Query 026941 Match_columns 230 No_of_seqs 126 out of 157 Neff 3.4 Searched_HMMs 46136 Date Fri Mar 29 02:46:31 2013 Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026941.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026941hhsearch_cdd -cpu 12 -v 0 No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PF09788 Tmemb_55A: Transmembr 99.5 1.4E-13 3E-18 123.9 9.2 114 63-177 64-195 (256) 2 TIGR01053 LSD1 zinc finger dom 99.3 9.8E-13 2.1E-17 84.9 2.2 30 103-132 1-30 (31) 3 PF06943 zf-LSD1: LSD1 zinc fi 99.3 2.4E-12 5.3E-17 79.9 2.2 25 106-130 1-25 (25) 4 TIGR01053 LSD1 zinc finger dom 99.3 2.5E-12 5.5E-17 83.0 2.3 31 141-171 1-31 (31) 5 PF06943 zf-LSD1: LSD1 zinc fi 99.2 9E-12 1.9E-16 77.4 2.5 25 144-168 1-25 (25) 6 KOG4684 Uncharacterized conser 99.0 6.4E-10 1.4E-14 99.9 5.2 113 64-177 80-207 (275) 7 KOG1546 Metacaspase involved i 95.0 0.025 5.3E-07 54.0 3.9 30 141-172 4-33 (362) 8 PF10122 Mu-like_Com: Mu-like 94.4 0.023 5E-07 40.9 1.6 33 140-172 3-37 (51) 9 PF10122 Mu-like_Com: Mu-like 94.2 0.021 4.6E-07 41.1 1.1 34 102-135 3-38 (51) 10 PF09788 Tmemb_55A: Transmembr 94.0 0.12 2.7E-06 47.5 5.9 92 35-135 65-191 (256) 11 PF11331 DUF3133: Protein of u 92.9 0.11 2.4E-06 36.5 2.9 38 79-116 3-44 (46) 12 PF01667 Ribosomal_S27e: Ribos 92.2 0.13 2.9E-06 37.3 2.6 40 121-161 7-46 (55) 13 PTZ00083 40S ribosomal protein 91.6 0.31 6.6E-06 38.5 4.2 38 82-121 35-72 (85) 14 PLN00209 ribosomal protein S27 91.5 0.3 6.5E-06 38.6 4.1 39 82-122 36-74 (86) 15 TIGR02098 MJ0042_CXXC MJ0042 f 91.5 0.23 5E-06 32.0 2.9 30 122-151 3-35 (38) 16 PRK00415 rps27e 30S ribosomal 91.2 0.19 4.2E-06 37.1 2.6 37 121-158 11-47 (59) 17 PF13719 zinc_ribbon_5: zinc-r 91.1 0.24 5.2E-06 32.6 2.7 27 142-168 3-34 (37) 18 PF13719 zinc_ribbon_5: zinc-r 90.6 0.26 5.6E-06 32.4 2.6 30 122-151 3-35 (37) 19 PRK14890 putative Zn-ribbon RN 89.8 0.34 7.3E-06 35.9 2.8 52 101-168 5-57 (59) 20 KOG1779 40s ribosomal protein 89.4 0.66 1.4E-05 36.5 4.3 39 82-122 34-72 (84) 21 COG2051 RPS27A Ribosomal prote 89.0 0.67 1.5E-05 35.2 4.0 35 122-157 20-54 (67) 22 PF11331 DUF3133: Protein of u 89.0 0.43 9.4E-06 33.6 2.8 37 117-153 2-43 (46) 23 PRK00398 rpoP DNA-directed RNA 88.5 0.59 1.3E-05 31.5 3.1 28 141-168 3-30 (46) 24 PRK00398 rpoP DNA-directed RNA 88.1 0.85 1.8E-05 30.8 3.7 25 104-128 4-28 (46) 25 PLN00209 ribosomal protein S27 87.7 0.49 1.1E-05 37.4 2.7 19 141-159 55-73 (86) 26 PF13717 zinc_ribbon_4: zinc-r 87.3 0.87 1.9E-05 29.9 3.3 14 122-135 3-16 (36) 27 PF13717 zinc_ribbon_4: zinc-r 86.0 0.92 2E-05 29.8 2.9 28 141-168 2-34 (36) 28 PTZ00083 40S ribosomal protein 85.7 0.93 2E-05 35.8 3.2 45 121-166 35-79 (85) 29 PF01667 Ribosomal_S27e: Ribos 85.5 0.83 1.8E-05 33.3 2.7 38 82-121 7-44 (55) 30 PRK00415 rps27e 30S ribosomal 84.2 0.66 1.4E-05 34.3 1.7 34 83-118 12-45 (59) 31 KOG1779 40s ribosomal protein 83.9 1.3 2.9E-05 34.8 3.4 39 122-161 35-73 (84) 32 TIGR02098 MJ0042_CXXC MJ0042 f 83.7 2.3 4.9E-05 27.3 3.9 29 141-169 2-35 (38) 33 PF04690 YABBY: YABBY protein; 82.5 2.3 5.1E-05 37.0 4.7 35 137-171 8-48 (170) 34 COG2888 Predicted Zn-ribbon RN 80.4 1.9 4E-05 32.3 2.8 50 104-168 10-59 (61) 35 PF11023 DUF2614: Protein of u 78.3 1.1 2.4E-05 37.1 1.2 15 81-95 68-82 (114) 36 COG2051 RPS27A Ribosomal prote 78.0 2.7 5.9E-05 31.9 3.1 37 82-120 19-55 (67) 37 PRK14714 DNA polymerase II lar 77.7 1.9 4.1E-05 47.4 3.1 56 99-168 663-718 (1337) 38 PRK02935 hypothetical protein; 77.6 1.5 3.2E-05 36.1 1.8 33 119-155 68-100 (110) 39 KOG4684 Uncharacterized conser 77.6 4.6 9.9E-05 37.3 5.0 30 119-148 78-107 (275) 40 PRK14890 putative Zn-ribbon RN 74.6 2.8 6.2E-05 31.1 2.4 53 61-130 4-57 (59) 41 PF12773 DZR: Double zinc ribb 73.2 1.4 3E-05 29.6 0.5 38 85-130 1-38 (50) 42 PF04690 YABBY: YABBY protein; 72.9 3.3 7.1E-05 36.1 2.8 48 98-159 7-54 (170) 43 COG4856 Uncharacterized protei 71.9 3.6 7.8E-05 40.2 3.1 65 16-80 5-89 (403) 44 PRK14873 primosome assembly pr 70.0 7.4 0.00016 39.8 5.0 67 68-155 368-436 (665) 45 PRK05580 primosome assembly pr 69.9 7.5 0.00016 39.4 4.9 67 71-156 368-436 (679) 46 TIGR00595 priA primosomal prot 68.3 9.4 0.0002 37.4 5.1 66 72-156 201-268 (505) 47 PF12773 DZR: Double zinc ribb 68.1 2.6 5.5E-05 28.3 0.9 40 124-170 1-40 (50) 48 smart00661 RPOL9 RNA polymeras 64.3 7.7 0.00017 25.9 2.7 29 144-172 3-33 (52) 49 COG4416 Com Mu-like prophage p 61.2 2.2 4.7E-05 31.7 -0.5 30 103-132 4-35 (60) 50 PF05495 zf-CHY: CHY zinc fing 60.3 12 0.00026 27.6 3.3 30 138-167 38-69 (71) 51 PF04810 zf-Sec23_Sec24: Sec23 60.2 7.6 0.00017 25.8 2.0 18 155-172 20-37 (40) 52 PRK14873 primosome assembly pr 59.2 9.2 0.0002 39.1 3.3 48 108-167 369-418 (665) 53 PRK05580 primosome assembly pr 58.3 12 0.00025 38.1 3.9 50 111-171 369-420 (679) 54 COG1198 PriA Primosomal protei 57.5 23 0.0005 37.0 5.9 63 69-150 420-484 (730) 55 KOG3267 Uncharacterized conser 57.4 1.6 3.4E-05 36.6 -2.0 51 4-61 11-61 (138) 56 PRK14559 putative protein seri 56.1 6.7 0.00015 40.1 1.8 36 83-131 2-37 (645) 57 PHA03030 hypothetical protein; 55.5 6.3 0.00014 32.7 1.2 13 25-37 10-22 (122) 58 PF07754 DUF1610: Domain of un 55.2 10 0.00022 23.5 1.9 21 145-166 2-23 (24) 59 PRK14714 DNA polymerase II lar 52.8 9.7 0.00021 42.2 2.4 40 105-152 681-720 (1337) 60 KOG1546 Metacaspase involved i 51.7 5.9 0.00013 38.3 0.5 29 104-134 5-33 (362) 61 PF07191 zinc-ribbons_6: zinc- 51.7 22 0.00047 27.2 3.5 57 104-169 2-60 (70) 62 PF12113 SVM_signal: SVM prote 50.1 6.3 0.00014 26.3 0.3 26 13-38 2-27 (33) 63 COG1096 Predicted RNA-binding 50.1 13 0.00029 33.1 2.4 29 138-168 146-174 (188) 64 COG4416 Com Mu-like prophage p 49.3 5.3 0.00011 29.7 -0.1 34 61-94 1-36 (60) 65 KOG2824 Glutaredoxin-related p 48.8 28 0.0006 32.8 4.4 11 79-89 237-247 (281) 66 COG4357 Zinc finger domain con 48.1 3.7 8E-05 33.5 -1.2 29 101-129 60-88 (105) 67 TIGR00595 priA primosomal prot 47.8 18 0.0004 35.4 3.3 42 119-171 211-252 (505) 68 COG4357 Zinc finger domain con 47.4 4.6 9.9E-05 33.0 -0.8 27 64-90 62-88 (105) 69 COG1198 PriA Primosomal protei 46.4 21 0.00046 37.3 3.6 52 110-172 422-475 (730) 70 PF09297 zf-NADH-PPase: NADH p 46.4 17 0.00036 22.8 1.9 25 143-167 5-29 (32) 71 TIGR01206 lysW lysine biosynth 45.7 23 0.00051 25.5 2.7 13 159-171 22-34 (54) 72 smart00661 RPOL9 RNA polymeras 45.4 22 0.00047 23.7 2.4 10 121-130 20-29 (52) 73 PF15616 TerY-C: TerY-C metal 43.2 34 0.00073 28.8 3.7 34 99-134 85-118 (131) 74 PF05129 Elf1: Transcription e 42.9 25 0.00053 26.9 2.7 38 120-157 21-62 (81) 75 TIGR00155 pqiA_fam integral me 41.5 23 0.00051 34.0 2.9 26 143-168 15-42 (403) 76 smart00659 RPOLCX RNA polymera 40.3 31 0.00068 23.7 2.6 29 123-154 4-32 (44) 77 COG1096 Predicted RNA-binding 39.6 25 0.00055 31.3 2.6 28 101-130 147-174 (188) 78 PF11023 DUF2614: Protein of u 39.0 13 0.00029 30.8 0.7 29 122-154 70-98 (114) 79 PRK04023 DNA polymerase II lar 38.7 18 0.00038 39.6 1.7 53 100-171 623-675 (1121) 80 PF04216 FdhE: Protein involve 38.4 49 0.0011 29.9 4.3 65 83-151 173-248 (290) 81 PF02591 DUF164: Putative zinc 37.9 28 0.0006 24.2 2.1 25 143-167 24-54 (56) 82 PF14369 zf-RING_3: zinc-finge 36.5 30 0.00064 22.7 1.9 24 66-89 4-28 (35) 83 COG1996 RPC10 DNA-directed RNA 35.4 26 0.00057 25.1 1.6 32 63-94 5-36 (49) 84 KOG3002 Zn finger protein [Gen 32.9 18 0.00039 33.8 0.6 62 82-153 48-122 (299) 85 PRK07219 DNA topoisomerase I; 32.4 85 0.0018 32.9 5.4 28 64-91 602-635 (822) 86 PF09082 DUF1922: Domain of un 31.4 46 0.00099 25.4 2.4 30 141-172 3-32 (68) 87 PF03604 DNA_RNApol_7kD: DNA d 31.4 19 0.00042 23.4 0.4 27 124-153 3-29 (32) 88 COG1996 RPC10 DNA-directed RNA 30.7 52 0.0011 23.6 2.5 32 140-171 5-36 (49) 89 PF10571 UPF0547: Uncharacteri 30.5 24 0.00053 21.9 0.7 10 158-167 13-22 (26) 90 PRK02935 hypothetical protein; 30.1 35 0.00075 28.3 1.7 34 79-117 67-100 (110) 91 PF12172 DUF35_N: Rubredoxin-l 29.3 31 0.00066 22.1 1.1 21 104-128 12-32 (37) 92 PRK14892 putative transcriptio 28.8 59 0.0013 26.0 2.8 11 157-167 40-50 (99) 93 PRK15103 paraquat-inducible me 28.7 41 0.00089 32.6 2.3 13 122-134 11-23 (419) 94 COG1579 Zn-ribbon protein, pos 28.0 29 0.00063 31.7 1.1 12 156-167 218-229 (239) 95 TIGR01384 TFS_arch transcripti 26.9 44 0.00096 25.5 1.8 27 143-171 2-28 (104) 96 COG2023 RPR2 RNase P subunit R 26.9 40 0.00087 27.6 1.6 35 138-172 53-95 (105) 97 PF00541 Adeno_knob: Adenovira 26.8 60 0.0013 28.3 2.7 27 33-59 45-71 (171) 98 PF02150 RNA_POL_M_15KD: RNA p 26.6 31 0.00067 22.5 0.7 28 144-171 4-32 (35) 99 KOG2824 Glutaredoxin-related p 26.6 87 0.0019 29.6 3.9 49 104-166 230-280 (281) 100 PRK03564 formate dehydrogenase 26.4 1.1E+02 0.0025 28.9 4.7 45 81-129 186-234 (309) 101 PRK04351 hypothetical protein; 26.4 52 0.0011 27.7 2.3 14 140-153 131-144 (149) 102 PF07191 zinc-ribbons_6: zinc- 26.3 1.6E+02 0.0035 22.5 4.7 59 64-132 1-61 (70) 103 smart00731 SprT SprT homologue 26.2 76 0.0016 25.8 3.1 32 83-114 113-144 (146) 104 PF06589 CRA: Circumsporozoite 26.1 33 0.00071 29.7 1.0 14 26-40 7-20 (157) 105 TIGR01562 FdhE formate dehydro 25.9 1.1E+02 0.0024 28.8 4.5 61 85-149 187-260 (305) 106 smart00647 IBR In Between Ring 25.5 76 0.0016 21.3 2.6 21 108-128 25-47 (64) 107 PRK11827 hypothetical protein; 25.4 81 0.0018 23.3 2.8 27 104-130 9-35 (60) 108 PF13248 zf-ribbon_3: zinc-rib 25.4 30 0.00065 21.0 0.5 9 122-130 3-11 (26) 109 PF00130 C1_1: Phorbol esters/ 25.3 63 0.0014 21.5 2.1 28 142-170 12-39 (53) 110 PF05458 Siva: Cd27 binding pr 25.3 24 0.00052 30.6 0.0 31 116-149 142-172 (175) 111 PRK03564 formate dehydrogenase 24.8 69 0.0015 30.3 2.9 14 117-130 208-221 (309) 112 PF07295 DUF1451: Protein of u 24.5 76 0.0016 26.9 2.9 30 63-92 111-140 (146) 113 KOG2907 RNA polymerase I trans 23.7 27 0.00058 29.1 0.1 31 104-134 8-38 (116) 114 PF14353 CpXC: CpXC protein 23.2 72 0.0016 25.2 2.4 16 138-153 35-50 (128) 115 PF14803 Nudix_N_2: Nudix N-te 23.2 83 0.0018 20.7 2.3 9 101-109 20-28 (34) 116 PF06677 Auto_anti-p27: Sjogre 23.2 84 0.0018 21.5 2.4 22 143-165 19-40 (41) 117 cd00029 C1 Protein kinase C co 23.0 44 0.00096 21.5 1.0 26 143-169 13-38 (50) 118 KOG3002 Zn finger protein [Gen 22.7 33 0.00072 32.1 0.4 41 120-167 47-88 (299) 119 PF01485 IBR: IBR domain; Int 22.7 62 0.0013 21.7 1.7 26 143-168 20-49 (64) 120 PRK14559 putative protein seri 22.4 52 0.0011 33.9 1.8 51 104-170 2-52 (645) 121 PF12273 RCR: Chitin synthesis 22.1 29 0.00063 27.8 -0.0 15 25-39 11-25 (130) 122 smart00109 C1 Protein kinase C 21.9 44 0.00096 21.2 0.8 25 142-168 12-36 (49) 123 TIGR00100 hypA hydrogenase nic 21.7 68 0.0015 25.6 2.0 28 140-169 69-96 (115) 124 COG5416 Uncharacterized integr 21.6 69 0.0015 26.1 2.0 28 26-53 31-58 (98) 125 PF07282 OrfB_Zn_ribbon: Putat 21.6 1.1E+02 0.0025 21.4 2.9 13 120-132 27-39 (69) 126 TIGR00155 pqiA_fam integral me 21.5 91 0.002 30.1 3.1 34 120-153 12-45 (403) 127 PF08792 A2L_zn_ribbon: A2L zi 21.4 1.3E+02 0.0028 19.6 2.9 25 105-129 5-29 (33) 128 cd00069 GHB Glycoprotein hormo 21.3 76 0.0016 25.8 2.2 44 49-93 31-90 (102) 129 PF14634 zf-RING_5: zinc-RING 21.0 10 0.00023 25.0 -2.4 10 157-166 34-43 (44) 130 PRK04023 DNA polymerase II lar 20.9 59 0.0013 35.8 1.9 9 83-91 639-647 (1121) 131 PF03119 DNA_ligase_ZBD: NAD-d 20.8 70 0.0015 20.0 1.5 21 143-163 1-21 (28) 132 COG2191 Formylmethanofuran deh 20.6 61 0.0013 29.4 1.6 29 82-110 172-200 (206) 133 smart00834 CxxC_CXXC_SSSS Puta 20.1 92 0.002 19.6 2.0 26 65-90 6-34 (41) 134 PF14599 zinc_ribbon_6: Zinc-r 20.0 94 0.002 22.9 2.3 49 45-93 11-59 (61) No 1 >PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction:1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate. Probab=99.48 E-value=1.4e-13 Score=123.89 Aligned_cols=114 Identities=23% Similarity=0.501 Sum_probs=100.5 Q ss_pred ceeeccccceeeeecCCC--CeeecCCCCcccccCCCCCceeEEEeCCcceeEEeecCCCeEeCCC--CCcceecCC--- Q 026941 63 SQLVCSGCRSVLLYPRGA--TNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSVRCSC--CHTVNLAPA--- 135 (230) Q Consensus 63 sQlvC~gCr~lL~YP~GA--~~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~sVrC~~--C~tVn~Vp~--- 135 (230) .-+.|+.|+.++...... -.|+|..|++.|+..++++++.+++|. |+.||+....++.+-|+. |..|....+ T Consensus 64 p~v~CrVCq~~I~i~gk~~QhVVkC~~CnEATPIr~aPpGKKYVRCP-CNCLLICk~sS~rIaCPRp~CkRiI~L~~~~~ 142 (256) T PF09788_consen 64 PVVTCRVCQSLIDIEGKMHQHVVKCSVCNEATPIRNAPPGKKYVRCP-CNCLLICKSSSQRIACPRPNCKRIINLGPSHQ 142 (256) T ss_pred ceEEeecCCceecccCccceeeEECCCCCccccccCCCCCCeeEecC-CceEEEeecccccccCCCCCCcceEEeCCccC Confidence 578999999999998766 369999999999999999999999997 999999999999999996 998875432 Q ss_pred ---------CCceeEEEcCCCCeeeeccCCC--CeEeCCCCCcceeeccCCCC Q 026941 136 ---------PNQFAHIICGHCRTTLMYPHGA--PSVKCAVCQYVTNVNMANAR 177 (230) Q Consensus 136 ---------~~q~a~V~Cg~Crt~LmyP~GA--~sVrCa~C~~VT~V~~~n~R 177 (230) .+.+..++||+|+.+++++.=. ..