Query 005101
Match_columns 714
No_of_seqs 215 out of 507
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 18:04:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005101.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005101hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5192 BMS1 GTP-binding prote 100.0 3E-123 6E-128 1008.5 21.9 572 85-709 487-1076(1077)
2 PF04950 DUF663: Protein of un 100.0 4.8E-93 1E-97 741.4 6.2 289 241-546 9-297 (297)
3 KOG1980 Uncharacterized conser 100.0 3.7E-70 8.1E-75 600.1 20.5 230 322-555 522-751 (754)
4 COG5177 Uncharacterized conser 100.0 1E-54 2.2E-59 469.0 7.0 226 321-549 533-761 (769)
5 KOG1951 GTP-binding protein AA 99.5 4.8E-14 1E-18 129.9 9.5 102 605-706 1-104 (115)
6 KOG0461 Selenocysteine-specifi 94.5 0.036 7.8E-07 61.2 4.1 210 317-535 255-493 (522)
7 KOG1029 Endocytic adaptor prot 80.6 3 6.6E-05 50.3 6.1 31 674-704 372-402 (1118)
8 COG2451 Ribosomal protein L35A 67.9 7.1 0.00015 36.3 3.9 84 449-544 6-97 (100)
9 PRK04337 50S ribosomal protein 65.4 7.1 0.00015 35.7 3.4 55 479-533 18-76 (87)
10 PTZ00041 60S ribosomal protein 61.8 12 0.00025 36.2 4.2 85 447-543 17-116 (120)
11 cd03706 mtEFTU_III Domain III 49.4 1E+02 0.0022 27.2 8.0 71 375-459 21-93 (93)
12 PF01247 Ribosomal_L35Ae: Ribo 48.8 11 0.00023 35.1 1.7 55 479-533 18-84 (95)
13 PRK04000 translation initiatio 45.0 3.8E+02 0.0083 30.2 13.4 119 317-456 283-410 (411)
14 TIGR03680 eif2g_arch translati 43.3 3.4E+02 0.0074 30.4 12.7 64 375-456 341-405 (406)
15 PRK12317 elongation factor 1-a 36.5 4.3E+02 0.0093 29.6 12.1 133 317-462 278-423 (425)
16 PRK00247 putative inner membra 34.7 2.2E+02 0.0049 32.9 9.6 46 637-684 315-360 (429)
17 KOG4364 Chromatin assembly fac 33.1 2.5E+02 0.0054 34.4 9.8 22 598-619 221-242 (811)
18 TIGR00483 EF-1_alpha translati 32.6 5E+02 0.011 29.1 11.9 129 317-460 280-423 (426)
19 cd03708 GTPBP_III Domain III o 32.1 2.1E+02 0.0045 24.7 7.0 68 375-458 16-86 (87)
20 CHL00071 tufA elongation facto 31.6 5.8E+02 0.013 28.6 12.2 128 318-459 276-407 (409)
21 PRK10512 selenocysteinyl-tRNA- 30.4 3.6E+02 0.0079 32.3 10.8 115 317-463 227-344 (614)
22 COG1866 PckA Phosphoenolpyruva 28.5 50 0.0011 38.5 3.2 106 353-479 147-259 (529)
23 KOG1832 HIV-1 Vpr-binding prot 28.1 59 0.0013 40.8 3.8 18 203-220 1421-1438(1516)
24 PLN03126 Elongation factor Tu; 23.5 8.5E+02 0.018 28.4 11.9 75 376-459 400-476 (478)
25 TIGR00485 EF-Tu translation el 22.9 8.1E+02 0.018 27.3 11.3 122 318-459 266-392 (394)
26 PRK12735 elongation factor Tu; 22.5 8.3E+02 0.018 27.3 11.3 124 317-459 267-394 (396)
27 PTZ00141 elongation factor 1- 21.5 1.3E+03 0.027 26.6 13.1 129 317-460 286-430 (446)
28 PRK00049 elongation factor Tu; 21.2 1.2E+03 0.026 26.2 12.4 123 317-459 267-394 (396)
No 1
>COG5192 BMS1 GTP-binding protein required for 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.9e-123 Score=1008.51 Aligned_cols=572 Identities=31% Similarity=0.548 Sum_probs=498.5
Q ss_pred HHhhhcccc-ccCchhhhccCCCCCchhhccccc-cC-CC--CC--CCCCCCCCccccccCcccccCC-C-CCCCCCccc
Q 005101 85 LKLTKSSLR-RCANLIQLVYGKSTSTSETLSKEV-QD-SI--EG--EESDEDEFFKPKVEGNKLREGL-D-SGIVNTDDC 155 (714)
Q Consensus 85 ~~~~~~~~~-r~~nL~klvYg~~~~~~~~~~~~~-~~-~~--e~--~~~~~~~fFk~~~~~~~~~e~~-~-~~~~~~~d~ 155 (714)
+++|.|++. |..|+++++|+++++|++|+..|+ ++ .+ ++ .++++++||++++..+.+ .. + ....+ -..
T Consensus 487 ~kl~~sqs~kr~~ni~ki~y~e~lspeeci~e~kge~~~s~e~~~v~~D~~edff~vsk~~n~~--~s~~~ek~~~-~~f 563 (1077)
T COG5192 487 SKLAYSQSGKRGRNIQKIFYDESLSPEECIEEYKGESAKSSESDLVVQDEPEDFFDVSKVANES--ISSNHEKLME-SEF 563 (1077)
T ss_pred hhhhhhhcccccccccceeccccCCHHHHHHHhccccccccccccccccCchhhhhhhhhcccc--cccchhhhch-hHH
Confidence 456666654 567999999999999999999998 31 11 12 346777899976544432 10 0 11111 112
Q ss_pred ccccccccccCCCchHhHHHHhhhcccCccchhhhhccccCCCCCCCCCcccccCCCcccccCccccCCCCCCC-CC---
Q 005101 156 SKIKSYEDLKSWKQEEVYESIRDRFVTGDWSKAAQRNQVSKGKSEDDDSDDAVYGDYEDLETGEKQEGQRKDNS-GC--- 231 (714)
Q Consensus 156 ~~~~~~~~~~~W~~ee~~~~ir~~FvTg~w~~~~~~d~~~~~~~~~~~~d~e~~GdFEDLEtge~~~~~~~~~~-~~--- 231 (714)
+.+ ...|+ .++.|+.||.++...+.. ++ .++. -.|++.|+|||||..|.....+.+++ +.
T Consensus 564 e~L-----~kkw~---s~~~lk~RF~~~~~lds~-eg------~EEl-~qd~E~gn~ed~~d~e~~~d~e~ees~G~s~t 627 (1077)
T COG5192 564 EEL-----KKKWS---SLAQLKSRFQKDATLDSI-EG------EEEL-IQDDEKGNFEDLEDEENSSDNEMEESRGSSVT 627 (1077)
T ss_pred HHH-----HHHHh---hHHHHHHHhhcccccccc-cc------hhhh-hhchhccCcccccccccccccchhhccCCccc
Confidence 333 57895 489999999998765321 22 1111 13455789999998776543221111 10
Q ss_pred --CC--CCccc-hHHHHHHHHHHHHHhhhhhcccCCCCCcchhhccccccccCCCCCCccchHHHHHHHHHHHHHhhHHH
Q 005101 232 --EG--IENED-ESAVEERRLKKLSLRAKFDVQYDGSESPEEEMNEKDGAKFHCGQPNEIGLVDQMKEEIEFRKQMNIAE 306 (714)
Q Consensus 232 --~~--~~~~~-e~~~~~~~~kK~~lk~~F~~e~d~~~~~~~~~~~~~~~~~~~~~~~~~~~yd~~K~e~~~q~~~N~~e 306 (714)
++ .++-+ +.+++.+++||++|+.+|+.+..+ +++..+.+||+.+|+.+++|+.||+.|
T Consensus 628 ~~~~e~~~e~~~e~ErE~na~kKE~lr~~Fe~eer~-----------------d~e~~d~dwy~~eK~ki~~ql~inr~e 690 (1077)
T COG5192 628 AENEESADEVDYETEREENARKKEELRGNFELEERG-----------------DPEKKDVDWYTEEKRKIEEQLKINRSE 690 (1077)
T ss_pred ccchhhccccchHHHhhhhhhhhhhhhcceeehhcc-----------------CccccccchHHHHHHHHHHHHhhhhhh
Confidence 11 11123 778999999999999999987753 233455679999999999999999999
Q ss_pred hcCCCHHHHHHhcCCCCCcEEEEEEeecChhhhhccCCCCceeEeecccccceeeEEEEEEEecCcccccccccCCcEEE
Q 005101 307 LNDLDEVTRLELEGFRTGTYLRMEIHDVPFEMVEYFDPCHPVLVGGIGLGEQNVGYMQVRLKRHRWWHKKVLKSRDPIIV 386 (714)
Q Consensus 307 f~~~d~e~R~~~EG~~~G~YVrI~I~~VP~e~v~~fdp~~PlIlgGLl~~E~k~~vv~~riKRhrw~~~kiLKSkDpLIf 386 (714)
|++|++++|+.+|||++|.||||+|+.||.+|+.+|+|.+|||+|||||.|.++|+||++|+|||| |++|||++|||||
T Consensus 691 ~e~M~Pe~r~~Ieg~raG~YVriv~~~vP~efv~~fn~r~piV~GGlLp~E~~~giVq~rikrhrW-hKKILKTNdPlif 769 (1077)
T COG5192 691 FETMVPESRVVIEGYRAGRYVRIVLSHVPLEFVDEFNSRYPIVLGGLLPAEKEMGIVQGRIKRHRW-HKKILKTNDPLIF 769 (1077)
T ss_pred hhhcCCcceeEeecccccceEEEEeccCCHHHHhhcCCCCcEEeccccchhhhhhhhhhHHHHhHH-HHHHhccCCCeEE
Confidence 999999999999999999999999999999999999999999999999999999999999999999 9999999999999
Q ss_pred EeeeeeeeeeeeeeecCCCccceeeeecCCCceEEEEEEeecCCCCceEEEEEeccCCCCCeEEEEEEEeecccCceeEE
Q 005101 387 SIGWRRFQTIPVYAIEDRSGRHRMLKYTPEHMHCLATFWGPLAPPQTGVVAVQNLSNNQASFRIAATAVVLEFNHEVKIK 466 (714)
Q Consensus 387 siGwRRFqt~PIyS~~d~n~R~K~lKYtpeh~~c~ATfyGPit~p~tpvlafq~~s~~~~~frI~ATG~vl~~D~sr~Iv 466 (714)
