Query 030512
Match_columns 176
No_of_seqs 91 out of 93
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 14:51:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030512.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030512hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04755 PAP_fibrillin: PAP_fi 99.9 7.4E-27 1.6E-31 185.9 12.4 109 65-176 1-113 (198)
2 TIGR02116 toxin_Txe_YoeB toxin 85.7 2.1 4.5E-05 30.3 4.8 32 85-117 16-48 (80)
3 PF05973 Gp49: Phage derived p 70.7 20 0.00043 25.5 6.0 42 84-125 6-50 (91)
4 TIGR02683 upstrm_HI1419 probab 70.2 11 0.00024 27.5 4.8 35 85-121 18-52 (95)
5 PF14834 GST_C_4: Glutathione 69.5 6.7 0.00015 31.3 3.6 42 75-119 31-72 (117)
6 PF05015 Plasmid_killer: Plasm 68.1 24 0.00051 25.9 6.1 56 70-125 8-81 (93)
7 TIGR02530 flg_new flagellar op 63.3 9.1 0.0002 29.6 3.2 30 79-108 27-56 (96)
8 PF11010 DUF2848: Protein of u 60.0 8.5 0.00018 33.0 2.8 27 87-113 6-32 (194)
9 PF06251 Caps_synth_GfcC: Caps 54.8 19 0.0004 30.2 3.9 77 48-127 40-130 (229)
10 cd01645 RT_Rtv RT_Rtv: Reverse 51.8 34 0.00074 28.0 5.0 42 80-121 5-55 (213)
11 COG2026 RelE Cytotoxic transla 46.2 39 0.00084 24.7 4.0 25 84-108 18-42 (90)
12 PF07624 PSD2: Protein of unkn 39.6 46 0.00099 23.6 3.5 41 63-103 8-59 (76)
13 PRK10324 translation inhibitor 37.8 33 0.00072 26.2 2.7 27 78-104 6-32 (113)
14 PF14805 THDPS_N_2: Tetrahydro 37.4 76 0.0016 22.9 4.3 33 83-119 21-55 (70)
15 PRK10470 ribosome hibernation 35.4 36 0.00079 24.5 2.5 27 78-104 6-32 (95)
16 PF04536 TPM: TLP18.3, Psb32 a 35.0 45 0.00098 23.9 2.9 21 84-104 2-22 (119)
17 PF10047 DUF2281: Protein of u 34.0 66 0.0014 22.5 3.5 36 83-118 11-46 (66)
18 PF00356 LacI: Bacterial regul 31.6 58 0.0012 21.4 2.7 25 73-100 18-42 (46)
19 TIGR00053 addiction module tox 30.9 45 0.00098 23.5 2.3 33 86-118 22-55 (89)
20 PF05511 ATP-synt_F6: Mitochon 30.4 48 0.001 25.8 2.5 53 50-102 20-80 (99)
21 COG0097 RplF Ribosomal protein 30.1 53 0.0011 27.8 2.9 37 82-118 131-169 (178)
22 PF07813 LTXXQ: LTXXQ motif fa 29.3 65 0.0014 22.3 2.9 30 75-104 6-35 (100)
23 PRK10455 periplasmic protein; 28.9 50 0.0011 27.0 2.5 22 80-101 53-74 (161)
24 PF12124 Nsp3_PL2pro: Coronavi 27.5 61 0.0013 23.3 2.4 32 131-172 22-55 (66)
25 COG4115 Uncharacterized protei 27.4 1.1E+02 0.0024 23.4 3.9 39 86-124 21-71 (84)
26 TIGR00741 yfiA ribosomal subun 26.5 70 0.0015 22.5 2.7 27 78-104 6-32 (95)
27 COG4683 Uncharacterized protei 25.7 88 0.0019 25.2 3.3 27 85-111 19-47 (120)
28 cd00552 RaiA RaiA ("ribosome-a 25.7 73 0.0016 22.3 2.6 27 78-104 5-31 (93)
29 cd03715 RT_ZFREV_like RT_ZFREV 25.2 1.5E+02 0.0032 23.9 4.6 42 80-121 5-56 (210)
30 PF03367 zf-ZPR1: ZPR1 zinc-fi 24.8 1E+02 0.0022 25.1 3.6 39 64-102 100-139 (161)
31 PRK10363 cpxP periplasmic repr 24.5 72 0.0016 26.8 2.7 22 79-100 46-67 (166)
32 PRK11041 DNA-binding transcrip 24.0 71 0.0015 26.0 2.6 17 83-99 3-19 (309)
33 COG3590 PepO Predicted metallo 23.4 60 0.0013 32.5 2.3 46 56-104 349-395 (654)
34 TIGR03176 AllC allantoate amid 23.2 1.6E+02 0.0035 26.5 4.9 56 82-139 26-94 (406)
35 cd01395 HMT_MBD Methyl-CpG bin 23.0 21 0.00045 25.3 -0.6 47 107-153 1-49 (60)
36 PF06769 Plasmid_Txe: Plasmid 22.3 1.4E+02 0.0031 21.9 3.6 31 86-117 17-52 (80)
37 PRK12751 cpxP periplasmic stre 21.8 86 0.0019 25.9 2.6 19 80-98 53-71 (162)
38 PF02482 Ribosomal_S30AE: Sigm 21.3 98 0.0021 21.7 2.5 27 78-104 5-31 (97)
39 KOG0729 26S proteasome regulat 21.0 1.6E+02 0.0036 27.7 4.5 45 72-125 279-325 (435)
40 PRK10727 DNA-binding transcrip 21.0 1.5E+02 0.0033 24.9 4.0 18 83-100 27-44 (343)
41 PF07095 IgaA: Intracellular g 20.9 2.9E+02 0.0063 28.2 6.5 91 82-176 44-150 (705)
42 TIGR02574 stabl_TIGR02574 puta 20.0 2.9E+02 0.0062 18.9 4.6 38 64-101 8-45 (63)
No 1
>PF04755 PAP_fibrillin: PAP_fibrillin; InterPro: IPR006843 This family identifies a conserved domain found in a number of plastid lipid-associated proteins (PAPs) that are thought to form together with other plastoglobulins a coat on the surface of the lipoprotein particle. The coat may contain receptors for attachment to the thylakoid membrane as well as regulatory proteins that may function in the transfer of lipids to and from the thylakoid membranes.). This entry also represents a number of putative fibrillin proteins.; GO: 0005198 structural molecule activity, 0009507 chloroplast
Probab=99.94 E-value=7.4e-27 Score=185.90 Aligned_cols=109 Identities=29% Similarity=0.543 Sum_probs=98.5
Q ss_pred hHHHHHHHHhhccCCCCccCCHHHHHHHHHHHHHHhhhCC-CCCCCC-CCccceEEEEEecCCCCCCCCccccccee-ee
Q 030512 65 DDLVASILSKVNQSDGGVSLAKEEHKEVAEVAQELQKYCV-EAPVKC-PLIFGEWDVVYCSVPTSPGGGYRSAFGRL-FF 141 (176)
Q Consensus 65 ~~Lk~~LL~aIagtdRG~~aS~e~r~~V~~~i~qLE~~np-p~Pl~s-pLL~G~W~LlYTSs~~~~GG~~Rs~lgR~-lf 141 (176)
++||++||+++++||||+.+++++|++|+++|.+||++|| |+|+++ ++|+|+|+|+|||++...+...+ ++. ++
T Consensus 1 ~~~K~~Ll~~~~~~~rG~~~~~~~~~~i~~~v~~LE~~np~~~p~~s~~~L~G~W~Lvytt~~~~~~~l~~---~~~~~~ 77 (198)
T PF04755_consen 1 QDLKQELLQAVAGTNRGLRASPEDREEIEELVEELEALNPTPDPADSLPLLDGRWELVYTTSPEIRSLLQR---GRLPGV 77 (198)
T ss_pred ChHHHHHHHHHhccCCCccCCHHHHHHHHHHHHHHHHhCCCCCCcCCchhcCcEEEEEeecCCCccccccc---cccccc
Confidence 4799999999999999999999999999999999999999 999999 79999999999999988764333 333 57
Q ss_pred eecceEEEeeCCc-eEeEEEEEEEecceeeEEEeeC
Q 030512 142 KTKEMIQAVEAPD-TVRNKVSFTALGFLDGEVSLKA 176 (176)
Q Consensus 142 k~~ei~Q~I~~p~-~V~N~Vef~~~g~L~G~Vsl~g 176 (176)
++++|+|.|+..+ ++.|.|+|..||+++|.+.+.+
T Consensus 78 ~~~~v~Q~id~~~~~~~N~v~~~~~~~~~~~~~v~a 113 (198)
T PF04755_consen 78 RVGRVFQTIDADNGRVENVVELSGFPLLEGSVSVRA 113 (198)
T ss_pred cccceEEEEECCCceEEEEEEEeccCceEEEEEEEE
Confidence 8899999999999 9999999999999999888753
No 2
>TIGR02116 toxin_Txe_YoeB toxin-antitoxin system, toxin component, Txe/YoeB family. The Axe-Txe pair in Enterococcus faecium and the homologous YefM-YoeB pair in Escherichia coli have been shown to act as an antitoxin-toxin pair. This model describes the toxin component. Nearly every example found is next to an identifiable antitoxin, as indicated by matches to TIGR01552 and/or pfam02604.