+||++|++|++|+...+| T Consensus 143 ~p~~~~~~~~p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG~~faR 195 (256) T PF09788_consen 143 GPVTPPVPTQPGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVGPRFAR 195 (256) T ss_pred CCCCCCCCCCCCceeEECCCCCCcEeccCCCCCccccCCCCceeccccchHhh Confidence 2367899999999999999744 67899999999999977776 No 2 >TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC Probab=99.30 E-value=9.8e-13 Score=84.88 Aligned_cols=30 Identities=77% Similarity=1.488 Sum_probs=15.9 Q ss_pred EEEeCCcceeEEeecCCCeEeCCCCCccee Q 026941 103 QLICGGCRTLLMYTRGATSVRCSCCHTVNL 132 (230) Q Consensus 103 qLvCggCr~lL~YP~GA~sVrC~~C~tVn~ 132 (230) |++|++||++|+||+||++|||+.|++||. T Consensus 1 q~~C~~C~t~L~yP~gA~~vrCs~C~~vt~ 30 (31) T TIGR01053 1 QVVCGGCRTLLMYPRGASSVRCALCQTVNL 30 (31) T ss_pred CcCcCCCCcEeecCCCCCeEECCCCCeEec Confidence 345555555555555555555555555543 No 3 >PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers []. Probab=99.26 E-value=2.4e-12 Score=79.90 Aligned_cols=25 Identities=88% Similarity=1.799 Sum_probs=14.1 Q ss_pred eCCcceeEEeecCCCeEeCCCCCcc Q 026941 106 CGGCRTLLMYTRGATSVRCSCCHTV 130 (230) Q Consensus 106 CggCr~lL~YP~GA~sVrC~~C~tV 130 (230) |++||++||||+||++|||+.|++| T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~V 25 (25) T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHTV 25 (25) T ss_pred CCCCCceEEcCCCCCCeECCccCcC Confidence 4555555555555555555555554 No 4 >TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC Probab=99.26 E-value=2.5e-12 Score=82.97 Aligned_cols=31 Identities=61% Similarity=1.243 Sum_probs=29.3 Q ss_pred EEEcCCCCeeeeccCCCCeEeCCCCCcceee Q 026941 141 HIICGHCRTTLMYPHGAPSVKCAVCQYVTNV 171 (230) Q Consensus 141 ~V~Cg~Crt~LmyP~GA~sVrCa~C~~VT~V 171 (230) |++|++||++|+||+||++|||+.|++||.| T Consensus 1 q~~C~~C~t~L~yP~gA~~vrCs~C~~vt~v 31 (31) T TIGR01053 1 QVVCGGCRTLLMYPRGASSVRCALCQTVNLV 31 (31) T ss_pred CcCcCCCCcEeecCCCCCeEECCCCCeEecC Confidence 5799999999999999999999999999975 No 5 >PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers []. Probab=99.20 E-value=9e-12 Score=77.38 Aligned_cols=25 Identities=72% Similarity=1.483 Sum_probs=24.2 Q ss_pred cCCCCeeeeccCCCCeEeCCCCCcc Q 026941 144 CGHCRTTLMYPHGAPSVKCAVCQYV 168 (230) Q Consensus 144 Cg~Crt~LmyP~GA~sVrCa~C~~V 168 (230) |++||++||||+||++|||+.|++| T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~V 25 (25) T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHTV 25 (25) T ss_pred CCCCCceEEcCCCCCCeECCccCcC Confidence 8999999999999999999999986 No 6 >KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only] Probab=98.97 E-value=6.4e-10 Score=99.85 Aligned_cols=113 Identities=21% Similarity=0.475 Sum_probs=94.9 Q ss_pred eeeccccceeeeecCCC--CeeecCCCCcccccCCCCCceeEEEeCCcceeEEeecCCCeEeCC--CCCcceecCC---- Q 026941 64 QLVCSGCRSVLLYPRGA--TNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSVRCS--CCHTVNLAPA---- 135 (230) Q Consensus 64 QlvC~gCr~lL~YP~GA--~~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~sVrC~--~C~tVn~Vp~---- 135 (230) -+.|+.|+.++..-.-- -.|.|..||+.|+..++++...+++|. |+.||+.....+..-|+ .|..|....+ T Consensus 80 mvtCRVCq~~i~~egk~~QHVVKC~~CnEATPIrnAPpGKKYVRCP-CNCLLICK~sSqRIACPRpnCkRiInL~p~~~~ 158 (275) T KOG4684|consen 80 MVTCRVCQVAISLEGKNQQHVVKCHSCNEATPIRNAPPGKKYVRCP-CNCLLICKASSQRIACPRPNCKRIINLDPLIEK 158 (275) T ss_pred eEeehhhhHHhccccccceeeEeecccCccccCCCCCCCCceeecC-CcEEEEEecccceeccCCCCcceeeecCCCCCC Confidence 47899999998874333 369999999999999889999999997 99999999999999998 8988764321 Q ss_pred ------CCceeEEEcCCCCeeeeccC-CCCeEeCCCCCcceeeccCCCC Q 026941 136 ------PNQFAHIICGHCRTTLMYPH-GAPSVKCAVCQYVTNVNMANAR 177 (230) Q Consensus 136 ------~~q~a~V~Cg~Crt~LmyP~-GA~sVrCa~C~~VT~V~~~n~R 177 (230) ++.+-+|.||+|+.++++.. -....+|++|++|.+|+-..+| T Consensus 159 p~~P~~~P~gcRV~CgHC~~tFLfnt~tnaLArCPHCrKvSsvGsrfar 207 (275) T KOG4684|consen 159 PRDPGTAPTGCRVKCGHCNETFLFNTLTNALARCPHCRKVSSVGSRFAR 207 (275) T ss_pred CCCCCCCCcceEEEecCccceeehhhHHHHHhcCCcccchhhhhhHHhh Confidence 24668999999999999985 2367899999999999865554 No 7 >KOG1546 consensus Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones] Probab=95.02 E-value=0.025 Score=53.98 Aligned_cols=30 Identities=33% Similarity=0.724 Sum_probs=28.0 Q ss_pred EEEcCCCCeeeeccCCCCeEeCCCCCcceeec Q 026941 141 HIICGHCRTTLMYPHGAPSVKCAVCQYVTNVN 172 (230) Q Consensus 141 ~V~Cg~Crt~LmyP~GA~sVrCa~C~~VT~V~ 172 (230) .+.|. |+++++.|+||+. +|+.|++||.++ T Consensus 4 ~~~~~-~~~p~~~pp~ar~-q~~~~~~~~~~~ 33 (362) T KOG1546|consen 4 LVGCN-CQRPMAPPPGARY-QCAGCHAVTQIA 33 (362) T ss_pred cccCC-CCCCCCCCCCCcc-cccccceeeeec Confidence 46787 9999999999999 999999999997 No 8 >PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ]. Probab=94.41 E-value=0.023 Score=40.92 Aligned_cols=33 Identities=30% Similarity=0.662 Sum_probs=27.6 Q ss_pred eEEEcCCCCeeeeccC--CCCeEeCCCCCcceeec Q 026941 140 AHIICGHCRTTLMYPH--GAPSVKCAVCQYVTNVN 172 (230) Q Consensus 140 a~V~Cg~Crt~LmyP~--GA~sVrCa~C~~VT~V~ 172 (230) -.++|++|+.+|.--. ....+||+.|.+++.|. T Consensus 3 ~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~ 37 (51) T PF10122_consen 3 KEIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVR 37 (51) T ss_pred cceeccchhHHHhhhcCccEEEEECCCCCccceEe Confidence 3589999999999863 44589999999999996 No 9 >PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ]. Probab=94.20 E-value=0.021 Score=41.12 Aligned_cols=34 Identities=29% Similarity=0.686 Sum_probs=27.2 Q ss_pred eEEEeCCcceeEEeecCC--CeEeCCCCCcceecCC Q 026941 102 AQLICGGCRTLLMYTRGA--TSVRCSCCHTVNLAPA 135 (230) Q Consensus 102 ~qLvCggCr~lL~YP~GA--~sVrC~~C~tVn~Vp~ 135 (230) ..++|++|+.+|+.--++ ..++||.|.++|.+.. T Consensus 3 ~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a 38 (51) T PF10122_consen 3 KEIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRA 38 (51) T ss_pred cceeccchhHHHhhhcCccEEEEECCCCCccceEec Confidence 468899999999885444 4889999999998764 No 10 >PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction:1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate. Probab=94.02 E-value=0.12 Score=47.48 Aligned_cols=92 Identities=26% Similarity=0.500 Sum_probs=59.0 Q ss_pred hhcceeeEEEEeeeecCCcccccCcCccceeeccccceeeee---cCCCCeeecC-----------------C--C-Ccc Q 026941 35 YINHTITQLSIDFDFSNDSILLSLQGMQSQLVCSGCRSVLLY---PRGATNVCCA-----------------L--C-NTI 91 (230) Q Consensus 35 ~~~~~~~~~~~~~~f~~~~~l~~~~~mqsQlvC~gCr~lL~Y---P~GA~~VrCa-----------------~--C-~tV 91 (230) .|+-.+=|-.||++=..+ |--..|..|.+---. |.|-..|||+ + | ..| T Consensus 65 ~v~CrVCq~~I~i~gk~~---------QhVVkC~~CnEATPIr~aPpGKKYVRCPCNCLLICk~sS~rIaCPRp~CkRiI 135 (256) T PF09788_consen 65 VVTCRVCQSLIDIEGKMH---------QHVVKCSVCNEATPIRNAPPGKKYVRCPCNCLLICKSSSQRIACPRPNCKRII 135 (256) T ss_pred eEEeecCCceecccCccc---------eeeEECCCCCccccccCCCCCCeeEecCCceEEEeecccccccCCCCCCcceE Confidence 345566677777764433 344556656553332 4455555554 4 6 334 Q ss_pred cccCC---C-------CCceeEEEeCCcceeEEeecCC--CeEeCCCCCcceecCC Q 026941 92 TSVPI---P-------GMEMAQLICGGCRTLLMYTRGA--TSVRCSCCHTVNLAPA 135 (230) Q Consensus 92 t~Vpp---~-------~~q~~qLvCggCr~lL~YP~GA--~sVrC~~C~tVn~Vp~ 135 (230) |..+. | ...+--++||+|+...+++.=. +..|||.|+.|++|.. T Consensus 136 ~L~~~~~~p~~~~~~~~p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG~ 191 (256) T PF09788_consen 136 NLGPSHQGPVTPPVPTQPGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVGP 191 (256) T ss_pred EeCCccCCCCCCCCCCCCCceeEECCCCCCcEeccCCCCCccccCCCCceeccccc Confidence 44432 1 2357889999999999999755 6789999999999853 No 11 >PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function. Probab=92.90 E-value=0.11 Score=36.54 Aligned_cols=38 Identities=29% Similarity=0.693 Sum_probs=25.6 Q ss_pred CCCeeecCCCCcccccCCC----CCceeEEEeCCcceeEEee Q 026941 79 GATNVCCALCNTITSVPIP----GMEMAQLICGGCRTLLMYT 116 (230) Q Consensus 79 GA~~VrCa~C~tVt~Vpp~----~~q~~qLvCggCr~lL~YP 116 (230) ||+.|-|..|..+-.+|.. .....+|.||.|-.+|.|. T Consensus 3 GAPFv~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl~~s 44 (46) T PF11331_consen 3 GAPFVVCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVLSFS 44 (46) T ss_pred CCCEeECccHHHHHcCCCccCCCccceeEEeCCCCceeEEEe Confidence 6677777777666666432 2236788888888888774 No 12 >PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b. Probab=92.21 E-value=0.13 Score=37.35 Aligned_cols=40 Identities=25% Similarity=0.467 Sum_probs=25.6 Q ss_pred eEeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCCeEe Q 026941 121 SVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVK 161 (230) Q Consensus 121 sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~sVr 161 (230) .|+|+.|..++.|=+-++. .|.|..|.+.|.-|.|-.+-- T Consensus 7 ~VkCp~C~~~q~vFSha~t-~V~C~~Cg~~L~~PtGGKa~l 46 (55) T PF01667_consen 7 DVKCPGCYNIQTVFSHAQT-VVKCVVCGTVLAQPTGGKARL 46 (55) T ss_dssp EEE-TTT-SEEEEETT-SS--EE-SSSTSEEEEE-SSSEEE T ss_pred EEECCCCCCeeEEEecCCe-EEEcccCCCEecCCCCcCeEE Confidence 5888888888877554444 788999999998888865543 No 13 >PTZ00083 40S ribosomal protein S27; Provisional Probab=91.57 E-value=0.31 Score=38.45 Aligned_cols=38 Identities=32% Similarity=0.680 Sum_probs=20.5 Q ss_pred eeecCCCCcccccCCCCCceeEEEeCCcceeEEeecCCCe Q 026941 82 NVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATS 121 (230) Q Consensus 82 ~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~s 121 (230) -|+|+.|..++.+= ++....+.|.+|.++|..|.|--. T Consensus 35 ~VkCp~C~n~q~VF--ShA~t~V~C~~Cg~~L~~PTGGKa 72 (85) T PTZ00083 35 DVKCPGCSQITTVF--SHAQTVVLCGGCSSQLCQPTGGKA 72 (85) T ss_pred EEECCCCCCeeEEE--ecCceEEEccccCCEeeccCCCCe Confidence 36666665555552 344455555555555555555443 No 14 >PLN00209 ribosomal protein S27; Provisional Probab=91.55 E-value=0.3 Score=38.57 Aligned_cols=39 Identities=31% Similarity=0.615 Sum_probs=21.8 Q ss_pred eeecCCCCcccccCCCCCceeEEEeCCcceeEEeecCCCeE Q 026941 82 NVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSV 122 (230) Q Consensus 82 ~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~sV 122 (230) -|+|+.|..++.+= ++....+.|.+|.++|..|.|--.. T Consensus 36 ~VkCp~C~n~q~VF--ShA~t~V~C~~Cg~~L~~PTGGKa~ 74 (86) T PLN00209 36 DVKCQGCFNITTVF--SHSQTVVVCGSCQTVLCQPTGGKAR 74 (86) T ss_pred EEECCCCCCeeEEE--ecCceEEEccccCCEeeccCCCCeE Confidence 36666666666552 3444556666666666666654443 No 15 >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=91.50 E-value=0.23 Score=31.97 Aligned_cols=30 Identities=20% Similarity=0.519 Sum_probs=15.9 Q ss_pred EeCCCCCcceecCCC---CceeEEEcCCCCeee Q 026941 122 VRCSCCHTVNLAPAP---NQFAHIICGHCRTTL 151 (230) Q Consensus 122 VrC~~C~tVn~Vp~~---~q~a~V~Cg~Crt~L 151 (230) +.||.|++...++++ ..-..++|++|+..+ T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38) T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38) T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE Confidence 556666666655532 112256666666554 No 16 >PRK00415 rps27e 30S ribosomal protein S27e; Reviewed Probab=91.25 E-value=0.19 Score=37.09 Aligned_cols=37 Identities=24% Similarity=0.464 Sum_probs=21.4 Q ss_pred eEeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCC Q 026941 121 SVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAP 158 (230) Q Consensus 121 sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~ 158 (230) .|+|+.|..++.+=+-.+. .|.|..|.++|.-|.|-. T Consensus 11 ~VkCp~C~n~q~vFsha~t-~V~C~~Cg~~L~~PtGGK 47 (59) T PRK00415 11 KVKCPDCGNEQVVFSHAST-VVRCLVCGKTLAEPTGGK 47 (59) T ss_pred EEECCCCCCeEEEEecCCc-EEECcccCCCcccCCCcc Confidence 3566666666654433333 566666666666666543 No 17 >PF13719 zinc_ribbon_5: zinc-ribbon domain Probab=91.11 E-value=0.24 Score=32.56 Aligned_cols=27 Identities=37% Similarity=0.864 Sum_probs=14.1 Q ss_pred EEcCCCCeeeecc-----CCCCeEeCCCCCcc Q 026941 142 IICGHCRTTLMYP-----HGAPSVKCAVCQYV 168 (230) Q Consensus 142 V~Cg~Crt~LmyP-----~GA~sVrCa~C~~V 168 (230) +.|.+|.+.+-+| .+...|||+.|+.+ T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~ 34 (37) T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHV 34 (37) T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcE Confidence 4455555554443 23456666666654 No 18 >PF13719 zinc_ribbon_5: zinc-ribbon domain Probab=90.62 E-value=0.26 Score=32.40 Aligned_cols=30 Identities=20% Similarity=0.495 Sum_probs=17.1 Q ss_pred EeCCCCCcceecCCC---CceeEEEcCCCCeee Q 026941 122 VRCSCCHTVNLAPAP---NQFAHIICGHCRTTL 151 (230) Q Consensus 122 VrC~~C~tVn~Vp~~---~q~a~V~Cg~Crt~L 151 (230) +.||.|++.-.++++ ..-..++|+.