Query 018653
Match_columns 352
No_of_seqs 273 out of 914
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 02:54:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018653.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018653hhsearch_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 1.4E-16 2.9E-21 110.2 4.9 36 70-105 1-36 (36)
2 cd00202 ZnF_GATA Zinc finger D 99.6 1.6E-15 3.6E-20 113.3 3.9 44 206-251 1-44 (54)
3 smart00401 ZnF_GATA zinc finge 99.5 5.6E-15 1.2E-19 109.5 2.9 46 204-251 3-49 (52)
4 PF00320 GATA: GATA zinc finge 99.5 1.1E-14 2.3E-19 100.4 1.2 36 207-244 1-36 (36)
5 PF06203 CCT: CCT motif; Inte 99.1 5.6E-11 1.2E-15 86.0 2.6 44 138-181 1-44 (45)
6 KOG1601 GATA-4/5/6 transcripti 98.6 2.1E-08 4.6E-13 90.4 3.0 47 204-252 199-245 (340)
7 COG5641 GAT1 GATA Zn-finger-co 98.3 2.3E-07 5E-12 96.2 3.2 60 195-256 149-213 (498)
8 PF09425 CCT_2: Divergent CCT 98.2 8.3E-07 1.8E-11 57.9 1.6 25 136-161 2-26 (27)
9 COG5641 GAT1 GATA Zn-finger-co 91.9 0.093 2E-06 55.2 2.2 52 204-256 297-348 (498)
10 KOG3554 Histone deacetylase co 75.9 3.3 7.2E-05 43.7 4.2 45 198-244 380-426 (693)
11 PF09889 DUF2116: Uncharacteri 65.9 3.1 6.7E-05 32.1 1.1 29 204-242 3-32 (59)
12 PF01783 Ribosomal_L32p: Ribos 65.3 1.6 3.4E-05 32.9 -0.6 25 204-240 26-50 (56)
13 PF13717 zinc_ribbon_4: zinc-r 64.9 1.5 3.2E-05 30.2 -0.7 33 205-238 3-35 (36)
14 PF14803 Nudix_N_2: Nudix N-te 64.7 2.1 4.6E-05 29.4 -0.0 30 205-236 1-30 (34)
15 PF06677 Auto_anti-p27: Sjogre 53.0 4.7 0.0001 28.9 0.1 25 204-235 17-41 (41)
16 smart00653 eIF2B_5 domain pres 52.2 4.9 0.00011 34.3 0.1 28 205-236 81-109 (110)
17 KOG1601 GATA-4/5/6 transcripti 52.1 5.4 0.00012 35.9 0.3 41 135-175 290-330 (340)
18 PRK11823 DNA repair protein Ra 49.2 6.1 0.00013 40.9 0.3 25 204-238 7-31 (446)
19 TIGR00416 sms DNA repair prote 46.9 7 0.00015 40.7 0.3 24 204-237 7-30 (454)
20 PF01412 ArfGap: Putative GTPa 45.7 16 0.00034 30.9 2.2 36 204-243 13-48 (116)
21 PF02701 zf-Dof: Dof domain, z 45.1 18 0.00039 28.3 2.2 47 204-252 5-54 (63)
22 KOG1598 Transcription initiati 44.5 9.9 0.00022 40.6 0.9 31 206-241 2-32 (521)
23 PF06689 zf-C4_ClpX: ClpX C4-t 44.2 11 0.00025 26.5 0.9 32 205-237 2-33 (41)
24 PF09297 zf-NADH-PPase: NADH p 43.4 5.1 0.00011 26.6 -0.9 29 204-238 3-31 (32)
25 TIGR02098 MJ0042_CXXC MJ0042 f 43.1 4.5 9.8E-05 27.4 -1.2 34 205-239 3-36 (38)
26 PRK12286 rpmF 50S ribosomal pr 43.0 7.6 0.00016 29.6 -0.1 23 204-237 27-49 (57)
27 PF13240 zinc_ribbon_2: zinc-r 43.0 13 0.00028 23.3 0.9 21 206-236 1-21 (23)
28 PRK00420 hypothetical protein; 42.7 9.8 0.00021 32.8 0.5 31 204-241 23-53 (112)
29 PF08271 TF_Zn_Ribbon: TFIIB z 41.6 9.7 0.00021 26.8 0.2 30 206-240 2-31 (43)
30 COG1645 Uncharacterized Zn-fin 41.2 9.3 0.0002 33.9 0.1 28 204-239 28-55 (131)
31 PF13248 zf-ribbon_3: zinc-rib 41.1 15 0.00033 23.3 1.1 24 204-237 2-25 (26)
32 cd01121 Sms Sms (bacterial rad 40.8 10 0.00023 38.5 0.4 23 206-238 2-24 (372)
33 COG3952 Predicted membrane pro 39.8 9 0.0002 33.0 -0.2 21 218-240 75-95 (113)
34 TIGR00311 aIF-2beta translatio 39.6 9.1 0.0002 33.8 -0.2 30 205-237 98-127 (133)
35 PRK03988 translation initiatio 38.7 9.3 0.0002 33.9 -0.3 31 204-237 102-132 (138)
36 COG5349 Uncharacterized protei 36.5 15 0.00033 32.3 0.7 35 203-242 20-54 (126)
37 PRK05978 hypothetical protein; 36.0 14 0.00031 33.3 0.5 34 204-242 33-66 (148)
38 PRK11788 tetratricopeptide rep 34.7 14 0.00031 35.6 0.3 24 204-237 354-377 (389)
39 PRK12336 translation initiatio 33.7 12 0.00027 34.9 -0.3 32 204-238 98-129 (201)
40 TIGR03573 WbuX N-acetyl sugar 32.3 28 0.00061 34.7 1.9 32 205-240 2-33 (343)
41 PF04810 zf-Sec23_Sec24: Sec23 32.1 18 0.0004 25.2 0.4 31 204-236 2-32 (40)
42 PRK05342 clpX ATP-dependent pr 31.8 25 0.00054 36.3 1.5 29 204-234 9-37 (412)
43 smart00834 CxxC_CXXC_SSSS Puta 30.3 17 0.00037 24.5 0.0 29 205-236 6-34 (41)
44 TIGR01031 rpmF_bact ribosomal 29.2 16 0.00034 27.6 -0.3 23 204-237 26-48 (55)
45 PF07282 OrfB_Zn_ribbon: Putat 29.0 17 0.00038 27.5 -0.1 30 204-239 28-57 (69)
46 COG2331 Uncharacterized protei 28.7 17 0.00037 29.7 -0.3 37 204-243 12-48 (82)
47 PRK14892 putative transcriptio 28.7 18 0.00038 30.6 -0.2 35 204-241 21-55 (99)
48 smart00105 ArfGap Putative GTP 28.7 47 0.001 27.9 2.4 37 204-244 3-39 (112)
49 PF01873 eIF-5_eIF-2B: Domain 28.5 20 0.00044 31.3 0.1 29 205-236 94-122 (125)
50 COG2816 NPY1 NTP pyrophosphohy 27.3 22 0.00048 35.3 0.2 31 204-240 111-141 (279)
51 KOG3740 Uncharacterized conser 27.2 28 0.00061 38.1 1.0 35 204-240 462-499 (706)
52 TIGR00244 transcriptional regu 26.0 26 0.00056 31.7 0.4 38 206-243 2-43 (147)