|+|||||||+||||+.|+.+|+|||||||+||||.+|||||+++||||||++|+. ..+|||+|+|+|.++|.+..||
T Consensus 770 S~GWRRFQsiPvys~~DsrTRnRMlKYTPEhmhCn~sFYGP~v~pntgFc~Vqse---~g~frv~a~g~i~dv~~~~~lv 846 (1077)
T COG5192 770 SVGWRRFQSIPVYSMKDSRTRNRMLKYTPEHMHCNVSFYGPVVPPNTGFCAVQSE---KGDFRVLALGTITDVNGDAKLV 846 (1077)
T ss_pred EechhhhcccceeeecchhhhhhhhhcCccceeeeeeeecCccCCCCCceeEEec---CCceEEEEeeeeEeccccHHHH
Confidence 9999999999999999999999999999999999999999999999999999984 4569999999999999999999
Q ss_pred EeEEEeeeeeEEeecceEEeccCCChhhhcccccccccccccCCCCcccCCCCCCeeEEEEeccccccCCEEEEecceec
Q 005101 467 KKIKLVGYPCKIFKKTALIKDMFTSDLEVAQCEGKEAAKEEIGNQPKRKGGQPREGIARCTFEDRILMSDIVFMRGWADV 546 (714)
Q Consensus 467 KKlkLtG~P~KI~K~TAfIr~MF~s~lEV~~Fkgkk~L~tk~G~rG~IKeslGthG~FKAtFedkI~~sDiVfLrlwkrV 546 (714)
|||+|+|||++|++||||||+||+|.+||++|+|.. |++.+|+||+||.|+|.+|++||.|+++|+|||||.||+|+||
T Consensus 847 kklklvg~p~qi~qnt~fvrdmfts~lev~kfega~-lk~vsglrgqvk~~~~k~g~yra~fe~kmlmsdii~lr~~~pv 925 (1077)
T COG5192 847 KKLKLVGYPKQIVQNTVFVRDMFTSDLEVLKFEGAS-LKAVSGLRGQVKGPHGKNGEYRAVFEGKMLMSDIITLRCFVPV 925 (1077)
T ss_pred hhhhhccCcHHHhhhhHhHHHhhhhhhHHHhhcccc-eeeeccccccccCccCCCccchheeccchhhhheeeEEeeeee
Confidence 999999999999999999999999999999999986 8899999999999999999999999999999999999999999
Q ss_pred ccCcccccccccCCCCCccccccccHHHHHHHcCCCCCCCCCCCCccccCCCCCCCCCCCChhhHhcCCCCCCCCCCCCC
Q 005101 547 EIPRFYNPLTTALQPRDKIWQGMKTVAELRREHNLSIPVNKNSLYKPIGRTPRKFNPLVIPKSLQAALPFESKPKDIPGR 626 (714)
Q Consensus 547 ~pk~fynPvt~~l~~~~~~W~gmrt~~elR~e~~i~~p~~~dS~Yk~ieR~~r~fnpl~iPk~Lq~~LPf~skpK~~~~~ 626 (714)
.+++||+||+|||+ .|+|+|.++|||..+|+.+|.++||.|-.++|..++|+.+.+|+.+|+.|||+ +
T Consensus 926 ~v~r~~~pv~~ll~----~wrglr~~~eir~sl~l~~~~~p~~~~~~~e~~~~~~~~~~~pr~ie~~lp~~--------k 993 (1077)
T COG5192 926 EVHRIFIPVDNLLG----KWRGLRRLHEIRESLGLTHSYAPQNDSSSEEMGYGAEEDYSLPREIESKLPLD--------K 993 (1077)
T ss_pred EEEEeeccHHHHHH----HHhhhHHHHHHHHHhCCCCCCCCCccchhhhhhccccccccCcHhHHhhCCcc--------h
Confidence 99999999999997 69999999999999999999999999999999999999999999999999998 5
Q ss_pred CCccccccccccCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 005101 627 KRPLLENRRAVVMEPHERKVHVLFQQLQLIRNEKMKKRKLKQQHRKKEIEAERAKDEQLTRKRQREERRERYREQDKLMK 706 (714)
Q Consensus 627 ~~~~~~~~~avv~~p~ekk~~~l~q~l~ti~~~k~~krk~k~~~~~~~~~k~~~k~e~~~~~~~ke~~K~~~r~~gk~~~ 706 (714)
+..+++.||++++.|.|++....+|..-++.+-|..++|++++-.++++.++.+|.|+++.+|.|+.+++.|...||++-
T Consensus 994 r~~~~~srr~~~~~~~e~r~k~~ik~~i~~~r~kd~~~ke~~~s~~r~k~~~i~k~e~er~qr~r~~~~d~~~e~~kkr~ 1073 (1077)
T COG5192 994 RSIAVVSRRIELPVPPECREKHEIKDRIVKERIKDQEEKERMESLQRAKEEEIGKKEKEREQRIRKTIHDNYKEMAKKRL 1073 (1077)
T ss_pred hhhhheeeeeeccCChhhhHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 56688999999999999999999999999999999999999999999999999999999999999999999999999976
Q ss_pred hhh
Q 005101 707 KIR 709 (714)
Q Consensus 707 ~~~ 709 (714)
++.
T Consensus 1074 kk~ 1076 (1077)
T COG5192 1074 KKK 1076 (1077)
T ss_pred hcc
Confidence 654
No 2
>PF04950 DUF663: Protein of unknown function (DUF663); InterPro: IPR007034 This domain is found at the C terminus of the ribosome biogenesis protein BMS1 and TSR1 families, which may act as a molecular switch during maturation of the 40S ribosomal subunit in the nucleolus.; PDB: 1WB1_D 1WB3_B 1WB2_A.
Probab=100.00 E-value=4.8e-93 Score=741.44 Aligned_cols=289 Identities=42% Similarity=0.657 Sum_probs=79.4
Q ss_pred HHHHHHHHHHHHhhhhhcccCCCCCcchhhccccccccCCCCCCccchHHHHHHHHHHHHHhhHHHhcCCCHHHHHHhcC
Q 005101 241 AVEERRLKKLSLRAKFDVQYDGSESPEEEMNEKDGAKFHCGQPNEIGLVDQMKEEIEFRKQMNIAELNDLDEVTRLELEG 320 (714)
Q Consensus 241 ~~~~~~~kK~~lk~~F~~e~d~~~~~~~~~~~~~~~~~~~~~~~~~~~yd~~K~e~~~q~~~N~~ef~~~d~e~R~~~EG 320 (714)
.+.++.+|++.||..+++++|..+. +.+...+...+|+....+..++..+|+. .+|++++.+.+|
T Consensus 9 ~ar~Rf~KyRgLKs~r~s~wD~~E~------------~~~lP~~y~ri~~f~n~~~~k~~~~~~~---~~~~~~~~~~~g 73 (297)
T PF04950_consen 9 PARERFQKYRGLKSFRTSEWDPDEK------------DPNLPEDYSRIFQFENFKRTKKRALKEA---ELDEEEREQEEG 73 (297)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred ccccccccccccccccccccccccc------------cccccccccccccccccccccccccccc---cccccccccccc
Confidence 3466788999999999999996532 1112234567888888888888888887 899999999999
Q ss_pred CCCCcEEEEEEeecChhhhhccCCCCceeEeecccccceeeEEEEEEEecCcccccccccCCcEEEEeeeeeeeeeeeee
Q 005101 321 FRTGTYLRMEIHDVPFEMVEYFDPCHPVLVGGIGLGEQNVGYMQVRLKRHRWWHKKVLKSRDPIIVSIGWRRFQTIPVYA 400 (714)
Q Consensus 321 ~~~G~YVrI~I~~VP~e~v~~fdp~~PlIlgGLl~~E~k~~vv~~riKRhrw~~~kiLKSkDpLIfsiGwRRFqt~PIyS 400 (714)
+.||+||+|+|++||++++++|++++||||||||+||+++||||++|+||+| |++||||+||||||||||||||+||||
T Consensus 74 ~~~G~YVrI~i~~vP~~~~~~~~~~~Plil~gLl~~E~k~svv~~~ikrh~~-~~~~lkSkd~li~~~G~Rrf~~~Pifs 152 (297)
T PF04950_consen 74 VRPGTYVRIEISNVPCEFVENFDPSYPLILGGLLPHEQKMSVVNFRIKRHRW-YEKPLKSKDPLIFSCGWRRFQTIPIFS 152 (297)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccccccc-ccccccccccccccccccccccccccc
Confidence 9999999999999999999999999999999999999999999999999999 999999999999999999999999999
Q ss_pred ecCCCccceeeeecCCCceEEEEEEeecCCCCceEEEEEeccCCCCCeEEEEEEEeecccCceeEEEeEEEeeeeeEEee
Q 005101 401 IEDRSGRHRMLKYTPEHMHCLATFWGPLAPPQTGVVAVQNLSNNQASFRIAATAVVLEFNHEVKIKKKIKLVGYPCKIFK 480 (714)
Q Consensus 401 ~~d~n~R~K~lKYtpeh~~c~ATfyGPit~p~tpvlafq~~s~~~~~frI~ATG~vl~~D~sr~IvKKlkLtG~P~KI~K 480 (714)
++++|+||||+||+|+|+||+||||||++|||||||+|+..++...+|||+|||+|+++|++++|+|||+|+||||||||
T Consensus 153 ~~~~~~r~k~~k~~~~~~~~~at~ygPi~~~~~~vl~f~~~~~~~~~~~l~atG~v~~~d~~~~i~Kki~L~G~P~ki~k 232 (297)
T PF04950_consen 153 QEDNNNRHKYEKYLPEGMHCVATFYGPITFPPTPVLAFKESSNSGSSFRLVATGSVLNVDPDRIIVKKIKLTGYPFKIHK 232 (297)
T ss_dssp -------------------------------------------TTTSS-B-EEEEEEEE--GGGS-B--EEEEEEEEEES
T ss_pred ccccccccccccccccccccccccccccccccccccccccccccCCCceEEEeeeEeCCCCcchhheeeeecCchheEEC
Confidence 99999999999999999999999999999999999999997665668999999999999999999999999999999999
Q ss_pred cceEEeccCCChhhhcccccccccccccCCCCcccCCCCCCeeEEEEeccccccCCEEEEecceec
Q 005101 481 KTALIKDMFTSDLEVAQCEGKEAAKEEIGNQPKRKGGQPREGIARCTFEDRILMSDIVFMRGWADV 546 (714)
Q Consensus 481 ~TAfIr~MF~s~lEV~~Fkgkk~L~tk~G~rG~IKeslGthG~FKAtFedkI~~sDiVfLrlwkrV 546 (714)
+|||||+||||++||+||+|.+ |+|++|++|+||+||||||+|||+||++|++||||||+||+||
T Consensus 233 ~~a~vr~MF~~~~dv~~F~~~~-l~T~~G~rG~Ik~~lgt~G~fka~F~~~i~~~D~V~~~lykrV 297 (297)
T PF04950_consen 233 RTAVVRGMFFNPEDVAWFKGAE-LRTKSGIRGHIKESLGTHGYFKATFEDKIKQSDIVFMRLYKRV 297 (297)