|+... T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37) T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37) T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcEe Confidence 456666666666542 234466666666543 No 19 >PRK14890 putative Zn-ribbon RNA-binding protein; Provisional Probab=89.80 E-value=0.34 Score=35.91 Aligned_cols=52 Identities=25% Similarity=0.571 Sum_probs=40.4 Q ss_pred eeEEEeCCcceeEEeecC-CCeEeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCCeEeCCCCCcc Q 026941 101 MAQLICGGCRTLLMYTRG-ATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYV 168 (230) Q Consensus 101 ~~qLvCggCr~lL~YP~G-A~sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~sVrCa~C~~V 168 (230) +.-.+|..|...| .|.+ +....||.|..+. ..+|..||.. +..++|+.|++. T Consensus 5 ~~~~~CtSCg~~i-~~~~~~~~F~CPnCG~~~---------I~RC~~CRk~------~~~Y~CP~CGF~ 57 (59) T PRK14890 5 MEPPKCTSCGIEI-APREKAVKFLCPNCGEVI---------IYRCEKCRKQ------SNPYTCPKCGFE 57 (59) T ss_pred ccCccccCCCCcc-cCCCccCEeeCCCCCCee---------EeechhHHhc------CCceECCCCCCc Confidence 3445799999988 5666 9999999996553 4579999986 367899999874 No 20 >KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis] Probab=89.41 E-value=0.66 Score=36.49 Aligned_cols=39 Identities=31% Similarity=0.600 Sum_probs=18.2 Q ss_pred eeecCCCCcccccCCCCCceeEEEeCCcceeEEeecCCCeE Q 026941 82 NVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSV 122 (230) Q Consensus 82 ~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~sV 122 (230) .|+|+.|-.||-+= .+...-++|+||.+.|.-|.|-..+ T Consensus 34 ~VkC~gc~~iT~vf--SHaqtvVvc~~c~~il~~~tggra~ 72 (84) T KOG1779|consen 34 DVKCPGCFKITTVF--SHAQTVVVCEGCSTILCQPTGGKAK 72 (84) T ss_pred EEEcCCceEEEEEe--ecCceEEEcCCCceEEEEecCCcEE Confidence 35555555555542 2223344555555555555444443 No 21 >COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis] Probab=89.02 E-value=0.67 Score=35.18 Aligned_cols=35 Identities=29% Similarity=0.533 Sum_probs=15.9 Q ss_pred EeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCC Q 026941 122 VRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGA 157 (230) Q Consensus 122 VrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA 157 (230) |+|+.|.....+=+-++. .++|..|.++|..|.|- T Consensus 20 VkCpdC~N~q~vFshast-~V~C~~CG~~l~~PTGG 54 (67) T COG2051 20 VKCPDCGNEQVVFSHAST-VVTCLICGTTLAEPTGG 54 (67) T ss_pred EECCCCCCEEEEeccCce-EEEecccccEEEecCCC Confidence 445545444433332222 44555555555555543 No 22 >PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function. Probab=89.01 E-value=0.43 Score=33.60 Aligned_cols=37 Identities=32% Similarity=0.659 Sum_probs=25.7 Q ss_pred cCCCeEeCCCCCcceecCCC-----CceeEEEcCCCCeeeec Q 026941 117 RGATSVRCSCCHTVNLAPAP-----NQFAHIICGHCRTTLMY 153 (230) Q Consensus 117 ~GA~sVrC~~C~tVn~Vp~~-----~q~a~V~Cg~Crt~Lmy 153 (230) .||+-|-|..|..+-.+|.. ....+++||.|...|.| T Consensus 2 GGAPFv~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl~~ 43 (46) T PF11331_consen 2 GGAPFVVCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVLSF 43 (46) T ss_pred CCCCEeECccHHHHHcCCCccCCCccceeEEeCCCCceeEEE Confidence 36777777777766666531 23668888888888776 No 23 >PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional Probab=88.50 E-value=0.59 Score=31.51 Aligned_cols=28 Identities=21% Similarity=0.596 Sum_probs=17.7 Q ss_pred EEEcCCCCeeeeccCCCCeEeCCCCCcc Q 026941 141 HIICGHCRTTLMYPHGAPSVKCAVCQYV 168 (230) Q Consensus 141 ~V~Cg~Crt~LmyP~GA~sVrCa~C~~V 168 (230) ...|++|...+.+..+...++|+.|+.- T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~ 30 (46) T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYR 30 (46) T ss_pred EEECCCCCCEEEECCCCCceECCCCCCe Confidence 3466666666666666656666666653 No 24 >PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional Probab=88.14 E-value=0.85 Score=30.76 Aligned_cols=25 Identities=28% Similarity=0.608 Sum_probs=11.5 Q ss_pred EEeCCcceeEEeecCCCeEeCCCCC Q 026941 104 LICGGCRTLLMYTRGATSVRCSCCH 128 (230) Q Consensus 104 LvCggCr~lL~YP~GA~sVrC~~C~ 128 (230) .+|+.|...+.+..+...++|+.|+ T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG 28 (46) T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCG 28 (46) T ss_pred EECCCCCCEEEECCCCCceECCCCC Confidence 3444444444444444444444444 No 25 >PLN00209 ribosomal protein S27; Provisional Probab=87.75 E-value=0.49 Score=37.37 Aligned_cols=19 Identities=37% Similarity=0.945 Sum_probs=9.4 Q ss_pred EEEcCCCCeeeeccCCCCe Q 026941 141 HIICGHCRTTLMYPHGAPS 159 (230) Q Consensus 141 ~V~Cg~Crt~LmyP~GA~s 159 (230) .|.|..|.++|..|.|-.+ T Consensus 55 ~V~C~~Cg~~L~~PTGGKa 73 (86) T PLN00209 55 VVVCGSCQTVLCQPTGGKA 73 (86) T ss_pred EEEccccCCEeeccCCCCe Confidence 4455555555555554443 No 26 >PF13717 zinc_ribbon_4: zinc-ribbon domain Probab=87.33 E-value=0.87 Score=29.91 Aligned_cols=14 Identities=14% Similarity=0.444 Sum_probs=7.4 Q ss_pred EeCCCCCcceecCC Q 026941 122 VRCSCCHTVNLAPA 135 (230) Q Consensus 122 VrC~~C~tVn~Vp~ 135 (230) +.|+.|++.-.+++ T Consensus 3 i~Cp~C~~~y~i~d 16 (36) T PF13717_consen 3 ITCPNCQAKYEIDD 16 (36) T ss_pred EECCCCCCEEeCCH Confidence 45555555555543 No 27 >PF13717 zinc_ribbon_4: zinc-ribbon domain Probab=86.05 E-value=0.92 Score=29.80 Aligned_cols=28 Identities=25% Similarity=0.581 Sum_probs=18.5 Q ss_pred EEEcCCCCeeeecc-----CCCCeEeCCCCCcc Q 026941 141 HIICGHCRTTLMYP-----HGAPSVKCAVCQYV 168 (230) Q Consensus 141 ~V~Cg~Crt~LmyP-----~GA~sVrCa~C~~V 168 (230) .+.|.+|++...+| .+...|+|+.|+.+ T Consensus 2 ~i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~ 34 (36) T PF13717_consen 2 IITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHV 34 (36) T ss_pred EEECCCCCCEEeCCHHHCCCCCcEEECCCCCCE Confidence 56777777776543 45567777777654 No 28 >PTZ00083 40S ribosomal protein S27; Provisional Probab=85.71 E-value=0.93 Score=35.77 Aligned_cols=45 Identities=24% Similarity=0.596 Sum_probs=29.7 Q ss_pred eEeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCCeEeCCCCC Q 026941 121 SVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQ 166 (230) Q Consensus 121 sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~sVrCa~C~ 166 (230) .|+|+.|..++.|=+-++. .|.|..|.++|.-|.|-.+.-=..|. T Consensus 35 ~VkCp~C~n~q~VFShA~t-~V~C~~Cg~~L~~PTGGKa~l~~gc~ 79 (85) T PTZ00083 35 DVKCPGCSQITTVFSHAQT-VVLCGGCSSQLCQPTGGKAKLTEGCS 79 (85) T ss_pred EEECCCCCCeeEEEecCce-EEEccccCCEeeccCCCCeEecCCce Confidence 4677777777766554444 67788888888888776655444443 No 29 >PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b. Probab=85.55 E-value=0.83 Score=33.27 Aligned_cols=38 Identities=26% Similarity=0.460 Sum_probs=21.0 Q ss_pred eeecCCCCcccccCCCCCceeEEEeCCcceeEEeecCCCe Q 026941 82 NVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATS 121 (230) Q Consensus 82 ~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~s 121 (230) .|+|+.|..++-+= ++....+.|.+|.++|..|.|--. T Consensus 7 ~VkCp~C~~~q~vF--Sha~t~V~C~~Cg~~L~~PtGGKa 44 (55) T PF01667_consen 7 DVKCPGCYNIQTVF--SHAQTVVKCVVCGTVLAQPTGGKA 44 (55) T ss_dssp EEE-TTT-SEEEEE--TT-SS-EE-SSSTSEEEEE-SSSE T ss_pred EEECCCCCCeeEEE--ecCCeEEEcccCCCEecCCCCcCe Confidence 47777777666662 233456777777777777777543 No 30 >PRK00415 rps27e 30S ribosomal protein S27e; Reviewed Probab=84.22 E-value=0.66 Score=34.33 Aligned_cols=34 Identities=24% Similarity=0.326 Sum_probs=15.7 Q ss_pred eecCCCCcccccCCCCCceeEEEeCCcceeEEeecC Q 026941 83 VCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRG 118 (230) Q Consensus 83 VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~G 118 (230) |+|+.|..++.+= ++-...+.|..|.++|..|.| T Consensus 12 VkCp~C~n~q~vF--sha~t~V~C~~Cg~~L~~PtG 45 (59) T PRK00415 12 VKCPDCGNEQVVF--SHASTVVRCLVCGKTLAEPTG 45 (59) T ss_pred EECCCCCCeEEEE--ecCCcEEECcccCCCcccCCC Confidence 5555554444331 122244555555555555554 No 31 >KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis] Probab=83.91 E-value=1.3 Score=34.80 Aligned_cols=39 Identities=26% Similarity=0.560 Sum_probs=21.2 Q ss_pred EeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCCeEe Q 026941 122 VRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVK 161 (230) Q Consensus 122 VrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~sVr 161 (230) |+|+.|-.+|.+=+-.|+ -|.|++|.+.|.-|.|-.+.. T Consensus 35 VkC~gc~~iT~vfSHaqt-vVvc~~c~~il~~~tggra~l 73 (84) T KOG1779|consen 35 VKCPGCFKITTVFSHAQT-VVVCEGCSTILCQPTGGKAKL 73 (84) T ss_pred EEcCCceEEEEEeecCce-EEEcCCCceEEEEecCCcEEe Confidence 455555555554443344 456666666666666555443 No 32 >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=83.65 E-value=2.3 Score=27.29 Aligned_cols=29 Identities=28% Similarity=0.619 Sum_probs=18.1 Q ss_pred EEEcCCCCeeeeccC-----CCCeEeCCCCCcce Q 026941 141 HIICGHCRTTLMYPH-----GAPSVKCAVCQYVT 169 (230) Q Consensus 141 ~V~Cg~Crt~LmyP~-----GA~sVrCa~C~~VT 169 (230) .+.|.+|.+...++. +...++|+.|+.+- T Consensus 2 ~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38) T TIGR02098 2 RIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38) T ss_pred EEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE Confidence 466777777766663 22367777777653 No 33 >PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ]. Probab=82.49 E-value=2.3 Score=37.01 Aligned_cols=35 Identities=26% Similarity=0.582 Sum_probs=15.8 Q ss_pred CceeEEEcCCCCeeeeccC------CCCeEeCCCCCcceee Q 026941 137 NQFAHIICGHCRTTLMYPH------GAPSVKCAVCQYVTNV 171 (230) Q Consensus 137 ~q~a~V~Cg~Crt~LmyP~------GA~sVrCa~C~~VT~V 171 (230) .+..+|.|+-|.|.|.+-- ..-+|||.+|...-+| T Consensus 8 E~lCYVhCnFC~TiLaVsVP~ssL~~~VTVRCGHCtNLLSV 48 (170) T PF04690_consen 8 EQLCYVHCNFCNTILAVSVPCSSLLKTVTVRCGHCTNLLSV 48 (170) T ss_pred CcEEEEEcCCcCeEEEEecchhhhhhhhceeccCccceeee Confidence 3444455555555444321 2234555555554444 No 34 >COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis] Probab=80.38 E-value=1.9 Score=32.30 Aligned_cols=50 Identities=22% Similarity=0.595 Sum_probs=40.2 Q ss_pred EEeCCcceeEEeecCCCeEeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCCeEeCCCCCcc Q 026941 104 LICGGCRTLLMYTRGATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYV 168 (230) Q Consensus 104 LvCggCr~lL~YP~GA~sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~sVrCa~C~~V 168 (230) -+|..|...|.--.++...-||.|.-+ ...+|..||.+ ...++|+.|.+. T Consensus 10 ~~CtSCg~~i~p~e~~v~F~CPnCGe~---------~I~Rc~~CRk~------g~~Y~Cp~CGF~ 59 (61) T COG2888 10 PVCTSCGREIAPGETAVKFPCPNCGEV---------EIYRCAKCRKL------GNPYRCPKCGFE 59 (61) T ss_pred ceeccCCCEeccCCceeEeeCCCCCce---------eeehhhhHHHc------CCceECCCcCcc Confidence 589999999988889999999999633 35689999975 346789988864 No 35 >PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane Probab=78.31 E-value=1.1 Score=37.07 Aligned_cols=15 Identities=27% Similarity=0.487 Sum_probs=7.5 Q ss_pred CeeecCCCCcccccC Q 026941 81 TNVCCALCNTITSVP 95 (230) Q Consensus 81 ~~VrCa~C~tVt~Vp 95 (230) ..|.||.|+..|-+. T Consensus 68 v~V~CP~C~K~TKmL 82 (114) T PF11023_consen 68 VQVECPNCGKQTKML 82 (114) T ss_pred eeeECCCCCChHhhh Confidence 345555555555543 No 36 >COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis] Probab=77.96 E-value=2.7 Score=31.93 Aligned_cols=37 Identities=24% Similarity=0.335 Sum_probs=21.2 Q ss_pred eeecCCCCcccccCCCCCceeEEEeCCcceeEEeecCCC Q 026941 82 NVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGAT 120 (230) Q Consensus 82 ~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~ 120 (230) .|+|+.|...+-+= ++....+.|..|.++|.+|.|-- T Consensus 19 ~VkCpdC~N~q~vF--shast~V~C~~CG~~l~~PTGGk 55 (67) T COG2051 19 RVKCPDCGNEQVVF--SHASTVVTCLICGTTLAEPTGGK 55 (67) T ss_pred EEECCCCCCEEEEe--ccCceEEEecccccEEEecCCCe Confidence 37777775444441 22235566777777777776643 No 37 >PRK14714 DNA polymerase II large subunit; Provisional Probab=77.72 E-value=1.9 Score=47.38 Aligned_cols=56 Identities=23% Similarity=0.492 Sum_probs=42.5 Q ss_pred CceeEEEeCCcceeEEeecCCCeEeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCCeEeCCCCCcc Q 026941 99 MEMAQLICGGCRTLLMYTRGATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYV 168 (230) Q Consensus 99 ~q~~qLvCggCr~lL~YP~GA~sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~sVrCa~C~~V 168 (230) .+++...|..|...... .+|+.|.+-+.. ...|..|+..+-..... +.+|+-|..- T Consensus 663 VEV~~rkCPkCG~~t~~------~fCP~CGs~te~-------vy~CPsCGaev~~des~-a~~CP~CGtp 718 (1337) T PRK14714 663 VEVGRRRCPSCGTETYE------NRCPDCGTHTEP-------VYVCPDCGAEVPPDESG-RVECPRCDVE 718 (1337) T ss_pred EEEEEEECCCCCCcccc------ccCcccCCcCCC-------ceeCccCCCccCCCccc-cccCCCCCCc Confidence 36778999999996422 399999988642 34899999987655434 7899999963 No 38 >PRK02935 hypothetical protein; Provisional Probab=77.64 E-value=1.5 Score=36.12 Aligned_cols=33 Identities=24% Similarity=0.485 Sum_probs=16.7 Q ss_pred CCeEeCCCCCcceecCCCCceeEEEcCCCCeeeeccC Q 026941 119 ATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPH 155 (230) Q Consensus 119 A~sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~ 155 (230) |..|.||.|+..|.+..-.+ .|-+|+++|.+.