
|.||++ ++||+||+||.|..+|||+||++|++++++
T Consensus 1 C~~C~t--t~t~~WR~~~~g~~~LCn~Cg~~~kk~~~~ 36 (36)
T PF00320_consen 1 CSNCGT--TETPQWRRGPNGNRTLCNACGLYYKKYGKM 36 (36)
T ss_dssp -TTT----ST-SSEEEETTSEE-EEHHHHHHHHHHSS-
T ss_pred CcCCcC--CCCchhhcCCCCCCHHHHHHHHHHHHhCCC
Confidence 899999 789999999999888999999999999863
No 5
>PF06203 CCT: CCT motif; InterPro: IPR010402 The CCT (CONSTANS, CO-like, and TOC1) domain is a highly conserved basic module of ~43 amino acids, which is found near the C terminus of plant proteins often involved in light signal transduction. The CCT domain is found in association with other domains, such as the B-box zinc finger, the GATA-type zinc finger, the ZIM motif or the response regulatory domain. The CCT domain contains a putative nuclear localisation signal within the second half of the CCT motif and has been shown to be involved in nuclear localization and probably also has a role in protein-protein interaction [].; GO: 0005515 protein binding
Probab=99.50 E-value=8.3e-15 Score=98.42 Aligned_cols=44 Identities=57% Similarity=0.801 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHhhhhccccceeccccHHHHHHHHhhcCccccCC
Q 027756 65 RLASLIRFREKRKERNFEKKIRYTVRKEVALRMQRNKGQFTSAK 108 (219)
Q Consensus 65 R~~sl~rf~eKrk~R~~~k~~rY~~Rk~~A~~r~R~kGrf~s~~ 108 (219)
|+++|+||+|||++|+|+|+|+|++||.+|+.+||++|+|++..
T Consensus 1 R~~~l~Ry~~Kr~~R~f~kkirY~~Rk~~A~~R~RvkGRFvk~~ 44 (45)
T PF06203_consen 1 REEKLQRYREKRKRRNFEKKIRYESRKAVADKRPRVKGRFVKKS 44 (45)
T ss_pred CHHHHHHHHHHHHhhcccccCCcchHHHHHhhCCccCCcccCCC
Confidence 67899999999999999999999999999999999999999874
No 6
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.71 E-value=8.8e-09 Score=86.79 Aligned_cols=46 Identities=48% Similarity=1.001 Sum_probs=39.9
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHHHhcCCCCCCccCC
Q 027756 138 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKGTLRDLSKAA 185 (219)
Q Consensus 138 ~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~~~~~~r~~~~~~ 185 (219)
...|.+|++ +.||+||++|.|+..||||||++|+++...+++....
T Consensus 199 ~~~c~~~~~--~~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~~ 244 (340)
T KOG1601|consen 199 LRQCSNCGT--TKTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEKR 244 (340)
T ss_pred CcccCCCCC--CCCcceecCCCCCccccccchhhhhhcCccccccccC
Confidence 589999999 7899999999999999999999999997555555543
No 7
>PF09425 CCT_2: Divergent CCT motif; InterPro: IPR018467 The short CCT (CO, COL, TOC1) motif is found in a number of plant proteins, including Constans (CO), Constans-like (COL) and TOC1. The CCT motif is about 45 amino acids long and contains a putative nuclear localisation signal within the second half of the CCT motif []. The CCT motif is found in the Arabidopsis circadian rhythm protein TOC1, an autoregulatory response regulator homologue the controls the photoperiodic flowering through its clock function []. ; GO: 0005515 protein binding; PDB: 3OGK_V 3OGL_S 3OGM_W.
Probab=98.58 E-value=2.3e-08 Score=60.34 Aligned_cols=26 Identities=50% Similarity=0.508 Sum_probs=10.0
Q ss_pred hHHHHHHHHHHHHHhhhhccccceecc
Q 027756 62 NNRRLASLIRFREKRKERNFEKKIRYT 88 (219)
Q Consensus 62 ~~~R~~sl~rf~eKrk~R~~~k~~rY~ 88 (219)
|++|++||+||+||||+|+.. +..|.
T Consensus 1 P~aRK~SLqRFLeKRK~R~~~-~~PY~ 26 (27)
T PF09425_consen 1 PIARKASLQRFLEKRKDRLAA-KSPYQ 26 (27)
T ss_dssp -----HHHHHHHHHH------------
T ss_pred CchHHHHHHHHHHHHHHhhcc-CCCCC
Confidence 578999999999999999997 56775
No 8
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.40 E-value=1.5e-07 Score=90.82 Aligned_cols=59 Identities=36% Similarity=0.610 Sum_probs=47.3
Q ss_pred CCCCcccccccccccccCCCCccccCCCC----CcccchhhhHHHHhcCCCC-CCccCCCCCCccc
Q 027756 132 NGSQNQDIVCRHCGISEKSTPMMRRGPEG----PRTLCNACGLMWANKGTLR-DLSKAAPQAGQTS 192 (219)
Q Consensus 132 ~~~~~~~~~C~~C~~~~~~Tp~wR~Gp~G----~~~LCNaCGl~~~~~~~~r-~~~~~~~~~~~~~ 192 (219)
.+......+|.||.+ +.||+|||+..+ .-.|||||||+|+.|+.+| |+..+........
T Consensus 152 ~~~s~~~~vc~Nc~t--~stPlwrR~~~~~s~~~n~lcnaCgl~~klhg~~r~P~t~ks~~~ks~~ 215 (498)
T COG5641 152 SDNSNQPHVCSNCKT--TSTPLWRRASSESSLPGNNLCNACGLYLKLHGSPRAPISLKSDSIKSRS 215 (498)
T ss_pred cccccccchhccccc--cCCccccccccccccCCccccccccccccccCCcCCCcccccccccccc
Confidence 344555669999999 789999999993 2699999999999999999 8877655444444
No 9
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=92.62 E-value=0.3 Score=47.64 Aligned_cols=56 Identities=21% Similarity=0.460 Sum_probs=38.8
Q ss_pred cccccccccccCCCCcccc-C-CCCCcccchhhhHHHHhcCC------CCCCccCCCCCCccccCC
Q 027756 138 DIVCRHCGISEKSTPMMRR-G-PEGPRTLCNACGLMWANKGT------LRDLSKAAPQAGQTSSLN 195 (219)
Q Consensus 138 ~~~C~~C~~~~~~Tp~wR~-G-p~G~~~LCNaCGl~~~~~~~------~r~~~~~~~~~~~~~~~~ 195 (219)
.+.|-+|+| ++.-+|=. | |.-...||--|=+||++-+- +..-.++.++++-.+...
T Consensus 386 g~~CEsC~t--tqs~qWYsWGppnmqcrLCasCWiyWKKygGLk~ptqle~~~~~~~p~~e~p~~r 449 (693)
T KOG3554|consen 386 GRACESCYT--TQSLQWYSWGPPNMQCRLCASCWIYWKKYGGLKMPTQLEGEDKGPPPPVEPPAPR 449 (693)
T ss_pred CCccccccc--ccccceeccCCCCccchhhHHHHHHHHHhcCcCCcchhccccCCCCCCCCCCCCC
Confidence 678999999 78888865 4 44445899999999999762 334455555555444333
No 10
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=91.61 E-value=0.093 Score=51.27 Aligned_cols=52 Identities=25% Similarity=0.275 Sum_probs=44.0
Q ss_pred CCcccccccccccccCCCCccccCCCCCcccchhhhHHHHhcCCCCCCccCCC
Q 027756 134 SQNQDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKGTLRDLSKAAP 186 (219)
Q Consensus 134 ~~~~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~~~~~~r~~~~~~~ 186 (219)
.......|.+|++. +.||.||+...-.-.+||+||++.+..+..+|+.++.-
T Consensus 293 ~~ps~~~~s~~~~~-~~tp~~~r~~~~~s~~~n~~~~~~~~~~~~~p~~pk~d 344 (498)
T COG5641 293 VLPSDKKRSTLTTS-TATPLWRRTSDKSSFSCNASGSALKPPGSKRPLLPKPD 344 (498)
T ss_pred cchhhcCccccccc-ccCcccccccccccccccccccccCCcccccccCCCCC
Confidence 44457889999987 67999999988778999999999999999999888533
No 11
>PF13619 KTSC: KTSC domain
Probab=82.83 E-value=2.1 Score=29.76 Aligned_cols=37 Identities=30% Similarity=0.464 Sum_probs=30.3
Q ss_pred hhhhhccCCCCceEEEe-ccEEEEecCCCHHHHHHHHH
Q 027756 5 MRVMVLERIGDQLTLSF-QGQVYVFDSVSPEKVQAVLL 41 (219)
Q Consensus 5 ~~~~~~~~~~~qLTifY-~G~v~Vfd~v~~~ka~~im~ 41 (219)
++.+-=+.++..|.|.| +|.++.|.+||++-.+++|.