53 PF11228 DUF3027: Protein of u 25.9 20 0.00043 33.8 -0.4 30 217-246 126-163 (193)
54 PF13719 zinc_ribbon_5: zinc-r 25.1 16 0.00035 25.1 -0.9 33 205-238 3-35 (37)
55 PF09723 Zn-ribbon_8: Zinc rib 25.0 24 0.00051 24.9 -0.0 29 205-236 6-34 (42)
56 PRK12496 hypothetical protein; 24.4 35 0.00075 30.9 0.9 32 204-243 127-158 (164)
57 PRK01110 rpmF 50S ribosomal pr 23.7 24 0.00053 27.1 -0.2 23 204-238 27-49 (60)
58 KOG0712 Molecular chaperone (D 23.3 50 0.0011 33.6 1.9 36 204-239 143-181 (337)
59 TIGR02605 CxxC_CxxC_SSSS putat 21.5 32 0.0007 24.7 0.1 29 205-236 6-34 (52)
60 COG1096 Predicted RNA-binding 21.2 33 0.00071 32.3 0.1 29 204-240 149-177 (188)
61 PRK00241 nudC NADH pyrophospha 20.8 27 0.00059 33.6 -0.5 31 204-240 99-129 (256)
62 PF10083 DUF2321: Uncharacteri 20.3 50 0.0011 30.2 1.1 33 204-238 39-78 (158)
63 COG4260 Membrane protease subu 20.2 70 0.0015 32.3 2.1 29 204-237 315-343 (345)
64 COG1066 Sms Predicted ATP-depe 20.2 37 0.0008 35.8 0.2 24 204-237 7-30 (456)
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=1.4e-16 Score=110.17 Aligned_cols=36 Identities=42% Similarity=0.683 Sum_probs=33.2
Q ss_pred CCCCCccceEEEccEEEEeCCCChHHHHHHHHHhcC
Q 018653 70 TSTRTSELTVAYEGEVYVFPAVTPHKVQALLLLLGE 105 (352)
Q Consensus 70 ~~~~taQLTIfY~G~V~VFDdVp~eKaqaImlLa~~ 105 (352)
+.+.++||||||+|+|+|||+||+|||++||+||++
T Consensus 1 ~~~~~~qLTIfY~G~V~Vfd~v~~~Ka~~im~lA~r 36 (36)
T PF06200_consen 1 PSPETAQLTIFYGGQVCVFDDVPPDKAQEIMLLASR 36 (36)
T ss_pred CCCCCCcEEEEECCEEEEeCCCCHHHHHHHHHHhcC
Confidence 356789999999999999999999999999999973
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=99.57 E-value=1.6e-15 Score=113.32 Aligned_cols=44 Identities=52% Similarity=1.129 Sum_probs=40.6
Q ss_pred cccccccccCCCCccccCCCCCchhchHhhhhHHhcCCCCCCCcCc
Q 018653 206 ICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTLRDLTKGA 251 (352)
Q Consensus 206 ~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~~~~~~~r~~~~~~ 251 (352)
.|+||+++ .||+||+||.|..+|||||||||++++..||.....
T Consensus 1 ~C~~C~~~--~Tp~WR~g~~~~~~LCNaCgl~~~k~~~~rp~~~~~ 44 (54)
T cd00202 1 ACSNCGTT--TTPLWRRGPSGGSTLCNACGLYWKKHGVMRPLSKRK 44 (54)
T ss_pred CCCCCCCC--CCcccccCCCCcchHHHHHHHHHHhcCCCCCcccCc
Confidence 59999997 599999999998999999999999999999988755
No 3
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=99.52 E-value=5.6e-15 Score=109.52 Aligned_cols=46 Identities=50% Similarity=1.014 Sum_probs=41.1
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhhHHhcCCC-CCCCcCc
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTL-RDLTKGA 251 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~~~~~~~-r~~~~~~ 251 (352)
...|+||+++ .||+||+||.|..+|||||||||++++.+ ||..+.+
T Consensus 3 ~~~C~~C~~~--~T~~WR~g~~g~~~LCnaCgl~~~k~~~~~rp~~~~~ 49 (52)
T smart00401 3 GRSCSNCGTT--ETPLWRRGPSGNKTLCNACGLYYKKHGGLKRPLSLKK 49 (52)
T ss_pred CCCcCCCCCC--CCCccccCCCCCCcEeecccHHHHHcCCCCCcccccc
Confidence 5799999997 59999999999889999999999999988 8776543
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=99.47 E-value=1.1e-14 Score=100.41 Aligned_cols=36 Identities=58% Similarity=1.258 Sum_probs=28.3
Q ss_pred ccccccccCCCCccccCCCCCchhchHhhhhHHhcCCC
Q 018653 207 CQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTL 244 (352)
Q Consensus 207 C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~~~~~~~ 244 (352)
|+||+++. ||+||+||.|..+||||||++|++++++
T Consensus 1 C~~C~tt~--t~~WR~~~~g~~~LCn~Cg~~~kk~~~~ 36 (36)
T PF00320_consen 1 CSNCGTTE--TPQWRRGPNGNRTLCNACGLYYKKYGKM 36 (36)
T ss_dssp -TTT--ST---SSEEEETTSEE-EEHHHHHHHHHHSS-
T ss_pred CcCCcCCC--CchhhcCCCCCCHHHHHHHHHHHHhCCC
Confidence 89999984 9999999999889999999999999864
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=99.08 E-value=5.6e-11 Score=86.05 Aligned_cols=44 Identities=52% Similarity=0.819 Sum_probs=41.8
Q ss_pred HHHHHHHHHHhhhhccccccccccchhhhHHHHhhhcccccccc
Q 018653 138 RIASLVRFREKRKERSFEKKIRYSCRKEVAQRMQRKNGQFTSSK 181 (352)
Q Consensus 138 R~aSL~Rf~eKRk~R~~~k~i~Y~~RK~~A~rr~R~kGqFa~~k 181 (352)
|.++|+||++||+.|+|.|+|+|.+||.+|+.++|.+|+|++..
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 67899999999999999999999999999999999999998764
No 6
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=98.61 E-value=2.1e-08 Score=90.38 Aligned_cols=47 Identities=47% Similarity=0.971 Sum_probs=39.5
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhhHHhcCCCCCCCcCcc
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTLRDLTKGAR 252 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~~~~~~~r~~~~~~~ 252 (352)
...|.+|+++ .||+||++|.|+..||||||++|++++..|++.....
