Query 003543
Match_columns 811
No_of_seqs 314 out of 798
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 01:25:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003543.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003543hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0401 Translation initiation 100.0 4.8E-69 1E-73 652.4 42.0 759 2-810 142-940 (970)
2 PF02854 MIF4G: MIF4G domain; 100.0 1.6E-31 3.6E-36 268.6 20.2 202 199-458 1-209 (209)
3 smart00543 MIF4G Middle domain 99.9 9.4E-27 2E-31 234.3 21.3 194 200-458 2-200 (200)
4 smart00544 MA3 Domain in DAP-5 99.9 1.5E-22 3.3E-27 188.5 13.3 113 646-758 1-113 (113)
5 PF02847 MA3: MA3 domain; Int 99.9 8E-23 1.7E-27 190.1 10.8 113 646-758 1-113 (113)
6 KOG0403 Neoplastic transformat 99.8 3.5E-20 7.6E-25 202.3 14.1 151 642-793 340-490 (645)
7 KOG2140 Uncharacterized conser 99.8 1.4E-19 3.1E-24 200.2 15.3 424 195-786 161-593 (739)
8 KOG0403 Neoplastic transformat 99.8 1.4E-18 3.1E-23 189.8 14.2 146 643-789 46-191 (645)
9 KOG2141 Protein involved in hi 99.4 1E-11 2.2E-16 142.9 19.2 200 196-462 317-524 (822)
10 KOG3942 MIF4G domain-containin 98.7 1E-07 2.2E-12 101.6 13.0 163 268-463 169-337 (348)
11 KOG2051 Nonsense-mediated mRNA 98.7 2.3E-07 4.9E-12 111.5 15.3 152 268-454 462-613 (1128)
12 KOG0401 Translation initiation 98.2 2.5E-07 5.3E-12 114.8 -0.8 277 173-481 588-892 (970)
13 KOG2051 Nonsense-mediated mRNA 97.5 0.0025 5.3E-08 77.9 17.5 103 353-456 722-835 (1128)
14 KOG1104 Nuclear cap-binding co 94.2 1.7 3.6E-05 52.6 17.2 161 268-463 67-248 (759)
15 PF12152 eIF_4G1: Eukaryotic t 86.8 0.44 9.5E-06 42.1 2.1 26 55-80 43-69 (75)
16 PF02847 MA3: MA3 domain; Int 79.8 18 0.00039 33.3 10.1 30 268-297 36-66 (113)
17 PF05918 API5: Apoptosis inhib 76.6 30 0.00065 41.5 12.9 156 196-413 177-346 (556)
18 smart00544 MA3 Domain in DAP-5 67.8 25 0.00054 32.5 7.8 30 268-297 36-66 (113)
19 PLN00131 hypothetical protein; 55.8 1.5E+02 0.0033 29.9 10.9 68 632-710 117-185 (218)
20 PF02854 MIF4G: MIF4G domain; 55.8 63 0.0014 32.1 8.8 121 648-770 2-132 (209)
21 KOG2140 Uncharacterized conser 53.0 71 0.0015 38.0 9.4 23 118-140 75-97 (739)
22 PRK14703 glutaminyl-tRNA synth 48.9 4.1E+02 0.0089 33.6 15.7 85 697-793 663-760 (771)
23 PLN03081 pentatricopeptide (PP 43.8 1.8E+02 0.0039 35.7 11.7 61 651-715 263-323 (697)
24 PF05456 eIF_4EBP: Eukaryotic 43.3 7.2 0.00016 37.4 -0.3 21 59-79 42-62 (116)
25 PLN03218 maturation of RBCL 1; 41.2 1.5E+02 0.0032 38.8 10.7 67 650-717 582-649 (1060)
26 PF04844 Ovate: Transcriptiona 41.2 67 0.0015 27.3 5.2 46 643-688 5-52 (59)
27 KOG2141 Protein involved in hi 37.5 1.1E+02 0.0025 37.6 8.2 79 268-380 653-731 (822)
28 PRK05477 gatB aspartyl/glutamy 37.4 3.9E+02 0.0085 31.8 12.5 32 697-729 367-398 (474)
29 PF08146 BP28CT: BP28CT (NUC21 36.3 1.7E+02 0.0037 29.2 8.2 109 196-328 39-149 (153)
30 PF07817 GLE1: GLE1-like prote 35.4 6E+02 0.013 27.4 16.7 181 196-417 27-241 (256)
31 cd03567 VHS_GGA VHS domain fam 33.5 2.8E+02 0.0061 27.3 9.1 95 359-460 19-119 (139)
32 TIGR01568 A_thal_3678 uncharac 32.6 1.3E+02 0.0029 26.1 5.7 47 642-688 10-59 (66)
33 PRK14137 recX recombination re 31.9 6.1E+02 0.013 26.5 13.6 99 637-770 29-129 (195)
34 PLN03218 maturation of RBCL 1; 31.5 2.6E+02 0.0057 36.5 10.8 65 650-715 617-682 (1060)
35 PF08044 DUF1707: Domain of un 31.5 65 0.0014 26.6 3.6 45 694-738 4-53 (53)
36 TIGR01446 DnaD_dom DnaD and ph 30.9 1.5E+02 0.0033 25.2 6.0 54 664-720 19-72 (73)
37 PF10602 RPN7: 26S proteasome 30.9 1.6E+02 0.0034 30.0 7.1 56 640-695 29-88 (177)
38 PF02284 COX5A: Cytochrome c o 29.8 3.4E+02 0.0074 25.9 8.3 93 641-739 6-102 (108)
39 cd03568 VHS_STAM VHS domain fa 29.4 4.9E+02 0.011 25.7 10.1 109 359-478 18-128 (144)
40 PF08876 DUF1836: Domain of un 28.9 38 0.00083 31.9 2.1 52 692-743 53-104 (105)
41 cd00923 Cyt_c_Oxidase_Va Cytoc 28.3 5E+02 0.011 24.6 9.1 93 641-739 3-99 (103)
42 PF04286 DUF445: Protein of un 28.3 5.3E+02 0.011 28.4 11.4 93 642-734 102-200 (367)
43 PF12854 PPR_1: PPR repeat 28.2 79 0.0017 23.2 3.3 25 650-674 10-34 (34)
44 smart00543 MIF4G Middle domain 28.1 5.2E+02 0.011 25.5 10.4 31 739-769 94-124 (200)
45 cd03561 VHS VHS domain family; 27.8 5.2E+02 0.011 24.9 9.8 95 359-460 18-115 (133)
46 PF08321 PPP5: PPP5 TPR repeat 27.5 38 0.00082 31.3 1.7 72 714-791 9-91 (95)
47 cd03569 VHS_Hrs_Vps27p VHS dom 25.4 3.5E+02 0.0075 26.7 8.2 109 359-478 22-132 (142)
48 PF02650 HTH_WhiA: WhiA C-term 25.1 4.7E+02 0.01 23.8 8.2 64 357-435 21-84 (85)
49 COG1421 CRISPR system related 24.8 1.6E+02 0.0034 29.2 5.4 60 713-772 43-110 (137)
50 PLN03081 pentatricopeptide (PP 24.7 4.1E+02 0.009 32.5 10.5 62 650-715 161-222 (697)
51 PLN03077 Protein ECB2; Provisi 24.6 3.1E+02 0.0068 34.4 9.7 63 649-715 325-387 (857)
52 COG5537 IRR1 Cohesin [Cell div 24.1 1E+03 0.022 29.3 12.8 137 644-788 328-469 (740)
53 PF10884 DUF2683: Protein of u 23.6 2E+02 0.0042 26.0 5.3 44 647-690 12-60 (80)
54 TIGR00756 PPR pentatricopeptid 23.3 91 0.002 21.4 2.8 26 651-676 4-29 (35)
55 PTZ00009 heat shock 70 kDa pro 23.2 3.4E+02 0.0074 33.4 9.3 79 395-477 512-597 (653)
56 PF13041 PPR_2: PPR repeat fam 22.3 1.6E+02 0.0035 22.9 4.3 41 650-690 6-47 (50)
57 COG5538 SEC66 Endoplasmic reti 22.3 8.4E+02 0.018 24.9 10.8 119 278-445 36-154 (180)
58 KOG4699 Preprotein translocase 22.3 8.4E+02 0.018 24.9 10.8 119 278-445 36-154 (180)
59 PF12612 TFCD_C: Tubulin foldi 21.8 2.4E+02 0.0053 28.9 6.7 37 676-712 2-38 (193)
60 PRK09498 sifA secreted effecto 21.2 1.7E+02 0.0037 32.4 5.4 28 649-676 29-56 (336)
61 PF08542 Rep_fac_C: Replicatio 20.6 4.9E+02 0.011 22.7 7.5 47 680-730 5-51 (89)
62 PF10363 DUF2435: Protein of u 20.6 6.6E+02 0.014 23.0 8.7 81 684-769 6-86 (92)
63 PF01535 PPR: PPR repeat; Int 20.2 1.3E+02 0.0029 20.3 3.1 25 651-675 4-28 (31)
No 1
>KOG0401 consensus Translation initiation factor 4F, ribosome/mRNA-bridging subunit (eIF-4G) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.8e-69 Score=652.44 Aligned_cols=759 Identities=30% Similarity=0.427 Sum_probs=553.1
Q ss_pred CcCCcc---eEEeccCCCCCCCCCccccccCCCCC--CC--CCCCCCCCCCCCCCc---ccccCCCccCCCcccccCHHH
Q 003543 2 QAADQT---VISLRPGGGGGPRGTRLFTHRFDSSS--TP--SSDSQTLPPHGGVAS---AFKMGDLRFEGHERVRYTREQ 71 (811)
Q Consensus 2 ~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~--~~--~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~y~~~~ 71 (811)
+.+++. +++++|+|.. ...+.|+.....+. +. ++....++.+++.+. .....+.++....+..|....
T Consensus 142 ~~~~~s~~~~l~~~~~~~~--~~~~~~~~~~~~s~~~~~~~~s~~~~~~~~~~~~~~~~~e~~~~~~~~~~l~~~~~~~~ 219 (970)
T KOG0401|consen 142 QEGEPSSTKALILKKSGEE--ADDKAFGEPKESSLGEGQADSSTPKTSEDGIPFEKPPDPEEQKASDRMDALTLAFSEEL 219 (970)
T ss_pred cCCCCCccccccccccccc--ccccccccccccccccccCCCCCcccccccCCCCCCCCcccccccccchhhhhhhhhhh
Confidence 345555 9999999995 33445555433222 21 222222455666543 444566677777788999999
Q ss_pred HHHHHHHhhccHHHHHhhhhhccccccCCCCCCCCCCCCcccchhhhhhcccCCccccccCCCC--CcccchhhhHhhhh
Q 003543 72 LLQLKEVAQLTEDILKIKQEIESEFDGEGQSWGGRAENNNLQSQFQARYLEADNRDWRTRSTTS--GQEKSLEANQEKME 149 (811)
Q Consensus 72 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~ 149 (811)
++.......++..++..+......+..++.+|. + ..+........|..++.++||.....+. ...+.++..++..-
T Consensus 220 ~~~~e~~~~~~d~~~~~~e~~~~~~~~e~~~~~-~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~ 297 (970)
T KOG0401|consen 220 LLEAENTPRSSDEYVRRIEAEQEPLRPEEPSGL-R-AIQKIPEKATERRAEESGRDKPEHEDQTKPAGNRLLDEPRESQP 297 (970)
T ss_pred hhhhhhcCCcchHHHHHHHHHhhccCCccchhh-h-cccccccccccccccccccccccccccccccccccccchhhhcc
Confidence 998887788999988887778888999999982 2 2222466778899999999998776665 22244544444332
Q ss_pred ccccccc---ccchhhhhhcccCCCCCCCcccccccCCCccccCCCChHHHHHHHHHHHhhcCChhhHHHHHHHHHHccC
Q 003543 150 FGAHEGQ---LNSQFASAQISTNQGAGPAPALIKAEVPWSARRGNLSEKDRVLKTVKGILNKLTPEKFDVLKGQLIDSGI 226 (811)
Q Consensus 150 ~~~~~~~---~~~~~~~~~~~~~~~~~p~~~l~~~e~~w~~~~~~~~~~e~l~r~Vk~iLNKLTpenFd~l~~ql~~~~i 226 (811)
...+..+ ....+.........+..|.+...++..+|...+...+..+++.+.|++|||||||++|+.++.++++.+|
T Consensus 298 ~~~~e~~~~~~~~~~~~~~~~~~~~~~ps~k~a~~~~~~~~~~~~~~~~~el~~~vrsilnkltp~~~~~l~~q~~~~~i 377 (970)
T KOG0401|consen 298 AENGEPAKKGVEEVEEVVLNFAQKAPSPSPKRAKSKSDQGAERKDVELKEELAKRVRSLLNKLTPERKELLIEQLIELNV 377 (970)
T ss_pred ccccccccccchhhhHHHHHhccCCCCCcchhhccccccccccchhHHHHHHHHHHhhhcCCCchHHHHHHHHHHHhhcc
Confidence 2221110 1222222233344666788888889999988888888889999999999999999999999999999999
Q ss_pred CchhhhhhhhhhhccchhhHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHhhcCCCchHHHHHHHHHHhhhCCCCCCCCC
Q 003543 227 TTPDILKVTITHLECHNLLQVIIFLYSIFFLLKLRSLFAFQGVIELIFDKAVLEPTFCPMYALLCSDLNEKLPPFPSDEP 306 (811)
Q Consensus 227 ~~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~VI~lIfeKAi~Ep~fs~mYA~LC~~L~~~l~~~~~~e~ 306 (811)
++.++|+ +||.+||||||.||+||.|||+||..|.. .+.++..+.
T Consensus 378 ~t~~~l~----------------------------------~vi~~vfdkAi~EP~f~~~yA~lc~~l~~-~~~~~~~~~ 422 (970)
T KOG0401|consen 378 DTDDALK----------------------------------EVIELVFDKAINEPTFCAMYARLCFDLEG-PPSEPELDM 422 (970)
T ss_pred CcHHHHh----------------------------------HHHHHHHHhhhcccccchhcchhcccccC-CccCCCcCC
Confidence 9999998 99999999999999999999999999998 555555556
Q ss_pred CCcchhHHHHHHHHHHHHHhhhh-hhHHHHhhcCChHH-HHHHHHHHHHHHHhhhhhHHHHHHHHhcCCCCHHHHHHHHH
Q 003543 307 GGKDITFKRILLNHCQEAFEGAD-NTRAEIRQMTAPEQ-EMERMDQERLVKLRTLGNIRLIGELLKQKMVPEKIVHHIVQ 384 (811)
Q Consensus 307 ~gk~~~FRrlLLnrcQeeFe~~~-~~~~ei~~l~~~e~-E~E~~e~e~~~KrR~LGnIrFIGELfk~~mL~e~Ii~~cI~ 384 (811)
.+..++||++||++||++|+... ....++..+..+++ |.++.+.+++.++|++|||+|||+||+..|++++|||.||+
T Consensus 423 ~~~~~~fr~~lL~rcq~~fe~~~~~~~~~~~~~~~~~~~e~~le~~k~~~~~rtlgn~~~ig~l~~~~ml~e~i~~~~v~ 502 (970)
T KOG0401|consen 423 GGDEINFRRLLLNRCQKEFEGEDDKIADEYSEAEEPDELEEELEEEKYILRRRTLGNFRFIGELFKLKMLTEKIVHACVQ 502 (970)
T ss_pred CCCcccHHHHHHHHhHHHhhcccHHHHHHhhhhcCchhHHHHHHhccceecCCccchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67779999999999999999988 56667777666655 55566666788999999999999999999999999999999
Q ss_pred HHhhcCCCCCCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHhhCCCCChHHHHHHHHHHHHHhCCCCcccc
Q 003543 385 ELLENDGKTCPAEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTTNSQLVPRLRFMIHDVLDLRANNWVPRRE 464 (811)
Q Consensus 385 ~LL~~~~~~~p~Ee~IEcLc~LL~tiGk~Ld~~~k~~~~mD~yF~rL~~l~~~~~lSsRIRFmI~dvIdLR~n~W~~r~~ 464 (811)
.||..+. ++|++|||+|+|++|||+.||........||.||.+++.+...+.+++|+|||++++||||.++|++|+.
T Consensus 503 ~Ll~~~~---~~ee~ie~lc~f~~tig~~lD~~~~s~r~md~~~~~~k~~~~~~~~s~r~RfM~~~~idlR~~~w~~rr~ 579 (970)
T KOG0401|consen 503 KLLSDDQ---PSEESIECLCRFLTTIGKKLDFSKESPRNMDEYFNSMKNLKRKPQRSNRIRFMLQSVIDLRKSGWGPRRA 579 (970)
T ss_pred Hhhcccc---ccchhhhhHHhhhhcccccccccCcccchhHHHHHHHHHhhhhhhhccchhhhhccccccccccccchhc
Confidence 9998642 7899999999999999999997544333499999999999999999999999999999999999999999
Q ss_pred ccCcc-cHHHHHHHHHHhcCCCCchhhhhhcCCCCC---CCCC-----CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 003543 465 EMKAK-TITEIHSEAEKNLGLRPGATAMMRNGRTGA---TGGM-----GPGGFPIARPGTGGMMPGMPGTQKMPGMPGFD 535 (811)
Q Consensus 465 ~~~pk-ti~eIh~Eae~~~~~~~~~~~~~r~~r~~~---~g~~-----~pg~~~~~~p~~gg~~p~~~~~r~~p~~pg~~ 535 (811)
+.+++ +|++||.++.+..+..++....+++++.+. .+.. .+.+....+...+.|+++++...-+..++.++
T Consensus 580 ~~~~~~~ieei~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~i~~~~~~~~~~~~~ 659 (970)
T KOG0401|consen 580 EETNDKPIEEIAPEAPSANRWSPKSLSKKTEGRLAEESDSGLLGKEVVERKGKSGLRKLTPEMFDKISDPILDIADQSMD 659 (970)
T ss_pred ccCCCCchhhcchhhhhhcccCcccccccccccccccccccccCccccccccccccccCChhhcccccccccccchhhcc
Confidence 88877 999999999888765555443344433211 0000 01112223344455566665443444455666
Q ss_pred CCCCCccCCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCcCC--CCccccC---CCCCCCCCC
Q 003543 536 TDNWEVPRSR--TMPRGDSKSPSQFPGRVQSPLIGKSPSIN----SKFLPQGSGGIISG--KTSALLQ---GSPTPSARP 604 (811)
Q Consensus 536 ~d~~~~~~~~--s~~r~~~~~~~~~~~~~~~~~~~k~~~~n----~~~~p~gs~~~~sg--k~sall~---~~~~p~~r~ 604 (811)
.++|++.... ..++..+.. +++ ...+.+..++..... ....++|+.+.... ..++... ..+....++
T Consensus 660 e~~~~~~k~~~~~~~~k~~~~-~~~-~~~~~~~~~~~~~~~s~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 737 (970)
T KOG0401|consen 660 EEDGEASKQKGEQGGRKASDE-QHF-SSMRAPALEKVVPSLSSDIDDKRNRGSNGELLSDSYLSARCHEEFENGWSRELP 737 (970)
T ss_pred ccccchhhhcccccccccCcc-ccc-cccCCccccccccccccccccccccCCccccccccccchhhhhhccccccccCC
Confidence 6677655332 222221111 011 011222222211111 12334444431111 1111111 111011111
Q ss_pred CCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCC--CCCHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHH
Q 003543 605 SGIASGVEPLTQYTKPVAPAASVVASPEKPSAPVT--KLNLADLRKKTVSLLEEYFSIRILDEALQCVEELRAPTYHPEV 682 (811)
Q Consensus 605 ~~~~~~~~~~~q~~~~~k~~~~~p~~~~~~~~~~~--~ls~EEl~kki~sil~EY~~~~D~~EA~~cikEL~~p~~~~ev 682 (811)
++....+ .+.-+.+. -.++.+.+.++... .++.+.+..++++|++||++..+.+|++.|+++|++|.+|+.+
T Consensus 738 s~~~~~~-----~~e~~~~~-~~~~~~~~~~~~~~v~~~~~~~l~~~sk~l~ee~~~~~~~~~~~~~ie~l~S~~~~~~~ 811 (970)
T KOG0401|consen 738 SGKDGER-----EPEMMSPE-YYAAKAAKRAGLGLVIALSSELLELLSKSLLEEFLSLRLEKEALKCIEELESPSLLLKT 811 (970)
T ss_pred CCccccc-----chhhcCcc-cchhhhhhccCCcchhhhhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcccchhhhHHH
Confidence 1111111 00001010 00111222333344 7889999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCCChHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcchhhhcCCCchhHHHHHHHHHHHHcCCCChHH-
Q 003543 683 VKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTGCLLYGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLDFIV- 761 (811)
Q Consensus 683 V~~~I~~aLEkk~~erElvs~LL~~L~~~~lls~~q~~~Gf~~vle~LdDl~iDiP~A~~~La~fiaraV~dg~l~~~~- 761 (811)
|..+|+..|++++..++++++||..|+..+.++.+++..||..++..++|+.||+|++|.|+++|++.++..+++++..