Probab=85.66 E-value=2.1 Score=30.26 Aligned_cols=32 Identities=16% Similarity=0.185 Sum_probs=20.6
Q ss_pred CHHHHHHHHHHHHHHhhhCC-CCCCCCCCccceE
Q 030512 85 AKEEHKEVAEVAQELQKYCV-EAPVKCPLIFGEW 117 (176)
Q Consensus 85 S~e~r~~V~~~i~qLE~~np-p~Pl~spLL~G~W 117 (176)
.++.+++|.+++.+|+ .|| +...+.--|.|+|
T Consensus 16 ~~~~~~~i~~~i~~l~-~~P~~~~~~~~~L~G~~ 48 (80)
T TIGR02116 16 DKKLKKKINELIKDVR-RDPFKGKGKPEPLKGDL 48 (80)
T ss_pred CHHHHHHHHHHHHHHH-cCCCCCCCCcccCCCCC
Confidence 3678899999999887 355 3223333466655
No 3
>PF05973 Gp49: Phage derived protein Gp49-like (DUF891); InterPro: IPR009241 This entry consists of several hypothetical viral and bacterial proteins some are annotated as addiction module killer proteins.
Probab=70.72 E-value=20 Score=25.49 Aligned_cols=42 Identities=14% Similarity=0.135 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHHHHHHhhhCC--CCCCCCCCc-cceEEEEEecCC
Q 030512 84 LAKEEHKEVAEVAQELQKYCV--EAPVKCPLI-FGEWDVVYCSVP 125 (176)
Q Consensus 84 aS~e~r~~V~~~i~qLE~~np--p~Pl~spLL-~G~W~LlYTSs~ 125 (176)
+++..+++|...+..|+..+| ..|.-..+= +|=|+|=.....
T Consensus 6 L~~~~~~~i~~~l~~l~~~G~~l~~~~~k~l~~~~i~ElR~~~~~ 50 (91)
T PF05973_consen 6 LPDKERAKILAQLERLEEHGPSLGEPLFKHLKGDGIYELRVRGGS 50 (91)
T ss_pred CCHHHHHHHHHHHHHHHhcCCccCCCcccccCcCCeEEEEEeecC
Confidence 578899999999999999986 566666565 788888765554
No 4
>TIGR02683 upstrm_HI1419 probable addiction module killer protein. Members of this strictly bacterial protein family are small, at roughly 100 amino acids. The gene is almost invariably the upstream member of a gene pair, where the downstream member is a predicted DNA-binding protein from a clade within Pfam helix-turn-helix family pfam01381. These gene pairs, when found on the bacterial chromosome, often are located with prophage regions, but also in both integrated plasmid regions and near housekeeping genes. Analysis suggests that the gene pair may serve as an addiction module.
Probab=70.24 E-value=11 Score=27.46 Aligned_cols=35 Identities=9% Similarity=-0.076 Sum_probs=21.8
Q ss_pred CHHHHHHHHHHHHHHhhhCCCCCCCCCCccceEEEEE
Q 030512 85 AKEEHKEVAEVAQELQKYCVEAPVKCPLIFGEWDVVY 121 (176)
Q Consensus 85 S~e~r~~V~~~i~qLE~~npp~Pl~spLL~G~W~LlY 121 (176)
.+.++++|.+.+..|+..++ |.--+|-+|.|++=+
T Consensus 18 d~~~~~kI~~~i~~l~~g~~--~~~K~l~~~~~ElR~ 52 (95)
T TIGR02683 18 DPRAKARILARIDRLALGNF--GDVKPVGEGVSELRI 52 (95)
T ss_pred CHHHHHHHHHHHHHHhccCC--CCccCCCCCcEEEEe
Confidence 67789999999999996322 222234344455443
No 5
>PF14834 GST_C_4: Glutathione S-transferase, C-terminal domain; PDB: 3BBY_A.
Probab=69.50 E-value=6.7 Score=31.30 Aligned_cols=42 Identities=17% Similarity=0.393 Sum_probs=24.3
Q ss_pred hccCCCCccCCHHHHHHHHHHHHHHhhhCCCCCCCCCCccceEEE
Q 030512 75 VNQSDGGVSLAKEEHKEVAEVAQELQKYCVEAPVKCPLIFGEWDV 119 (176)
Q Consensus 75 IagtdRG~~aS~e~r~~V~~~i~qLE~~npp~Pl~spLL~G~W~L 119 (176)
+..-.+...+|++.+++|.++++..|.+-+. ..+-|||+|-+
T Consensus 31 vf~~~~~~pLs~~a~~~a~kL~~~a~~ll~~---g~~~LFGewsI 72 (117)
T PF14834_consen 31 VFRGARKPPLSEAAQAAAQKLIAVAERLLAD---GGPNLFGEWSI 72 (117)
T ss_dssp HHS--------HHHHHHHHHHHHHHHHHTTT-----SSTTSS--H
T ss_pred hhcCCCCCCCCHHHHHHHHHHHHHHHHHhcc---CCCCccccchH
Confidence 4444556778999999999999999988652 23459999954
No 6
>PF05015 Plasmid_killer: Plasmid maintenance system killer protein; InterPro: IPR007711 Several plasmids with proteic killer gene systems have been reported. All of them encode a stable toxin and an unstable antidote. Upon loss of the plasmid, the less stable inhibitor is inactivated more rapidly than the toxin, allowing the toxin to be activated. The activation of those systems result in cell filamentation and cessation of viable cell production. It has been verified that both the stable killer and the unstable inhibitor of the systems are short polypeptides. This family corresponds to the toxin.
Probab=68.13 E-value=24 Score=25.92 Aligned_cols=56 Identities=14% Similarity=0.178 Sum_probs=36.4
Q ss_pred HHHHhhccCCCCccCCHHHHHHHHHHHHHHhhh------CC-----CCCCCCC-------CccceEEEEEecCC
Q 030512 70 SILSKVNQSDGGVSLAKEEHKEVAEVAQELQKY------CV-----EAPVKCP-------LIFGEWDVVYCSVP 125 (176)
Q Consensus 70 ~LL~aIagtdRG~~aS~e~r~~V~~~i~qLE~~------np-----p~Pl~sp-------LL~G~W~LlYTSs~ 125 (176)
.=|+++.-+++-....++-.+.+...+++|++. .. .+||+.. -|+|+|+|+|.-..