+ T Consensus 68 avqV~CP~C~K~TKmLGrvD----~CM~C~~PLTLd~ 100 (110) T PRK02935 68 AVQVICPSCEKPTKMLGRVD----ACMHCNQPLTLDR 100 (110) T ss_pred ceeeECCCCCchhhhcccee----ecCcCCCcCCcCc Confidence 44455555555555433222 3555555555544 No 39 >KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only] Probab=77.58 E-value=4.6 Score=37.35 Aligned_cols=30 Identities=23% Similarity=0.454 Sum_probs=13.1 Q ss_pred CCeEeCCCCCcceecCCCCceeEEEcCCCC Q 026941 119 ATSVRCSCCHTVNLAPAPNQFAHIICGHCR 148 (230) Q Consensus 119 A~sVrC~~C~tVn~Vp~~~q~a~V~Cg~Cr 148 (230) ++.|-|..|+....+-.-+|.--|.|+.|+ T Consensus 78 ~PmvtCRVCq~~i~~egk~~QHVVKC~~Cn 107 (275) T KOG4684|consen 78 FPMVTCRVCQVAISLEGKNQQHVVKCHSCN 107 (275) T ss_pred CceEeehhhhHHhccccccceeeEeecccC Confidence 334444444444443333344444444444 No 40 >PRK14890 putative Zn-ribbon RNA-binding protein; Provisional Probab=74.64 E-value=2.8 Score=31.08 Aligned_cols=53 Identities=25% Similarity=0.575 Sum_probs=39.4 Q ss_pred ccceeeccccceeeeecCC-CCeeecCCCCcccccCCCCCceeEEEeCCcceeEEeecCCCeEeCCCCCcc Q 026941 61 MQSQLVCSGCRSVLLYPRG-ATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSVRCSCCHTV 130 (230) Q Consensus 61 mqsQlvC~gCr~lL~YP~G-A~~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~sVrC~~C~tV 130 (230) |..-.+|..|...| .|.+ +..-.|+.|.++.-. +|..||.+ +...+||.|... T Consensus 4 ~~~~~~CtSCg~~i-~~~~~~~~F~CPnCG~~~I~----------RC~~CRk~------~~~Y~CP~CGF~ 57 (59) T PRK14890 4 MMEPPKCTSCGIEI-APREKAVKFLCPNCGEVIIY----------RCEKCRKQ------SNPYTCPKCGFE 57 (59) T ss_pred cccCccccCCCCcc-cCCCccCEeeCCCCCCeeEe----------echhHHhc------CCceECCCCCCc Confidence 34555899999887 5666 788899999765443 58889976 356789888764 No 41 >PF12773 DZR: Double zinc ribbon Probab=73.17 E-value=1.4 Score=29.60 Aligned_cols=38 Identities=24% Similarity=0.478 Sum_probs=22.7 Q ss_pred cCCCCcccccCCCCCceeEEEeCCcceeEEeecCCCeEeCCCCCcc Q 026941 85 CALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSVRCSCCHTV 130 (230) Q Consensus 85 Ca~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~sVrC~~C~tV 130 (230) |+.|.+.+.. ....|..|.+.|. ......+.|+.|.+. T Consensus 1 Cp~Cg~~~~~-------~~~fC~~CG~~l~-~~~~~~~~C~~Cg~~ 38 (50) T PF12773_consen 1 CPHCGTPNPD-------DAKFCPHCGTPLP-PPDQSKKICPNCGAE 38 (50) T ss_pred CCCcCCcCCc-------cccCChhhcCChh-hccCCCCCCcCCcCC Confidence 5556555442 4566777777776 444555666666665 No 42 >PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ]. Probab=72.91 E-value=3.3 Score=36.12 Aligned_cols=48 Identities=29% Similarity=0.508 Sum_probs=29.7 Q ss_pred CCceeEEEeCCcceeEEeecCCCeEeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCCe Q 026941 98 GMEMAQLICGGCRTLLMYTRGATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPS 159 (230) Q Consensus 98 ~~q~~qLvCggCr~lL~YP~GA~sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~s 159 (230) +.+.-++.|+-|.|+|. -+|=|+.= -.+-.|+||+|-.+|.+--++.. T Consensus 7 sE~lCYVhCnFC~TiLa-----VsVP~ssL---------~~~VTVRCGHCtNLLSVNm~~~~ 54 (170) T PF04690_consen 7 SEQLCYVHCNFCNTILA-----VSVPCSSL---------LKTVTVRCGHCTNLLSVNMRALL 54 (170) T ss_pred CCcEEEEEcCCcCeEEE-----Eecchhhh---------hhhhceeccCccceeeeeccccc Confidence 34556666666666664 23444421 13447899999999887766554 No 43 >COG4856 Uncharacterized protein conserved in bacteria [Function unknown] Probab=71.85 E-value=3.6 Score=40.22 Aligned_cols=65 Identities=25% Similarity=0.457 Sum_probs=49.4 Q ss_pred CCcccceeee-hhhHHHHHhhhcce-------------------eeEEEEeeeecCCcccccCcCccceeeccccceeee Q 026941 16 PNQTKQIKLS-FFIFLFLFIYINHT-------------------ITQLSIDFDFSNDSILLSLQGMQSQLVCSGCRSVLL 75 (230) Q Consensus 16 ~~~~~~~~~~-~~~~~~~~~~~~~~-------------------~~~~~~~~~f~~~~~l~~~~~mqsQlvC~gCr~lL~ 75 (230) -|+..-++++ ||+-++||+|+|.. ++.+-+|.-+|.+-.+++-...+-+..=.|=+.++. T Consensus 5 lns~W~irIiaff~A~~Lfl~vn~~n~~N~~~t~~~~~~t~~~tltdvpvdvlYD~~~y~isg~~etV~Vtl~G~ns~~~ 84 (403) T COG4856 5 LNSPWLIRIIAFFFAILLFLYVNNNNFNNPISTIKPTSETYTLTLTDVPVDVLYDSDKYFISGQPETVTVTLKGPNSIVL 84 (403) T ss_pred hcCcHhHHHHHHHHHHHhheeecccccCCcccccccccccccceeeeceeEEEEccccccccCCceEEEEEEeCCcceee Confidence 3555556666 77778899998754 899999999999998888777666666677777777 Q ss_pred ecCCC Q 026941 76 YPRGA 80 (230) Q Consensus 76 YP~GA 80 (230) |-+-+ T Consensus 85 ~~~~~ 89 (403) T COG4856 85 KSEKP 89 (403) T ss_pred eeecC Confidence 76544 No 44 >PRK14873 primosome assembly protein PriA; Provisional Probab=70.04 E-value=7.4 Score=39.80 Aligned_cols=67 Identities=24% Similarity=0.509 Sum_probs=49.0 Q ss_pred cccceeeeecC-CC-CeeecCCCCcccccCCCCCceeEEEeCCcceeEEeecCCCeEeCCCCCcceecCCCCceeEEEcC Q 026941 68 SGCRSVLLYPR-GA-TNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSVRCSCCHTVNLAPAPNQFAHIICG 145 (230) Q Consensus 68 ~gCr~lL~YP~-GA-~~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~sVrC~~C~tVn~Vp~~~q~a~V~Cg 145 (230) .| +.+|+.+| |- +.+.|..|..+ ..|..|..-|.|..+....+|..|..- .. --.|. T Consensus 368 ~g-qvll~lnRrGyap~l~C~~Cg~~------------~~C~~C~~~L~~h~~~~~l~Ch~CG~~-~~-------p~~Cp 426 (665) T PRK14873 368 HG-PVLVQVPRRGYVPSLACARCRTP------------ARCRHCTGPLGLPSAGGTPRCRWCGRA-AP-------DWRCP 426 (665) T ss_pred cC-cEEEEecCCCCCCeeEhhhCcCe------------eECCCCCCceeEecCCCeeECCCCcCC-Cc-------CccCC Confidence 58 88888875 54 67899999754 568899999999888778888888763 11 23677 Q ss_pred CCCeeeeccC Q 026941 146 HCRTTLMYPH 155 (230) Q Consensus 146 ~Crt~LmyP~ 155 (230) +|...-+-+. T Consensus 427 ~Cgs~~l~~~ 436 (665) T PRK14873 427 RCGSDRLRAV 436 (665) T ss_pred CCcCCcceee Confidence 7776544443 No 45 >PRK05580 primosome assembly protein PriA; Validated Probab=69.89 E-value=7.5 Score=39.41 Aligned_cols=67 Identities=27% Similarity=0.551 Sum_probs=50.1 Q ss_pred ceeeeecC-CC-CeeecCCCCcccccCCCCCceeEEEeCCcceeEEeecCCCeEeCCCCCcceecCCCCceeEEEcCCCC Q 026941 71 RSVLLYPR-GA-TNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSVRCSCCHTVNLAPAPNQFAHIICGHCR 148 (230) Q Consensus 71 r~lL~YP~-GA-~~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~sVrC~~C~tVn~Vp~~~q~a~V~Cg~Cr 148 (230) +.++..|+ |- +.+.|..|..+ +.|..|..-|.|.......+|..|......+. .|.+|. T Consensus 368 qvll~~nrrGy~~~~~C~~Cg~~------------~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~-------~Cp~Cg 428 (679) T PRK05580 368 QVLLFLNRRGYAPFLLCRDCGWV------------AECPHCDASLTLHRFQRRLRCHHCGYQEPIPK-------ACPECG 428 (679) T ss_pred eEEEEEcCCCCCCceEhhhCcCc------------cCCCCCCCceeEECCCCeEECCCCcCCCCCCC-------CCCCCc Confidence 45666664 54 68999999754 46889999999999999999999987755432 488886 Q ss_pred eeeeccCC Q 026941 149 TTLMYPHG 156 (230) Q Consensus 149 t~LmyP~G 156 (230) ..-+.+.| T Consensus 429 ~~~l~~~g 436 (679) T PRK05580 429 STDLVPVG 436 (679) T ss_pred CCeeEEee Confidence 66555533 No 46 >TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Probab=68.31 E-value=9.4 Score=37.40 Aligned_cols=66 Identities=30% Similarity=0.674 Sum_probs=48.1 Q ss_pred eeeeec-CCC-CeeecCCCCcccccCCCCCceeEEEeCCcceeEEeecCCCeEeCCCCCcceecCCCCceeEEEcCCCCe Q 026941 72 SVLLYP-RGA-TNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSVRCSCCHTVNLAPAPNQFAHIICGHCRT 149 (230) Q Consensus 72 ~lL~YP-~GA-~~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt 149 (230) .++..| +|- +.+.|..|..+ +.|..|..-|.|-......+|.-|.....+|. .|..|.. T Consensus 201 vLvflnrrGya~~~~C~~Cg~~------------~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~-------~Cp~C~s 261 (505) T TIGR00595 201 SILFLNRRGYSKNLLCRSCGYI------------LCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPK-------TCPQCGS 261 (505) T ss_pred EEEEEeCCcCCCeeEhhhCcCc------------cCCCCCCCceEEecCCCeEEcCCCcCcCCCCC-------CCCCCCC Confidence 344444 454 68999999754 45889999999999988999999987755432 5888876 Q ss_pred eeeccCC Q 026941 150 TLMYPHG 156 (230) Q Consensus 150 ~LmyP~G 156 (230) .-+-+.| T Consensus 262 ~~l~~~g 268 (505) T TIGR00595 262 EDLVYKG 268 (505) T ss_pred CeeEeec Confidence 6555544 No 47 >PF12773 DZR: Double zinc ribbon Probab=68.09 E-value=2.6 Score=28.30 Aligned_cols=40 Identities=30% Similarity=0.546 Sum_probs=29.1 Q ss_pred CCCCCcceecCCCCceeEEEcCCCCeeeeccCCCCeEeCCCCCccee Q 026941 124 CSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTN 170 (230) Q Consensus 124 C~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~sVrCa~C~~VT~ 170 (230) |+.|++.+. .....|.+|.+.|. ......+.|+.|.+... T Consensus 1 Cp~Cg~~~~------~~~~fC~~CG~~l~-~~~~~~~~C~~Cg~~~~ 40 (50) T PF12773_consen 1 CPHCGTPNP------DDAKFCPHCGTPLP-PPDQSKKICPNCGAENP 40 (50) T ss_pred CCCcCCcCC------ccccCChhhcCChh-hccCCCCCCcCCcCCCc Confidence 677777743 22567999999888 55666788999988643 No 48 >smart00661 RPOL9 RNA polymerase subunit 9. Probab=64.31 E-value=7.7 Score=25.93 Aligned_cols=29 Identities=24% Similarity=0.646 Sum_probs=20.4 Q ss_pred cCCCCeeeeccCCC--CeEeCCCCCcceeec Q 026941 144 CGHCRTTLMYPHGA--PSVKCAVCQYVTNVN 172 (230) Q Consensus 144 Cg~Crt~LmyP~GA--~sVrCa~C~~VT~V~ 172 (230) |..|..+|..+.+. ....|+.|.+.-.+. T Consensus 3 Cp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~~ 33 (52) T smart00661 3 CPKCGNMLIPKEGKEKRRFVCRKCGYEEPIE 33 (52) T ss_pred CCCCCCccccccCCCCCEEECCcCCCeEECC Confidence 77787766555443 367899999887763 No 49 >COG4416 Com Mu-like prophage protein Com [General function prediction only] Probab=61.15 E-value=2.2 Score=31.70 Aligned_cols=30 Identities=30% Similarity=0.680 Sum_probs=14.4 Q ss_pred EEEeCCcceeEEeecCC--CeEeCCCCCccee Q 026941 103 QLICGGCRTLLMYTRGA--TSVRCSCCHTVNL 132 (230) Q Consensus 103 qLvCggCr~lL~YP~GA--~sVrC~~C~tVn~ 132 (230) -++|..|+.+|.=..|. .-++||.|..||. T Consensus 4 tiRC~~CnKlLa~a~~~~yle~KCPrCK~vN~ 35 (60) T COG4416 4 TIRCAKCNKLLAEAEGQAYLEKKCPRCKEVNE 35 (60) T ss_pred eeehHHHhHHHHhcccceeeeecCCccceeee Confidence 34455555555443333 2345555555554 No 50 >PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A. Probab=60.27 E-value=12 Score=27.63 Aligned_cols=30 Identities=27% Similarity=0.611 Sum_probs=17.2 Q ss_pred ceeEEEcCCCCeeeeccCCCC--eEeCCCCCc Q 026941 138 QFAHIICGHCRTTLMYPHGAP--SVKCAVCQY 167 (230) Q Consensus 138 q~a~V~Cg~Crt~LmyP~GA~--sVrCa~C~~ 167 (230) ....|.||.|++.+.+-.-.- ...|+.|+. T Consensus 38 ~~~~v~Cg~C~~~~~~~~~~c~~~~~C~~C~~ 69 (71) T PF05495_consen 38 PVKRVICGKCRTEQPIDEYSCGADYFCPICGL 69 (71) T ss_dssp T--EEEETTT--EEES-SBTT--SEEETTTTE T ss_pred cccCeECCCCCCccChhhhhcCCCccCcCcCC Confidence 334888888888887765322 367887764 No 51 >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=60.24 E-value=7.6 Score=25.77 Aligned_cols=18 Identities=17% Similarity=0.416 Sum_probs=10.5 Q ss_pred CCCCeEeCCCCCcceeec Q 026941 155 HGAPSVKCAVCQYVTNVN 172 (230) Q Consensus 155 ~GA~sVrCa~C~~VT~V~ 172 (230) .+..+-+|..|.+.+.+. T Consensus 20 ~~~~~w~C~~C~~~N~lp 37 (40) T PF04810_consen 20 DGGKTWICNFCGTKNPLP 37 (40) T ss_dssp TTTTEEEETTT--EEE-- T ss_pred CCCCEEECcCCCCcCCCC Confidence 366778888888877774 No 52 >PRK14873 primosome assembly protein PriA; Provisional Probab=59.15 E-value=9.2 Score=39.12 Aligned_cols=48 Identities=31% Similarity=0.680 Sum_probs=29.4 Q ss_pred CcceeEEeec-C-CCeEeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCCeEeCCCCCc Q 026941 108 GCRTLLMYTR-G-ATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQY 167 (230) Q Consensus 108 gCr~lL~YP~-G-A~sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~sVrCa~C~~ 167 (230) | .++|+-++ | ++.+.|..|..+ ..|.+|...|.|..+....+|..|++ T Consensus 369 g-qvll~lnRrGyap~l~C~~Cg~~-----------~~C~~C~~~L~~h~~~~~l~Ch~CG~ 418 (665) T PRK14873 369 G-PVLVQVPRRGYVPSLACARCRTP-----------ARCRHCTGPLGLPSAGGTPRCRWCGR 418 (665) T ss_pred C-cEEEEecCCCCCCeeEhhhCcCe-----------eECCCCCCceeEecCCCeeECCCCcC Confidence 5 56666553 3 456677777654 35666666666665555666666665 No 53 >PRK05580 primosome assembly protein PriA; Validated Probab=58.29 E-value=12 Score=38.05 Aligned_cols=50 Identities=30% Similarity=0.620 Sum_probs=35.9 Q ss_pred eeEEeec-C-CCeEeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCCeEeCCCCCcceee Q 026941 111 TLLMYTR-G-ATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNV 171 (230) Q Consensus 111 ~lL~YP~-G-A~sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~sVrCa~C~~VT~V 171 (230) .+|..++ | |+.+.|..|..+ ..|.+|...|.|.......+|..|++...+ T Consensus 369 vll~~nrrGy~~~~~C~~Cg~~-----------~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~ 420 (679) T PRK05580 369 VLLFLNRRGYAPFLLCRDCGWV-----------AECPHCDASLTLHRFQRRLRCHHCGYQEPI 420 (679) T ss_pred EEEEEcCCCCCCceEhhhCcCc-----------cCCCCCCCceeEECCCCeEECCCCcCCCCC Confidence 4555663 4 678999999765 468888888888877777777777765543 No 54 >COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair] Probab=57.51 E-value=23 Score=37.02 Aligned_cols=63 Identities=25% Similarity=0.587 Sum_probs=47.6 Q ss_pred ccceeeeecC-CC-CeeecCCCCcccccCCCCCceeEEEeCCcceeEEeecCCCeEeCCCCCcceecCCCCceeEEEcCC Q 026941 69 GCRSVLLYPR-GA-TNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSVRCSCCHTVNLAPAPNQFAHIICGH 146 (230) Q Consensus 69 gCr~lL~YP~-GA-~~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~sVrC~~C~tVn~Vp~~~q~a~V~Cg~ 146 (230) |=+.