T Consensus 812 v~~~v~~~l~~~~~~~~~~~~ll~~l~~~~~~~~~~~~~~~~~~~~~~~d~~~d~pk~w~~~~e~~gp~~~~~~~~~~e~ 891 (970)
T KOG0401|consen 812 VGENIEPTLEKSPQAVEELLQLLDILVSKNPLSIETLEIGYREKFKLADDKELDLPKGWNYIKEFLGPLIHQKILDESEL 891 (970)
T ss_pred HHHhcCcccccChhHHHHHHHHHHHHHhcCcccHHHHhhhHHHHHhhhHHHhcccccchhHHHHhhhhHhhhccccHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999954
Q ss_pred HHHHHhhhcchhHHHHHHHHHHHHHhcCCCchhhHhhhhhhHHHHhhhh
Q 003543 762 LKEVLKKVEDNMFRRSIFTAAMKSIQSSPAGQEVLAVQGAEVQACESLL 810 (811)
Q Consensus 762 i~~~~~~~~d~~~~~~~l~~~l~~l~~~~~g~~v~~~~~~~~~~~~~~~ 810 (811)
+..+...+++.+++..++.+++..+...-++.++.+..+....+|+.++
T Consensus 892 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~ 940 (970)
T KOG0401|consen 892 VREILKNMRPNGRRSNVLFSVLEIVEKELGRADLGDIQRESFLSTKTLL 940 (970)
T ss_pred HHHHhhcCCccccccchHHHHHHHHHHhhhHHHHHHHHHHhcccchhcc
Confidence 5677778899999999999999999988899999999999999998764
No 2
>PF02854 MIF4G: MIF4G domain; InterPro: IPR003890 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 3", and is found in nuclear cap-binding proteins, eIF4G, and UPF2. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA. Nonsense-mediated mRNA decay (NMD) in eukaryotes involves UPF1, UPF2 and UPF3 to accelerate the decay rate of two unique classes of transcripts: (1) nonsense mRNAs that arise through errors in gene expression, and (2) naturally occurring transcripts that lack coding errors but have built-in features that target them for accelerated decay (error-free mRNAs). NMD can trigger decay during any round of translation and can target CBC-bound or eIF-4E-bound transcripts []. UPF2 contains MIF4G domains, while UPF3 contains an RNP domain []. ; GO: 0005515 protein binding, 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A 1HU3_A 3RK6_A ....
Probab=99.98 E-value=1.6e-31 Score=268.64 Aligned_cols=202 Identities=42% Similarity=0.776 Sum_probs=172.4
Q ss_pred HHHHHHHhhcCChhhHHHHHHHHHHccCCc-hhhhhhhhhhhccchhhHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHh
Q 003543 199 LKTVKGILNKLTPEKFDVLKGQLIDSGITT-PDILKVTITHLECHNLLQVIIFLYSIFFLLKLRSLFAFQGVIELIFDKA 277 (811)
Q Consensus 199 ~r~Vk~iLNKLTpenFd~l~~ql~~~~i~~-~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~VI~lIfeKA 277 (811)
+|+|+++|||||++||+.++++|..+.+.. .+.++ .+++.||++|
T Consensus 1 ~r~v~~~lnklt~~n~~~~~~~l~~~~~~~~~~~~~----------------------------------~i~~~i~~~a 46 (209)
T PF02854_consen 1 LRKVRGILNKLTPSNFESIIDELIKLNWSDDPETLK----------------------------------EIVKLIFEKA 46 (209)
T ss_dssp HHHHHHHHHHCSSTTHHHHHHHHHHHHHHSCHHHHH----------------------------------HHHHHHHHHH
T ss_pred CchHHHHHHHCCHHHHHHHHHHHHHHHhhccHHHHH----------------------------------HHHHHHhhhh
Confidence 589999999999999999999999876554 44444 8999999999
Q ss_pred hcCCCchHHHHHHHHHHhhhCCCCCCCCCCCcchhHHHHHHHHHHHHHhhhhhhHHHHhhcCChHHHHHHHHHHHHHHHh
Q 003543 278 VLEPTFCPMYALLCSDLNEKLPPFPSDEPGGKDITFKRILLNHCQEAFEGADNTRAEIRQMTAPEQEMERMDQERLVKLR 357 (811)
Q Consensus 278 i~Ep~fs~mYA~LC~~L~~~l~~~~~~e~~gk~~~FRrlLLnrcQeeFe~~~~~~~ei~~l~~~e~E~E~~e~e~~~KrR 357 (811)
+.+|.|+.+||+||..|+...+ ..|+..||++||++|+.... ..+.+ +.....+++
T Consensus 47 ~~~~~~~~~~a~l~~~l~~~~~-----------~~f~~~ll~~~~~~f~~~~~-----------~~~~~--~~~~~~~~~ 102 (209)
T PF02854_consen 47 VEEPNFSPLYARLCAALNSRFP-----------SEFRSLLLNRCQEEFEERYS-----------NEELE--ENRQSSKQR 102 (209)
T ss_dssp HHSGGGHHHHHHHHHHHHHHCH-----------HHHHHHHHHHHHHHHHHHT------------HHHHH--HHHHHHHHH
T ss_pred hcCchHHHHHHHHHHHHhccch-----------hhHHHHHHHHHHHHHHHhhh-----------hhhHH--HHHHHHHHH
Confidence 9999999999999999999753 58999999999999999541 00111 122356778
Q ss_pred hhhhHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCC---CCCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHH
Q 003543 358 TLGNIRLIGELLKQKMVPEKIVHHIVQELLENDGK---TCPAEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKEL 434 (811)
Q Consensus 358 ~LGnIrFIGELfk~~mL~e~Ii~~cI~~LL~~~~~---~~p~Ee~IEcLc~LL~tiGk~Ld~~~k~~~~mD~yF~rL~~l 434 (811)
+.|+++||||||+.+++++++|++|+..|+..... ..+++++|||+|.+|.+||+.|+.....+..|+.||..++.+
T Consensus 103 ~~~~~~fl~eL~~~~vv~~~~i~~~l~~ll~~~~~~~~~~~~~~~ie~~~~lL~~~G~~l~~~~~~~~~l~~~~~~~~~~ 182 (209)
T PF02854_consen 103 RRGNIRFLAELFNFGVVSEKIIFDILRELLSDGTDECQPPPDEENIECLCTLLKTCGKKLENSEESPKALDEIFERLQKY 182 (209)
T ss_dssp HHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHTSHHCCHHTCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH
T ss_pred HhhhhhHHHhhHhhccccchhHHHHHHHHHhcccccccCCCcHhHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHH
Confidence 99999999999999999999999999999986421 125679999999999999999994445667899999999999
Q ss_pred hhC---CCCChHHHHHHHHHHHHHhCC
Q 003543 435 TTN---SQLVPRLRFMIHDVLDLRANN 458 (811)
Q Consensus 435 ~~~---~~lSsRIRFmI~dvIdLR~n~ 458 (811)
..+ +.+++|+||||++++|+|+||
T Consensus 183 ~~~~~~~~~~~r~~~~l~~l~~lr~~~ 209 (209)
T PF02854_consen 183 ANSKKDPNLSSRIRFMLEDLIELRNNK 209 (209)
T ss_dssp HHHCHSSSSSHHHHHHHHHHHHHHHTC
T ss_pred HHhhcccCCCHHHHHHHHHHHHHhcCC
Confidence 887 799999999999999999986
No 3
>smart00543 MIF4G Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)
Probab=99.95 E-value=9.4e-27 Score=234.26 Aligned_cols=194 Identities=37% Similarity=0.609 Sum_probs=166.2
Q ss_pred HHHHHHhhcCChhhHHHHHHHHHHccCCchhhhhhhhhhhccchhhHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHhhc
Q 003543 200 KTVKGILNKLTPEKFDVLKGQLIDSGITTPDILKVTITHLECHNLLQVIIFLYSIFFLLKLRSLFAFQGVIELIFDKAVL 279 (811)
Q Consensus 200 r~Vk~iLNKLTpenFd~l~~ql~~~~i~~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~VI~lIfeKAi~ 279 (811)
++|+++|||||++||+.++++|..+.+.+.+..+ .+++.||++|+.
T Consensus 2 ~~v~~~lnkLs~~n~~~~~~~l~~~~~~~~~~~~----------------------------------~l~~~i~~~~~~ 47 (200)
T smart00543 2 KKVKGLINKLSPSNFESIIKELLKLNNSDKNLRK----------------------------------YILELIFEKAVE 47 (200)
T ss_pred hHHHHHHhhCCHHHHHHHHHHHHHHHccCHHHHH----------------------------------HHHHHHHHHHHc
Confidence 6899999999999999999999998877655554 899999999999
Q ss_pred CCCchHHHHHHHHHHhhhCCCCCCCCCCCcchhHHHHHHHHHHHHHhhhhhhHHHHhhcCChHHHHHHHHHHHHHHHhhh
Q 003543 280 EPTFCPMYALLCSDLNEKLPPFPSDEPGGKDITFKRILLNHCQEAFEGADNTRAEIRQMTAPEQEMERMDQERLVKLRTL 359 (811)
Q Consensus 280 Ep~fs~mYA~LC~~L~~~l~~~~~~e~~gk~~~FRrlLLnrcQeeFe~~~~~~~ei~~l~~~e~E~E~~e~e~~~KrR~L 359 (811)
+|.|+.+||+||..|+...+ .|+..|++.|+++|++.-. ..+...++++.
T Consensus 48 ~~~~~~~ya~L~~~l~~~~~------------~f~~~ll~~~~~~f~~~~e------------------~~~~~~~~~~~ 97 (200)
T smart00543 48 EPNFIPAYARLCALLNAKNP------------DFGSLLLERLQEEFEKGLE------------------SEEESDKQRRL 97 (200)
T ss_pred CcchHHHHHHHHHHHHHHHH------------HHHHHHHHHHHHHHHHHHH------------------HHHHHhhhhHH
Confidence 99999999999999998742 6999999999999988511 00123457889
Q ss_pred hhHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCC--CCCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHhhC
Q 003543 360 GNIRLIGELLKQKMVPEKIVHHIVQELLENDGK--TCPAEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTTN 437 (811)
Q Consensus 360 GnIrFIGELfk~~mL~e~Ii~~cI~~LL~~~~~--~~p~Ee~IEcLc~LL~tiGk~Ld~~~k~~~~mD~yF~rL~~l~~~ 437 (811)
|+++||||||+.++++..++.+|+..|+..... ...++++|||+|.+|.+||+.|+. +..+..|+.+|..++....+
T Consensus 98 ~~i~fl~eL~~~~~i~~~~i~~~l~~ll~~~~~~~~~~~~~~ve~l~~lL~~~G~~l~~-~~~~~~~~~~l~~l~~~~~~ 176 (200)
T smart00543 98 GLVRFLGELYNFQVLTSKIILELLKELLNDLTKLDPPRSDFSVECLLSLLPTCGKDLER-EKSPKLLDEILERLQDYLLK 176 (200)
T ss_pred hHHHHHHHHHHcccCcHHHHHHHHHHHHhccCCCCCCCcHHHHHHHHHHHHHhhHHHcC-cccHHHHHHHHHHHHHHHhc
Confidence 999999999999999999999999999986311 113568999999999999999994 23456899999999999887
Q ss_pred C---CCChHHHHHHHHHHHHHhCC
Q 003543 438 S---QLVPRLRFMIHDVLDLRANN 458 (811)
Q Consensus 438 ~---~lSsRIRFmI~dvIdLR~n~ 458 (811)
. .+++|+||||+++++||++.
T Consensus 177 ~~~~~~~~r~~~~l~~l~~l~~~~ 200 (200)
T smart00543 177 KDKTELSSRLRFMLELLIELRKNK 200 (200)
T ss_pred ccccCCChHHHHHHHHHHHHhhCc
Confidence 6 79999999999999999863
No 4
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=99.88 E-value=1.5e-22 Score=188.46 Aligned_cols=113 Identities=35% Similarity=0.472 Sum_probs=110.4
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 003543 646 LRKKTVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTGCLL 725 (811)
Q Consensus 646 l~kki~sil~EY~~~~D~~EA~~cikEL~~p~~~~evV~~~I~~aLEkk~~erElvs~LL~~L~~~~lls~~q~~~Gf~~ 725 (811)
++|++..+|+||++++|.+||++||.+|+.|++|++||+.+|..+||+++.+|+.+++||.+|++.+++++++|..||..
T Consensus 1 ~~k~i~~~l~ey~~~~D~~ea~~~l~~L~~~~~~~~vv~~~i~~~le~~~~~~~~~~~Ll~~L~~~~~~~~~~~~~~f~~ 80 (113)
T smart00544 1 LKKKIFLIIEEYLSSGDTDEAVHCLLELKLPEQHHEVVKVLLTCALEEKRTYREMYSVLLSRLCQANVISTKQFEKGFWR 80 (113)
T ss_pred ChhHHHHHHHHHHHcCCHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCccHHHHHHHHHHHHHHcCCcCHHHHHHHHHH
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcchhhhcCCCchhHHHHHHHHHHHHcCCCC
Q 003543 726 YGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLD 758 (811)
Q Consensus 726 vle~LdDl~iDiP~A~~~La~fiaraV~dg~l~ 758 (811)
+++.++|+++|+|+++.++|+|+|++|.+|+||
T Consensus 81 ~~~~l~dl~~D~P~a~~~la~~~a~~v~~~~l~ 113 (113)
T smart00544 81 LLEDIEDLELDIPNAWRNLAEFVARLISDGILP 113 (113)
T ss_pred HHhhChhhhcccccHHHHHHHHHHHHHHcCCCC
Confidence 999999999999999999999999999999986
No 5
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=99.88 E-value=8e-23 Score=190.06 Aligned_cols=113 Identities=35% Similarity=0.537 Sum_probs=107.3
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 003543 646 LRKKTVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTGCLL 725 (811)
Q Consensus 646 l~kki~sil~EY~~~~D~~EA~~cikEL~~p~~~~evV~~~I~~aLEkk~~erElvs~LL~~L~~~~lls~~q~~~Gf~~ 725 (811)
++|++..+|.|||+++|.+||+.||+||+.|.+|++||+.+|..+||+++.+|+.++.||.+|++.++++.++|..||..
T Consensus 1 ~rk~i~~~l~ey~~~~d~~ea~~~l~el~~~~~~~~vv~~~l~~~le~~~~~r~~~~~Ll~~L~~~~~~~~~~~~~gf~~ 80 (113)
T PF02847_consen 1 LRKKIFSILMEYFSSGDVDEAVECLKELKLPSQHHEVVKVILECALEEKKSYREYYSKLLSHLCKRKLISKEQFQEGFED 80 (113)
T ss_dssp HHHHHHHHHHHHHHHT-HHHHHHHHHHTT-GGGHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHH
T ss_pred ChHHHHHHHHHHhcCCCHHHHHHHHHHhCCCccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 68999999999999999999999999999998899999999999999999999999999999999999999999999999
Q ss_pred HhhcchhhhcCCCchhHHHHHHHHHHHHcCCCC
Q 003543 726 YGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLD 758 (811)
Q Consensus 726 vle~LdDl~iDiP~A~~~La~fiaraV~dg~l~ 758 (811)
+++.++|+.+|+|++|+++|+|++++|.+|+||
T Consensus 81 ~l~~l~Dl~~D~P~~~~~la~~~~~~i~~~~lp 113 (113)
T PF02847_consen 81 LLESLEDLELDIPKAPEYLAKFLARLIADGILP 113 (113)
T ss_dssp HHHHHHHHHHHSTTHHHHHHHHHHHHHHTTSS-
T ss_pred HHhHhhhccccchHHHHHHHHHHHHHHHcCCcC
Confidence 999999999999999999999999999999986
No 6
>KOG0403 consensus Neoplastic transformation suppressor Pdcd4/MA-3, contains MA3 domain [Signal transduction mechanisms]
Probab=99.83 E-value=3.5e-20 Score=202.27 Aligned_cols=151 Identities=24% Similarity=0.360 Sum_probs=143.1
Q ss_pred CHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHHhCCCCCHHHHHH
Q 003543 642 NLADLRKKTVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGT 721 (811)
Q Consensus 642 s~EEl~kki~sil~EY~~~~D~~EA~~cikEL~~p~~~~evV~~~I~~aLEkk~~erElvs~LL~~L~~~~lls~~q~~~ 721 (811)
+...|++.+..||+|||.++|+.|.++|+++|+.|.|.+-|++.+|++|||+++.++|+++.||+.|+- .++|++++..