T Consensus 8 k~l~~l~~~~~~k~~~~~~~~~~~~~L~~L~aa~~~~dl~~~p~~r~h~L~G~~~g~~Si~i~~~~RliF~~~~ 81 (93)
T PF05015_consen 8 KKLEKLFEDGKTKKIPADIAKKLRRRLDQLDAATSLEDLRSPPSNRLHKLKGDRKGQWSIRINGNWRLIFRFED 81 (93)
T ss_pred HHHHHHHCCCCcCCcCHHHHHHHHHHHHHHHhCCCHHHHhcCcCCCcccccCCCCCcEEEEeCCCEEEEEEEeC
Confidence 446667767666667777777777888877653 22 3555442 37788888886544
No 7
>TIGR02530 flg_new flagellar operon protein. Members of this family are found in a subset of bacterial flagellar operons, generally between genes designated flgD and flgE, in species as diverse as Bacillus halodurans and various other Firmicutes, Geobacter sulfurreducens, and Bdellovibrio bacteriovorus. The specific molecular function is unknown.
Probab=63.33 E-value=9.1 Score=29.56 Aligned_cols=30 Identities=17% Similarity=0.346 Sum_probs=27.5
Q ss_pred CCCccCCHHHHHHHHHHHHHHhhhCCCCCC
Q 030512 79 DGGVSLAKEEHKEVAEVAQELQKYCVEAPV 108 (176)
Q Consensus 79 dRG~~aS~e~r~~V~~~i~qLE~~npp~Pl 108 (176)
.||+.++++|-++|.+.+.+.+..+..++|
T Consensus 27 ~R~I~l~~~~~~~i~~av~~A~~KG~kesL 56 (96)
T TIGR02530 27 ERNISINPDDWKKLLEAVEEAESKGVKDSL 56 (96)
T ss_pred HcCCCCCHHHHHHHHHHHHHHHhcCCCceE
Confidence 699999999999999999999999887654
No 8
>PF11010 DUF2848: Protein of unknown function (DUF2848); InterPro: IPR021269 This bacterial family of proteins has no known function.
Probab=59.98 E-value=8.5 Score=33.02 Aligned_cols=27 Identities=26% Similarity=0.442 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHhhhCCCCCCCCCCc
Q 030512 87 EEHKEVAEVAQELQKYCVEAPVKCPLI 113 (176)
Q Consensus 87 e~r~~V~~~i~qLE~~npp~Pl~spLL 113 (176)
-|+++|..-|++|+++++|.|-+.|++
T Consensus 6 Rd~~av~~HI~EL~~lGVp~Ps~vP~~ 32 (194)
T PF11010_consen 6 RDQEAVEHHIEELAALGVPPPSSVPLF 32 (194)
T ss_pred CCHHHHHHHHHHHHHhCCCCCCCCCEE
Confidence 478999999999999999999999865
No 9
>PF06251 Caps_synth_GfcC: Capsule biosynthesis GfcC; InterPro: IPR010425 This entry represents uncharacterised bacterial proteins that contain a central beta-grasp like domain related to the SLBB domain [].; PDB: 3P42_B.
Probab=54.79 E-value=19 Score=30.18 Aligned_cols=77 Identities=16% Similarity=0.142 Sum_probs=46.6
Q ss_pred eEEEEEeecCCcccCChhHHHHHHHHhhccCCCCccCCHHHHHHHHHHHHHHhhhCC--------------CCCCCCCCc
Q 030512 48 KIVRAVSISSPDLRTGPDDLVASILSKVNQSDGGVSLAKEEHKEVAEVAQELQKYCV--------------EAPVKCPLI 113 (176)
Q Consensus 48 ~~~~~vs~~~p~~~~~~~~Lk~~LL~aIagtdRG~~aS~e~r~~V~~~i~qLE~~np--------------p~Pl~spLL 113 (176)
+|.+.+= +....++..+..+++|+..++-... ....+..+....++++|+.... .+|-..|+|
T Consensus 40 y~~~a~L-~~~~~~~~~~~~~~~ll~~L~~l~~--~~~~~~~~~~~~l~~qL~~~~~~gR~~i~lD~d~~r~~~~~n~~L 116 (229)
T PF06251_consen 40 YWPGAAL-FRRSKQAEAEQQKQQLLAQLAQLEQ--SADSDQAAAAQQLIQQLQSLEATGRVVINLDPDWVRLNPEYNPLL 116 (229)
T ss_dssp -GGG-EE-E-HHHHHHHHHHHHHHHHHHHHHHH--HS-HHHHHHHHHHHHHHTT--B----S----TTS-EESTTSS-B-
T ss_pred ccCccee-ecccchHHHHHHHHHHHHHHHHHhh--ccchhHHHHHHHHHHHHHhccccceEEEecCHHHhhccccCCCcC
Confidence 5554433 3344445588899999888887665 6778888999999999976432 134466789
Q ss_pred cceEEEEEecCCCC
Q 030512 114 FGEWDVVYCSVPTS 127 (176)
Q Consensus 114 ~G~W~LlYTSs~~~ 127 (176)
.|.+.|...+.++.
T Consensus 117 ~ggd~L~vP~rp~~ 130 (229)
T PF06251_consen 117 EGGDRLYVPPRPNT 130 (229)
T ss_dssp ECEEEEE-----SE
T ss_pred CCCcEEEECCCCCE
Confidence 99999999888854
No 10
>cd01645 RT_Rtv RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.
Probab=51.81 E-value=34 Score=27.95 Aligned_cols=42 Identities=21% Similarity=0.396 Sum_probs=32.2
Q ss_pred CCccCCHHHHHHHHHHHHHHhhhCC----CCCCCCC-Cc----cceEEEEE
Q 030512 80 GGVSLAKEEHKEVAEVAQELQKYCV----EAPVKCP-LI----FGEWDVVY 121 (176)
Q Consensus 80 RG~~aS~e~r~~V~~~i~qLE~~np----p~Pl~sp-LL----~G~W~LlY 121 (176)
|..-+++++++++.+.|++|-+.+. ..|-.+| .+ +|+||+..
T Consensus 5 ~~~p~~~~~~~~~~~~i~~ll~~g~I~~~~s~~~sp~~~v~K~~g~~R~~~ 55 (213)
T cd01645 5 KQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLH 55 (213)
T ss_pred CccCCCHHHHHHHHHHHHHHHHCCceecCCCCCcCcEEEEEcCCCCeEEEe
Confidence 4456899999999999999988763 4566666 22 69999873
No 11
>COG2026 RelE Cytotoxic translational repressor of toxin-antitoxin stability system [Translation, ribosomal structure and biogenesis / Cell division and chromosome partitioning]
Probab=46.20 E-value=39 Score=24.74 Aligned_cols=25 Identities=20% Similarity=0.150 Sum_probs=19.7
Q ss_pred CCHHHHHHHHHHHHHHhhhCCCCCC
Q 030512 84 LAKEEHKEVAEVAQELQKYCVEAPV 108 (176)
Q Consensus 84 aS~e~r~~V~~~i~qLE~~npp~Pl 108 (176)
+++..++.+.+.+.+|+...||.+.
T Consensus 18 L~~~~~~~~~~~l~~~~~~~~p~~~ 42 (90)
T COG2026 18 LDKKIRKKIKDKLKELLENPPPIRH 42 (90)
T ss_pred CCHHHHHHHHHHHHHhhccCCchhh
Confidence 6889999999999999887544444
No 12
>PF07624 PSD2: Protein of unknown function (DUF1585); InterPro: IPR011478 This entry represents a conserved region at the C terminus of a family of cytochrome-like proteins found in bacteria such as Rhodopirellula baltica and Solibacter usitatus. These proteins also contain IPR013036 from INTERPRO, IPR013039 from INTERPRO, IPR013042 from INTERPRO and IPR013043 from INTERPRO.
