Query gi|254781067|ref|YP_003065480.1| elongation factor P [Candidatus Liberibacter asiaticus str. psy62] Match_columns 189 No_of_seqs 126 out of 1788 Neff 6.0 Searched_HMMs 39220 Date Mon May 30 05:19:03 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781067.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR00038 efp translation elon 100.0 0 0 502.4 17.7 189 1-189 1-194 (194) 2 PRK00529 elongation factor P; 100.0 0 0 495.4 22.0 186 3-188 1-186 (186) 3 PRK12426 elongation factor P; 100.0 0 0 488.4 21.7 185 3-187 1-185 (185) 4 PRK04542 elongation factor P; 100.0 0 0 483.4 22.0 186 3-188 1-189 (189) 5 TIGR02178 yeiP elongation fact 100.0 0 0 360.5 16.6 183 5-187 1-187 (187) 6 COG0231 Efp Translation elonga 100.0 2.6E-43 0 286.1 15.1 131 1-131 1-131 (131) 7 PRK03999 translation initiatio 100.0 1.7E-32 4.3E-37 219.9 14.1 120 1-122 1-123 (129) 8 pfam09285 Elong-fact-P_C Elong 99.9 1.3E-22 3.3E-27 159.3 6.2 56 131-186 1-56 (56) 9 smart00841 Elong-fact-P_C Elon 99.9 1.5E-22 3.9E-27 158.9 6.2 56 131-186 1-56 (56) 10 cd05794 S1_EF-P_repeat_2 S1_EF 99.9 2.6E-22 6.7E-27 157.4 6.2 56 131-186 1-56 (56) 11 cd04470 S1_EF-P_repeat_1 S1_EF 99.8 7.2E-20 1.8E-24 142.5 6.9 61 68-128 1-61 (61) 12 pfam08207 EFP_N Elongation fac 99.7 1.9E-17 4.8E-22 127.7 7.8 58 5-62 1-58 (58) 13 pfam01132 EFP Elongation facto 99.7 3.3E-17 8.3E-22 126.3 6.0 55 69-123 1-55 (55) 14 TIGR00037 eIF_5A translation i 99.6 1.1E-15 2.7E-20 117.0 8.7 113 4-116 7-123 (137) 15 PTZ00328 eukaryotic initiation 99.4 1.2E-11 3.1E-16 92.1 12.7 115 4-118 23-149 (166) 16 KOG3271 consensus 99.2 1.7E-10 4.4E-15 85.1 9.4 121 5-125 22-150 (156) 17 cd04467 S1_aIF5A S1_aIF5A: Arc 96.9 0.0017 4.3E-08 42.2 5.0 53 67-121 1-53 (57) 18 COG1499 NMD3 NMD protein affec 96.7 0.024 6.2E-07 35.1 9.6 104 7-126 245-352 (355) 19 cd04463 S1_EF_like S1_EF_like: 96.0 0.0077 2E-07 38.2 3.7 54 70-124 1-54 (55) 20 cd04463 S1_EF_like S1_EF_like: 95.0 0.045 1.1E-06 33.5 4.8 36 151-186 11-55 (55) 21 pfam01287 eIF-5a Eukaryotic el 92.6 0.37 9.4E-06 27.9 5.6 60 66-125 1-68 (69) 22 PRK08463 acetyl-CoA carboxylas 81.2 4.9 0.00012 21.0 6.1 65 70-140 272-344 (478) 23 PRK08591 acetyl-CoA carboxylas 79.2 2.8 7.1E-05 22.5 3.7 26 70-96 272-297 (449) 24 TIGR00514 accC acetyl-CoA carb 77.1 0.98 2.5E-05 25.3 0.9 73 71-150 274-355 (451) 25 KOG0238 consensus 74.4 7.5 0.00019 19.9 4.9 69 70-138 268-356 (670) 26 cd04468 S1_eIF5A S1_eIF5A: Euk 68.2 9.3 0.00024 19.3 4.2 50 67-116 1-53 (69) 27 KOG0267 consensus 63.5 13 0.00034 18.4 5.5 161 5-172 137-313 (825) 28 PRK08654 pyruvate carboxylase 61.6 14 0.00036 18.2 6.4 26 70-96 272-297 (497) 29 PRK12833 acetyl-CoA carboxylas 59.9 14 0.00035 18.3 3.8 27 70-96 274-301 (458) 30 COG1153 FwdD Formylmethanofura 58.2 6.2 0.00016 20.4 1.7 32 66-97 16-47 (128) 31 pfam00900 Ribosomal_S4e Riboso 55.6 18 0.00046 17.6 4.4 37 146-182 36-73 (74) 32 cd02779 MopB_CT_Arsenite-Ox Th 52.3 10 0.00026 19.1 2.1 14 107-120 47-60 (115) 33 cd02789 MopB_CT_FmdC-FwdD The 52.1 9.7 0.00025 19.2 2.0 55 45-120 4-58 (106) 34 cd02792 MopB_CT_Formate-Dh-Na- 48.5 12 0.0003 18.7 1.9 32 78-121 32-63 (122) 35 TIGR02102 pullulan_Gpos pullul 48.4 13 0.00033 18.4 2.1 19 119-137 1008-1026(1164) 36 cd02791 MopB_CT_Nitrate-R-NapA 46.5 14 0.00035 18.3 2.0 30 79-120 33-62 (122) 37 cd02780 MopB_CT_Tetrathionate_ 45.9 14 0.00036 18.2 2.0 31 79-121 28-58 (143) 38 cd02785 MopB_CT_4 The MopB_CT_ 45.1 14 0.00036 18.2 1.9 16 106-121 45-60 (124) 39 TIGR01591 Fdh-alpha formate de 45.0 13 0.00034 18.3 1.7 23 166-188 623-646 (694) 40 pfam00498 FHA FHA domain. The 44.6 27 0.00069 16.5 4.0 55 61-115 12-66 (67) 41 cd02790 MopB_CT_Formate-Dh_H F 44.4 15 0.00038 18.1 1.9 31 79-121 33-63 (116) 42 PRK13480 3'-5' exoribonuclease 43.9 27 0.0007 16.4 5.6 57 1-62 1-57 (314) 43 cd02777 MopB_CT_DMSOR-like The 42.8 18 0.00046 17.6 2.1 17 106-122 47-63 (127) 44 PRK06111 acetyl-CoA carboxylas 41.4 28 0.00071 16.4 2.9 27 70-96 272-298 (449) 45 PRK05586 biotin carboxylase; V 40.0 32 0.00081 16.1 5.8 97 70-173 272-377 (447) 46 cd02786 MopB_CT_3 The MopB_CT_ 38.7 21 0.00053 17.2 1.9 32 79-122 29-60 (116) 47 pfam02941 FeThRed_A Ferredoxin 38.5 21 0.00054 17.1 2.0 30 106-135 24-57 (67) 48 PRK08462 biotin carboxylase; V 38.4 34 0.00086 15.9 6.4 97 69-174 273-379 (446) 49 cd00508 MopB_CT_Fdh-Nap-like T 38.3 21 0.00054 17.1 1.9 31 78-120 32-62 (120) 50 cd02776 MopB_CT_Nitrate-R-NarG 38.3 23 0.00058 17.0 2.1 30 106-135 44-78 (141) 51 TIGR01540 portal_PBSX phage po 38.1 11 0.00028 18.8 0.5 21 166-186 169-189 (386) 52 cd02778 MopB_CT_Thiosulfate-R- 36.8 24 0.00061 16.8 2.0 31 79-121 28-58 (123) 53 cd02793 MopB_CT_DMSOR-BSOR-TMA 36.2 26 0.00067 16.5 2.1 17 106-122 46-62 (129) 54 pfam01568 Molydop_binding Moly 35.1 25 0.00065 16.7 1.9 15 107-121 44-58 (110) 55 KOG1708 consensus 35.1 23 0.0006 16.9 1.7 52 118-184 122-173 (236) 56 cd02781 MopB_CT_Acetylene-hydr 34.9 26 0.00066 16.6 1.9 15 107-121 47-61 (130) 57 PRK03955 hypothetical protein; 33.6 29 0.00074 16.3 2.0 16 167-182 111-126 (132) 58 cd02775 MopB_CT Molybdopterin- 33.1 27 0.0007 16.5 1.8 15 107-121 37-51 (101) 59 PRK07178 acetyl-CoA carboxylas 32.2 42 0.0011 15.3 7.4 96 71-174 272-376 (471) 60 cd02782 MopB_CT_1 The MopB_CT_ 31.1 34 0.00086 15.9 2.0 16 107-122 47-62 (129) 61 cd02794 MopB_CT_DmsA-EC The Mo 31.0 34 0.00088 15.8 2.0 17 106-122 43-59 (121) 62 TIGR01363 strep_his_triad stre 29.4 39 0.001 15.5 2.1 75 6-87 122-206 (376) 63 TIGR02087 LEUD_arch 3-isopropy 25.7 46 0.0012 15.1 1.9 19 166-184 108-126 (159) 64 TIGR01196 edd phosphogluconate 25.4 42 0.0011 15.3 1.6 16 168-183 546-561 (614) 65 TIGR01017 rpsD_bact ribosomal 25.2 56 0.0014 14.5 2.9 27 154-180 126-153 (217) 66 TIGR02517 type_II_gspD general 24.9 51 0.0013 14.8 2.0 36 142-177 558-595 (697) 67 PRK06302 acetyl-CoA carboxylas 24.8 31 0.00079 16.1 0.9 14 165-178 99-112 (155) 68 pfam08968 DUF1885 Domain of un 24.7 47 0.0012 15.0 1.8 52 73-124 59-124 (128) 69 TIGR03479 DMSO_red_II_alp DMSO 24.5 50 0.0013 14.8 1.9 22 167-188 823-844 (912) 70 cd00060 FHA Forkhead associate 23.5 60 0.0015 14.3 3.7 56 61-116 36-92 (102) 71 PRK03947 prefoldin subunit alp 23.4 61 0.0015 14.3 3.1 46 142-187 47-92 (141) 72 pfam11871 DUF3391 Domain of un 23.0 57 0.0014 14.5 1.9 21 2-22 3-23 (127) 73 PRK08166 NADH dehydrogenase su 23.0 50 0.0013 14.8 1.7 23 166-188 800-822 (858) 74 COG3173 Predicted aminoglycosi 22.8 62 0.0016 14.3 2.7 19 9-27 205-223 (321) 75 TIGR01348 PDHac_trf_long pyruv 22.3 64 0.0016 14.2 2.3 23 143-165 230-253 (655) 76 PRK08493 NADH dehydrogenase su 21.6 58 0.0015 14.5 1.8 23 166-188 759-781 (819) 77 COG0243 BisC Anaerobic dehydro 21.3 67 0.0017 14.1 2.0 21 168-188 685-705 (765) 78 smart00359 PUA Putative RNA-bi 21.2 67 0.0017 14.1 2.9 33 155-187 18-50 (77) 79 PRK13532 nitrate reductase; Pr 21.1 61 0.0016 14.3 1.8 23 166-188 756-778 (828) 80 smart00166 UBX Domain present 20.7 49 0.0012 14.9 1.2 48 35-87 3-50 (80) 81 pfam10709 DUF2511 Protein of u 20.5 69 0.0018 14.0 4.2 56 65-120 34-89 (110) 82 pfam00789 UBX UBX domain. This 20.1 71 0.0018 13.9 2.1 49 35-86 3-51 (81) No 1 >TIGR00038 efp translation elongation factor P; InterPro: IPR011768 Members of this family possess translation elongation factor activity. They have been shown to stimulate efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro, possibly indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase (by similarity) . This family does not include members of IPR011897 from INTERPRO, an EFP-like protein of certain gammaproteobacteria.; GO: 0003746 translation elongation factor activity, 0006414 translational elongation, 0005737 cytoplasm. Probab=100.00 E-value=0 Score=502.38 Aligned_cols=189 Identities=35% Similarity=0.620 Sum_probs=187.7 Q ss_pred CC-EEEHHHCCCCCEEEE-CCEEEEEEEEEEECCCCCCCEEEEEEEECCCCCCEEEEECCCCCEEEEEECCCEEEEEEEE Q ss_conf 92-366432167758998-8937999998753688876389999998246871001342787200101056405789961 Q gi|254781067|r 1 MV-KVIASAVRKGNVLDV-DGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQD 78 (189) Q Consensus 1 m~-~i~an~lk~G~~i~~-dg~~~~V~~~~~~kpgkg~a~v~~klknL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~d 78 (189) || ++.+|+||+|..|.. ||+||+|++++|+|||||+||+|+|||||+||++++++||++|++|.|++++..|||||.| T Consensus 1 MA~~~~s~d~r~Gl~i~~~~G~~~~VvE~~fvKpGkG~AfVR~Klk~L~tG~v~~~tFk~Gd~~e~~~i~~~~mqylYkD 80 (194) T TIGR00038 1 MAEMISSNDFRKGLKILLIDGEPYRVVENEFVKPGKGQAFVRTKLKNLRTGAVVEKTFKAGDKVEQANIEEKTMQYLYKD 80 (194) T ss_pred CCCEEEEECCCCCCEEEECCCEEEEEEECCCCCCCCCCCEEEEEEEECCCCCEEEEECCCCCCCCCCEEEEEEEEEEEEC T ss_conf 97405520456885387229838999812457875666166766531358848999417668635416764334477706 Q ss_pred CCEEEEEECCCCCCCCCCHHH---HHHHHHHCCCCCEEEEEEECCEEEEECCCCEEEEEEEECCCCCCCCCCCCCEEEEE Q ss_conf 988999946887643211543---00133201378615689766777440158749999998285421310247700089 Q gi|254781067|r 79 QEGFHFMNPETYDQVTVSEEV---IGDQKVYFQEGMEVKLLIHEGVALSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAI 155 (189) Q Consensus 79 g~~~~FMd~etyeqi~i~~~~---ig~~~~fL~eg~~v~i~~~~~~~i~i~lP~~v~l~V~~t~p~~kG~t~~~~~K~A~ 155 (189) ||.|+|||++||||++|+.+. |||+.+||.|+++|+|.+|+|++|+|+||++|.|+|++||||+|||||++++|||+ T Consensus 81 gd~~vFMD~etyeQ~~~~~~~sanl~d~~kfl~e~~~v~v~~~~~~~l~v~lP~~V~levVetepg~KGDTa~~g~KpA~ 160 (194) T TIGR00038 81 GDQYVFMDLETYEQISLDAKQSANLGDEAKFLLEEMEVSVVLYNDEILGVELPNLVELEVVETEPGVKGDTATGGTKPAT 160 (194) T ss_pred CCEEEECCCCCHHHEECCCCCCCCCHHHHCCCCCCCEEEEEEECCEEEECCCCCEEEEEEEECCCCCCCCCCCCCCCCEE T ss_conf 97688667886555311611154520110023566338999768948413078725789987588974663678604558 Q ss_pred EECCCEEECCCCCCCCCEEEEECCCCCEEHHCCC Q ss_conf 9379599847401688799998899724021029 Q gi|254781067|r 156 LSNDIRTTVPPHINIGDDIVILTEDNSYVERVKK 189 (189) Q Consensus 156 letG~~i~VP~FI~~Gd~IkV~T~~g~Y~~Rakk 189 (189) |+||++|+||+||++||+|+|||+||||++|+|+ T Consensus 161 L~TG~vV~VPlFv~~Gd~i~v~T~~geY~eR~k~ 194 (194) T TIGR00038 161 LETGAVVKVPLFVNEGDKIKVNTRDGEYVERVKK 194 (194) T ss_pred ECCCCEEECCEEEEECCEEEEECCCCCHHCCCCC T ss_conf 6168688254054208889892577731100269 No 2 >PRK00529 elongation factor P; Validated Probab=100.00 E-value=0 Score=495.42 Aligned_cols=186 Identities=38% Similarity=0.645 Sum_probs=184.6 Q ss_pred EEEHHHCCCCCEEEECCEEEEEEEEEEECCCCCCCEEEEEEEECCCCCCEEEEECCCCCEEEEEECCCEEEEEEEECCEE Q ss_conf 36643216775899889379999987536888763899999982468710013427872001010564057899619889 Q gi|254781067|r 3 KVIASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQDQEGF 82 (189) Q Consensus 3 ~i~an~lk~G~~i~~dg~~~~V~~~~~~kpgkg~a~v~~klknL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~dg~~~ 82 (189) |++||+||+|++|++||+||+|++++|++||||+||+|+|||||.||+++++||+++|++|.|+++++++||||.||+.| T Consensus 1 Mi~~~~ik~G~~i~~~g~~~~V~~~~~~kpgkg~A~~~~klknl~tG~~~e~~f~s~d~ve~a~~~~~~~qylY~dg~~~ 80 (186) T PRK00529 1 MISANDFRPGNVIELDGEPWVVLEFEHVKPGKGQAFVRVKLKNLLTGKVVEKTFKAGDKVERADVERKEMQYLYFDGEMY 80 (186) T ss_pred CCCHHHCCCCCEEEECCEEEEEEEEEEECCCCCCEEEEEEEEECCCCCEEEEEECCCCEEEEEEEEEEEEEEEEECCCCE T ss_conf 98568667878999999999999988873888952899999982789748999858977788689634569999779953 Q ss_pred EEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCEEEEECCCCEEEEEEEECCCCCCCCCCCCCEEEEEEECCCEE Q ss_conf 99946887643211543001332013786156897667774401587499999982854213102477000899379599 Q gi|254781067|r 83 HFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVALSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRT 162 (189) Q Consensus 83 ~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~~i~i~lP~~v~l~V~~t~p~~kG~t~~~~~K~A~letG~~i 162 (189) +|||++||||++|+++++|++.+||+||++|.+.+|+|+||+|+||++|+|+|++|+|++|||||++++|||+||||++| T Consensus 81 ~FMd~etyEQi~l~~~~ig~~~~~L~e~~~v~v~~~~~~~i~v~lP~~V~l~V~et~p~vKGdTas~~~KpA~letG~~v 160 (186) T PRK00529 81 VFMDTETYEQIEVPAEQVGDAAKFLKEGMEVTVTFYNGEPISVELPNTVELEVTETEPGVKGDTASGGTKPATLETGAVV 160 (186) T ss_pred EEECCCCCCCEECCHHHHHHHHHHHCCCCEEEEEEECCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCEEEECCCCEE T ss_conf 99769974114347889777887423797899999899998555898599999988996444456788661998289999 Q ss_pred ECCCCCCCCCEEEEECCCCCEEHHCC Q ss_conf 84740168879999889972402102 Q gi|254781067|r 163 TVPPHINIGDDIVILTEDNSYVERVK 188 (189) Q Consensus 163 ~VP~FI~~Gd~IkV~T~~g~Y~~Rak 188 (189) +||+||++||+|+||||+|+|++||| T Consensus 161 ~VP~FI~~Gd~IkVdT~~geYv~RaK 186 (186) T PRK00529 161 QVPLFINEGEKIKVDTRTGEYVSRAK 186 (186) T ss_pred EECCCCCCCCEEEEECCCCEEEHHCC T ss_conf 83883218999999899976800249 No 3 >PRK12426 elongation factor P; Provisional Probab=100.00 E-value=0 Score=488.35 Aligned_cols=185 Identities=23% Similarity=0.484 Sum_probs=183.4 Q ss_pred EEEHHHCCCCCEEEECCEEEEEEEEEEECCCCCCCEEEEEEEECCCCCCEEEEECCCCCEEEEEECCCEEEEEEEECCEE Q ss_conf 36643216775899889379999987536888763899999982468710013427872001010564057899619889 Q gi|254781067|r 3 KVIASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQDQEGF 82 (189) Q Consensus 3 ~i~an~lk~G~~i~~dg~~~~V~~~~~~kpgkg~a~v~~klknL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~dg~~~ 82 (189) |++||+||+|++|+++|+||+|++++|++||||+||+|+|||||.