T Consensus 340 ~~r~Fkk~~~~IIqEYFlsgDt~Evi~~L~DLn~~E~~~~f~k~lITLAldrK~~ekEMasvllS~L~~-e~fsteDv~~ 418 (645)
T KOG0403|consen 340 NLRAFKKDLTPIIQEYFLSGDTPEVIRSLRDLNLPEYNPGFLKLLITLALDRKNSEKEMASVLLSDLHG-EVFSTEDVEK 418 (645)
T ss_pred HHHHHHHhhHHHHHHHHhcCChHHHHHHHHHcCCccccchHHHHHHHHHhccchhHHHHHHHHHHHhhc-ccCCHHHHHH
Confidence 366799999999999999999999999999999999999999999999999999999999999999998 5999999999
Q ss_pred HHHHHhhcchhhhcCCCchhHHHHHHHHHHHHcCCCChHHHHHHHhhhcchhHHHHHHHHHHHHHhcCCCch
Q 003543 722 GCLLYGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLDFIVLKEVLKKVEDNMFRRSIFTAAMKSIQSSPAGQ 793 (811)
Q Consensus 722 Gf~~vle~LdDl~iDiP~A~~~La~fiaraV~dg~l~~~~i~~~~~~~~d~~~~~~~l~~~l~~l~~~~~g~ 793 (811)
||..+|+.++|+++|+|.|++.||.|+||||.|++|.+..|+++...+.+..-.++.+..|-..|+...+|+
T Consensus 419 ~F~mLLesaedtALD~p~a~~elalFlARAViDdVLap~~leei~~~lp~~s~g~et~~~ArsLlsar~aGe 490 (645)
T KOG0403|consen 419 GFDMLLESAEDTALDIPRASQELALFLARAVIDDVLAPTNLEEISGTLPPVSQGRETLDKARSLLSARHAGE 490 (645)
T ss_pred HHHHHHhcchhhhccccccHHHHHHHHHHHHhhcccccCcHHHHcCCCCCchhhHHHHHHHHHHHHHhhccc
Confidence 999999999999999999999999999999999999999999999999888778888999988888876553
No 7
>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]
Probab=99.81 E-value=1.4e-19 Score=200.21 Aligned_cols=424 Identities=19% Similarity=0.256 Sum_probs=267.2
Q ss_pred HHHHHHHHHHHhhcCChhhHHHHHHHHHHccCCchhhhhhhhhhhccchhhHHHHHHHHHHHHHHhhhhhhHHHHHHHHH
Q 003543 195 KDRVLKTVKGILNKLTPEKFDVLKGQLIDSGITTPDILKVTITHLECHNLLQVIIFLYSIFFLLKLRSLFAFQGVIELIF 274 (811)
Q Consensus 195 ~e~l~r~Vk~iLNKLTpenFd~l~~ql~~~~i~~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~VI~lIf 274 (811)
+|.+.+.|.+|+||+|..|+..++.+|+..+|..+.. .+...|+
T Consensus 161 WEalkksInglInkvn~sNi~~ii~eLfqeNiirgRg------------------------------------l~crsv~ 204 (739)
T KOG2140|consen 161 WEALKKSINGLINKVNASNIQEIIRELFQENIIRGRG------------------------------------LLCRSVM 204 (739)
T ss_pred HHHHHHHhHHHHhhhhHHHHHHHHHHHHHHHHHhccc------------------------------------hhHHHHH
Confidence 4679999999999999999999999999988765544 4677888
Q ss_pred HHhhcCCCchHHHHHHHHHHhhhCCCCCCCCCCCcchhHHHHHHHHHHHHHhhhhhhHHHHhhcCChHHHHHHHHHHHHH
Q 003543 275 DKAVLEPTFCPMYALLCSDLNEKLPPFPSDEPGGKDITFKRILLNHCQEAFEGADNTRAEIRQMTAPEQEMERMDQERLV 354 (811)
Q Consensus 275 eKAi~Ep~fs~mYA~LC~~L~~~l~~~~~~e~~gk~~~FRrlLLnrcQeeFe~~~~~~~ei~~l~~~e~E~E~~e~e~~~ 354 (811)
+-....|.|+.+||.|++.|+.++|.+. .+||.+..-.|.+..+ ++.
T Consensus 205 ~aq~asp~ft~vyaALvAviNskfP~Ig------------ElLlkrLilqf~r~f~---------------------RnD 251 (739)
T KOG2140|consen 205 QAQAASPGFTPVYAALVAVINSKFPQIG------------ELLLKRLILQFKRSFR---------------------RND 251 (739)
T ss_pred HHHhcCCCCcHHHHHHHHHHccCCchHH------------HHHHHHHHHHHHHHhc---------------------ccc
Confidence 8888999999999999999999998663 2555555555666442 123
Q ss_pred HHhhhhhHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHH
Q 003543 355 KLRTLGNIRLIGELLKQKMVPEKIVHHIVQELLENDGKTCPAEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKEL 434 (811)
Q Consensus 355 KrR~LGnIrFIGELfk~~mL~e~Ii~~cI~~LL~~~~~~~p~Ee~IEcLc~LL~tiGk~Ld~~~k~~~~mD~yF~rL~~l 434 (811)
|..|+..++||++|++++|.+|.+..+++.-||+. |++++||.++.+|+.||.+|-... +..+|.+|++|+.|
T Consensus 252 k~~c~~~~kfiahLinq~VahEIv~Leil~lLLe~-----PTddSvevaI~flkecGakL~~VS--pr~~n~IfErlR~I 324 (739)
T KOG2140|consen 252 KVSCLNASKFIAHLINQQVAHEIVALEILTLLLER-----PTDDSVEVAIAFLKECGAKLAEVS--PRALNGIFERLRYI 324 (739)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-----CCCchHHHHHHHHHHHHHHHHHhC--hHHHhHHHHHHHHH
Confidence 45688889999999999999999999999999975 899999999999999999999753 35689999999999
Q ss_pred hhCCCCChHHHHHHHHHHHHHhCCCCccccccCcccHHHHHHHHHHhcCCCCchhhhhhcCCCCCCCCCCCCCCCCCCCC
Q 003543 435 TTNSQLVPRLRFMIHDVLDLRANNWVPRREEMKAKTITEIHSEAEKNLGLRPGATAMMRNGRTGATGGMGPGGFPIARPG 514 (811)
Q Consensus 435 ~~~~~lSsRIRFmI~dvIdLR~n~W~~r~~~~~pkti~eIh~Eae~~~~~~~~~~~~~r~~r~~~~g~~~pg~~~~~~p~ 514 (811)
+....++.|++|||+.++..|+.+++.. ..++..++-|.++..--+-+.-.... .... .=|.|.
T Consensus 325 Lhe~Eld~rvqy~iEtlf~iRkdkfk~~--p~v~~~LDlvee~dq~tH~l~l~de~----dpe~-----~L~vFk----- 388 (739)
T KOG2140|consen 325 LHEGELDRRVQYMIETLFQIRKDKFKSH--PAVLEELDLVEEEDQITHSLSLEDED----DPEK-----ELGVFK----- 388 (739)
T ss_pred HhHhhHHHHHHHHHHHHHHHHHHhhccC--CccccccCccchhhheeeeeeccccc----Chhh-----hhcccc-----
Confidence 9999999999999999999999999876 33455555555543211111000000 0000 000000
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCC-cc-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCcc
Q 003543 515 TGGMMPGMPGTQKMPGMPGFDTDNWE-VP-RSRTMPRGDSKSPSQFPGRVQSPLIGKSPSINSKFLPQGSGGIISGKTSA 592 (811)
Q Consensus 515 ~gg~~p~~~~~r~~p~~pg~~~d~~~-~~-~~~s~~r~~~~~~~~~~~~~~~~~~~k~~~~n~~~~p~gs~~~~sgk~sa 592 (811)
.|. +|+ .. ....- |.--.|+. .+.|.- .-.|++ -
T Consensus 389 -------------------~dp-~f~ene~kydai-kkeiLgn~--------------dsen~d-~~~~s~--------E 424 (739)
T KOG2140|consen 389 -------------------KDP-NFEENEEKYDAI-KKEILGNE--------------DSENED-DEDGSS--------E 424 (739)
T ss_pred -------------------cCc-cHHHHHHHHHHH-HHHHhcCC--------------cccccc-cccccc--------c
Confidence 000 110 00 00000 00000000 000000 000000 0
Q ss_pred ccCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhcCCCHHHHHHHHHH
Q 003543 593 LLQGSPTPSARPSGIASGVEPLTQYTKPVAPAASVVASPEKPSAPVTKLNLADLRKKTVSLLEEYFSIRILDEALQCVEE 672 (811)
Q Consensus 593 ll~~~~~p~~r~~~~~~~~~~~~q~~~~~k~~~~~p~~~~~~~~~~~~ls~EEl~kki~sil~EY~~~~D~~EA~~cikE 672 (811)
..+... -. + ..+. +-++ ..-.....+.-.|+++|=-.| -++-|.+||..-+--
T Consensus 425 ~~~eee----~e-~---~ee~------~e~~----------qI~D~T~~Nlv~frr~IYLti---~SSldfeEaaHKLLK 477 (739)
T KOG2140|consen 425 DDDEEE----DE-S---VEED------EEKL----------QIIDMTETNLVNFRRTIYLTI---QSSLDFEEAAHKLLK 477 (739)
T ss_pred cccccc----cc-c---cccc------cccc----------eeeccccchhHHhhhhheeee---eccCcHHHHHHHHHh
Confidence 000000 00 0 0000 0000 001122234556666552222 256799999999998
Q ss_pred hCCCCC-hHHHHHHHHHHHhcCCCCChHHHHHHHH-HHHhCCCCCHHHHHHHHHHHhhcchhhhcCCCchhHHHHHHHHH
Q 003543 673 LRAPTY-HPEVVKEAIALALEKIPPCVEPVIQLLE-FLLNKNVLTTRDIGTGCLLYGSLLDDIGIDLPKAPNNFGEMVGK 750 (811)
Q Consensus 673 L~~p~~-~~evV~~~I~~aLEkk~~erElvs~LL~-~L~~~~lls~~q~~~Gf~~vle~LdDl~iDiP~A~~~La~fiar 750 (811)
|+.|.- ..+++..+|.....-.. -+..-.||. .++.-+..=.+.|.+-|...++++.+++.+- -..||+|+|+
T Consensus 478 mkip~~q~~elc~mii~cc~QerT--y~kFYglL~eRfc~l~r~~q~~fe~~f~q~YstIhr~Etnk---LRnlakffah 552 (739)
T KOG2140|consen 478 MKIPESQEKELCNMIIDCCAQERT--YEKFYGLLGERFCMLHREWQEAFEKCFKQQYSTIHRYETNK---LRNLAKFFAH 552 (739)
T ss_pred ccCCchhhHHHHHHHHHHhhhHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHH---HHHHHHHHHH
Confidence 888764 47788777776543221 122222222 2332233456788999999999999998653 4569999999
Q ss_pred HHHcCCCChHHHHHHHhhhcch-----hHHHHHHHHHHHHH
Q 003543 751 LVVAKSLDFIVLKEVLKKVEDN-----MFRRSIFTAAMKSI 786 (811)
Q Consensus 751 aV~dg~l~~~~i~~~~~~~~d~-----~~~~~~l~~~l~~l 786 (811)
++.-+.||...++-+---=++. -|.+-+|.++.+.|
T Consensus 553 Llstd~lpw~vl~~ikLTEEdTtsssRIfiKilFqELve~l 593 (739)
T KOG2140|consen 553 LLSTDALPWDVLACIKLTEEDTTSSSRIFIKILFQELVEAL 593 (739)
T ss_pred HhcccccchHHHHHhhcccccCCccceehHHHHHHHHHHHh
Confidence 9999999998877552222222 26666677666655
No 8
>KOG0403 consensus Neoplastic transformation suppressor Pdcd4/MA-3, contains MA3 domain [Signal transduction mechanisms]
Probab=99.78 E-value=1.4e-18 Score=189.76 Aligned_cols=146 Identities=29% Similarity=0.385 Sum_probs=133.0
Q ss_pred HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHHhCCCCCHHHHHHH
Q 003543 643 LADLRKKTVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTG 722 (811)
Q Consensus 643 ~EEl~kki~sil~EY~~~~D~~EA~~cikEL~~p~~~~evV~~~I~~aLEkk~~erElvs~LL~~L~~~~lls~~q~~~G 722 (811)
.++++|+..+||+|||+.+|+.-|+.-++||.+..||+.||++++.+||||.+++.|+++-||+.||. -+|+++|+..|
T Consensus 46 l~dykk~~~sii~eyfstgdv~vaa~dl~elg~seyhpyfvkrlvsmamdrhdkekemasvlls~lya-dvi~p~qir~g 124 (645)
T KOG0403|consen 46 LSDYKKKAVSIIDEYFSTGDVVVAASDLKELGSSEYHPYFVKRLVSMAMDRHDKEKEMASVLLSALYA-DVIDPDQIRDG 124 (645)
T ss_pred HHHHHHHHHHHHHHHccCCCchhhHHHHHHhccccccHHHHHHHHHHHhhccchHHHHHHHHHHHHHH-HhcChHHHHHH
Confidence 67999999999999999999999999999999999999999999999999999999999999999999 79999999999
Q ss_pred HHHHhhcchhhhcCCCchhHHHHHHHHHHHHcCCCChHHHHHHHhhhcchhHHHHHHHHHHHHHhcC
Q 003543 723 CLLYGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLDFIVLKEVLKKVEDNMFRRSIFTAAMKSIQSS 789 (811)
Q Consensus 723 f~~vle~LdDl~iDiP~A~~~La~fiaraV~dg~l~~~~i~~~~~~~~d~~~~~~~l~~~l~~l~~~ 789 (811)
|.+++++.+|+++|||+|-+.||-||||||.|++||+.|+....+-+.+..-.-.++..+-+.+-+.
T Consensus 125 f~~ll~s~ddl~vdipdavnvlalfiaraivddilpp~fl~r~~k~lp~~skg~qV~~~aeksylsa 191 (645)
T KOG0403|consen 125 FIRLLESADDLAVDIPDAVNVLALFIARAIVDDILPPAFLKRAKKLLPDSSKGFQVINTAEKSYLSA 191 (645)
T ss_pred HHHHHHhcccceecCchHHHHHHHHHHHHHHHhccChHHHHHHHhhCCCcccchhHHHHHHhhccCC
Confidence 9999999999999999999999999999999999999999999887766544445555554444433
No 9
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=99.39 E-value=1e-11 Score=142.90 Aligned_cols=200 Identities=21% Similarity=0.276 Sum_probs=148.5
Q ss_pred HHHHHHHHHHhhcCChhhHHHHHHHHHHccCCchhhhhhhhhhhccchhhHHHHHHHHHHHHHHhhhhhhHHHHHHHHHH
Q 003543 196 DRVLKTVKGILNKLTPEKFDVLKGQLIDSGITTPDILKVTITHLECHNLLQVIIFLYSIFFLLKLRSLFAFQGVIELIFD 275 (811)
Q Consensus 196 e~l~r~Vk~iLNKLTpenFd~l~~ql~~~~i~~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~VI~lIfe 275 (811)
.++.|+|+|+||||+..|+.+|+..|-.+ |-.+.++.+.+ -+.-...
T Consensus 317 ~rl~rkv~g~LNKLSdaNi~~I~~~i~~L---------------------------y~~~sr~~v~~------sLtk~l~ 363 (822)
T KOG2141|consen 317 QRLRRKVNGSLNKLSDANIIKIIAGIAEL---------------------------YMNNSRYDVTS------SLTKLLL 363 (822)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------------------HHhcchhhHHH------HHHHHHH
Confidence 57999999999999999999998877654 44444444442 2222223
Q ss_pred HhhcC-----CCchHHHHHHHHHHhhhCCCCCCCCCCCcchhHHHHHHHHHHHHHhhhhhhHHHHhhcCChHHHHHHHHH
Q 003543 276 KAVLE-----PTFCPMYALLCSDLNEKLPPFPSDEPGGKDITFKRILLNHCQEAFEGADNTRAEIRQMTAPEQEMERMDQ 350 (811)
Q Consensus 276 KAi~E-----p~fs~mYA~LC~~L~~~l~~~~~~e~~gk~~~FRrlLLnrcQeeFe~~~~~~~ei~~l~~~e~E~E~~e~ 350 (811)
+|+.- -.+|..||-|...|..... ..|--.++....+.|-...+..+ ++...
T Consensus 364 ~~~~~~~~~ld~~~~~y~AL~~~l~~~vg-----------~eigahf~q~~ve~f~~~~~~~~----------~~~~~-- 420 (822)
T KOG2141|consen 364 KALLGPFRLLDSLLTTYAALAAMLHTMVG-----------NEIGAHFLQTFVEDFLKSYKEEE----------EMDLK-- 420 (822)
T ss_pred HHhhhhHHHHHHHHHHHHHHHHHHHHHHh-----------hHHHHHHHHHHHHHHHHHHHHHH----------hcccc--
Confidence 44443 3578999999999988753 23445677777777777653211 11111
Q ss_pred HHHHHHhhhhhHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHH
Q 003543 351 ERLVKLRTLGNIRLIGELLKQKMVPEKIVHHIVQELLENDGKTCPAEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSR 430 (811)
Q Consensus 351 e~~~KrR~LGnIrFIGELfk~~mL~e~Ii~~cI~~LL~~~~~~~p~Ee~IEcLc~LL~tiGk~Ld~~~k~~~~mD~yF~r 430 (811)
-+.+-+.+.|+++||+.+++...+|+++|..|..+ ++|-++|||..++..||..|-.++. ..+.+++..