T ss_dssp SSCEECSSSSTCCHHHHS-S---BEETTS-BEEEEE-BTTTTBBEEEESS---SS-EEEEE-----
T ss_pred ceEEhhhhcCCHHHHHhhcCCE-EEeeccCCCEECeeECCCCcEEEEECCcCCCCCEEEEecCCCC
Confidence 9999999999999999999997 8999999999999999999999999999999999999999998
No 3
>KOG1980 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=3.7e-70 Score=600.06 Aligned_cols=230 Identities=23% Similarity=0.357 Sum_probs=224.2
Q ss_pred CCCcEEEEEEeecChhhhhccCCCCceeEeecccccceeeEEEEEEEecCcccccccccCCcEEEEeeeeeeeeeeeeee
Q 005101 322 RTGTYLRMEIHDVPFEMVEYFDPCHPVLVGGIGLGEQNVGYMQVRLKRHRWWHKKVLKSRDPIIVSIGWRRFQTIPVYAI 401 (714)
Q Consensus 322 ~~G~YVrI~I~~VP~e~v~~fdp~~PlIlgGLl~~E~k~~vv~~riKRhrw~~~kiLKSkDpLIfsiGwRRFqt~PIyS~ 401 (714)
.+|+||+|+|.|||..+++.|.+..+|||+||||||+||+|+||.++||+. |+.||||+++|||+||+|||.++|+||+
T Consensus 522 ~~G~~V~v~l~nvP~~i~E~~~~~~~lvvfglL~hEhKmtV~Nfvl~r~p~-~e~Plkske~livq~G~Rrf~i~PlfSs 600 (754)
T KOG1980|consen 522 IPGQYVRVFLRNVPVSILEAIKKQLLLVVFGLLPHEHKMTVLNFVLQRHPG-YEEPLKSKEELIVQCGFRRFDINPLFSS 600 (754)
T ss_pred CCCceEEEEeecCcHHHHHHHhhccceeeeeccchhhhheeeEEEEecCCC-CCccccccceeEEEeccceEEecccccc
Confidence 599999999999999999999999999999999999999999999999999 9999999999999999999999999999
Q ss_pred cCCCccceeeeecCCCceEEEEEEeecCCCCceEEEEEeccCCCCCeEEEEEEEeecccCceeEEEeEEEeeeeeEEeec
Q 005101 402 EDRSGRHRMLKYTPEHMHCLATFWGPLAPPQTGVVAVQNLSNNQASFRIAATAVVLEFNHEVKIKKKIKLVGYPCKIFKK 481 (714)
Q Consensus 402 ~d~n~R~K~lKYtpeh~~c~ATfyGPit~p~tpvlafq~~s~~~~~frI~ATG~vl~~D~sr~IvKKlkLtG~P~KI~K~ 481 (714)
++.|++|||.||.|+.+..+|||||||+|+|+|||+|+..+++ +.+++|||+++++||+|+|+||.+|+||||||||+
T Consensus 601 ~t~ndkhK~eRfl~~~~a~vaTviaPI~F~ps~vL~FK~s~~~--~~~LiAtG~~l~~dpdRiv~KRaVLsGhPfKi~kk 678 (754)
T KOG1980|consen 601 HTPNDKHKYERFLPPDEAVVATVIAPITFGPSPVLIFKKSSDG--SLELIATGSLLNCDPDRIVAKRAVLSGHPFKIHKK 678 (754)
T ss_pred CCccchhhhhhhcCccceEEEEEEeccccCCcceEEEEeCCCc--ccceeeeeeeeccCCcceeEeeeeecCCCceeeee
Confidence 9999999999999999999999999999999999999998654 77999999999999999999999999999999999
Q ss_pred ceEEeccCCChhhhcccccccccccccCCCCcccCCCCCCeeEEEEeccccccCCEEEEecceecccCcccccc
Q 005101 482 TALIKDMFTSDLEVAQCEGKEAAKEEIGNQPKRKGGQPREGIARCTFEDRILMSDIVFMRGWADVEIPRFYNPL 555 (714)
Q Consensus 482 TAfIr~MF~s~lEV~~Fkgkk~L~tk~G~rG~IKeslGthG~FKAtFedkI~~sDiVfLrlwkrV~pk~fynPv 555 (714)
.|+|||||||++||.||+|++ |+||+|++||||+||||||+|||+|+++|+.+|+|+|+|||||||.|.|++-
T Consensus 679 ~v~VRYMFFn~EDV~wFKpIq-L~Tk~gR~GhIKEplGTHG~fKc~FdgkLksqDtV~MsLYKRvfP~~~y~~~ 751 (754)
T KOG1980|consen 679 YVVVRYMFFNREDVEWFKPIQ-LYTKSGRTGHIKEPLGTHGYFKCYFDGKLKSQDTVMMSLYKRVFPKWTYWNG 751 (754)
T ss_pred eEEEeeecCCHhHeeeeccee-eeccccccccccccccCcceeEEEecCcccccchHHHHHHHhhccccccccc
Confidence 999999999999999999998 8899999999999999999999999999999999999999999999999543
No 4
>COG5177 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1e-54 Score=468.96 Aligned_cols=226 Identities=21% Similarity=0.247 Sum_probs=215.1
Q ss_pred CCCCcEEEEEEeecChhhhhcc-CCCCceeEeecccccceeeEEEEEEEecCcccccccccCCcEEEEeeeeeeeeeeee
Q 005101 321 FRTGTYLRMEIHDVPFEMVEYF-DPCHPVLVGGIGLGEQNVGYMQVRLKRHRWWHKKVLKSRDPIIVSIGWRRFQTIPVY 399 (714)
Q Consensus 321 ~~~G~YVrI~I~~VP~e~v~~f-dp~~PlIlgGLl~~E~k~~vv~~riKRhrw~~~kiLKSkDpLIfsiGwRRFqt~PIy 399 (714)
.++|+.|||.|. +|..+.+.+ +|..-|+|+|||.||+|.+|.||+++||.. |+.||+|+++|++++|.|||.++|+|
T Consensus 533 a~~G~~vri~lr-~p~~l~E~~~~p~~llvvygll~yE~k~tV~nFs~~rh~e-ye~P~~s~E~~vvq~G~rr~~i~Pl~ 610 (769)
T COG5177 533 APDGQMVRIKLR-FPKFLYEGLIEPQILLVVYGLLEYEDKKTVHNFSLQRHFE-YEVPLKSEESMVVQLGHRRVDICPLI 610 (769)
T ss_pred CCCCcEEEEEEe-ccHHHHhhhcccceeeeeeehhhhcchhhhhhhhhhhhhc-ccCCCCcccceeeeeccceEEEeehh
Confidence 789999999999 999999987 466677889999999999999999999999 99999999999999999999999999
Q ss_pred eecCC--CccceeeeecCCCceEEEEEEeecCCCCceEEEEEeccCCCCCeEEEEEEEeecccCceeEEEeEEEeeeeeE
Q 005101 400 AIEDR--SGRHRMLKYTPEHMHCLATFWGPLAPPQTGVVAVQNLSNNQASFRIAATAVVLEFNHEVKIKKKIKLVGYPCK 477 (714)
Q Consensus 400 S~~d~--n~R~K~lKYtpeh~~c~ATfyGPit~p~tpvlafq~~s~~~~~frI~ATG~vl~~D~sr~IvKKlkLtG~P~K 477 (714)
|...+ |+-|||.||+|+....+|||+|||+|.++|+|+|+..+....+.+++|||+.+++|++++|+||.+|||||||
T Consensus 611 s~~s~s~Nn~qKy~r~l~p~~~~vas~I~Pi~Fg~spvi~fkkS~~d~~s~~l~a~g~~~n~d~~rviakrAvLtGhPFk 690 (769)
T COG5177 611 SKGSNSPNNNQKYFRRLKPLESGVASFIGPISFGLSPVIIFKKSALDELSATLLASGGMNNFDGDRVIAKRAVLTGHPFK 690 (769)
T ss_pred ccCCCCCcchHHHHhhcCccceeeeEEEcceeccCcceEEEccCccchhhhhhhhcccccccCcchhhhhhhhhcCCCcc
Confidence 99432 6789999999999999999999999999999999998666678999999999999999999999999999999
Q ss_pred EeecceEEeccCCChhhhcccccccccccccCCCCcccCCCCCCeeEEEEeccccccCCEEEEecceecccC
Q 005101 478 IFKKTALIKDMFTSDLEVAQCEGKEAAKEEIGNQPKRKGGQPREGIARCTFEDRILMSDIVFMRGWADVEIP 549 (714)
Q Consensus 478 I~K~TAfIr~MF~s~lEV~~Fkgkk~L~tk~G~rG~IKeslGthG~FKAtFedkI~~sDiVfLrlwkrV~pk 549 (714)
+||+.++||||||||+||.||+++. |.||+|++|.||+||||||||||||+++|..+|+|.|+||+|+||-
T Consensus 691 ~hK~~vtvryMFf~pEdV~wFk~Iq-lftk~grtGfIKeplGThGyFKatF~gki~~qD~VaMSLYKRm~p~ 761 (769)
T COG5177 691 NHKRYVTVRYMFFSPEDVMWFKNIQ-LFTKRGRTGFIKEPLGTHGYFKATFSGKIKSQDKVAMSLYKRMFPE 761 (769)
T ss_pred cceeEEEEeeecCCHhHeeeecchh-hhhhcCccceecccccCcceeeEEecCcccccchhhHHHHHHhccC
Confidence 9999999999999999999999997 7899999999999999999999999999999999999999999985
No 5
>KOG1951 consensus GTP-binding protein AARP2 involved in 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]
Probab=99.51 E-value=4.8e-14 Score=129.89 Aligned_cols=102 Identities=39% Similarity=0.596 Sum_probs=97.4
Q ss_pred CCChhhHhcCCCCCCCCCCCCCCCcccccccc--ccCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 005101 605 VIPKSLQAALPFESKPKDIPGRKRPLLENRRA--VVMEPHERKVHVLFQQLQLIRNEKMKKRKLKQQHRKKEIEAERAKD 682 (714)
Q Consensus 605 ~iPk~Lq~~LPf~skpK~~~~~~~~~~~~~~a--vv~~p~ekk~~~l~q~l~ti~~~k~~krk~k~~~~~~~~~k~~~k~ 682 (714)
.||++||++|||+|+||.+.+++++.+...|| ||+.|+|+|+++++|++.|+++++..++++.+..++++++++.++.
T Consensus 1 ~iPKalqk~LPfkskpka~~~~k~~l~~~~r~~~vv~~p~e~K~~~~~~~v~t~~~~~~qk~K~~~~~krk~~~e~k~~~ 80 (115)
T KOG1951|consen 1 MIPKALQKALPFKSKPKAAKKRKRPLQDLQRADEVVAKPRERKARAVIDAVETARSFKRQKAKKTKKKKRKEYREKKAKK 80 (115)
T ss_pred CccHHHHHhCCccccchhhccccccccchhhcchhhcCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 59999999999999999999999999988887 9999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 005101 683 EQLTRKRQREERRERYREQDKLMK 706 (714)
Q Consensus 683 e~~~~~~~ke~~K~~~r~~gk~~~ 706 (714)
++...++.++.+++.|+..|+.-.