Probab=39.55 E-value=46 Score=23.62 Aligned_cols=41 Identities=12% Similarity=0.197 Sum_probs=27.2
Q ss_pred ChhHHHHHHHHh-----------hccCCCCccCCHHHHHHHHHHHHHHhhhC
Q 030512 63 GPDDLVASILSK-----------VNQSDGGVSLAKEEHKEVAEVAQELQKYC 103 (176)
Q Consensus 63 ~~~~Lk~~LL~a-----------IagtdRG~~aS~e~r~~V~~~i~qLE~~n 103 (176)
++.+||..|++. +..=-=|+..+.+|+..|+++++++++-+
T Consensus 8 ~~~eLk~~L~~~~~~~~~~~~~kl~~YAlGR~~~~~D~~~i~~i~~~~~~~~ 59 (76)
T PF07624_consen 8 GAAELKQYLAERKDQFARCFAEKLLTYALGRPLEFSDRCEIDRIVEAFKANG 59 (76)
T ss_pred CHHHHHHHHHHCHHHHHHHHHHHHHHHHcCCCCCcchHHHHHHHHHHHHHcC
Confidence 355555555544 33333355557899999999999997743
No 13
>PRK10324 translation inhibitor protein RaiA; Provisional
Probab=37.80 E-value=33 Score=26.17 Aligned_cols=27 Identities=15% Similarity=0.263 Sum_probs=25.4
Q ss_pred CCCCccCCHHHHHHHHHHHHHHhhhCC
Q 030512 78 SDGGVSLAKEEHKEVAEVAQELQKYCV 104 (176)
Q Consensus 78 tdRG~~aS~e~r~~V~~~i~qLE~~np 104 (176)
|.|++.+|++-|+.|.+-+++|+++.+
T Consensus 6 tgr~v~~tdalr~~ie~Kl~kL~k~~~ 32 (113)
T PRK10324 6 TSKQMEITPAIRQHVADRLAKLEKWQT 32 (113)
T ss_pred EEEcCcCCHHHHHHHHHHHHHHHHhcC
Confidence 578999999999999999999999986
No 14
>PF14805 THDPS_N_2: Tetrahydrodipicolinate N-succinyltransferase N-terminal; PDB: 3EG4_A 3TDT_A 2TDT_A 1KGT_A 1TDT_A 1KGQ_A 3BXY_A 3GOS_A 3TK8_A.
Probab=37.38 E-value=76 Score=22.94 Aligned_cols=33 Identities=30% Similarity=0.275 Sum_probs=23.4
Q ss_pred cCCHHHHHHHHHHHHHHhhhC--CCCCCCCCCccceEEE
Q 030512 83 SLAKEEHKEVAEVAQELQKYC--VEAPVKCPLIFGEWDV 119 (176)
Q Consensus 83 ~aS~e~r~~V~~~i~qLE~~n--pp~Pl~spLL~G~W~L 119 (176)
.+.++.|+.|.++|+.|++=- +.+|.+ +|.|.+
T Consensus 21 ~~~~~~~~av~~~i~~Ld~G~lRvAek~~----~g~W~v 55 (70)
T PF14805_consen 21 NADPELRDAVEEVIELLDSGELRVAEKDA----DGEWVV 55 (70)
T ss_dssp T--HHHHHHHHHHHHHHHTTSS-SEEEET----TTEEEE
T ss_pred cCCHHHHHHHHHHHHHhcCCCeEEEeecC----CCCEEe
Confidence 347999999999999998743 356653 288875
No 15
>PRK10470 ribosome hibernation promoting factor HPF; Provisional
Probab=35.43 E-value=36 Score=24.51 Aligned_cols=27 Identities=15% Similarity=0.202 Sum_probs=25.0
Q ss_pred CCCCccCCHHHHHHHHHHHHHHhhhCC
Q 030512 78 SDGGVSLAKEEHKEVAEVAQELQKYCV 104 (176)
Q Consensus 78 tdRG~~aS~e~r~~V~~~i~qLE~~np 104 (176)
+.|++.+|++.|+.|.+-+++|+++.+
T Consensus 6 ~~r~i~~t~al~~~v~~kl~kL~r~~~ 32 (95)
T PRK10470 6 TGHNVEITEALREFVTAKFAKLEQYFD 32 (95)
T ss_pred EEEeeccCHHHHHHHHHHHHHHHHhcC
Confidence 568899999999999999999999986
No 16
>PF04536 TPM: TLP18.3, Psb32 and MOLO-1 founding proteins of phosphatase; InterPro: IPR007621 This is a family of uncharacterised proteins. They are found in both eukarya and eubacteria. In eubacteria the region is towards the N-terminal of the protein and is accompanied by an N-terminal signal sequence. The C-terminal of eubacterial proteins typically contains one or more putative transmembrane regions. In eukaryotes the region is not accompanied by a signal sequence.; PDB: 3PTJ_A 3PW9_A 3PVH_A 2KPT_A 2KW7_A.
Probab=34.98 E-value=45 Score=23.93 Aligned_cols=21 Identities=24% Similarity=0.352 Sum_probs=17.7
Q ss_pred CCHHHHHHHHHHHHHHhhhCC
Q 030512 84 LAKEEHKEVAEVAQELQKYCV 104 (176)
Q Consensus 84 aS~e~r~~V~~~i~qLE~~np 104 (176)
+|+++++++++.+++||+...
T Consensus 2 Ls~~~~~~l~~~l~~~~~~t~ 22 (119)
T PF04536_consen 2 LSQEERERLNQALAKLEKKTG 22 (119)
T ss_dssp S-HHHHHHHHHHHHHHHHHC-
T ss_pred CCHHHHHHHHHHHHHHHHhhC
Confidence 689999999999999999754
No 17
>PF10047 DUF2281: Protein of unknown function (DUF2281); InterPro: IPR018739 This domain is found in putative uncharacterised proteins, though some proteins contaning this domain are described as a transcritional regulator of the Xre family.
Probab=33.95 E-value=66 Score=22.47 Aligned_cols=36 Identities=22% Similarity=0.380 Sum_probs=27.3
Q ss_pred cCCHHHHHHHHHHHHHHhhhCCCCCCCCCCccceEE
Q 030512 83 SLAKEEHKEVAEVAQELQKYCVEAPVKCPLIFGEWD 118 (176)
Q Consensus 83 ~aS~e~r~~V~~~i~qLE~~npp~Pl~spLL~G~W~ 118 (176)
.++++.+++|..-|.=|....+...-...-+.|+|+
T Consensus 11 ~LP~~~~~Evldfi~fL~~k~~~~~~~~~~~~~~~~ 46 (66)
T PF10047_consen 11 QLPEELQQEVLDFIEFLLQKYQQKESKKKKLLGDWK 46 (66)
T ss_pred HCCHHHHHHHHHHHHHHHHhcccccccccccccccC
Confidence 468999999999999998877633334445677776
No 18
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=31.61 E-value=58 Score=21.44 Aligned_cols=25 Identities=24% Similarity=0.364 Sum_probs=19.5
Q ss_pred HhhccCCCCccCCHHHHHHHHHHHHHHh
Q 030512 73 SKVNQSDGGVSLAKEEHKEVAEVAQELQ 100 (176)
Q Consensus 73 ~aIagtdRG~~aS~e~r~~V~~~i~qLE 100 (176)
.+|.|. -..+++.|++|.+++++|.
T Consensus 18 r~ln~~---~~vs~~tr~rI~~~a~~lg 42 (46)
T PF00356_consen 18 RVLNGP---PRVSEETRERILEAAEELG 42 (46)
T ss_dssp HHHTTC---SSSTHHHHHHHHHHHHHHT
T ss_pred HHHhCC---CCCCHHHHHHHHHHHHHHC
Confidence 344444 3689999999999999884
No 19
>TIGR00053 addiction module toxin component, YafQ family. This model represents a cluster of eubacterial proteins and a cluster of archaeal proteins, all of which are uncharacterized, from 85 to 102 residues in length, and similar in sequence. These include YafQ, a ribosome-associated endoribonuclease that serves as part of a toxin-antitoxin system, for which DinJ is the antidote component.