T Consensus 6 I~~v~Yd~~~~~L~V~F~~G~~Y~Y~~Vp~~~~~~l~~ 43 (60)
T PF13619_consen 6 IRSVGYDPETRTLEVEFKSGSVYRYFGVPPEVYEALLN 43 (60)
T ss_pred ccEEeECCCCCEEEEEEcCCCEEEECCCCHHHHHHHHc
Confidence 33444567788999999 89999999999999998876
No 12
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=81.01 E-value=0.5 Score=29.95 Aligned_cols=30 Identities=30% Similarity=0.738 Sum_probs=14.4
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhH
Q 027756 139 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 170 (219)
Q Consensus 139 ~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl 170 (219)
+.|.+||.. .+..-=.|.+-.+..|.+||-
T Consensus 1 kfC~~CG~~--l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGP--LERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B---EEE--TT-SS-EEEETTTTE
T ss_pred CccccccCh--hhhhcCCCCCccceECCCCCC
Confidence 369999982 222222455566689999984
No 13
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=78.45 E-value=0.59 Score=39.13 Aligned_cols=41 Identities=44% Similarity=0.657 Sum_probs=39.0
Q ss_pred hHHHHHHHHHHHHHhhhhccccceeccccHHHHHHHHhhcC
Q 027756 62 NNRRLASLIRFREKRKERNFEKKIRYTVRKEVALRMQRNKG 102 (219)
Q Consensus 62 ~~~R~~sl~rf~eKrk~R~~~k~~rY~~Rk~~A~~r~R~kG 102 (219)
...|...+.|+++++..|.|.+.++|..|+..|..+++.++
T Consensus 290 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (340)
T KOG1601|consen 290 SHQRVAEVRRYRESRDGRYFDKGIRYASRKSNAESRPRLKG 330 (340)
T ss_pred cchHHHHHhhccCccCCcccccccccccccccchhcccccc
Confidence 56899999999999999999999999999999999999988
No 14
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=65.95 E-value=7 Score=28.19 Aligned_cols=47 Identities=28% Similarity=0.673 Sum_probs=33.8
Q ss_pred cccccccccccccCCCCc--cc-cCCCCCcccchhhhHHHHhcCCCCCCccC
Q 027756 136 NQDIVCRHCGISEKSTPM--MR-RGPEGPRTLCNACGLMWANKGTLRDLSKA 184 (219)
Q Consensus 136 ~~~~~C~~C~~~~~~Tp~--wR-~Gp~G~~~LCNaCGl~~~~~~~~r~~~~~ 184 (219)
.+...|..|.. ++|-. .= -...-|+..|-+|-.+|-..|.+|.++-+
T Consensus 3 ~~~~~CPRC~S--~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvg 52 (63)
T PF02701_consen 3 EQPLPCPRCDS--TNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVG 52 (63)
T ss_pred ccCCCCCCcCC--CCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccC
Confidence 45677999987 45533 11 12344568999999999999999998655
No 15
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 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 [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=65.42 E-value=1.8 Score=29.98 Aligned_cols=26 Identities=27% Similarity=0.846 Sum_probs=18.5
Q ss_pred ccccccccccccCCCCccccCCCCCcccchhhhHHHHh
Q 027756 137 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWAN 174 (219)
Q Consensus 137 ~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~~ 174 (219)
....|.+||.. .-+..+|..|| ||+.
T Consensus 25 ~l~~c~~cg~~-----------~~~H~vc~~cG-~y~~ 50 (56)
T PF01783_consen 25 NLVKCPNCGEP-----------KLPHRVCPSCG-YYKG 50 (56)
T ss_dssp SEEESSSSSSE-----------ESTTSBCTTTB-BSSS
T ss_pred ceeeeccCCCE-----------ecccEeeCCCC-eECC
Confidence 45679999983 22368999999 5543
No 16
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=64.54 E-value=2.8 Score=27.58 Aligned_cols=25 Identities=44% Similarity=1.163 Sum_probs=19.2
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhh
Q 027756 138 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACG 169 (219)
Q Consensus 138 ~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCG 169 (219)
...|..|++ |++| ..+| ..+|-+|+
T Consensus 17 ~~~Cp~C~~-----PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCGT-----PLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred cCccCCCCC-----eeEE-ecCC-CEECCCCC
Confidence 456999965 9999 3466 68999985
No 17
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=64.52 E-value=2.9 Score=26.99 Aligned_cols=31 Identities=29% Similarity=0.681 Sum_probs=20.4
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhH
Q 027756 138 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 170 (219)
Q Consensus 138 ~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl 170 (219)
..+|.+|++ ---|.-.-...|....||-|+.
T Consensus 2 p~rC~~C~a--ylNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCRRCRA--YLNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp S-B-TTT----BS-TTSEEETTTTEEEETTT--
T ss_pred ccccCCCCC--EECCcceEcCCCCEEECcCCCC
Confidence 468999999 5588888888888889999985
No 18
>COG3952 Predicted membrane protein [Function unknown]
Probab=59.45 E-value=2.4 Score=33.66 Aligned_cols=21 Identities=33% Similarity=0.408 Sum_probs=16.7
Q ss_pred CccccCCCCCcccchhhhHHHHh
Q 027756 152 PMMRRGPEGPRTLCNACGLMWAN 174 (219)
Q Consensus 152 p~wR~Gp~G~~~LCNaCGl~~~~ 174 (219)
-+||.+|-+ .||++||++-..
T Consensus 75 fi~~~DpV~--Vl~~~~glF~~l 95 (113)
T COG3952 75 FIRRQDPVF--VLGQACGLFIYL 95 (113)
T ss_pred HHHhcchHH--HHHHhhhHHHHH
Confidence 357888888 799999998543
No 19
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=58.57 E-value=3 Score=26.44 Aligned_cols=33 Identities=24% Similarity=0.652 Sum_probs=27.9
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhHHH
Q 027756 139 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMW 172 (219)
Q Consensus 139 ~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~ 172 (219)
..|.+|++. -..+..+-.+.|...-|-.||-.|
T Consensus 3 i~Cp~C~~~-y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAK-YEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCE-EeCCHHHCCCCCcEEECCCCCCEe
Confidence 469999997 578888888999889999998655
No 20
>KOG1561 consensus CCAAT-binding factor, subunit B (HAP2) [Transcription]
Probab=58.07 E-value=7.2 Score=36.13 Aligned_cols=30 Identities=30% Similarity=0.477 Sum_probs=25.5
Q ss_pred eec--cccHHHHHHHHh-hcCccccCCCCCccc
Q 027756 85 IRY--TVRKEVALRMQR-NKGQFTSAKSNNEDS 114 (219)
Q Consensus 85 ~rY--~~Rk~~A~~r~R-~kGrf~s~~~~~d~S 114 (219)
..| ++|..+|++|+| ..|||...++.++++
T Consensus 217 kpYLHESRH~HAmkR~RG~GGRFln~k~~~~~s 249 (307)
T KOG1561|consen 217 KPYLHESRHLHAMKRARGEGGRFLNTKEYHDDS 249 (307)
T ss_pred CccccchhhHHHhhcccCCCCCCCchhhhhhhc
Confidence 347 899999999999 899999998766553
No 21
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=57.61 E-value=8.9 Score=29.97 Aligned_cols=38 Identities=26% Similarity=0.500 Sum_probs=27.6
Q ss_pred cccccccccccccCCCCccccCCCCCcccchhhhHHHHhcCC
Q 027756 136 NQDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKGT 177 (219)
Q Consensus 136 ~~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~~~~~ 177 (219)
..+..|..|+.. -|.|-.=.-| -.||-.|.-.++.-|+
T Consensus 11 ~~N~~CaDCg~~---~p~w~s~~~G-iflC~~Cag~HR~lg~ 48 (116)
T PF01412_consen 11 PGNKVCADCGAP---NPTWASLNYG-IFLCLECAGIHRSLGV 48 (116)
T ss_dssp TTCTB-TTT-SB---S--EEETTTT-EEE-HHHHHHHHHHTT
T ss_pred cCcCcCCCCCCC---CCCEEEeecC-hhhhHHHHHHHHHhcc
Confidence 456889999984 5899998889 6999999988888775
No 22
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=56.43 E-value=3.7 Score=33.69 Aligned_cols=30 Identities=30% Similarity=0.744 Sum_probs=21.9
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhHH
Q 027756 139 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGLM 171 (219)
Q Consensus 139 ~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~ 171 (219)
-.|..|+. .+|-+-+.+-.= -.-|+|||-.