T Consensus 81 ~~~~~~r~~~kkr~~~kk~~k~~~ 104 (115)
T KOG1951|consen 81 EEPLEQREKEKKREGPKKVGKSTL 104 (115)
T ss_pred hhhhhhhHHHHHHhhhcccchhHH
Confidence 999999999999999999887654
No 6
>KOG0461 consensus Selenocysteine-specific elongation factor [Translation, ribosomal structure and biogenesis]
Probab=94.49 E-value=0.036 Score=61.20 Aligned_cols=210 Identities=14% Similarity=0.187 Sum_probs=132.4
Q ss_pred HhcCCCCCcEEEEEEeecChhhhhccCCCCceeEeecccccceeeEEEEEEEecCcccccccccCCcEEEEeeeeeeeee
Q 005101 317 ELEGFRTGTYLRMEIHDVPFEMVEYFDPCHPVLVGGIGLGEQNVGYMQVRLKRHRWWHKKVLKSRDPIIVSIGWRRFQTI 396 (714)
Q Consensus 317 ~~EG~~~G~YVrI~I~~VP~e~v~~fdp~~PlIlgGLl~~E~k~~vv~~riKRhrw~~~kiLKSkDpLIfsiGwRRFqt~ 396 (714)
.+..+..|..+-+.+......+.++---+- .|.|- ..-.+-+.++.-++ |.++|+|+.-+-+++|+---...
T Consensus 255 ~vtsa~~GdR~g~cVtqFd~klleRgi~~~---pg~Lk----~~~avl~~vepI~y-fr~~i~sk~K~Hi~VgheTVMa~ 326 (522)
T KOG0461|consen 255 RVTSAAAGDRAGFCVTQFDEKLLERGICGP---PGTLK----STKAVLATVEPIQY-FRKSINSKSKIHIAVGHETVMAE 326 (522)
T ss_pred hhhhhhcccceeeeeeccCHHHHhccccCC---Ccccc----eeeeeeEeecchHH-HhhhhhhcceEEEEehhhhhhhh
Confidence 344566677777766655444443310011 12222 23345567788888 99999999999999999765554
Q ss_pred eeeeecCCCc---------cceee-eecCC-CceE-----EEEEEeecCCCCceEEEEEecc--CCCCCeEEEEEEEeec
Q 005101 397 PVYAIEDRSG---------RHRML-KYTPE-HMHC-----LATFWGPLAPPQTGVVAVQNLS--NNQASFRIAATAVVLE 458 (714)
Q Consensus 397 PIyS~~d~n~---------R~K~l-KYtpe-h~~c-----~ATfyGPit~p~tpvlafq~~s--~~~~~frI~ATG~vl~ 458 (714)
-.|..++.+. ...+. -.+|. -.+| ..+|=.|+..|+..-++-.... -...+-|++.+|.+.-
T Consensus 327 ~~ff~d~d~~~~tf~~~kEye~~E~d~~Pa~~~~~~~~~aL~~FEkpv~~P~~s~~i~s~ld~d~h~~~CRlAF~Gi~~~ 406 (522)
T KOG0461|consen 327 CQFFKDTDGTTSTFQLDKEYENGEFDMLPALLAPCDVIQALFSFEKPVFLPEYSNPIMSALDEDQHGSGCRLAFSGIFSQ 406 (522)
T ss_pred eEEeeccCCcccccccchhhhccccccChhhcCCchheeeeeeecccccCcccccHHHHhhhhhcCCCceEEEeeeehhh
Confidence 4443322111 01111 22332 2344 6788889888874333322111 1245789999999876
Q ss_pred ccCc----------eeEEEeEEEeeeeeEEeec-ceEEeccCCChhhhcccccccccccccCCCCcccCCCCCCeeEEEE
Q 005101 459 FNHE----------VKIKKKIKLVGYPCKIFKK-TALIKDMFTSDLEVAQCEGKEAAKEEIGNQPKRKGGQPREGIARCT 527 (714)
Q Consensus 459 ~D~s----------r~IvKKlkLtG~P~KI~K~-TAfIr~MF~s~lEV~~Fkgkk~L~tk~G~rG~IKeslGthG~FKAt 527 (714)
.-++ ..|.||=-=.|+--++.+. .+++++||--.--..-|.|.+ +.+-.|-+|+|-.+.|..|.||.|
T Consensus 407 ~l~~~~y~~~~LP~lrifkrK~k~G~veRv~~d~svI~~~lFK~etn~dlfvG~~-v~lStGe~G~Ie~aFGqsgKf~it 485 (522)
T KOG0461|consen 407 ILPESKYNGKNLPPLRIFKRKCKKGHVERVEKDFSVICTGLFKAETNFDLFVGFQ-VCLSTGERGKIEGAFGQSGKFRIT 485 (522)
T ss_pred hCcccccccccCCchhhhhhhhcccchhhhhccHHHHHhhhhccccccceeeeeE-EEeccCCccceeccccCcceEEEE
Confidence 5555 3344544445666555554 356789998777778899966 445569999999999999999999
Q ss_pred eccccccC
Q 005101 528 FEDRILMS 535 (714)
Q Consensus 528 FedkI~~s 535 (714)
|-++|..-
T Consensus 486 f~~~lspe 493 (522)
T KOG0461|consen 486 FAEKLSPE 493 (522)
T ss_pred ecccCChh
Confidence 99998653
No 7
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=80.55 E-value=3 Score=50.28 Aligned_cols=31 Identities=23% Similarity=0.456 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 005101 674 EIEAERAKDEQLTRKRQREERRERYREQDKL 704 (714)
Q Consensus 674 ~~~k~~~k~e~~~~~~~ke~~K~~~r~~gk~ 704 (714)
+..++.+++-+...+|+.|+||++-|++..+
T Consensus 372 ElekqLerQReiE~qrEEerkkeie~rEaar 402 (1118)
T KOG1029|consen 372 ELEKQLERQREIERQREEERKKEIERREAAR 402 (1118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555555555666677777777665533
No 8
>COG2451 Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis]
Probab=67.94 E-value=7.1 Score=36.29 Aligned_cols=84 Identities=21% Similarity=0.248 Sum_probs=60.0
Q ss_pred EEEEEEEeecccCceeEEEeEEEeeeeeEEeecceEEecc-CCChhhhcccccccccc-ccc-CC--CCcccCCCCCCee
Q 005101 449 RIAATAVVLEFNHEVKIKKKIKLVGYPCKIFKKTALIKDM-FTSDLEVAQCEGKEAAK-EEI-GN--QPKRKGGQPREGI 523 (714)
Q Consensus 449 rI~ATG~vl~~D~sr~IvKKlkLtG~P~KI~K~TAfIr~M-F~s~lEV~~Fkgkk~L~-tk~-G~--rG~IKeslGthG~ 523 (714)
|...-|++++.--+.. + +|-+++.||-- -.|++|...+.|+.... .++ |+ .|.|..+.|..|.
T Consensus 6 r~~ikgv~lsyrR~k~-------~-----q~P~~~liKi~gv~s~~eA~~y~gk~v~yk~~~~G~Vi~G~V~R~HGnsGa 73 (100)
T COG2451 6 RLRIKGVVLSYRRSKR-------T-----QHPNVSLIKIEGVDSPEEAQFYLGKRVCYKYRSSGRVIKGKVVRTHGNSGA 73 (100)
T ss_pred eEEEeeEEEEEEeccc-------c-----cCCceEEEEEecCCCHHHHHhhhccEEEEEeCCCCcEEEEEEEEecCCcce
Confidence 5556666665433322 2 34467788877 89999999999965442 222 65 8999999999999
Q ss_pred EEEEeccccc---cCCEEEEecce
Q 005101 524 ARCTFEDRIL---MSDIVFMRGWA 544 (714)
Q Consensus 524 FKAtFedkI~---~sDiVfLrlwk 544 (714)
.||.|+..+- .++.|++.||.
T Consensus 74 VrarF~~~LP~qa~G~~v~v~ly~ 97 (100)
T COG2451 74 VRARFERNLPGQALGTSVEVKLYP 97 (100)
T ss_pred EEEEecCCCCchhcCcEEEEEEcc
Confidence 9999999874 45777777763
No 9
>PRK04337 50S ribosomal protein L35Ae; Validated
Probab=65.38 E-value=7.1 Score=35.70 Aligned_cols=55 Identities=20% Similarity=0.293 Sum_probs=41.8
Q ss_pred eecceEEecc-CCChhhhcccccccccc-cccCC--CCcccCCCCCCeeEEEEeccccc
Q 005101 479 FKKTALIKDM-FTSDLEVAQCEGKEAAK-EEIGN--QPKRKGGQPREGIARCTFEDRIL 533 (714)
Q Consensus 479 ~K~TAfIr~M-F~s~lEV~~Fkgkk~L~-tk~G~--rG~IKeslGthG~FKAtFedkI~ 533 (714)
+-|||.||== .++.+|..+|.||+... .+.|+ -|+|..+.|..|.+||.|...+-
T Consensus 18 ~~~~aLlkiegv~~~~~a~fylGKrv~yvyk~grviwGKItR~HGnsGvVrAkF~~nLP 76 (87)
T PRK04337 18 YNRQVIIKPLGVDDREEAAKLIGRKVIWKDPTGNKYVGKIVRVHGNRGEVRARFKPGLP 76 (87)
T ss_pred CCceEEEEEcCcCCHHHHHhhcCceEEEEeCCCCEEEEEEEeeeCCCceEEEEECCCCC
Confidence 4456666643 78899999999976442 33454 79999999999999999987653
No 10
>PTZ00041 60S ribosomal protein L35a; Provisional
Probab=61.76 E-value=12 Score=36.20 Aligned_cols=85 Identities=19% Similarity=0.223 Sum_probs=55.7
Q ss_pred CeEEEEEEEeecccCceeEEEeEEEeeeeeEEeecceEEecc-CCChhhhcccccccccc---c---ccC-----CCCcc
Q 005101 447 SFRIAATAVVLEFNHEVKIKKKIKLVGYPCKIFKKTALIKDM-FTSDLEVAQCEGKEAAK---E---EIG-----NQPKR 514 (714)
Q Consensus 447 ~frI~ATG~vl~~D~sr~IvKKlkLtG~P~KI~K~TAfIr~M-F~s~lEV~~Fkgkk~L~---t---k~G-----~rG~I 514 (714)
.-|+-+-|++++.--+. -.-+-|||.||== .++.+|..+|-|++... . +.| +-|.|
T Consensus 17 ~~Rly~kgv~lgYkRg~------------~nQ~~~~aLlKieGV~~~~~a~fYlGKrvayvyka~~~~~~~k~RviwGKV 84 (120)
T PTZ00041 17 PVRLYVKAVFLGYKRSK------------VNQYPNVALLKIEGVNTREDARFYLGKRVAYVYKAKKLKNGTKFRAIWGKI 84 (120)
T ss_pred CcceEEEEEEEEecccc------------ccCCCceEEEEecCcCChhhhHhhccceEEEEEcCccccCCcceeEEEEEE
Confidence 44666666666542221 1234567777743 78889999999955432 1 112 35999
Q ss_pred cCCCCCCeeEEEEeccccc---cCCEEEEecc
Q 005101 515 KGGQPREGIARCTFEDRIL---MSDIVFMRGW 543 (714)
Q Consensus 515 KeslGthG~FKAtFedkI~---~sDiVfLrlw 543 (714)
..+.|..|.+||.|...+- ++..|.+-||
T Consensus 85 tR~HGnsGvVrAkF~~nLPp~A~G~~VrVmly 116 (120)
T PTZ00041 85 TRPHGNSGVVRARFNKNLPPKAIGSRVRVFLY 116 (120)
T ss_pred EcccCCCcEEEEEeCCCCChHHcCCeEEEEEc
Confidence 9999999999999998764 3555655543
No 11
>cd03706 mtEFTU_III Domain III of mitochondrial EF-TU (mtEF-TU). mtEF-TU is highly conserved and is 55-60% identical to bacterial EF-TU. The overall structure is similar to that observed in the Escherichia coli and Thermus aquaticus EF-TU. However, compared with that observed in prokaryotic EF-TU the nucleotide-binding domain (domain I) of EF-TUmt is in a different orientation relative to the rest of the structure. Furthermore, domain III is followed by a short 11-amino acid extension that forms one helical turn. This extension seems to be specific to the mitochondrial factors and has not been observed in any of the prokaryotic factors.