||+++++||+++|++|.|+++++++||||.||+.| T Consensus 1 Mi~~n~lk~G~~i~~~g~~~~V~~~~h~kpGkg~a~v~~klknl~tG~~~e~tf~s~ekve~a~~~~~~~qyLY~dg~~~ 80 (185) T PRK12426 1 MVLSSQLSVGMFISTKDGLYKVVSVSKVTGPKGESFIKVSLQAADSDVIVERNFKAGQEVKEAQFEPRNLEYLYLEDDSY 80 (185) T ss_pred CCCHHHCCCCCEEEECCEEEEEEEEEECCCCCCCEEEEEEEEECCCCCEEEEEECCCCEEEEEEEEEEEEEEEEECCCEE T ss_conf 97456257888999999899999976137999850899999983789989988989999978889887889999789838 Q ss_pred EEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCEEEEECCCCEEEEEEEECCCCCCCCCCCCCEEEEEEECCCEE Q ss_conf 99946887643211543001332013786156897667774401587499999982854213102477000899379599 Q gi|254781067|r 83 HFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVALSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRT 162 (189) Q Consensus 83 ~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~~i~i~lP~~v~l~V~~t~p~~kG~t~~~~~K~A~letG~~i 162 (189) +|||++||||++|+++.+|++.+||+||++|+++||+++||+|+||++|+|+|++|+|++||||+++++|||+||||++| T Consensus 81 ~FMd~etyEQ~~v~~~~lg~~~~~L~e~~~v~v~~~~~~~i~v~lP~~V~l~V~et~p~~kg~t~s~~~KpA~leTG~~I 160 (185) T PRK12426 81 LFLDLGNYEKIYIPKEIMKDNFLFLKAGVTVSALVYDNTVFSVELPHFLELMVSKTDFPGDSLSLSGGAKKALLETGVEV 160 (185) T ss_pred EEECCCCCCCEECCHHHCCHHHHHHCCCCEEEEEEECCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCCEEECCCCEE T ss_conf 99579983317814556003565303786699999188389988899799999989999678535787250898189999 Q ss_pred ECCCCCCCCCEEEEECCCCCEEHHC Q ss_conf 8474016887999988997240210 Q gi|254781067|r 163 TVPPHINIGDDIVILTEDNSYVERV 187 (189) Q Consensus 163 ~VP~FI~~Gd~IkV~T~~g~Y~~Ra 187 (189) +||+||++||+|+||||+|+|++|+ T Consensus 161 ~VP~FI~~Gd~IkVdT~~g~Yv~RV 185 (185) T PRK12426 161 LVPPFVEIGDVIKVDTRTCEYIQRV 185 (185) T ss_pred EECCCCCCCCEEEEECCCCEEEECC T ss_conf 8188402999999989987577059 No 4 >PRK04542 elongation factor P; Provisional Probab=100.00 E-value=0 Score=483.36 Aligned_cols=186 Identities=26% Similarity=0.512 Sum_probs=182.3 Q ss_pred EEEHHHCCCCCEEEECCEEEEEEEEEEECCC--CCCCEEEEEEEECCCCCCEEEEECCCCCEEEEEECCCEEEEEEEECC Q ss_conf 3664321677589988937999998753688--87638999999824687100134278720010105640578996198 Q gi|254781067|r 3 KVIASAVRKGNVLDVDGKLYIVLVAKNFHPG--KGTPITQVEMRRISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQDQE 80 (189) Q Consensus 3 ~i~an~lk~G~~i~~dg~~~~V~~~~~~kpg--kg~a~v~~klknL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~dg~ 80 (189) |++||+||+|++|++||+||+|++++|++|| +|+|++|+|||||+||+++++||+++|+||.|+++++++||||.||+ T Consensus 1 M~~a~dik~G~~i~~~g~~~~V~~~~~~kpg~r~g~~~~r~klKnl~tG~~~e~tf~~~d~ve~a~ve~~~~qyLY~dg~ 80 (189) T PRK04542 1 MPKASEIKKGMAVEYNGKLLLVKDIERSSPQGRGGATLYKMRFYDVRTGLKVEERFKGDDILDTVTLTRRQVTFSYVDGD 80 (189) T ss_pred CCCHHHCCCCCEEEECCEEEEEEEEEEECCCCCCCCEEEEEEEEECCCCCEEEEEECCCCEEEEEEEEEEEEEEEEECCC T ss_conf 98556367988999999899999999888998886169999997627898899998699999887886788899995899 Q ss_pred EEEEEECCCCCCCCCCHHHHHHHHHHCCCCCE-EEEEEECCEEEEECCCCEEEEEEEECCCCCCCCCCCCCEEEEEEECC Q ss_conf 89999468876432115430013320137861-56897667774401587499999982854213102477000899379 Q gi|254781067|r 81 GFHFMNPETYDQVTVSEEVIGDQKVYFQEGME-VKLLIHEGVALSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSND 159 (189) Q Consensus 81 ~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~-v~i~~~~~~~i~i~lP~~v~l~V~~t~p~~kG~t~~~~~K~A~letG 159 (189) .|+|||++||||++|+++++|++.+||+||++ |.+++|+|+||+|+||++|+|+|++|||++||||+++++|||+|||| T Consensus 81 ~~~FMd~etyEQi~l~~~~vg~~~~~L~e~~~~v~v~~~~~~~i~v~lP~~V~l~V~etep~vKGdTas~~~K~AtletG 160 (189) T PRK04542 81 EYVFMDNEDYTPYTFTKDQIEEELLFIPEGTPGMQVLTVDGQPVALELPQTVDLEIVETAPSIKGASASARTKPATLSTG 160 (189) T ss_pred EEEEEECCCHHHEEECHHHHHHHHHHHHCCCEEEEEEEECCEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCEEEECCC T ss_conf 17999699833265278995118765126998999999899789998898399999988996445357888760998289 Q ss_pred CEEECCCCCCCCCEEEEECCCCCEEHHCC Q ss_conf 59984740168879999889972402102 Q gi|254781067|r 160 IRTTVPPHINIGDDIVILTEDNSYVERVK 188 (189) Q Consensus 160 ~~i~VP~FI~~Gd~IkV~T~~g~Y~~Rak 188 (189) ++|+||+||++||+|+||||+|+|++||+ T Consensus 161 ~~I~VPlFI~~Gd~IkVdT~~g~Yv~RAn 189 (189) T PRK04542 161 LVIQVPEYISTGEKIRINTAERKFMGRAD 189 (189) T ss_pred CEEEECCCCCCCCEEEEECCCCEEHHHCC T ss_conf 99982884039999999899873611269 No 5 >TIGR02178 yeiP elongation factor P-like protein YeiP; InterPro: IPR011897 This entry represents homologs of elongation factor P (IPR011768 from INTERPRO) and probably are translation factors. Member of this family are found only in some gammaproteobacteria, including Escherichia coli (YeiP) and Vibrio cholerae.. Probab=100.00 E-value=0 Score=360.45 Aligned_cols=183 Identities=28% Similarity=0.552 Sum_probs=178.6 Q ss_pred EHHHCCCCCEEEECCEEEEEEEEEEECC-CCCCC-EEEEEEEECCCCCCEEEEECCCCCEEEEEECCCEEEEEEEECCEE Q ss_conf 6432167758998893799999875368-88763-899999982468710013427872001010564057899619889 Q gi|254781067|r 5 IASAVRKGNVLDVDGKLYIVLVAKNFHP-GKGTP-ITQVEMRRISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQDQEGF 82 (189) Q Consensus 5 ~an~lk~G~~i~~dg~~~~V~~~~~~kp-gkg~a-~v~~klknL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~dg~~~ 82 (189) .|||||||++|+++|+.|+|-|++..+| |||++ .+|+.+.++.||.++|.+|+++|-++-|.+.||++.|+|.||+.| T Consensus 1 kAsE~KKG~~~~yngktllikDI~~~sP~gRGg~~~yk~r~~dv~tG~kveerfk~Dd~ldtVel~rR~~sFSY~DG~ey 80 (187) T TIGR02178 1 KASELKKGSVVEYNGKTLLIKDIEVSSPQGRGGAVLYKLRMSDVRTGSKVEERFKADDVLDTVELLRREVSFSYVDGEEY 80 (187) T ss_pred CCCCCCCCEEEEECCCEEEEEEEEECCCCCCCCCEEEEEEEEECCCCCEEEECCCCCCEEEEEEEEECEEEEEEECCCEE T ss_conf 95421124389835987889865542899876233888998656878524201076722311121100046777637506 Q ss_pred EEEECCCCCCCCCCHHHHHHHHHHCCCC-CE-EEEEEECCEEEEECCCCEEEEEEEECCCCCCCCCCCCCEEEEEEECCC Q ss_conf 9994688764321154300133201378-61-568976677744015874999999828542131024770008993795 Q gi|254781067|r 83 HFMNPETYDQVTVSEEVIGDQKVYFQEG-ME-VKLLIHEGVALSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDI 160 (189) Q Consensus 83 ~FMd~etyeqi~i~~~~ig~~~~fL~eg-~~-v~i~~~~~~~i~i~lP~~v~l~V~~t~p~~kG~t~~~~~K~A~letG~ 160 (189) +|||.|+|..|++.+|.++|.+.|+.|| |. |+|++||+.+++++||++|+|+|.+|+|.+||.|||+++|||+|.||+ T Consensus 81 VFmd~eDYTpYtf~kd~Iedellfi~EgG~~gm~V~l~Dg~~vAleLPq~V~leiveT~P~iKGasAs~R~KPA~l~TGl 160 (187) T TIGR02178 81 VFMDEEDYTPYTFDKDEIEDELLFISEGGLSGMSVLLIDGEAVALELPQSVELEIVETDPEIKGASASKRPKPAKLITGL 160 (187) T ss_pred EEECCCCCCCCCCCHHHHCCCCCEECCCCCCCCEEEEECCCHHHHHCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCC T ss_conf 83058788742577445001000205577688679998130042318874589988479998453247788886115652 Q ss_pred EEECCCCCCCCCEEEEECCCCCEEHHC Q ss_conf 998474016887999988997240210 Q gi|254781067|r 161 RTTVPPHINIGDDIVILTEDNSYVERV 187 (189) Q Consensus 161 ~i~VP~FI~~Gd~IkV~T~~g~Y~~Ra 187 (189) +||||.||.+||+|.|||+++.|++|| T Consensus 161 vv~VPEYi~tGerI~in~~er~fmgRA 187 (187) T TIGR02178 161 VVQVPEYITTGERILINTEERKFMGRA 187 (187) T ss_pred EEECCCCCCCCCEEEEECCCCCCCCCC T ss_conf 786776238998699962457656889 No 6 >COG0231 Efp Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis] Probab=100.00 E-value=2.6e-43 Score=286.13 Aligned_cols=131 Identities=36% Similarity=0.661 Sum_probs=129.5 Q ss_pred CCEEEHHHCCCCCEEEECCEEEEEEEEEEECCCCCCCEEEEEEEECCCCCCEEEEECCCCCEEEEEECCCEEEEEEEECC Q ss_conf 92366432167758998893799999875368887638999999824687100134278720010105640578996198 Q gi|254781067|r 1 MVKVIASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQDQE 80 (189) Q Consensus 1 m~~i~an~lk~G~~i~~dg~~~~V~~~~~~kpgkg~a~v~~klknL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~dg~ 80 (189) |+++++|+||+|++|.+||+||+|++++|+|||||+|++|+++|||.||++.+.+|+++|++|.|.++++++||||.||+ T Consensus 1 ~~~i~~~~lr~G~~i~~dg~~~~V~~~~~~KpGKg~a~vrvk~k~l~tG~~~e~~f~~~~kve~a~ie~~~~q~lY~dg~ 80 (131) T COG0231 1 MAMISASELRKGLYIVIDGEPYVVVEISHVKPGKGGAFVRVKLKNLFTGKKVEKTFKADDKVEVAIVERKTAQYLYIDGD 80 (131) T ss_pred CCEEEHHHCCCCCEEEECCEEEEEEEEEECCCCCCCCEEEEEEEECCCCCEEEEEECCCCEEEEEEEEEEEEEEEECCCC T ss_conf 94056777268779998996899999787269999857999999845898999997578889886996005699994899 Q ss_pred EEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCEEEEECCCCEE Q ss_conf 899994688764321154300133201378615689766777440158749 Q gi|254781067|r 81 GFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVALSVEVPRHV 131 (189) Q Consensus 81 ~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~~i~i~lP~~v 131 (189) .|+|||++||||++++.+.+||.++||+||++|++++|+|++++|+||++| T Consensus 81 ~~~FMD~etyeq~~v~~~~~~d~~~~l~eg~~v~v~~~~g~~i~v~lP~~v 131 (131) T COG0231 81 FYVFMDLETYEQYELPKDQIGDAAKFLKEGMEVEVLLYNGEPIAVELPNFV 131 (131) T ss_pred EEEECCCCCCEEEEECHHHHHHHHHHCCCCCEEEEEEECCEEEEEECCCCC T ss_conf 589814898268996402414588635799899999999999999889879 No 7 >PRK03999 translation initiation factor IF-5A; Provisional Probab=100.00 E-value=1.7e-32 Score=219.86 Aligned_cols=120 Identities=25% Similarity=0.305 Sum_probs=113.2 Q ss_pred CCE--EEHHHCCCCCEEEECCEEEEEEEEEEECCCC-CCCEEEEEEEECCCCCCEEEEECCCCCEEEEEECCCEEEEEEE Q ss_conf 923--6643216775899889379999987536888-7638999999824687100134278720010105640578996 Q gi|254781067|r 1 MVK--VIASAVRKGNVLDVDGKLYIVLVAKNFHPGK-GTPITQVEMRRISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQ 77 (189) Q Consensus 1 m~~--i~an~lk~G~~i~~dg~~~~V~~~~~~kpgk-g~a~v~~klknL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~ 77 (189) |++ ++|++||+|..|+++|+||+|++++|+|||| |+|++|++++||+||++.+.+|++++++|.|.++++++||||. T Consensus 1 m~~~~i~~~dlK~G~~i~idg~pckVve~~~sKpGKHG~Akvr~~~~~i~tG~k~e~~~~~~~kve~p~i~kk~~Q~l~~ 80 (129) T PRK03999 1 MSKKQVEVGELKEGSYVVIDGEPCRIVEISKSKPGKHGSAKARIVAIGIFDGQKRSLVAPVDAKVEVPIIEKRTGQVLSI 80 (129) T ss_pred CCCCEEEHHHCCCCCEEEECCEEEEEEEEEEECCCCCCCEEEEEEEEECCCCCEEEEEECCCCEEECCEEEEEEEEEEEE T ss_conf 97222678992689999999985999998886499985369999999646797899988798805646698768899995 Q ss_pred ECCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCEE Q ss_conf 198899994688764321154300133201378615689766777 Q gi|254781067|r 78 DQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVA 122 (189) Q Consensus 78 dg~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~~ 122 (189) +|+.|+|||+|||||+++|.+ .+...+|++|++|.++-..