T Consensus 199 ~~~c~~~~~~--~t~~~r~~~~g~~~~cnacgl~~k~~~~~r~~~~~~~ 245 (340)
T KOG1601|consen 199 LRQCSNCGTT--KTPLWRRGPEGPKSLCNACGLRYKKGGVRRPLPEKRP 245 (340)
T ss_pred CcccCCCCCC--CCcceecCCCCCccccccchhhhhhcCccccccccCc
Confidence 4799999987 5999999999999999999999999985555444333
No 7
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=98.35 E-value=2.3e-07 Score=96.16 Aligned_cols=60 Identities=28% Similarity=0.548 Sum_probs=47.4
Q ss_pred CCCCCCCCCCccccccccccCCCCccccCCCC----CchhchHhhhhHHhcCCCC-CCCcCcccccc
Q 018653 195 NGSAPPESVSRICQHCGISEKLTPAMRRGPAG----PRTLCNACGLMWANKGTLR-DLTKGARNICF 256 (352)
Q Consensus 195 ~~~~~~~~~~~~C~~Cg~t~~~Tp~wR~GP~G----~~~LCNaCGl~~~~~~~~r-~~~~~~~~~~~ 256 (352)
......+.+...|.||.++ .||+|||+..+ .-.|||||||+|+.||++| |+..+...+..
T Consensus 149 ~n~~~~s~~~~vc~Nc~t~--stPlwrR~~~~~s~~~n~lcnaCgl~~klhg~~r~P~t~ks~~~ks 213 (498)
T COG5641 149 NNQSDNSNQPHVCSNCKTT--STPLWRRASSESSLPGNNLCNACGLYLKLHGSPRAPISLKSDSIKS 213 (498)
T ss_pred CCccccccccchhcccccc--CCccccccccccccCCccccccccccccccCCcCCCcccccccccc
Confidence 3344455556699999997 69999999993 3899999999999999999 87765544433
No 8
>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=98.17 E-value=8.3e-07 Score=57.93 Aligned_cols=25 Identities=52% Similarity=0.579 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHHhhhhcccccccccc
Q 018653 136 SQRIASLVRFREKRKERSFEKKIRYS 161 (352)
Q Consensus 136 ~~R~aSL~Rf~eKRk~R~~~k~i~Y~ 161 (352)
.+|++||+||+||||+|..+ +.+|.
T Consensus 2 ~aRK~SLqRFLeKRK~R~~~-~~PY~ 26 (27)
T PF09425_consen 2 IARKASLQRFLEKRKDRLAA-KSPYQ 26 (27)
T ss_dssp ----HHHHHHHHHH------------
T ss_pred chHHHHHHHHHHHHHHhhcc-CCCCC
Confidence 47999999999999999998 48886
No 9
>COG5641 GAT1 GATA Zn-finger-containing transcription factor [Transcription]
Probab=91.94 E-value=0.093 Score=55.24 Aligned_cols=52 Identities=23% Similarity=0.200 Sum_probs=43.2
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhhHHhcCCCCCCCcCcccccc
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTLRDLTKGARNICF 256 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~~~~~~~r~~~~~~~~~~~ 256 (352)
...|.+|++. +.||.||+...-.-.+|||||++-+..+..+++.++..-..+
T Consensus 297 ~~~~s~~~~~-~~tp~~~r~~~~~s~~~n~~~~~~~~~~~~~p~~pk~d~n~~ 348 (498)
T COG5641 297 DKKRSTLTTS-TATPLWRRTSDKSSFSCNASGSALKPPGSKRPLLPKPDPNSK 348 (498)
T ss_pred hcCccccccc-ccCcccccccccccccccccccccCCcccccccCCCCChhhh
Confidence 5689999975 469999999887799999999999999999998875543333
No 10
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=75.88 E-value=3.3 Score=43.72 Aligned_cols=45 Identities=22% Similarity=0.462 Sum_probs=34.0
Q ss_pred CCCCCCCccccccccccCCCCcc--ccCCCCCchhchHhhhhHHhcCCC
Q 018653 198 APPESVSRICQHCGISEKLTPAM--RRGPAGPRTLCNACGLMWANKGTL 244 (352)
Q Consensus 198 ~~~~~~~~~C~~Cg~t~~~Tp~w--R~GP~G~~~LCNaCGl~~~~~~~~ 244 (352)
......++.|-+|+++ ..-+| .-+|.-...||-.|=+||++.|-+
T Consensus 380 t~~~~~g~~CEsC~tt--qs~qWYsWGppnmqcrLCasCWiyWKKygGL 426 (693)
T KOG3554|consen 380 TFQNQDGRACESCYTT--QSLQWYSWGPPNMQCRLCASCWIYWKKYGGL 426 (693)
T ss_pred cccCCCCCcccccccc--cccceeccCCCCccchhhHHHHHHHHHhcCc
Confidence 3344447899999997 46666 446666779999999999998753
No 11
>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=65.90 E-value=3.1 Score=32.07 Aligned_cols=29 Identities=21% Similarity=0.657 Sum_probs=23.4
Q ss_pred CccccccccccCCCCccccCCCCCchhc-hHhhhhHHhcC
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLC-NACGLMWANKG 242 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LC-NaCGl~~~~~~ 242 (352)
-++|.+||.+. |.. +..| ..|+.-|.++.
T Consensus 3 HkHC~~CG~~I---------p~~-~~fCS~~C~~~~~k~q 32 (59)
T PF09889_consen 3 HKHCPVCGKPI---------PPD-ESFCSPKCREEYRKRQ 32 (59)
T ss_pred CCcCCcCCCcC---------Ccc-hhhhCHHHHHHHHHHH
Confidence 36899999885 444 7899 59999999865
No 12
>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=65.30 E-value=1.6 Score=32.88 Aligned_cols=25 Identities=28% Similarity=0.810 Sum_probs=18.7
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhhHHh
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~~~ 240 (352)
...|.+||.. --++.+|..|| ||+-
T Consensus 26 l~~c~~cg~~-----------~~~H~vc~~cG-~y~~ 50 (56)
T PF01783_consen 26 LVKCPNCGEP-----------KLPHRVCPSCG-YYKG 50 (56)
T ss_dssp EEESSSSSSE-----------ESTTSBCTTTB-BSSS
T ss_pred eeeeccCCCE-----------ecccEeeCCCC-eECC
Confidence 5799999974 23478999999 5543
No 13
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=64.93 E-value=1.5 Score=30.22 Aligned_cols=33 Identities=21% Similarity=0.569 Sum_probs=29.0
Q ss_pred ccccccccccCCCCccccCCCCCchhchHhhhhH
Q 018653 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (352)
Q Consensus 205 ~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~ 238 (352)
..|-+|++. ...+-.+-.+.|....|-.||-.|
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 579999987 588999999999999999999766
No 14
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=64.69 E-value=2.1 Score=29.43 Aligned_cols=30 Identities=30% Similarity=0.780 Sum_probs=14.5
Q ss_pred ccccccccccCCCCccccCCCCCchhchHhhh
Q 018653 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (352)
Q Consensus 205 ~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl 236 (352)
+.|.+||..- +..-=.|.+-.+..|.+||.