T Consensus 103 VlC~~C~s--pdT~l~k~~r~~-~l~C~ACGa~ 132 (138)
T PRK03988 103 VICPECGS--PDTKLIKEGRIW-VLKCEACGAE 132 (138)
T ss_pred EECCCCCC--CCcEEEEcCCeE-EEEcccCCCC
Confidence 57999999 568888753222 3679999953
No 23
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=55.02 E-value=4.1 Score=33.24 Aligned_cols=30 Identities=30% Similarity=0.786 Sum_probs=21.6
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhHH
Q 027756 139 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGLM 171 (219)
Q Consensus 139 ~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~ 171 (219)
-.|..|+. .+|-+-+.+-. --.-|+|||-.
T Consensus 98 VlC~~C~s--PdT~l~k~~r~-~~l~C~ACGa~ 127 (133)
T TIGR00311 98 VICRECNR--PDTRIIKEGRV-SLLKCEACGAK 127 (133)
T ss_pred EECCCCCC--CCcEEEEeCCe-EEEecccCCCC
Confidence 57999999 56888875322 12579999954
No 24
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=53.55 E-value=5 Score=40.52 Aligned_cols=37 Identities=19% Similarity=0.453 Sum_probs=29.5
Q ss_pred ccccccccccccCCCCccccCCCC---CcccchhhhHHHHhc
Q 027756 137 QDIVCRHCGISEKSTPMMRRGPEG---PRTLCNACGLMWANK 175 (219)
Q Consensus 137 ~~~~C~~C~~~~~~Tp~wR~Gp~G---~~~LCNaCGl~~~~~ 175 (219)
+...|..|.+ .-||.|+.-+.+ ..++|..|----.++
T Consensus 461 ~P~~caqckt--dftp~wk~ekstq~d~~i~cE~cvtSnqkk 500 (706)
T KOG3740|consen 461 EPYACAQCKT--DFTPAWKKEKSTQADAAIVCENCVTSNQKK 500 (706)
T ss_pred Cchhhhhccc--ccccccccccccCcchHHHHHhhhhhcccc
Confidence 3678999999 889999998888 348999997554443
No 25
>PRK05978 hypothetical protein; Provisional
Probab=53.25 E-value=5.8 Score=33.04 Aligned_cols=34 Identities=26% Similarity=0.522 Sum_probs=26.2
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHHHhcC
Q 027756 138 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKG 176 (219)
Q Consensus 138 ~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~~~~ 176 (219)
..+|.+||. ..+++ |-..-..-|.+||+.|..+.
T Consensus 33 ~grCP~CG~----G~LF~-g~Lkv~~~C~~CG~~~~~~~ 66 (148)
T PRK05978 33 RGRCPACGE----GKLFR-AFLKPVDHCAACGEDFTHHR 66 (148)
T ss_pred cCcCCCCCC----Ccccc-cccccCCCccccCCccccCC
Confidence 468999998 57776 45555689999999997653
No 26
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=52.27 E-value=4.9 Score=31.72 Aligned_cols=29 Identities=28% Similarity=0.679 Sum_probs=21.0
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhH
Q 027756 139 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 170 (219)
Q Consensus 139 ~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl 170 (219)
-.|..|+. .+|-+-+.+-.= -.-|+|||-
T Consensus 81 VlC~~C~s--pdT~l~k~~r~~-~l~C~aCGa 109 (110)
T smart00653 81 VLCPECGS--PDTELIKENRLF-FLKCEACGA 109 (110)
T ss_pred EECCCCCC--CCcEEEEeCCeE-EEEccccCC
Confidence 56999999 578888873211 245999994
No 27
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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 ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=51.49 E-value=7.2 Score=25.34 Aligned_cols=32 Identities=28% Similarity=0.668 Sum_probs=20.0
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhHH
Q 027756 139 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGLM 171 (219)
Q Consensus 139 ~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~ 171 (219)
..|+-||.+....-..=.||.+ ...|+.|=..
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~-~~IC~~Cv~~ 33 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNG-AYICDECVEQ 33 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-S-EEEEHHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCC-cEECHHHHHH
Confidence 5799999976555555588977 6899999543
No 28
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=51.40 E-value=7.8 Score=27.49 Aligned_cols=30 Identities=23% Similarity=0.661 Sum_probs=23.1
Q ss_pred ccccccccccccCCCCccccCCCCCcccc-hhhhHHHHhcC
Q 027756 137 QDIVCRHCGISEKSTPMMRRGPEGPRTLC-NACGLMWANKG 176 (219)
Q Consensus 137 ~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LC-NaCGl~~~~~~ 176 (219)
+.+.|.+||.+. | | . ...| ..|+.-|.++.
T Consensus 2 ~HkHC~~CG~~I---p-----~-~-~~fCS~~C~~~~~k~q 32 (59)
T PF09889_consen 2 PHKHCPVCGKPI---P-----P-D-ESFCSPKCREEYRKRQ 32 (59)
T ss_pred CCCcCCcCCCcC---C-----c-c-hhhhCHHHHHHHHHHH
Confidence 467899999965 2 2 2 6899 59999998765
No 29
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=50.78 E-value=5.9 Score=32.43 Aligned_cols=27 Identities=33% Similarity=0.924 Sum_probs=22.4
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHH
Q 027756 138 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMW 172 (219)
Q Consensus 138 ~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~ 172 (219)
..+|.-||+ |++| -+| ...|--||...
T Consensus 28 ~~hCp~Cg~-----PLF~--KdG-~v~CPvC~~~~ 54 (131)
T COG1645 28 AKHCPKCGT-----PLFR--KDG-EVFCPVCGYRE 54 (131)
T ss_pred HhhCcccCC-----ccee--eCC-eEECCCCCceE
Confidence 467999988 9999 588 69999999543
No 30
>PRK00420 hypothetical protein; Validated
Probab=49.29 E-value=7.9 Score=30.83 Aligned_cols=30 Identities=23% Similarity=0.707 Sum_probs=23.6
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHHHh
Q 027756 138 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWAN 174 (219)
Q Consensus 138 ~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~~ 174 (219)
...|..||+ |+.|- .+| ...|-.||-.+..
T Consensus 23 ~~~CP~Cg~-----pLf~l-k~g-~~~Cp~Cg~~~~v 52 (112)
T PRK00420 23 SKHCPVCGL-----PLFEL-KDG-EVVCPVHGKVYIV 52 (112)
T ss_pred cCCCCCCCC-----cceec-CCC-ceECCCCCCeeee
Confidence 367999987 88885 466 6999999987654
No 31
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=48.65 E-value=5.8 Score=34.27 Aligned_cols=33 Identities=24% Similarity=0.644 Sum_probs=23.6
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhHHHHh
Q 027756 139 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWAN 174 (219)
Q Consensus 139 ~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~~ 174 (219)
-.|..|+. .+|-+-+.+-.= -.-|+|||-..-.
T Consensus 99 V~C~~C~~--pdT~l~k~~~~~-~l~C~aCGa~~~v 131 (201)
T PRK12336 99 VICSECGL--PDTRLVKEDRVL-MLRCDACGAHRPV 131 (201)
T ss_pred EECCCCCC--CCcEEEEcCCeE-EEEcccCCCCccc
Confidence 57999999 568888764221 3579999976543
No 32
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.45 E-value=7.9 Score=31.47 Aligned_cols=34 Identities=26% Similarity=0.475 Sum_probs=23.6
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHHHhcC
Q 027756 138 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKG 176 (219)
Q Consensus 138 ~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~~~~ 176 (219)
..+|.+||. -=+.|. =-....-|.|||+-|..+.
T Consensus 21 ~grCP~CGe----GrLF~g-FLK~~p~C~aCG~dyg~~~ 54 (126)
T COG5349 21 RGRCPRCGE----GRLFRG-FLKVVPACEACGLDYGFAD 54 (126)
T ss_pred cCCCCCCCC----chhhhh-hcccCchhhhccccccCCc
Confidence 457999998 344443 2334578999999997654
No 33
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=44.03 E-value=8.5 Score=24.88 Aligned_cols=29 Identities=28% Similarity=0.763 Sum_probs=15.2
Q ss_pred cccccccccCCCCccccCCCCCcccchhhhHHHH
Q 027756 140 VCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWA 173 (219)
Q Consensus 140 ~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~ 173 (219)
.|.+|+.. . .--.--.| ...|..||+-..