Probab=30.92 E-value=45 Score=23.52 Aligned_cols=33 Identities=18% Similarity=0.224 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHHHhhhCC-CCCCCCCCccceEE
Q 030512 86 KEEHKEVAEVAQELQKYCV-EAPVKCPLIFGEWD 118 (176)
Q Consensus 86 ~e~r~~V~~~i~qLE~~np-p~Pl~spLL~G~W~ 118 (176)
+.++++|.+++.+|..-+| |...+.--|-|+|.
T Consensus 22 ~~~~~~i~~~i~~l~~~~~~p~~~~~~~L~G~~~ 55 (89)
T TIGR00053 22 GKDLKKLLKKMEELINTLPLPEHYKDHPLRGPWK 55 (89)
T ss_pred CccHHHHHHHHHHHHcCCCCCcccCCccCcCCcC
Confidence 3677888888888877444 44344334555543
No 20
>PF05511 ATP-synt_F6: Mitochondrial ATP synthase coupling factor 6; InterPro: IPR008387 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit F6 (or coupling factor 6) found in the F0 complex of F-ATPases in mitochondria. The F6 subunit is part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In mitochondria, the peripheral stalk is composed of one copy each of subunits OSCP (oligomycin sensitivity conferral protein), F6, B and D []. There is no homologue of subunit F6 in bacterial or chloroplast F-ATPase, whose peripheral stalks are composed of one copy of the delta subunit (homologous to OSCP), and two copies of subunit B in bacteria, or one copy each of subunits B and B' in chloroplasts and photosynthetic bacteria. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0000276 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o); PDB: 2WSS_V 2CLY_C 1VZS_A.
Probab=30.44 E-value=48 Score=25.76 Aligned_cols=53 Identities=25% Similarity=0.353 Sum_probs=27.0
Q ss_pred EEEEeecCCcccCChhHHHHHHHHhhccC------CCC--ccCCHHHHHHHHHHHHHHhhh
Q 030512 50 VRAVSISSPDLRTGPDDLVASILSKVNQS------DGG--VSLAKEEHKEVAEVAQELQKY 102 (176)
Q Consensus 50 ~~~vs~~~p~~~~~~~~Lk~~LL~aIagt------dRG--~~aS~e~r~~V~~~i~qLE~~ 102 (176)
+.+++++++-..+..|.+..--|++|..- ..| ++++||-+++.++-+.+|...
T Consensus 20 ~Rni~~sa~~~~k~~DPIQklFldKIREY~~Ksks~gGklVD~~Pe~~kel~eel~kL~r~ 80 (99)
T PF05511_consen 20 RRNIGTSAVAFNKALDPIQKLFLDKIREYNQKSKSSGGKLVDAGPEYEKELNEELEKLARQ 80 (99)
T ss_dssp -------------S--TTTHHHHHHHHHHHHHHTTTSS-STT--THHHHHHHHHHHHHHHH
T ss_pred HHHhhhhHHHHhcccChHHHHHHHHHHHHHHHhccCCCCCCCCCHHHHHHHHHHHHHHHHH
Confidence 33445454443344566666667777432 445 889999999999999999774
No 21
>COG0097 RplF Ribosomal protein L6P/L9E [Translation, ribosomal structure and biogenesis]
Probab=30.11 E-value=53 Score=27.79 Aligned_cols=37 Identities=19% Similarity=0.195 Sum_probs=29.7
Q ss_pred ccCCHHHHHHHHHHHHHHhhhCCCCCCCCC--CccceEE
Q 030512 82 VSLAKEEHKEVAEVAQELQKYCVEAPVKCP--LIFGEWD 118 (176)
Q Consensus 82 ~~aS~e~r~~V~~~i~qLE~~npp~Pl~sp--LL~G~W~ 118 (176)
+..+--|+|.|-+.++.++++++|+|-+-. ..+|++-
T Consensus 131 I~v~GidKe~VGQ~AA~Ir~~r~pepykgKgi~ydge~I 169 (178)
T COG0097 131 IVVEGIDKELVGQVAANIRAARKPEPYKGKGIRYDGEYI 169 (178)
T ss_pred EEEEcCCHHHHhHHHHHHHhccCCCCCCCcceEEcCEEE
Confidence 445566899999999999999999999876 4555543
No 22
>PF07813 LTXXQ: LTXXQ motif family protein; InterPro: IPR012899 This five residue motif is found in a number of bacterial proteins bearing similarity to the protein CpxP (P32158 from SWISSPROT). This is a periplasmic protein that aids in combating extracytoplasmic protein-mediated toxicity, and may also be involved in the response to alkaline pH []. Another member of this family, Spy (P77754 from SWISSPROT) is also a periplasmic protein that may be involved in the response to stress []. The homology between CpxP and Spy may indicate that these two proteins are functionally related []. The motif is found repeated twice in many members of this entry. ; GO: 0042597 periplasmic space; PDB: 3ITF_B 3QZC_B 3OEO_D 3O39_A.
Probab=29.28 E-value=65 Score=22.35 Aligned_cols=30 Identities=10% Similarity=0.216 Sum_probs=21.1
Q ss_pred hccCCCCccCCHHHHHHHHHHHHHHhhhCC
Q 030512 75 VNQSDGGVSLAKEEHKEVAEVAQELQKYCV 104 (176)
Q Consensus 75 IagtdRG~~aS~e~r~~V~~~i~qLE~~np 104 (176)
+...-..+.+|++|++.+.++..+..+...
T Consensus 6 ~~~l~~~L~LT~eQ~~~~~~i~~~~~~~~~ 35 (100)
T PF07813_consen 6 IDRLKEELNLTDEQKAKWRAIRQAMKAKMK 35 (100)
T ss_dssp --STTTTS--THHHHHHHHHHHHHHCTTS-
T ss_pred HHHHHhhCCCCHHHHHHHHHHHHHHHHHHH
Confidence 344567899999999999999999877643
No 23
>PRK10455 periplasmic protein; Reviewed
Probab=28.92 E-value=50 Score=27.00 Aligned_cols=22 Identities=9% Similarity=0.430 Sum_probs=18.6
Q ss_pred CCccCCHHHHHHHHHHHHHHhh
Q 030512 80 GGVSLAKEEHKEVAEVAQELQK 101 (176)
Q Consensus 80 RG~~aS~e~r~~V~~~i~qLE~ 101 (176)
+|+.+|++||++|.+|..+-..
T Consensus 53 ~~L~LT~~Qrqqir~im~~~r~ 74 (161)
T PRK10455 53 KGLNLTDAQKQQIRDIMKAQRD 74 (161)
T ss_pred hhCCCCHHHHHHHHHHHHHHHH
Confidence 4699999999999999887533
No 24
>PF12124 Nsp3_PL2pro: Coronavirus polyprotein cleavage domain; InterPro: IPR022733 This domain is found in SARS coronaviruses, and is about 70 amino acids in length. It is found associated with various other coronavirus proteins due to the polyprotein nature of most viral translation. PL2pro is a domain of the non-structural protein nsp3. The domain performs three of the cleavages required to separate the translated polyprotein into its distinct proteins. ; GO: 0004197 cysteine-type endopeptidase activity, 0008242 omega peptidase activity, 0016740 transferase activity, 0016788 hydrolase activity, acting on ester bonds, 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2KAF_A 2KQW_A.