T Consensus 1 kfC~~CG~~l--~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPL--ERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B---EEE--TT-SS-EEEETTTTE
T ss_pred CccccccChh--hhhcCCCCCccceECCCCCC
Confidence 3699999641 22222445556789999995
No 15
>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=52.99 E-value=4.7 Score=28.86 Aligned_cols=25 Identities=44% Similarity=1.103 Sum_probs=19.8
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhh
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACG 235 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCG 235 (352)
...|..|+ +|++| .-+| +.+|-+|+
T Consensus 17 ~~~Cp~C~-----~PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCG-----TPLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred cCccCCCC-----CeeEE-ecCC-CEECCCCC
Confidence 45899995 89999 3466 78999986
No 16
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=52.22 E-value=4.9 Score=34.34 Aligned_cols=28 Identities=29% Similarity=0.712 Sum_probs=21.0
Q ss_pred ccccccccccCCCCccccCCCCC-chhchHhhh
Q 018653 205 RICQHCGISEKLTPAMRRGPAGP-RTLCNACGL 236 (352)
Q Consensus 205 ~~C~~Cg~t~~~Tp~wR~GP~G~-~~LCNaCGl 236 (352)
-.|..|+.+. |-+-+. .+. -.-|+|||-
T Consensus 81 VlC~~C~spd--T~l~k~--~r~~~l~C~aCGa 109 (110)
T smart00653 81 VLCPECGSPD--TELIKE--NRLFFLKCEACGA 109 (110)
T ss_pred EECCCCCCCC--cEEEEe--CCeEEEEccccCC
Confidence 5899999984 888887 232 244999995
No 17
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=52.15 E-value=5.4 Score=35.91 Aligned_cols=41 Identities=44% Similarity=0.678 Sum_probs=37.7
Q ss_pred hHHHHHHHHHHHHhhhhccccccccccchhhhHHHHhhhcc
Q 018653 135 LSQRIASLVRFREKRKERSFEKKIRYSCRKEVAQRMQRKNG 175 (352)
Q Consensus 135 l~~R~aSL~Rf~eKRk~R~~~k~i~Y~~RK~~A~rr~R~kG 175 (352)
...|.+.+.|++++++.+.|.+.++|..++..+..+++.++
T Consensus 290 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (340)
T KOG1601|consen 290 SHQRVAEVRRYRESRDGRYFDKGIRYASRKSNAESRPRLKG 330 (340)
T ss_pred cchHHHHHhhccCccCCcccccccccccccccchhcccccc
Confidence 45788999999999999999999999999999999999887
No 18
>PRK11823 DNA repair protein RadA; Provisional
Probab=49.18 E-value=6.1 Score=40.93 Aligned_cols=25 Identities=36% Similarity=0.897 Sum_probs=18.2
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhhH
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~ 238 (352)
..+|.+||-+ ++.|- | .|.+||-+=
T Consensus 7 ~y~C~~Cg~~---~~~~~----g---~Cp~C~~w~ 31 (446)
T PRK11823 7 AYVCQECGAE---SPKWL----G---RCPECGAWN 31 (446)
T ss_pred eEECCcCCCC---CcccC----e---eCcCCCCcc
Confidence 6899999986 55552 2 599997653
No 19
>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=46.93 E-value=7 Score=40.66 Aligned_cols=24 Identities=33% Similarity=0.641 Sum_probs=17.3
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhh
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~ 237 (352)
..+|.+||-+. ..|+| .|.+||-+
T Consensus 7 ~y~C~~Cg~~~-~~~~g---------~Cp~C~~w 30 (454)
T TIGR00416 7 KFVCQHCGADS-PKWQG---------KCPACHAW 30 (454)
T ss_pred eEECCcCCCCC-ccccE---------ECcCCCCc
Confidence 68999999862 44444 48888765
No 20
>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=45.72 E-value=16 Score=30.95 Aligned_cols=36 Identities=25% Similarity=0.594 Sum_probs=27.1
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhhHHhcCC
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGT 243 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~~~~~~ 243 (352)
...|..||.. -|.|-.=..| -.||-.|.-.++.-|+
T Consensus 13 N~~CaDCg~~---~p~w~s~~~G-iflC~~Cag~HR~lg~ 48 (116)
T PF01412_consen 13 NKVCADCGAP---NPTWASLNYG-IFLCLECAGIHRSLGV 48 (116)
T ss_dssp CTB-TTT-SB---S--EEETTTT-EEE-HHHHHHHHHHTT
T ss_pred cCcCCCCCCC---CCCEEEeecC-hhhhHHHHHHHHHhcc
Confidence 5899999975 7899999999 9999999988887765
No 21
>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=45.10 E-value=18 Score=28.34 Aligned_cols=47 Identities=28% Similarity=0.640 Sum_probs=32.6
Q ss_pred CccccccccccCCCCcc--c-cCCCCCchhchHhhhhHHhcCCCCCCCcCcc
Q 018653 204 SRICQHCGISEKLTPAM--R-RGPAGPRTLCNACGLMWANKGTLRDLTKGAR 252 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~w--R-~GP~G~~~LCNaCGl~~~~~~~~r~~~~~~~ 252 (352)
...|..|..+. |--- = -...-|+..|-+|..+|-..|++|.+--++.
T Consensus 5 ~~~CPRC~S~n--TKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvggg 54 (63)
T PF02701_consen 5 PLPCPRCDSTN--TKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVGGG 54 (63)
T ss_pred CCCCCCcCCCC--CEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccCCC
Confidence 57888888753 2110 0 0123457899999999999999999866554
No 22
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=44.50 E-value=9.9 Score=40.56 Aligned_cols=31 Identities=29% Similarity=0.712 Sum_probs=23.2
Q ss_pred cccccccccCCCCccccCCCCCchhchHhhhhHHhc
Q 018653 206 ICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANK 241 (352)
Q Consensus 206 ~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~~~~ 241 (352)
.|.|||.+ ++.-+- -.| ...|++||......
T Consensus 2 ~C~~C~~s---~fe~d~-a~g-~~~C~~CG~v~E~~ 32 (521)
T KOG1598|consen 2 VCKNCGGS---NFERDE-ATG-NLYCTACGTVLEYN 32 (521)
T ss_pred cCCCCCCC---Cccccc-ccC-Cceeccccceeecc
Confidence 79999985 555443 566 89999999876653
No 23
>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=44.15 E-value=11 Score=26.53 Aligned_cols=32 Identities=28% Similarity=0.686 Sum_probs=21.5
Q ss_pred ccccccccccCCCCccccCCCCCchhchHhhhh
Q 018653 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (352)
Q Consensus 205 ~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~ 237 (352)
.+|+-||.++...-..=.||.| ...|+.|=..