|+- T Consensus 81 ~gd~~~fMD~etyE~~elp~~--~e~~~~l~~G~eV~~~~a~G~~ 123 (129) T PRK03999 81 MGDTVQLMDLETYETFEVPIP--EELKDKIEPGVEVEYWEAMGRR 123 (129) T ss_pred CCCEEEEECCCCCEEEEECCC--HHHHHHCCCCCEEEEEEECCEE T ss_conf 699999975999426770199--8998505399879999828937 No 8 >pfam09285 Elong-fact-P_C Elongation factor P, C-terminal. Members of this family of nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology. Probab=99.87 E-value=1.3e-22 Score=159.35 Aligned_cols=56 Identities=38% Similarity=0.588 Sum_probs=55.1 Q ss_pred EEEEEEECCCCCCCCCCCCCEEEEEEECCCEEECCCCCCCCCEEEEECCCCCEEHH Q ss_conf 99999982854213102477000899379599847401688799998899724021 Q gi|254781067|r 131 VVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYVER 186 (189) Q Consensus 131 v~l~V~~t~p~~kG~t~~~~~K~A~letG~~i~VP~FI~~Gd~IkV~T~~g~Y~~R 186 (189) |+|+|++|+|++||||+++++|||+||||++|+||+||++||+|+|||++|+|++| T Consensus 1 V~l~V~etep~vKG~Ta~~~~K~A~letG~~i~VP~FI~~Gd~I~VdT~~g~Y~~R 56 (56) T pfam09285 1 VELEVVETEPGVKGDTASSGTKPATLETGAEVQVPLFIEEGEKIKVDTRTGEYVSR 56 (56) T ss_pred CEEEEEECCCCCCCCCCCCCCCEEEECCCCEEECCCCCCCCCEEEEECCCCEEECC T ss_conf 98999978985235345777342898389899838740489999998998858778 No 9 >smart00841 Elong-fact-P_C Elongation factor P, C-terminal. These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology PUBMED:15210970. Probab=99.87 E-value=1.5e-22 Score=158.88 Aligned_cols=56 Identities=41% Similarity=0.577 Sum_probs=55.1 Q ss_pred EEEEEEECCCCCCCCCCCCCEEEEEEECCCEEECCCCCCCCCEEEEECCCCCEEHH Q ss_conf 99999982854213102477000899379599847401688799998899724021 Q gi|254781067|r 131 VVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYVER 186 (189) Q Consensus 131 v~l~V~~t~p~~kG~t~~~~~K~A~letG~~i~VP~FI~~Gd~IkV~T~~g~Y~~R 186 (189) |+|+|++|+|++||||+++++|||+||||++||||+||++||+|+|||++|+|++| T Consensus 1 V~l~V~etep~vKG~Tas~~~K~A~letG~~i~VP~FI~~Gd~I~IdT~~g~Y~~R 56 (56) T smart00841 1 VELEVTETEPGVKGDTASGGTKPATLETGAVVQVPLFINEGDKIKVDTRTGEYVSR 56 (56) T ss_pred CEEEEEECCCCCCCCCCCCCCCEEEECCCCEEECCCCCCCCCEEEEECCCCEEECC T ss_conf 98999978997335455786031898489899838740389999998999858778 No 10 >cd05794 S1_EF-P_repeat_2 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P Probab=99.86 E-value=2.6e-22 Score=157.43 Aligned_cols=56 Identities=39% Similarity=0.586 Sum_probs=55.1 Q ss_pred EEEEEEECCCCCCCCCCCCCEEEEEEECCCEEECCCCCCCCCEEEEECCCCCEEHH Q ss_conf 99999982854213102477000899379599847401688799998899724021 Q gi|254781067|r 131 VVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYVER 186 (189) Q Consensus 131 v~l~V~~t~p~~kG~t~~~~~K~A~letG~~i~VP~FI~~Gd~IkV~T~~g~Y~~R 186 (189) |+|+|++|+|++||||+++++|||+||||++|+||+||++||+|+|||++|+|++| T Consensus 1 v~l~V~etep~~kG~Tas~~~K~A~letG~~i~VP~FI~~Gd~I~VdT~~g~Y~~R 56 (56) T cd05794 1 VELEVTETEPGVKGDTASSGTKPATLETGAEVQVPLFIKEGEKIKVDTRTGEYVER 56 (56) T ss_pred CEEEEEECCCCCCCCCCCCCCCEEEECCCCEEECCCCCCCCCEEEEECCCCEEECC T ss_conf 98999988986335445777452897389999848740489999998998848678 No 11 >cd04470 S1_EF-P_repeat_1 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P Probab=99.80 E-value=7.2e-20 Score=142.52 Aligned_cols=61 Identities=39% Similarity=0.840 Sum_probs=60.0 Q ss_pred CCCEEEEEEEECCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCEEEEECCC Q ss_conf 5640578996198899994688764321154300133201378615689766777440158 Q gi|254781067|r 68 EDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVALSVEVP 128 (189) Q Consensus 68 e~~~~qylY~dg~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~~i~i~lP 128 (189) +++++||||.||+.|+|||++||||++|+++.+|++.+||+||++|.+.+|+|+||+|+|| T Consensus 1 e~~~~qyLY~dg~~~~FMd~etyEQi~v~~~~igd~~~~L~e~~~v~i~~~~~~~i~i~lP 61 (61) T cd04470 1 EEREMQYLYKDGDNYVFMDTETYEQIELPKEALGDAAKFLKEGMEVIVLFYNGEPIGVELP 61 (61) T ss_pred CCCEEEEEEECCCEEEEECCCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCEEEEEECC T ss_conf 9831699896899089954886412216677863278635589899999989998988895 No 12 >pfam08207 EFP_N Elongation factor P (EF-P) KOW-like domain. Probab=99.72 E-value=1.9e-17 Score=127.71 Aligned_cols=58 Identities=31% Similarity=0.678 Sum_probs=56.6 Q ss_pred EHHHCCCCCEEEECCEEEEEEEEEEECCCCCCCEEEEEEEECCCCCCEEEEECCCCCE Q ss_conf 6432167758998893799999875368887638999999824687100134278720 Q gi|254781067|r 5 IASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQV 62 (189) Q Consensus 5 ~an~lk~G~~i~~dg~~~~V~~~~~~kpgkg~a~v~~klknL~tG~~~e~~f~~~ekv 62 (189) +|||||+|++|++||+||+|++++|++||||+|++|+|||||.||+++|++|+++|+| T Consensus 1 ~a~elkkG~~i~~~g~l~~V~~~~~~~pgkg~a~~~~klknl~tG~~~e~~f~~~dkv 58 (58) T pfam08207 1 SASDLKKGLVIEIDGEPYVVLEFEHVKPGKGQAFVRTKLKNLRTGAKVEKTFKSGDKV 58 (58) T ss_pred CHHHCCCCCEEEECCEEEEEEEEEEECCCCCCEEEEEEEEECCCCCEEEEEECCCCCC T ss_conf 9425459879999999999999888759998538999988625698999888788739 No 13 >pfam01132 EFP Elongation factor P (EF-P) OB domain. Probab=99.69 E-value=3.3e-17 Score=126.25 Aligned_cols=55 Identities=36% Similarity=0.803 Sum_probs=53.6 Q ss_pred CCEEEEEEEECCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCEEE Q ss_conf 6405789961988999946887643211543001332013786156897667774 Q gi|254781067|r 69 DQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVAL 123 (189) Q Consensus 69 ~~~~qylY~dg~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~~i 123 (189) ++++||||.||+.|||||++||||++|+++.+|++.+||+||++|.+.+|+|+|| T Consensus 1 ~~~~qylY~dg~~~~FMd~etyEQi~i~~~~ig~~~~~L~e~~~v~v~~~~~~~i 55 (55) T pfam01132 1 RREMQYLYKDGDNYVFMDTETYEQIELPKEALGDAAKFLKEGMEVTVLFYNGEPI 55 (55) T ss_pred CCCEEEEEECCCCEEEEECCCCEEEECCHHHHCCHHHHCCCCCEEEEEEECCEEC T ss_conf 9846999948991899618975067638789672887587999999999999999 No 14 >TIGR00037 eIF_5A translation initiation factor eIF-5A; InterPro: IPR001884 Translation initiation factor 5A (IF-5A) is reported to be involved in the first step of peptide bond formation in translation, to be involved in cell-cycle regulation and to be a cofactor for the Rev and Rex transactivator proteins of human immunodeficiency virus-1 and T-cell leukaemia virus I, respectively , , . IF-5A contains an unusual amino acid, hypusine N-epsilon-(4-aminobutyl-2-hydroxy)lysine), that is required for its function. The first step in the post-translational modification of lysine to hypusine is catalyzed by the enzyme deoxyhypusine synthase, the structure of which has been reported. The crystal structure of IF-5A from the archaeon Pyrobaculum aerophilum has been determined to 1.75 A. Unmodified P. aerophilum IF-5A is found to be a beta structure with two domains and three separate hydrophobic cores. The lysine (Lys42) that is post-translationally modified by deoxyhypusine synthase is found at one end of the IF-5A molecule in a turn between beta strands beta4 and beta5; this lysine residue is freely solvent accessible. The C-terminal domain is found to be homologous to the cold-shock protein CspA of E. coli, which has a well characterised RNA-binding fold, suggesting that IF-5A is involved in RNA binding . ; GO: 0003743 translation initiation factor activity, 0006413 translational initiation. Probab=99.64 E-value=1.1e-15 Score=116.96 Aligned_cols=113 Identities=27% Similarity=0.274 Sum_probs=98.6 Q ss_pred EEHHHCCCCCEEEECCEEEEEEEEEEECCCC-CCCEEEEEEEECCCCCCEEEEECCCCCEEEEEECCCEEEEEEEECCEE Q ss_conf 6643216775899889379999987536888-763899999982468710013427872001010564057899619889 Q gi|254781067|r 4 VIASAVRKGNVLDVDGKLYIVLVAKNFHPGK-GTPITQVEMRRISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQDQEGF 82 (189) Q Consensus 4 i~an~lk~G~~i~~dg~~~~V~~~~~~kpgk-g~a~v~~klknL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~dg~~~ 82 (189) +..+.||+|.++.+||+||.|++.+.+|||| |+|.+|+..-.++++++.+.--+++.++|.+.++|+++|.|-.+|+.. T Consensus 7 v~v~~Lr~g~yVvIdg~PC~IvdiS~SkpGKHG~AKar~~aigIF~~~K~e~v~P~~~k~~VPiv~r~~~Q~l~i~g~~~ 86 (137) T TIGR00037 7 VEVSALRVGGYVVIDGEPCKIVDISTSKPGKHGHAKARVVAIGIFDGQKREFVSPVTSKVEVPIVDRREAQVLAIMGGVV 86 (137) T ss_pred EEEEECCCCCEEEECCCCCEEEECCCCCCCCCCCCEEEEEEEECCCCCCEEEECCCCCCEEECEEECCCCEEEEECCCEE T ss_conf 46345124866887686760676131498986752789988612266542101775562141437367503888618837 Q ss_pred EEEECCCCCCCCCCHH--HHHHHHHHCC-CCCEEEEE Q ss_conf 9994688764321154--3001332013-78615689 Q gi|254781067|r 83 HFMNPETYDQVTVSEE--VIGDQKVYFQ-EGMEVKLL 116 (189) Q Consensus 83 ~FMd~etyeqi~i~~~--~ig~~~~fL~-eg~~v~i~ 116 (189) -+||++|||.++++.- -++|...-=. ||-.+-|. T Consensus 87 qLMdl~tyet~e~~~PeGEL~d~l~~g~DEGkDLmV~ 123 (137) T TIGR00037 87 QLMDLETYETFELPIPEGELGDSLEEGFDEGKDLMVE 123 (137) T ss_pred EEECCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH T ss_conf 8632788730220278775734300013666022034 No 15 >PTZ00328 eukaryotic initiation factor 5a; Provisional Probab=99.39 E-value=1.2e-11 Score=92.10 Aligned_cols=115 Identities=21% Similarity=0.344 Sum_probs=96.7 Q ss_pred EEHHHCCCCCEEEECCEEEEEEEEEEECCCC-CCCEEEEEEEECCCCCCEEEEECCCCCEEEEEECCCEEEEEEEECC-- Q ss_conf 6643216775899889379999987536888-7638999999824687100134278720010105640578996198-- Q gi|254781067|r 4 VIASAVRKGNVLDVDGKLYIVLVAKNFHPGK-GTPITQVEMRRISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQDQE-- 80 (189) Q Consensus 4 i~an~lk~G~~i~~dg~~~~V~~~~~~kpgk-g~a~v~~klknL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~dg~-- 80 (189) +.++.||+|..+.++|.||+|++...+|+|| |.|.+++-..+|.||++.+...+++++++.+.+.+.++|.+-.+++ T Consensus 23 ~q~~~lrkgg~vvikgrPCkVv~~stSKtGKHGhAK~~lvgiDIFtgkk~ed~~Ps~hn~~vP~V~r~~yqli~I~dd~d 102 (166) T PTZ00328 23 LPAGALKKGGYVCINGRPCKVIDLSVSKTGKHGHAKVSIVATDIFTGNRLEDQAPSTHNVEVPFVKTFTYSVLDIQPNED 102 (166) T ss_pred EECCCEEECCEEEECCCCEEEEEEEECCCCCCCCCEEEEEEEECCCCCEEEEEEECCCCCCCCEEECCEEEEEEECCCCC T ss_conf 68661338899998885418999884679866630467898861468666788605786225678802879986315666 Q ss_pred -----EEEEEEC--CCCCCCCCCHH-HHHHHHH-HCCCCCEEEEEEE Q ss_conf -----8999946--88764321154-3001332-0137861568976 Q gi|254781067|r 81 -----GFHFMNP--ETYDQVTVSEE-VIGDQKV-YFQEGMEVKLLIH 118 (189) Q Consensus 81 -----~~~FMd~--etyeqi~i~~~-~ig~~~~-fL~eg~~v~i~~~ 118 (189) ...+|+. ++-|.+.||.+ -++...+ -..+|-++.+... T Consensus 103 ~~~~G~lsLm~e~G~~k~Dlklp~~~~l~~~I~~~f~~gk~~~vtVl 149 (166) T PTZ00328 103 PSLPAHLSLMDDEGESREDLDMPPDAALATQIKEQFDSGKEVLVVVV 149 (166) T ss_pred CCCCCEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEEE T ss_conf 55541599996899823576389827999999999867990999998 No 16 >KOG3271 consensus Probab=99.19 E-value=1.7e-10 Score=85.07 Aligned_cols=121 Identities=18% Similarity=0.228 Sum_probs=101.2 Q ss_pred EHHHCCCCCEEEECCEEEEEEEEEEECCCC-CCCEEEEEEEECCCCCCEEEEECCCCCEEEEEECCCEEEEEEEECCEEE Q ss_conf 643216775899889379999987536888-7638999999824687100134278720010105640578996198899 Q gi|254781067|r 5 IASAVRKGNVLDVDGKLYIVLVAKNFHPGK-GTPITQVEMRRISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQDQEGFH 83 (189) Q Consensus 5 ~an~lk~G~~i~~dg~~~~V~~~~~~kpgk-g~a~v~~klknL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~dg~~~~ 83 (189) .++.||++-++.++|.||+|++...+|.|| |.|.+.+-..+|.||++.+--.+++++++++.++|.++|.+-.+++... T Consensus 22 q~salrkNG~vviK~rpckivEmSTsKtGKHGhAKvh~vaidifTgkk~edI~psthnmdVp~vkr~~yqLidIsd~~~s 101 (156) T KOG3271 22 QCSALRKNGHVVIKGRPCKIVEMSTSKTGKHGHAKVHIVAIDIFTGKKLEDICPSTHNMDVPVVKRVDYQLIDISDGYLS 101 (156) T ss_pred HHHHEEECCEEEECCCCCEEEEEECCCCCCCCCEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCEEE T ss_conf 22212317889973887369984512377677417899999964376425535777750147635010489973288489 Q ss_pred EEECCCC--CCCCCCHHHHHHHHHHCCCCC-EEEEE----EECCEEEEE Q ss_conf 9946887--643211543001332013786-15689----766777440 Q gi|254781067|r 84 FMNPETY--DQVTVSEEVIGDQKVYFQEGM-EVKLL----IHEGVALSV 125 (189) Q Consensus 84 FMd~ety--eqi~i~~~~ig~~~~fL~eg~-~v~i~----~~~~~~i~i 125 (189) ||+.+.+ +.+-+|..-+|+++.-=-|+. .+.+. ++++..+++ T Consensus 102 l~~~sG~~kdDlklp~~el~~~i~~~~e~g~dl~v~Vlsa~gee~~~a~ 150 (156) T KOG3271 102 LMTDSGETKDDLKLPEGELGNQIRQGFEEGKDLLVTVLSAMGEEAAVAP 150 (156) T ss_pred EECCCCCCCHHCCCCCHHHHHHHHHHHCCCCCEEEEEHHHHCHHHHEEE T ss_conf 8868997120004764157899998642687279997564170443242 No 17 >cd04467 S1_aIF5A S1_aIF5A: Archaeal translation Initiation Factor 5A (aIF5A), S1-like RNA-binding domain. aIF5A is a homolog of eukaryotic eIF5A. IF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is a post-translationally modified lysine and is essential for IF5A function. In yeast, eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) in a hypusine-dependent manner. This C-terminal S1 domain resembles the cold-shock domain which binds RNA. Moreover, IF5A prefers binding to the actively translating ribosome. This evidence suggests that IF5A plays a role in translation elongation instead of translation initiation as previously proposed. Probab=96.92 E-value=0.0017 Score=42.23 Aligned_cols=53 Identities=25% Similarity=0.251 Sum_probs=42.7 Q ss_pred ECCCEEEEEEEECCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCE Q ss_conf 0564057899619889999468876432115430013320137861568976677 Q gi|254781067|r 67 VEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGV 121 (189) Q Consensus 67 ie~~~~qylY~dg~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~ 121 (189) ++|+..|.+-..|+....||+||||.++++.. .+...=|.+|.+|.-.-..|+ T Consensus 1 Iekk~gQVlsi~G~~vQlMD~etYeTfe~~ip--ee~~~~l~~G~eVeY~e~mG~ 53 (57) T cd04467 1 IERKTGQVLSIMGDVVQLMDLETYETFEVPIP--EEIKDKLEPGKEVEYWESMGK 53 (57) T ss_pred CCCCEEEEEEECCCEEEEEECCCCEEEEEECC--HHHHHCCCCCCEEEEEEECCC T ss_conf 96521269997598379850666111776588--788724679974988311583 No 18 >COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis] Probab=96.73 E-value=0.024 Score=35.15 Aligned_cols=104 Identities=25% Similarity=0.424 Sum_probs=76.5 Q ss_pred HHCCCCCEEEECCEEEEEEEEEEECCCCCCCEEEEEEEECCCCCCEEEEECCCCCEE--EEE--ECCCEEEEEEEECCEE Q ss_conf 321677589988937999998753688876389999998246871001342787200--101--0564057899619889 Q gi|254781067|r 7 SAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQVE--RAF--VEDQRFQFLYQDQEGF 82 (189) Q Consensus 7 n~lk~G~~i~~dg~~~~V~~~~~~kpgkg~a~v~~klknL~tG~~~e~~f~~~ekve--~~~--ie~~~~qylY~dg~~~ 82 (189) -++++|.++.++|..+.++... |+ .+.++++.|+...+.++.-...-+ .+. -+-+.+.+.-.