+|+.+| |- +.+.|..|..+- .|..|...|.|-+....-+|--|+.-..+| ..|.. T Consensus 420 geQ~llflnRRGys~~l~C~~Cg~v~------------~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p-------~~Cp~ 480 (730) T COG1198 420 GEQVLLFLNRRGYAPLLLCRDCGYIA------------ECPNCDSPLTLHKATGQLRCHYCGYQEPIP-------QSCPE 480 (730) T ss_pred CCeEEEEEccCCccceeecccCCCcc------------cCCCCCcceEEecCCCeeEeCCCCCCCCCC-------CCCCC Confidence 3455666655 44 689999998764 478999999999999999999998875543 24777 Q ss_pred CCee Q 026941 147 CRTT 150 (230) Q Consensus 147 Crt~ 150 (230) |... T Consensus 481 Cgs~ 484 (730) T COG1198 481 CGSE 484 (730) T ss_pred CCCC Confidence 7666 No 55 >KOG3267 consensus Uncharacterized conserved protein [Function unknown] Probab=57.36 E-value=1.6 Score=36.64 Aligned_cols=51 Identities=29% Similarity=0.465 Sum_probs=36.6 Q ss_pred cceeeeeccccCCCcccceeeehhhHHHHHhhhcceeeEEEEeeeecCCcccccCcCc Q 026941 4 RGFHLIHNEIKKPNQTKQIKLSFFIFLFLFIYINHTITQLSIDFDFSNDSILLSLQGM 61 (230) Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~l~~~~~m 61 (230) ||||+|-|+|-|.-.. .|+-|---..-+||.||-..|.|.=.+|.|- -.|| T Consensus 11 kg~~iit~~ilkeir~---dl~~fn~g~~~~fiqhtsaaltinen~d~d~----qad~ 61 (138) T KOG3267|consen 11 KGCHIITNDILKEIRE---DLKDFNCGLAHFFIQHTSAALTINENWDADT----QADM 61 (138) T ss_pred CccEEecHHHHHHHHH---HHhhccccceeeeeeccceeeEecccCCcch----hhhH Confidence 6999999998764221 2333433344557899999999999999987 5555 No 56 >PRK14559 putative protein serine/threonine phosphatase; Provisional Probab=56.08 E-value=6.7 Score=40.14 Aligned_cols=36 Identities=25% Similarity=0.492 Sum_probs=22.3 Q ss_pred eecCCCCcccccCCCCCceeEEEeCCcceeEEeecCCCeEeCCCCCcce Q 026941 83 VCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTRGATSVRCSCCHTVN 131 (230) Q Consensus 83 VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~GA~sVrC~~C~tVn 131 (230) ..|+.|.+.|+. +.-.|..|.+.|.. -.|+.|.+-+ T Consensus 2 ~~Cp~Cg~~n~~-------~akFC~~CG~~l~~------~~Cp~CG~~~ 37 (645) T PRK14559 2 LICPQCQFENPN-------NNRFCQKCGTSLTH------KPCPQCGTEV 37 (645) T ss_pred CcCCCCCCcCCC-------CCccccccCCCCCC------CcCCCCCCCC Confidence 367888777653 34467777776621 2477776663 No 57 >PHA03030 hypothetical protein; Provisional Probab=55.48 E-value=6.3 Score=32.68 Aligned_cols=13 Identities=62% Similarity=1.308 Sum_probs=9.0 Q ss_pred ehhhHHHHHhhhc Q 026941 25 SFFIFLFLFIYIN 37 (230) Q Consensus 25 ~~~~~~~~~~~~~ 37 (230) ..|||||+|.||- T Consensus 10 ~lfifl~iffYI~ 22 (122) T PHA03030 10 FLFIFLFIFFYIR 22 (122) T ss_pred HHHHHHHHHHHhe Confidence 3577777888873 No 58 >PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues. Probab=55.24 E-value=10 Score=23.52 Aligned_cols=21 Identities=24% Similarity=0.623 Sum_probs=9.3 Q ss_pred CCCCeeeeccCC-CCeEeCCCCC Q 026941 145 GHCRTTLMYPHG-APSVKCAVCQ 166 (230) Q Consensus 145 g~Crt~LmyP~G-A~sVrCa~C~ 166 (230) ..|...|. |++ +....|+.|. T Consensus 2 ~sC~~~i~-~r~~~v~f~CPnCG 23 (24) T PF07754_consen 2 TSCGRPIA-PREQAVPFPCPNCG 23 (24) T ss_pred ccCCCccc-CcccCceEeCCCCC Confidence 33444333 444 4455555553 No 59 >PRK14714 DNA polymerase II large subunit; Provisional Probab=52.75 E-value=9.7 Score=42.22 Aligned_cols=40 Identities=20% Similarity=0.433 Sum_probs=17.7 Q ss_pred EeCCcceeEEeecCCCeEeCCCCCcceecCCCCceeEEEcCCCCeeee Q 026941 105 ICGGCRTLLMYTRGATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLM 152 (230) Q Consensus 105 vCggCr~lL~YP~GA~sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~Lm 152 (230) .|..|...+ .....|+.|+.-....+ .. ...|..|.+.+. T Consensus 681 fCP~CGs~t-----e~vy~CPsCGaev~~de-s~--a~~CP~CGtplv 720 (1337) T PRK14714 681 RCPDCGTHT-----EPVYVCPDCGAEVPPDE-SG--RVECPRCDVELT 720 (1337) T ss_pred cCcccCCcC-----CCceeCccCCCccCCCc-cc--cccCCCCCCccc Confidence 555555543 11235555655322111 11 345666665543 No 60 >KOG1546 consensus Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones] Probab=51.67 E-value=5.9 Score=38.30 Aligned_cols=29 Identities=28% Similarity=0.653 Sum_probs=26.0 Q ss_pred EEeCCcceeEEeecCCCeEeCCCCCcceecC Q 026941 104 LICGGCRTLLMYTRGATSVRCSCCHTVNLAP 134 (230) Q Consensus 104 LvCggCr~lL~YP~GA~sVrC~~C~tVn~Vp 134 (230) +.|. |++-++-|.||.. +|+.|++++.+. T Consensus 5 ~~~~-~~~p~~~pp~ar~-q~~~~~~~~~~~ 33 (362) T KOG1546|consen 5 VGCN-CQRPMAPPPGARY-QCAGCHAVTQIA 33 (362) T ss_pred ccCC-CCCCCCCCCCCcc-cccccceeeeec Confidence 3576 9999999999999 999999999875 No 61 >PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A. Probab=51.65 E-value=22 Score=27.20 Aligned_cols=57 Identities=23% Similarity=0.470 Sum_probs=28.6 Q ss_pred EEeCCcceeEEeecCCCeEeCCCCCcceecCCCCceeEEEcCCCCeeeeccC--CCCeEeCCCCCcce Q 026941 104 LICGGCRTLLMYTRGATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPH--GAPSVKCAVCQYVT 169 (230) Q Consensus 104 LvCggCr~lL~YP~GA~sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~--GA~sVrCa~C~~VT 169 (230) +.|..|...|. +.| ....|..|+.-- ..+-.|..|+..|..=. ||..+-|-.|+..- T Consensus 2 ~~CP~C~~~L~-~~~-~~~~C~~C~~~~-------~~~a~CPdC~~~Le~LkACGAvdYFC~~c~gLi 60 (70) T PF07191_consen 2 NTCPKCQQELE-WQG-GHYHCEACQKDY-------KKEAFCPDCGQPLEVLKACGAVDYFCNHCHGLI 60 (70) T ss_dssp -B-SSS-SBEE-EET-TEEEETTT--EE-------EEEEE-TTT-SB-EEEEETTEEEEE-TTTT-EE T ss_pred CcCCCCCCccE-EeC-CEEECccccccc-------eecccCCCcccHHHHHHHhcccceeeccCCcee Confidence 45667777633 333 566777776532 12567777777776543 77777777777643 No 62 >PF12113 SVM_signal: SVM protein signal sequence; InterPro: IPR021970 This domain is presumed to be a signal peptide sequence found in Sequence-variable mosaic (SVM) proteins []. It is found in phytoplasmas. This presumed signal sequence is about 30 amino acids in length. Probab=50.13 E-value=6.3 Score=26.34 Aligned_cols=26 Identities=46% Similarity=0.595 Sum_probs=18.8 Q ss_pred ccCCCcccceeeehhhHHHHHhhhcc Q 026941 13 IKKPNQTKQIKLSFFIFLFLFIYINH 38 (230) Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 38 (230) +|-.||-|-|.+-.|+||-||..+|. T Consensus 2 fKlknq~~ii~i~Lf~~LGL~fI~NN 27 (33) T PF12113_consen 2 FKLKNQFKIINIFLFIFLGLFFITNN 27 (33) T ss_pred cchhhchhhhhhHHHHHHHHHheecC Confidence 35567888887778888877766664 No 63 >COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis] Probab=50.13 E-value=13 Score=33.08 Aligned_cols=29 Identities=24% Similarity=0.536 Sum_probs=21.1 Q ss_pred ceeEEEcCCCCeeeeccCCCCeEeCCCCCcc Q 026941 138 QFAHIICGHCRTTLMYPHGAPSVKCAVCQYV 168 (230) Q Consensus 138 q~a~V~Cg~Crt~LmyP~GA~sVrCa~C~~V 168 (230) .+-.-.|.+|+..|++ .-...+|+.|..+ T Consensus 146 GVI~A~CsrC~~~L~~--~~~~l~Cp~Cg~t 174 (188) T COG1096 146 GVIYARCSRCRAPLVK--KGNMLKCPNCGNT 174 (188) T ss_pred eEEEEEccCCCcceEE--cCcEEECCCCCCE Confidence 4445678888888887 6677788888764 No 64 >COG4416 Com Mu-like prophage protein Com [General function prediction only] Probab=49.25 E-value=5.3 Score=29.71 Aligned_cols=34 Identities=21% Similarity=0.583 Sum_probs=26.4 Q ss_pred ccceeeccccceeeeecCCCC--eeecCCCCccccc Q 026941 61 MQSQLVCSGCRSVLLYPRGAT--NVCCALCNTITSV 94 (230) Q Consensus 61 mqsQlvC~gCr~lL~YP~GA~--~VrCa~C~tVt~V 94 (230) |.-.+.|..|..||.=-.|.. .+.|+.|-+||.. T Consensus 1 ~~~tiRC~~CnKlLa~a~~~~yle~KCPrCK~vN~~ 36 (60) T COG4416 1 MMQTIRCAKCNKLLAEAEGQAYLEKKCPRCKEVNEF 36 (60) T ss_pred CceeeehHHHhHHHHhcccceeeeecCCccceeeee Confidence 345688999999988766664 5889999888875 No 65 >KOG2824 consensus Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones] Probab=48.84 E-value=28 Score=32.83 Aligned_cols=11 Identities=36% Similarity=0.809 Sum_probs=5.0 Q ss_pred CCCeeecCCCC Q 026941 79 GATNVCCALCN 89 (230) Q Consensus 79 GA~~VrCa~C~ 89 (230) |+..+-|..|+ T Consensus 237 g~rFlpC~~C~ 247 (281) T KOG2824|consen 237 GARFLPCSNCH 247 (281) T ss_pred CcceEecCCCC Confidence 34444444443 No 66 >COG4357 Zinc finger domain containing protein (CHY type) [Function unknown] Probab=48.13 E-value=3.7 Score=33.52 Aligned_cols=29 Identities=31% Similarity=0.685 Sum_probs=24.5 Q ss_pred eeEEEeCCcceeEEeecCCCeEeCCCCCc Q 026941 101 MAQLICGGCRTLLMYTRGATSVRCSCCHT 129 (230) Q Consensus 101 ~~qLvCggCr~lL~YP~GA~sVrC~~C~t 129 (230) ..-++||-||.+|.+..=-..++|+.|+. T Consensus 60 ~~~iiCGvC~~~LT~~EY~~~~~Cp~C~s 88 (105) T COG4357 60 PKAIICGVCRKLLTRAEYGMCGSCPYCQS 88 (105) T ss_pred CccEEhhhhhhhhhHHHHhhcCCCCCcCC Confidence 44589999999999988888888999874 No 67 >TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Probab=47.84 E-value=18 Score=35.41 Aligned_cols=42 Identities=21% Similarity=0.722 Sum_probs=27.0 Q ss_pred CCeEeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCCeEeCCCCCcceee Q 026941 119 ATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNV 171 (230) Q Consensus 119 A~sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~sVrCa~C~~VT~V 171 (230) |+.+.|..|..+ ..|.+|...|.|-......+|..|++...+ T Consensus 211 a~~~~C~~Cg~~-----------~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~ 252 (505) T TIGR00595 211 SKNLLCRSCGYI-----------LCCPNCDVSLTYHKKEGKLRCHYCGYQEPI 252 (505) T ss_pred CCeeEhhhCcCc-----------cCCCCCCCceEEecCCCeEEcCCCcCcCCC Confidence 567788888665 346666666666666666666666655443 No 68 >COG4357 Zinc finger domain containing protein (CHY type) [Function unknown] Probab=47.43 E-value=4.6 Score=33.00 Aligned_cols=27 Identities=22% Similarity=0.623 Sum_probs=23.7 Q ss_pred eeeccccceeeeecCCCCeeecCCCCc Q 026941 64 QLVCSGCRSVLLYPRGATNVCCALCNT 90 (230) Q Consensus 64 QlvC~gCr~lL~YP~GA~~VrCa~C~t 90 (230) -++|+.|+.+|.+-.=-..++|+.|++ T Consensus 62 ~iiCGvC~~~LT~~EY~~~~~Cp~C~s 88 (105) T COG4357 62 AIICGVCRKLLTRAEYGMCGSCPYCQS 88 (105) T ss_pred cEEhhhhhhhhhHHHHhhcCCCCCcCC Confidence 389999999999988888889999954 No 69 >COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair] Probab=46.42 E-value=21 Score=37.28 Aligned_cols=52 Identities=25% Similarity=0.625 Sum_probs=40.4 Q ss_pred ceeEEeec-C-CCeEeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCCeEeCCCCCcceeec Q 026941 110 RTLLMYTR-G-ATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNVN 172 (230) Q Consensus 110 r~lL~YP~-G-A~sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~sVrCa~C~~VT~V~ 172 (230) +.+|+.+| | ++.+.|..|..+ ..|.+|...|.|-......+|-.|++...+. T Consensus 422 Q~llflnRRGys~~l~C~~Cg~v-----------~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p 475 (730) T COG1198 422 QVLLFLNRRGYAPLLLCRDCGYI-----------AECPNCDSPLTLHKATGQLRCHYCGYQEPIP 475 (730) T ss_pred eEEEEEccCCccceeecccCCCc-----------ccCCCCCcceEEecCCCeeEeCCCCCCCCCC Confidence 34555554 4 558999999876 4599999999999999999999998876653 No 70 >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=46.36 E-value=17 Score=22.83 Aligned_cols=25 Identities=24% Similarity=0.631 Sum_probs=13.6 Q ss_pred EcCCCCeeeeccCCCCeEeCCCCCc Q 026941 143 ICGHCRTTLMYPHGAPSVKCAVCQY 167 (230) Q Consensus 143 ~Cg~Crt~LmyP~GA~sVrCa~C~~ 167 (230) .|+.|...+..-.+..+-+|+.|.. T Consensus 5 fC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32) T PF09297_consen 5 FCGRCGAPTKPAPGGWARRCPSCGH 29 (32) T ss_dssp B-TTT--BEEE-SSSS-EEESSSS- T ss_pred ccCcCCccccCCCCcCEeECCCCcC Confidence 4777777777777777777777765 No 71 >TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway. Probab=45.75 E-value=23 Score=25.51 Aligned_cols=13 Identities=31% Similarity=0.460 Sum_probs=6.0 Q ss_pred eEeCCCCCcceee Q 026941 159 SVKCAVCQYVTNV 171 (230) Q Consensus 159 sVrCa~C~~VT~V 171 (230) -|.|+.|..-=.| T Consensus 22 iV~Cp~CGaeleV 34 (54) T TIGR01206 22 LVICDECGAELEV 34 (54) T ss_pred EEeCCCCCCEEEE Confidence 3455555544443 No 72 >smart00661 RPOL9 RNA polymerase subunit 9. Probab=45.42 E-value=22 Score=23.73 Aligned_cols=10 Identities=20% Similarity=0.424 Sum_probs=4.5 Q ss_pred eEeCCCCCcc Q 026941 121 SVRCSCCHTV 130 (230) Q Consensus 121 sVrC~~C~tV 130 (230) ...|+.|... T Consensus 20 ~~vC~~Cg~~ 29 (52) T smart00661 20 RFVCRKCGYE 29 (52) T ss_pred EEECCcCCCe Confidence 3444444444 No 73 >PF15616 TerY-C: TerY-C metal binding domain Probab=43.23 E-value=34 Score=28.80 Aligned_cols=34 Identities=24% Similarity=0.485 Sum_probs=24.4 Q ss_pred CceeEEEeCCcceeEEeecCCCeEeCCCCCcceecC Q 026941 99 MEMAQLICGGCRTLLMYTRGATSVRCSCCHTVNLAP 134 (230) Q Consensus 99 ~q~~qLvCggCr~lL~YP~GA~sVrC~~C~tVn~Vp 134 (230) ++.+-.+| +|..++-|-- ...|.||.|...-... T Consensus 85 n~~~fa~C-~CGkl~Ci~g-~~~~~CPwCg~~g~~~ 118 (131) T PF15616_consen 85 NQYAFAVC-GCGKLFCIDG-EGEVTCPWCGNEGSFG 118 (131) T ss_pred ChhcEEEe-cCCCEEEeCC-CCCEECCCCCCeeeec Confidence 44566788 6998887765 5588899998765543 No 74 >PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A. Probab=42.93 E-value=25 Score=26.92 Aligned_cols=38 Identities=11% Similarity=0.320 Sum_probs=16.6 Q ss_pred CeEeCCCCCcceecC----CCCceeEEEcCCCCeeeeccCCC Q 026941 120 TSVRCSCCHTVNLAP----APNQFAHIICGHCRTTLMYPHGA 157 (230) Q Consensus 120 ~sVrC~~C~tVn~Vp----~~~q~a~V~Cg~Crt~LmyP~GA 157 (230) ....