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 5899999987666666689988 8999999544
No 24
>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=43.39 E-value=5.1 Score=26.57 Aligned_cols=29 Identities=31% Similarity=0.785 Sum_probs=16.4
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhhH
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~ 238 (352)
.+.|..||... ...+.|....|.+||..+
T Consensus 3 ~rfC~~CG~~t------~~~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 3 HRFCGRCGAPT------KPAPGGWARRCPSCGHEH 31 (32)
T ss_dssp TSB-TTT--BE------EE-SSSS-EEESSSS-EE
T ss_pred CcccCcCCccc------cCCCCcCEeECCCCcCEe
Confidence 46899999763 233557778999999753
No 25
>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=43.10 E-value=4.5 Score=27.43 Aligned_cols=34 Identities=26% Similarity=0.627 Sum_probs=24.5
Q ss_pred ccccccccccCCCCccccCCCCCchhchHhhhhHH
Q 018653 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWA 239 (352)
Q Consensus 205 ~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~~ 239 (352)
..|.+|++. ..-+..+.+..|....|-.||..|.
T Consensus 3 ~~CP~C~~~-~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTS-FRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCE-EEeCHHHcCCCCCEEECCCCCCEEE
Confidence 578999986 2556666666777788999987654
No 26
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=43.02 E-value=7.6 Score=29.57 Aligned_cols=23 Identities=30% Similarity=0.836 Sum_probs=17.6
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhh
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~ 237 (352)
.-.|.+||... =+..+|..||.|
T Consensus 27 l~~C~~CG~~~-----------~~H~vC~~CG~Y 49 (57)
T PRK12286 27 LVECPNCGEPK-----------LPHRVCPSCGYY 49 (57)
T ss_pred ceECCCCCCcc-----------CCeEECCCCCcC
Confidence 46899999852 237899999954
No 27
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=43.00 E-value=13 Score=23.29 Aligned_cols=21 Identities=29% Similarity=0.865 Sum_probs=12.4
Q ss_pred cccccccccCCCCccccCCCCCchhchHhhh
Q 018653 206 ICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (352)
Q Consensus 206 ~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl 236 (352)
.|.+||... +++ ...|.-||.
T Consensus 1 ~Cp~CG~~~---------~~~-~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEI---------EDD-AKFCPNCGT 21 (23)
T ss_pred CCcccCCCC---------CCc-CcchhhhCC
Confidence 367777653 334 456777764
No 28
>PRK00420 hypothetical protein; Validated
Probab=42.68 E-value=9.8 Score=32.84 Aligned_cols=31 Identities=29% Similarity=0.674 Sum_probs=24.8
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhhHHhc
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANK 241 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~~~~ 241 (352)
...|..|| +|+.|. .+| ...|-.||..+...
T Consensus 23 ~~~CP~Cg-----~pLf~l-k~g-~~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 23 SKHCPVCG-----LPLFEL-KDG-EVVCPVHGKVYIVK 53 (112)
T ss_pred cCCCCCCC-----Ccceec-CCC-ceECCCCCCeeeec
Confidence 46899998 788885 566 89999999977653
No 29
>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=41.58 E-value=9.7 Score=26.77 Aligned_cols=30 Identities=27% Similarity=0.700 Sum_probs=17.8
Q ss_pred cccccccccCCCCccccCCCCCchhchHhhhhHHh
Q 018653 206 ICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (352)
Q Consensus 206 ~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~~~ 240 (352)
+|.+||.+ . .--.--.| ..+|..||+-+.-
T Consensus 2 ~Cp~Cg~~---~-~~~D~~~g-~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 2 KCPNCGSK---E-IVFDPERG-ELVCPNCGLVLEE 31 (43)
T ss_dssp SBTTTSSS---E-EEEETTTT-EEEETTT-BBEE-
T ss_pred CCcCCcCC---c-eEEcCCCC-eEECCCCCCEeec
Confidence 58888874 2 22333345 7789999876654
No 30
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=41.20 E-value=9.3 Score=33.89 Aligned_cols=28 Identities=36% Similarity=0.926 Sum_probs=23.5
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhhHH
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWA 239 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~~ 239 (352)
..+|.-|| ||++| -+| ...|-.||....
T Consensus 28 ~~hCp~Cg-----~PLF~--KdG-~v~CPvC~~~~~ 55 (131)
T COG1645 28 AKHCPKCG-----TPLFR--KDG-EVFCPVCGYREV 55 (131)
T ss_pred HhhCcccC-----Cccee--eCC-eEECCCCCceEE
Confidence 56899998 89999 688 899999996433
No 31
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=41.12 E-value=15 Score=23.35 Aligned_cols=24 Identities=25% Similarity=0.747 Sum_probs=15.8
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhh
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~ 237 (352)
.+.|.+||... +.+ ...|..||..
T Consensus 2 ~~~Cp~Cg~~~---------~~~-~~fC~~CG~~ 25 (26)
T PF13248_consen 2 EMFCPNCGAEI---------DPD-AKFCPNCGAK 25 (26)
T ss_pred cCCCcccCCcC---------Ccc-cccChhhCCC
Confidence 35788888753 333 5688888853
No 32
>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=40.83 E-value=10 Score=38.48 Aligned_cols=23 Identities=35% Similarity=0.911 Sum_probs=16.5
Q ss_pred cccccccccCCCCccccCCCCCchhchHhhhhH
Q 018653 206 ICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (352)
Q Consensus 206 ~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~ 238 (352)
+|.+||-. ++.|- | -|.+||-+=
T Consensus 2 ~c~~cg~~---~~~~~----g---~cp~c~~w~ 24 (372)
T cd01121 2 VCSECGYV---SPKWL----G---KCPECGEWN 24 (372)
T ss_pred CCCCCCCC---CCCcc----E---ECcCCCCce
Confidence 69999985 66663 3 588887653
No 33
>COG3952 Predicted membrane protein [Function unknown]
Probab=39.81 E-value=9 Score=33.01 Aligned_cols=21 Identities=33% Similarity=0.387 Sum_probs=16.1
Q ss_pred CccccCCCCCchhchHhhhhHHh
Q 018653 218 PAMRRGPAGPRTLCNACGLMWAN 240 (352)
Q Consensus 218 p~wR~GP~G~~~LCNaCGl~~~~ 240 (352)
-.||.+|-+ .||++||++-..