T Consensus 421 ----~K~~~Nl~~~l~ylynF~ivs~~LiydiI~kl~~~-----l~e~~ve~ll~ii~~~G~~LRkDDp--~alk~~i~e 489 (822)
T KOG2141|consen 421 ----DKSLNNIVLFLSYLYNFGIVSCSLIYDIIRKLAEN-----LNETNVEALLTIIANCGFSLRKDDP--LALKDIITE 489 (822)
T ss_pred ----cchhhhHHHHHHHHHHhhcccHHHHHHHHHHHHhc-----hhhhhHHHHHHHHHHccchhcCCCh--HHHHHHHHH
Confidence 13577889999999999999999999999999986 6899999999999999999997543 456777777
Q ss_pred HHHHhhCCC---CChHHHHHHHHHHHHHhCCCCcc
Q 003543 431 LKELTTNSQ---LVPRLRFMIHDVLDLRANNWVPR 462 (811)
Q Consensus 431 L~~l~~~~~---lSsRIRFmI~dvIdLR~n~W~~r 462 (811)
|+....+.. .++|+|||+..++.|++|+-.+-
T Consensus 490 iq~~a~~a~~s~~~pR~rFmleti~aLKnN~~kki 524 (822)
T KOG2141|consen 490 IQSKAASAKISAISPRLRFMLETISALKNNKLKKI 524 (822)
T ss_pred HHHHhhcCCccccchHHHHHHHHHHHHhcCCCcCC
Confidence 777665533 47999999999999999876654
No 10
>KOG3942 consensus MIF4G domain-containing protein [Translation, ribosomal structure and biogenesis]
Probab=98.73 E-value=1e-07 Score=101.56 Aligned_cols=163 Identities=18% Similarity=0.134 Sum_probs=128.8
Q ss_pred HHHHHHHHHhhcCCCchHHHHHHHHHHhhhCCCCCCCCCCCcchhHHHHHHHHHHHHHhhhhhhHHHHhhcCChHHHHHH
Q 003543 268 GVIELIFDKAVLEPTFCPMYALLCSDLNEKLPPFPSDEPGGKDITFKRILLNHCQEAFEGADNTRAEIRQMTAPEQEMER 347 (811)
Q Consensus 268 ~VI~lIfeKAi~Ep~fs~mYA~LC~~L~~~l~~~~~~e~~gk~~~FRrlLLnrcQeeFe~~~~~~~ei~~l~~~e~E~E~ 347 (811)
.++-.|+.+||..-.|.-.-++||..|..... +.+.|+..||+.|++-|+-+..++.
T Consensus 169 rc~~~~~r~avegg~ggl~v~klC~n~~~~~~---------~gt~f~~~Lln~lrq~f~~r~gl~s-------------- 225 (348)
T KOG3942|consen 169 RCGPTIARQAVEGGGGGLFVCKLCTNLGSSWR---------NGTQFMDELLNLLRQGFLLRTGLSS-------------- 225 (348)
T ss_pred HHHHHHHHHHHhcCCCchhHHHHhhhhhhhhh---------ccchHHHHHHHHHHHhhccchhccc--------------
Confidence 67779999999999999999999998876531 2356999999999999998754321
Q ss_pred HHHHHHHHHhhhhhHHHHHHHHhcC-----CCCHHHHHHHHHHHhhcCCCCCCChhhHHHHHHHHHHHhhhhhcCCcchh
Q 003543 348 MDQERLVKLRTLGNIRLIGELLKQK-----MVPEKIVHHIVQELLENDGKTCPAEENVEAICQFFNTIGKQLDENPKSRR 422 (811)
Q Consensus 348 ~e~e~~~KrR~LGnIrFIGELfk~~-----mL~e~Ii~~cI~~LL~~~~~~~p~Ee~IEcLc~LL~tiGk~Ld~~~k~~~ 422 (811)
....|+++.|.|++|||-+- ++=..++..|++.|+..- +-.+..+|||...|...|..|++.- ..
T Consensus 226 -----~~~~rw~~fisfltelf~nlgs~p~~vL~~~l~~cl~~llrsp---d~~~~e~ecl~~~L~~~g~dle~ql--P~ 295 (348)
T KOG3942|consen 226 -----LASCRWWRFISFLTELFDNLGSCPQVVLQRSLRLCLQILLRSP---DWPEFEYECLSMKLAVEGLDLEKQL--PF 295 (348)
T ss_pred -----hhHHHHHHHHHHHHHHHhhcCCCChhhHHHHHHHHHHHHccCC---CcchHHHHHHHHHHHHcCccchhhh--hH
Confidence 13468999999999999874 556688999999999862 2357899999999999999999632 24
Q ss_pred hHHHHHHHHHHHhhCCCCC-hHHHHHHHHHHHHHhCCCCccc
Q 003543 423 VNDVYFSRLKELTTNSQLV-PRLRFMIHDVLDLRANNWVPRR 463 (811)
Q Consensus 423 ~mD~yF~rL~~l~~~~~lS-sRIRFmI~dvIdLR~n~W~~r~ 463 (811)
.|-.+|.-.++..-...-| .-+|.||..+|||.++.|.++.
T Consensus 296 ql~lL~~s~rDafL~~sep~a~~r~~lllliel~As~wqlpt 337 (348)
T KOG3942|consen 296 QLLLLFPSRRDAFLVRSEPLAPWRCPLLLLIELPASAWQLPT 337 (348)
T ss_pred HHHHHHHHHHHhhhccccccccccchhhhccccCccccCCCC
Confidence 5667777777655444433 3469999999999999999874
No 11
>KOG2051 consensus Nonsense-mediated mRNA decay 2 protein [RNA processing and modification]
Probab=98.68 E-value=2.3e-07 Score=111.53 Aligned_cols=152 Identities=22% Similarity=0.382 Sum_probs=112.1
Q ss_pred HHHHHHHHHhhcCCCchHHHHHHHHHHhhhCCCCCCCCCCCcchhHHHHHHHHHHHHHhhhhhhHHHHhhcCChHHHHHH
Q 003543 268 GVIELIFDKAVLEPTFCPMYALLCSDLNEKLPPFPSDEPGGKDITFKRILLNHCQEAFEGADNTRAEIRQMTAPEQEMER 347 (811)
Q Consensus 268 ~VI~lIfeKAi~Ep~fs~mYA~LC~~L~~~l~~~~~~e~~gk~~~FRrlLLnrcQeeFe~~~~~~~ei~~l~~~e~E~E~ 347 (811)
.+|..+|.---+.-.-...|++|++.|....|.+. .-|++....+|...-.... ++ +.|
T Consensus 462 rLvKal~~vprt~ldllPyYsRlVAtl~~~M~dva------------t~lv~~L~~eFr~~~hkK~---q~-----~ie- 520 (1128)
T KOG2051|consen 462 RLVKALFVVPRTRLDLLPYYSRLVATLSKCMPDVA------------TELVTMLRKEFRSHLHKKA---QI-----NIE- 520 (1128)
T ss_pred HHHHhhhcccchhhhhhhHHHHHHHHHHhhhhHHH------------HHHHHHHHHHHHHHHhhhh---hh-----hhh-
Confidence 67777776655666778999999999999887653 3577777778876432110 00 011
Q ss_pred HHHHHHHHHhhhhhHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHH
Q 003543 348 MDQERLVKLRTLGNIRLIGELLKQKMVPEKIVHHIVQELLENDGKTCPAEENVEAICQFFNTIGKQLDENPKSRRVNDVY 427 (811)
Q Consensus 348 ~e~e~~~KrR~LGnIrFIGELfk~~mL~e~Ii~~cI~~LL~~~~~~~p~Ee~IEcLc~LL~tiGk~Ld~~~k~~~~mD~y 427 (811)
..+-+|+|||||.|.++++..-+..|++.||... .-.+||.+|.||++||..|-.++.++-.|..+
T Consensus 521 ---------tk~~~VrfIsEL~KF~lv~~~~if~cLk~ll~dF-----~~hnIEm~c~lLE~~GrfLlr~pEt~lrM~~~ 586 (1128)
T KOG2051|consen 521 ---------TKLKIVRFISELCKFQLVPKFEIFSCLKMLLNDF-----THHNIEMACVLLESCGRFLLRSPETKLRMRVF 586 (1128)
T ss_pred ---------hhhhhhhhHHhhhhhCccChHHHHHHHHHHHHhc-----ccccHHHHHHHHHhcchhhhcChhHHHHHHHH
Confidence 1245799999999999999999999999998753 44579999999999999999988888788888
Q ss_pred HHHHHHHhhCCCCChHHHHHHHHHHHH
Q 003543 428 FSRLKELTTNSQLVPRLRFMIHDVLDL 454 (811)
Q Consensus 428 F~rL~~l~~~~~lSsRIRFmI~dvIdL 454 (811)
+++|+.......+.+|-.-+|.+++=+
T Consensus 587 Le~i~rkK~a~~lDsr~~~~iENay~~ 613 (1128)
T KOG2051|consen 587 LEQIKRKKRASALDSRQATLIENAYYL 613 (1128)
T ss_pred HHHHHHHHHHhhhchHHHHHHHHhHHh
Confidence 888885554455555555555554433
No 12
>KOG0401 consensus Translation initiation factor 4F, ribosome/mRNA-bridging subunit (eIF-4G) [Translation, ribosomal structure and biogenesis]
Probab=98.19 E-value=2.5e-07 Score=114.82 Aligned_cols=277 Identities=19% Similarity=0.191 Sum_probs=181.5
Q ss_pred CCCcccccccCCCcccc------CCC---Ch-----HHHHHHHHHHHhhcCChhhHHHHHHHHHHccCCchhhhhhhhhh
Q 003543 173 GPAPALIKAEVPWSARR------GNL---SE-----KDRVLKTVKGILNKLTPEKFDVLKGQLIDSGITTPDILKVTITH 238 (811)
Q Consensus 173 ~p~~~l~~~e~~w~~~~------~~~---~~-----~e~l~r~Vk~iLNKLTpenFd~l~~ql~~~~i~~~~~L~~~~~~ 238 (811)
...+++..+.+.|.+.. ..+ ++ .+.+.+.+++.+|++|+++|+.+...++.....+
T Consensus 588 eei~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~i~~~~~~~~~~~---------- 657 (970)
T KOG0401|consen 588 EEIAPEAPSANRWSPKSLSKKTEGRLAEESDSGLLGKEVVERKGKSGLRKLTPEMFDKISDPILDIADQS---------- 657 (970)
T ss_pred hhcchhhhhhcccCcccccccccccccccccccccCccccccccccccccCChhhcccccccccccchhh----------
Confidence 33467778888998742 111 11 1345789999999999999999998877542211
Q ss_pred hccchhhHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHhhcCCCchHHHHHHHHHHhhhCCCCCC---CCCCCcchhHHH
Q 003543 239 LECHNLLQVIIFLYSIFFLLKLRSLFAFQGVIELIFDKAVLEPTFCPMYALLCSDLNEKLPPFPS---DEPGGKDITFKR 315 (811)
Q Consensus 239 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~VI~lIfeKAi~Ep~fs~mYA~LC~~L~~~l~~~~~---~e~~gk~~~FRr 315 (811)
....+|.+...++..++.|+..+++|+.||+..|.........-.. .........+.+
T Consensus 658 -------------------~~e~~~~~~k~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~g~~~~~~~~~ 718 (970)
T KOG0401|consen 658 -------------------MDEEDGEASKQKGEQGGRKASDEQHFSSMRAPALEKVVPSLSSDIDDKRNRGSNGELLSDS 718 (970)
T ss_pred -------------------ccccccchhhhcccccccccCccccccccCCccccccccccccccccccccCCcccccccc
Confidence 1123344455899999999999999999999999887665431100 011122356788
Q ss_pred HHHHHHHHHHhhhhhhHHHHhhcCCh--HHHHHHHHHHHHHHHhhhhhHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCC
Q 003543 316 ILLNHCQEAFEGADNTRAEIRQMTAP--EQEMERMDQERLVKLRTLGNIRLIGELLKQKMVPEKIVHHIVQELLENDGKT 393 (811)
Q Consensus 316 lLLnrcQeeFe~~~~~~~ei~~l~~~--e~E~E~~e~e~~~KrR~LGnIrFIGELfk~~mL~e~Ii~~cI~~LL~~~~~~ 393 (811)
.+..+|+.+|.+.+.-+.-....... +.-.+..+....++++++|++ +......+.+.+..|++.|+...+... .
T Consensus 719 ~~~~~~~~~~~~~~~~~~~s~~~~~~~~e~~~~~~~~~~~~~~~~~~~v-~~~~~~~l~~~sk~l~ee~~~~~~~~~--~ 795 (970)
T KOG0401|consen 719 YLSARCHEEFENGWSRELPSGKDGEREPEMMSPEYYAAKAAKRAGLGLV-IALSSELLELLSKSLLEEFLSLRLEKE--A 795 (970)
T ss_pred ccchhhhhhccccccccCCCCcccccchhhcCcccchhhhhhccCCcch-hhhhHHHHHHHHHHHHHHHHHHhhhhh--h
Confidence 99999999999987421100000011 100012233456789999999 777777788899999999988766542 3
Q ss_pred CCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHh-h-C------CCCChHHHHHHHHHHHHHh-CCCCcccc
Q 003543 394 CPAEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELT-T-N------SQLVPRLRFMIHDVLDLRA-NNWVPRRE 464 (811)
Q Consensus 394 ~p~Ee~IEcLc~LL~tiGk~Ld~~~k~~~~mD~yF~rL~~l~-~-~------~~lSsRIRFmI~dvIdLR~-n~W~~r~~ 464 (811)
.+..+.++..|.++++||..++..-.....+..+..+|..++ . + -..+.+..|-+.|.+.++- ++|.--..
T Consensus 796 ~~~ie~l~S~~~~~~~v~~~v~~~l~~~~~~~~~~~~ll~~l~~~~~~~~~~~~~~~~~~~~~~~d~~~d~pk~w~~~~e 875 (970)
T KOG0401|consen 796 LKCIEELESPSLLLKTVGENIEPTLEKSPQAVEELLQLLDILVSKNPLSIETLEIGYREKFKLADDKELDLPKGWNYIKE 875 (970)
T ss_pred hhhhhcccchhhhHHHHHHhcCcccccChhHHHHHHHHHHHHHhcCcccHHHHhhhHHHHHhhhHHHhcccccchhHHHH
Confidence 467889999999999999999853322222333333332221 1 1 1346677777777777764 78887777
Q ss_pred ccCcccHHHHHHHHHHh
Q 003543 465 EMKAKTITEIHSEAEKN 481 (811)
Q Consensus 465 ~~~pkti~eIh~Eae~~ 481 (811)
..+|.+++.++.+.+..
T Consensus 876 ~~gp~~~~~~~~~~e~~ 892 (970)
T KOG0401|consen 876 FLGPLIHQKILDESELV 892 (970)
T ss_pred hhhhHhhhccccHHHHH
Confidence 77888888888776543
No 13
>KOG2051 consensus Nonsense-mediated mRNA decay 2 protein [RNA processing and modification]
Probab=97.53 E-value=0.0025 Score=77.94 Aligned_cols=103 Identities=17% Similarity=0.338 Sum_probs=79.8
Q ss_pred HHHHhhhhhHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCC-------CChh--hHHHHHHHHHHHhhhhhcCCcchhh
Q 003543 353 LVKLRTLGNIRLIGELLKQKMVPEKIVHHIVQELLENDGKTC-------PAEE--NVEAICQFFNTIGKQLDENPKSRRV 423 (811)
Q Consensus 353 ~~KrR~LGnIrFIGELfk~~mL~e~Ii~~cI~~LL~~~~~~~-------p~Ee--~IEcLc~LL~tiGk~Ld~~~k~~~~ 423 (811)
..+.|++.++|||||||+..|+...+|...+-.++--..... |.++ -|-.+|.||.|||..++. ..++..
T Consensus 722 ~~nQrriA~aryL~ELynfemvds~vIl~tLy~~i~~g~~~~~~~~~ldppddlFRirlV~~lL~tc~~yf~r-gs~kkk 800 (1128)
T KOG2051|consen 722 VSNQRRIALARYLGELYNFEMVDSDVILNTLYHLISLGHFENLTPSALDPPDDLFRIRLVCMLLQTCGPYFTR-GSTKKK 800 (1128)
T ss_pred HHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHhcccccCCCCcccCCChHHHHHHHHHHHHHHHccccccc-chhHHH
Confidence 456788999999999999999999999998888875321111 3332 678899999999999996 445667
Q ss_pred HHHHHHHHHHHhhCC--CCChHHHHHHHHHHHHHh
Q 003543 424 NDVYFSRLKELTTNS--QLVPRLRFMIHDVLDLRA 456 (811)
Q Consensus 424 mD~yF~rL~~l~~~~--~lSsRIRFmI~dvIdLR~ 456 (811)
|+.|+--.+...--+ ..|--+.++++|++.+-.
T Consensus 801 l~~fL~~fq~Y~~iKk~~~Pld~~~~f~d~~~~~r 835 (1128)
T KOG2051|consen 801 LDQFLVAFQRYILIKKSQQPLDMEYEFEDFLELVR 835 (1128)
T ss_pred HHHHHHHHHHHhhcccccCCCchhhhHHhhhhhcc
Confidence 888877777654333 378899999999998854
No 14
>KOG1104 consensus Nuclear cap-binding complex, subunit NCBP1/CBP80 [RNA processing and modification]
Probab=94.21 E-value=1.7 Score=52.63 Aligned_cols=161 Identities=16% Similarity=0.200 Sum_probs=113.1
Q ss_pred HHHHHHHHHhhcCCCchHHHHHHHHHHhhhCCCCCCCCCCCcchhHHHHHHHHHHHHHhhhhhhHHHHhhcCChHHHHHH
Q 003543 268 GVIELIFDKAVLEPTFCPMYALLCSDLNEKLPPFPSDEPGGKDITFKRILLNHCQEAFEGADNTRAEIRQMTAPEQEMER 347 (811)
Q Consensus 268 ~VI~lIfeKAi~Ep~fs~mYA~LC~~L~~~l~~~~~~e~~gk~~~FRrlLLnrcQeeFe~~~~~~~ei~~l~~~e~E~E~ 347 (811)
.+++.|-.=|+.-|.=+..||-|...|+.+-+.| -.-+++..-.+|...-+ ..
T Consensus 67 ~iL~~L~~ca~~lP~K~~~yaTLvgllN~kn~~f------------g~~~v~~~~~~~q~sl~------~~--------- 119 (759)
T KOG1104|consen 67 KILDILNTCAVYLPEKITAYATLVGLLNLKNFNF------------GGEFVEYMIEELQESLK------SG--------- 119 (759)
T ss_pred HHHHHHHHHHHHcccchhHHHHHHHHHhccchhh------------HHHHHHHHHHHHHHHhh------cC---------
Confidence 6888888899999999999999999998874433 22333333333332110 00
Q ss_pred HHHHHHHHHhhhhhHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCC-CCC---ChhhHHHHHHHHHHHhhhhhcCCcchhh
Q 003543 348 MDQERLVKLRTLGNIRLIGELLKQKMVPEKIVHHIVQELLENDGK-TCP---AEENVEAICQFFNTIGKQLDENPKSRRV 423 (811)
Q Consensus 348 ~e~e~~~KrR~LGnIrFIGELfk~~mL~e~Ii~~cI~~LL~~~~~-~~p---~Ee~IEcLc~LL~tiGk~Ld~~~k~~~~ 423 (811)
.-.+.-+.+||+..|++-+||...-|...+..|+..... ..| .+.-+-|+..-|--+|+.|.+. .+..