+.+.. T Consensus 245 p~~~~gDiV~~~~~~~~~v~~~----~~-----~~~~~dl~t~e~~~~~~~~~~~~~~~~~~~~~~~~~~~vvs~~~~~~ 315 (355) T COG1499 245 PEFRPGDIVSVRGRQLVLVRSI----GK-----GIVVLDLETGEPVEITWSVYKRNEGKVAVKEPRLKKAVVVSRDPSAI 315 (355) T ss_pred CCCCCCCEEEECCCEEEEEEEE----CC-----CEEEEECCCCCCCCCCHHHCCCCCCEEEECCCCCEEEEEEECCCCEE T ss_conf 8879887899779738999993----68-----44898556587033675450067641552145526899996588803 Q ss_pred EEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCEEEEEC Q ss_conf 99946887643211543001332013786156897667774401 Q gi|254781067|r 83 HFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVALSVE 126 (189) Q Consensus 83 ~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~~i~i~ 126 (189) .|||++|||-+++... =|.+|.+|.+..+.+....++ T Consensus 316 ~v~d~et~e~~~~~~~-------~~~~g~~v~v~~~~~~~~~~~ 352 (355) T COG1499 316 QVLDPETYEARTVKGP-------SLEEGDEVKVFKVRGRNYVVE 352 (355) T ss_pred EEEECCEEEEEECCCC-------CCCCCCEEEEEEECCEEEEEE T ss_conf 8970553898861688-------778997899999804387610 No 19 >cd04463 S1_EF_like S1_EF_like: EF-like, S1-like RNA-binding domain. The EF-like superfamily contains the bacterial translation elongation factor P and its archeal and eukaryotic homologs, aIF5A and eIF5A. All proteins in this superfamily contain an S1 domain, which binds RNA or single-stranded DNA and often interacts with the ribosome. Hex-1, the SI-like domain of which is also found in this group, is structurally homologous to eIF5A and might have evolved from an ancestral eIF5A through gene duplication. Probab=96.01 E-value=0.0077 Score=38.20 Aligned_cols=54 Identities=24% Similarity=0.184 Sum_probs=34.1 Q ss_pred CEEEEEEEECCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCEEEE Q ss_conf 4057899619889999468876432115430013320137861568976677744 Q gi|254781067|r 70 QRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVALS 124 (189) Q Consensus 70 ~~~qylY~dg~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~~i~ 124 (189) +++|+||..++..+|||.++||+..++.-.--. .-++.+|+.+.+..+.|+.+. T Consensus 1 ~e~qVLd~q~~~~~~Md~e~~~~~~~p~~~~~~-~E~f~~G~~vlv~~~~Gq~~~ 54 (55) T cd04463 1 RELQVLDIQGSKPVTMDLETYEVVQVPPPVDQS-FESFEPGEVVLVDTRTGQYVG 54 (55) T ss_pred CCCEEEECCCCEEEEEEEEEEEEEECCCCCCCC-CCCCCCCEEEEEECCCCCEEC T ss_conf 950688106872389871213677238985644-223489608999746662743 No 20 >cd04463 S1_EF_like S1_EF_like: EF-like, S1-like RNA-binding domain. The EF-like superfamily contains the bacterial translation elongation factor P and its archeal and eukaryotic homologs, aIF5A and eIF5A. All proteins in this superfamily contain an S1 domain, which binds RNA or single-stranded DNA and often interacts with the ribosome. Hex-1, the SI-like domain of which is also found in this group, is structurally homologous to eIF5A and might have evolved from an ancestral eIF5A through gene duplication. Probab=95.05 E-value=0.045 Score=33.51 Aligned_cols=36 Identities=25% Similarity=0.394 Sum_probs=30.9 Q ss_pred EEEEEEEC--CCEEECCCCC-------CCCCEEEEECCCCCEEHH Q ss_conf 00089937--9599847401-------688799998899724021 Q gi|254781067|r 151 YKPAILSN--DIRTTVPPHI-------NIGDDIVILTEDNSYVER 186 (189) Q Consensus 151 ~K~A~let--G~~i~VP~FI-------~~Gd~IkV~T~~g~Y~~R 186 (189) .++++++. +-+.+||+++ +.|..|.+++++|+|+.+ T Consensus 11 ~~~~~Md~e~~~~~~~p~~~~~~~E~f~~G~~vlv~~~~Gq~~~v 55 (55) T cd04463 11 SKPVTMDLETYEVVQVPPPVDQSFESFEPGEVVLVDTRTGQYVGV 55 (55) T ss_pred CEEEEEEEEEEEEEECCCCCCCCCCCCCCCEEEEEECCCCCEECC T ss_conf 723898712136772389856442234896089997466627439 No 21 >pfam01287 eIF-5a Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold. eIF5A, previously thought to be an initiation factor, has been shown to be required for peptide chain elongation in yeast. Probab=92.57 E-value=0.37 Score=27.90 Aligned_cols=60 Identities=23% Similarity=0.376 Sum_probs=41.3 Q ss_pred EECCCEEEEEEEECC-EEEEEEC--CCCCCCCCCHHHHHHHHH-HCCCCCEEEEEEE----CCEEEEE Q ss_conf 105640578996198-8999946--887643211543001332-0137861568976----6777440 Q gi|254781067|r 66 FVEDQRFQFLYQDQE-GFHFMNP--ETYDQVTVSEEVIGDQKV-YFQEGMEVKLLIH----EGVALSV 125 (189) Q Consensus 66 ~ie~~~~qylY~dg~-~~~FMd~--etyeqi~i~~~~ig~~~~-fL~eg~~v~i~~~----~~~~i~i 125 (189) .+.|+.+|.+..++| ....||. +++|.+.+|..-+++..+ -+.+|.++.+.++ +..++++ T Consensus 1 ~V~r~eyQli~I~~Dg~lsLMde~g~t~eDl~lP~~~l~~eI~~~~~~Gk~~~V~v~~amGee~ii~~ 68 (69) T pfam01287 1 NVKRTEYQLIDISGDGFLSLMDEDGETKEDLKLPEGELGEEIKEKFEEGKEVLVTVLSAMGEEKIVAV 68 (69) T ss_pred CCCCCEEEEEEECCCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHCCCCEEEEEEHHCCEEEEEEC T ss_conf 96322148986668863776648898831466994689999999986799389999042881335762 No 22 >PRK08463 acetyl-CoA carboxylase; Validated Probab=81.16 E-value=4.9 Score=21.03 Aligned_cols=65 Identities=20% Similarity=0.190 Sum_probs=37.6 Q ss_pred CEEEEEEEECCEEEEEECCCCCCCCCC-------HHHHHHHHHHCCCCCEEEEEEECCEEEEECC-CCEEEEEEEECCC Q ss_conf 405789961988999946887643211-------5430013320137861568976677744015-8749999998285 Q gi|254781067|r 70 QRFQFLYQDQEGFHFMNPETYDQVTVS-------EEVIGDQKVYFQEGMEVKLLIHEGVALSVEV-PRHVVFTVIDTEP 140 (189) Q Consensus 70 ~~~qylY~dg~~~~FMd~etyeqi~i~-------~~~ig~~~~fL~eg~~v~i~~~~~~~i~i~l-P~~v~l~V~~t~p 140 (189) -.++|||.+.+.|+||...+==|++=+ .|++..+.. +..|..+.+.-. .+.+ -..+++.|.--+| T Consensus 272 GTvEFL~d~~~~fyFlEmNtRlQVEHpVTE~vTGvDLV~~Qi~-iA~G~~L~~~q~-----~i~~~GhAIE~RI~AEdp 344 (478) T PRK08463 272 GTIEFLLDDYNNFYFMEMNTRIQVEHGVTEEITGIDLIVRQIR-IAAGEILDLEQS-----DIKPRGFAIEARITAENV 344 (478) T ss_pred CEEEEEECCCCCEEEEEEECCCCCCCCCCCEECCCCHHHHHHH-HHCCCCCCCCCC-----CCCCCCEEEEEEEECCCC T ss_conf 3389888389978999607554556654110038868999999-867998885400-----346674599999851477 No 23 >PRK08591 acetyl-CoA carboxylase biotin carboxylase subunit; Validated Probab=79.19 E-value=2.8 Score=22.53 Aligned_cols=26 Identities=31% Similarity=0.464 Sum_probs=19.4 Q ss_pred CEEEEEEEECCEEEEEECCCCCCCCCC Q ss_conf 405789961988999946887643211 Q gi|254781067|r 70 QRFQFLYQDQEGFHFMNPETYDQVTVS 96 (189) Q Consensus 70 ~~~qylY~dg~~~~FMd~etyeqi~i~ 96 (189) -.++|||. ++.|+||...|==|++=| T Consensus 272 GTvEFL~d-~~~fyFlEmNtRlQVEHp 297 (449) T PRK08591 272 GTIEFLYE-NGEFYFIEMNTRIQVEHP 297 (449) T ss_pred EEEEEEEE-CCEEEEEEEECCCCCCCC T ss_conf 03899997-890899962434124565 No 24 >TIGR00514 accC acetyl-CoA carboxylase, biotin carboxylase; InterPro: IPR004549 This family represents the biotin carboxylase subunit found usually as a component of acetyl-CoA carboxylase. Acetyl-CoA carboxylase (6.4.1.2 from EC) is a heterohexamer of biotin carboxyl carrier protein, biotin carboxylase (6.3.4.14 from EC), and two subunits of carboxyl transferase in a 2:2 complex. In the first step of long-chain fatty acid synthesis, biotin carboxylase catalyses the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-coA. Homologous domains are found in eukaryotic forms of acetyl-CoA carboxylase and in a number of other carboxylases (e.g. pyruvate carboxylase). In some systems, the biotin carboxyl carrier protein and this protein (biotin carboxylase) may be shared by different carboxyltransferases. However, this model is not intended to identify the biotin carboxylase domain of propionyl-coA carboxylase. The model should hit the full length of proteins, except for chloroplast transit peptides in plants. If it hits a domain only of a longer protein, there may be a problem with the identification.; GO: 0016874 ligase activity. Probab=77.15 E-value=0.98 Score=25.31 Aligned_cols=73 Identities=21% Similarity=0.259 Sum_probs=45.0 Q ss_pred EEEEEEEECCE-EEEEECCCCCCCCCC-------HHHHHHHHHHCCCCCEEEEEEECCEEEEECC-CCEEEEEEEECCCC Q ss_conf 05789961988-999946887643211-------5430013320137861568976677744015-87499999982854 Q gi|254781067|r 71 RFQFLYQDQEG-FHFMNPETYDQVTVS-------EEVIGDQKVYFQEGMEVKLLIHEGVALSVEV-PRHVVFTVIDTEPS 141 (189) Q Consensus 71 ~~qylY~dg~~-~~FMd~etyeqi~i~-------~~~ig~~~~fL~eg~~v~i~~~~~~~i~i~l-P~~v~l~V~~t~p~ 141 (189) +++|||...+. ||||.+.|==|+|=| -|+|.+|.+ +..|+++.+- ++. |.| =..++|.| .||.. T Consensus 274 TvEFLld~~~~rFYFmEMNTRIQVEHPVTEmvtGvDL~keQir-vA~G~~L~~k--Qe~---v~~~GHaieCRI-NAEDP 346 (451) T TIGR00514 274 TVEFLLDKNGQRFYFMEMNTRIQVEHPVTEMVTGVDLIKEQIR-VAAGEKLSLK--QED---VKLRGHAIECRI-NAEDP 346 (451) T ss_pred EEEEEEECCCCEEEEEEECCEEEEEECCEEEEECHHHHHHHHH-HHCCCCCCCC--CCE---EEEEEEEEEEEE-CCCCC T ss_conf 1688862588735776517602111032014600257888998-7378956643--114---799988998651-45587 Q ss_pred CCCCCCCCC Q ss_conf 213102477 Q gi|254781067|r 142 SKGQTVTAS 150 (189) Q Consensus 142 ~kG~t~~~~ 150 (189) .|+=+=|.+ T Consensus 347 ~~~F~PsPG 355 (451) T TIGR00514 347 IKNFLPSPG 355 (451) T ss_pred CCCCCCCCC T ss_conf 877868885 No 25 >KOG0238 consensus Probab=74.40 E-value=7.5 Score=19.88 Aligned_cols=69 Identities=17% Similarity=0.140 Sum_probs=40.4 Q ss_pred CEEEEEEEECCEEEEEECCCCCCCCCC-------HHHHHHHH--------HHCC-----CCCEEEEEEECCEEEEECCCC Q ss_conf 405789961988999946887643211-------54300133--------2013-----786156897667774401587 Q gi|254781067|r 70 QRFQFLYQDQEGFHFMNPETYDQVTVS-------EEVIGDQK--------VYFQ-----EGMEVKLLIHEGVALSVEVPR 129 (189) Q Consensus 70 ~~~qylY~dg~~~~FMd~etyeqi~i~-------~~~ig~~~--------~fL~-----eg~~v~i~~~~~~~i~i~lP~ 129 (189) -.++|++...++|+||.+.|-=|++-| .|++.+++ ++-+ .|--+....|-+.|.+--||. T Consensus 268 GTVEFi~D~~~~FyFmEmNTRLQVEHPvTEmItg~DLVewqiRvA~ge~lp~~q~ei~l~GhafE~RiyAEdp~~~f~P~ 347 (670) T KOG0238 268 GTVEFIVDSKDNFYFMEMNTRLQVEHPVTEMITGTDLVEWQIRVAAGEPLPLKQEEIPLNGHAFEARIYAEDPYKGFLPS 347 (670) T ss_pred CEEEEEECCCCCEEEEEEECEEEECCCCHHHCCCHHHHHHHHHHHCCCCCCCCCCEEEECCEEEEEEEEECCCCCCCCCC T ss_conf 44999983788579998402253036416321222789999998649999977020136454789998500775467778 Q ss_pred EEEEEEEEC Q ss_conf 499999982 Q gi|254781067|r 130 HVVFTVIDT 138 (189) Q Consensus 130 ~v~l~V~~t 138 (189) .=-|.-..+ T Consensus 348 ~G~L~~~~~ 356 (670) T KOG0238 348 AGRLVYYSF 356 (670) T ss_pred CCCCEEECC T ss_conf 741112026 No 26 >cd04468 S1_eIF5A S1_eIF5A: Eukaryotic translation Initiation Factor 5A (eIF5A), S1-like RNA-binding domain. eIF5A is an evolutionarily conserved protein found in eukaryotes. eIF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is essential for eIF5A function and is a post-translationally modified lysine. eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) in a hypusine-dependent manner. This C-terminal S1 domain resembles the oligonucleotides-binding fold (OB fold) which binds RNA. Moreover, eIF5A prefers binding to the actively translating ribosome. This evidence suggests that eIF5A plays a role in translation elongation instead of translation initiation as previously proposed. Probab=68.22 E-value=9.3 Score=19.32 Aligned_cols=50 Identities=24% Similarity=0.410 Sum_probs=36.4 Q ss_pred ECCCEEEEEEEECCEEEEEEC--CCCCCCCCCHHHHHHHHH-HCCCCCEEEEE Q ss_conf 056405789961988999946--887643211543001332-01378615689 Q gi|254781067|r 67 VEDQRFQFLYQDQEGFHFMNP--ETYDQVTVSEEVIGDQKV-YFQEGMEVKLL 116 (189) Q Consensus 67 ie~~~~qylY~dg~~~~FMd~--etyeqi~i~~~~ig~~~~-fL~eg~~v~i~ 116 (189) +.|.++|.+..+++....|+. ++-|.+.+|..-+|...+ -.-+|-.+.+. T Consensus 1 V~R~eYqLidIdDGflsLm~d~G~~keDlklP~~elg~~I~~~f~~gk~~~Vt 53 (69) T cd04468 1 VKRTEYQLIDIDDGFLSLMDDDGETREDLKLPEGELGKEIREKFDEGKDVLVT 53 (69) T ss_pred CCHHHEEEEEECCCCEEEECCCCCCHHCCCCCCHHHHHHHHHHHHCCCCEEEE T ss_conf 94131589841156200356899832125699479999999997679918999 No 27 >KOG0267 consensus Probab=63.48 E-value=13 Score=18.40 Aligned_cols=161 Identities=16% Similarity=0.195 Sum_probs=97.8 Q ss_pred EHHHCC-CCCEEEECCEEEEEEEEEEECCCC----CCCEEEEEEEECCCCCCEEEEECCCC-CEEEEEECCCEEEEEEEE Q ss_conf 643216-775899889379999987536888----76389999998246871001342787-200101056405789961 Q gi|254781067|r 5 IASAVR-KGNVLDVDGKLYIVLVAKNFHPGK----GTPITQVEMRRISDGVKVSNRWRTTE-QVERAFVEDQRFQFLYQD 78 (189) Q Consensus 5 ~an~lk-~G~~i~~dg~~~~V~~~~~~kpgk----g~a~v~~klknL~tG~~~e~~f~~~e-kve~~~ie~~~~qylY~d 78 (189) ...|+| +|....++|-++.|--.++.--|| |+--.-+++=++.-|+.+ ..|++.+ ++..++ -.+..||-.- T Consensus 137 ~iwD~Rk~Gc~~~~~s~~~vv~~l~lsP~Gr~v~~g~ed~tvki~d~~agk~~-~ef~~~e~~v~sle--~hp~e~Lla~ 213 (825) T KOG0267 137 KIWDIRKKGCSHTYKSHTRVVDVLRLSPDGRWVASGGEDNTVKIWDLTAGKLS-KEFKSHEGKVQSLE--FHPLEVLLAP 213 (825) T ss_pred EEHHHHCCCCEEEECCCCCEEEEEEECCCCCEEECCCCCCEEEEECCCCCCCC-CCCCCCCCCCCCCC--CCCHHHHHCC T ss_conf 11000004742450587632577753699706610688654562034432002-22566655510134--6823542166 Q ss_pred C---CEEEEEECCCCCCCCCCHHHHHH--HHHHCCCCCEE----EEEEECCEEEEECCCCEEEEEEEECCCCCCCCCCCC Q ss_conf 9---88999946887643211543001--33201378615----689766777440158749999998285421310247 Q gi|254781067|r 79 Q---EGFHFMNPETYDQVTVSEEVIGD--QKVYFQEGMEV----KLLIHEGVALSVEVPRHVVFTVIDTEPSSKGQTVTA 149 (189) Q Consensus 79 g---~~~~FMd~etyeqi~i~~~~ig~--~~~fL~eg~~v----~i~~~~~~~i~i~lP~~v~l~V~~t~p~~kG~t~~~ 149 (189) | ...