T Consensus 75 fi~~~DpV~--Vl~~~~glF~~l 95 (113)
T COG3952 75 FIRRQDPVF--VLGQACGLFIYL 95 (113)
T ss_pred HHHhcchHH--HHHHhhhHHHHH
Confidence 356777776 799999998654
No 34
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=39.60 E-value=9.1 Score=33.82 Aligned_cols=30 Identities=30% Similarity=0.691 Sum_probs=21.5
Q ss_pred ccccccccccCCCCccccCCCCCchhchHhhhh
Q 018653 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (352)
Q Consensus 205 ~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~ 237 (352)
-.|..|+-+. |-+-+.+ .---.-|+|||-.
T Consensus 98 VlC~~C~sPd--T~l~k~~-r~~~l~C~ACGa~ 127 (133)
T TIGR00311 98 VICRECNRPD--TRIIKEG-RVSLLKCEACGAK 127 (133)
T ss_pred EECCCCCCCC--cEEEEeC-CeEEEecccCCCC
Confidence 5899999985 8888753 1112579999954
No 35
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=38.70 E-value=9.3 Score=33.95 Aligned_cols=31 Identities=32% Similarity=0.624 Sum_probs=21.9
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhh
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~ 237 (352)
--.|..|+.+. |-+-+.+= ---.-|+|||-.
T Consensus 102 yVlC~~C~spd--T~l~k~~r-~~~l~C~ACGa~ 132 (138)
T PRK03988 102 YVICPECGSPD--TKLIKEGR-IWVLKCEACGAE 132 (138)
T ss_pred cEECCCCCCCC--cEEEEcCC-eEEEEcccCCCC
Confidence 35899999984 88877521 113679999954
No 36
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.49 E-value=15 Score=32.35 Aligned_cols=35 Identities=29% Similarity=0.580 Sum_probs=23.3
Q ss_pred CCccccccccccCCCCccccCCCCCchhchHhhhhHHhcC
Q 018653 203 VSRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKG 242 (352)
Q Consensus 203 ~~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~~~~~ 242 (352)
.-.+|-+||-- -+.| |=--...-|.|||+-|..+.
T Consensus 20 l~grCP~CGeG----rLF~-gFLK~~p~C~aCG~dyg~~~ 54 (126)
T COG5349 20 LRGRCPRCGEG----RLFR-GFLKVVPACEACGLDYGFAD 54 (126)
T ss_pred hcCCCCCCCCc----hhhh-hhcccCchhhhccccccCCc
Confidence 35789999952 2232 22233578999999998764
No 37
>PRK05978 hypothetical protein; Provisional
Probab=35.99 E-value=14 Score=33.27 Aligned_cols=34 Identities=26% Similarity=0.537 Sum_probs=26.2
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhhHHhcC
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKG 242 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~~~~~ 242 (352)
..+|-+||. -.++| |-..-..-|.+||+.|..+.
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 578999996 45555 55666788999999998764
No 38
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=34.65 E-value=14 Score=35.58 Aligned_cols=24 Identities=21% Similarity=0.642 Sum_probs=14.8
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhh
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~ 237 (352)
.+.|.|||.+ +..| ..+|-.||-+
T Consensus 354 ~~~c~~cg~~---~~~~-------~~~c~~c~~~ 377 (389)
T PRK11788 354 RYRCRNCGFT---ARTL-------YWHCPSCKAW 377 (389)
T ss_pred CEECCCCCCC---Cccc-------eeECcCCCCc
Confidence 4778888876 3333 2357777644
No 39
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=33.71 E-value=12 Score=34.88 Aligned_cols=32 Identities=28% Similarity=0.626 Sum_probs=22.6
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhhH
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~ 238 (352)
--.|..|+-.. |-+-+.+ .---.-|+|||-..
T Consensus 98 yV~C~~C~~pd--T~l~k~~-~~~~l~C~aCGa~~ 129 (201)
T PRK12336 98 YVICSECGLPD--TRLVKED-RVLMLRCDACGAHR 129 (201)
T ss_pred eEECCCCCCCC--cEEEEcC-CeEEEEcccCCCCc
Confidence 35899999985 8887763 11135799999643
No 40
>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=32.30 E-value=28 Score=34.72 Aligned_cols=32 Identities=22% Similarity=0.647 Sum_probs=26.1
Q ss_pred ccccccccccCCCCccccCCCCCchhchHhhhhHHh
Q 018653 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (352)
Q Consensus 205 ~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~~~ 240 (352)
..|..|..++ ..|--.-..+| +||+|--+-.+
T Consensus 2 ~~C~~C~~~~-t~p~i~fd~~G---vC~~C~~~~~~ 33 (343)
T TIGR03573 2 KFCKRCVMPT-TRPGITFDEDG---VCSACRNFEEK 33 (343)
T ss_pred CcCCCCCCCC-CCCCeeECCCC---CchhhhhHHhh
Confidence 5899999985 67777777888 99999987643
No 41
>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=32.09 E-value=18 Score=25.21 Aligned_cols=31 Identities=29% Similarity=0.639 Sum_probs=20.4
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhh
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl 236 (352)
..+|.+|++- --|..+-...|..-.||-|+.
T Consensus 2 p~rC~~C~ay--lNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCRRCRAY--LNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp S-B-TTT--B--S-TTSEEETTTTEEEETTT--
T ss_pred ccccCCCCCE--ECCcceEcCCCCEEECcCCCC
Confidence 3689999986 488888888888889999986
No 42
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=31.79 E-value=25 Score=36.29 Aligned_cols=29 Identities=28% Similarity=0.693 Sum_probs=25.0
Q ss_pred CccccccccccCCCCccccCCCCCchhchHh
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNAC 234 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaC 234 (352)
..+|+.||.+...+...-.||.. ..|+.|
T Consensus 9 ~~~CSFCGr~~~ev~~li~g~~~--~IC~~C 37 (412)
T PRK05342 9 LLYCSFCGKSQHEVRKLIAGPGV--YICDEC 37 (412)
T ss_pred ccccCCCCCChhhccccccCCCC--cccchH
Confidence 56999999998888888889844 699999
No 43
>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=30.29 E-value=17 Score=24.54 Aligned_cols=29 Identities=24% Similarity=0.643 Sum_probs=20.6
Q ss_pred ccccccccccCCCCccccCCCCCchhchHhhh
Q 018653 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (352)
Q Consensus 205 ~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl 236 (352)
-+|..||.. -..|..--++....|-.||.
T Consensus 6 y~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHT---FEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEcCCCCCE---EEEEEecCCCCCCCCCCCCC
Confidence 479999974 44555444466778999997
No 44
>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=29.17 E-value=16 Score=27.58 Aligned_cols=23 Identities=30% Similarity=0.850 Sum_probs=17.0
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhh
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~ 237 (352)
...|.+||.. -=+..+|-.||.|
T Consensus 26 l~~C~~cG~~-----------~~~H~vc~~cG~Y 48 (55)
T TIGR01031 26 LVVCPNCGEF-----------KLPHRVCPSCGYY 48 (55)
T ss_pred ceECCCCCCc-----------ccCeeECCccCeE
Confidence 4679999974 2237899999943
No 45
>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=29.03 E-value=17 Score=27.46 Aligned_cols=30 Identities=30% Similarity=0.658 Sum_probs=21.6
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhhHH
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWA 239 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~~ 239 (352)
...|..||..... ...+....|..||..+.