T Consensus 120 ------~~n~ar~llrfL~dL~~~~vl~~~sli~l~esl~~~~~e~~~Pqvr~D~~v~~vLs~lPw~g~el~e~--~~~~ 191 (759)
T KOG1104|consen 120 ------NWNEARYLLRFLSDLSNCHVLQADSLINLFESLLDAAIEENVPQVRRDYYVYCVLSSLPWFGRELNEK--KPTE 191 (759)
T ss_pred ------ChHHHHHHHHHHHHHhcCCccChHHHHHHHHHHHHHHHhhcCcchhhhHHHHHHHhccchhhhhhccc--chHH
Confidence 012344789999999999999998888888888874211 112 4557788888888999999863 3467
Q ss_pred HHHHHHHHHHHhhCCC---------------CCh--HHHHHHHHHHHHHhCCCCccc
Q 003543 424 NDVYFSRLKELTTNSQ---------------LVP--RLRFMIHDVLDLRANNWVPRR 463 (811)
Q Consensus 424 mD~yF~rL~~l~~~~~---------------lSs--RIRFmI~dvIdLR~n~W~~r~ 463 (811)
|+.++..++..+..++ ... =++.+...|..+|.|+|+-..
T Consensus 192 ~e~ll~~ie~Yl~~R~~shi~lL~vw~~~~~~~qeeyle~L~~qI~~lr~n~w~e~h 248 (759)
T KOG1104|consen 192 MEELLVYIEIYLKKRKKSHINLLNVWSGEPDHPQEEYLELLWAQIQKLRQNDWAENH 248 (759)
T ss_pred HHHHHHHHHHHHHHhcccccchhhcCCCCCCchHHHHHHHHHHHHHHHHhcCccccc
Confidence 8988888876553221 122 278899999999999999754
No 15
>PF12152 eIF_4G1: Eukaryotic translation initiation factor 4G1; InterPro: IPR022745 The eukaryotic initiation factor 4G (eIF4G) is the core of a multicomponent switch controlling gene expression at the level of translation initiation. It interacts with the small ribosomal subunit interacting protein, eIF3, and the eIF4E/cap-mRNA complex in order to load the ribosome onto mRNA during cap-dependent translation. This entry represents the eIF4E-binding domain of eIF4G []. Binding of this domain to its substrate triggers a coupled folding transition where it forms a right-handed helical ring that wraps around the N terminus of eIF4E.; PDB: 1RF8_B.
Probab=86.77 E-value=0.44 Score=42.06 Aligned_cols=26 Identities=27% Similarity=0.468 Sum_probs=15.6
Q ss_pred CCCccCCC-cccccCHHHHHHHHHHhh
Q 003543 55 GDLRFEGH-ERVRYTREQLLQLKEVAQ 80 (811)
Q Consensus 55 ~~~~~~~~-~~~~y~~~~l~~~~~~~~ 80 (811)
-|++.+.. -+.||.++|||||+.+|.
T Consensus 43 P~~~ln~~~~kf~Yd~~FLLQF~~v~~ 69 (75)
T PF12152_consen 43 PDPALNKAAKKFRYDPDFLLQFQDVFK 69 (75)
T ss_dssp SSTTGGGSS-SS---HHHHHHHHHHH-
T ss_pred CCHHHccccCccccCHHHHHHHHHHhc
Confidence 33344333 689999999999999993
No 16
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=79.80 E-value=18 Score=33.32 Aligned_cols=30 Identities=27% Similarity=0.453 Sum_probs=27.7
Q ss_pred HHHHHHHHHhhcC-CCchHHHHHHHHHHhhh
Q 003543 268 GVIELIFDKAVLE-PTFCPMYALLCSDLNEK 297 (811)
Q Consensus 268 ~VI~lIfeKAi~E-p~fs~mYA~LC~~L~~~ 297 (811)
.||..|++.++++ ..+..+|+.|...|...
T Consensus 36 ~vv~~~l~~~le~~~~~r~~~~~Ll~~L~~~ 66 (113)
T PF02847_consen 36 EVVKVILECALEEKKSYREYYSKLLSHLCKR 66 (113)
T ss_dssp HHHHHHHHHHHTSSHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHhhccHHHHHHHHHHHHHHHhc
Confidence 7999999999999 99999999999999874
No 17
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=76.64 E-value=30 Score=41.52 Aligned_cols=156 Identities=22% Similarity=0.313 Sum_probs=83.9
Q ss_pred HHHHHHHHHHhhcCChhhHHHHHHHHHHccC----CchhhhhhhhhhhccchhhHHHHHHHHHHHHHHhhhhhhHHHHHH
Q 003543 196 DRVLKTVKGILNKLTPEKFDVLKGQLIDSGI----TTPDILKVTITHLECHNLLQVIIFLYSIFFLLKLRSLFAFQGVIE 271 (811)
Q Consensus 196 e~l~r~Vk~iLNKLTpenFd~l~~ql~~~~i----~~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~VI~ 271 (811)
+-|...|+.+|..+|.+-|+.++.=|-.+.+ .+.+... .+++
T Consensus 177 ~~i~~~ikkvL~DVTaeEF~l~m~lL~~lk~~~~~~t~~g~q----------------------------------eLv~ 222 (556)
T PF05918_consen 177 EFIVDEIKKVLQDVTAEEFELFMSLLKSLKIYGGKQTIEGRQ----------------------------------ELVD 222 (556)
T ss_dssp HHHHHHHHHHCTT--HHHHHHHHHHHHTSGG---GSSHHHHH----------------------------------HHHH
T ss_pred HHHHHHHHHHHHhccHHHHHHHHHHHHhCccccccCChHHHH----------------------------------HHHH
Confidence 3477888999999999999888855545555 3443433 8999
Q ss_pred HHHHHhhcCC----CchHHHHHHHHHHhhhCCCCCCCCCCCcchhHHHHHHHHHHHHHhhhhhhHHHHhhcCChHHHHHH
Q 003543 272 LIFDKAVLEP----TFCPMYALLCSDLNEKLPPFPSDEPGGKDITFKRILLNHCQEAFEGADNTRAEIRQMTAPEQEMER 347 (811)
Q Consensus 272 lIfeKAi~Ep----~fs~mYA~LC~~L~~~l~~~~~~e~~gk~~~FRrlLLnrcQeeFe~~~~~~~ei~~l~~~e~E~E~ 347 (811)
+|.+.|--+. .....+.+|...+...+|-|.. +...+.|-.++.. +-|=.... + ++ +
T Consensus 223 ii~eQa~Ld~~f~~sD~e~Idrli~C~~~Alp~fs~---~v~Sskfv~y~~~---kvlP~l~~-------l--~e-~--- 283 (556)
T PF05918_consen 223 IIEEQADLDQPFDPSDPESIDRLISCLRQALPFFSR---GVSSSKFVNYMCE---KVLPKLSD-------L--PE-D--- 283 (556)
T ss_dssp HHHHHHTTTS---SSSHHHHHHHHHHHHHHGGG-BT---TB--HHHHHHHHH---HTCCCTT------------------
T ss_pred HHHHHhccCCCCCCcCHHHHHHHHHHHHHhhHHhcC---CCChHHHHHHHHH---HhcCChhh-------C--Ch-H---
Confidence 9999995333 3457888898888888875532 1233455555533 32222111 1 00 0
Q ss_pred HHHHHHHHHhhhhhHHHHHHHHhcC--CCCHHHHHHHHHHHhhcCC--CCCCC--hhhHHHHHHHHHHHhhh
Q 003543 348 MDQERLVKLRTLGNIRLIGELLKQK--MVPEKIVHHIVQELLENDG--KTCPA--EENVEAICQFFNTIGKQ 413 (811)
Q Consensus 348 ~e~e~~~KrR~LGnIrFIGELfk~~--mL~e~Ii~~cI~~LL~~~~--~~~p~--Ee~IEcLc~LL~tiGk~ 413 (811)
+.+-.++.++|+--.- +-...++-.+...|+.--. ...|+ --.||||.-.+..+|++
T Consensus 284 ---------~kl~lLk~lAE~s~~~~~~d~~~~L~~i~~~L~~ymP~~~~~~~l~fs~vEcLL~afh~La~k 346 (556)
T PF05918_consen 284 ---------RKLDLLKLLAELSPFCGAQDARQLLPSIFQLLKKYMPSKKTEPKLQFSYVECLLYAFHQLARK 346 (556)
T ss_dssp ---------HHHHHHHHHHHHHTT----THHHHHHHHHHHHHTTS----------HHHHHHHHHHHHHHHTT
T ss_pred ---------HHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHHHhCCCCCCCCcccchHhhHHHHHHHHHhhh
Confidence 1133556677766541 1122333233333332111 11122 24899999999888876
No 18
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=67.79 E-value=25 Score=32.52 Aligned_cols=30 Identities=30% Similarity=0.474 Sum_probs=26.8
Q ss_pred HHHHHHHHHhhcC-CCchHHHHHHHHHHhhh
Q 003543 268 GVIELIFDKAVLE-PTFCPMYALLCSDLNEK 297 (811)
Q Consensus 268 ~VI~lIfeKAi~E-p~fs~mYA~LC~~L~~~ 297 (811)
.|+..++.-++++ .+|..+|+.|...|++.
T Consensus 36 ~vv~~~i~~~le~~~~~~~~~~~Ll~~L~~~ 66 (113)
T smart00544 36 EVVKVLLTCALEEKRTYREMYSVLLSRLCQA 66 (113)
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHHHHHHHc
Confidence 7888999999988 58999999999999864
No 19
>PLN00131 hypothetical protein; Provisional
Probab=55.85 E-value=1.5e+02 Score=29.89 Aligned_cols=68 Identities=19% Similarity=0.251 Sum_probs=38.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHH-HHhcCCCCChHHHHHHHHHHHh
Q 003543 632 EKPSAPVTKLNLADLRKKTVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIA-LALEKIPPCVEPVIQLLEFLLN 710 (811)
Q Consensus 632 ~~~~~~~~~ls~EEl~kki~sil~EY~~~~D~~EA~~cikEL~~p~~~~evV~~~I~-~aLEkk~~erElvs~LL~~L~~ 710 (811)
+..+.++|.+.+.++..|-+..-+| ++.+-.+.+-.....+..+++. +.|| ++.+|.++-+|..||++
T Consensus 117 eqepepapplddqdlltkrkrvsee----------lrlllqigavkrknkiadqlldwmgld-netdrtllddlynhlyd 185 (218)
T PLN00131 117 EQEPEPAPPLDDQDLLTKRKRVSEE----------LRLLLQIGAVKRKNKIADQLLDWMGLD-NETDRTLLDDLYNHLYD 185 (218)
T ss_pred ccCCCCCCCCCcHHHHHHHHHHHHH----------HHHHHHHhhhhhhhHHHHHHHHHhccC-ccchHHHHHHHHHHHhh
Confidence 3344567778887776655543222 3333333332333445555554 3444 45678899999999987
No 20
>PF02854 MIF4G: MIF4G domain; InterPro: IPR003890 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 3", and is found in nuclear cap-binding proteins, eIF4G, and UPF2. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA. Nonsense-mediated mRNA decay (NMD) in eukaryotes involves UPF1, UPF2 and UPF3 to accelerate the decay rate of two unique classes of transcripts: (1) nonsense mRNAs that arise through errors in gene expression, and (2) naturally occurring transcripts that lack coding errors but have built-in features that target them for accelerated decay (error-free mRNAs). NMD can trigger decay during any round of translation and can target CBC-bound or eIF-4E-bound transcripts []. UPF2 contains MIF4G domains, while UPF3 contains an RNP domain []. ; GO: 0005515 protein binding, 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A 1HU3_A 3RK6_A ....
Probab=55.77 E-value=63 Score=32.12 Aligned_cols=121 Identities=12% Similarity=0.031 Sum_probs=70.8
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHhCCCC---ChHHHHHHHHHHHhcCCCCChHHHHHHHHHHHhCCC-CCHHHHHHHH
Q 003543 648 KKTVSLLEEYFSIRILDEALQCVEELRAPT---YHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNV-LTTRDIGTGC 723 (811)
Q Consensus 648 kki~sil~EY~~~~D~~EA~~cikEL~~p~---~~~evV~~~I~~aLEkk~~erElvs~LL~~L~~~~l-ls~~q~~~Gf 723 (811)
|+++.+|...- ..++++.+..+..+.... ....+|+.+++.+.+.. ......++|...|....- -=...+...+
T Consensus 2 r~v~~~lnklt-~~n~~~~~~~l~~~~~~~~~~~~~~i~~~i~~~a~~~~-~~~~~~a~l~~~l~~~~~~~f~~~ll~~~ 79 (209)
T PF02854_consen 2 RKVRGILNKLT-PSNFESIIDELIKLNWSDDPETLKEIVKLIFEKAVEEP-NFSPLYARLCAALNSRFPSEFRSLLLNRC 79 (209)
T ss_dssp HHHHHHHHHCS-STTHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHSG-GGHHHHHHHHHHHHHHCHHHHHHHHHHHH
T ss_pred chHHHHHHHCC-HHHHHHHHHHHHHHHhhccHHHHHHHHHHHhhhhhcCc-hHHHHHHHHHHHHhccchhhHHHHHHHHH
Confidence 45566665544 677777777777765443 34555555555555444 446677777777766322 1112233333
Q ss_pred HHHhhc------chhhhcCCCchhHHHHHHHHHHHHcCCCChHHHHHHHhhhc
Q 003543 724 LLYGSL------LDDIGIDLPKAPNNFGEMVGKLVVAKSLDFIVLKEVLKKVE 770 (811)
Q Consensus 724 ~~vle~------LdDl~iDiP~A~~~La~fiaraV~dg~l~~~~i~~~~~~~~ 770 (811)
...+.. +++..--.=.-..-+..|+|.+..-+.++...+-+++..+-
T Consensus 80 ~~~f~~~~~~~~~~~~~~~~~~~~~~~~~fl~eL~~~~vv~~~~i~~~l~~ll 132 (209)
T PF02854_consen 80 QEEFEERYSNEELEENRQSSKQRRRGNIRFLAELFNFGVVSEKIIFDILRELL 132 (209)
T ss_dssp HHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHH
T ss_pred HHHHHHhhhhhhHHHHHHHHHHHHhhhhhHHHhhHhhccccchhHHHHHHHHH
Confidence 333332 22222222234556788999999999999988888777653
No 21
>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]
Probab=52.98 E-value=71 Score=38.03 Aligned_cols=23 Identities=17% Similarity=0.166 Sum_probs=12.6
Q ss_pred hhhcccCCccccccCCCCCcccc
Q 003543 118 ARYLEADNRDWRTRSTTSGQEKS 140 (811)
Q Consensus 118 ~~~~~~~~~~~~~~~~~~~~~~~ 140 (811)
.+-.+.+.|+|+.|-..+...+|
T Consensus 75 ~s~~~~~~~~~~~R~~~~~~~~s 97 (739)
T KOG2140|consen 75 RSERESPVRSRSPRRSARSPSRS 97 (739)
T ss_pred cccccCCcccccccccCCCcccC
Confidence 33445667777777554443333
No 22
>PRK14703 glutaminyl-tRNA synthetase/YqeY domain fusion protein; Provisional
Probab=48.91 E-value=4.1e+02 Score=33.57 Aligned_cols=85 Identities=13% Similarity=0.058 Sum_probs=48.8
Q ss_pred ChHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcchhhhcCCCchhHHHHHHHHHHHHcCCCChHHHHHHHhhhcc-----
Q 003543 697 CVEPVIQLLEFLLNKNVLTTRDIGTGCLLYGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLDFIVLKEVLKKVED----- 771 (811)
Q Consensus 697 erElvs~LL~~L~~~~lls~~q~~~Gf~~vle~LdDl~iDiP~A~~~La~fiaraV~dg~l~~~~i~~~~~~~~d----- 771 (811)
.-+.++.|+ .|+..|.||.....+-|..+++.=. + ...+|...=...+-+...|+.+++++..
T Consensus 663 ~pe~LaeLv-~lV~~g~IS~~~AK~VL~~m~~~~~----~-------p~~IIee~GL~qisDe~~Le~iV~eVI~~NP~~ 730 (771)
T PRK14703 663 TPAALARLV-ALVDAGRISTRIAKDVLAELAASGG----D-------PEAIVEAKGLEQVSDAGALEPIVEEVLAAHPDK 730 (771)
T ss_pred CHHHHHHHH-HHHHcCCccHHHHHHHHHHHHhcCC----C-------HHHHHHhcCCcccCCHHHHHHHHHHHHHHCHHH
Confidence 347788886 5667799999999988888775411 1 1122222211112223445555544321
Q ss_pred --------hhHHHHHHHHHHHHHhcCCCch
Q 003543 772 --------NMFRRSIFTAAMKSIQSSPAGQ 793 (811)
Q Consensus 772 --------~~~~~~~l~~~l~~l~~~~~g~ 793 (811)
.....-++|.||+..+..=+++
T Consensus 731 Ve~yk~GK~kalgfLVGqVMK~tkGKAdP~ 760 (771)
T PRK14703 731 VAAYRAGKTKLLGFFVGQVMRETGGKANPQ 760 (771)
T ss_pred HHHHhcchHHHHHHHHHHHHHHhCCCCCHH
Confidence 3455777889998887653333
No 23
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=43.80 E-value=1.8e+02 Score=35.67 Aligned_cols=61 Identities=13% Similarity=0.110 Sum_probs=37.5
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHHhCCCCC
Q 003543 651 VSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLT 715 (811)
Q Consensus 651 ~sil~EY~~~~D~~EA~~cikEL~~p~~~~evV~~~I~~aLEkk~~erElvs~LL~~L~~~~lls 715 (811)
..+|+-|...|++++|...++++..+. .++...+..++-+.. ..+.+.+++..+...|+-.
T Consensus 263 n~Li~~y~k~g~~~~A~~vf~~m~~~~---~vt~n~li~~y~~~g-~~~eA~~lf~~M~~~g~~p 323 (697)
T PLN03081 263 CALIDMYSKCGDIEDARCVFDGMPEKT---TVAWNSMLAGYALHG-YSEEALCLYYEMRDSGVSI 323 (697)
T ss_pred HHHHHHHHHCCCHHHHHHHHHhCCCCC---hhHHHHHHHHHHhCC-CHHHHHHHHHHHHHcCCCC
Confidence 556777777888888888888776542 344444444444432 3455667777776655443
No 24
>PF05456 eIF_4EBP: Eukaryotic translation initiation factor 4E binding protein (EIF4EBP); InterPro: IPR008606 This family consists of several eukaryotic translation initiation factor 4E binding proteins (EIF4EBP1, -2 and -3). Translation initiation in eukaryotes is mediated by the cap structure (m7GpppN, where N is any nucleotide) present at the 5' end of all cellular mRNAs, except organellar. The cap is recognised by eukaryotic initiation factor 4F (eIF4F), which consists of three polypeptides, including eIF4E, the cap-binding protein subunit. The interaction of the cap with eIF4E facilitates the binding of the ribosome to the mRNA. eIF4E activity is regulated in part by translational repressors, 4E-BP1, 4E-BP2 and 4E-BP3 which bind to it and prevent its assembly into eIF4F [].; GO: 0008190 eukaryotic initiation factor 4E binding, 0045947 negative regulation of translational initiation; PDB: 2JGB_B 2V8Y_F 1WKW_B 3HXG_C 3U7X_D 3M94_C 3M93_C 2V8X_B 3HXI_C 2V8W_B ....