-|-|+|+||-|.-.+-...+ ...|-.+|+.+ ++.+-+.. .--.+|...+..+||...|+++.. T Consensus 214 Gs~d~tv~f~dletfe~I~s~~~~~~~v~~~~fn~~~~~~~~G~q~sl~~~~----~a~ah~~~~~~~~Ep~~~~~~vqs 289 (825) T KOG0267 214 GSSDRTVRFWDLETFEVISSGKPETDGVRSLAFNPDGKIVLSGEQISLSESR----TASAHVRKTLARWEPEMDGAVVQS 289 (825) T ss_pred CCCCCEEEEECCCEEEEEECCCCCCCCCEEEEECCCCEEEECCCHHHHHHHH----CCCCEEECCCCCCCCCCCCCEEEE T ss_conf 7777506643141368861268755772221016874032047503222221----033102101245564424522444 Q ss_pred C-EEEEEEECCCEEECCCCCCCCC Q ss_conf 7-0008993795998474016887 Q gi|254781067|r 150 S-YKPAILSNDIRTTVPPHINIGD 172 (189) Q Consensus 150 ~-~K~A~letG~~i~VP~FI~~Gd 172 (189) . .|+..+--|-.=+.--|+..++ T Consensus 290 ~~~~ek~v~v~~d~~~ln~~~s~~ 313 (825) T KOG0267 290 NSHKEKVVAVGRDPQDLNAFSSKV 313 (825) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCC T ss_conf 377542001345743100210355 No 28 >PRK08654 pyruvate carboxylase subunit A; Validated Probab=61.61 E-value=14 Score=18.19 Aligned_cols=26 Identities=31% Similarity=0.450 Sum_probs=19.1 Q ss_pred CEEEEEEEECCEEEEEECCCCCCCCCC Q ss_conf 405789961988999946887643211 Q gi|254781067|r 70 QRFQFLYQDQEGFHFMNPETYDQVTVS 96 (189) Q Consensus 70 ~~~qylY~dg~~~~FMd~etyeqi~i~ 96 (189) -++||||. ++.|+||...+==|.+-+ T Consensus 272 GTVEFl~d-~g~fyFlEmNtRlQVEHp 297 (497) T PRK08654 272 GTVEFLYS-NGNFYFLEMNTRLQVEHP 297 (497) T ss_pred CEEEEEEE-CCEEEEEEEECCCCCCCC T ss_conf 32799874-883999961244224554 No 29 >PRK12833 acetyl-CoA carboxylase biotin carboxylase subunit; Provisional Probab=59.86 E-value=14 Score=18.27 Aligned_cols=27 Identities=26% Similarity=0.460 Sum_probs=19.5 Q ss_pred CEEEEEEEE-CCEEEEEECCCCCCCCCC Q ss_conf 405789961-988999946887643211 Q gi|254781067|r 70 QRFQFLYQD-QEGFHFMNPETYDQVTVS 96 (189) Q Consensus 70 ~~~qylY~d-g~~~~FMd~etyeqi~i~ 96 (189) -.++|||.+ .+.|+||...+==|.+-+ T Consensus 274 gTvEFl~d~~~~~fyFlEvNtRlQVEH~ 301 (458) T PRK12833 274 GTLEYLFDDARGEFYFIEMNTRIQVEHP 301 (458) T ss_pred EEEEEEEECCCCCEEEEEEECCCCCCCC T ss_conf 0266678658896899962136444442 No 30 >COG1153 FwdD Formylmethanofuran dehydrogenase subunit D [Energy production and conversion] Probab=58.15 E-value=6.2 Score=20.42 Aligned_cols=32 Identities=31% Similarity=0.375 Sum_probs=23.7 Q ss_pred EECCCEEEEEEEECCEEEEEECCCCCCCCCCH Q ss_conf 10564057899619889999468876432115 Q gi|254781067|r 66 FVEDQRFQFLYQDQEGFHFMNPETYDQVTVSE 97 (189) Q Consensus 66 ~ie~~~~qylY~dg~~~~FMd~etyeqi~i~~ 97 (189) .++.-...=.|.+-..+.-||+++++|.-+++ T Consensus 16 aie~gK~~~~Y~~a~a~~~inp~D~~~Lgv~E 47 (128) T COG1153 16 AIEGGKFTDEYFNACAVCEINPEDMKQLGVSE 47 (128) T ss_pred HHHCCCCHHHHHHHEEEEEECHHHHHHHCCCC T ss_conf 22236325666301058997999999848876 No 31 >pfam00900 Ribosomal_S4e Ribosomal family S4e. Probab=55.55 E-value=18 Score=17.56 Aligned_cols=37 Identities=24% Similarity=0.305 Sum_probs=30.0 Q ss_pred CCCCCEEEEEEECCCEEECC-CCCCCCCEEEEECCCCC Q ss_conf 02477000899379599847-40168879999889972 Q gi|254781067|r 146 TVTASYKPAILSNDIRTTVP-PHINIGDDIVILTEDNS 182 (189) Q Consensus 146 t~~~~~K~A~letG~~i~VP-~FI~~Gd~IkV~T~~g~ 182 (189) ++.++--...+.-|-.|.+| .-++.||.++|+..+++ T Consensus 36 ~~kgG~~ql~~hDGrni~~~~~~~k~~Dtv~i~l~~~k 73 (74) T pfam00900 36 TVKGGKPQLNLHDGRNIRYPDPDYKTGDTLVIDLPTQK 73 (74) T ss_pred EECCCEEEEEECCCCEEEECCCCCCCCCEEEEECCCCC T ss_conf 90399389995487589827898226999999877783 No 32 >cd02779 MopB_CT_Arsenite-Ox This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of Arsenite oxidase (Arsenite-Ox) and related proteins. Arsenite oxidase oxidizes arsenite to the less toxic arsenate; it transfers the electrons obtained from the oxidation of arsenite towards the soluble periplasmic electron carriers cytochrome c and/or amicyanin. Probab=52.25 E-value=10 Score=19.09 Aligned_cols=14 Identities=21% Similarity=0.313 Sum_probs=5.6 Q ss_pred CCCCCEEEEEEECC Q ss_conf 13786156897667 Q gi|254781067|r 107 FQEGMEVKLLIHEG 120 (189) Q Consensus 107 L~eg~~v~i~~~~~ 120 (189) |++|..|.+.--.| T Consensus 47 I~~Gd~V~v~s~rG 60 (115) T cd02779 47 LKNGDLVEVYNDYG 60 (115) T ss_pred CCCCCEEEEECCCE T ss_conf 99989999987990 No 33 >cd02789 MopB_CT_FmdC-FwdD The MopB_FmdC-FwdD CD includes the C-terminus of subunit C of molybdenum formylmethanofuran dehydrogenase (FmdC) and subunit D of tungsten formylmethanofuran dehydrogenase (FwdD), and other related proteins. Formylmethanofuran dehydrogenase catalyzes the first step in methane formation from CO2 in methanogenic archaea and some eubacteria. Members of this CD belong to the molybdopterin_binding superfamily of proteins. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=52.11 E-value=9.7 Score=19.20 Aligned_cols=55 Identities=22% Similarity=0.290 Sum_probs=31.5 Q ss_pred ECCCCCCEEEEECCCCCEEEEEECCCEEEEEEEECCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECC Q ss_conf 8246871001342787200101056405789961988999946887643211543001332013786156897667 Q gi|254781067|r 45 RISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEG 120 (189) Q Consensus 45 nL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~dg~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~ 120 (189) .|.||+.+++ +. .+++...-=.|.+-..|.+|+++++..+-+ .+|..|.+.--.| T Consensus 4 iL~TGRti~q----g~-----~m~~~~~~~~y~~~~a~~~i~P~D~~~lGi------------~~Gd~V~v~s~~G 58 (106) T cd02789 4 ILNSGRTIDQ----GR-----IIEGGNKLTYEVDACAYCEINPEDYKLLGK------------PEGDKVKVTSEFG 58 (106) T ss_pred EECCCCHHHH----HH-----HHHCCCCCHHHCCCCEEEEECHHHHHHCCC------------CCCCEEEEECCCE T ss_conf 9824754755----75-----200768732321666499989999998098------------9999999987987 No 34 >cd02792 MopB_CT_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. This CD (MopB_CT_Formate-Dh-Na-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=48.48 E-value=12 Score=18.68 Aligned_cols=32 Identities=22% Similarity=0.162 Sum_probs=16.2 Q ss_pred ECCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCE Q ss_conf 19889999468876432115430013320137861568976677 Q gi|254781067|r 78 DQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGV 121 (189) Q Consensus 78 dg~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~ 121 (189) ..+.|++|++++=+.. =|.+|..|.|.--.|. T Consensus 32 ~pe~~v~i~p~dA~~l------------gi~dGd~V~v~s~~G~ 63 (122) T cd02792 32 QPEMFVEISPELAAER------------GIKNGDMVWVSSPRGK 63 (122) T ss_pred CCCCEEEECHHHHHHC------------CCCCCCEEEEECCCEE T ss_conf 9998999999999874------------9988988999889989 No 35 >TIGR02102 pullulan_Gpos pullulanase, extracellular; InterPro: IPR011838 Pullulan is an unusual, industrially important polysaccharide in which short alpha-1,4 chains (maltotriose) are connected in alpha-1,6 linkages. Enzymes that cleave alpha-1,6 linkages in pullulan and release maltotriose are called pullulanases although pullulan itself may not be the natural substrate. In contrast, a glycogen debranching enzyme such GlgX, homologous to this family, can release glucose at alpha,1-6 linkages from glycogen first subjected to limit degradation by phosphorylase. Characterised members of this family include a surface-located pullulanase from Streptococcus pneumoniae and an extracellular bifunctional amylase/pullulanase with C-terminal pullulanase activity .. Probab=48.40 E-value=13 Score=18.41 Aligned_cols=19 Identities=21% Similarity=0.163 Sum_probs=8.2 Q ss_pred CCEEEEECCCCEEEEEEEE Q ss_conf 6777440158749999998 Q gi|254781067|r 119 EGVALSVEVPRHVVFTVID 137 (189) Q Consensus 119 ~~~~i~i~lP~~v~l~V~~ 137 (189) ..+-|.++-=+.++++|-+ T Consensus 1008 ~~~~l~ldpLTa~v~~Vg~ 1026 (1164) T TIGR02102 1008 TKEGLKLDPLTAVVVRVGE 1026 (1164) T ss_pred ECCCEEECCCEEEEEEECC T ss_conf 1033156141579998557 No 36 >cd02791 MopB_CT_Nitrate-R-NapA-like Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. This CD (MopB_CT_Nitrate-R-Nap) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs Probab=46.49 E-value=14 Score=18.27 Aligned_cols=30 Identities=23% Similarity=0.400 Sum_probs=14.4 Q ss_pred CCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECC Q ss_conf 988999946887643211543001332013786156897667 Q gi|254781067|r 79 QEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEG 120 (189) Q Consensus 79 g~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~ 120 (189) .+.++.|++++-+..- |.||..|.|.--.| T Consensus 33 pe~~v~inp~dA~~~g------------i~dgd~V~v~s~~G 62 (122) T cd02791 33 PEPYVEIHPEDAARLG------------LKEGDLVRVTSRRG 62 (122) T ss_pred CCCEEEECHHHHHHCC------------CCCCCEEEEECCCE T ss_conf 9978999999998869------------98999999984880 No 37 >cd02780 MopB_CT_Tetrathionate_Arsenate-R This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins. Probab=45.88 E-value=14 Score=18.20 Aligned_cols=31 Identities=23% Similarity=0.379 Sum_probs=17.5 Q ss_pred CCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCE Q ss_conf 9889999468876432115430013320137861568976677 Q gi|254781067|r 79 QEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGV 121 (189) Q Consensus 79 g~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~ 121 (189) .++|+.|++++=++ .=|++|..|.|.--.|. T Consensus 28 pen~v~inp~dA~~------------~Gi~~Gd~V~v~s~~G~ 58 (143) T cd02780 28 PENPVWINPEDAAK------------LGIKTGDRVRVVTPGGS 58 (143) T ss_pred CCCEEEECHHHHHH------------CCCCCCCEEEEECCCEE T ss_conf 99859999999998------------69998999999879857 No 38 >cd02785 MopB_CT_4 The MopB_CT_4 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=45.15 E-value=14 Score=18.21 Aligned_cols=16 Identities=19% Similarity=0.169 Sum_probs=8.3 Q ss_pred HCCCCCEEEEEEECCE Q ss_conf 0137861568976677 Q gi|254781067|r 106 YFQEGMEVKLLIHEGV 121 (189) Q Consensus 106 fL~eg~~v~i~~~~~~ 121 (189) =|++|..|.+.---|+ T Consensus 45 GI~dgd~V~v~n~rG~ 60 (124) T cd02785 45 GIAHGDLVEVYNDRGS 60 (124) T ss_pred CCCCCCEEEEECCCEE T ss_conf 9999999999859999 No 39 >TIGR01591 Fdh-alpha formate dehydrogenase, alpha subunit; InterPro: IPR006478 This group of sequences describe a subset of formate dehydrogenase alpha chains found mainly in the archaea but also in alpha and gamma proteobacteria and a small number of Gram-positive bacteria. The alpha chain contains domains for molybdopterin dinucleotide binding and molybdopterin oxidoreductase. The holo-enzyme also contains beta and gamma subunits. The enzyme catalyzes the oxidation of formate (produced from pyruvate during anaerobic growth) to carbon dioxide with the concomitant release of two electrons and two protons. The enzyme's purpose is to allow growth on formate in some circumstances and, in the case of FdhH in gamma proteobacteria, to pass electrons to hydrogenase (by which process acid is neutralized) . The alpha subunit of a version of nitrate reductase is closely related.; GO: 0008863 formate dehydrogenase activity, 0015942 formate metabolic process, 0009326 formate dehydrogenase complex. Probab=44.95 E-value=13 Score=18.35 Aligned_cols=23 Identities=22% Similarity=0.200 Sum_probs=19.7 Q ss_pred CCCCCCCEEEEECCCC-CEEHHCC Q ss_conf 4016887999988997-2402102 Q gi|254781067|r 166 PHINIGDDIVILTEDN-SYVERVK 188 (189) Q Consensus 166 ~FI~~Gd~IkV~T~~g-~Y~~Rak 188 (189) +=|+.||.|+|.+|.| +-.-||+ T Consensus 623 lgI~dgd~V~V~Sr~GG~~~~rA~ 646 (694) T TIGR01591 623 LGIKDGDLVKVKSRRGGEITLRAK 646 (694) T ss_pred CCCCCCCEEEEEECCCCCEEEEEE T ss_conf 588356778998414710143441 No 40 >pfam00498 FHA FHA domain. The FHA (Forkhead-associated) domain is a phosphopeptide binding motif. Probab=44.56 E-value=27 Score=16.50 Aligned_cols=55 Identities=15% Similarity=0.272 Sum_probs=37.9 Q ss_pred CEEEEEECCCEEEEEEEECCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEE Q ss_conf 2001010564057899619889999468876432115430013320137861568 Q gi|254781067|r 61 QVERAFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKL 115 (189) Q Consensus 61 kve~~~ie~~~~qylY~dg~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i 115 (189) .++...+.++-+.+.+.++..|+..|..+-.-..++...++...--|.+|..+.