||.|+.-+.|. .....+.+.|+.|.....+..+. T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~i~~ 62 (81) T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTKINP 62 (81) T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE--S T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEccCc Confidence 345677777444432 23577788888887666555443 No 75 >TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A. Probab=41.52 E-value=23 Score=34.02 Aligned_cols=26 Identities=19% Similarity=0.685 Sum_probs=10.6 Q ss_pred EcCCCCeeeeccC--CCCeEeCCCCCcc Q 026941 143 ICGHCRTTLMYPH--GAPSVKCAVCQYV 168 (230) Q Consensus 143 ~Cg~Crt~LmyP~--GA~sVrCa~C~~V 168 (230) .|..|......|+ .....+|+.|+++ T Consensus 15 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~ 42 (403) T TIGR00155 15 LCSQCDMLVALPRIESGQKAACPRCGTT 42 (403) T ss_pred eCCCCCCcccccCCCCCCeeECCCCCCC Confidence 3444444444432 2223445555443 No 76 >smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III Probab=40.35 E-value=31 Score=23.67 Aligned_cols=29 Identities=21% Similarity=0.478 Sum_probs=14.1 Q ss_pred eCCCCCcceecCCCCceeEEEcCCCCeeeecc Q 026941 123 RCSCCHTVNLAPAPNQFAHIICGHCRTTLMYP 154 (230) Q Consensus 123 rC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP 154 (230) +|+.|+..+... ....++|..|.--++|- T Consensus 4 ~C~~Cg~~~~~~---~~~~irC~~CG~rIlyK 32 (44) T smart00659 4 ICGECGRENEIK---SKDVVRCRECGYRILYK 32 (44) T ss_pred ECCCCCCEeecC---CCCceECCCCCceEEEE Confidence 455555544432 22345555555555543 No 77 >COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis] Probab=39.65 E-value=25 Score=31.32 Aligned_cols=28 Identities=21% Similarity=0.573 Sum_probs=22.3 Q ss_pred eeEEEeCCcceeEEeecCCCeEeCCCCCcc Q 026941 101 MAQLICGGCRTLLMYTRGATSVRCSCCHTV 130 (230) Q Consensus 101 ~~qLvCggCr~lL~YP~GA~sVrC~~C~tV 130 (230) .-.-.|..|+..|++ .-...+|+.|+.+ T Consensus 147 VI~A~CsrC~~~L~~--~~~~l~Cp~Cg~t 174 (188) T COG1096 147 VIYARCSRCRAPLVK--KGNMLKCPNCGNT 174 (188) T ss_pred EEEEEccCCCcceEE--cCcEEECCCCCCE Confidence 445679999999999 6677899999765 No 78 >PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane Probab=39.00 E-value=13 Score=30.81 Aligned_cols=29 Identities=24% Similarity=0.534 Sum_probs=13.1 Q ss_pred EeCCCCCcceecCCCCceeEEEcCCCCeeeecc Q 026941 122 VRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYP 154 (230) Q Consensus 122 VrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP 154 (230) |.||.|+..|.+..-.+ .|-+|+++|.+. T Consensus 70 V~CP~C~K~TKmLGr~D----~CM~C~~pLTLd 98 (114) T PF11023_consen 70 VECPNCGKQTKMLGRVD----ACMHCKEPLTLD 98 (114) T ss_pred eECCCCCChHhhhchhh----ccCcCCCcCccC Confidence 34555555554433322 355555555444 No 79 >PRK04023 DNA polymerase II large subunit; Validated Probab=38.73 E-value=18 Score=39.57 Aligned_cols=53 Identities=21% Similarity=0.427 Sum_probs=39.5 Q ss_pred ceeEEEeCCcceeEEeecCCCeEeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCCeEeCCCCCcceee Q 026941 100 EMAQLICGGCRTLLMYTRGATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTNV 171 (230) Q Consensus 100 q~~qLvCggCr~lL~YP~GA~sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~sVrCa~C~~VT~V 171 (230) +.+.-.|..|.... ...+|+.|...|.. ..+|..|++..- ...|+.|.+.+.- T Consensus 623 EVg~RfCpsCG~~t------~~frCP~CG~~Te~-------i~fCP~CG~~~~------~y~CPKCG~El~~ 675 (1121) T PRK04023 623 EIGRRKCPSCGKET------FYRRCPFCGTHTEP-------VYRCPRCGIEVE------EDECEKCGREPTP 675 (1121) T ss_pred cccCccCCCCCCcC------CcccCCCCCCCCCc-------ceeCccccCcCC------CCcCCCCCCCCCc Confidence 45666899999984 55799999988431 459999977643 2459999987764 No 80 >PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B. Probab=38.42 E-value=49 Score=29.88 Aligned_cols=65 Identities=18% Similarity=0.413 Sum_probs=29.0 Q ss_pred eecCCCCccccc---CCCC-CceeEEEeCCcceeEEeecCCCeEeCCCCCcceecC-------CCCceeEEEcCCCCeee Q 026941 83 VCCALCNTITSV---PIPG-MEMAQLICGGCRTLLMYTRGATSVRCSCCHTVNLAP-------APNQFAHIICGHCRTTL 151 (230) Q Consensus 83 VrCa~C~tVt~V---pp~~-~q~~qLvCggCr~lL~YP~GA~sVrC~~C~tVn~Vp-------~~~q~a~V~Cg~Crt~L 151 (230) -.|+.|.+-... ...+ ....++.|+-|.+.=-|+|. +|+.|..-.... +....---.|..|+.=| T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~----~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~Yl 248 (290) T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRI----KCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYL 248 (290) T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TT----S-TTT---SS-EEE--------SEEEEEETTTTEEE T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCC----CCcCCCCCCCcceeeEecCCCCcEEEEECCcccchH Confidence 467777544332 1111 14699999999999999986 599998765421 12233344566666533 No 81 >PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function. Probab=37.90 E-value=28 Score=24.22 Aligned_cols=25 Identities=28% Similarity=0.559 Sum_probs=12.7 Q ss_pred EcCCCCeeeec------cCCCCeEeCCCCCc Q 026941 143 ICGHCRTTLMY------PHGAPSVKCAVCQY 167 (230) Q Consensus 143 ~Cg~Crt~Lmy------P~GA~sVrCa~C~~ 167 (230) .|++|++.|-- -.+..-+.|+.|+. T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgR 54 (56) T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNCGR 54 (56) T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCCCc Confidence 56666655421 13345566666654 No 82 >PF14369 zf-RING_3: zinc-finger Probab=36.47 E-value=30 Score=22.70 Aligned_cols=24 Identities=25% Similarity=0.746 Sum_probs=14.4 Q ss_pred eccccceeeee-cCCCCeeecCCCC Q 026941 66 VCSGCRSVLLY-PRGATNVCCALCN 89 (230) Q Consensus 66 vC~gCr~lL~Y-P~GA~~VrCa~C~ 89 (230) -|..|++.+.. +.+.+.+.|+.|+ T Consensus 4 wCh~C~~~V~~~~~~~~~~~CP~C~ 28 (35) T PF14369_consen 4 WCHQCNRFVRIAPSPDSDVACPRCH 28 (35) T ss_pred eCccCCCEeEeCcCCCCCcCCcCCC Confidence 46667766666 3444455677775 No 83 >COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription] Probab=35.38 E-value=26 Score=25.07 Aligned_cols=32 Identities=16% Similarity=0.447 Sum_probs=23.2 Q ss_pred ceeeccccceeeeecCCCCeeecCCCCccccc Q 026941 63 SQLVCSGCRSVLLYPRGATNVCCALCNTITSV 94 (230) Q Consensus 63 sQlvC~gCr~lL~YP~GA~~VrCa~C~tVt~V 94 (230) -.-+|..|...+.-.+.-..++|+.|..=-.+ T Consensus 5 ~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl~ 36 (49) T COG1996 5 MEYKCARCGREVELDQETRGIRCPYCGSRILV 36 (49) T ss_pred EEEEhhhcCCeeehhhccCceeCCCCCcEEEE Confidence 34578888888877777788888888654433 No 84 >KOG3002 consensus Zn finger protein [General function prediction only] Probab=32.95 E-value=18 Score=33.84 Aligned_cols=62 Identities=24% Similarity=0.643 Sum_probs=40.5 Q ss_pred eeecCCC-CcccccCCCCC--ceeEEEeCCcceeEEeecCCCeEeCCCCCc-ceecCC-----CCceeEEEcC----CCC Q 026941 82 NVCCALC-NTITSVPIPGM--EMAQLICGGCRTLLMYTRGATSVRCSCCHT-VNLAPA-----PNQFAHIICG----HCR 148 (230) Q Consensus 82 ~VrCa~C-~tVt~Vpp~~~--q~~qLvCggCr~lL~YP~GA~sVrC~~C~t-Vn~Vp~-----~~q~a~V~Cg----~Cr 148 (230) ..-|+.| +.+.+ |.+ +.+||.|..|++ -.+.+||-|.- ++.++. ..+-..+-|. +|. T Consensus 48 lleCPvC~~~l~~---Pi~QC~nGHlaCssC~~-------~~~~~CP~Cr~~~g~~R~~amEkV~e~~~vpC~~~~~GC~ 117 (299) T KOG3002|consen 48 LLDCPVCFNPLSP---PIFQCDNGHLACSSCRT-------KVSNKCPTCRLPIGNIRCRAMEKVAEAVLVPCKNAKLGCT 117 (299) T ss_pred hccCchhhccCcc---cceecCCCcEehhhhhh-------hhcccCCccccccccHHHHHHHHHHHhceecccccccCCc Confidence 3678888 55544 444 479999999997 44679999863 223332 1245567776 577 Q ss_pred eeeec Q 026941 149 TTLMY 153 (230) Q Consensus 149 t~Lmy 153 (230) -.+.| T Consensus 118 ~~~~Y 122 (299) T KOG3002|consen 118 KSFPY 122 (299) T ss_pred eeecc Confidence 77665 No 85 >PRK07219 DNA topoisomerase I; Validated Probab=32.39 E-value=85 Score=32.86 Aligned_cols=28 Identities=25% Similarity=0.428 Sum_probs=14.8 Q ss_pred eeeccccceeeeecCCC---CeeecCC---CCcc Q 026941 64 QLVCSGCRSVLLYPRGA---TNVCCAL---CNTI 91 (230) Q Consensus 64 QlvC~gCr~lL~YP~GA---~~VrCa~---C~tV 91 (230) ...|..|..-|.+-.+. ..+.|.. |... T Consensus 602 ~~~CP~Cg~~l~~r~~~~g~~F~gCs~yp~C~~t 635 (822) T PRK07219 602 IGKCPECGGDLIIIRTDKGSRFVGCSGYPDCRNT 635 (822) T ss_pred cCcCCCCCCcceeeeccCCceeeecCCCcCCCCe Confidence 35677777655543322 3366655 6543 No 86 >PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A. Probab=31.39 E-value=46 Score=25.41 Aligned_cols=30 Identities=33% Similarity=0.628 Sum_probs=22.4 Q ss_pred EEEcCCCCeeeeccCCCCeEeCCCCCcceeec Q 026941 141 HIICGHCRTTLMYPHGAPSVKCAVCQYVTNVN 172 (230) Q Consensus 141 ~V~Cg~Crt~LmyP~GA~sVrCa~C~~VT~V~ 172 (230) ..+| .|+..|.-..|+..-+| .|.+...|. T Consensus 3 ifrC-~Cgr~lya~e~~kTkkC-~CG~~l~vk 32 (68) T PF09082_consen 3 IFRC-DCGRYLYAKEGAKTKKC-VCGKTLKVK 32 (68) T ss_dssp EEEE-TTS--EEEETT-SEEEE-TTTEEEE-- T ss_pred EEEe-cCCCEEEecCCcceeEe-cCCCeeeee Confidence 4689 69999999999999999 899999985 No 87 >PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L .... Probab=31.38 E-value=19 Score=23.39 Aligned_cols=27 Identities=22% Similarity=0.538 Sum_probs=11.4 Q ss_pred CCCCCcceecCCCCceeEEEcCCCCeeeec Q 026941 124 CSCCHTVNLAPAPNQFAHIICGHCRTTLMY 153 (230) Q Consensus 124 C~~C~tVn~Vp~~~q~a~V~Cg~Crt~Lmy 153 (230) |+.|...+...+. ..++|..|.--+|| T Consensus 3 C~~Cg~~~~~~~~---~~irC~~CG~RIly 29 (32) T PF03604_consen 3 CGECGAEVELKPG---DPIRCPECGHRILY 29 (32) T ss_dssp ESSSSSSE-BSTS---STSSBSSSS-SEEB T ss_pred CCcCCCeeEcCCC---CcEECCcCCCeEEE Confidence 5555555553221 22455555544444 No 88 >COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription] Probab=30.72 E-value=52 Score=23.59 Aligned_cols=32 Identities=16% Similarity=0.441 Sum_probs=24.3 Q ss_pred eEEEcCCCCeeeeccCCCCeEeCCCCCcceee Q 026941 140 AHIICGHCRTTLMYPHGAPSVKCAVCQYVTNV 171 (230) Q Consensus 140 a~V~Cg~Crt~LmyP~GA~sVrCa~C~~VT~V 171 (230) ..-.|..|...+-......-++|+.|++---+ T Consensus 5 ~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl~ 36 (49) T COG1996 5 MEYKCARCGREVELDQETRGIRCPYCGSRILV 36 (49) T ss_pred EEEEhhhcCCeeehhhccCceeCCCCCcEEEE Confidence 35578888888877778888888888876555 No 89 >PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases. Probab=30.54 E-value=24 Score=21.90 Aligned_cols=10 Identities=30% Similarity=0.820 Sum_probs=5.3 Q ss_pred CeEeCCCCCc Q 026941 158 PSVKCAVCQY 167 (230) Q Consensus 158 ~sVrCa~C~~ 167 (230) .+.+|+.|++ T Consensus 13 ~~~~Cp~CG~ 22 (26) T PF10571_consen 13 SAKFCPHCGY 22 (26) T ss_pred hcCcCCCCCC Confidence 3445666654 No 90 >PRK02935 hypothetical protein; Provisional Probab=30.06 E-value=35 Score=28.28 Aligned_cols=34 Identities=26% Similarity=0.380 Sum_probs=21.3 Q ss_pred CCCeeecCCCCcccccCCCCCceeEEEeCCcceeEEeec Q 026941 79 GATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMYTR 117 (230) Q Consensus 79 GA~~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~YP~ 117 (230) -|..|.|+.|+-.|-+.. .--.|-.|++.|--.+ T Consensus 67 kavqV~CP~C~K~TKmLG-----rvD~CM~C~~PLTLd~ 100 (110) T PRK02935 67 KAVQVICPSCEKPTKMLG-----RVDACMHCNQPLTLDR 100 (110) T ss_pred cceeeECCCCCchhhhcc-----ceeecCcCCCcCCcCc Confidence 345677888877777653 3346777777665443 No 91 >PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A. Probab=29.33 E-value=31 Score=22.09 Aligned_cols=21 Identities=24% Similarity=0.593 Sum_probs=9.4 Q ss_pred EEeCCcceeEEeecCCCeEeCCCCC Q 026941 104 LICGGCRTLLMYTRGATSVRCSCCH 128 (230) Q Consensus 104 LvCggCr~lL~YP~GA~sVrC~~C~ 128 (230) -+|..|..+..||+ ..|+.|. T Consensus 12 ~rC~~Cg~~~~pPr----~~Cp~C~ 32 (37) T PF12172_consen 12 QRCRDCGRVQFPPR----PVCPHCG 32 (37) T ss_dssp EE-TTT--EEES------SEETTTT T ss_pred EEcCCCCCEecCCC----cCCCCcC Confidence 35666666666665 3456664 No 92 >PRK14892 putative transcription elongation factor Elf1; Provisional Probab=28.78 E-value=59 Score=26.03 Aligned_cols=11 Identities=18% Similarity=0.643 Sum_probs=4.7 Q ss_pred CCeEeCCCCCc Q 026941 157 APSVKCAVCQY 167 (230) Q Consensus 157 A~sVrCa~C~~ 167 (230) -..+.|+.|++ T Consensus 40 ~~h~~C~~CG~ 50 (99) T PRK14892 40 IAIITCGNCGL 50 (99) T ss_pred cceEECCCCCC Confidence 33444444443 No 93 >PRK15103 paraquat-inducible membrane protein A; Provisional Probab=28.72 E-value=41 Score=32.60 Aligned_cols=13 Identities=23% Similarity=0.680 Sum_probs=5.9 Q ss_pred EeCCCCCcceecC Q 026941 122 VRCSCCHTVNLAP 134 (230) Q Consensus 122 VrC~~C~tVn~Vp 134 (230) +.|+.|+.+...+ T Consensus 11 ~~C~~Cd~l~~~~ 23 (419) T PRK15103 11 ILCPQCDMLVALP 23 (419) T ss_pred ccCCCCCceeecC Confidence 3344554444443 No 94 >COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only] Probab=28.04 E-value=29 Score=31.73 Aligned_cols=12 Identities=25% Similarity=0.440 Sum_probs=5.9 Q ss_pred CCCeEeCCCCCc Q 026941 156 GAPSVKCAVCQY 167 (230) Q Consensus 156 GA~sVrCa~C~~ 167 (230) +-.-|+||.