Probab=43.25 E-value=7.2 Score=37.35 Aligned_cols=21 Identities=29% Similarity=0.477 Sum_probs=8.6
Q ss_pred cCCCcccccCHHHHHHHHHHh
Q 003543 59 FEGHERVRYTREQLLQLKEVA 79 (811)
Q Consensus 59 ~~~~~~~~y~~~~l~~~~~~~ 79 (811)
.-++-||-|+|+|||++|..-
T Consensus 42 TPGGTRIIYdR~FLL~~RnSP 62 (116)
T PF05456_consen 42 TPGGTRIIYDRKFLLECRNSP 62 (116)
T ss_dssp ----------HHHHHCTCG--
T ss_pred ccCCcEEEEeHHHHHHhcCCC
Confidence 445679999999999999763
No 25
>PLN03218 maturation of RBCL 1; Provisional
Probab=41.19 E-value=1.5e+02 Score=38.77 Aligned_cols=67 Identities=9% Similarity=0.025 Sum_probs=38.5
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHhCCCCCh-HHHHHHHHHHHhcCCCCChHHHHHHHHHHHhCCCCCHH
Q 003543 650 TVSLLEEYFSIRILDEALQCVEELRAPTYH-PEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTR 717 (811)
Q Consensus 650 i~sil~EY~~~~D~~EA~~cikEL~~p~~~-~evV~~~I~~aLEkk~~erElvs~LL~~L~~~~lls~~ 717 (811)
...+|.-|...+++++|...++++...... ..++...+..++-+. ...+.+.+++..+...|+.+..
T Consensus 582 ynaLI~ay~k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~-G~~deAl~lf~eM~~~Gv~PD~ 649 (1060)
T PLN03218 582 VGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQK-GDWDFALSIYDDMKKKGVKPDE 649 (1060)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhc-CCHHHHHHHHHHHHHcCCCCCH
Confidence 456677777777777777777777543332 223344444444332 2345666777777666655443
No 26
>PF04844 Ovate: Transcriptional repressor, ovate; InterPro: IPR006458 This group of sequences contain an uncharacterised domain of about 70 residues found exclusively in plants, generally toward the C terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana (Mouse-ear cress). Other regions of these proteins tend to consist largely of low-complexity sequence. Function is not known.
Probab=41.17 E-value=67 Score=27.31 Aligned_cols=46 Identities=28% Similarity=0.418 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHHHHh--cCCCHHHHHHHHHHhCCCCChHHHHHHHHH
Q 003543 643 LADLRKKTVSLLEEYF--SIRILDEALQCVEELRAPTYHPEVVKEAIA 688 (811)
Q Consensus 643 ~EEl~kki~sil~EY~--~~~D~~EA~~cikEL~~p~~~~evV~~~I~ 688 (811)
-++|++.+..+|.|-- .-.+++|-+.|.-.||.|.+|..+|.-...
T Consensus 5 ~~DFr~SM~EMI~~~~i~~~~~LeeLL~cYL~LN~~~~H~~Iv~aF~d 52 (59)
T PF04844_consen 5 YEDFRESMVEMIEENGIRDWDDLEELLACYLSLNSPEHHKFIVEAFVD 52 (59)
T ss_pred HHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCChhhhhHHHHHHHH
Confidence 5688888888777764 335899999999999999888766655543
No 27
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=37.47 E-value=1.1e+02 Score=37.58 Aligned_cols=79 Identities=20% Similarity=0.317 Sum_probs=53.4
Q ss_pred HHHHHHHHHhhcCCCchHHHHHHHHHHhhhCCCCCCCCCCCcchhHHHHHHHHHHHHHhhhhhhHHHHhhcCChHHHHHH
Q 003543 268 GVIELIFDKAVLEPTFCPMYALLCSDLNEKLPPFPSDEPGGKDITFKRILLNHCQEAFEGADNTRAEIRQMTAPEQEMER 347 (811)
Q Consensus 268 ~VI~lIfeKAi~Ep~fs~mYA~LC~~L~~~l~~~~~~e~~gk~~~FRrlLLnrcQeeFe~~~~~~~ei~~l~~~e~E~E~ 347 (811)
.|+..|++=++.|-.|-..||-|+.++++.-..| ..+|.-.| |..-.+++.+
T Consensus 653 EI~~VllhC~l~EK~yNpfYa~lA~KfCe~~~~~--------~~tfQF~~-----------WD~f~ele~l--------- 704 (822)
T KOG2141|consen 653 EIARVLLHCCLNEKTYNPFYALLALKFCEFNKNL--------KKTFQFAL-----------WDRFKELEQL--------- 704 (822)
T ss_pred HHHHHHHHHHhhhcccchHHHHHHHHHHHHhhhh--------HHHHHHHH-----------HHHHHHhhhc---------
Confidence 7999999999999999999999999999863221 12332222 2221222221
Q ss_pred HHHHHHHHHhhhhhHHHHHHHHhcCCCCHHHHH
Q 003543 348 MDQERLVKLRTLGNIRLIGELLKQKMVPEKIVH 380 (811)
Q Consensus 348 ~e~e~~~KrR~LGnIrFIGELfk~~mL~e~Ii~ 380 (811)
...|.....+|+++|.....++-.|+.
T Consensus 705 ------s~~ri~nLa~l~a~Li~~~~lsLtVLK 731 (822)
T KOG2141|consen 705 ------SLFRISNLAKLLASLISNAVLSLTVLK 731 (822)
T ss_pred ------chhhHhHHHHHHHHHHHhcccceeeee
Confidence 123556678999999998888766655
No 28
>PRK05477 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated
Probab=37.41 E-value=3.9e+02 Score=31.78 Aligned_cols=32 Identities=9% Similarity=0.069 Sum_probs=25.5
Q ss_pred ChHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhc
Q 003543 697 CVEPVIQLLEFLLNKNVLTTRDIGTGCLLYGSL 729 (811)
Q Consensus 697 erElvs~LL~~L~~~~lls~~q~~~Gf~~vle~ 729 (811)
.-+.++.|+. |+..|.||..+..+-|..+++.
T Consensus 367 ~~~~l~~Li~-lv~~g~Is~~~ak~vl~~~~~~ 398 (474)
T PRK05477 367 TPEQLAELIK-LIDDGTISGKIAKEVFEEMLET 398 (474)
T ss_pred CHHHHHHHHH-HHHcCCccHHHHHHHHHHHHhc
Confidence 3467888874 6677999999999999988765
No 29
>PF08146 BP28CT: BP28CT (NUC211) domain; InterPro: IPR012954 This C-terminal domain is found in BAP28-like nucleolar proteins []. The bap28 mutation leads to abnormalities in the brain, starting at midsomitogenesis stages. Mutant zebrafish embryos display excessive apoptosis, especially in the central nervous system (CNS) that results in death. The mutation affects a gene that encodes a large protein with high similarity to the uncharacterised human protein BAP28 and lower similarity to yeast Utp10. Utp10 is a component of a nucleolar U3 small nucleolar RNA-containing RNP complex that is required for transcription of ribosomal DNA and for processing of 18 S rRNA. Zebrafish Bap28 is also required for rRNA transcription and processing, with a major effect on 18S rRNA maturation. Bap28 is therefore required for cell survival in the CNS through its role in rRNA synthesis and processing [].
Probab=36.32 E-value=1.7e+02 Score=29.16 Aligned_cols=109 Identities=17% Similarity=0.215 Sum_probs=61.9
Q ss_pred HHHHHHHHHHhhcCChhhHHHHHHHHHHccCCchhhhhhhhhhhccchhhHHHHHHHHHHHHHHhhhhhhHHHHHHHHHH
Q 003543 196 DRVLKTVKGILNKLTPEKFDVLKGQLIDSGITTPDILKVTITHLECHNLLQVIIFLYSIFFLLKLRSLFAFQGVIELIFD 275 (811)
Q Consensus 196 e~l~r~Vk~iLNKLTpenFd~l~~ql~~~~i~~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~VI~lIfe 275 (811)
+.+..-+-.+.=||+...|-.+..+|++|.......- ....-..=.+++| .++..+++
T Consensus 39 ~~v~~~~~~lV~KLnE~~FRPlF~~l~dWA~~~l~~~-------~~~~~~~R~itfy---------------~l~~~l~e 96 (153)
T PF08146_consen 39 SSVISAFVSLVLKLNEATFRPLFLKLVDWATSGLPKS-------DSSGSRARLITFY---------------RLLNALAE 96 (153)
T ss_pred HHHHHHHHHHHHHcccchhHhHHHHHHHHHcccCCcc-------cCcCchhHHHHHH---------------HHHHHHHH
Confidence 3466677788889999999999999999975410000 0000001145667 56777776
Q ss_pred --HhhcCCCchHHHHHHHHHHhhhCCCCCCCCCCCcchhHHHHHHHHHHHHHhhh
Q 003543 276 --KAVLEPTFCPMYALLCSDLNEKLPPFPSDEPGGKDITFKRILLNHCQEAFEGA 328 (811)
Q Consensus 276 --KAi~Ep~fs~mYA~LC~~L~~~l~~~~~~e~~gk~~~FRrlLLnrcQeeFe~~ 328 (811)
|.+--|-|+.+--..+..|...-..- .+...+....++.+|...+..|+..
T Consensus 97 ~LKslf~~Y~~~ll~~~~~~L~~~~~~~--~~~~~~~~~L~~~vL~~L~~~F~~D 149 (153)
T PF08146_consen 97 KLKSLFTPYFSYLLDNAVDLLKQFNSSK--TESKSKSWELWRLVLSTLQKCFLHD 149 (153)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhcc--ccchhhHHHHHHHHHHHHHHHHhhc
Confidence 44444444444444444443321100 0101123578888888888888764
No 30
>PF07817 GLE1: GLE1-like protein; InterPro: IPR012476 The members of this family are sequences that are similar to the human protein GLE1 (O75458 from SWISSPROT). This protein is localised at the nuclear pore complexes and functions in poly(A)+ RNA export to the cytoplasm []. ; GO: 0016973 poly(A)+ mRNA export from nucleus, 0005643 nuclear pore; PDB: 3PEV_B 3RRN_B 3PEU_B 3RRM_B.
Probab=35.42 E-value=6e+02 Score=27.43 Aligned_cols=181 Identities=17% Similarity=0.207 Sum_probs=93.4
Q ss_pred HHHHHHHHHHhhcCChh--hHHHHHHHHHHc--c--CCchhhhhhhhhhhccchhhHHHHHHHHHHHHHHhhhhhhHHHH
Q 003543 196 DRVLKTVKGILNKLTPE--KFDVLKGQLIDS--G--ITTPDILKVTITHLECHNLLQVIIFLYSIFFLLKLRSLFAFQGV 269 (811)
Q Consensus 196 e~l~r~Vk~iLNKLTpe--nFd~l~~ql~~~--~--i~~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~V 269 (811)
..+.|+|+.-+|.||.. .+.+++.+|.++ + +...+... ...++.. +|.+ ++..+
T Consensus 27 ~~~kr~I~~~vgQls~~~~qi~~i~~~i~~ll~~~~~~~~~~~~----~~~~~~~--~~~~--------------~l~~l 86 (256)
T PF07817_consen 27 FDLKRKINPKVGQLSNSSSQINRIINQISNLLSGQPVKSNDLQQ----SKNDHPL--AYKY--------------LLNFL 86 (256)
T ss_dssp HHHHHHHCCHHHC--SBHHHHHHHHHHHHHH----------HHT----TTT-SHH--HHHH--------------HHHHH
T ss_pred HHhhhhCcCcHhhccCcHHHHHHHHHHHHHHhhhhhhchhhhhh----hccCCch--HHHH--------------HHHHH
Confidence 45778888888999844 555666666654 1 11111100 0011111 2222 23356
Q ss_pred HHHHHHHhhc----CCCchHHHHHHHHHHhhhCCCCCCCCCCCcchhHHHHHHHHHHHH----H------hhhhhhHHHH
Q 003543 270 IELIFDKAVL----EPTFCPMYALLCSDLNEKLPPFPSDEPGGKDITFKRILLNHCQEA----F------EGADNTRAEI 335 (811)
Q Consensus 270 I~lIfeKAi~----Ep~fs~mYA~LC~~L~~~l~~~~~~e~~gk~~~FRrlLLnrcQee----F------e~~~~~~~ei 335 (811)
++.|...|-. .|..+.-||.++..|....|.| -.+|+.++... + ..... .++.
T Consensus 87 Ak~iv~Q~e~ev~~~~~~A~PlA~v~~~l~~~~p~~------------~dillA~l~k~Cp~~vP~~~~~~~~~~-~e~~ 153 (256)
T PF07817_consen 87 AKKIVSQAETEVSANPESAFPLARVAVQLWSQHPEF------------GDILLARLHKKCPYLVPKYPGFTCDQS-TEEY 153 (256)
T ss_dssp HHHHHHHHHHHHHH-GGGHHHHHHHHHHHHHHSTCH------------HHHHHHHHHHH-GGGG----T-----S-SHHH
T ss_pred HHHHHHHHHHHhccCCchhhhHHHHHHHHHHcCCcH------------HHHHHHHHHHcCceeEeecCcccCCCC-HHHH
Confidence 6666655544 6888888999999999887644 35666655443 1 11100 1111
Q ss_pred h-hcC---ChHHHHHHHHHHHHHHHhhhhhHHHHHHHHhcCC---------CCHHHHHHHHHHHhhcCCCCCC-ChhhHH
Q 003543 336 R-QMT---APEQEMERMDQERLVKLRTLGNIRLIGELLKQKM---------VPEKIVHHIVQELLENDGKTCP-AEENVE 401 (811)
Q Consensus 336 ~-~l~---~~e~E~E~~e~e~~~KrR~LGnIrFIGELfk~~m---------L~e~Ii~~cI~~LL~~~~~~~p-~Ee~IE 401 (811)
. .|. .++. .| .+...-.|+-|.+++-+-+..... .+-.--=..+..+|+.. | .+-...
T Consensus 154 ~k~lGyk~~~~~-~E---~~~~y~~Rm~Gi~~lyaAi~~~~~~~~~~~~~p~~~~~~W~wlAr~lN~~----p~~~~~~~ 225 (256)
T PF07817_consen 154 RKRLGYKRDDGG-WE---SEDQYLKRMTGIIRLYAAIIQTPPPKGQKTSNPHGLEHGWRWLARILNLP----PAPNITAT 225 (256)
T ss_dssp HHHTT--B-TTS-B-----HHHHHHHHHHHHHHHHHHHHS---CCCCTT-SS-THHHHHHHHHHHCS-----CC-HHHHH
T ss_pred HHHcCCccCCCC-cc---chHHHHHHHHHHHHHHHHHHhccCCcCCCCCCCCCcHHHHHHHHHHhCCC----CCcccHHH
Confidence 1 010 0000 11 112233688999999999887542 22222344566666642 3 456788
Q ss_pred HHHHHHHHHhhhhhcC
Q 003543 402 AICQFFNTIGKQLDEN 417 (811)
Q Consensus 402 cLc~LL~tiGk~Ld~~ 417 (811)
+|..+|+.+|..|-..
T Consensus 226 lL~~~Le~ag~~l~~~ 241 (256)
T PF07817_consen 226 LLHSFLEVAGFRLLQI 241 (256)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHH
Confidence 9999999999999863
No 31
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=33.49 E-value=2.8e+02 Score=27.34 Aligned_cols=95 Identities=11% Similarity=0.138 Sum_probs=59.0
Q ss_pred hhhHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCCh--hhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHhh
Q 003543 359 LGNIRLIGELLKQKMVPEKIVHHIVQELLENDGKTCPAE--ENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTT 436 (811)
Q Consensus 359 LGnIrFIGELfk~~mL~e~Ii~~cI~~LL~~~~~~~p~E--e~IEcLc~LL~tiGk~Ld~~~k~~~~mD~yF~rL~~l~~ 436 (811)
.+.|.-|+++.+.+-...+.....|..-|.+. +|.. -.+..|=.+++.||..+...-..+.+++. |.+++.
T Consensus 19 w~~ileicD~In~~~~~~k~a~rai~krl~~~---n~~v~l~AL~LLe~~vkNCG~~fh~evas~~Fl~e----l~kl~~ 91 (139)
T cd03567 19 WEAIQAFCEQINKEPEGPQLAVRLLAHKIQSP---QEKEALQALTVLEACMKNCGERFHSEVGKFRFLNE----LIKLVS 91 (139)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHHHHHcCC---CHHHHHHHHHHHHHHHHHcCHHHHHHHHhHHHHHH----HHHHhc
Confidence 45677788888877555554444444444431 1221 25556666777889988753223344444 444443
Q ss_pred C----CCCChHHHHHHHHHHHHHhCCCC
Q 003543 437 N----SQLVPRLRFMIHDVLDLRANNWV 460 (811)
Q Consensus 437 ~----~~lSsRIRFmI~dvIdLR~n~W~ 460 (811)
. +..+..|+-+|..+|......+.
T Consensus 92 ~k~~~~~~~~~Vk~kil~li~~W~~~f~ 119 (139)
T cd03567 92 PKYLGSRTSEKVKTKIIELLYSWTLELP 119 (139)
T ss_pred cccCCCCCCHHHHHHHHHHHHHHHHHhc
Confidence 2 45789999999999998876664
No 32
>TIGR01568 A_thal_3678 uncharacterized plant-specific domain TIGR01568. This model describes an uncharacterized domain of about 70 residues found exclusively in plants, generally toward the C-terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana. Other regions of these proteins tend to consist largely of low-complexity sequence.
Probab=32.56 E-value=1.3e+02 Score=26.15 Aligned_cols=47 Identities=23% Similarity=0.345 Sum_probs=35.9
Q ss_pred CHHHHHHHHHHHHHHHhc--C-CCHHHHHHHHHHhCCCCChHHHHHHHHH
Q 003543 642 NLADLRKKTVSLLEEYFS--I-RILDEALQCVEELRAPTYHPEVVKEAIA 688 (811)
Q Consensus 642 s~EEl~kki~sil~EY~~--~-~D~~EA~~cikEL~~p~~~~evV~~~I~ 688 (811)
+-++|++.+.++|.|-=- . .+++|-+.|.-.||.+.+|+.+|.-...