T Consensus 2 ~Cp~Cg~~--~--~~~D~~~g-~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 2 KCPNCGSK--E--IVFDPERG-ELVCPNCGLVLE 30 (43)
T ss_dssp SBTTTSSS--E--EEEETTTT-EEEETTT-BBEE
T ss_pred CCcCCcCC--c--eEEcCCCC-eEECCCCCCEee
Confidence 57777772 2 22222233 567888876543
No 34
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=43.34 E-value=5.3 Score=24.94 Aligned_cols=33 Identities=30% Similarity=0.734 Sum_probs=21.0
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhHHH
Q 027756 139 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMW 172 (219)
Q Consensus 139 ~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~ 172 (219)
..|.+|++. -.-+....+..|....|--||..|
T Consensus 3 ~~CP~C~~~-~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTS-FRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCE-EEeCHHHcCCCCCEEECCCCCCEE
Confidence 458888874 234445555556567888887654
No 35
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=42.19 E-value=9.1 Score=30.82 Aligned_cols=29 Identities=31% Similarity=0.757 Sum_probs=22.3
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhH
Q 027756 139 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 170 (219)
Q Consensus 139 ~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl 170 (219)
-.|..|+. .+|-+-+.+..- -.-|+|||-
T Consensus 94 VlC~~C~s--pdT~l~k~~r~~-~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGS--PDTELIKEGRLI-FLKCKACGA 122 (125)
T ss_dssp SSCTSTSS--SSEEEEEETTCC-EEEETTTSC
T ss_pred EEcCCCCC--CccEEEEcCCEE-EEEecccCC
Confidence 46999999 568888875443 478999994
No 36
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=41.90 E-value=6.3 Score=24.00 Aligned_cols=28 Identities=29% Similarity=0.719 Sum_probs=15.0
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHH
Q 027756 138 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLM 171 (219)
Q Consensus 138 ~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~ 171 (219)
.+.|..||... ..-+.|-...|..||..
T Consensus 3 ~rfC~~CG~~t------~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAPT------KPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--BE------EE-SSSS-EEESSSS-E
T ss_pred CcccCcCCccc------cCCCCcCEeECCCCcCE
Confidence 56899999842 22334667899999875
No 37
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=40.99 E-value=13 Score=36.74 Aligned_cols=35 Identities=29% Similarity=0.647 Sum_probs=24.4
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhHHHHhcCCC
Q 027756 139 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKGTL 178 (219)
Q Consensus 139 ~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~~~~~~ 178 (219)
..|.||+.+ ++.-+ --+| ...|++||.-.-.....
T Consensus 1 ~~C~~C~~s---~fe~d-~a~g-~~~C~~CG~v~E~~~iv 35 (521)
T KOG1598|consen 1 MVCKNCGGS---NFERD-EATG-NLYCTACGTVLEYNNIV 35 (521)
T ss_pred CcCCCCCCC---Ccccc-cccC-Cceeccccceeecccee
Confidence 369999993 45433 3455 59999999877665543
No 38
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=40.30 E-value=21 Score=34.06 Aligned_cols=30 Identities=27% Similarity=0.720 Sum_probs=24.6
Q ss_pred ccccccccccccCCCCccccCCCCCcccchhh
Q 027756 137 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNAC 168 (219)
Q Consensus 137 ~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaC 168 (219)
....|+.||.+...++..-.||.. ..|+.|
T Consensus 8 ~~~~CSFCGr~~~ev~~li~g~~~--~IC~~C 37 (412)
T PRK05342 8 KLLYCSFCGKSQHEVRKLIAGPGV--YICDEC 37 (412)
T ss_pred CccccCCCCCChhhccccccCCCC--cccchH
Confidence 355899999987777778888854 699999
No 39
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=39.89 E-value=12 Score=26.16 Aligned_cols=25 Identities=28% Similarity=0.829 Sum_probs=17.9
Q ss_pred cccccccccccccCCCCccccCCCCCcccchhhhHH
Q 027756 136 NQDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLM 171 (219)
Q Consensus 136 ~~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~ 171 (219)
.....|.+||... - +..+|..||.|
T Consensus 25 ~~l~~C~~CG~~~--~---------~H~vC~~CG~Y 49 (57)
T PRK12286 25 PGLVECPNCGEPK--L---------PHRVCPSCGYY 49 (57)
T ss_pred CcceECCCCCCcc--C---------CeEECCCCCcC
Confidence 3456799999932 2 26899999954
No 40
>smart00521 CBF CCAAT-Binding transcription Factor.
Probab=39.73 E-value=36 Score=24.51 Aligned_cols=21 Identities=29% Similarity=0.354 Sum_probs=17.6
Q ss_pred eccccHHHHHHHHh-hcCcccc
Q 027756 86 RYTVRKEVALRMQR-NKGQFTS 106 (219)
Q Consensus 86 rY~~Rk~~A~~r~R-~kGrf~s 106 (219)
-+++|..+|++|+| .-|+|..
T Consensus 40 lhESRH~HAm~R~Rg~gGRFl~ 61 (62)
T smart00521 40 LHESRHLHAMRRPRGSGGRFLN 61 (62)
T ss_pred ccchhHHHHHccCcCCCCCCCC
Confidence 35999999999999 5668864
No 41
>PF12773 DZR: Double zinc ribbon
Probab=38.87 E-value=19 Score=23.51 Aligned_cols=30 Identities=27% Similarity=0.792 Sum_probs=19.0
Q ss_pred CcccccccccccccCCCCccccCCCCCcccchhhhHH
Q 027756 135 QNQDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLM 171 (219)
Q Consensus 135 ~~~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~ 171 (219)
......|.+||+.. . .+......|..||-.
T Consensus 9 ~~~~~fC~~CG~~l--~-----~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 9 PDDAKFCPHCGTPL--P-----PPDQSKKICPNCGAE 38 (50)
T ss_pred CccccCChhhcCCh--h-----hccCCCCCCcCCcCC
Confidence 34467788888842 2 334445678888764
No 42
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=37.80 E-value=13 Score=35.74 Aligned_cols=26 Identities=35% Similarity=0.879 Sum_probs=16.9
Q ss_pred cccccccccccccCCCCccccCCCCCcccchhhhHH
Q 027756 136 NQDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLM 171 (219)
Q Consensus 136 ~~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~ 171 (219)
+...+|.+||-. +|.|- .-|.+||-+
T Consensus 5 ~~~y~C~~Cg~~---~~~~~-------g~Cp~C~~w 30 (454)
T TIGR00416 5 KSKFVCQHCGAD---SPKWQ-------GKCPACHAW 30 (454)
T ss_pred CCeEECCcCCCC---Ccccc-------EECcCCCCc
Confidence 345789999884 45552 258888755
No 43
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=37.60 E-value=22 Score=32.48 Aligned_cols=25 Identities=28% Similarity=0.597 Sum_probs=17.5
Q ss_pred CCCCcccccccccccc-----cCCCCcccc
Q 027756 132 NGSQNQDIVCRHCGIS-----EKSTPMMRR 156 (219)
Q Consensus 132 ~~~~~~~~~C~~C~~~-----~~~Tp~wR~ 156 (219)
.|...+...|.+||.- ....|+||.
T Consensus 24 ~d~~~Ge~vC~~CG~Vl~e~~iD~g~EWR~ 53 (310)
T PRK00423 24 YDYERGEIVCADCGLVIEENIIDQGPEWRA 53 (310)
T ss_pred EECCCCeEeecccCCcccccccccCCCccC
Confidence 4566778888888873 234788885
No 44
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=37.16 E-value=15 Score=32.71 Aligned_cols=26 Identities=23% Similarity=0.644 Sum_probs=14.7
Q ss_pred cccccccccccccCCCCccccCCCCCcccchhhhHH
Q 027756 136 NQDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLM 171 (219)
Q Consensus 136 ~~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~ 171 (219)
.+.+.|.|||.. +..| ..+|..||-+
T Consensus 352 ~p~~~c~~cg~~---~~~~-------~~~c~~c~~~ 377 (389)
T PRK11788 352 KPRYRCRNCGFT---ARTL-------YWHCPSCKAW 377 (389)
T ss_pred CCCEECCCCCCC---Cccc-------eeECcCCCCc
Confidence 344677777773 3344 2456666643
No 45
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=37.01 E-value=21 Score=20.79 Aligned_cols=22 Identities=27% Similarity=0.871 Sum_probs=12.8
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhH
Q 027756 139 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 170 (219)
Q Consensus 139 ~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl 170 (219)
+.|.+||... . .+ ...|..||.