Probab=27.47 E-value=61 Score=23.31 Aligned_cols=32 Identities=38% Similarity=0.722 Sum_probs=19.0
Q ss_pred Ccccccceeeeeecc--eEEEeeCCceEeEEEEEEEecceeeEE
Q 030512 131 GYRSAFGRLFFKTKE--MIQAVEAPDTVRNKVSFTALGFLDGEV 172 (176)
Q Consensus 131 ~~Rs~lgR~lfk~~e--i~Q~I~~p~~V~N~Vef~~~g~L~G~V 172 (176)
++|+-+|..|+|-|+ +|.++ .|.+||- ++|+|
T Consensus 22 gqrtelgveflkrgdkivyht~------~~~iefh----~~gev 55 (66)
T PF12124_consen 22 GQRTELGVEFLKRGDKIVYHTV------ENPIEFH----MDGEV 55 (66)
T ss_dssp --EETTEEEEEEETTEEEEE-S------SSS--EE----ETTEE
T ss_pred cceehhhhHHHhcCCEEEEEec------CCceEEE----ecCcE
Confidence 479999999999876 34444 4448874 56665
No 25
>COG4115 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.35 E-value=1.1e+02 Score=23.35 Aligned_cols=39 Identities=26% Similarity=0.339 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHhh-----hCCCCCCCCC-------CccceEEEEEecC
Q 030512 86 KEEHKEVAEVAQELQK-----YCVEAPVKCP-------LIFGEWDVVYCSV 124 (176)
Q Consensus 86 ~e~r~~V~~~i~qLE~-----~npp~Pl~sp-------LL~G~W~LlYTSs 124 (176)
.-....|+++|..+.. .++||||+.. .|+-+=+|+||-.
T Consensus 21 ~~~~kki~~Li~~i~rdPfkg~gkpEpLk~~~~g~wSRRIn~eHRlVY~v~ 71 (84)
T COG4115 21 KKLKKKINELIKEIKRDPFKGIGKPEPLKGDYSGYWSRRINHEHRLVYTVD 71 (84)
T ss_pred HHHHHHHHHHHHHhccCccccCCCCccCcccccchhhhhcccceeEEEEec
Confidence 3456778888888754 4559999865 4556667888754
No 26
>TIGR00741 yfiA ribosomal subunit interface protein. The member of this family from E. coli is now recognized as a protein at the interace between ribosomal large and small subunits, with about 1/3 as many copies per cell as the number of ribosomes.
Probab=26.49 E-value=70 Score=22.53 Aligned_cols=27 Identities=19% Similarity=0.311 Sum_probs=24.7
Q ss_pred CCCCccCCHHHHHHHHHHHHHHhhhCC
Q 030512 78 SDGGVSLAKEEHKEVAEVAQELQKYCV 104 (176)
Q Consensus 78 tdRG~~aS~e~r~~V~~~i~qLE~~np 104 (176)
+.|++.+|++.++.|.+-+++|+++.+
T Consensus 6 ~~~~~~~t~~l~~~i~~k~~kl~k~~~ 32 (95)
T TIGR00741 6 TGKNVEITEALREYVEEKLARLERYFT 32 (95)
T ss_pred EEeccccCHHHHHHHHHHHHHHHHhcC
Confidence 358999999999999999999999986
No 27
>COG4683 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.68 E-value=88 Score=25.17 Aligned_cols=27 Identities=15% Similarity=0.096 Sum_probs=23.2
Q ss_pred CHHHHHHHHHHHHHHhhhCC--CCCCCCC
Q 030512 85 AKEEHKEVAEVAQELQKYCV--EAPVKCP 111 (176)
Q Consensus 85 S~e~r~~V~~~i~qLE~~np--p~Pl~sp 111 (176)
-.+.++.|..+|..||..+| |.|.-+.
T Consensus 19 e~~tq~~V~a~i~lle~~Gp~L~~Py~dk 47 (120)
T COG4683 19 ERETQESVTAAIDLLEMEGPTLGRPYVDK 47 (120)
T ss_pred hHHHHHHHHHHHHHHHHhCCCCCCccccc
Confidence 45778999999999999999 8998654
No 28
>cd00552 RaiA RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site. RaiA is also thought to counteract miscoding at the A site thus reducing translation errors. The RaiA fold structurally resembles the double-stranded RNA-binding domain (dsRBD).
Probab=25.66 E-value=73 Score=22.31 Aligned_cols=27 Identities=19% Similarity=0.292 Sum_probs=24.6
Q ss_pred CCCCccCCHHHHHHHHHHHHHHhhhCC
Q 030512 78 SDGGVSLAKEEHKEVAEVAQELQKYCV 104 (176)
Q Consensus 78 tdRG~~aS~e~r~~V~~~i~qLE~~np 104 (176)
+.|++.+|++-++.|.+-+.+|+++.+
T Consensus 5 ~~r~~~~t~al~~~i~~k~~kl~r~~~ 31 (93)
T cd00552 5 TGRNIEVTDALREYVEEKLEKLEKYFD 31 (93)
T ss_pred EEEcccCCHHHHHHHHHHHHHHHHhcC
Confidence 468999999999999999999999974
No 29
>cd03715 RT_ZFREV_like RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.
Probab=25.21 E-value=1.5e+02 Score=23.93 Aligned_cols=42 Identities=21% Similarity=0.364 Sum_probs=31.5
Q ss_pred CCccCCHHHHHHHHHHHHHHhhhCC----CCCCCCC--Cc---cc-eEEEEE
Q 030512 80 GGVSLAKEEHKEVAEVAQELQKYCV----EAPVKCP--LI---FG-EWDVVY 121 (176)
Q Consensus 80 RG~~aS~e~r~~V~~~i~qLE~~np----p~Pl~sp--LL---~G-~W~LlY 121 (176)
+....++++++++.+.+.+|++.+. ..|-.+| ++ +| +|+++.
T Consensus 5 ~~~~~~~~~~~~~~~~v~~ll~~G~I~~~~s~~~sp~~~V~Kk~g~~~R~~v 56 (210)
T cd03715 5 KQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNDYRMVQ 56 (210)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHCCCeECCCCCCCCceEEEEeCCCCcceEEE
Confidence 4456899999999999999999874 3455555 22 67 899863
No 30
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 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 ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=24.82 E-value=1e+02 Score=25.14 Aligned_cols=39 Identities=18% Similarity=0.299 Sum_probs=33.6
Q ss_pred hhHHHHHHHHhhccCC-CCccCCHHHHHHHHHHHHHHhhh
Q 030512 64 PDDLVASILSKVNQSD-GGVSLAKEEHKEVAEVAQELQKY 102 (176)
Q Consensus 64 ~~~Lk~~LL~aIagtd-RG~~aS~e~r~~V~~~i~qLE~~ 102 (176)
++.|..++.+.+.... .+...++++++++.+++++|+++
T Consensus 100 VEGlL~~i~~~L~~~~~~~~~~~~e~~~~~~~~i~~L~~~ 139 (161)
T PF03367_consen 100 VEGLLMRIIDNLERLQPERDSDDPEEKEKIEEFIEKLDEL 139 (161)
T ss_dssp HHHHHHHHHHHHHTTHHCCCHH-HHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHhhhhccccCCHHHHHHHHHHHHHHHHH
Confidence 8889888888888874 57788999999999999999987
No 31
>PRK10363 cpxP periplasmic repressor CpxP; Reviewed
Probab=24.53 E-value=72 Score=26.80 Aligned_cols=22 Identities=18% Similarity=0.436 Sum_probs=18.6
Q ss_pred CCCccCCHHHHHHHHHHHHHHh
Q 030512 79 DGGVSLAKEEHKEVAEVAQELQ 100 (176)
Q Consensus 79 dRG~~aS~e~r~~V~~~i~qLE 100 (176)
=+|+.+|++||++|.++..+=.