T Consensus 10 Py~DFr~SM~EMI~~~~i~~~w~~LeeLL~cYL~LN~~~~H~~Iv~AF~d 59 (66)
T TIGR01568 10 PYEDFRRSMEEMIEERELEADWKELEELLACYLDLNPKKSHRFIVRAFVD 59 (66)
T ss_pred hHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCchhhhHHHHHHHH
Confidence 367899988888887632 2 4689999999999999888766655443
No 33
>PRK14137 recX recombination regulator RecX; Provisional
Probab=31.86 E-value=6.1e+02 Score=26.45 Aligned_cols=99 Identities=11% Similarity=0.046 Sum_probs=57.1
Q ss_pred CCCCCCHHHHHHHHHHHHHHHhcCCCHHHHHH--HHHHhCCCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHHhCCCC
Q 003543 637 PVTKLNLADLRKKTVSLLEEYFSIRILDEALQ--CVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVL 714 (811)
Q Consensus 637 ~~~~ls~EEl~kki~sil~EY~~~~D~~EA~~--cikEL~~p~~~~evV~~~I~~aLEkk~~erElvs~LL~~L~~~~ll 714 (811)
....++.+|+..++....-.|++.++-.+... -|... .|.. +.+-..|..|...|+|
T Consensus 29 ~~~~~~~~e~~~~~~~~Al~~Ls~R~rS~~ELr~KL~~k---g~~~------------------e~Ie~vI~rL~e~gyL 87 (195)
T PRK14137 29 RRTPPTPDEAREALLAYAFRALAARAMTAAELRAKLERR---SEDE------------------ALVTEVLERVQELGYQ 87 (195)
T ss_pred ccCCCCHHHHHHHHHHHHHHHHhcchhhHHHHHHHHHhc---CCCH------------------HHHHHHHHHHHHcCCC
Confidence 45567899999999998888888887665432 22221 2333 4444555566666677
Q ss_pred CHHHHHHHHHHHhhcchhhhcCCCchhHHHHHHHHHHHHcCCCChHHHHHHHhhhc
Q 003543 715 TTRDIGTGCLLYGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLDFIVLKEVLKKVE 770 (811)
Q Consensus 715 s~~q~~~Gf~~vle~LdDl~iDiP~A~~~La~fiaraV~dg~l~~~~i~~~~~~~~ 770 (811)
+-..|...+.. --..- ...|-.-+...+|+...|++++..+.
T Consensus 88 DD~rfAe~~~~----------~k~~G----p~rI~~eL~qKGI~~~lI~~al~~~d 129 (195)
T PRK14137 88 DDAQVARAENS----------RRGVG----ALRVRQTLRRRGVEETLIEETLAARD 129 (195)
T ss_pred CHHHHHHHHHH----------hcCch----HHHHHHHHHHcCCCHHHHHHHHHhcC
Confidence 66666655410 00111 11344455556666666666666553
No 34
>PLN03218 maturation of RBCL 1; Provisional
Probab=31.50 E-value=2.6e+02 Score=36.51 Aligned_cols=65 Identities=12% Similarity=0.087 Sum_probs=40.8
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHhCCCCChH-HHHHHHHHHHhcCCCCChHHHHHHHHHHHhCCCCC
Q 003543 650 TVSLLEEYFSIRILDEALQCVEELRAPTYHP-EVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLT 715 (811)
Q Consensus 650 i~sil~EY~~~~D~~EA~~cikEL~~p~~~~-evV~~~I~~aLEkk~~erElvs~LL~~L~~~~lls 715 (811)
...+|.-|...+++++|...++++......+ .++..++..++-+. ...+.+.+++..+.+.|+-.
T Consensus 617 ynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~-G~~eeA~~l~~eM~k~G~~p 682 (1060)
T PLN03218 617 YTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHA-GDLDKAFEILQDARKQGIKL 682 (1060)
T ss_pred HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhC-CCHHHHHHHHHHHHHcCCCC
Confidence 4677888888888888888888886544332 34444444444433 23456666777776665543
No 35
>PF08044 DUF1707: Domain of unknown function (DUF1707); InterPro: IPR012551 This domain is found in a variety of actinomycetales proteins. All of the proteins containing this domain are hypothetical and probably membrane bound or associated. Currently, it is unclear to the function of this domain.
Probab=31.47 E-value=65 Score=26.64 Aligned_cols=45 Identities=20% Similarity=0.138 Sum_probs=36.2
Q ss_pred CCCChHHHHHHHHHHHhCCCCCHHHHHHHHHHHh-----hcchhhhcCCC
Q 003543 694 IPPCVEPVIQLLEFLLNKNVLTTRDIGTGCLLYG-----SLLDDIGIDLP 738 (811)
Q Consensus 694 k~~erElvs~LL~~L~~~~lls~~q~~~Gf~~vl-----e~LdDl~iDiP 738 (811)
++.+|+.+..+|...+..|-|+.+.|..=...++ ..|..+.-|+|
T Consensus 4 sd~dR~~~~~~L~~a~a~GrL~~~Ef~~R~~~a~~A~t~~eL~~l~~DLP 53 (53)
T PF08044_consen 4 SDADRERAVDLLRAAFAEGRLSLDEFDERLDAAYAARTRGELDALFADLP 53 (53)
T ss_pred cHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCcHHHHHHHHccCc
Confidence 5678999999999999999999999998777654 34555555555
No 36
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=30.94 E-value=1.5e+02 Score=25.22 Aligned_cols=54 Identities=20% Similarity=0.285 Sum_probs=40.4
Q ss_pred HHHHHHHHHhCCCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHHhCCCCCHHHHH
Q 003543 664 DEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIG 720 (811)
Q Consensus 664 ~EA~~cikEL~~p~~~~evV~~~I~~aLEkk~~erElvs~LL~~L~~~~lls~~q~~ 720 (811)
+....-+.+.. +.+++|..+|..+++++.....-+-..|..-.++|+-|.+|+.
T Consensus 19 ~~i~~~~~~~~---~~~evI~~ai~~a~~~~~~~~~Yi~~Il~~W~~~gi~T~e~~~ 72 (73)
T TIGR01446 19 EDLKYWLDEFG---NSPELIKEALKEAVSNNKANYKYIDAILNNWKNNGIKTVEDVE 72 (73)
T ss_pred HHHHHHHHHhC---CCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHcCCCCHHHHh
Confidence 33333444443 4489999999999987655567888999999999999988864
No 37
>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome. This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.
Probab=30.90 E-value=1.6e+02 Score=30.03 Aligned_cols=56 Identities=21% Similarity=0.198 Sum_probs=41.5
Q ss_pred CCCHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhCCC----CChHHHHHHHHHHHhcCCC
Q 003543 640 KLNLADLRKKTVSLLEEYFSIRILDEALQCVEELRAP----TYHPEVVKEAIALALEKIP 695 (811)
Q Consensus 640 ~ls~EEl~kki~sil~EY~~~~D~~EA~~cikEL~~p----~~~~evV~~~I~~aLEkk~ 695 (811)
.+-+++++.....+-+-|+.+||+++|++|+...... ...-.+.-.+|..++..++
T Consensus 29 n~~kesir~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d 88 (177)
T PF10602_consen 29 NLGKESIRMALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGD 88 (177)
T ss_pred ccchHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCC
Confidence 4567888888889999999999999999999986432 2234555666666666553
No 38
>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....
Probab=29.79 E-value=3.4e+02 Score=25.85 Aligned_cols=93 Identities=15% Similarity=0.116 Sum_probs=59.8
Q ss_pred CCHHHHHHHHHHHHHHHhcCC--CHHHHHHHHHHhCCCCCh--HHHHHHHHHHHhcCCCCChHHHHHHHHHHHhCCCCCH
Q 003543 641 LNLADLRKKTVSLLEEYFSIR--ILDEALQCVEELRAPTYH--PEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTT 716 (811)
Q Consensus 641 ls~EEl~kki~sil~EY~~~~--D~~EA~~cikEL~~p~~~--~evV~~~I~~aLEkk~~erElvs~LL~~L~~~~lls~ 716 (811)
-|.|||..+. ..||+.. |.=|+.+.+.+|..-+.. |.+|..++-.+ |.-.+-.++...|..+..+.--..
T Consensus 6 Et~eeF~ary----~~~F~~~~iD~we~rrglN~l~~~DlVP~P~ii~aALrAc--RRvND~a~AVR~lE~iK~K~~~~~ 79 (108)
T PF02284_consen 6 ETDEEFDARY----EKYFNRPDIDGWELRRGLNNLFGYDLVPEPKIIEAALRAC--RRVNDFALAVRILEGIKDKCGNKK 79 (108)
T ss_dssp --HHHHHHHH----HHHHH-TT--HHHHHHHHHHHTTSSB---HHHHHHHHHHH--HHTT-HHHHHHHHHHHHHHTTT-T
T ss_pred cCHHHHHHHH----HHHhCCccccHHHHHHHHHHHhccccCCChHHHHHHHHHH--HHhhhHHHHHHHHHHHHHHccChH
Confidence 4677777664 4588755 555888999998765543 66777776544 334456788899998877554444
Q ss_pred HHHHHHHHHHhhcchhhhcCCCc
Q 003543 717 RDIGTGCLLYGSLLDDIGIDLPK 739 (811)
Q Consensus 717 ~q~~~Gf~~vle~LdDl~iDiP~ 739 (811)
+++..=++++--.+++|.|+.|-
T Consensus 80 ~~Y~~~lqElkPtl~ELGI~t~E 102 (108)
T PF02284_consen 80 EIYPYILQELKPTLEELGIPTPE 102 (108)
T ss_dssp THHHHHHHHHHHHHHHHT---TT
T ss_pred HHHHHHHHHHhhHHHHhCCCCHH
Confidence 47777788888889999998874
No 39
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=29.38 E-value=4.9e+02 Score=25.73 Aligned_cols=109 Identities=15% Similarity=0.214 Sum_probs=68.7
Q ss_pred hhhHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCCh--hhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHhh
Q 003543 359 LGNIRLIGELLKQKMVPEKIVHHIVQELLENDGKTCPAE--ENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTT 436 (811)
Q Consensus 359 LGnIrFIGELfk~~mL~e~Ii~~cI~~LL~~~~~~~p~E--e~IEcLc~LL~tiGk~Ld~~~k~~~~mD~yF~rL~~l~~ 436 (811)
.+.|.=|+++.+.+-...+-...+|+.-|.+. +|.. -.+..|=.+++.||..+...-.++ .+.+.|..++.
T Consensus 18 w~~il~icD~I~~~~~~~k~a~ral~KRl~~~---n~~v~l~AL~LLe~~vkNCG~~fh~evask----~Fl~eL~kl~~ 90 (144)
T cd03568 18 WGLILDVCDKVKSDENGAKDCLKAIMKRLNHK---DPNVQLRALTLLDACAENCGKRFHQEVASR----DFTQELKKLIN 90 (144)
T ss_pred HHHHHHHHHHHhcCCccHHHHHHHHHHHHcCC---CHHHHHHHHHHHHHHHHHCCHHHHHHHhhH----HHHHHHHHHhc
Confidence 45677788888887666655555555555431 1221 256666667778888887532233 45566777766
Q ss_pred CCCCChHHHHHHHHHHHHHhCCCCccccccCcccHHHHHHHH
Q 003543 437 NSQLVPRLRFMIHDVLDLRANNWVPRREEMKAKTITEIHSEA 478 (811)
Q Consensus 437 ~~~lSsRIRFmI~dvIdLR~n~W~~r~~~~~pkti~eIh~Ea 478 (811)
.+ ....|+-+|..+|......+.. +...+-|.+++++-
T Consensus 91 ~~-~~~~Vk~kil~li~~W~~~f~~---~~~l~~i~~~y~~L 128 (144)
T cd03568 91 DR-VHPTVKEKLREVVKQWADEFKN---DPSLSLMSDLYKKL 128 (144)
T ss_pred cc-CCHHHHHHHHHHHHHHHHHhCC---CcccHHHHHHHHHH
Confidence 55 7889999999999987655542 22334566666654
No 40
>PF08876 DUF1836: Domain of unknown function (DUF1836); InterPro: IPR014975 This group of proteins are functionally uncharacterised.
Probab=28.90 E-value=38 Score=31.92 Aligned_cols=52 Identities=27% Similarity=0.110 Sum_probs=42.4
Q ss_pred cCCCCChHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcchhhhcCCCchhHH
Q 003543 692 EKIPPCVEPVIQLLEFLLNKNVLTTRDIGTGCLLYGSLLDDIGIDLPKAPNN 743 (811)
Q Consensus 692 Ekk~~erElvs~LL~~L~~~~lls~~q~~~Gf~~vle~LdDl~iDiP~A~~~ 743 (811)
++|-=.|++++.|+.--.-+.++|-+++.++|..+.....+-.++...||++
T Consensus 53 ~kKkYsr~qla~li~I~~lK~vlsi~dI~~ll~~~~~~~~~~~~~~~~~Y~~ 104 (105)
T PF08876_consen 53 IKKKYSREQLAYLIVISILKQVLSIDDIKKLLDLQFNNYEDDEISLEDAYNY 104 (105)
T ss_pred ccCccCHHHHHHHHHHHHHHccCCHHHHHHHHHHHHhcccccCCCHHHHHhc
Confidence 3444468999999988777899999999999999999987777777666654
No 41
>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.
Probab=28.35 E-value=5e+02 Score=24.56 Aligned_cols=93 Identities=15% Similarity=0.102 Sum_probs=67.3
Q ss_pred CCHHHHHHHHHHHHHHHhcCC--CHHHHHHHHHHhCCCCCh--HHHHHHHHHHHhcCCCCChHHHHHHHHHHHhCCCCCH
Q 003543 641 LNLADLRKKTVSLLEEYFSIR--ILDEALQCVEELRAPTYH--PEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTT 716 (811)
Q Consensus 641 ls~EEl~kki~sil~EY~~~~--D~~EA~~cikEL~~p~~~--~evV~~~I~~aLEkk~~erElvs~LL~~L~~~~lls~ 716 (811)
.|.|||..+-. -||+.- |.=|+.+.+.+|..=+.. |.+|..++-.+ |.-.+-.++...|..+..+.--..
T Consensus 3 Et~EeF~aRye----~~F~~~~iD~we~rr~mN~l~~~DlVP~P~ii~aaLrAc--RRvND~alAVR~lE~vK~K~~~~~ 76 (103)
T cd00923 3 ETDEEFDARYE----TYFNRPDIDGWELRRGLNNLFGYDLVPEPKVIEAALRAC--RRVNDFALAVRILEAIKDKCGAHK 76 (103)
T ss_pred ccHHHHHHHHH----HHhCCcCccHHHHHHHHHHHhccccCCCcHHHHHHHHHH--HHhhhHHHHHHHHHHHHHHccCch
Confidence 35677776654 488765 788999999988654432 67777777644 444466788899998875543466
Q ss_pred HHHHHHHHHHhhcchhhhcCCCc
Q 003543 717 RDIGTGCLLYGSLLDDIGIDLPK 739 (811)
Q Consensus 717 ~q~~~Gf~~vle~LdDl~iDiP~ 739 (811)
.++..-++++-..+++|.|+.|-
T Consensus 77 ~~y~~~lqeikp~l~ELGI~t~E 99 (103)
T cd00923 77 EIYPYILQEIKPTLKELGISTPE 99 (103)
T ss_pred hhHHHHHHHHhHHHHHHCCCCHH
Confidence 67888888888889999998874
No 42
>PF04286 DUF445: Protein of unknown function (DUF445); InterPro: IPR007383 This entry contains proteins of unknown function. They are predicted to be transmembrane proteins with 2 or 3 TM domains.
Probab=28.32 E-value=5.3e+02 Score=28.39 Aligned_cols=93 Identities=17% Similarity=0.134 Sum_probs=51.5
Q ss_pred CHHHHHHHHHHHHHHHhcCCCHHHHHHHH-HHhCCCCChHHHHHHHHHHHhcC--CCCChHHHHHHHHHHHhCCCCC--H
Q 003543 642 NLADLRKKTVSLLEEYFSIRILDEALQCV-EELRAPTYHPEVVKEAIALALEK--IPPCVEPVIQLLEFLLNKNVLT--T 716 (811)
Q Consensus 642 s~EEl~kki~sil~EY~~~~D~~EA~~ci-kEL~~p~~~~evV~~~I~~aLEk--k~~erElvs~LL~~L~~~~lls--~ 716 (811)
..+.+.+.+...+..++...+.......+ ..+-...++..++..++....+. ++..++.+.+++.....+..-+ .
T Consensus 102 ~~~~i~~~i~~~~~~~l~~~~~~~~~~~~l~~ll~~~~~~~l~~~il~~i~~~l~~~e~~~~I~~~i~~~~~~~~~~~~~ 181 (367)
T PF04286_consen 102 DQEKIAEFIEKNLRKKLSEIILAPLLQKLLRSLLEEEQHQKLLDRILEKIKEYLKSEETRERIRDLIEEFLEEYLGKSFL 181 (367)
T ss_pred hhHHHHHHHHHHHHHHHHHhccchhHHHHHHHHHhccchHHHHHHHHHHHHHHHcCchHHHHHHHHHHHHHHHhcccchh
Confidence 34455555555555555555555444333 44444455666666666544442 3555667777777777644333 6
Q ss_pred HHHHHHHHHH-hhcchhhh
Q 003543 717 RDIGTGCLLY-GSLLDDIG 734 (811)
Q Consensus 717 ~q~~~Gf~~v-le~LdDl~ 734 (811)
+.+...|... ...++++.
T Consensus 182 ~~l~~~i~~~l~~~l~~l~ 200 (367)
T PF04286_consen 182 DKLAEKIQDELDSLLEKLQ 200 (367)
T ss_pred hHHHHHHHHHHHHHHHHHH
Confidence 6666666654 44566665
No 43
>PF12854 PPR_1: PPR repeat
Probab=28.22 E-value=79 Score=23.20 Aligned_cols=25 Identities=24% Similarity=0.476 Sum_probs=22.4
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHhC
Q 003543 650 TVSLLEEYFSIRILDEALQCVEELR 674 (811)
Q Consensus 650 i~sil~EY~~~~D~~EA~~cikEL~ 674 (811)
...+|.-|...|.++||.+.++++.