Probab=49.44 E-value=1e+02 Score=27.16 Aligned_cols=71 Identities=11% Similarity=-0.022 Sum_probs=45.3
Q ss_pred ccccccCCcEEEEeeeeeeeeeeeeeecCCCccceeeeecCCCceEEEEEE--eecCCCCceEEEEEeccCCCCCeEEEE
Q 005101 375 KKVLKSRDPIIVSIGWRRFQTIPVYAIEDRSGRHRMLKYTPEHMHCLATFW--GPLAPPQTGVVAVQNLSNNQASFRIAA 452 (714)
Q Consensus 375 ~kiLKSkDpLIfsiGwRRFqt~PIyS~~d~n~R~K~lKYtpeh~~c~ATfy--GPit~p~tpvlafq~~s~~~~~frI~A 452 (714)
+.+|++...+.|++|-..-... |... ++ -.+.+.+..|.|.+. .|+...+.+-++++..+ +.+|
T Consensus 21 ~~~i~~g~~~~~~~~t~~~~~~-i~~~---~~----~~~l~~g~~~~v~i~l~~p~~~~~g~rf~lR~~~------~tvg 86 (93)
T cd03706 21 HKPFVSNFQPQMFSLTWDCAAR-IDLP---PG----KEMVMPGEDTKVTLILRRPMVLEKGQRFTLRDGN------RTIG 86 (93)
T ss_pred CccccCCCeeEEEeccceEEEE-EECC---CC----CcEeCCCCEEEEEEEECCcEEEeeCCEEEEEECC------EEEE
Confidence 3699999999999987653321 1111 11 234566778888887 88764444455555542 7999
Q ss_pred EEEeecc
Q 005101 453 TAVVLEF 459 (714)
Q Consensus 453 TG~vl~~ 459 (714)
.|.|+++
T Consensus 87 ~G~V~~~ 93 (93)
T cd03706 87 TGLVTDT 93 (93)
T ss_pred EEEEEeC
Confidence 9998753
No 12
>PF01247 Ribosomal_L35Ae: Ribosomal protein L35Ae; InterPro: IPR001780 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The ribosomal L35A eukaryotic and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of: Vertebrate L35A. Caenorhabditis elegans L35A (F10E7.7). Saccharomyces cerevisiae L37A/L37B (Rp47). Plant L35A. Pyrococcus woesei L35A homologue []. These proteins have 87 to 110 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_j 2LP6_A 1SQR_A 4A18_H 4A1D_H 4A19_H 4A1B_H 3IZS_j.
Probab=48.81 E-value=11 Score=35.06 Aligned_cols=55 Identities=22% Similarity=0.218 Sum_probs=37.5
Q ss_pred eecceEEecc-CCChhhhcccccccccc-cc--------cC--CCCcccCCCCCCeeEEEEeccccc
Q 005101 479 FKKTALIKDM-FTSDLEVAQCEGKEAAK-EE--------IG--NQPKRKGGQPREGIARCTFEDRIL 533 (714)
Q Consensus 479 ~K~TAfIr~M-F~s~lEV~~Fkgkk~L~-tk--------~G--~rG~IKeslGthG~FKAtFedkI~ 533 (714)
+-++|.||== .++.+|..+|.|++... .+ .+ +-|.|..+.|..|.+||.|...|-
T Consensus 18 ~~~~aLlKiegV~~~~~a~fylGKrv~yvyk~~~~~~~~k~r~iwGkV~r~HGnsGvVrAkF~~nLP 84 (95)
T PF01247_consen 18 HPNTALLKIEGVNTKEDAQFYLGKRVAYVYKAKNKKNGSKGRVIWGKVTRPHGNSGVVRAKFKKNLP 84 (95)
T ss_dssp CEEEEEEEESS-STCHHHHTTTT-EEEEEECE-SSSTTECSEEEEEEEEEESTTTTEEEEEESS--S
T ss_pred CCCeeEEeecCccCHHHHHhhcCcEEEEEEecccccCCCcEeEEEEEEEeEEcCCCEEEEEeCCCCC
Confidence 3456666643 68889999999955432 11 12 378999999999999999987664
No 13
>PRK04000 translation initiation factor IF-2 subunit gamma; Validated
Probab=45.04 E-value=3.8e+02 Score=30.24 Aligned_cols=119 Identities=10% Similarity=0.091 Sum_probs=66.6
Q ss_pred HhcCCCCCcEEEEEEe---ecChhhhhccCCCCceeEeecccccceeeEEEEEEEec-Cc----ccccccccCCcEEEEe
Q 005101 317 ELEGFRTGTYLRMEIH---DVPFEMVEYFDPCHPVLVGGIGLGEQNVGYMQVRLKRH-RW----WHKKVLKSRDPIIVSI 388 (714)
Q Consensus 317 ~~EG~~~G~YVrI~I~---~VP~e~v~~fdp~~PlIlgGLl~~E~k~~vv~~riKRh-rw----~~~kiLKSkDpLIfsi 388 (714)
.++.+.||..|-|.|. ++...-+. .+..|.--+-.+.-..-=.+++.+-.| .| +++.+|+..-.+++++
T Consensus 283 ~~~~a~~G~~v~i~l~~~~~i~~~~i~---~G~vl~~~~~~~~~~~~f~a~v~~l~~~~~~~~~~~~~~i~~g~~~~l~~ 359 (411)
T PRK04000 283 KVEEARPGGLVGVGTKLDPSLTKADAL---AGSVAGKPGTLPPVWESLTIEVHLLERVVGTKEELKVEPIKTGEPLMLNV 359 (411)
T ss_pred ECCEEcCCCEEEEEeccCCCCCHHHcc---CccEEEcCCCCCCceEEEEEEEEEEEhhcCccccccCCCCCCCCEEEEEE
Confidence 3455889999999986 34332221 111110001111111111234444444 23 1357999999999999
Q ss_pred eeeeeeeeeeeeecCCCccceeeeecCCCceEEEEEEeecC-CCCceEEEEEeccCCCCCeEEEEEEEe
Q 005101 389 GWRRFQTIPVYAIEDRSGRHRMLKYTPEHMHCLATFWGPLA-PPQTGVVAVQNLSNNQASFRIAATAVV 456 (714)
Q Consensus 389 GwRRFqt~PIyS~~d~n~R~K~lKYtpeh~~c~ATfyGPit-~p~tpvlafq~~s~~~~~frI~ATG~v 456 (714)
|-.+-...-.. .. +..|...++-|+. +++..|+..+.. ....|++|+|.+
T Consensus 360 ~t~~~~~~i~~-i~--------------~~~~~~~l~~p~~~~~g~r~~~~~~~---~~~~~~~~~~~~ 410 (411)
T PRK04000 360 GTATTVGVVTS-AR--------------KDEAEVKLKRPVCAEEGDRVAISRRV---GGRWRLIGYGII 410 (411)
T ss_pred eccEEEEEEEE-cC--------------CcEEEEEECCcEecCCCCEEEEEEec---CCcEEEEEEEEe
Confidence 98765443332 21 1256677888954 557777776543 346799999975
No 14
>TIGR03680 eif2g_arch translation initiation factor 2 subunit gamma. eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA.
Probab=43.27 E-value=3.4e+02 Score=30.42 Aligned_cols=64 Identities=8% Similarity=0.180 Sum_probs=45.4
Q ss_pred ccccccCCcEEEEeeeeeeeeeeeeeecCCCccceeeeecCCCceEEEEEEeecC-CCCceEEEEEeccCCCCCeEEEEE
Q 005101 375 KKVLKSRDPIIVSIGWRRFQTIPVYAIEDRSGRHRMLKYTPEHMHCLATFWGPLA-PPQTGVVAVQNLSNNQASFRIAAT 453 (714)
Q Consensus 375 ~kiLKSkDpLIfsiGwRRFqt~PIyS~~d~n~R~K~lKYtpeh~~c~ATfyGPit-~p~tpvlafq~~s~~~~~frI~AT 453 (714)
..+|+....+++++|-.+-...-. ... + ..|...+.-|+. .++..|+.++.. ...+||+|+
T Consensus 341 ~~~i~~g~~~~l~~gt~~~~~~v~-~~~--~------------~~~~l~l~~p~~~~~g~r~~~~~~~---~~~~~~~g~ 402 (406)
T TIGR03680 341 VEPIKTGEVLMLNVGTATTVGVVT-SAR--K------------DEIEVKLKRPVCAEEGDRVAISRRV---GGRWRLIGY 402 (406)
T ss_pred cccCCCCCEEEEEEccceEEEEEE-EcC--C------------cEEEEEECCcEEcCCCCEEEEEEec---CCceEEEEE
Confidence 579999999999999776544433 222 1 235566778854 457788888765 357999999
Q ss_pred EEe
Q 005101 454 AVV 456 (714)
Q Consensus 454 G~v 456 (714)
|.+
T Consensus 403 g~~ 405 (406)
T TIGR03680 403 GII 405 (406)
T ss_pred EEe
Confidence 976
No 15
>PRK12317 elongation factor 1-alpha; Reviewed
Probab=36.53 E-value=4.3e+02 Score=29.60 Aligned_cols=133 Identities=11% Similarity=0.081 Sum_probs=67.2
Q ss_pred HhcCCCCCcEEEEEEeecChhhhhccCCCCceeEeecccccceeeEEEEEEEecCcccccccccCCcEEEEeeeeeeee-
Q 005101 317 ELEGFRTGTYLRMEIHDVPFEMVEYFDPCHPVLVGGIGLGEQNVGYMQVRLKRHRWWHKKVLKSRDPIIVSIGWRRFQT- 395 (714)
Q Consensus 317 ~~EG~~~G~YVrI~I~~VP~e~v~~fdp~~PlIlgGLl~~E~k~~vv~~riKRhrw~~~kiLKSkDpLIfsiGwRRFqt- 395 (714)
.++-..+|..|.|.|.++...-+. .+..|.-.+-.+...+-=.+++.+-.| +.+|+.....++++|-.+-..