|+. T Consensus 218 ~d~iv~CP~CgR 229 (239) T COG1579 218 KDEIVFCPYCGR 229 (239) T ss_pred CCCCccCCccch Confidence 334455555544 No 95 >TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae. Probab=26.92 E-value=44 Score=25.51 Aligned_cols=27 Identities=22% Similarity=0.668 Sum_probs=19.4 Q ss_pred EcCCCCeeeeccCCCCeEeCCCCCcceee Q 026941 143 ICGHCRTTLMYPHGAPSVKCAVCQYVTNV 171 (230) Q Consensus 143 ~Cg~Crt~LmyP~GA~sVrCa~C~~VT~V 171 (230) .|..|+.+|. |.+ ..+.|+.|.+...+ T Consensus 2 fC~~Cg~~l~-~~~-~~~~C~~C~~~~~~ 28 (104) T TIGR01384 2 FCPKCGSLMT-PKN-GVYVCPSCGYEKEK 28 (104) T ss_pred CCcccCcccc-cCC-CeEECcCCCCcccc Confidence 4888888774 443 36889999887665 No 96 >COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis] Probab=26.88 E-value=40 Score=27.60 Aligned_cols=35 Identities=26% Similarity=0.504 Sum_probs=23.6 Q ss_pred ceeEEEcCCCCeeeeccCCC--------CeEeCCCCCcceeec Q 026941 138 QFAHIICGHCRTTLMYPHGA--------PSVKCAVCQYVTNVN 172 (230) Q Consensus 138 q~a~V~Cg~Crt~LmyP~GA--------~sVrCa~C~~VT~V~ 172 (230) ++-...|.+|.+.|....++ -.+.|-.|+++.+.. T Consensus 53 ~iKR~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~R~p 95 (105) T COG2023 53 EIKRTICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIRRYP 95 (105) T ss_pred HHHHHhccccCcccccCcceEEEEcCCeEEEEecCCCcEEEec Confidence 44455677777777766555 367787788777764 No 97 >PF00541 Adeno_knob: Adenoviral fibre protein (knob domain); InterPro: IPR000978 Adenoviruses are responsible for diseases such as pneumonia, cystitis, conjunctivitis and diarrhoea, all of which can be fatal to patients who are immunocompromised []. Viral infection commences with recognition of host cell receptors by means of specialised proteins on viral surfaces. Specific attachment of adenovirus is achieved through interactions between host-cell receptors and the adenovirus fibre protein and is mediated by the globular carboxy-terminal domain of the adenovirus fibre protein, termed the carboxy-terminal knob domain.; GO: 0007155 cell adhesion, 0019058 viral infectious cycle, 0019062 virion attachment to host cell surface receptor; PDB: 3EXW_A 3F0Y_I 2W9L_S 2J1K_I 2J2J_F 2WBV_E 2WGU_C 1UXE_B 2WGT_B 3QND_E .... Probab=26.84 E-value=60 Score=28.31 Aligned_cols=27 Identities=30% Similarity=0.445 Sum_probs=22.5 Q ss_pred HhhhcceeeEEEEeeeecCCcccccCc Q 026941 33 FIYINHTITQLSIDFDFSNDSILLSLQ 59 (230) Q Consensus 33 ~~~~~~~~~~~~~~~~f~~~~~l~~~~ 59 (230) +..|+.+..+++|-|.||+++.|+... T Consensus 45 ~~~i~~~~~~~~i~L~FD~~G~Ll~~~ 71 (171) T PF00541_consen 45 YNNITNTTNSFSIKLLFDSNGVLLSGS 71 (171) T ss_dssp GHGGGGSSEEEEEEEEEETTSEBETTT T ss_pred ceecCCCceeEEEEEEECCCCCEeeCC Confidence 456788878999999999999998533 No 98 >PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I .... Probab=26.58 E-value=31 Score=22.52 Aligned_cols=28 Identities=25% Similarity=0.617 Sum_probs=14.5 Q ss_pred cCCCCeeeeccCCC-CeEeCCCCCcceee Q 026941 144 CGHCRTTLMYPHGA-PSVKCAVCQYVTNV 171 (230) Q Consensus 144 Cg~Crt~LmyP~GA-~sVrCa~C~~VT~V 171 (230) |..|..+|....+. ..+.|..|.++-.+ T Consensus 4 Cp~C~nlL~p~~~~~~~~~C~~C~Y~~~~ 32 (35) T PF02150_consen 4 CPECGNLLYPKEDKEKRVACRTCGYEEPI 32 (35) T ss_dssp ETTTTSBEEEEEETTTTEEESSSS-EEE- T ss_pred CCCCCccceEcCCCccCcCCCCCCCccCC Confidence 66676666444322 22357777776655 No 99 >KOG2824 consensus Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones] Probab=26.56 E-value=87 Score=29.62 Aligned_cols=49 Identities=29% Similarity=0.640 Sum_probs=37.6 Q ss_pred EEeCCcceeEEeecCCCeEeCCCCCcceecCC--CCceeEEEcCCCCeeeeccCCCCeEeCCCCC Q 026941 104 LICGGCRTLLMYTRGATSVRCSCCHTVNLAPA--PNQFAHIICGHCRTTLMYPHGAPSVKCAVCQ 166 (230) Q Consensus 104 LvCggCr~lL~YP~GA~sVrC~~C~tVn~Vp~--~~q~a~V~Cg~Crt~LmyP~GA~sVrCa~C~ 166 (230) ..|.+|. |+.-+-|..|+.=..+-+ ......++|..|+- .-.|||+.|. T Consensus 230 ~~C~~CG-------g~rFlpC~~C~GS~kv~~~~~~~~~~~rC~~CNE-------NGLvrCp~Cs 280 (281) T KOG2824|consen 230 GVCESCG-------GARFLPCSNCHGSCKVHEEEEDDGGVLRCLECNE-------NGLVRCPVCS 280 (281) T ss_pred CcCCCcC-------CcceEecCCCCCceeeeeeccCCCcEEECcccCC-------CCceeCCccC Confidence 6788885 788888998888777765 56777888888875 3568888885 No 100 >PRK03564 formate dehydrogenase accessory protein FdhE; Provisional Probab=26.41 E-value=1.1e+02 Score=28.86 Aligned_cols=45 Identities=22% Similarity=0.501 Sum_probs=29.5 Q ss_pred CeeecCCCCccccc----CCCCCceeEEEeCCcceeEEeecCCCeEeCCCCCc Q 026941 81 TNVCCALCNTITSV----PIPGMEMAQLICGGCRTLLMYTRGATSVRCSCCHT 129 (230) Q Consensus 81 ~~VrCa~C~tVt~V----pp~~~q~~qLvCggCr~lL~YP~GA~sVrC~~C~t 129 (230) ..-.|+.|.+...+ ........++.|+-|.+.=-|+| ++|+.|.. T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R----~~C~~Cg~ 234 (309) T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVR----VKCSNCEQ 234 (309) T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccC----ccCCCCCC Confidence 34567777554321 11123468899999999888875 67999974 No 101 >PRK04351 hypothetical protein; Provisional Probab=26.38 E-value=52 Score=27.72 Aligned_cols=14 Identities=36% Similarity=0.800 Sum_probs=9.7 Q ss_pred eEEEcCCCCeeeec Q 026941 140 AHIICGHCRTTLMY 153 (230) Q Consensus 140 a~V~Cg~Crt~Lmy 153 (230) ..-+||.|+..|.+ T Consensus 131 ~~yrCg~C~g~L~~ 144 (149) T PRK04351 131 KRYRCGKCRGKLKL 144 (149) T ss_pred CcEEeCCCCcEeee Confidence 46677777777765 No 102 >PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A. Probab=26.29 E-value=1.6e+02 Score=22.48 Aligned_cols=59 Identities=24% Similarity=0.541 Sum_probs=33.3 Q ss_pred eeeccccceeeeecCCCCeeecCCCCcccccCCCCCceeEEEeCCcceeEEe--ecCCCeEeCCCCCccee Q 026941 64 QLVCSGCRSVLLYPRGATNVCCALCNTITSVPIPGMEMAQLICGGCRTLLMY--TRGATSVRCSCCHTVNL 132 (230) Q Consensus 64 QlvC~gCr~lL~YP~GA~~VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~Y--P~GA~sVrC~~C~tVn~ 132 (230) ++.|..|++.|.. +| ..-+|..|+.-- ..+..|..|...|-- .=||...-|-.|+...+ T Consensus 1 e~~CP~C~~~L~~-~~-~~~~C~~C~~~~--------~~~a~CPdC~~~Le~LkACGAvdYFC~~c~gLiS 61 (70) T PF07191_consen 1 ENTCPKCQQELEW-QG-GHYHCEACQKDY--------KKEAFCPDCGQPLEVLKACGAVDYFCNHCHGLIS 61 (70) T ss_dssp --B-SSS-SBEEE-ET-TEEEETTT--EE--------EEEEE-TTT-SB-EEEEETTEEEEE-TTTT-EE- T ss_pred CCcCCCCCCccEE-eC-CEEECccccccc--------eecccCCCcccHHHHHHHhcccceeeccCCceee Confidence 3578889888654 34 678888886521 256788888887743 45788888888877654 No 103 >smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function. Probab=26.19 E-value=76 Score=25.81 Aligned_cols=32 Identities=19% Similarity=0.361 Sum_probs=16.4 Q ss_pred eecCCCCcccccCCCCCceeEEEeCCcceeEE Q 026941 83 VCCALCNTITSVPIPGMEMAQLICGGCRTLLM 114 (230) Q Consensus 83 VrCa~C~tVt~Vpp~~~q~~qLvCggCr~lL~ 114 (230) -+|..|.....-........+.+|+.|+-.|. T Consensus 113 y~C~~C~~~~~~~rr~~~~~~y~C~~C~g~l~ 144 (146) T smart00731 113 YRCTGCGQRYLRVRRSNNVSRYRCGKCGGKLI 144 (146) T ss_pred EECCCCCCCCceEccccCcceEEcCCCCCEEE Confidence 45666654433222223336666766766654 No 104 >PF06589 CRA: Circumsporozoite-related antigen (CRA); InterPro: IPR009512 The mode of choroquine action or resistance of the malarial parasite Plasmodium falciparum is not fully elucidated and presents a huge challenge world wide. Plasmodial EXP-1 protein, also called circumsporozoite-related antigen, changes under chloroquine treatment, making it a potential chloroquine resistance marker []. Although there are no authentic repeats in this antigen, there are a number of internal homologies (N-A-N-P) and (N-A-D-P). The first of these tetramers is the dominant repeat found in the circumsporozoite protein (CSP) of P. falciparum and reacts with antibodies against circumsporozoite-related antigen (CRA). It is possible that immune responses to CRA may act against the CSP also. The CRA is found in many parasitic strains. Probab=26.12 E-value=33 Score=29.69 Aligned_cols=14 Identities=43% Similarity=1.018 Sum_probs=9.8 Q ss_pred hhhHHHHHhhhccee Q 026941 26 FFIFLFLFIYINHTI 40 (230) Q Consensus 26 ~~~~~~~~~~~~~~~ 40 (230) ||| ||+.|++||.. T Consensus 7 ~Fl-lF~~il~~~A~ 20 (157) T PF06589_consen 7 FFL-LFCLILCDHAL 20 (157) T ss_pred HHH-HHHHHHhhhhh Confidence 455 77788888764 No 105 >TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553). Probab=25.86 E-value=1.1e+02 Score=28.81 Aligned_cols=61 Identities=23% Similarity=0.507 Sum_probs=0.0 Q ss_pred cCCCCcccccC-----CCCCceeEEEeCCcceeEEeecCCCeEeCCCCC------cceecC--CCCceeEEEcCCCCe Q 026941 85 CALCNTITSVP-----IPGMEMAQLICGGCRTLLMYTRGATSVRCSCCH------TVNLAP--APNQFAHIICGHCRT 149 (230) Q Consensus 85 Ca~C~tVt~Vp-----p~~~q~~qLvCggCr~lL~YP~GA~sVrC~~C~------tVn~Vp--~~~q~a~V~Cg~Crt 149 (230) |+.|.+...+- .......++.|+-|.+.=-|. .++|+.|. ..+... +....---.|+.|++ T Consensus 187 CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~----R~~C~~Cg~~~~l~y~~~e~~~~~~~~r~e~C~~C~~ 260 (305) T TIGR01562 187 CPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYV----RVKCSHCEESKHLAYLSLEHDAEKAVLKAETCDSCQG 260 (305) T ss_pred CCCCCChhhhhhhcccCCCCCceEEEcCCCCCccccc----CccCCCCCCCCceeeEeecCCCCCcceEEeecccccc No 106 >smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers Probab=25.50 E-value=76 Score=21.32 Aligned_cols=21 Identities=29% Similarity=0.757 Sum_probs=9.4 Q ss_pred CcceeEEeec--CCCeEeCCCCC Q 026941 108 GCRTLLMYTR--GATSVRCSCCH 128 (230) Q Consensus 108 gCr~lL~YP~--GA~sVrC~~C~ 128 (230) +|...+.... +...|.|+.|+ T Consensus 25 ~C~~~~~~~~~~~~~~v~C~~C~ 47 (64) T smart00647 25 DCSAAIIVTEEEGCNRVTCPKCG 47 (64) T ss_pred CCcceEEecCCCCCCeeECCCCC Confidence 4444444432 44455554443 No 107 >PRK11827 hypothetical protein; Provisional Probab=25.44 E-value=81 Score=23.31 Aligned_cols=27 Identities=19% Similarity=0.437 Sum_probs=13.3 Q ss_pred EEeCCcceeEEeecCCCeEeCCCCCcc Q 026941 104 LICGGCRTLLMYTRGATSVRCSCCHTV 130 (230) Q Consensus 104 LvCggCr~lL~YP~GA~sVrC~~C~tV 130 (230) |+|..|+.-|.|-.++....|..|+-. T Consensus 9 LaCP~ckg~L~~~~~~~~Lic~~~~la 35 (60) T PRK11827 9 IACPVCNGKLWYNQEKQELICKLDNLA 35 (60) T ss_pred eECCCCCCcCeEcCCCCeEECCccCee Confidence 445555555555444444444444433 No 108 >PF13248 zf-ribbon_3: zinc-ribbon domain Probab=25.36 E-value=30 Score=20.97 Aligned_cols=9 Identities=22% Similarity=0.641 Sum_probs=5.0 Q ss_pred EeCCCCCcc Q 026941 122 VRCSCCHTV 130 (230) Q Consensus 122 VrC~~C~tV 130 (230) +.|+.|++. T Consensus 3 ~~Cp~Cg~~ 11 (26) T PF13248_consen 3 MFCPNCGAE 11 (26) T ss_pred CCCcccCCc Confidence 346666653 No 109 >PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A .... Probab=25.27 E-value=63 Score=21.51 Aligned_cols=28 Identities=21% Similarity=0.628 Sum_probs=19.4 Q ss_pred EEcCCCCeeeeccCCCCeEeCCCCCccee Q 026941 142 IICGHCRTTLMYPHGAPSVKCAVCQYVTN 170 (230) Q Consensus 142 V~Cg~Crt~LmyP~GA~sVrCa~C~~VT~ 170 (230) ..|..|+..| +..+...++|..|+.+-. T Consensus 12 ~~C~~C~~~i-~g~~~~g~~C~~C~~~~H 39 (53) T PF00130_consen 12 TYCDVCGKFI-WGLGKQGYRCSWCGLVCH 39 (53) T ss_dssp EB-TTSSSBE-CSSSSCEEEETTTT-EEE T ss_pred CCCcccCccc-CCCCCCeEEECCCCChHh Confidence 4688888888 336778888888887644 No 110 >PF05458 Siva: Cd27 binding protein (Siva); InterPro: IPR022773 Siva binds to the CD27 cytoplasmic tail. It has a DD homology region, a box-B-like ring finger, and a zinc finger-like domain. Overexpression of Siva in various cell lines induces apoptosis, suggesting an important role for Siva in the CD27-transduced apoptotic pathway []. Siva-1 binds to and inhibits BCL-X(L)-mediated protection against UV radiation-induced apoptosis. Indeed, the unique amphipathic helical region (SAH) present in Siva-1 is required for its binding to BCL-X(L) and sensitising cells to UV radiation. Natural complexes of Siva-1/BCL-X(L) are detected in HUT78 and murine thymocyte, suggesting a potential role for Siva-1 in regulating T cell homeostasis []. This family contains both Siva-1 and the shorter Siva-2 lacking the sequence coded by exon 2. It has been suggested that Siva-2 could regulate the function of Siva-1 []. Probab=25.25 E-value=24 Score=30.59 Aligned_cols=31 Identities=32% Similarity=0.758 Sum_probs=16.1 Q ss_pred ecCCCeEeCCCCCcceecCCCCceeEEEcCCCCe Q 026941 116 TRGATSVRCSCCHTVNLAPAPNQFAHIICGHCRT 149 (230) Q Consensus 116 P~GA~sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt 149 (230) ..+=..+.|+.|.+++.. .+...+-|-+|.+ T Consensus 142 C~~C~~~~Cs~Cs~~~y~---~~~e~~lC~~C~m 172 (175) T PF05458_consen 142 CSSCSEVFCSLCSTVNYS---DQYERVLCLSCSM 172 (175) T ss_pred hhchhhhhhcCccccccC---CcccccccCCCCC Confidence 444455566666665543 2334555655543 No 111 >PRK03564 formate dehydrogenase accessory protein FdhE; Provisional Probab=24.78 E-value=69 Score=30.32 Aligned_cols=14 Identities=21% Similarity=0.705 Sum_probs=7.3 Q ss_pred cCCCeEeCCCCCcc Q 026941 117 RGATSVRCSCCHTV 130 (230) Q Consensus 117 ~GA~sVrC~~C~tV 130 (230) .|.....|+.|.+- T Consensus 208 ~G~RyL~CslC~te 221 (309) T PRK03564 208 QGLRYLHCNLCESE 221 (309) T ss_pred CCceEEEcCCCCCc Confidence 45555555555544 No 112 >PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown. Probab=24.54 E-value=76 Score=26.87 Aligned_cols=30 Identities=20% Similarity=0.433 Sum_probs=15.6 Q ss_pred ceeeccccceeeeecCCCCeeecCCCCccc Q 026941 63 SQLVCSGCRSVLLYPRGATNVCCALCNTIT 92 (230) Q Consensus 63 sQlvC~gCr~lL~YP~GA~~VrCa~C~tVt 92 (230) +.