+ T Consensus 12 ~l~~~~iSr~Ha~i~~~~~~~~~i~Dl~S~nGt~vNg~~i~~~~~~L~~GD~i~i 66 (67) T pfam00498 12 VLDDPSVSRRHAEIRYDGGGRFYLEDLGSTNGTFVNGQRLGPEPVRLKDGDVIRL 66 (67) T ss_pred EECCCCCCHHHEEEEEECCCEEEEEECCCCCCEEECCEECCCCCEECCCCCEEEE T ss_conf 9898360702499999249869999799886859999996788769999999984 No 41 >cd02790 MopB_CT_Formate-Dh_H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a Mo active site region and a [4Fe-4S] center. This CD (MopB_CT_Formate-Dh_H) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=44.45 E-value=15 Score=18.07 Aligned_cols=31 Identities=23% Similarity=0.448 Sum_probs=14.7 Q ss_pred CCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCE Q ss_conf 9889999468876432115430013320137861568976677 Q gi|254781067|r 79 QEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGV 121 (189) Q Consensus 79 g~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~ 121 (189) .+.|+.|++++-+..- |++|..|.|.--.|. T Consensus 33 pep~v~i~p~dA~~lG------------i~~Gd~V~v~s~~G~ 63 (116) T cd02790 33 PEEYVEINPEDAKRLG------------IEDGEKVRVSSRRGS 63 (116) T ss_pred CCCEEEECHHHHHHCC------------CCCCCEEEEECCCEE T ss_conf 9988998999998859------------988998999879989 No 42 >PRK13480 3'-5' exoribonuclease YhaM; Provisional Probab=43.94 E-value=27 Score=16.44 Aligned_cols=57 Identities=16% Similarity=0.310 Sum_probs=44.1 Q ss_pred CCEEEHHHCCCCCEEEECCEEEEEEEEEEECCCCCCCEEEEEEEECCCCCCEEEEECCCCCE Q ss_conf 92366432167758998893799999875368887638999999824687100134278720 Q gi|254781067|r 1 MVKVIASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQV 62 (189) Q Consensus 1 m~~i~an~lk~G~~i~~dg~~~~V~~~~~~kpgkg~a~v~~klknL~tG~~~e~~f~~~ekv 62 (189) ||+ .-++++.|..+. ..|.|.+.+..+.-.|.+|.++.|++ .||.+--+-|..++.. T Consensus 1 m~~-~i~~l~~G~~v~---~~~lv~~~~~~~tknG~~Yl~l~L~D-~tG~I~ak~W~~~~~~ 57 (314) T PRK13480 1 MMK-GIENLEVGESVD---HFLLIKSATKGVASNGKPFLTLILQD-KSGDIEAKLWDVSKED 57 (314) T ss_pred CCC-CHHHCCCCCEEE---EEEEEEECHHHCCCCCCCEEEEEEEC-CCCEEEEEECCCCHHH T ss_conf 965-141089998888---99999871433189998147999983-7876889967898666 No 43 >cd02777 MopB_CT_DMSOR-like The MopB_CT_DMSOR-like CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Also included in this group is the pyrogallol-phloroglucinol transhydroxylase from Pelobacter acidigallici. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB hom Probab=42.80 E-value=18 Score=17.56 Aligned_cols=17 Identities=18% Similarity=0.331 Sum_probs=9.3 Q ss_pred HCCCCCEEEEEEECCEE Q ss_conf 01378615689766777 Q gi|254781067|r 106 YFQEGMEVKLLIHEGVA 122 (189) Q Consensus 106 fL~eg~~v~i~~~~~~~ 122 (189) =|.+|..|.+.--.|++ T Consensus 47 gI~dGd~V~v~n~~G~i 63 (127) T cd02777 47 GIKDGDIVRVFNDRGAV 63 (127) T ss_pred CCCCCCEEEEECCCCEE T ss_conf 99898999998789649 No 44 >PRK06111 acetyl-CoA carboxylase biotin carboxylase subunit; Validated Probab=41.39 E-value=28 Score=16.41 Aligned_cols=27 Identities=30% Similarity=0.420 Sum_probs=21.0 Q ss_pred CEEEEEEEECCEEEEEECCCCCCCCCC Q ss_conf 405789961988999946887643211 Q gi|254781067|r 70 QRFQFLYQDQEGFHFMNPETYDQVTVS 96 (189) Q Consensus 70 ~~~qylY~dg~~~~FMd~etyeqi~i~ 96 (189) -.++|||.++..|+||...+==|++-+ T Consensus 272 gTvEFl~d~~~~fyFlEvNtRlQVEHp 298 (449) T PRK06111 272 GTIEFLVDNQKNFYFLEMNTRLQVEHP 298 (449) T ss_pred EEEEEEEECCCCEEEEEEECCCCCCCC T ss_conf 689999948986899953435444664 No 45 >PRK05586 biotin carboxylase; Validated Probab=40.01 E-value=32 Score=16.06 Aligned_cols=97 Identities=14% Similarity=0.247 Sum_probs=47.4 Q ss_pred CEEEEEEEECCEEEEEECCCCCCCCCC-------HHHHHHHHHHCCCCCEEEEEEECCEEEEEC-CCCEEEEEEEECCCC Q ss_conf 405789961988999946887643211-------543001332013786156897667774401-587499999982854 Q gi|254781067|r 70 QRFQFLYQDQEGFHFMNPETYDQVTVS-------EEVIGDQKVYFQEGMEVKLLIHEGVALSVE-VPRHVVFTVIDTEPS 141 (189) Q Consensus 70 ~~~qylY~dg~~~~FMd~etyeqi~i~-------~~~ig~~~~fL~eg~~v~i~~~~~~~i~i~-lP~~v~l~V~~t~p~ 141 (189) -.++|||..++.|+||...+==|++=+ .|++..+. .+..|..+... .+ .|. -...+++.| ++|.. T Consensus 272 GTvEFl~d~~~~fyFlEvNtRlQVEH~VTE~vtGvDLV~~Qi-~iA~G~~L~~~--q~---~i~~~GhAIe~Ri-~AEdp 344 (447) T PRK05586 272 GTIEFLLDKDGNFYFMEMNTRIQVEHPITEMITGVDLVKEQI-KIAYGEKLSIT--QE---DIKINGHAIECRI-NAEDP 344 (447) T ss_pred CEEEEEECCCCCEEEEEEECCCCCCCCCEEECCCCCHHHHHH-HHHCCCCCCCC--CC---CCCCCCEEEEEEE-ECCCC T ss_conf 247888758997899933435555664110003776899999-98679999977--01---0787856999982-14578 Q ss_pred CCC-CCCCCCEEEEEEECCCEEECCCCCCCCCE Q ss_conf 213-10247700089937959984740168879 Q gi|254781067|r 142 SKG-QTVTASYKPAILSNDIRTTVPPHINIGDD 173 (189) Q Consensus 142 ~kG-~t~~~~~K~A~letG~~i~VP~FI~~Gd~ 173 (189) .++ -.+++.-..-..-+|--|.|-..+..|+. T Consensus 345 ~~~f~Ps~G~i~~~~~P~g~gvRvDt~~~~G~~ 377 (447) T PRK05586 345 ENGFMPCPGKIEELYIPGGLGVRLDSAIYSGYT 377 (447) T ss_pred CCCCCCCCCEEEEEECCCCCCEEEECCCCCCCC T ss_conf 878505875665897699998898787458796 No 46 >cd02786 MopB_CT_3 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=38.75 E-value=21 Score=17.18 Aligned_cols=32 Identities=16% Similarity=0.158 Sum_probs=16.8 Q ss_pred CCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCEE Q ss_conf 98899994688764321154300133201378615689766777 Q gi|254781067|r 79 QEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVA 122 (189) Q Consensus 79 g~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~~ 122 (189) ++.+++|++++-++ .=|++|..|.+.---|++ T Consensus 29 ~~p~v~i~p~DA~~------------~GI~dGd~V~v~n~~G~v 60 (116) T cd02786 29 GEPTLLIHPADAAA------------RGIADGDLVVVFNDRGSV 60 (116) T ss_pred CCCEEEECHHHHHH------------CCCCCCCEEEEECCCEEE T ss_conf 99869999999988------------599999999997899899 No 47 >pfam02941 FeThRed_A Ferredoxin thioredoxin reductase variable alpha chain. Probab=38.54 E-value=21 Score=17.12 Aligned_cols=30 Identities=27% Similarity=0.351 Sum_probs=21.6 Q ss_pred HCCCCCE----EEEEEECCEEEEECCCCEEEEEE Q ss_conf 0137861----56897667774401587499999 Q gi|254781067|r 106 YFQEGME----VKLLIHEGVALSVEVPRHVVFTV 135 (189) Q Consensus 106 fL~eg~~----v~i~~~~~~~i~i~lP~~v~l~V 135 (189) |=..||+ =.+..|+|+|||..||-.|.+.+ T Consensus 24 fDl~G~eGeV~~~v~~wkGr~ISanlP~~V~F~~ 57 (67) T pfam02941 24 FDLKGMEGEIKQYVGDWKGRPISANLPFKVQFSK 57 (67) T ss_pred CCCCCCEEEEEEEEECCCCCEECCCCCEEEEECH T ss_conf 4446777777567631369695699879999800 No 48 >PRK08462 biotin carboxylase; Validated Probab=38.38 E-value=34 Score=15.91 Aligned_cols=97 Identities=19% Similarity=0.221 Sum_probs=45.8 Q ss_pred CCEEEEEEEE-CCEEEEEECCCCCCCCCC-------HHHHHHHHHHCCCCCEEEEEEECCEEEEECC-CCEEEEEEEECC Q ss_conf 6405789961-988999946887643211-------5430013320137861568976677744015-874999999828 Q gi|254781067|r 69 DQRFQFLYQD-QEGFHFMNPETYDQVTVS-------EEVIGDQKVYFQEGMEVKLLIHEGVALSVEV-PRHVVFTVIDTE 139 (189) Q Consensus 69 ~~~~qylY~d-g~~~~FMd~etyeqi~i~-------~~~ig~~~~fL~eg~~v~i~~~~~~~i~i~l-P~~v~l~V~~t~ 139 (189) --.+||||.. ++.|+||...+==|++=+ -|++..+.. +..|..+ .+... +.+ -..+++.|.--+ T Consensus 273 aGTvEFl~d~~~~~fyFlE~NtRlQVEH~VTE~vtGiDLV~~Qi~-iA~G~~l----~~q~~--i~~~GhaIe~Ri~AEd 345 (446) T PRK08462 273 AGTFEFLLDSNMKDFYFMEMNTRLQVEHTVSEMVSGLDLIEWMIK-IAEGEEL----PSQES--IKLKGHAIECRITAED 345 (446) T ss_pred CCEEEEEECCCCCEEEEEEEECCCCEECCCCCCCCCCCHHHHHHH-HHCCCCC----CCCCC--CCCCCEEEEEEEECCC T ss_conf 433899980799718999743342100111122148779999999-8679998----75666--6726434223420458 Q ss_pred CCCCCCCCC-CCEEEEEEECCCEEECCCCCCCCCEE Q ss_conf 542131024-77000899379599847401688799 Q gi|254781067|r 140 PSSKGQTVT-ASYKPAILSNDIRTTVPPHINIGDDI 174 (189) Q Consensus 140 p~~kG~t~~-~~~K~A~letG~~i~VP~FI~~Gd~I 174 (189) | ..-.-+ +.-..-..-+|.-|.|-.++..|+.| T Consensus 346 p--~~F~Ps~G~i~~~~~P~g~gvRvDt~~~~G~~v 379 (446) T PRK08462 346 P--KKFYPSPGKITKWIAPGGRNVRMDSHAYAGYVV 379 (446) T ss_pred C--CCCCCCCEEEEEEECCCCCCEEEECCCCCCCEE T ss_conf 7--767998758878987999998963887785987 No 49 >cd00508 MopB_CT_Fdh-Nap-like This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. Formate dehydrogenase N (alpha subunit) is the major electron donor to the bacterial nitrate respiratory chain and nitrate reductases, Nap and Nas, catalyze the reduction of nitrate to nitrite. This CD (MopB_CT_Fdh-Nap-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=38.32 E-value=21 Score=17.13 Aligned_cols=31 Identities=23% Similarity=0.375 Sum_probs=15.8 Q ss_pred ECCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECC Q ss_conf 1988999946887643211543001332013786156897667 Q gi|254781067|r 78 DQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEG 120 (189) Q Consensus 78 dg~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~ 120 (189) ..+.++.|++++-++.- |++|..|.|.--.| T Consensus 32 ~pep~v~~~p~dA~~lg------------i~~Gd~V~v~s~~G 62 (120) T cd00508 32 APEPFVEIHPEDAARLG------------IKDGDLVRVSSRRG 62 (120) T ss_pred CCCCEEEECHHHHHHCC------------CCCCCEEEEECCCE T ss_conf 99988999999998859------------99999999981773 No 50 >cd02776 MopB_CT_Nitrate-R-NarG-like Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. Found in prokaryotes and some archaea, NarGHI usually functions as a heterotrimer. The alpha chain contains the molybdenum cofactor-containing Mo-bisMGD catalytic subunit. This CD (MopB_CT_Nitrate-R-NarG-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=38.28 E-value=23 Score=16.95 Aligned_cols=30 Identities=27% Similarity=0.402 Sum_probs=14.0 Q ss_pred HCCCCCEEEEEEECCE-----EEEECCCCEEEEEE Q ss_conf 0137861568976677-----74401587499999 Q gi|254781067|r 106 YFQEGMEVKLLIHEGV-----ALSVEVPRHVVFTV 135 (189) Q Consensus 106 fL~eg~~v~i~~~~~~-----~i~i~lP~~v~l~V 135 (189) =++||.-|.+.--.|. .++=.+|.-+++.= T Consensus 44 GI~DgD~Vev~N~~G~v~arA~Vs~rip~G~v~my 78 (141) T cd02776 44 GIKDNDWVEVFNDNGVVVARAKVSPRIPRGTVFMY 78 (141) T ss_pred CCCCCCEEEEECCCCEEEEEEEECCCCCCCEEEEE T ss_conf 99889999998489259999998998799989997 No 51 >TIGR01540 portal_PBSX phage portal protein, PBSX family; InterPro: IPR006430 This group of sequences, from phage and prophage, represent one of several distantly related families of portal proteins. This protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins. It functions as a dodecamer of a single polypeptide of average molecular weight of 40-90 kDa. This family shows clear homology to sequences represented by IPR006427 from INTERPRO.. Probab=38.10 E-value=11 Score=18.84 Aligned_cols=21 Identities=24% Similarity=0.327 Sum_probs=17.5 Q ss_pred CCCCCCCEEEEECCCCCEEHH Q ss_conf 401688799998899724021 Q gi|254781067|r 166 PHINIGDDIVILTEDNSYVER 186 (189) Q Consensus 166 ~FI~~Gd~IkV~T~~g~Y~~R 186 (189) .||+.+|-+|.|-|||||+.- T Consensus 169 ~F~~~~dp~kmdirtGeyvnt 189 (386) T TIGR01540 169 IFIELPDPIKMDIRTGEYVNT 189 (386) T ss_pred EEEECCCCCEEECCCCHHHHH T ss_conf 986168974121134226787 No 52 >cd02778 MopB_CT_Thiosulfate-R-like The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Also included in this CD is the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), which has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. The MopB_CT_Thiosulfate-R-like CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=36.80 E-value=24 Score=16.80 Aligned_cols=31 Identities=26% Similarity=0.392 Sum_probs=14.6 Q ss_pred CCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECCE Q ss_conf 9889999468876432115430013320137861568976677 Q gi|254781067|r 79 QEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGV 121 (189) Q Consensus 79 g~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~~ 121 (189) .+.++.|++++=+.. =|++|..|.|.--.|. T Consensus 28 ~~~~v~inp~dA~~~------------Gi~dGd~V~v~s~~G~ 58 (123) T cd02778 28 PENTLWINPETAARL------------GIKDGDRVEVSSARGK 58 (123) T ss_pred CCCEEEECHHHHHHC------------CCCCCCEEEEECCCEE T ss_conf 998899999999984------------9999999999889968 No 53 >cd02793 MopB_CT_DMSOR-BSOR-TMAOR The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO.This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=36.18 E-value=26 Score=16.54 Aligned_cols=17 Identities=18% Similarity=0.305 Sum_probs=10.1 Q ss_pred HCCCCCEEEEEEECCEE Q ss_conf 01378615689766777 Q gi|254781067|r 106 YFQEGMEVKLLIHEGVA 122 (189) Q Consensus 106 fL~eg~~v~i~~~~~~~ 122 (189) =|++|..|.|.--.|++ T Consensus 46 GI~dGd~V~V~n~rG~v 62 (129) T cd02793 46 GIADGDIVRVFNDRGAC 62 (129) T ss_pred CCCCCCEEEEECCCCEE T ss_conf 99898999998889569 No 54 >pfam01568 Molydop_binding Molydopterin dinucleotide binding domain. This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a molybdopterin dinucleotide cofactor. This domain corresponds to the C-terminal domain IV in dimethyl sulfoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules. Probab=35.08 E-value=25 Score=16.66 Aligned_cols=15 Identities=20% Similarity=0.355 Sum_probs=8.7 Q ss_pred CCCCCEEEEEEECCE Q ss_conf 137861568976677 Q gi|254781067|r 107 FQEGMEVKLLIHEGV 121 (189) Q Consensus 107 L~eg~~v~i~~~~~~ 121 (189) |.