T Consensus 46 F~gLdLTdaQRqQmRdLm~~~r 67 (166)
T PRK10363 46 FDGISLTEHQRQQMRDLMQQAR 67 (166)
T ss_pred ccCCCCCHHHHHHHHHHHHHHH
Confidence 4789999999999999985543
No 32
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=23.99 E-value=71 Score=26.01 Aligned_cols=17 Identities=12% Similarity=0.315 Sum_probs=15.8
Q ss_pred cCCHHHHHHHHHHHHHH
Q 030512 83 SLAKEEHKEVAEVAQEL 99 (176)
Q Consensus 83 ~aS~e~r~~V~~~i~qL 99 (176)
..|++.|++|.++|++|
T Consensus 3 ~Vs~~Tr~rV~~~a~el 19 (309)
T PRK11041 3 KVSQATRQRVEQAVLEV 19 (309)
T ss_pred cCCHHHHHHHHHHHHHH
Confidence 37999999999999999
No 33
>COG3590 PepO Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]
Probab=23.40 E-value=60 Score=32.53 Aligned_cols=46 Identities=15% Similarity=0.363 Sum_probs=36.0
Q ss_pred cCCcccCChhHHHHHHHHhhccCCCCcc-CCHHHHHHHHHHHHHHhhhCC
Q 030512 56 SSPDLRTGPDDLVASILSKVNQSDGGVS-LAKEEHKEVAEVAQELQKYCV 104 (176)
Q Consensus 56 ~~p~~~~~~~~Lk~~LL~aIagtdRG~~-aS~e~r~~V~~~i~qLE~~np 104 (176)
++|+.+++.++|++.|.++..-.=.-+. +|||.|++ ++++|++..|
T Consensus 349 Fpp~aKa~m~~lVa~l~~ayk~Ri~~ldWmtpeTrek---Al~KL~~ft~ 395 (654)
T COG3590 349 FPPEAKADMEELVANLIKAYKARISKLDWMTPETREK---ALEKLNKFTA 395 (654)
T ss_pred CChHHHHHHHHHHHHHHHHHHHHhhhccccCHHHHHH---HHHHHhcccc
Confidence 5799999999999999988765533333 89999975 6788888876
No 34
>TIGR03176 AllC allantoate amidohydrolase. This enzyme catalyzes the breakdown of allantoate, first to ureidoglycine by hydrolysis and then decarboxylation of one of the two equivalent ureido groups. Ureidoglycine then spontaneously exchanges ammonia for water resulting in ureidoglycolate. This enzyme is an alternative to allantoicase (3.5.3.4) which releases urea.
Probab=23.17 E-value=1.6e+02 Score=26.45 Aligned_cols=56 Identities=16% Similarity=0.216 Sum_probs=39.2
Q ss_pred ccCCHHHHHHHHHHHHHHhhhCC---CCCCCCCCccceEE--------EEEecCCCC--CCCCccccccee
Q 030512 82 VSLAKEEHKEVAEVAQELQKYCV---EAPVKCPLIFGEWD--------VVYCSVPTS--PGGGYRSAFGRL 139 (176)
Q Consensus 82 ~~aS~e~r~~V~~~i~qLE~~np---p~Pl~spLL~G~W~--------LlYTSs~~~--~GG~~Rs~lgR~ 139 (176)
+..|++++++-+-+.+++++.+- -+..- =|+|.|+ |+..|=-.+ .||.|...+|.+
T Consensus 26 ~~~s~~~~~a~~~~~~~~~~~Gl~v~~D~~g--N~~~~~~g~~~~~~~i~~gsHlDtv~~gG~~dg~~Gv~ 94 (406)
T TIGR03176 26 LLYSPEWLAAQQQFKKRMAESGLETRFDDVG--NLYGRLVGTEFPEETILTGSHIDTVVNGGNLDGQFGAL 94 (406)
T ss_pred eeCCHHHHHHHHHHHHHHHHcCCEEEEcCCC--cEEEEecCCCCCCCeEEEeccccCCCCCCccCchhhHH
Confidence 34899999999999999999875 23332 3555553 333333333 788999999986
No 35
>cd01395 HMT_MBD Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated transcriptional repression. SETDB1 and other proteins in this group have a similar domain architecture. SETDB1 is a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins.
Probab=23.05 E-value=21 Score=25.26 Aligned_cols=47 Identities=19% Similarity=0.270 Sum_probs=34.7
Q ss_pred CCCCCCccceEEEEEecCCCCCC--CCcccccceeeeeecceEEEeeCC
Q 030512 107 PVKCPLIFGEWDVVYCSVPTSPG--GGYRSAFGRLFFKTKEMIQAVEAP 153 (176)
Q Consensus 107 Pl~spLL~G~W~LlYTSs~~~~G--G~~Rs~lgR~lfk~~ei~Q~I~~p 153 (176)
||.-||+.|==+..++.+.+... -.||+|=||.|=...|+.|.++.-
T Consensus 1 PL~~Pll~gw~R~~~~~~~~~~k~~V~Y~aPCGr~Lr~~~EV~~YL~~t 49 (60)
T cd01395 1 PLHTPLLCGFQRMKYRARVGKVKKHVIYKAPCGRSLRNMSEVHRYLRET 49 (60)
T ss_pred CcccccccCeEEEEEeccCCCcccceEEECCcchhhhcHHHHHHHHHhc
Confidence 88899999977888877653211 279999999888888877665543
No 36
>PF06769 Plasmid_Txe: Plasmid encoded toxin Txe; InterPro: IPR009614 The Axe-Txe pair in Enterococcus faecium (Streptococcus faecium) and the homologous YefM-YoeB pair in Escherichia coli have been shown to act as an antitoxin-toxin pair. This family describes the toxin component. Nearly every example found is next to an identifiable antitoxin, as indicated by match to IPR006442 from INTERPRO [].; GO: 0004519 endonuclease activity, 0006401 RNA catabolic process; PDB: 3OEI_L 2A6R_F 2A6Q_E 2A6S_D.
Probab=22.25 E-value=1.4e+02 Score=21.94 Aligned_cols=31 Identities=23% Similarity=0.521 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHHhhh---CC--CCCCCCCCccceE
Q 030512 86 KEEHKEVAEVAQELQKY---CV--EAPVKCPLIFGEW 117 (176)
Q Consensus 86 ~e~r~~V~~~i~qLE~~---np--p~Pl~spLL~G~W 117 (176)
+.-.+.|.++|.+|... +. ||||+.. +.|-|
T Consensus 17 ~kl~kki~~li~~i~r~P~~G~gkpE~Lk~~-~~g~~ 52 (80)
T PF06769_consen 17 KKLLKKINKLIKEIKRNPFTGIGKPEPLKGD-LSGYW 52 (80)
T ss_dssp HHHHHHHHHHHHHHHHSTTSSTT--EE-SGG-GTTEE
T ss_pred HHHHHHHHHHHHHHHhcccCCCCCCcccccC-CCCeE
Confidence 45678899999999773 11 6777654 44444
No 37
>PRK12751 cpxP periplasmic stress adaptor protein CpxP; Reviewed
Probab=21.79 E-value=86 Score=25.87 Aligned_cols=19 Identities=11% Similarity=0.557 Sum_probs=17.2
Q ss_pred CCccCCHHHHHHHHHHHHH
Q 030512 80 GGVSLAKEEHKEVAEVAQE 98 (176)
Q Consensus 80 RG~~aS~e~r~~V~~~i~q 98 (176)
+|+.+|++||++|-++..+
T Consensus 53 ~~l~LTd~QR~qmr~im~~ 71 (162)
T PRK12751 53 DGINLTEQQRQQMRDLMRQ 71 (162)
T ss_pred ccCCCCHHHHHHHHHHHHH
Confidence 6899999999999998766
No 38
>PF02482 Ribosomal_S30AE: Sigma 54 modulation protein / S30EA ribosomal protein; InterPro: IPR003489 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the sigma-54 modulation protein family and the S30Ae family of ribosomal proteins which includes the light-repressed protein (lrtA) [].; GO: 0005488 binding, 0044238 primary metabolic process; PDB: 1L4S_A 1VOX_a 1VOV_a 3V2E_Y 3V2C_Y 1N3G_A 1VOS_a 1VOZ_a 1VOQ_a 1IMU_A ....