++|-.|...+.|-.-..--.|+.|+... T Consensus 111 G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~~ 140 (146) T PF07295_consen 111 GTLVCENCGHEVELTHPERLPPCPKCGHTE 140 (146) T ss_pred ceEecccCCCEEEecCCCcCCCCCCCCCCe Confidence 555555555555554433345555555443 No 113 >KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription] Probab=23.67 E-value=27 Score=29.13 Aligned_cols=31 Identities=23% Similarity=0.459 Sum_probs=26.8 Q ss_pred EEeCCcceeEEeecCCCeEeCCCCCcceecC Q 026941 104 LICGGCRTLLMYTRGATSVRCSCCHTVNLAP 134 (230) Q Consensus 104 LvCggCr~lL~YP~GA~sVrC~~C~tVn~Vp 134 (230) .-|+-|..+|.-|.-++.|-|..|.....+. T Consensus 8 ~FC~~CG~ll~~~~~~~~~~C~~Ck~~~~v~ 38 (116) T KOG2907|consen 8 DFCSDCGSLLEEPSAQSTVLCIRCKIEYPVS 38 (116) T ss_pred chhhhhhhhcccccccCceEeccccccCCHH Confidence 5688899999999999999999999888765 No 114 >PF14353 CpXC: CpXC protein Probab=23.23 E-value=72 Score=25.17 Aligned_cols=16 Identities=13% Similarity=0.426 Sum_probs=8.2 Q ss_pred ceeEEEcCCCCeeeec Q 026941 138 QFAHIICGHCRTTLMY 153 (230) Q Consensus 138 q~a~V~Cg~Crt~Lmy 153 (230) +.-..+|.+|.....+ T Consensus 35 ~l~~~~CP~Cg~~~~~ 50 (128) T PF14353_consen 35 SLFSFTCPSCGHKFRL 50 (128) T ss_pred CcCEEECCCCCCceec Confidence 4445555555554443 No 115 >PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C. Probab=23.21 E-value=83 Score=20.69 Aligned_cols=9 Identities=33% Similarity=1.066 Sum_probs=3.3 Q ss_pred eeEEEeCCc Q 026941 101 MAQLICGGC 109 (230) Q Consensus 101 ~~qLvCggC 109 (230) ..-++|..| T Consensus 20 r~R~vC~~C 28 (34) T PF14803_consen 20 RERLVCPAC 28 (34) T ss_dssp S-EEEETTT T ss_pred ccceECCCC Confidence 334444444 No 116 >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=23.18 E-value=84 Score=21.47 Aligned_cols=22 Identities=32% Similarity=0.779 Sum_probs=10.0 Q ss_pred EcCCCCeeeeccCCCCeEeCCCC Q 026941 143 ICGHCRTTLMYPHGAPSVKCAVC 165 (230) Q Consensus 143 ~Cg~Crt~LmyP~GA~sVrCa~C 165 (230) .|..|.++||=..+. .+.|+.| T Consensus 19 ~Cp~C~~PL~~~k~g-~~~Cv~C 40 (41) T PF06677_consen 19 HCPDCGTPLMRDKDG-KIYCVSC 40 (41) T ss_pred ccCCCCCeeEEecCC-CEECCCC Confidence 455555555543322 2445544 No 117 >cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis). Probab=23.01 E-value=44 Score=21.51 Aligned_cols=26 Identities=19% Similarity=0.548 Sum_probs=18.2 Q ss_pred EcCCCCeeeeccCCCCeEeCCCCCcce Q 026941 143 ICGHCRTTLMYPHGAPSVKCAVCQYVT 169 (230) Q Consensus 143 ~Cg~Crt~LmyP~GA~sVrCa~C~~VT 169 (230) .|..|+..|... +....+|+.|..+- T Consensus 13 ~C~~C~~~i~~~-~~~~~~C~~C~~~~ 38 (50) T cd00029 13 FCDVCRKSIWGL-FKQGLRCSWCKVKC 38 (50) T ss_pred Chhhcchhhhcc-ccceeEcCCCCCch Confidence 477777777543 57788888887643 No 118 >KOG3002 consensus Zn finger protein [General function prediction only] Probab=22.72 E-value=33 Score=32.14 Aligned_cols=41 Identities=29% Similarity=0.653 Sum_probs=27.4 Q ss_pred CeEeCCCCCcceecCCC-CceeEEEcCCCCeeeeccCCCCeEeCCCCCc Q 026941 120 TSVRCSCCHTVNLAPAP-NQFAHIICGHCRTTLMYPHGAPSVKCAVCQY 167 (230) Q Consensus 120 ~sVrC~~C~tVn~Vp~~-~q~a~V~Cg~Crt~LmyP~GA~sVrCa~C~~ 167 (230) ...-||.|----..|.. -+.+|+.|..|++ -.+.+|+.|+. T Consensus 47 ~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~-------~~~~~CP~Cr~ 88 (299) T KOG3002|consen 47 DLLDCPVCFNPLSPPIFQCDNGHLACSSCRT-------KVSNKCPTCRL 88 (299) T ss_pred hhccCchhhccCcccceecCCCcEehhhhhh-------hhcccCCcccc Confidence 34668877433333332 2778999999998 44678888874 No 119 >PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A. Probab=22.68 E-value=62 Score=21.68 Aligned_cols=26 Identities=27% Similarity=0.597 Sum_probs=10.7 Q ss_pred EcCC--CCeeeeccCCCCe--EeCCCCCcc Q 026941 143 ICGH--CRTTLMYPHGAPS--VKCAVCQYV 168 (230) Q Consensus 143 ~Cg~--Crt~LmyP~GA~s--VrCa~C~~V 168 (230) .|.+ |...+....+... +.|+.|++. T Consensus 20 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 49 (64) T PF01485_consen 20 WCPNPDCEYIIEKDDGCNSPIVTCPSCGTE 49 (64) T ss_dssp --TTSST---ECS-SSTTS--CCTTSCCSE T ss_pred CCCCCCCcccEEecCCCCCCeeECCCCCCc Confidence 4544 5555555555554 555555544 No 120 >PRK14559 putative protein serine/threonine phosphatase; Provisional Probab=22.42 E-value=52 Score=33.89 Aligned_cols=51 Identities=29% Similarity=0.548 Sum_probs=28.4 Q ss_pred EEeCCcceeEEeecCCCeEeCCCCCcceecCCCCceeEEEcCCCCeeeeccCCCCeEeCCCCCccee Q 026941 104 LICGGCRTLLMYTRGATSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMYPHGAPSVKCAVCQYVTN 170 (230) Q Consensus 104 LvCggCr~lL~YP~GA~sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~LmyP~GA~sVrCa~C~~VT~ 170 (230) ++|..|.... | +.+.-|+.|.+--. +..|.+|... .|.|+. .|+.|++-.. T Consensus 2 ~~Cp~Cg~~n--~--~~akFC~~CG~~l~--------~~~Cp~CG~~--~~~~~~--fC~~CG~~~~ 52 (645) T PRK14559 2 LICPQCQFEN--P--NNNRFCQKCGTSLT--------HKPCPQCGTE--VPVDEA--HCPNCGAETG 52 (645) T ss_pred CcCCCCCCcC--C--CCCccccccCCCCC--------CCcCCCCCCC--CCcccc--cccccCCccc Confidence 3566666542 2 23335666654321 1357777776 455655 6888877544 No 121 >PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 []. Probab=22.14 E-value=29 Score=27.81 Aligned_cols=15 Identities=40% Similarity=0.815 Sum_probs=7.8 Q ss_pred ehhhHHHHHhhhcce Q 026941 25 SFFIFLFLFIYINHT 39 (230) Q Consensus 25 ~~~~~~~~~~~~~~~ 39 (230) .||||||+|+.+|.. T Consensus 11 ~i~l~~~~~~~~~rR 25 (130) T PF12273_consen 11 AILLFLFLFYCHNRR 25 (130) T ss_pred HHHHHHHHHHHHHHH Confidence 344555555555543 No 122 >smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains. Probab=21.94 E-value=44 Score=21.19 Aligned_cols=25 Identities=20% Similarity=0.608 Sum_probs=16.6 Q ss_pred EEcCCCCeeeeccCCCCeEeCCCCCcc Q 026941 142 IICGHCRTTLMYPHGAPSVKCAVCQYV 168 (230) Q Consensus 142 V~Cg~Crt~LmyP~GA~sVrCa~C~~V 168 (230) ..|..|+..|.... ..++|+.|+.+ T Consensus 12 ~~C~~C~~~i~~~~--~~~~C~~C~~~ 36 (49) T smart00109 12 TKCCVCRKSIWGSF--QGLRCSWCKVK 36 (49) T ss_pred CCccccccccCcCC--CCcCCCCCCch Confidence 35777777776433 46788888654 No 123 >TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes. Probab=21.68 E-value=68 Score=25.62 Aligned_cols=28 Identities=14% Similarity=0.425 Sum_probs=16.6 Q ss_pred eEEEcCCCCeeeeccCCCCeEeCCCCCcce Q 026941 140 AHIICGHCRTTLMYPHGAPSVKCAVCQYVT 169 (230) Q Consensus 140 a~V~Cg~Crt~LmyP~GA~sVrCa~C~~VT 169 (230) +..+|..|... ++.......||.|+... T Consensus 69 ~~~~C~~Cg~~--~~~~~~~~~CP~Cgs~~ 96 (115) T TIGR00100 69 VECECEDCSEE--VSPEIDLYRCPKCHGIM 96 (115) T ss_pred cEEEcccCCCE--EecCCcCccCcCCcCCC Confidence 45667777633 33333456788887643 No 124 >COG5416 Uncharacterized integral membrane protein [Function unknown] Probab=21.63 E-value=69 Score=26.07 Aligned_cols=28 Identities=18% Similarity=0.411 Sum_probs=17.4 Q ss_pred hhhHHHHHhhhcceeeEEEEeeeecCCc Q 026941 26 FFIFLFLFIYINHTITQLSIDFDFSNDS 53 (230) Q Consensus 26 ~~~~~~~~~~~~~~~~~~~~~~~f~~~~ 53 (230) +.|++.++|++-|..+.+.++|-|-.-+ T Consensus 31 ilillLllifav~Nt~~V~~~~lfg~~~ 58 (98) T COG5416 31 ILILLLLLIFAVINTDSVEFNYLFGQWE 58 (98) T ss_pred HHHHHHHHHHHHhccCceEEEeecchhh Confidence 3445555555555566777787776644 No 125 >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=21.57 E-value=1.1e+02 Score=21.43 Aligned_cols=13 Identities=38% Similarity=0.570 Sum_probs=6.4 Q ss_pred CeEeCCCCCccee Q 026941 120 TSVRCSCCHTVNL 132 (230) Q Consensus 120 ~sVrC~~C~tVn~ 132 (230) +|-.|+.|..+.. T Consensus 27 TSq~C~~CG~~~~ 39 (69) T PF07282_consen 27 TSQTCPRCGHRNK 39 (69) T ss_pred CccCccCcccccc Confidence 4445555555443 No 126 >TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A. Probab=21.50 E-value=91 Score=30.09 Aligned_cols=34 Identities=26% Similarity=0.471 Sum_probs=26.3 Q ss_pred CeEeCCCCCcceecCCCCceeEEEcCCCCeeeec Q 026941 120 TSVRCSCCHTVNLAPAPNQFAHIICGHCRTTLMY 153 (230) Q Consensus 120 ~sVrC~~C~tVn~Vp~~~q~a~V~Cg~Crt~Lmy 153 (230) ..+.|+.|+.+..+++-..-..-.|..|+..|.- T Consensus 12 ~~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~ 45 (403) T TIGR00155 12 KHILCSQCDMLVALPRIESGQKAACPRCGTTLTV 45 (403) T ss_pred CeeeCCCCCCcccccCCCCCCeeECCCCCCCCcC Confidence 3678999999998886444446779999999953 No 127 >PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors []. Probab=21.41 E-value=1.3e+02 Score=19.56 Aligned_cols=25 Identities=16% Similarity=0.386 Sum_probs=10.5 Q ss_pred EeCCcceeEEeecCCCeEeCCCCCc Q 026941 105 ICGGCRTLLMYTRGATSVRCSCCHT 129 (230) Q Consensus 105 vCggCr~lL~YP~GA~sVrC~~C~t 129 (230) .|.+|+.-++|-.-...-.|.-|.. T Consensus 5 ~C~~C~~~~i~~~~~~~~~C~~Cg~ 29 (33) T PF08792_consen 5 KCSKCGGNGIVNKEDDYEVCIFCGS 29 (33) T ss_pred EcCCCCCCeEEEecCCeEEcccCCc Confidence 3444444444433333344444433 No 128 >cd00069 GHB Glycoprotein hormone beta chain homologues. Gonadotropins; reproductive hormones consisting of two glycosylated chains (alpha and beta) of similar topology with Cysteine-knot motifs. Probab=21.28 E-value=76 Score=25.76 Aligned_cols=44 Identities=34% Similarity=0.614 Sum_probs=31.1 Q ss_pred ecCCcccccCcCccceeecc------------ccce----eeeecCCCCeeecCCCCcccc Q 026941 49 FSNDSILLSLQGMQSQLVCS------------GCRS----VLLYPRGATNVCCALCNTITS 93 (230) Q Consensus 49 f~~~~~l~~~~~mqsQlvC~------------gCr~----lL~YP~GA~~VrCa~C~tVt~ 93 (230) +..|+++.++-....|-+|. ||.. ...|| =|-+.+|..|++-+. T Consensus 31 ~T~dpv~~~~~~~~~Q~vCtY~~~~Y~tv~lpgCp~gvdp~~tYP-VAlsC~C~~C~t~~t 90 (102) T cd00069 31 YTKDPVYKSPLSPLPQRVCTYRELSYETVRLPGCPPGVDPGVTYP-VALSCHCGKCNTDTT 90 (102) T ss_pred ccccccccccCCCcccCcccCCcEEEEEEECCCCcCCCCCCEEee-eecccccCCcCCCCc Confidence 44566666666666888884 6766 77777 467888888877654 No 129 >PF14634 zf-RING_5: zinc-RING finger domain Probab=20.99 E-value=10 Score=25.00 Aligned_cols=10 Identities=50% Similarity=1.218 Sum_probs=4.5 Q ss_pred CCeEeCCCCC Q 026941 157 APSVKCAVCQ 166 (230) Q Consensus 157 A~sVrCa~C~ 166 (230) ...++|+.|+ T Consensus 34 ~~~~~CP~C~ 43 (44) T PF14634_consen 34 GKSVKCPICR 43 (44) T ss_pred CCCCCCcCCC Confidence 3444444443 No 130 >PRK04023 DNA polymerase II large subunit; Validated Probab=20.88 E-value=59 Score=35.80 Aligned_cols=9 Identities=33% Similarity=0.807 Sum_probs=4.3 Q ss_pred eecCCCCcc Q 026941 83 VCCALCNTI 91 (230) Q Consensus 83 VrCa~C~tV 91 (230) -+|+.|.+. T Consensus 639 frCP~CG~~ 647 (1121) T PRK04023 639 RRCPFCGTH 647 (1121) T ss_pred ccCCCCCCC Confidence 445555444 No 131 >PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A. Probab=20.76 E-value=70 Score=19.99 Aligned_cols=21 Identities=24% Similarity=0.730 Sum_probs=10.3 Q ss_pred EcCCCCeeeeccCCCCeEeCC Q 026941 143 ICGHCRTTLMYPHGAPSVKCA 163 (230) Q Consensus 143 ~Cg~Crt~LmyP~GA~sVrCa 163 (230) +|.-|.+.|....|...++|. T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~ 21 (28) T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCP 21 (28) T ss_dssp B-TTT--BEEE-CCTTCEEE- T ss_pred CcCCCCCEeEcCCCCEeEECC Confidence 366666666666666666664 No 132 >COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion] Probab=20.59 E-value=61 Score=29.38 Aligned_cols=29 Identities=21% Similarity=0.495 Sum_probs=22.7 Q ss_pred eeecCCCCcccccCCCCCceeEEEeCCcc Q 026941 82 NVCCALCNTITSVPIPGMEMAQLICGGCR 110 (230) Q Consensus 82 ~VrCa~C~tVt~Vpp~~~q~~qLvCggCr 110 (230) +|+|..|.....-+..-...+.++|..|. T Consensus 172 ~v~C~kCGE~~~e~~~~~~ng~~vC~~C~ 200 (206) T COG2191 172 SVRCSKCGELFMEPRAVVLNGKPVCKPCA 200 (206) T ss_pred eeeccccCcccccchhhhcCCceeccccc Confidence 58888888877776656677888998885 No 133 >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=20.10 E-value=92 Score=19.58 Aligned_cols=26 Identities=15% Similarity=0.418 Sum_probs=14.4 Q ss_pred eeccccceeeeecCC---CCeeecCCCCc Q 026941 65 LVCSGCRSVLLYPRG---ATNVCCALCNT 90 (230) Q Consensus 65 lvC~gCr~lL~YP~G---A~~VrCa~C~t 90 (230) ..|..|.......++ ...+.|+.|.. T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41) T smart00834 6 YRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41) T ss_pred EEcCCCCCEEEEEEecCCCCCCCCCCCCC Confidence 456666665544333 23566766654 No 134 >PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A. Probab=20.01 E-value=94 Score=22.94 Aligned_cols=49 Identities=12% Similarity=0.333 Sum_probs=15.1 Q ss_pred EeeeecCCcccccCcCccceeeccccceeeeecCCCCeeecCCCCcccc Q 026941 45 IDFDFSNDSILLSLQGMQSQLVCSGCRSVLLYPRGATNVCCALCNTITS 93 (230) Q Consensus 45 ~~~~f~~~~~l~~~~~mqsQlvC~gCr~lL~YP~GA~~VrCa~C~tVt~ 93 (230) +|-+-...+|+..-.+....+.|..|..--.-+-+--.-+|..|.+-|. T Consensus 11 LD~~i~~~pmP~~Y~~~~v~IlCNDC~~~s~v~fH~lg~KC~~C~SYNT 59 (61) T PF14599_consen 11 LDAEIAATPMPEEYRNKKVWILCNDCNAKSEVPFHFLGHKCSHCGSYNT 59 (61) T ss_dssp -----------------EEEEEESSS--EEEEE--TT----TTTS---E T ss_pred HHHHHHhCCCCHHHhCCEEEEECCCCCCccceeeeHhhhcCCCCCCccc Confidence 3444444554444444446777888887776676666777888866553 Done!