T Consensus 3 ~~Cp~Cg~~~--~-------~~-~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEI--D-------PD-AKFCPNCGA 24 (26)
T ss_pred CCCcccCCcC--C-------cc-cccChhhCC
Confidence 4677787732 1 22 357777774
No 46
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=36.94 E-value=20 Score=23.07 Aligned_cols=30 Identities=20% Similarity=0.436 Sum_probs=18.6
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhh
Q 027756 138 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACG 169 (219)
Q Consensus 138 ~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCG 169 (219)
...|..|+- ++.=.|..-.......|+.||
T Consensus 3 ~~pCP~CGG--~DrFr~~d~~g~G~~~C~~Cg 32 (37)
T smart00778 3 HGPCPNCGG--SDRFRFDDKDGRGTWFCSVCG 32 (37)
T ss_pred ccCCCCCCC--ccccccccCCCCcCEEeCCCC
Confidence 346888988 445446543222257899886
No 47
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=35.17 E-value=12 Score=29.11 Aligned_cols=36 Identities=22% Similarity=0.436 Sum_probs=22.9
Q ss_pred ccccccccccccCCCCccccCCCCCcccchhhhHHHHhc
Q 027756 137 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANK 175 (219)
Q Consensus 137 ~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~~~ 175 (219)
....|.+|+.....-++=| ..+...|..||.|+...
T Consensus 20 t~f~CP~Cge~~v~v~~~k---~~~h~~C~~CG~y~~~~ 55 (99)
T PRK14892 20 KIFECPRCGKVSISVKIKK---NIAIITCGNCGLYTEFE 55 (99)
T ss_pred cEeECCCCCCeEeeeecCC---CcceEECCCCCCccCEE
Confidence 4567999995211112222 35578999999998653
No 48
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=35.04 E-value=21 Score=33.18 Aligned_cols=39 Identities=23% Similarity=0.475 Sum_probs=31.9
Q ss_pred CcccccccccccccCCCCccccCCCCCcccchhhhHHHHhcCC
Q 027756 135 QNQDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKGT 177 (219)
Q Consensus 135 ~~~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~~~~~ 177 (219)
......|..|+. .. |+|=.=.-| ..||=-|-=-.+.-|+
T Consensus 17 ~~~Nk~CaDCga--~~-P~W~S~nlG-vfiCi~CagvHRsLGv 55 (319)
T COG5347 17 DSSNKKCADCGA--PN-PTWASVNLG-VFLCIDCAGVHRSLGV 55 (319)
T ss_pred ccccCccccCCC--CC-CceEecccC-eEEEeecchhhhcccc
Confidence 455788999999 56 999999999 6999999766666553
No 49
>TIGR03573 WbuX N-acetyl sugar amidotransferase. This enzyme has been implicated in the formation of the acetamido moiety (sugar-NC(=NH)CH3) which is found on some exopolysaccharides and is positively charged at neutral pH. The reaction involves ligation of ammonia with a sugar N-acetyl group, displacing water. In E. coli (O145 strain) and Pseudomonas aeruginosa (O12 strain) this gene is known as wbuX and ifnA respectively and likely acts on sialic acid. In Campylobacter jejuni, the gene is known as pseA and acts on pseudaminic acid in the process of flagellin glycosylation. In other Pseudomonas strains and various organisms it is unclear what the identity of the sugar substrate is, and in fact, the phylogenetic tree of this family sports a considerably deep branching suggestive of possible major differences in substrate structure. Nevertheless, the family is characterized by a conserved tetracysteine motif (CxxC.....[GN]xCxxC) possibly indicative of a metal binding site, as well as an
Probab=34.99 E-value=24 Score=32.58 Aligned_cols=32 Identities=22% Similarity=0.621 Sum_probs=25.0
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhHHHHh
Q 027756 139 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWAN 174 (219)
Q Consensus 139 ~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~~ 174 (219)
+.|+.|..+ ++.|--.-..+| +||+|--+-.+
T Consensus 2 ~~C~~C~~~-~t~p~i~fd~~G---vC~~C~~~~~~ 33 (343)
T TIGR03573 2 KFCKRCVMP-TTRPGITFDEDG---VCSACRNFEEK 33 (343)
T ss_pred CcCCCCCCC-CCCCCeeECCCC---CchhhhhHHhh
Confidence 579999997 467766667777 99999987643
No 50
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=33.71 E-value=21 Score=24.91 Aligned_cols=28 Identities=25% Similarity=0.620 Sum_probs=18.5
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhHHH
Q 027756 139 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMW 172 (219)
Q Consensus 139 ~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~ 172 (219)
..|+.||... .. ...+....|..||..+
T Consensus 29 q~C~~CG~~~-~~-----~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 29 QTCPRCGHRN-KK-----RRSGRVFTCPNCGFEM 56 (69)
T ss_pred cCccCccccc-cc-----ccccceEEcCCCCCEE
Confidence 4599998843 12 3444467888888764
No 51
>PRK11823 DNA repair protein RadA; Provisional
Probab=33.69 E-value=16 Score=35.06 Aligned_cols=27 Identities=30% Similarity=0.719 Sum_probs=18.1
Q ss_pred cccccccccccccCCCCccccCCCCCcccchhhhHHH
Q 027756 136 NQDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMW 172 (219)
Q Consensus 136 ~~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~ 172 (219)
+...+|.+||-. ++.|- .-|.+||-+=
T Consensus 5 ~~~y~C~~Cg~~---~~~~~-------g~Cp~C~~w~ 31 (446)
T PRK11823 5 KTAYVCQECGAE---SPKWL-------GRCPECGAWN 31 (446)
T ss_pred CCeEECCcCCCC---CcccC-------eeCcCCCCcc
Confidence 445789999884 56653 3588887653
No 52
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=32.29 E-value=18 Score=33.13 Aligned_cols=37 Identities=27% Similarity=0.498 Sum_probs=26.1
Q ss_pred CCCCcccccccccccccCCCCccccCCCCCcccchhhhHHHHh
Q 027756 132 NGSQNQDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWAN 174 (219)
Q Consensus 132 ~~~~~~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~~ 174 (219)
-+.....+.|..||+ .+.| + ..|-+.+|+.||..+-.
T Consensus 105 ~~w~~~~RFCg~CG~--~~~~--~--~~g~~~~C~~cg~~~fP 141 (279)
T COG2816 105 LEWYRSHRFCGRCGT--KTYP--R--EGGWARVCPKCGHEHFP 141 (279)
T ss_pred HHHHhhCcCCCCCCC--cCcc--c--cCceeeeCCCCCCccCC
Confidence 445667889999999 3333 2 24556899999988754
No 53
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=32.18 E-value=21 Score=24.13 Aligned_cols=29 Identities=31% Similarity=0.688 Sum_probs=17.0
Q ss_pred ccccccccccCCCCc-cccCCC---CCcc-cchhhhHH
Q 027756 139 IVCRHCGISEKSTPM-MRRGPE---GPRT-LCNACGLM 171 (219)
Q Consensus 139 ~~C~~C~~~~~~Tp~-wR~Gp~---G~~~-LCNaCGl~ 171 (219)
+.|..||. ++. ||++.+ +... .|..||-.
T Consensus 2 kPCPfCGg----~~~~~~~~~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 2 KPCPFCGG----ADVYLRRGFDPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCC----cceeeEeccCCCCCEEEEECCCCCCC
Confidence 57999988 344 663322 2112 58888865
No 54
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=29.49 E-value=13 Score=26.81 Aligned_cols=33 Identities=24% Similarity=0.428 Sum_probs=23.4
Q ss_pred cccccccccccCCCCc-cccCCCCCcccchhhhHHHH
Q 027756 138 DIVCRHCGISEKSTPM-MRRGPEGPRTLCNACGLMWA 173 (219)
Q Consensus 138 ~~~C~~C~~~~~~Tp~-wR~Gp~G~~~LCNaCGl~~~ 173 (219)
.-.|..|.+ .+|=+ ||.. .-+..-|-+||-.-+
T Consensus 10 GA~CP~C~~--~Dtl~mW~En-~ve~vECV~CG~~~~ 43 (66)
T COG3529 10 GAVCPACQA--QDTLAMWREN-NVEIVECVKCGHHMR 43 (66)
T ss_pred cCCCcccch--hhHHHHHHhc-CCceEehhhcchHhh
Confidence 356999999 55555 5554 444689999997764
No 55
>PHA00626 hypothetical protein
Probab=29.26 E-value=20 Score=25.48 Aligned_cols=31 Identities=26% Similarity=0.637 Sum_probs=21.4
Q ss_pred cccccccccCCCCccc----cCCCCCcccchhhhHHHHhc
Q 027756 140 VCRHCGISEKSTPMMR----RGPEGPRTLCNACGLMWANK 175 (219)
Q Consensus 140 ~C~~C~~~~~~Tp~wR----~Gp~G~~~LCNaCGl~~~~~ 175 (219)
.|.+|+.. -..| +++.. ...|.-||..|-+.