Probab=21.31 E-value=98 Score=21.68 Aligned_cols=27 Identities=11% Similarity=0.239 Sum_probs=21.5
Q ss_pred CCCCccCCHHHHHHHHHHHHHHhhhCC
Q 030512 78 SDGGVSLAKEEHKEVAEVAQELQKYCV 104 (176)
Q Consensus 78 tdRG~~aS~e~r~~V~~~i~qLE~~np 104 (176)
+.|++.+|++-++.|.+-+.+|+++.+
T Consensus 5 ~~~~~~~t~~l~~~i~~kl~kl~~~~~ 31 (97)
T PF02482_consen 5 TGRNFELTDALREYIEEKLEKLERFFD 31 (97)
T ss_dssp EECSS---HHHHHHHHHHHHHHHTTSS
T ss_pred EEEcccCCHHHHHHHHHHHHHHHhhcC
Confidence 358899999999999999999999875
No 39
>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]
Probab=20.96 E-value=1.6e+02 Score=27.67 Aligned_cols=45 Identities=16% Similarity=0.285 Sum_probs=38.1
Q ss_pred HHhhccC--CCCccCCHHHHHHHHHHHHHHhhhCCCCCCCCCCccceEEEEEecCC
Q 030512 72 LSKVNQS--DGGVSLAKEEHKEVAEVAQELQKYCVEAPVKCPLIFGEWDVVYCSVP 125 (176)
Q Consensus 72 L~aIagt--dRG~~aS~e~r~~V~~~i~qLE~~npp~Pl~spLL~G~W~LlYTSs~ 125 (176)
++||-|. |-|+--..|-+.-.+++|.||..+.| -||-+|++.|+.
T Consensus 279 idaiggarfddg~ggdnevqrtmleli~qldgfdp---------rgnikvlmatnr 325 (435)
T KOG0729|consen 279 IDAIGGARFDDGAGGDNEVQRTMLELINQLDGFDP---------RGNIKVLMATNR 325 (435)
T ss_pred cccccCccccCCCCCcHHHHHHHHHHHHhccCCCC---------CCCeEEEeecCC
Confidence 4677777 88999899999999999999998876 388899988765
No 40
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=20.96 E-value=1.5e+02 Score=24.89 Aligned_cols=18 Identities=11% Similarity=0.154 Sum_probs=16.4
Q ss_pred cCCHHHHHHHHHHHHHHh
Q 030512 83 SLAKEEHKEVAEVAQELQ 100 (176)
Q Consensus 83 ~aS~e~r~~V~~~i~qLE 100 (176)
..|++.|++|.+++++|.
T Consensus 27 ~Vs~~tr~rV~~~a~elg 44 (343)
T PRK10727 27 KASEASRLAVHSAMESLS 44 (343)
T ss_pred CCCHHHHHHHHHHHHHHC
Confidence 489999999999999984
No 41
>PF07095 IgaA: Intracellular growth attenuator protein IgaA; InterPro: IPR010771 This family consists of several bacterial intracellular growth attenuator (IgaA) proteins. IgaA is involved in negative control of bacterial proliferation within fibroblasts. IgaA is homologous to the Escherichia coli YrfF and Proteus mirabilis UmoB proteins. Whereas the biological function of YrfF is currently unknown, UmoB has been shown elsewhere to act as a positive regulator of FlhDC, the master regulator of flagella and swarming. FlhDC has been shown to repress cell division during P. mirabilis swarming, suggesting that UmoB could repress cell division via FlhDC. This biological function, if maintained in Salmonella enterica, could sustain a putative negative control of cell division and growth exerted by IgaA in intracellular bacteria [].; GO: 0009276 Gram-negative-bacterium-type cell wall, 0016021 integral to membrane
Probab=20.91 E-value=2.9e+02 Score=28.20 Aligned_cols=91 Identities=18% Similarity=0.108 Sum_probs=54.2
Q ss_pred ccCCHHHHHHHHHHHHHHhhh-CCCCCCC------CCCccceEEEEEecCCCC--------CCCCcccccceeeeee-cc
Q 030512 82 VSLAKEEHKEVAEVAQELQKY-CVEAPVK------CPLIFGEWDVVYCSVPTS--------PGGGYRSAFGRLFFKT-KE 145 (176)
Q Consensus 82 ~~aS~e~r~~V~~~i~qLE~~-npp~Pl~------spLL~G~W~LlYTSs~~~--------~GG~~Rs~lgR~lfk~-~e 145 (176)
+++|+|+|++|..-+.++.+. ++|.|.. .+-+..+=+-+||=.... -...+|=.||-.=+.+ -.
T Consensus 44 RKLt~eEr~aIe~YL~~~~~~~~~~~~s~~~~~~~~~~l~~qs~~Vy~vt~aItRygl~td~~n~WRYylD~vEVhLP~~ 123 (705)
T PF07095_consen 44 RKLTAEERQAIEQYLNQLNKSQQTPKPSGSSSAPQKLALTLQSDNVYTVTHAITRYGLATDDPNKWRYYLDSVEVHLPPF 123 (705)
T ss_pred CCCCHHHHHHHHHHHHHhhhccCCCCCCccccCccCccccCCCCeEEEeecceEeeeccCCCCccceeeeCcEEEECChH
Confidence 458999999999999988876 4455542 223334444566644422 1224554444332222 22
Q ss_pred eEEEeeCCceEeEEEEEEEecceeeEEEeeC
Q 030512 146 MIQAVEAPDTVRNKVSFTALGFLDGEVSLKA 176 (176)
Q Consensus 146 i~Q~I~~p~~V~N~Vef~~~g~L~G~Vsl~g 176 (176)
..|.|... |.||+----.++=.|||+|
T Consensus 124 wEqyI~~~----N~vElI~T~slPLVIsLNG 150 (705)
T PF07095_consen 124 WEQYIAQE----NVVELIKTDSLPLVISLNG 150 (705)
T ss_pred HHHHhccc----CeEEEEEeCCccEEEEecc
Confidence 34666555 7788876666777888877
No 42
>TIGR02574 stabl_TIGR02574 putative addiction module component, TIGR02574 family. Members of this family are bacterial proteins, typically are about 75 amino acids long, always found as part of a pair (at least) of two small genes. The other in the pair always belongs to a subfamily of the larger family pfam05016 (although not necessarily scoring above the designated cutoff), which contains plasmid stabilization proteins. It is likely that this protein and its pfam05016 member partner comprise some form of addiction module, although these gene pairs usually are found on the bacterial main chromosome.
Probab=20.00 E-value=2.9e+02 Score=18.88 Aligned_cols=38 Identities=13% Similarity=0.191 Sum_probs=29.5
Q ss_pred hhHHHHHHHHhhccCCCCccCCHHHHHHHHHHHHHHhh
Q 030512 64 PDDLVASILSKVNQSDGGVSLAKEEHKEVAEVAQELQK 101 (176)
Q Consensus 64 ~~~Lk~~LL~aIagtdRG~~aS~e~r~~V~~~i~qLE~ 101 (176)
.-.|++.|++.|..-+-....++.++++.++=.+.+++
T Consensus 8 Rl~Lve~LwdSL~~~~~~~~~~~~~~~el~~R~~~~~~ 45 (63)
T TIGR02574 8 RIQLVEDIWDSIAAEAKHLILTEAQKAELDRRLADYKA 45 (63)
T ss_pred HHHHHHHHHHHhccCcccCCCCHHHHHHHHHHHHHHHc
Confidence 44688899999998777888888888887776666554
Done!