+|..|.+.--.|+ T Consensus 44 i~~Gd~V~v~s~~G~ 58 (110) T pfam01568 44 IKDGDLVEVTSRRGS 58 (110) T ss_pred CCCCCEEEEECCCEE T ss_conf 988999999768989 No 55 >KOG1708 consensus Probab=35.05 E-value=23 Score=16.85 Aligned_cols=52 Identities=17% Similarity=0.273 Sum_probs=32.6 Q ss_pred ECCEEEEECCCCEEEEEEEECCCCCCCCCCCCCEEEEEEECCCEEECCCCCCCCCEEEEECCCCCEE Q ss_conf 6677744015874999999828542131024770008993795998474016887999988997240 Q gi|254781067|r 118 HEGVALSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYV 184 (189) Q Consensus 118 ~~~~~i~i~lP~~v~l~V~~t~p~~kG~t~~~~~K~A~letG~~i~VP~FI~~Gd~IkV~T~~g~Y~ 184 (189) +.|.++-.+-|-++.-.|.=-+|.-. .-.|-+. -|-+.|++|+|+||+|.-+ T Consensus 122 ~pgtivk~EaPlhvsk~VmLvdp~d~----------q~te~~w-----r~~e~GekVRvstrSG~iI 173 (236) T KOG1708 122 EPGTIVKSEAPLHVSKQVMLVDPEDD----------QPTEVEW-----RFTEDGEKVRVSTRSGRII 173 (236) T ss_pred CCCEEEEECCCCEEECCEEEECCCCC----------CCCEEEE-----EECCCCCEEEEEECCCCCC T ss_conf 88627750377234040698773236----------7732015-----7747885799983055161 No 56 >cd02781 MopB_CT_Acetylene-hydratase The MopB_CT_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=34.93 E-value=26 Score=16.60 Aligned_cols=15 Identities=20% Similarity=0.114 Sum_probs=8.1 Q ss_pred CCCCCEEEEEEECCE Q ss_conf 137861568976677 Q gi|254781067|r 107 FQEGMEVKLLIHEGV 121 (189) Q Consensus 107 L~eg~~v~i~~~~~~ 121 (189) |++|..|.|.---|+ T Consensus 47 i~~Gd~V~v~s~~G~ 61 (130) T cd02781 47 IADGDWVWVETPRGR 61 (130) T ss_pred CCCCCEEEEECCCEE T ss_conf 999999999848978 No 57 >PRK03955 hypothetical protein; Reviewed Probab=33.55 E-value=29 Score=16.30 Aligned_cols=16 Identities=13% Similarity=0.312 Sum_probs=14.2 Q ss_pred CCCCCCEEEEECCCCC Q ss_conf 0168879999889972 Q gi|254781067|r 167 HINIGDDIVILTEDNS 182 (189) Q Consensus 167 FI~~Gd~IkV~T~~g~ 182 (189) .|+.||+|+||+.+|. T Consensus 111 ~i~~Gd~v~vd~~~G~ 126 (132) T PRK03955 111 ELKDGDRVRVDGDTGT 126 (132) T ss_pred CCCCCCEEEEECCCCE T ss_conf 0479999999689638 No 58 >cd02775 MopB_CT Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is Probab=33.07 E-value=27 Score=16.46 Aligned_cols=15 Identities=20% Similarity=0.355 Sum_probs=8.2 Q ss_pred CCCCCEEEEEEECCE Q ss_conf 137861568976677 Q gi|254781067|r 107 FQEGMEVKLLIHEGV 121 (189) Q Consensus 107 L~eg~~v~i~~~~~~ 121 (189) |++|..|.+.--.+. T Consensus 37 i~~Gd~v~v~~~~g~ 51 (101) T cd02775 37 IKDGDLVRVESRRGS 51 (101) T ss_pred CCCCCEEEEEECCEE T ss_conf 988999999969858 No 59 >PRK07178 acetyl-CoA carboxylase; Validated Probab=32.16 E-value=42 Score=15.29 Aligned_cols=96 Identities=16% Similarity=0.196 Sum_probs=43.8 Q ss_pred EEEEEEEECCEEEEEECCCCCCCCCC-------HHHHHHHHHHCCCCCEEEEEEECCEEEEECC-CCEEEEEEEECCCCC Q ss_conf 05789961988999946887643211-------5430013320137861568976677744015-874999999828542 Q gi|254781067|r 71 RFQFLYQDQEGFHFMNPETYDQVTVS-------EEVIGDQKVYFQEGMEVKLLIHEGVALSVEV-PRHVVFTVIDTEPSS 142 (189) Q Consensus 71 ~~qylY~dg~~~~FMd~etyeqi~i~-------~~~ig~~~~fL~eg~~v~i~~~~~~~i~i~l-P~~v~l~V~~t~p~~ 142 (189) .++|||.+ +.|+||...+==|++=+ -|++..+. .+..|..+... ++ . +.+ -..+++.| ++|... T Consensus 272 TvEFlv~~-~~~yFlEvNtRlQVEH~VTE~vtGiDLV~~Qi-~iA~G~~L~~~--q~-~--i~~~GhAIe~Ri-~AEDp~ 343 (471) T PRK07178 272 TVEFLLAD-GEVYFMEMNTRVQVEHTITEEITGIDIVREQI-RIASGLPLSVK--QE-D--IQHRGFALQFRI-NAEDPK 343 (471) T ss_pred EEEEEEEC-CCEEEEECCCCCCCCCCHHHHHHCCCHHHHHH-HHHCCCCCCCC--CC-C--CCCCCCEEEEEE-ECCCCC T ss_conf 69999867-94799832466655542136661675899999-98679978831--02-4--455885899998-513776 Q ss_pred CCC-CCCCCEEEEEEECCCEEECCCCCCCCCEE Q ss_conf 131-02477000899379599847401688799 Q gi|254781067|r 143 KGQ-TVTASYKPAILSNDIRTTVPPHINIGDDI 174 (189) Q Consensus 143 kG~-t~~~~~K~A~letG~~i~VP~FI~~Gd~I 174 (189) ++= .+.+.-..-..-.|--|.+-..+..|+.| T Consensus 344 ~~F~Ps~G~i~~~~~P~g~gvR~Dt~~~~G~~v 376 (471) T PRK07178 344 NNFLPSFGKITRYYAPGGPGVRTDTAIYTGYTI 376 (471) T ss_pred CCCCCCCCEEEEEECCCCCCEEEECCCCCCCEE T ss_conf 686568725778976999988986677688961 No 60 >cd02782 MopB_CT_1 The MopB_CT_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=31.06 E-value=34 Score=15.88 Aligned_cols=16 Identities=19% Similarity=0.397 Sum_probs=9.6 Q ss_pred CCCCCEEEEEEECCEE Q ss_conf 1378615689766777 Q gi|254781067|r 107 FQEGMEVKLLIHEGVA 122 (189) Q Consensus 107 L~eg~~v~i~~~~~~~ 122 (189) |++|..|.|.---|.+ T Consensus 47 i~~Gd~V~v~s~~G~~ 62 (129) T cd02782 47 LADGDKVRVTSAAGSV 62 (129) T ss_pred CCCCCEEEEECCCEEE T ss_conf 9899999998698479 No 61 >cd02794 MopB_CT_DmsA-EC The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-terminal iron-sulfur [4Fe-4S] cluster binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=30.99 E-value=34 Score=15.84 Aligned_cols=17 Identities=18% Similarity=0.262 Sum_probs=10.1 Q ss_pred HCCCCCEEEEEEECCEE Q ss_conf 01378615689766777 Q gi|254781067|r 106 YFQEGMEVKLLIHEGVA 122 (189) Q Consensus 106 fL~eg~~v~i~~~~~~~ 122 (189) =|.+|..|.|.---|++ T Consensus 43 gi~dGd~V~v~n~~G~i 59 (121) T cd02794 43 GIKDGDRVLVFNDRGKV 59 (121) T ss_pred CCCCCCEEEEECCCCEE T ss_conf 99899999998199069 No 62 >TIGR01363 strep_his_triad streptococcal histidine triad protein; InterPro: IPR006270 The sequences represented in this group are identified by a domain which consists of the N-terminal half of a family of Streptococcal proteins that contain a signal peptide and then up to five repeats of a region that includes a His-X-X-His-X-His (histidine triad) motif. Additional copies of the repeats are found in more poorly conserved regions. Members of this family from Streptococcus pneumoniae are suggested to cleave human C3, and the member PhpA has been shown in vaccine studies to be a protective antigen in mice . . Probab=29.42 E-value=39 Score=15.48 Aligned_cols=75 Identities=20% Similarity=0.307 Sum_probs=43.3 Q ss_pred HHHCCCCCEEEECCEEEEEEEEEEECCCCCCCEEEEEEEECCCCCCEEEEECCCCC--EEEEEECCC--------EEEEE Q ss_conf 43216775899889379999987536888763899999982468710013427872--001010564--------05789 Q gi|254781067|r 6 ASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTEQ--VERAFVEDQ--------RFQFL 75 (189) Q Consensus 6 an~lk~G~~i~~dg~~~~V~~~~~~kpgkg~a~v~~klknL~tG~~~e~~f~~~ek--ve~~~ie~~--------~~qyl 75 (189) .|||+-|-+|.++|+.|.=| |+|.-+-.+|+|- =+...+.+.+-...++ -..+.+..+ ..|== T Consensus 122 vNEi~~GYVIKV~G~YYVYL-----K~aa~~~NiRTK~--~I~~Q~~~~~~~~~~~Glaqvahl~~~~~~AV~~A~~QGR 194 (376) T TIGR01363 122 VNEIKGGYVIKVNGKYYVYL-----KDAAHADNIRTKE--EIARQKQERSKEAKEKGLAQVAHLSKREDAAVAEARRQGR 194 (376) T ss_pred EEEECCCEEEEECCEEEEEE-----CCCCCCCCCCHHH--HHHHHHHHHHHHHHCCCEEEHHHHCHHHHHHHHHHHHCCC T ss_conf 02203866898858188961-----7212210130178--9999987433433225401011203246789999984788 Q ss_pred EEECCEEEEEEC Q ss_conf 961988999946 Q gi|254781067|r 76 YQDQEGFHFMNP 87 (189) Q Consensus 76 Y~dg~~~~FMd~ 87 (189) |+-+|+|+|--. T Consensus 195 YTTDDGYIF~a~ 206 (376) T TIGR01363 195 YTTDDGYIFNAS 206 (376) T ss_pred CCCCCCCEECCH T ss_conf 104576222712 No 63 >TIGR02087 LEUD_arch 3-isopropylmalate dehydratase, small subunit; InterPro: IPR011827 3-isopropylmalate dehydratase (or isopropylmalate isomerase; 4.2.1.33 from EC) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family . Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S] cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively , . LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase 4.2.1.36 from EC, converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis . Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus . This entry is most closely related to the 3-isopropylmalate dehydratase IPR004431 from INTERPRO. It also includes members, which cluster with other genes of leucine biosynthesis. The structure of the Pyrococcus horikoshii small subunit (O59393 from SWISSPROT) has recently been determined . As expected the structure of this polypeptide is similar to that of aconitase domain 4, though one alpha helix is replaced by a short loop with relatively high temperature factor values. This loop region is thought to be important for substrate recognition. Unlike other aconitase family proteins, this subunit formed a tetramer through disulphide linkages, though it is not expected to interfere with its interaction with the large subunit. These disulphide linkages would be expected to confer thermostability on the enzyme, reflecting the thermophilic lifestyle of the organism.; GO: 0003861 3-isopropylmalate dehydratase activity, 0009098 leucine biosynthetic process, 0009316 3-isopropylmalate dehydratase complex. Probab=25.72 E-value=46 Score=15.08 Aligned_cols=19 Identities=21% Similarity=0.240 Sum_probs=13.9 Q ss_pred CCCCCCCEEEEECCCCCEE Q ss_conf 4016887999988997240 Q gi|254781067|r 166 PHINIGDDIVILTEDNSYV 184 (189) Q Consensus 166 ~FI~~Gd~IkV~T~~g~Y~ 184 (189) .-++.||.|.||-++|+=+ T Consensus 108 e~~~dGD~V~vdl~~geir 126 (159) T TIGR02087 108 ELIKDGDEVEVDLEKGEIR 126 (159) T ss_pred EEECCCCEEEEECCCCEEE T ss_conf 0213788789975766088 No 64 >TIGR01196 edd phosphogluconate dehydratase; InterPro: IPR004786 Two dehydratases, dihydroxy-acid dehydratase (gene ilvD or ILV3) and 6-phosphogluconate dehydratase (gene edd) have been shown to be evolutionary related . Dihydroxy-acid dehydratase catalyzes the fourth step in the biosynthesis of isoleucine and valine, the dehydratation of 2,3-dihydroxy-isovaleic acid into alpha-ketoisovaleric acid. 6-Phosphogluconate dehydratase catalyzes the first step in the Entner-Doudoroff pathway, the dehydratation of 6-phospho-D-gluconate into 6-phospho-2-dehydro-3-deoxy-D-gluconate. Another protein containing this signature is the Escherichia coli hypothetical protein yjhG. The N-terminal part of the proteins contains a cysteine that could be involved in the binding of a 2Fe-2S iron-sulphur cluster . This family defines the 6-phosphogluconate dehydratases.; GO: 0004456 phosphogluconate dehydratase activity, 0009255 Entner-Doudoroff pathway. Probab=25.39 E-value=42 Score=15.33 Aligned_cols=16 Identities=25% Similarity=0.219 Sum_probs=13.7 Q ss_pred CCCCCEEEEECCCCCE Q ss_conf 1688799998899724 Q gi|254781067|r 168 INIGDDIVILTEDNSY 183 (189) Q Consensus 168 I~~Gd~IkV~T~~g~Y 183 (189) |+.||.|+||--+|+- T Consensus 546 irdGD~iR~D~~nG~L 561 (614) T TIGR01196 546 IRDGDLIRVDAVNGEL 561 (614) T ss_pred EECCCEEEECCCCCEE T ss_conf 6238788980778804 No 65 >TIGR01017 rpsD_bact ribosomal protein S4; InterPro: IPR005709 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 of 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 , . The S4 domain is a small domain consisting of 60-65 amino acid residues that probably mediates binding to RNA. This family consists of organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit. Probab=25.15 E-value=56 Score=14.54 Aligned_cols=27 Identities=30% Similarity=0.426 Sum_probs=18.7 Q ss_pred EEEECCCEEECCCC-CCCCCEEEEECCC Q ss_conf 89937959984740-1688799998899 Q gi|254781067|r 154 AILSNDIRTTVPPH-INIGDDIVILTED 180 (189) Q Consensus 154 A~letG~~i~VP~F-I~~Gd~IkV~T~~ 180 (189) .++=||-.|..|.| +++||.|.|--.+ T Consensus 126 hi~vNGk~VdIPSy~v~~Gd~i~ikEk~ 153 (217) T TIGR01017 126 HILVNGKKVDIPSYQVRPGDIISIKEKS 153 (217) T ss_pred EEEECCEEECCCEEEECCCCEEEEEECC T ss_conf 0787981852240670799889981032 No 66 >TIGR02517 type_II_gspD general secretion pathway protein D; InterPro: IPR013356 In Gram-negative bacteria, proteins that have first crossed the inner member by Sec-dependent protein transport can be exported across the outer membrane by type II secretion (also referred to as the main terminal branch of the general secretion pathway). Members of this family are general secretion pathway protein D. In Yersinia enterocolitica, a second member of this family is part of a novel second type II secretion system specifically associated with virulence (See ). This family is closely homologous to the type IV pilus outer membrane secretin PilQ (IPR013355 from INTERPRO) and to the type III secretion system pore YscC/HrcC (IPR003522 from INTERPRO).; GO: 0008565 protein transporter activity, 0015628 protein secretion by the type II secretion system, 0015627 type II protein secretion system complex, 0019867 outer membrane. Probab=24.90 E-value=51 Score=14.80 Aligned_cols=36 Identities=22% Similarity=0.348 Sum_probs=26.3 Q ss_pred CCCCCCCCCEEEEEE-ECCCEEECCCCCC-CCCEEEEE Q ss_conf 213102477000899-3795998474016-88799998 Q gi|254781067|r 142 SKGQTVTASYKPAIL-SNDIRTTVPPHIN-IGDDIVIL 177 (189) Q Consensus 142 ~kG~t~~~~~K~A~l-etG~~i~VP~FI~-~Gd~IkV~ 177 (189) +.