T Consensus 2 ~CP~CGS~----~Ivrcg~cr~~sn-rYkCkdCGY~ft~~ 36 (59)
T PHA00626 2 SCPKCGSG----NIAKEKTMRGWSD-DYVCCDCGYNDSKD 36 (59)
T ss_pred CCCCCCCc----eeeeeceecccCc-ceEcCCCCCeechh
Confidence 58899882 2234 23455 58999999998764
No 56
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=29.05 E-value=46 Score=25.78 Aligned_cols=38 Identities=24% Similarity=0.437 Sum_probs=31.4
Q ss_pred ccccccccccccCCCCccccCCCCCcccchhhhHHHHhcCCC
Q 027756 137 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKGTL 178 (219)
Q Consensus 137 ~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~~~~~~ 178 (219)
++..|..|+.. -|.|=.=.-| ..||-.|.-..+..+.+
T Consensus 2 ~N~~CaDC~~~---~p~w~s~~~G-ifvC~~CsgiHR~lg~h 39 (112)
T smart00105 2 GNKKCFDCGAP---NPTWASVNLG-VFLCIECSGIHRSLGVH 39 (112)
T ss_pred CCCcccCCCCC---CCCcEEeccc-eeEhHHhHHHHHhcCCC
Confidence 46789999994 5999988888 69999999888877654
No 57
>PF12553 DUF3742: Protein of unknown function (DUF3742); InterPro: IPR022213 This domain family is found in bacteria, and is approximately 50 amino acids in length. There is a single completely conserved residue Y that may be functionally important.
Probab=28.66 E-value=21 Score=24.84 Aligned_cols=12 Identities=42% Similarity=0.711 Sum_probs=9.9
Q ss_pred CCccccCCCCCc
Q 027756 151 TPMMRRGPEGPR 162 (219)
Q Consensus 151 Tp~wR~Gp~G~~ 162 (219)
.|+||.||.|-.
T Consensus 33 ~~E~R~G~~GfG 44 (54)
T PF12553_consen 33 EPEWREGPAGFG 44 (54)
T ss_pred cHhheecCCCcc
Confidence 388999999853
No 58
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=28.44 E-value=7.9 Score=35.33 Aligned_cols=32 Identities=19% Similarity=0.377 Sum_probs=23.0
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHHHh
Q 027756 138 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWAN 174 (219)
Q Consensus 138 ~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~~ 174 (219)
-..|.+|+. ..|++.=...-..|..||-+++.
T Consensus 26 ~~~c~~c~~-----~~~~~~l~~~~~vc~~c~~h~rl 57 (285)
T TIGR00515 26 WTKCPKCGQ-----VLYTKELERNLEVCPKCDHHMRM 57 (285)
T ss_pred eeECCCCcc-----hhhHHHHHhhCCCCCCCCCcCcC
Confidence 346999998 34555433445799999998876
No 59
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=27.44 E-value=25 Score=21.79 Aligned_cols=29 Identities=24% Similarity=0.697 Sum_probs=19.2
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhH
Q 027756 139 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 170 (219)
Q Consensus 139 ~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl 170 (219)
-+|..|+.. -..|..-.++....|-.||.
T Consensus 6 y~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHT---FEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEcCCCCCE---EEEEEecCCCCCCCCCCCCC
Confidence 468899883 23455433355678999997
No 60
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=26.88 E-value=18 Score=23.85 Aligned_cols=32 Identities=31% Similarity=0.664 Sum_probs=21.6
Q ss_pred ccccccccccccCCCCccccCCCCCcccchhhhHHHHhc
Q 027756 137 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANK 175 (219)
Q Consensus 137 ~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~~~ 175 (219)
....|..|+. .+|-.+..| ..|..|++..+++
T Consensus 10 ~~~~C~~C~~-----~i~g~~~~g--~~C~~C~~~~H~~ 41 (53)
T PF00130_consen 10 KPTYCDVCGK-----FIWGLGKQG--YRCSWCGLVCHKK 41 (53)
T ss_dssp STEB-TTSSS-----BECSSSSCE--EEETTTT-EEETT
T ss_pred CCCCCcccCc-----ccCCCCCCe--EEECCCCChHhhh
Confidence 4567999988 456644444 8999999988654
No 61
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=26.78 E-value=32 Score=22.49 Aligned_cols=31 Identities=26% Similarity=0.473 Sum_probs=18.3
Q ss_pred cccccccccCCCCccccCCCCCcccchhhhHHHHh
Q 027756 140 VCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWAN 174 (219)
Q Consensus 140 ~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~~ 174 (219)
.|..||.-. ..+.|. ......|..||..+..
T Consensus 2 FCp~Cg~~l-~~~~~~---~~~~~vC~~Cg~~~~~ 32 (52)
T smart00661 2 FCPKCGNML-IPKEGK---EKRRFVCRKCGYEEPI 32 (52)
T ss_pred CCCCCCCcc-ccccCC---CCCEEECCcCCCeEEC
Confidence 699998831 122232 1236789999965443
No 62
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=25.94 E-value=22 Score=31.70 Aligned_cols=36 Identities=19% Similarity=0.347 Sum_probs=24.6
Q ss_pred CCCcccccccccccccCCCCccccCCCCCcccchhhhHHHHh
Q 027756 133 GSQNQDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWAN 174 (219)
Q Consensus 133 ~~~~~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~~ 174 (219)
+.....+.|..||.. ... ...|....|.+||..+..
T Consensus 94 ~w~~~~~fC~~CG~~--~~~----~~~~~~~~C~~c~~~~yp 129 (256)
T PRK00241 94 EFYRSHRFCGYCGHP--MHP----SKTEWAMLCPHCRERYYP 129 (256)
T ss_pred HHhhcCccccccCCC--Cee----cCCceeEECCCCCCEECC
Confidence 445567899999994 222 245666789999976654
No 63
>PF02007 MtrH: Tetrahydromethanopterin S-methyltransferase MtrH subunit; InterPro: IPR023467 In archaea the enzyme tetrahydromethanopterin S-methyltransferase is composed of eight subunits, MtrA-H. The enzyme is a membrane- associated enzyme complex which catalyzes an energy-conserving, sodium-ion-translocating step in methanogenesis from hydrogen and carbon dioxide []. Subunit MtrH catalyzes the methylation reaction and was shown to exhibit methyltetrahydromethanopterin:cob(I)alamin methyltransferase activity []. CH3-H4MPT + cob(I)alamin --> H4MPT + CH3-cob(III)alamin (H4MPT = tetrahydromethanopterin); GO: 0008168 methyltransferase activity, 0006730 one-carbon metabolic process
Probab=25.66 E-value=70 Score=29.64 Aligned_cols=26 Identities=19% Similarity=0.287 Sum_probs=22.3
Q ss_pred EEEeccEEEEecC----CCHHHHHHHHHHh
Q 027756 18 TLSFQGQVYVFDS----VSPEKVQAVLLLL 43 (219)
Q Consensus 18 TifY~G~v~Vfd~----v~~~ka~~im~la 43 (219)
||||+|--.|-|. |.-++|++++..-
T Consensus 27 SIFY~gHkIV~D~~~G~FDk~~Ae~Li~~q 56 (296)
T PF02007_consen 27 SIFYNGHKIVEDEKKGIFDKEAAEALINRQ 56 (296)
T ss_pred eeeecCceeeeccCCCccCHHHHHHHHHHH
Confidence 6999999999887 8999999886643
No 64
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=25.46 E-value=26 Score=24.30 Aligned_cols=24 Identities=33% Similarity=0.866 Sum_probs=17.0
Q ss_pred cccccccccccccCCCCccccCCCCCcccchhhhH
Q 027756 136 NQDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 170 (219)
Q Consensus 136 ~~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl 170 (219)
.....|.+||.. --+..+|-.||.