T Consensus 28 Sq~C~~CG~~~~~------~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 28 SQTCPRCGHRNKK------RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred ccCccCccccccc------ccccceEEcCCCCCEEC
Confidence 4689999987422 44555789999998654
No 46
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.74 E-value=17 Score=29.72 Aligned_cols=37 Identities=30% Similarity=0.515 Sum_probs=26.1
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhhHHhcCC
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGT 243 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~~~~~~ 243 (352)
.-.|.+||-...-...++..| -+.|.+||-++++--.
T Consensus 12 ~Y~c~~cg~~~dvvq~~~ddp---lt~ce~c~a~~kk~l~ 48 (82)
T COG2331 12 SYECTECGNRFDVVQAMTDDP---LTTCEECGARLKKLLN 48 (82)
T ss_pred EEeecccchHHHHHHhcccCc---cccChhhChHHHHhhc
Confidence 468999997533345566555 5699999998887543
No 47
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=28.74 E-value=18 Score=30.59 Aligned_cols=35 Identities=20% Similarity=0.329 Sum_probs=22.9
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhhHHhc
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANK 241 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~~~~ 241 (352)
.-.|.+|+.....-+.=| .-....|..||.|+.+.
T Consensus 21 ~f~CP~Cge~~v~v~~~k---~~~h~~C~~CG~y~~~~ 55 (99)
T PRK14892 21 IFECPRCGKVSISVKIKK---NIAIITCGNCGLYTEFE 55 (99)
T ss_pred EeECCCCCCeEeeeecCC---CcceEECCCCCCccCEE
Confidence 568999994321112222 34489999999998763
No 48
>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=28.69 E-value=47 Score=27.91 Aligned_cols=37 Identities=24% Similarity=0.516 Sum_probs=31.6
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhhHHhcCCC
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGTL 244 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~~~~~~~ 244 (352)
...|..|+.. -|.|=.=..| -.||-.|.-..+.-|+.
T Consensus 3 N~~CaDC~~~---~p~w~s~~~G-ifvC~~CsgiHR~lg~h 39 (112)
T smart00105 3 NKKCFDCGAP---NPTWASVNLG-VFLCIECSGIHRSLGVH 39 (112)
T ss_pred CCcccCCCCC---CCCcEEeccc-eeEhHHhHHHHHhcCCC
Confidence 5799999985 7999988889 89999999888877653
No 49
>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=28.45 E-value=20 Score=31.27 Aligned_cols=29 Identities=31% Similarity=0.749 Sum_probs=21.7
Q ss_pred ccccccccccCCCCccccCCCCCchhchHhhh
Q 018653 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (352)
Q Consensus 205 ~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl 236 (352)
-.|..|+.+. |-+-+.+-. --.-|+|||-
T Consensus 94 VlC~~C~spd--T~l~k~~r~-~~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSPD--TELIKEGRL-IFLKCKACGA 122 (125)
T ss_dssp SSCTSTSSSS--EEEEEETTC-CEEEETTTSC
T ss_pred EEcCCCCCCc--cEEEEcCCE-EEEEecccCC
Confidence 5799999884 888877332 2577999994
No 50
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=27.27 E-value=22 Score=35.25 Aligned_cols=31 Identities=29% Similarity=0.665 Sum_probs=22.4
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhhHHh
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~~~ 240 (352)
.+.|..||+.. .+ ...|-+.+|+.||..+--
T Consensus 111 ~RFCg~CG~~~--~~----~~~g~~~~C~~cg~~~fP 141 (279)
T COG2816 111 HRFCGRCGTKT--YP----REGGWARVCPKCGHEHFP 141 (279)
T ss_pred CcCCCCCCCcC--cc----ccCceeeeCCCCCCccCC
Confidence 57999999852 22 235667899999987764
No 51
>KOG3740 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.20 E-value=28 Score=38.12 Aligned_cols=35 Identities=20% Similarity=0.511 Sum_probs=28.1
Q ss_pred CccccccccccCCCCccccCCCC---CchhchHhhhhHHh
Q 018653 204 SRICQHCGISEKLTPAMRRGPAG---PRTLCNACGLMWAN 240 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G---~~~LCNaCGl~~~~ 240 (352)
.-.|..|.+- -||.|+.-+.| ...+|.+|----.+
T Consensus 462 P~~caqcktd--ftp~wk~ekstq~d~~i~cE~cvtSnqk 499 (706)
T KOG3740|consen 462 PYACAQCKTD--FTPAWKKEKSTQADAAIVCENCVTSNQK 499 (706)
T ss_pred chhhhhcccc--cccccccccccCcchHHHHHhhhhhccc
Confidence 5789999996 49999998888 46899999654443
No 52
>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=25.98 E-value=26 Score=31.74 Aligned_cols=38 Identities=18% Similarity=0.284 Sum_probs=26.6
Q ss_pred cccccccccCCCCccccCCCC----CchhchHhhhhHHhcCC
Q 018653 206 ICQHCGISEKLTPAMRRGPAG----PRTLCNACGLMWANKGT 243 (352)
Q Consensus 206 ~C~~Cg~t~~~Tp~wR~GP~G----~~~LCNaCGl~~~~~~~ 243 (352)
+|..|+...+..--=|...+| .+--|.+||.+|-..-+
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyEr 43 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFER 43 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeee
Confidence 688998865454445555666 34789999999876543
No 53
>PF11228 DUF3027: Protein of unknown function (DUF3027); InterPro: IPR021391 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=25.92 E-value=20 Score=33.79 Aligned_cols=30 Identities=27% Similarity=0.593 Sum_probs=24.9
Q ss_pred CCccccCCCCCc--------hhchHhhhhHHhcCCCCC
Q 018653 217 TPAMRRGPAGPR--------TLCNACGLMWANKGTLRD 246 (352)
Q Consensus 217 Tp~wR~GP~G~~--------~LCNaCGl~~~~~~~~r~ 246 (352)
-..|++|+.||+ ..|.-||.|+...|.++.