T Consensus 278 ~~~~a~aG~~v~i~l~~~~~~~i~---rG~vl~~~~~~~~~~~~f~a~v~~l~~----~~~i~~G~~~~~~~~t~~~~~~ 350 (425)
T PRK12317 278 ELPQAEPGDNIGFNVRGVGKKDIK---RGDVCGHPDNPPTVAEEFTAQIVVLQH----PSAITVGYTPVFHAHTAQVACT 350 (425)
T ss_pred ccCEECCCCeEEEEECCCCHHHcc---CccEecCCCCCCCcccEEEEEEEEECC----CCcCCCCCeEEEEEcCcEEEEE
Confidence 345578999999999987644322 222111111111111222234444443 458888899999999665433
Q ss_pred -eeeeeecCCCccc---eeeeecCCCceEEEEEE--eecCC------CCceEEEEEeccCCCCCeEEEEEEEeecccCc
Q 005101 396 -IPVYAIEDRSGRH---RMLKYTPEHMHCLATFW--GPLAP------PQTGVVAVQNLSNNQASFRIAATAVVLEFNHE 462 (714)
Q Consensus 396 -~PIyS~~d~n~R~---K~lKYtpeh~~c~ATfy--GPit~------p~tpvlafq~~s~~~~~frI~ATG~vl~~D~s 462 (714)
..|.+.-|.++-. +--++.+.+..+++.|- -|++. +..+=++++.. + +.+|.|.|+++.+.
T Consensus 351 i~~i~~~~d~~t~~~~~~~p~~l~~g~~a~v~l~~~~p~~~~~~~~~~~lgrfilr~~-----g-~tv~~G~i~~v~~~ 423 (425)
T PRK12317 351 FEELVKKLDPRTGQVAEENPQFIKTGDAAIVKIKPTKPLVIEKVKEIPQLGRFAIRDM-----G-QTIAAGMVIDVKPA 423 (425)
T ss_pred EEEEEEEeccccccccCCCCcEECCCCEEEEEEEECCeeEEEeCCcCCCCccEEEEEC-----C-CeEEEEEEEEeccC
Confidence 3344443322111 11234445555555442 33321 12223334332 1 67999999888654
No 16
>PRK00247 putative inner membrane protein translocase component YidC; Validated
Probab=34.68 E-value=2.2e+02 Score=32.89 Aligned_cols=46 Identities=13% Similarity=0.309 Sum_probs=25.5
Q ss_pred ccCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 005101 637 VVMEPHERKVHVLFQQLQLIRNEKMKKRKLKQQHRKKEIEAERAKDEQ 684 (714)
Q Consensus 637 vv~~p~ekk~~~l~q~l~ti~~~k~~krk~k~~~~~~~~~k~~~k~e~ 684 (714)
.+..|. ++.++-.....+++++.+..++++..+++...++.+.+.+
T Consensus 315 ~~~~p~--~~~~~~~~~~~~~~~~~~~~~~~k~~~k~~~~~~~~~~~~ 360 (429)
T PRK00247 315 MIITPW--RAPELHAENAEIKKTRTAEKNEAKARKKEIAQKRRAAERE 360 (429)
T ss_pred ccCCcc--cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344454 6667766666676666665555555554444444444433
No 17
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=33.14 E-value=2.5e+02 Score=34.43 Aligned_cols=22 Identities=23% Similarity=0.283 Sum_probs=13.0
Q ss_pred CCCCCCCCCChhhHhcCCCCCC
Q 005101 598 PRKFNPLVIPKSLQAALPFESK 619 (714)
Q Consensus 598 ~r~fnpl~iPk~Lq~~LPf~sk 619 (714)
.+.|.+-.-|+.=-..+||.++
T Consensus 221 ~~~~s~q~p~k~~s~~~pk~tk 242 (811)
T KOG4364|consen 221 IRSFSDQMPQKNSSEMAPKDTK 242 (811)
T ss_pred cCcccccccccCCCcCCCCCCC
Confidence 3456665555555566777654
No 18
>TIGR00483 EF-1_alpha translation elongation factor EF-1 alpha. This model represents the counterpart of bacterial EF-Tu for the Archaea (aEF-1 alpha) and Eukaryotes (eEF-1 alpha). The trusted cutoff is set fairly high so that incomplete sequences will score between suggested and trusted cutoff levels.
Probab=32.62 E-value=5e+02 Score=29.12 Aligned_cols=129 Identities=9% Similarity=0.116 Sum_probs=64.6
Q ss_pred HhcCCCCCcEEEEEEeecChhhhhccCCCCceeEeec--ccccceeeEEEEEEEecCcccccccccCCcEEEEeeeeeee
Q 005101 317 ELEGFRTGTYLRMEIHDVPFEMVEYFDPCHPVLVGGI--GLGEQNVGYMQVRLKRHRWWHKKVLKSRDPIIVSIGWRRFQ 394 (714)
Q Consensus 317 ~~EG~~~G~YVrI~I~~VP~e~v~~fdp~~PlIlgGL--l~~E~k~~vv~~riKRhrw~~~kiLKSkDpLIfsiGwRRFq 394 (714)
.++...+|+.|.|.|.+++..-++ .+. ||+.- .+.-.+-=.+++.+-. ++.+|+..-..+|+||..+-.
T Consensus 280 ~~~~a~aG~~v~i~l~~i~~~~i~---rG~--vl~~~~~~~~~~~~f~a~v~~l~----~~~~i~~g~~~~~~~~t~~~~ 350 (426)
T TIGR00483 280 QIEQAEPGDNIGFNVRGVSKKDIR---RGD--VCGHPDNPPKVAKEFTAQIVVLQ----HPGAITVGYTPVFHCHTAQIA 350 (426)
T ss_pred ccCEEcCCCEEEEEECCCChhhcc---cce--EEecCCCCCceeeEEEEEEEEEC----CCCccCCCCeEEEEecCcEEE
Confidence 344578999999999987654332 111 12111 0100111122333322 345787776777999988754
Q ss_pred e--eeeeeecCCCccc---eeeeecCCCceEEEEEE--eecCCC------CceEEEEEeccCCCCCeEEEEEEEeeccc
Q 005101 395 T--IPVYAIEDRSGRH---RMLKYTPEHMHCLATFW--GPLAPP------QTGVVAVQNLSNNQASFRIAATAVVLEFN 460 (714)
Q Consensus 395 t--~PIyS~~d~n~R~---K~lKYtpeh~~c~ATfy--GPit~p------~tpvlafq~~s~~~~~frI~ATG~vl~~D 460 (714)
. ..|.+.-+.++-. +--++...+..+.+.|- -|++.- ..+=++++.. -+.+|.|.|+.+.
T Consensus 351 ~~i~~i~~~~~~~t~~~~~~~p~~l~~g~~a~v~l~~~~pi~~e~~~~~~~~grf~lr~~------g~tv~~G~v~~~~ 423 (426)
T TIGR00483 351 CRFDELLKKNDPRTGQVLEENPQFLKTGDAAIVKFKPTKPMVIEAVKEIPPLGRFAIRDM------GQTVAAGMIIDVD 423 (426)
T ss_pred EEEEEEEEEecCccccccCCCCceeCCCCEEEEEEEECCeeEEeecccCCCCccEEEEEC------CCEEEEEEEEEee
Confidence 3 4555554332211 11235555656555553 232211 1222223332 1678999888764
No 19
>cd03708 GTPBP_III Domain III of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
Probab=32.06 E-value=2.1e+02 Score=24.65 Aligned_cols=68 Identities=15% Similarity=0.054 Sum_probs=38.6
Q ss_pred ccccccCCcEEEEeeeeeeeeeeeeeecCCCccceeeeecCCCceEEEEEE---eecCCCCceEEEEEeccCCCCCeEEE
Q 005101 375 KKVLKSRDPIIVSIGWRRFQTIPVYAIEDRSGRHRMLKYTPEHMHCLATFW---GPLAPPQTGVVAVQNLSNNQASFRIA 451 (714)
Q Consensus 375 ~kiLKSkDpLIfsiGwRRFqt~PIyS~~d~n~R~K~lKYtpeh~~c~ATfy---GPit~p~tpvlafq~~s~~~~~frI~ 451 (714)
+.||.+.-..++++|-.+-...-. . ... ++...+..+.+.+. -|+..-+.+-++++. + +.+
T Consensus 16 ~~~i~~Gy~~~l~~~t~~~~~~i~--~--i~~-----~~l~~g~~~~v~i~f~~~p~~~e~~grf~lr~------g-~tv 79 (87)
T cd03708 16 PTTISPGYQATVHIGSIRQTARIV--S--IDK-----DVLRTGDRALVRFRFLYHPEYLREGQRLIFRE------G-RTK 79 (87)
T ss_pred CCcccCCCEeEEEEcCCEEEEEEE--e--ccH-----hhccCCCeEEEEEEECCCCcEEccCCeEEEEC------C-CcE
Confidence 468888888888887765332111 1 001 45556666665555 666423334444432 2 689
Q ss_pred EEEEeec
Q 005101 452 ATAVVLE 458 (714)
Q Consensus 452 ATG~vl~ 458 (714)
|.|.|.+
T Consensus 80 a~G~I~~ 86 (87)
T cd03708 80 GVGEVTK 86 (87)
T ss_pred EEEEEEE
Confidence 9999865
No 20
>CHL00071 tufA elongation factor Tu
Probab=31.58 E-value=5.8e+02 Score=28.65 Aligned_cols=128 Identities=12% Similarity=-0.040 Sum_probs=65.8
Q ss_pred hcCCCCCcEEEEEEeecChhhhhccCCCCceeEeecc-cccceeeEEEEEEEecCc-ccccccccCCcEEEEeeeeeeee
Q 005101 318 LEGFRTGTYLRMEIHDVPFEMVEYFDPCHPVLVGGIG-LGEQNVGYMQVRLKRHRW-WHKKVLKSRDPIIVSIGWRRFQT 395 (714)
Q Consensus 318 ~EG~~~G~YVrI~I~~VP~e~v~~fdp~~PlIlgGLl-~~E~k~~vv~~riKRhrw-~~~kiLKSkDpLIfsiGwRRFqt 395 (714)
++.+.+|..|.|.|.++...-+. .+. ||+.-- +.....=.+++.+-.|.- =...||+.....++++|-.+-..