T Consensus 24 p~l~~C~~cG~~-----------~~~H~vc~~cG~ 47 (55)
T TIGR01031 24 PTLVVCPNCGEF-----------KLPHRVCPSCGY 47 (55)
T ss_pred CcceECCCCCCc-----------ccCeeECCccCe
Confidence 345679999983 223679999993
No 65
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=25.35 E-value=26 Score=32.94 Aligned_cols=22 Identities=36% Similarity=0.874 Sum_probs=13.7
Q ss_pred cccccccccCCCCccccCCCCCcccchhhhHH
Q 027756 140 VCRHCGISEKSTPMMRRGPEGPRTLCNACGLM 171 (219)
Q Consensus 140 ~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~ 171 (219)
+|.+||-. +|.|- --|.+||-+
T Consensus 2 ~c~~cg~~---~~~~~-------g~cp~c~~w 23 (372)
T cd01121 2 VCSECGYV---SPKWL-------GKCPECGEW 23 (372)
T ss_pred CCCCCCCC---CCCcc-------EECcCCCCc
Confidence 58888773 45552 247777654
No 66
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=24.77 E-value=34 Score=33.34 Aligned_cols=40 Identities=30% Similarity=0.554 Sum_probs=34.1
Q ss_pred CcccccccccccccCCCCccccCCCCCcccchhhhHHHHhcCCC
Q 027756 135 QNQDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANKGTL 178 (219)
Q Consensus 135 ~~~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~~~~~~ 178 (219)
...+++|..|+.. -|-|=.=+-| ..||--|---.+.-|++
T Consensus 20 ~~~NKvCFDCgAk---nPtWaSVTYG-IFLCiDCSAvHRnLGVH 59 (454)
T KOG0706|consen 20 QSENKVCFDCGAK---NPTWASVTYG-IFLCIDCSAVHRNLGVH 59 (454)
T ss_pred CCCCceecccCCC---CCCceeecce-EEEEEecchhhhccccc
Confidence 3557899999994 6999999999 69999999888777765
No 67
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=24.75 E-value=30 Score=28.87 Aligned_cols=39 Identities=18% Similarity=0.319 Sum_probs=24.0
Q ss_pred ccccccccccCCCCccccCCCCC----cccchhhhHHHHhcCC
Q 027756 139 IVCRHCGISEKSTPMMRRGPEGP----RTLCNACGLMWANKGT 177 (219)
Q Consensus 139 ~~C~~C~~~~~~Tp~wR~Gp~G~----~~LCNaCGl~~~~~~~ 177 (219)
+.|..|+...+..--=|.-.+|. +--|.+||.+|-.--+
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyEr 43 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFER 43 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeee
Confidence 36899988432222234444542 3689999998866544
No 68
>KOG0712 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=24.62 E-value=38 Score=31.83 Aligned_cols=36 Identities=25% Similarity=0.503 Sum_probs=29.0
Q ss_pred cccccccccccCCCCccccCC---CCCcccchhhhHHHH
Q 027756 138 DIVCRHCGISEKSTPMMRRGP---EGPRTLCNACGLMWA 173 (219)
Q Consensus 138 ~~~C~~C~~~~~~Tp~wR~Gp---~G~~~LCNaCGl~~~ 173 (219)
...|..|..++-.+..|+-|| .-.++.|+.|+..-.
T Consensus 143 ~~~C~~C~GsGv~~~~~~~gPg~~qs~q~~C~~C~G~G~ 181 (337)
T KOG0712|consen 143 APKCTTCRGSGVQTRTRQMGPGMVQSPQLVCDSCNGSGE 181 (337)
T ss_pred CCCCCCCCCCCceeEEEeccccccccceeEeccCCCccc
Confidence 347999999988899999999 455688888876544
No 69
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=24.61 E-value=33 Score=29.01 Aligned_cols=36 Identities=17% Similarity=0.422 Sum_probs=20.0
Q ss_pred ccccccccccccCCCCcc-----ccCCCCCcccchhhhHHH
Q 027756 137 QDIVCRHCGISEKSTPMM-----RRGPEGPRTLCNACGLMW 172 (219)
Q Consensus 137 ~~~~C~~C~~~~~~Tp~w-----R~Gp~G~~~LCNaCGl~~ 172 (219)
....|.+|++++.-.--. =.++.-....|+.||..|
T Consensus 38 tI~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpy 78 (158)
T PF10083_consen 38 TITSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPY 78 (158)
T ss_pred HHHHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCC
Confidence 345678887754211100 013344457899999766
No 70
>PF02045 CBFB_NFYA: CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B; InterPro: IPR001289 The CCAAT-binding factor (CBFB/NF-YA) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin []. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding []. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The B subunit contains a region of similarity with the yeast protein HAP2 []. For the B subunit it has been suggested that the N-terminal portion of the conserved region is involved in subunit interaction and the C-terminal region involved in DNA-binding [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=23.63 E-value=57 Score=23.21 Aligned_cols=18 Identities=33% Similarity=0.501 Sum_probs=15.0
Q ss_pred ccccHHHHHHHHh-hcCcc
Q 027756 87 YTVRKEVALRMQR-NKGQF 104 (219)
Q Consensus 87 Y~~Rk~~A~~r~R-~kGrf 104 (219)
+++|..+|++++| ..|+|
T Consensus 40 heSRH~HA~~R~Rg~gGRF 58 (58)
T PF02045_consen 40 HESRHKHAMRRPRGPGGRF 58 (58)
T ss_pred HHHHHHHHHcCccCCCCCC
Confidence 5899999999999 55566
No 71
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.32 E-value=27 Score=26.32 Aligned_cols=35 Identities=26% Similarity=0.526 Sum_probs=24.2
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHHHhc
Q 027756 138 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANK 175 (219)
Q Consensus 138 ~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~~~ 175 (219)
.-.|.+|+-.-+--..++..| -+.|.+||-.+++-
T Consensus 12 ~Y~c~~cg~~~dvvq~~~ddp---lt~ce~c~a~~kk~ 46 (82)
T COG2331 12 SYECTECGNRFDVVQAMTDDP---LTTCEECGARLKKL 46 (82)
T ss_pred EEeecccchHHHHHHhcccCc---cccChhhChHHHHh
Confidence 457999987432234466554 56899999988764
No 72
>COG1962 MtrH Tetrahydromethanopterin S-methyltransferase, subunit H [Coenzyme metabolism]
Probab=22.84 E-value=82 Score=28.96 Aligned_cols=26 Identities=19% Similarity=0.198 Sum_probs=20.7
Q ss_pred EEEeccEEEEecC----CCHHHHHHHHHHh
Q 027756 18 TLSFQGQVYVFDS----VSPEKVQAVLLLL 43 (219)
Q Consensus 18 TifY~G~v~Vfd~----v~~~ka~~im~la 43 (219)
||||++--.|=|. |.-+.|++++..-
T Consensus 35 TIFY~~HkIVeDe~kGiFDr~aAE~Li~~q 64 (313)
T COG1962 35 TIFYAKHKIVEDEKKGIFDREAAEALINTQ 64 (313)
T ss_pred eeeeccceeeeccccccccHHHHHHHHHHH
Confidence 8999998888765 7888888886653
No 73
>PF10777 YlaC: Inner membrane protein YlaC; InterPro: IPR019713 The extracytoplasmic function (ECF) sigma factors are small regulatory proteins that are quite divergent in sequence relative to most other sigma factors. YlaC, regulated by YlaA, is important in oxidative stress resistance. It contributes to hydrogen peroxide resistance in Bacillus subtilis [].