T Consensus 126 a~RW~~g~~GP~s~~a~~a~~~C~tCgF~~plaG~L~~ 163 (193)
T PF11228_consen 126 AQRWYEGEFGPDSEMARAAPAQCSTCGFYVPLAGSLGQ 163 (193)
T ss_pred HHHHHcCCCCCCCHHHHhcccCCCcCccceEcCCchhc
Confidence 457888888877 479999999999888775
No 54
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=25.14 E-value=16 Score=25.13 Aligned_cols=33 Identities=21% Similarity=0.561 Sum_probs=24.4
Q ss_pred ccccccccccCCCCccccCCCCCchhchHhhhhH
Q 018653 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (352)
Q Consensus 205 ~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~ 238 (352)
..|.+|++. ..-|.=+-+..|.+.-|-.||-.|
T Consensus 3 i~CP~C~~~-f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTR-FRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCce-EEcCHHHcccCCcEEECCCCCcEe
Confidence 578888886 366666666777788888888665
No 55
>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=25.01 E-value=24 Score=24.88 Aligned_cols=29 Identities=21% Similarity=0.526 Sum_probs=18.8
Q ss_pred ccccccccccCCCCccccCCCCCchhchHhhh
Q 018653 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (352)
Q Consensus 205 ~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl 236 (352)
-+|..||.. --.|+..-+.....|-+||-
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 478888854 33444444455778888886
No 56
>PRK12496 hypothetical protein; Provisional
Probab=24.43 E-value=35 Score=30.92 Aligned_cols=32 Identities=25% Similarity=0.621 Sum_probs=22.0
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhhHHhcCC
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWANKGT 243 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~~~~~~ 243 (352)
..+|..|+.. .+. ++ ....|--||...+++..
T Consensus 127 ~~~C~gC~~~---~~~---~~--~~~~C~~CG~~~~r~~~ 158 (164)
T PRK12496 127 RKVCKGCKKK---YPE---DY--PDDVCEICGSPVKRKMV 158 (164)
T ss_pred eEECCCCCcc---ccC---CC--CCCcCCCCCChhhhcch
Confidence 3679999965 221 11 13589999999887665
No 57
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=23.73 E-value=24 Score=27.05 Aligned_cols=23 Identities=13% Similarity=0.079 Sum_probs=16.6
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhhH
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMW 238 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~ 238 (352)
...|.+||... =++.+|- ||.|-
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 46899999852 2367899 99553
No 58
>KOG0712 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=23.30 E-value=50 Score=33.61 Aligned_cols=36 Identities=25% Similarity=0.506 Sum_probs=29.9
Q ss_pred CccccccccccCCCCccccCC---CCCchhchHhhhhHH
Q 018653 204 SRICQHCGISEKLTPAMRRGP---AGPRTLCNACGLMWA 239 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP---~G~~~LCNaCGl~~~ 239 (352)
...|..|..++-.+..||-|| .-.++.|..|+..-.
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 458999999988999999999 556789999976544
No 59
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=21.46 E-value=32 Score=24.65 Aligned_cols=29 Identities=24% Similarity=0.602 Sum_probs=20.2
Q ss_pred ccccccccccCCCCccccCCCCCchhchHhhh
Q 018653 205 RICQHCGISEKLTPAMRRGPAGPRTLCNACGL 236 (352)
Q Consensus 205 ~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl 236 (352)
-+|..||.. --.|+.--+.....|-.||-
T Consensus 6 y~C~~Cg~~---fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHR---FEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCE---eEEEEecCCCCCCCCCCCCC
Confidence 579999974 45676533344677999997
No 60
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=21.22 E-value=33 Score=32.26 Aligned_cols=29 Identities=24% Similarity=0.573 Sum_probs=22.3
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhhHHh
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~~~ 240 (352)
--+|++|+ +++.+ .|...-|-.||.-=++
T Consensus 149 ~A~CsrC~-----~~L~~---~~~~l~Cp~Cg~tEkR 177 (188)
T COG1096 149 YARCSRCR-----APLVK---KGNMLKCPNCGNTEKR 177 (188)
T ss_pred EEEccCCC-----cceEE---cCcEEECCCCCCEEee
Confidence 45899998 67888 6778889999965443
No 61
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=20.79 E-value=27 Score=33.63 Aligned_cols=31 Identities=23% Similarity=0.462 Sum_probs=22.4
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhhHHh
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLMWAN 240 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~~~~ 240 (352)
.+.|.+||.. |-. ...|....|.+||..+..
T Consensus 99 ~~fC~~CG~~---~~~---~~~~~~~~C~~c~~~~yp 129 (256)
T PRK00241 99 HRFCGYCGHP---MHP---SKTEWAMLCPHCRERYYP 129 (256)
T ss_pred CccccccCCC---Cee---cCCceeEECCCCCCEECC
Confidence 5799999985 222 246777889999976654
No 62
>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=20.30 E-value=50 Score=30.23 Aligned_cols=33 Identities=18% Similarity=0.492 Sum_probs=20.0
Q ss_pred CccccccccccCCCCccc-------cCCCCCchhchHhhhhH
Q 018653 204 SRICQHCGISEKLTPAMR-------RGPAGPRTLCNACGLMW 238 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR-------~GP~G~~~LCNaCGl~~ 238 (352)
...|.+|++.+.. .|- .++.-...-|+.||..|
T Consensus 39 I~~Cp~C~~~IrG--~y~v~gv~~~g~~~~~PsYC~~CGkpy 78 (158)
T PF10083_consen 39 ITSCPNCSTPIRG--DYHVEGVFGLGGHYEAPSYCHNCGKPY 78 (158)
T ss_pred HHHCcCCCCCCCC--ceecCCeeeeCCCCCCChhHHhCCCCC
Confidence 5677777776411 121 13444567899999876
No 63
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=20.22 E-value=70 Score=32.29 Aligned_cols=29 Identities=28% Similarity=0.710 Sum_probs=21.3
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhh
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~ 237 (352)
...|.+||+.. |+-. |+|.--.|-+||.-
T Consensus 315 ~nfc~ncG~~~--t~~~---~ng~a~fcp~cgq~ 343 (345)
T COG4260 315 LNFCLNCGCGT--TADF---DNGKAKFCPECGQG 343 (345)
T ss_pred cccccccCccc--ccCC---ccchhhhChhhcCC
Confidence 45889999753 5533 67777899999964
No 64
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=20.21 E-value=37 Score=35.78 Aligned_cols=24 Identities=42% Similarity=0.984 Sum_probs=19.8
Q ss_pred CccccccccccCCCCccccCCCCCchhchHhhhh
Q 018653 204 SRICQHCGISEKLTPAMRRGPAGPRTLCNACGLM 237 (352)
Q Consensus 204 ~~~C~~Cg~t~~~Tp~wR~GP~G~~~LCNaCGl~ 237 (352)
...|++||.. .|.|- | -|..||-|
T Consensus 7 ~f~C~~CG~~---s~KW~----G---kCp~Cg~W 30 (456)
T COG1066 7 AFVCQECGYV---SPKWL----G---KCPACGAW 30 (456)
T ss_pred EEEcccCCCC---Ccccc----c---cCCCCCCc
Confidence 6899999985 89993 5 69999965
Done!