T Consensus 276 v~~a~aGd~v~i~l~~i~~~~i~---~G~--vl~~~~~~~~~~~f~a~i~~l~~~~~~~~~~i~~g~~~~~~~gt~~~~~ 350 (409)
T CHL00071 276 LDEGLAGDNVGILLRGIQKEDIE---RGM--VLAKPGTITPHTKFEAQVYILTKEEGGRHTPFFPGYRPQFYVRTTDVTG 350 (409)
T ss_pred CCEECCCceeEEEEcCCCHHHcC---CeE--EEecCCCCCcceEEEEEEEEEecccCCccccccCCceEEEEEcccEEEE
Confidence 34578999999999887643322 221 222210 101111123344434320 01468888899999999887554
Q ss_pred eeeeeecCCCccceeeeecCCCceEEEEEE--eecCCCCceEEEEEeccCCCCCeEEEEEEEeecc
Q 005101 396 IPVYAIEDRSGRHRMLKYTPEHMHCLATFW--GPLAPPQTGVVAVQNLSNNQASFRIAATAVVLEF 459 (714)
Q Consensus 396 ~PIyS~~d~n~R~K~lKYtpeh~~c~ATfy--GPit~p~tpvlafq~~s~~~~~frI~ATG~vl~~ 459 (714)
.-..-....+ .--++...+..|+|.|- .|+.+-..+-++++.. -+.+|.|.|+++
T Consensus 351 ~i~~i~~~~~---~~~~~l~~g~~a~v~l~~~~pi~~e~~~rfilR~~------~~tig~G~V~~~ 407 (409)
T CHL00071 351 KIESFTADDG---SKTEMVMPGDRIKMTVELIYPIAIEKGMRFAIREG------GRTVGAGVVSKI 407 (409)
T ss_pred EEEEEcccCC---CCCcEecCCCEEEEEEEECCeEEEeeCCEEEEecC------CeEEEEEEEEEe
Confidence 3322111111 11234556666655554 5554433334444432 278888888753
No 21
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=30.40 E-value=3.6e+02 Score=32.31 Aligned_cols=115 Identities=16% Similarity=0.077 Sum_probs=66.1
Q ss_pred HhcCCCCCcEEEEEEee-cChhhhhccCCCCceeEe-ecccccceeeEEEEEEEecCcccccccccCCcEEEEeeeeeee
Q 005101 317 ELEGFRTGTYLRMEIHD-VPFEMVEYFDPCHPVLVG-GIGLGEQNVGYMQVRLKRHRWWHKKVLKSRDPIIVSIGWRRFQ 394 (714)
Q Consensus 317 ~~EG~~~G~YVrI~I~~-VP~e~v~~fdp~~PlIlg-GLl~~E~k~~vv~~riKRhrw~~~kiLKSkDpLIfsiGwRRFq 394 (714)
.++-..||+.|-|.|.+ +..+-+. .+..|+-- .+.+.. .+-+.+. ...||+...++.|++|-.+-.
T Consensus 227 ~v~~a~aG~rval~l~g~~~~~~i~---rGdvl~~~~~~~~~~----~~~~~l~-----~~~~l~~~~~~~~~~gt~~~~ 294 (614)
T PRK10512 227 PTEQAQAGQRIALNIAGDAEKEQIN---RGDWLLADAPPEPFT----RVIVELQ-----THTPLTQWQPLHIHHAASHVT 294 (614)
T ss_pred CCCEEeCCCeEEEEecCCCChhhCC---CcCEEeCCCCCccce----eEEEEEc-----CCccCCCCCEEEEEEcccEEE
Confidence 34457899999999986 6554332 22211110 111111 1122221 246899999999999976544
Q ss_pred eeeeeeecCCCccceeeeecCCCceEEEEEEeecCCC-CceEEEEEeccCCCCCeEEEEEEEeecccCce
Q 005101 395 TIPVYAIEDRSGRHRMLKYTPEHMHCLATFWGPLAPP-QTGVVAVQNLSNNQASFRIAATAVVLEFNHEV 463 (714)
Q Consensus 395 t~PIyS~~d~n~R~K~lKYtpeh~~c~ATfyGPit~p-~tpvlafq~~s~~~~~frI~ATG~vl~~D~sr 463 (714)
..-.+- +...|...+.-|+... +.+|+. +..| .-+.+|.|.|++++|..
T Consensus 295 ~~i~~l---------------~~~~~~l~l~~p~~~~~gdr~il-r~~s----~~~tigGg~Vld~~~~~ 344 (614)
T PRK10512 295 GRVSLL---------------EDNLAELVLDTPLWLADNDRLVL-RDIS----ARNTLAGARVVMLNPPR 344 (614)
T ss_pred EEEEEc---------------CCeEEEEEECCcccccCCCEEEE-EeCC----CCEEEEEEEEcccCCcc
Confidence 322221 2234555566886554 556665 5543 35899999999987754
No 22
>COG1866 PckA Phosphoenolpyruvate carboxykinase (ATP) [Energy production and conversion]
Probab=28.49 E-value=50 Score=38.50 Aligned_cols=106 Identities=16% Similarity=0.159 Sum_probs=64.8
Q ss_pred cccccceeeEEEEEEEecCcccccccccCCcEEEEeeeeeeeeeee-eeecCCCccceeeeecCC-----CceEEEEEEe
Q 005101 353 IGLGEQNVGYMQVRLKRHRWWHKKVLKSRDPIIVSIGWRRFQTIPV-YAIEDRSGRHRMLKYTPE-----HMHCLATFWG 426 (714)
Q Consensus 353 Ll~~E~k~~vv~~riKRhrw~~~kiLKSkDpLIfsiGwRRFqt~PI-yS~~d~n~R~K~lKYtpe-----h~~c~ATfyG 426 (714)
|-.++-.++|+++---+--| ...=+.|..-++|.+-=+---+.-. |.-+-.-++-.++-|.-+ .|||.|.+ |
T Consensus 147 l~~~~~dftvin~p~f~~~~-~~~g~~Se~~i~~n~~~~~~lIggT~YaGEMKK~~fs~mnylLP~~~i~~MHcsANv-G 224 (529)
T COG1866 147 LSTFKPDFTVINAPSFKADP-KRDGLRSETFVAFNFTERIVLIGGTWYAGEMKKGIFSVMNYLLPLKGILSMHCSANV-G 224 (529)
T ss_pred hccCCCCeEEEeCCcCCCCh-hhcccccccEEEEecccceeeeeccchhhhhhhhHHHHhhccccccccccceecccc-C
Confidence 45667788899977667677 7777778777776643221111111 222212355678888754 48999854 5
Q ss_pred ecCCCCceEEEEEeccCCCCCeEEEEEEEe-ecccCceeEEEeEEEeeeeeEEe
Q 005101 427 PLAPPQTGVVAVQNLSNNQASFRIAATAVV-LEFNHEVKIKKKIKLVGYPCKIF 479 (714)
Q Consensus 427 Pit~p~tpvlafq~~s~~~~~frI~ATG~v-l~~D~sr~IvKKlkLtG~P~KI~ 479 (714)
|. +-..|+| -|+|||.. |+.||.| +|+|---.+.
T Consensus 225 ~~---gdvalFF----------GLSGTGKTTLSaDp~R------~LIGDDEHgW 259 (529)
T COG1866 225 EK---GDVALFF----------GLSGTGKTTLSADPHR------RLIGDDEHGW 259 (529)
T ss_pred cC---CCeEEEE----------eccCCCcceeccCCcc------ccccCccccc
Confidence 43 4444444 68888854 7999998 5777654443
No 23
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=28.06 E-value=59 Score=40.76 Aligned_cols=18 Identities=28% Similarity=0.291 Sum_probs=10.4
Q ss_pred CCcccccCCCcccccCcc
Q 005101 203 DSDDAVYGDYEDLETGEK 220 (714)
Q Consensus 203 ~~d~e~~GdFEDLEtge~ 220 (714)
++|+|.+||=.|++.|..
T Consensus 1421 ddd~edd~D~dd~~e~~~ 1438 (1516)
T KOG1832|consen 1421 DDDEEDDLDRDDGLEGDN 1438 (1516)
T ss_pred ccccccccccccchhccc
Confidence 345556666666666543
No 24
>PLN03126 Elongation factor Tu; Provisional
Probab=23.47 E-value=8.5e+02 Score=28.39 Aligned_cols=75 Identities=11% Similarity=-0.061 Sum_probs=46.0
Q ss_pred cccccCCcEEEEeeeeeeeeeeeeeecCCCccceeeeecCCCceEEEEE--EeecCCCCceEEEEEeccCCCCCeEEEEE
Q 005101 376 KVLKSRDPIIVSIGWRRFQTIPVYAIEDRSGRHRMLKYTPEHMHCLATF--WGPLAPPQTGVVAVQNLSNNQASFRIAAT 453 (714)
Q Consensus 376 kiLKSkDpLIfsiGwRRFqt~PIyS~~d~n~R~K~lKYtpeh~~c~ATf--yGPit~p~tpvlafq~~s~~~~~frI~AT 453 (714)
.||+..-..++++|--+-... |-.+....+ .--++...+..+++.| -.|+...+.+-++++.. -+.+|-
T Consensus 400 ~~I~~G~~~~lhigt~~~~~~-I~~i~~~~~--~~~~~l~~gd~a~v~l~~~~Pi~~~~~~RfilR~~------~~Tva~ 470 (478)
T PLN03126 400 SPFFAGYRPQFYMRTTDVTGK-VTSIMNDKD--EESKMVMPGDRVKMVVELIVPVACEQGMRFAIREG------GKTVGA 470 (478)
T ss_pred ccccCCcEEEEEEEecEEEEE-EEEEecccC--CCccEeCCCCEEEEEEEECCeEEEccCCEEEEecC------CceEEE
Confidence 588888888999997765433 222211111 1124555666666555 47877666666667654 278899
Q ss_pred EEeecc
Q 005101 454 AVVLEF 459 (714)
Q Consensus 454 G~vl~~ 459 (714)
|.|+++
T Consensus 471 G~V~~v 476 (478)
T PLN03126 471 GVIQSI 476 (478)
T ss_pred EEEEEe
Confidence 988764
No 25
>TIGR00485 EF-Tu translation elongation factor TU. This alignment models orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts, one of several GTP-binding translation factors found by the more general pfam model GTP_EFTU. The eukaryotic conterpart, eukaryotic translation elongation factor 1 (eEF-1 alpha), is excluded from this model. EF-Tu is one of the most abundant proteins in bacteria, as well as one of the most highly conserved, and in a number of species the gene is duplicated with identical function. When bound to GTP, EF-Tu can form a complex with any (correctly) aminoacylated tRNA except those for initiation and for selenocysteine, in which case EF-Tu is replaced by other factors. Transfer RNA is carried to the ribosome in these complexes for protein translation.
Probab=22.91 E-value=8.1e+02 Score=27.30 Aligned_cols=122 Identities=12% Similarity=0.006 Sum_probs=63.7
Q ss_pred hcCCCCCcEEEEEEeecChhhhhccCCCCceeEee--cccccceeeEEEEEEEecCcc-cccccccCCcEEEEeeeeeee
Q 005101 318 LEGFRTGTYLRMEIHDVPFEMVEYFDPCHPVLVGG--IGLGEQNVGYMQVRLKRHRWW-HKKVLKSRDPIIVSIGWRRFQ 394 (714)
Q Consensus 318 ~EG~~~G~YVrI~I~~VP~e~v~~fdp~~PlIlgG--Ll~~E~k~~vv~~riKRhrw~-~~kiLKSkDpLIfsiGwRRFq 394 (714)
++-..+|..|.|.|.++...-+. .+. ||+. ..+.-..+ -+++.+-.|.-. -..+|+...+.++++|--|-.