Probab=22.82 E-value=2.4e+02 Score=23.76 Aligned_cols=48 Identities=17% Similarity=0.242 Sum_probs=38.9
Q ss_pred ceEEEeccEEEEecCCCHHHHHHHHHHhcCCCCCCCCCCCCCCccchHHHHHHHHHHHHHhhhh
Q 027756 16 QLTLSFQGQVYVFDSVSPEKVQAVLLLLGGREVPSTTPAIPIANNQNNRRLASLIRFREKRKER 79 (219)
Q Consensus 16 qLTifY~G~v~Vfd~v~~~ka~~im~la~~~~~~~~~~~~~~~~~l~~~R~~sl~rf~eKrk~R 79 (219)
-|.+-|+|+=++...||++-+++|+.- |..+.+-|..|+|-.+++-+=
T Consensus 95 DLRVCYNGEWy~tr~vs~~ai~~iL~~----------------p~V~~~~K~~i~~i~~~Kgei 142 (155)
T PF10777_consen 95 DLRVCYNGEWYNTRFVSDQAIDKILQS----------------PQVPDEIKQGIQRIISTKGEI 142 (155)
T ss_pred EEeEEEcceeeeeccCCHHHHHHHHcC----------------CCCCHHHHHHHHHHHHhCCce
Confidence 478899999999999999999999872 445677888888888775543
No 74
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=22.61 E-value=39 Score=30.82 Aligned_cols=34 Identities=26% Similarity=0.754 Sum_probs=23.9
Q ss_pred ccccccccccccCCCCccccCCCCCcccchhhhHHHHhc
Q 027756 137 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMWANK 175 (219)
Q Consensus 137 ~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~~~~ 175 (219)
....|.+|+. ++.--+--.| ...|.-||+-..-+
T Consensus 10 ~~~~Cp~Cg~----~~iv~d~~~G-e~vC~~CG~Vl~e~ 43 (310)
T PRK00423 10 EKLVCPECGS----DKLIYDYERG-EIVCADCGLVIEEN 43 (310)
T ss_pred cCCcCcCCCC----CCeeEECCCC-eEeecccCCccccc
Confidence 3467999996 2343334566 69999999977654
No 75
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=22.39 E-value=46 Score=31.02 Aligned_cols=31 Identities=26% Similarity=0.593 Sum_probs=21.9
Q ss_pred cccccccccccccCCCCccccCCCCCcccchhhhHH
Q 027756 136 NQDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLM 171 (219)
Q Consensus 136 ~~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~ 171 (219)
.....|.+||+ ..|+-. |.|..-.|-+||--
T Consensus 313 ~k~nfc~ncG~--~~t~~~---~ng~a~fcp~cgq~ 343 (345)
T COG4260 313 AKLNFCLNCGC--GTTADF---DNGKAKFCPECGQG 343 (345)
T ss_pred cccccccccCc--ccccCC---ccchhhhChhhcCC
Confidence 33458999997 567644 45556799999853
No 76
>PRK00979 tetrahydromethanopterin S-methyltransferase subunit H; Provisional
Probab=22.27 E-value=92 Score=28.98 Aligned_cols=26 Identities=23% Similarity=0.336 Sum_probs=22.0
Q ss_pred EEEeccEEEEecC----CCHHHHHHHHHHh
Q 027756 18 TLSFQGQVYVFDS----VSPEKVQAVLLLL 43 (219)
Q Consensus 18 TifY~G~v~Vfd~----v~~~ka~~im~la 43 (219)
||||+|--.|-|. |.-++|++++..-
T Consensus 32 siFY~~h~iV~D~~~G~FDk~~Ae~Li~~~ 61 (308)
T PRK00979 32 SIFYAGHKIVSDEKKGIFDKEKAEALINRQ 61 (308)
T ss_pred EeeecCceeeeccccCccCHHHHHHHHHHH
Confidence 6999999999876 8999999886543
No 77
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=22.08 E-value=33 Score=24.21 Aligned_cols=23 Identities=17% Similarity=0.050 Sum_probs=15.8
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHH
Q 027756 138 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMW 172 (219)
Q Consensus 138 ~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~ 172 (219)
...|.+||... -+..+|. ||.|.
T Consensus 27 ~~~c~~cg~~~-----------~pH~vc~-cG~Y~ 49 (60)
T PRK01110 27 LSVDKTTGEYH-----------LPHHVSP-KGYYK 49 (60)
T ss_pred eeEcCCCCcee-----------ccceecC-CcccC
Confidence 46799999842 2356899 99543
No 78
>PRK14047 putative methyltransferase; Provisional
Probab=21.85 E-value=99 Score=28.84 Aligned_cols=26 Identities=19% Similarity=0.252 Sum_probs=22.2
Q ss_pred EEEeccEEEEecC----CCHHHHHHHHHHh
Q 027756 18 TLSFQGQVYVFDS----VSPEKVQAVLLLL 43 (219)
Q Consensus 18 TifY~G~v~Vfd~----v~~~ka~~im~la 43 (219)
||||+|--.|-|. |.-++|++++...
T Consensus 32 sIFY~~HkIV~D~~~GiFDk~~Ae~Lin~q 61 (310)
T PRK14047 32 TIFYNRHKIVTDEDKGLFDREAAEKLVNLQ 61 (310)
T ss_pred EEeecCceeeeccccCccCHHHHHHHHHHH
Confidence 7999999999876 8999999886654
No 79
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=21.65 E-value=60 Score=24.31 Aligned_cols=35 Identities=20% Similarity=0.571 Sum_probs=24.4
Q ss_pred ccccccccccCCCCccccCCCC--CcccchhhhHHHH
Q 027756 139 IVCRHCGISEKSTPMMRRGPEG--PRTLCNACGLMWA 173 (219)
Q Consensus 139 ~~C~~C~~~~~~Tp~wR~Gp~G--~~~LCNaCGl~~~ 173 (219)
..|.|||........|..-.+| ...=|+.|---|.
T Consensus 1 ~~C~HCg~~~p~~~~~~~~~~g~~~~FCC~GC~~V~~ 37 (88)
T PF12156_consen 1 MKCYHCGLPVPEGAKITVEIDGEERPFCCPGCQAVYQ 37 (88)
T ss_pred CCCCCCCCCCCCCCCeeeeeCCCccccccHHHHHHHH
Confidence 3699999975445567776666 4577899965443
No 80
>PF15321 ATAD4: ATPase family AAA domain containing 4
Probab=21.57 E-value=22 Score=27.03 Aligned_cols=12 Identities=58% Similarity=0.692 Sum_probs=9.7
Q ss_pred HHHHHHhhhhcc
Q 027756 70 IRFREKRKERNF 81 (219)
Q Consensus 70 ~rf~eKrk~R~~ 81 (219)
=||+||||-|..
T Consensus 69 GRFKEKrKvRat 80 (84)
T PF15321_consen 69 GRFKEKRKVRAT 80 (84)
T ss_pred cccccccccccc
Confidence 489999998854
No 81
>TIGR01114 mtrH N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit H. coenzyme M methyltransferase subunit H in methanogenic archaea. This methyltranfersae is membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.
Probab=21.53 E-value=1e+02 Score=28.79 Aligned_cols=26 Identities=12% Similarity=0.146 Sum_probs=22.1
Q ss_pred EEEeccEEEEecC----CCHHHHHHHHHHh
Q 027756 18 TLSFQGQVYVFDS----VSPEKVQAVLLLL 43 (219)
Q Consensus 18 TifY~G~v~Vfd~----v~~~ka~~im~la 43 (219)
||||+|--.|-|. |.-++|++++..-
T Consensus 32 SIFY~~HkIV~D~~~GiFDk~~Ae~Lin~q 61 (314)
T TIGR01114 32 TIFYARHKIVEDEDKGIFDKAAAETLIKTQ 61 (314)
T ss_pred EEeecCceeeeccccCccCHHHHHHHHHHH
Confidence 7999999999876 8999999886654
No 82
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=21.41 E-value=36 Score=21.96 Aligned_cols=29 Identities=24% Similarity=0.587 Sum_probs=17.4
Q ss_pred ccccccccccCCCCccccCCCCCcccchhhhH
Q 027756 139 IVCRHCGISEKSTPMMRRGPEGPRTLCNACGL 170 (219)
Q Consensus 139 ~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl 170 (219)
-+|..||.. --.|+..-+.....|-.||-
T Consensus 6 y~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHE---FEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCE---EEEEEEcCCCCCCcCCCCCC
Confidence 468888852 23334333344578888885
No 83
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=20.90 E-value=36 Score=29.51 Aligned_cols=27 Identities=26% Similarity=0.655 Sum_probs=20.9
Q ss_pred cccccccccccCCCCccccCCCCCcccchhhhHHH
Q 027756 138 DIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLMW 172 (219)
Q Consensus 138 ~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~~ 172 (219)
--.|++|+. ++.+ .|...-|..||---
T Consensus 149 ~A~CsrC~~-----~L~~---~~~~l~Cp~Cg~tE 175 (188)
T COG1096 149 YARCSRCRA-----PLVK---KGNMLKCPNCGNTE 175 (188)
T ss_pred EEEccCCCc-----ceEE---cCcEEECCCCCCEE
Confidence 457999988 7888 56667899999644
No 84
>PLN00162 transport protein sec23; Provisional
Probab=20.79 E-value=41 Score=34.67 Aligned_cols=33 Identities=21% Similarity=0.391 Sum_probs=28.3
Q ss_pred ccccccccccccCCCCccccCCCCCcccchhhhHH
Q 027756 137 QDIVCRHCGISEKSTPMMRRGPEGPRTLCNACGLM 171 (219)
Q Consensus 137 ~~~~C~~C~~~~~~Tp~wR~Gp~G~~~LCNaCGl~ 171 (219)
.+.+|..|++ ---|--+-...|....||-|+..
T Consensus 52 ~pvRC~~Cra--ylNPf~~~d~~~~~W~C~~C~~~ 84 (761)
T PLN00162 52 DPLRCRTCRA--VLNPYCRVDFQAKIWICPFCFQR 84 (761)
T ss_pred CCCccCCCcC--EECCceEEecCCCEEEccCCCCC
Confidence 5689999999 55899888888888999999854
Done!