+++.++.+....- ++|++++|=|+|. +|+.|+.+ T Consensus 558 ~~~~~~~n~f~t~~r~~vG~~L~v~PqIn~eg~~v~L~ 595 (697) T TIGR02517 558 GTGGTNANPFNTVERKDVGIKLKVTPQINGEGGTVRLE 595 (697) T ss_pred EEECCCCCEEEEEEEEEEEEEEEEEEEEECCCCEEEEE T ss_conf 63054553143016887228998887783799869999 No 67 >PRK06302 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated Probab=24.84 E-value=31 Score=16.12 Aligned_cols=14 Identities=29% Similarity=0.662 Sum_probs=10.3 Q ss_pred CCCCCCCCEEEEEC Q ss_conf 74016887999988 Q gi|254781067|r 165 PPHINIGDDIVILT 178 (189) Q Consensus 165 P~FI~~Gd~IkV~T 178 (189) |+||+.||+|+... T Consensus 99 ~pFV~vGd~V~~Gq 112 (155) T PRK06302 99 PPFVEVGDTVKEGQ 112 (155) T ss_pred CCCCCCCCEECCCC T ss_conf 97424686724898 No 68 >pfam08968 DUF1885 Domain of unknown function (DUF1885). This domain is found in a set of hypothetical proteins produced by bacteria of the Bacillus genus. Probab=24.72 E-value=47 Score=15.02 Aligned_cols=52 Identities=17% Similarity=0.432 Sum_probs=37.7 Q ss_pred EEEEEECCEEEEE-------ECCCCCCCCCCHHH-HHHH------HHHCCCCCEEEEEEECCEEEE Q ss_conf 7899619889999-------46887643211543-0013------320137861568976677744 Q gi|254781067|r 73 QFLYQDQEGFHFM-------NPETYDQVTVSEEV-IGDQ------KVYFQEGMEVKLLIHEGVALS 124 (189) Q Consensus 73 qylY~dg~~~~FM-------d~etyeqi~i~~~~-ig~~------~~fL~eg~~v~i~~~~~~~i~ 124 (189) -||-.+++.|.-| ..++|=|+.||... .||. .+||.--++=++.+|+|+.+- T Consensus 59 l~L~~~~~rY~~I~vgVg~e~~~sfIqi~LP~~AT~GDKgKANEfckfLAK~l~geL~LFNGRtmy 124 (128) T pfam08968 59 LYLQSDHDRYNGIYIGVGTEGEQTFIQISLPPTATFGDKGKANEFSKFLAKKLEGELQLFNGRTMY 124 (128) T ss_pred EEECCCCCCEEEEEEEECCCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHCEEEEECCEEEE T ss_conf 998047875505999635678715799988999877762227689999999741015775470798 No 69 >TIGR03479 DMSO_red_II_alp DMSO reductase family type II enzyme, molybdopterin subunit. This model represents the molybdopterin subunit, typically called the alpha subunit, of various proteins that also contain an iron-sulfur subunit and a heme b subunit. The group includes two distinct but very closely related periplasmic proteins of anaerobic respiration, selenate reductase and chlorate reductase. Other members of this family include dimethyl sulphide dehydrogenase, ethylbenzene dehydrogenase, and an archaeal respiratory nitrate reductase. This alpha subunit has a twin-arginine translocation (TAT) signal for Sec-independent translocation across the plasma membrane. Probab=24.45 E-value=50 Score=14.85 Aligned_cols=22 Identities=23% Similarity=0.347 Sum_probs=19.7 Q ss_pred CCCCCCEEEEECCCCCEEHHCC Q ss_conf 0168879999889972402102 Q gi|254781067|r 167 HINIGDDIVILTEDNSYVERVK 188 (189) Q Consensus 167 FI~~Gd~IkV~T~~g~Y~~Rak 188 (189) =|+.||.|+|-++.|+-.-||+ T Consensus 823 GI~dGD~V~V~N~~G~v~~~A~ 844 (912) T TIGR03479 823 GIKDGDQVRIFNDLAEFEAMAK 844 (912) T ss_pred CCCCCCEEEEECCCEEEEEEEE T ss_conf 9986999999869989999999 No 70 >cd00060 FHA Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation). Probab=23.55 E-value=60 Score=14.35 Aligned_cols=56 Identities=13% Similarity=0.225 Sum_probs=41.9 Q ss_pred CEEEEEECCCEEEEEEEECCEEEEEECCCCCCCCCCHHHHHHHH-HHCCCCCEEEEE Q ss_conf 20010105640578996198899994688764321154300133-201378615689 Q gi|254781067|r 61 QVERAFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQK-VYFQEGMEVKLL 116 (189) Q Consensus 61 kve~~~ie~~~~qylY~dg~~~~FMd~etyeqi~i~~~~ig~~~-~fL~eg~~v~i~ 116 (189) .+....+.++.+.+.|.+...++++|..+=.-..|+...+.... .-|.+|..+.+- T Consensus 36 ~l~~~~iSr~Ha~i~~~~~~~~~~~d~~S~nGt~vn~~~~~~~~~~~L~~gd~i~lG 92 (102) T cd00060 36 VLDDPSVSRRHAVIRYDGDGGVVLIDLGSTNGTFVNGQRVSPGEPVRLRDGDVIRLG 92 (102) T ss_pred EECCCCCCHHHEEEEECCCCEEEEEECCCCCCEEECCEECCCCCCEECCCCCEEEEC T ss_conf 918976482358999938706999989987468999999679960698999999999 No 71 >PRK03947 prefoldin subunit alpha; Reviewed Probab=23.44 E-value=61 Score=14.33 Aligned_cols=46 Identities=11% Similarity=0.063 Sum_probs=36.2 Q ss_pred CCCCCCCCCEEEEEEECCCEEECCCCCCCCCEEEEECCCCCEEHHC Q ss_conf 2131024770008993795998474016887999988997240210 Q gi|254781067|r 142 SKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYVERV 187 (189) Q Consensus 142 ~kG~t~~~~~K~A~letG~~i~VP~FI~~Gd~IkV~T~~g~Y~~Ra 187 (189) +++-...+..+...+.=|..+-||.-|...|+|.||--+|=|++|- T Consensus 47 l~~L~~~~~~~e~lvplg~~~~v~~~i~~~~kvlV~iG~g~~vE~~ 92 (141) T PRK03947 47 LEELKGAGEEKETLVPIGAGSFVKAKIKDPDKVIVSLGAGYSAEKD 92 (141) T ss_pred HHHHHCCCCCCEEEEECCCCEEEEEEECCCCEEEEECCCCEEEEEC T ss_conf 9975347999638896588728788846888689983898699975 No 72 >pfam11871 DUF3391 Domain of unknown function (DUF3391). This domain is functionally uncharacterized. This domain is found in bacteria. This presumed domain is typically between 122 to 139 amino acids in length. This domain is found associated with pfam01966. Probab=23.01 E-value=57 Score=14.51 Aligned_cols=21 Identities=14% Similarity=0.222 Sum_probs=16.0 Q ss_pred CEEEHHHCCCCCEEEECCEEE Q ss_conf 236643216775899889379 Q gi|254781067|r 2 VKVIASAVRKGNVLDVDGKLY 22 (189) Q Consensus 2 ~~i~an~lk~G~~i~~dg~~~ 22 (189) .+|..++|+.||+|.-=+.+| T Consensus 3 ~kI~v~~L~vGMyV~~l~~~W 23 (127) T pfam11871 3 KKIPVSQLQVGMYVSLLDRSW 23 (127) T ss_pred EEEEHHHCCCCCEEEECCCCC T ss_conf 077799957761898678775 No 73 >PRK08166 NADH dehydrogenase subunit G; Validated Probab=23.00 E-value=50 Score=14.82 Aligned_cols=23 Identities=13% Similarity=0.177 Sum_probs=19.1 Q ss_pred CCCCCCCEEEEECCCCCEEHHCC Q ss_conf 40168879999889972402102 Q gi|254781067|r 166 PHINIGDDIVILTEDNSYVERVK 188 (189) Q Consensus 166 ~FI~~Gd~IkV~T~~g~Y~~Rak 188 (189) +=|+.||.|+|.++.|+..-+|+ T Consensus 800 lGI~dGd~V~V~SrrG~v~~~a~ 822 (858) T PRK08166 800 LGVNAGTRVSFSYDGQTVRLPVR 822 (858) T ss_pred CCCCCCCEEEEEECCEEEEEEEE T ss_conf 59999798999969999999999 No 74 >COG3173 Predicted aminoglycoside phosphotransferase [General function prediction only] Probab=22.81 E-value=62 Score=14.26 Aligned_cols=19 Identities=32% Similarity=0.214 Sum_probs=5.9 Q ss_pred CCCCCEEEECCEEEEEEEE Q ss_conf 1677589988937999998 Q gi|254781067|r 9 VRKGNVLDVDGKLYIVLVA 27 (189) Q Consensus 9 lk~G~~i~~dg~~~~V~~~ 27 (189) ++.||+|..++.|-=|+++ T Consensus 205 ~~~gNlii~~~~~~gVlDw 223 (321) T COG3173 205 YRPGNLIIDPGRPTGVLDW 223 (321) T ss_pred CCCCCEEEECCCEEEEEEC T ss_conf 5568788728972589965 No 75 >TIGR01348 PDHac_trf_long pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase; InterPro: IPR006256 This group of sequences are a subset of pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase specifically close by both phylogenetic and percent identity (UPGMA) trees. Members contain two or three copies of the lipoyl-binding domain. Escherichia coli AceF is included in this set while mitochondrial and some other bacterial forms are excluded. dihydrolipoyllysine-residue acetyltransferase E2 component of pyruvate dehydrogenase complex; GO: 0004742 dihydrolipoyllysine-residue acetyltransferase activity, 0006096 glycolysis, 0045254 pyruvate dehydrogenase complex. Probab=22.29 E-value=64 Score=14.19 Aligned_cols=23 Identities=35% Similarity=0.434 Sum_probs=14.3 Q ss_pred CCCCCCCCEEEEEEECC-CEEECC Q ss_conf 13102477000899379-599847 Q gi|254781067|r 143 KGQTVTASYKPAILSND-IRTTVP 165 (189) Q Consensus 143 kG~t~~~~~K~A~letG-~~i~VP 165 (189) =|||++..+=-.|||+. .++.|| T Consensus 230 vGDtV~~~QslItLE~DKA~~EvP 253 (655) T TIGR01348 230 VGDTVSADQSLITLESDKASMEVP 253 (655) T ss_pred CCCEECCCCCEEEEECCEEEEEEC T ss_conf 377764788678870671478746 No 76 >PRK08493 NADH dehydrogenase subunit G; Validated Probab=21.58 E-value=58 Score=14.46 Aligned_cols=23 Identities=17% Similarity=0.380 Sum_probs=19.5 Q ss_pred CCCCCCCEEEEECCCCCEEHHCC Q ss_conf 40168879999889972402102 Q gi|254781067|r 166 PHINIGDDIVILTEDNSYVERVK 188 (189) Q Consensus 166 ~FI~~Gd~IkV~T~~g~Y~~Rak 188 (189) +=|+.||.|+|.++.|+-.-||+ T Consensus 759 lgi~dGd~V~v~S~~G~I~~~v~ 781 (819) T PRK08493 759 LNLKDGDRVTLKKEEEELTGSVR 781 (819) T ss_pred CCCCCCCEEEEEECCEEEEEEEE T ss_conf 39999997999979858999999 No 77 >COG0243 BisC Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion] Probab=21.27 E-value=67 Score=14.08 Aligned_cols=21 Identities=24% Similarity=0.254 Sum_probs=15.9 Q ss_pred CCCCCEEEEECCCCCEEHHCC Q ss_conf 168879999889972402102 Q gi|254781067|r 168 INIGDDIVILTEDNSYVERVK 188 (189) Q Consensus 168 I~~Gd~IkV~T~~g~Y~~Rak 188 (189) |+.||.|+|-++.|+-..||+ T Consensus 685 I~~GD~V~V~~~rG~v~~~a~ 705 (765) T COG0243 685 IKDGDLVRVENRRGEVEARAK 705 (765) T ss_pred CCCCCEEEEEECCCEEEEEEE T ss_conf 977998999908977999999 No 78 >smart00359 PUA Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase. Probab=21.24 E-value=67 Score=14.06 Aligned_cols=33 Identities=24% Similarity=0.121 Sum_probs=24.2 Q ss_pred EEECCCEEECCCCCCCCCEEEEECCCCCEEHHC Q ss_conf 993795998474016887999988997240210 Q gi|254781067|r 155 ILSNDIRTTVPPHINIGDDIVILTEDNSYVERV 187 (189) Q Consensus 155 ~letG~~i~VP~FI~~Gd~IkV~T~~g~Y~~Ra 187 (189) -|--.-.+.|..-++.||.|.|-+++|+.+.|. T Consensus 18 sll~~GI~~v~g~f~~gd~V~i~~~~g~~ia~G 50 (77) T smart00359 18 SLLAPGVVRVDGGIKEGDVVVIVDEKGEPLGIG 50 (77) T ss_pred CCCCCCEEEECCCCCCCCEEEEECCCCCEEEEE T ss_conf 706463186828727999999998999999999 No 79 >PRK13532 nitrate reductase; Provisional Probab=21.12 E-value=61 Score=14.30 Aligned_cols=23 Identities=17% Similarity=0.401 Sum_probs=18.8 Q ss_pred CCCCCCCEEEEECCCCCEEHHCC Q ss_conf 40168879999889972402102 Q gi|254781067|r 166 PHINIGDDIVILTEDNSYVERVK 188 (189) Q Consensus 166 ~FI~~Gd~IkV~T~~g~Y~~Rak 188 (189) +=|+.||.|+|.++-|+-.-||+ T Consensus 756 ~GI~~GD~V~V~S~RG~v~~~~~ 778 (828) T PRK13532 756 RGLRRGDEVKVVSRRGEVKSRVE 778 (828) T ss_pred CCCCCCCEEEEEECCEEEEEEEE T ss_conf 59999799999809889999999 No 80 >smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p. Probab=20.70 E-value=49 Score=14.91 Aligned_cols=48 Identities=15% Similarity=0.321 Sum_probs=30.4 Q ss_pred CCCEEEEEEEECCCCCCEEEEECCCCCEEEEEECCCEEEEEEEECCEEEEEEC Q ss_conf 76389999998246871001342787200101056405789961988999946 Q gi|254781067|r 35 GTPITQVEMRRISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQDQEGFHFMNP 87 (189) Q Consensus 35 g~a~v~~klknL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~dg~~~~FMd~ 87 (189) ..+-+|++ |-+|+.+..+|.++|.+..+.-=-. +-+..+.+.|.++-+ T Consensus 3 ~~~~iqiR---lpdG~~l~~~F~~~dtl~~v~~fV~--~~~~~~~~~f~L~t~ 50 (80) T smart00166 3 DQCRLQIR---LPDGSRLVRRFPSSDTLRTVYEFVS--AALTDGNDPFTLNSP 50 (80) T ss_pred CCEEEEEE---ECCCCEEEEECCCCCHHHHHHHHHH--HCCCCCCCCEEEEEC T ss_conf 74799999---1999989998389783999999998--647789950899738 No 81 >pfam10709 DUF2511 Protein of unknown function (DUF2511). This family is conserved in bacteria. The function is not known. Probab=20.50 E-value=69 Score=13.97 Aligned_cols=56 Identities=7% Similarity=-0.028 Sum_probs=37.6 Q ss_pred EEECCCEEEEEEEECCEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECC Q ss_conf 01056405789961988999946887643211543001332013786156897667 Q gi|254781067|r 65 AFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEG 120 (189) Q Consensus 65 ~~ie~~~~qylY~dg~~~~FMd~etyeqi~i~~~~ig~~~~fL~eg~~v~i~~~~~ 120 (189) =.+.+.+++..-..|..++.+|+.|..||.++.-.-......=..+..+++..-+| T Consensus 34 WpftrEevmL~Cr~g~alfViN~sTl~qYpLN~iA~~q~ksgk~~~~~id~i~~dd 89 (110) T pfam10709 34 WPFTREEVMLQCRNGNALFVANGSTLMQYPLNGVAESQGKSGKVPYQPIDVIWLDD 89 (110) T ss_pred CCCCCHHEEEEEECCCEEEEECCCCHHHCCCHHHHHHHHHCCCCCCCCCCEEECCC T ss_conf 87520306999826987999877500323623899998764775578677375279 No 82 >pfam00789 UBX UBX domain. This domain is present in ubiquitin-regulatory proteins and is a general Cdc48-interacting module. Probab=20.06 E-value=71 Score=13.91 Aligned_cols=49 Identities=16% Similarity=0.435 Sum_probs=28.3 Q ss_pred CCCEEEEEEEECCCCCCEEEEECCCCCEEEEEECCCEEEEEEEECCEEEEEE Q ss_conf 7638999999824687100134278720010105640578996198899994 Q gi|254781067|r 35 GTPITQVEMRRISDGVKVSNRWRTTEQVERAFVEDQRFQFLYQDQEGFHFMN 86 (189) Q Consensus 35 g~a~v~~klknL~tG~~~e~~f~~~ekve~~~ie~~~~qylY~dg~~~~FMd 86 (189) +...+++.+| |-+|+.+..+|.++|++..+.-=-. +.++.+...|.++- T Consensus 3 ~~~~t~I~iR-lpdG~r~~r~F~~~~tl~~v~~fV~--~~~~~~~~~f~L~t 51 (81) T pfam00789 3 AEDVCRLQIR-LPDGSRLVRRFNSSDPLQDVYDFVD--SNRYDDDEPFSLNT 51 (81) T ss_pred CCCEEEEEEE-CCCCCEEEEEECCCCCHHHHHHHHH--HHCCCCCCCEEEEE T ss_conf 9982899999-8999889999089983999999999--70879997689984 Done!