T Consensus 266 ~~~a~aGd~v~l~l~~i~~~~i~---rG~--vl~~~~~~~~~~~f-~a~i~vl~~~~g~~~~~i~~g~~~~l~~~t~~~~ 339 (394)
T TIGR00485 266 LDEGRAGDNVGLLLRGIKREEIE---RGM--VLAKPGSIKPHTKF-EAEVYVLKKEEGGRHTPFFSGYRPQFYFRTTDVT 339 (394)
T ss_pred EEEECCCCEEEEEeCCccHHHCC---ccE--EEecCCCCCcceEE-EEEEEEEecCCCCCCCccccCceEEEEEecceEE
Confidence 34577999999999876432221 111 1111 11111121 223333333100 035888888888999976643
Q ss_pred eeeeeeecCCCccceeeeecCCCceEEEEEE--eecCCCCceEEEEEeccCCCCCeEEEEEEEeecc
Q 005101 395 TIPVYAIEDRSGRHRMLKYTPEHMHCLATFW--GPLAPPQTGVVAVQNLSNNQASFRIAATAVVLEF 459 (714)
Q Consensus 395 t~PIyS~~d~n~R~K~lKYtpeh~~c~ATfy--GPit~p~tpvlafq~~s~~~~~frI~ATG~vl~~ 459 (714)
..-.+. + + -.+...+..|.|.|. -|+...+.+=++++.. -+.+|.|.|+.+
T Consensus 340 ~~i~~~--~-~-----~~~l~~g~~a~v~~~~~~p~~~~~~~rfilR~~------g~tv~~G~V~~v 392 (394)
T TIGR00485 340 GSITLP--E-G-----VEMVMPGDNVKMTVELISPIALEQGMRFAIREG------GRTVGAGVVSKI 392 (394)
T ss_pred EEEEec--C-C-----cceeCCCCEEEEEEEECceEEEeECCEEEEecC------CcEEEEEEEEEe
Confidence 332211 0 1 133455667777666 5665444444445532 278888988764
No 26
>PRK12735 elongation factor Tu; Reviewed
Probab=22.50 E-value=8.3e+02 Score=27.33 Aligned_cols=124 Identities=11% Similarity=-0.042 Sum_probs=63.6
Q ss_pred HhcCCCCCcEEEEEEeecChhhhhccCCCCceeEeecccccceeeEEEEEEEecCccc--ccccccCCcEEEEeeeeeee
Q 005101 317 ELEGFRTGTYLRMEIHDVPFEMVEYFDPCHPVLVGGIGLGEQNVGYMQVRLKRHRWWH--KKVLKSRDPIIVSIGWRRFQ 394 (714)
Q Consensus 317 ~~EG~~~G~YVrI~I~~VP~e~v~~fdp~~PlIlgGLl~~E~k~~vv~~riKRhrw~~--~kiLKSkDpLIfsiGwRRFq 394 (714)
.++-..+|..|.|.|.++..+-+. .+..|.-.+-++.=..+ -+++.+-.|.- . ..+|++....++++|--+..
T Consensus 267 ~v~~a~aGd~v~l~L~~i~~~~i~---rG~vl~~~~~~~~~~~f-~a~i~vl~~~~-~~~~~~i~~g~~~~l~~~t~~~~ 341 (396)
T PRK12735 267 LLDEGQAGDNVGVLLRGTKREDVE---RGQVLAKPGSIKPHTKF-EAEVYVLSKEE-GGRHTPFFNGYRPQFYFRTTDVT 341 (396)
T ss_pred EeCEECCCCEEEEEeCCCcHHHCC---cceEEEcCCCCCcceEE-EEEEEEEeccc-CCCCCcccCCCeeEEEeccceEE
Confidence 445578999999999987654322 22222111111111111 23344444321 1 35788888889999988754
Q ss_pred eeeeeeecCCCccceeeeecCCCceEEEEEE--eecCCCCceEEEEEeccCCCCCeEEEEEEEeecc
Q 005101 395 TIPVYAIEDRSGRHRMLKYTPEHMHCLATFW--GPLAPPQTGVVAVQNLSNNQASFRIAATAVVLEF 459 (714)
Q Consensus 395 t~PIyS~~d~n~R~K~lKYtpeh~~c~ATfy--GPit~p~tpvlafq~~s~~~~~frI~ATG~vl~~ 459 (714)
..-.. .+ + . .+...+..|+|.|. .|+..-..+=++++.. -+.+|.|.|+.+
T Consensus 342 ~~i~~--~~-~--~---~~l~~g~~a~v~l~~~~p~~~~~~~rfilR~~------g~tv~~G~V~~v 394 (396)
T PRK12735 342 GTIEL--PE-G--V---EMVMPGDNVKMTVELIAPIAMEEGLRFAIREG------GRTVGAGVVAKI 394 (396)
T ss_pred EEEEc--cC-C--C---ceeCCCCEEEEEEEECceEEEeECCEEEEEcC------CcEEEEEEEEEe
Confidence 33211 11 1 1 23444555555443 5554332234445432 278889988764
No 27
>PTZ00141 elongation factor 1- alpha; Provisional
Probab=21.46 E-value=1.3e+03 Score=26.59 Aligned_cols=129 Identities=13% Similarity=0.112 Sum_probs=66.1
Q ss_pred HhcCCCCCcEEEEEEeecChhhhhccCCCCceeEeec--cc-ccceeeEEEEEEEecCcccccccccCCcEEEEeeeeee
Q 005101 317 ELEGFRTGTYLRMEIHDVPFEMVEYFDPCHPVLVGGI--GL-GEQNVGYMQVRLKRHRWWHKKVLKSRDPIIVSIGWRRF 393 (714)
Q Consensus 317 ~~EG~~~G~YVrI~I~~VP~e~v~~fdp~~PlIlgGL--l~-~E~k~~vv~~riKRhrw~~~kiLKSkDpLIfsiGwRRF 393 (714)
.++-..+|+.|.|.|.++...-+. .+. ||+.- .| ...+-=-+++.+-. ++.+|+..-..+++||..+-
T Consensus 286 ~~~~a~aG~~v~i~L~~i~~~~v~---rG~--vl~~~~~~p~~~~~~f~a~i~~l~----~~~~i~~G~~~vl~~~t~~~ 356 (446)
T PTZ00141 286 QLAEAVPGDNVGFNVKNVSVKDIK---RGY--VASDSKNDPAKECADFTAQVIVLN----HPGQIKNGYTPVLDCHTAHI 356 (446)
T ss_pred ccCEECCCCEEEEEECCCCHHHcC---Cce--EEecCCCCCCccceEEEEEEEEEC----CCCccCCCCeEEEEEeceEE
Confidence 445578899999999987654322 222 11111 11 11111112222222 24578888777799998765
Q ss_pred ee--eeeeeecCCCc-c-c-eeeeecCCCceEEEEEE--eecCCC------CceEEEEEeccCCCCCeEEEEEEEeeccc
Q 005101 394 QT--IPVYAIEDRSG-R-H-RMLKYTPEHMHCLATFW--GPLAPP------QTGVVAVQNLSNNQASFRIAATAVVLEFN 460 (714)
Q Consensus 394 qt--~PIyS~~d~n~-R-~-K~lKYtpeh~~c~ATfy--GPit~p------~tpvlafq~~s~~~~~frI~ATG~vl~~D 460 (714)
.. ..|.+.-+.++ . . +.-++.+.+..+++.|- -||+.- ..+=++++.. + ..+|.|.|+.+.
T Consensus 357 ~~~i~~i~~~ld~~t~~~~~~~p~~l~~g~~a~v~l~~~~pi~~e~~~~~~~lgrfilrd~-----g-~tva~G~I~~v~ 430 (446)
T PTZ00141 357 ACKFAEIESKIDRRSGKVLEENPKAIKSGDAAIVKMVPTKPMCVEVFNEYPPLGRFAVRDM-----K-QTVAVGVIKSVE 430 (446)
T ss_pred EEEEEEEEEEeccccccccCCCCcEECCCCEEEEEEEECCceEEeecccCCCCccEEEEEC-----C-CEEEEEEEEEEe
Confidence 43 44555544321 1 1 22346666666666553 333221 2222333332 1 578999887765
No 28
>PRK00049 elongation factor Tu; Reviewed
Probab=21.17 E-value=1.2e+03 Score=26.16 Aligned_cols=123 Identities=10% Similarity=0.013 Sum_probs=65.0
Q ss_pred HhcCCCCCcEEEEEEeecChhhhhccCCCCceeEeec-ccccceeeEEEEEEEecCccc--ccccccCCcEEEEeeeeee
Q 005101 317 ELEGFRTGTYLRMEIHDVPFEMVEYFDPCHPVLVGGI-GLGEQNVGYMQVRLKRHRWWH--KKVLKSRDPIIVSIGWRRF 393 (714)
Q Consensus 317 ~~EG~~~G~YVrI~I~~VP~e~v~~fdp~~PlIlgGL-l~~E~k~~vv~~riKRhrw~~--~kiLKSkDpLIfsiGwRRF 393 (714)
.++-..+|+.|.|.|.++...-+ ..+. |++.- .+.-.+.=.+++.+-.|.- . ..+|++.-..++++|--+-
T Consensus 267 ~~~~a~~Gd~v~l~l~~i~~~~i---~~G~--vl~~~~~~~~~~~f~a~i~vl~~~~-~g~~~~i~~g~~~~~~~~t~~~ 340 (396)
T PRK00049 267 LLDEGQAGDNVGALLRGIKREDV---ERGQ--VLAKPGSITPHTKFEAEVYVLSKEE-GGRHTPFFNGYRPQFYFRTTDV 340 (396)
T ss_pred EeCEEcCCCEEEEEeCCCCHHHC---Ccce--EEecCCCCCcceEEEEEEEEEecCc-CCCCCcccCCCEEEEEEecCcE
Confidence 34557899999999998754322 2221 22221 1111111124444444421 1 3588888888999998874
Q ss_pred eeeeeeeecCCCccceeeeecCCCceEEEEEE--eecCCCCceEEEEEeccCCCCCeEEEEEEEeecc
Q 005101 394 QTIPVYAIEDRSGRHRMLKYTPEHMHCLATFW--GPLAPPQTGVVAVQNLSNNQASFRIAATAVVLEF 459 (714)
Q Consensus 394 qt~PIyS~~d~n~R~K~lKYtpeh~~c~ATfy--GPit~p~tpvlafq~~s~~~~~frI~ATG~vl~~ 459 (714)
... | ...+ + -+|...+..+++.|- .|++.-+.+=++++.. -+.+|-|.|+++
T Consensus 341 ~~~-i-~l~~-~-----~~~l~~g~~a~v~i~~~~p~~~e~~~RfilR~~------g~t~~~G~V~~v 394 (396)
T PRK00049 341 TGV-I-ELPE-G-----VEMVMPGDNVEMTVELIAPIAMEEGLRFAIREG------GRTVGAGVVTKI 394 (396)
T ss_pred EEE-E-EecC-C-----CcccCCCCEEEEEEEECceEEEeeCCEEEEecC------CcEEEEEEEEEe
Confidence 332 2 1111 1 135555656655554 5554333333445532 268888988764
Done!