T Consensus 10 y~~lI~~~Ck~G~~~~A~~l~~~M~ 34 (34)
T PF12854_consen 10 YNTLIDGYCKAGRVDEAFELFDEMK 34 (34)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHhCc
Confidence 4688999999999999999999873
No 44
>smart00543 MIF4G Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)
Probab=28.12 E-value=5.2e+02 Score=25.51 Aligned_cols=31 Identities=19% Similarity=0.271 Sum_probs=25.2
Q ss_pred chhHHHHHHHHHHHHcCCCChHHHHHHHhhh
Q 003543 739 KAPNNFGEMVGKLVVAKSLDFIVLKEVLKKV 769 (811)
Q Consensus 739 ~A~~~La~fiaraV~dg~l~~~~i~~~~~~~ 769 (811)
..+..+..|++.+..-+.++...+-+++..+
T Consensus 94 ~~~~~~i~fl~eL~~~~~i~~~~i~~~l~~l 124 (200)
T smart00543 94 QRRLGLVRFLGELYNFQVLTSKIILELLKEL 124 (200)
T ss_pred hhHHhHHHHHHHHHHcccCcHHHHHHHHHHH
Confidence 5567788999999999999988777776654
No 45
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=27.77 E-value=5.2e+02 Score=24.88 Aligned_cols=95 Identities=12% Similarity=0.136 Sum_probs=62.1
Q ss_pred hhhHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCCh--hhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHhh
Q 003543 359 LGNIRLIGELLKQKMVPEKIVHHIVQELLENDGKTCPAE--ENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTT 436 (811)
Q Consensus 359 LGnIrFIGELfk~~mL~e~Ii~~cI~~LL~~~~~~~p~E--e~IEcLc~LL~tiGk~Ld~~~k~~~~mD~yF~rL~~l~~ 436 (811)
...+..|+++.+..-...+-...+|+.-|+.. +|.. -.+..|=.+++.||..+...-.. ..++..|..++.
T Consensus 18 ~~~il~icd~I~~~~~~~k~a~raL~krl~~~---n~~vql~AL~lLd~~vkNcg~~f~~~i~s----~~fl~~l~~l~~ 90 (133)
T cd03561 18 WALNLELCDLINLKPNGPKEAARAIRKKIKYG---NPHVQLLALTLLELLVKNCGKPFHLQVAD----KEFLLELVKIAK 90 (133)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHHHHHhCChHHHHHHhh----HHHHHHHHHHhC
Confidence 35677889999888777676666676666642 1221 24555566666778877642211 245556677766
Q ss_pred CC-CCChHHHHHHHHHHHHHhCCCC
Q 003543 437 NS-QLVPRLRFMIHDVLDLRANNWV 460 (811)
Q Consensus 437 ~~-~lSsRIRFmI~dvIdLR~n~W~ 460 (811)
++ ..+..||-++..+|.-......
T Consensus 91 ~~~~~~~~Vk~kil~ll~~W~~~f~ 115 (133)
T cd03561 91 NSPKYDPKVREKALELILAWSESFG 115 (133)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHhc
Confidence 54 7899999999999987665444
No 46
>PF08321 PPP5: PPP5 TPR repeat region; InterPro: IPR013235 This domain is specific to the PPP5 subfamily of serine/threonine phosphatases.; GO: 0004722 protein serine/threonine phosphatase activity, 0046872 metal ion binding; PDB: 3ICF_B 3H60_B 3H63_A 3H66_A 3H62_B 1A17_A 1S95_B 3H69_A 3H68_D 3H64_D ....
Probab=27.48 E-value=38 Score=31.35 Aligned_cols=72 Identities=13% Similarity=0.214 Sum_probs=43.1
Q ss_pred CCHHHHHHHHHH------HhhcchhhhcCCCchhHHHHHHHHHHHHcCCCChHHHHHHHhhhcc-----hhHHHHHHHHH
Q 003543 714 LTTRDIGTGCLL------YGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLDFIVLKEVLKKVED-----NMFRRSIFTAA 782 (811)
Q Consensus 714 ls~~q~~~Gf~~------vle~LdDl~iDiP~A~~~La~fiaraV~dg~l~~~~i~~~~~~~~d-----~~~~~~~l~~~ 782 (811)
|-...|++|+.. +.+.++=-.++||..|+ ++-+.++-++.+||+.+++.+.+ -.|+-.++-++
T Consensus 9 ir~~~FekAI~~d~~~~s~~e~~d~~~i~Ve~sY~------GP~l~~~~it~efv~~mie~FK~~K~Lhkkyv~~Il~~~ 82 (95)
T PF08321_consen 9 IRRIAFEKAIAVDEEKKSVSESIDLESIDVEDSYD------GPRLEDEPITLEFVKAMIEWFKNQKKLHKKYVYQILLEA 82 (95)
T ss_dssp HHHHHHSHHHHHHHHHHSTTTS-TTSTT---SS--------SS--BTTB--HHHHHHHHHHHHCT----HHHHHHHHHHH
T ss_pred HHHHHHHHHhccCCcccCHHHhcCccceecCCCCC------CCCCCCCCCCHHHHHHHHHHHHhCCCccHHHHHHHHHHH
Confidence 334455555553 45555444577888765 66666689999999999986654 46888899999
Q ss_pred HHHHhcCCC
Q 003543 783 MKSIQSSPA 791 (811)
Q Consensus 783 l~~l~~~~~ 791 (811)
.+.++..|+
T Consensus 83 ~~llk~~Ps 91 (95)
T PF08321_consen 83 KKLLKQLPS 91 (95)
T ss_dssp HHHHHTS-S
T ss_pred HHHHHhCcC
Confidence 999988754
No 47
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=25.37 E-value=3.5e+02 Score=26.67 Aligned_cols=109 Identities=16% Similarity=0.198 Sum_probs=68.8
Q ss_pred hhhHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCCh--hhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHhh
Q 003543 359 LGNIRLIGELLKQKMVPEKIVHHIVQELLENDGKTCPAE--ENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTT 436 (811)
Q Consensus 359 LGnIrFIGELfk~~mL~e~Ii~~cI~~LL~~~~~~~p~E--e~IEcLc~LL~tiGk~Ld~~~k~~~~mD~yF~rL~~l~~ 436 (811)
.+.|.-|+++.+..-...+-...+|+.-|... +|.. -.++.|=.+++.||..+...-.. ..+.+.|..++.
T Consensus 22 w~~ileicD~In~~~~~~k~a~ral~krl~~~---n~~vql~AL~LLe~~vkNCG~~fh~evas----~~fl~~l~~l~~ 94 (142)
T cd03569 22 LASILEICDMIRSKDVQPKYAMRALKKRLLSK---NPNVQLYALLLLESCVKNCGTHFHDEVAS----REFMDELKDLIK 94 (142)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHHHcCC---ChHHHHHHHHHHHHHHHHCCHHHHHHHhh----HHHHHHHHHHHc
Confidence 46778889999887666665555555555531 2222 25666667777888888753222 345566777665
Q ss_pred CCCCChHHHHHHHHHHHHHhCCCCccccccCcccHHHHHHHH
Q 003543 437 NSQLVPRLRFMIHDVLDLRANNWVPRREEMKAKTITEIHSEA 478 (811)
Q Consensus 437 ~~~lSsRIRFmI~dvIdLR~n~W~~r~~~~~pkti~eIh~Ea 478 (811)
+ +.+.+|+-.|..+|.-....+... ..-.-+.+++++-
T Consensus 95 ~-~~~~~Vk~kil~li~~W~~~f~~~---~~l~~i~~~y~~L 132 (142)
T cd03569 95 T-TKNEEVRQKILELIQAWALAFRNK---PQLKYVVDTYQIL 132 (142)
T ss_pred c-cCCHHHHHHHHHHHHHHHHHhCCC---cccHHHHHHHHHH
Confidence 4 788999999999998877555422 1223455555543
No 48
>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA. It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.
Probab=25.10 E-value=4.7e+02 Score=23.77 Aligned_cols=64 Identities=17% Similarity=0.300 Sum_probs=42.8
Q ss_pred hhhhhHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHh
Q 003543 357 RTLGNIRLIGELLKQKMVPEKIVHHIVQELLENDGKTCPAEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELT 435 (811)
Q Consensus 357 R~LGnIrFIGELfk~~mL~e~Ii~~cI~~LL~~~~~~~p~Ee~IEcLc~LL~tiGk~Ld~~~k~~~~mD~yF~rL~~l~ 435 (811)
+-+-+|.||=+-.....++++....|--.|-. .|.++.-|+.+|.. +-+++-+..+|.+|+++.
T Consensus 21 ~qi~~I~~i~~~~~~~~l~~~l~~~a~lRl~~-------Pd~SL~EL~~~~~~--------~iSKSgvnhrlrKl~~ia 84 (85)
T PF02650_consen 21 KQIEAIEFIEENNGLDKLPEKLREFAELRLEN-------PDASLKELGELLEP--------PISKSGVNHRLRKLKKIA 84 (85)
T ss_dssp HHHHHHHHHHHHT-GGGS-HHHHHHHHHHHH--------TTS-HHHHHHTT----------T--HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcccccCCHHHHHHHHHHHHC-------ccccHHHHHHHHcC--------cCcHHHHHHHHHHHHHHh
Confidence 34668999999888889999988776655443 45677777776665 445677889999998875
No 49
>COG1421 CRISPR system related protein [Defense mechanisms]
Probab=24.79 E-value=1.6e+02 Score=29.19 Aligned_cols=60 Identities=25% Similarity=0.302 Sum_probs=44.6
Q ss_pred CCCHHHHHHHHHHH-------hhcchhhhcCCCchhHHHHHHHHHHHHcCCCC-hHHHHHHHhhhcch
Q 003543 713 VLTTRDIGTGCLLY-------GSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLD-FIVLKEVLKKVEDN 772 (811)
Q Consensus 713 lls~~q~~~Gf~~v-------le~LdDl~iDiP~A~~~La~fiaraV~dg~l~-~~~i~~~~~~~~d~ 772 (811)
-+|+.|+.+=+..+ .....+|.+|+|+..-.||.-++|.+..-.=. -.++++++.++.++
T Consensus 43 ~l~~~q~R~fy~~~~r~~~~~~~~~k~i~~~l~~m~~~lay~~gR~~~~~~e~lyevle~~idkid~D 110 (137)
T COG1421 43 NLTTTQLRKFYDYILRIDEENENSWKEIVLDLPKMKPQLAYAVGRDGKEALEGLYEVLEEMIDKIDDD 110 (137)
T ss_pred cCcHHHHHHHHHHHHHHhHhccCcHHHHHHHHHHHHHHHHHHHhhcchhhHHHHHHHHHHHHHHhhhh
Confidence 58888888777766 45568999999999998888888877653211 25677888888443
No 50
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=24.66 E-value=4.1e+02 Score=32.52 Aligned_cols=62 Identities=11% Similarity=0.014 Sum_probs=41.9
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHHhCCCCC
Q 003543 650 TVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLT 715 (811)
Q Consensus 650 i~sil~EY~~~~D~~EA~~cikEL~~p~~~~evV~~~I~~aLEkk~~erElvs~LL~~L~~~~lls 715 (811)
...+|.=|...+++++|...+.++..|.. +....+..++-+. ..-+.+..++..+...|+-.
T Consensus 161 ~n~Li~~y~k~g~~~~A~~lf~~m~~~~~---~t~n~li~~~~~~-g~~~~A~~lf~~M~~~g~~p 222 (697)
T PLN03081 161 MNRVLLMHVKCGMLIDARRLFDEMPERNL---ASWGTIIGGLVDA-GNYREAFALFREMWEDGSDA 222 (697)
T ss_pred HHHHHHHHhcCCCHHHHHHHHhcCCCCCe---eeHHHHHHHHHHC-cCHHHHHHHHHHHHHhCCCC
Confidence 35678889999999999999999877642 3344444444443 23456778888887766543
No 51
>PLN03077 Protein ECB2; Provisional
Probab=24.65 E-value=3.1e+02 Score=34.45 Aligned_cols=63 Identities=19% Similarity=0.194 Sum_probs=42.2
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHHhCCCCC
Q 003543 649 KTVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLT 715 (811)
Q Consensus 649 ki~sil~EY~~~~D~~EA~~cikEL~~p~~~~evV~~~I~~aLEkk~~erElvs~LL~~L~~~~lls 715 (811)
....+|.=|...|++++|...++++..|.. +....+..++-+.. .-+.+.+++..+...|+-.
T Consensus 325 ~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~---~s~n~li~~~~~~g-~~~~A~~lf~~M~~~g~~P 387 (857)
T PLN03077 325 VCNSLIQMYLSLGSWGEAEKVFSRMETKDA---VSWTAMISGYEKNG-LPDKALETYALMEQDNVSP 387 (857)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHhhCCCCCe---eeHHHHHHHHHhCC-CHHHHHHHHHHHHHhCCCC
Confidence 347788889999999999999999876642 33444444444433 3466777777776666543
No 52
>COG5537 IRR1 Cohesin [Cell division and chromosome partitioning]
Probab=24.14 E-value=1e+03 Score=29.34 Aligned_cols=137 Identities=12% Similarity=0.083 Sum_probs=88.0
Q ss_pred HHHHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHHhCCCCCHHHHHHHH
Q 003543 644 ADLRKKTVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTGC 723 (811)
Q Consensus 644 EEl~kki~sil~EY~~~~D~~EA~~cikEL~~p~~~~evV~~~I~~aLEkk~~erElvs~LL~~L~~~~lls~~q~~~Gf 723 (811)
+.++..+..+|.-+++..--..|++-+-| .|-..+++.+.--.+..|-+..+++.+|...|+|+...+..-.
T Consensus 328 ~~vRl~v~Kil~~L~s~~p~~d~ir~f~e--------RFk~rILE~~r~D~d~VRi~sik~l~~lr~lg~L~~SeIlIvs 399 (740)
T COG5537 328 EGVRLLVSKILLFLCSRIPHTDAIRRFVE--------RFKDRILEFLRTDSDCVRICSIKSLCYLRILGVLSSSEILIVS 399 (740)
T ss_pred HHHHHHHHHHHHHHHhcCCcchHHHHHHH--------HHHHHHHHHHhhccchhhHHHHHHHHHHHHhcccchhHHHHHH
Confidence 45666666677666655444444433322 3444444444433455678889999999999999999888777
Q ss_pred HHHhhcchhhhcCCCchhHHHHHHHHHHHHcCCCChHHHHHHHhhhc---chhH--HHHHHHHHHHHHhc
Q 003543 724 LLYGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLDFIVLKEVLKKVE---DNMF--RRSIFTAAMKSIQS 788 (811)
Q Consensus 724 ~~vle~LdDl~iDiP~A~~~La~fiaraV~dg~l~~~~i~~~~~~~~---d~~~--~~~~l~~~l~~l~~ 788 (811)
.-+++..+|--+-+-.+.+.++++.|+.|.+.+=-......++..+. ..+| .-.+|..+++.++.
T Consensus 400 scmlDi~pd~r~~~~E~v~~icK~~aevikEKipl~~k~n~lL~a~~qgse~~f~v~~~iFsr~~~llk~ 469 (740)
T COG5537 400 SCMLDIIPDSRENIVESVESICKIDAEVIKEKIPLATKTNRLLEAMKQGSERYFVVCEEIFSRFVHLLKK 469 (740)
T ss_pred HHHhcCCCcchHHHHHHHHHHHHHHHHHHHhhcchhhhhhhHHHHHHhhhhccchhHHHHHHHHHHHHHH
Confidence 77888777765557788999999999999844322222233333332 2344 55667777777654
No 53
>PF10884 DUF2683: Protein of unknown function (DUF2683); InterPro: IPR020271 This entry contains proteins with no known function.
Probab=23.56 E-value=2e+02 Score=26.01 Aligned_cols=44 Identities=11% Similarity=0.339 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHH-----HhCCCCChHHHHHHHHHHH
Q 003543 647 RKKTVSLLEEYFSIRILDEALQCVE-----ELRAPTYHPEVVKEAIALA 690 (811)
Q Consensus 647 ~kki~sil~EY~~~~D~~EA~~cik-----EL~~p~~~~evV~~~I~~a 690 (811)
.+++-.|++-=|+..|..+|+.-+- ++..|.+.|+||+++....
T Consensus 12 ~n~ilnIiKaky~lkdks~aId~~ieeye~~~lEpElkPEfVeki~~i~ 60 (80)
T PF10884_consen 12 TNQILNIIKAKYNLKDKSAAIDKIIEEYEEKILEPELKPEFVEKIKKIM 60 (80)
T ss_pred chHHHHHHHHHhCCchHHHHHHHHHHHHHHHhcccccCHHHHHHHHHHH
Confidence 4678899999999999999986443 4567899999999998854
No 54
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=23.33 E-value=91 Score=21.39 Aligned_cols=26 Identities=19% Similarity=0.289 Sum_probs=22.5
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHhCCC
Q 003543 651 VSLLEEYFSIRILDEALQCVEELRAP 676 (811)
Q Consensus 651 ~sil~EY~~~~D~~EA~~cikEL~~p 676 (811)
..+|.-|...++.++|...+.++...
T Consensus 4 n~li~~~~~~~~~~~a~~~~~~M~~~ 29 (35)
T TIGR00756 4 NTLIDGLCKAGRVEEALELFKEMLER 29 (35)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHc
Confidence 57889999999999999999998543
No 55
>PTZ00009 heat shock 70 kDa protein; Provisional
Probab=23.16 E-value=3.4e+02 Score=33.36 Aligned_cols=79 Identities=9% Similarity=0.186 Sum_probs=40.7
Q ss_pred CChhhHHHHHHHHHHHhhhhhc---CCcchhhHHHHHHHHHHHhhC----CCCChHHHHHHHHHHHHHhCCCCccccccC
Q 003543 395 PAEENVEAICQFFNTIGKQLDE---NPKSRRVNDVYFSRLKELTTN----SQLVPRLRFMIHDVLDLRANNWVPRREEMK 467 (811)
Q Consensus 395 p~Ee~IEcLc~LL~tiGk~Ld~---~~k~~~~mD~yF~rL~~l~~~----~~lSsRIRFmI~dvIdLR~n~W~~r~~~~~ 467 (811)
.++++++.+.+.+...-..-.. ....+..++.|.-.++..+.. ..++..-|--|.+.++--. .|.... .
T Consensus 512 ls~~~i~~~~~~~~~~~~~d~~~~~~~eakN~lEs~Iy~~r~~L~~~~~~~~~t~ee~~~l~~~l~~~~-~wL~~~---~ 587 (653)
T PTZ00009 512 LSKADIDRMVNEAEKYKAEDEANRERVEAKNGLENYCYSMKNTLQDEKVKGKLSDSDKATIEKAIDEAL-EWLEKN---Q 587 (653)
T ss_pred ccHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhhHHHHHHHHHHHhhhhhhccCCHHHHHHHHHHHHHHH-HHHhcC---C
Confidence 4566777776666543221110 001223466777777776642 3556666666666655543 577532 1
Q ss_pred cccHHHHHHH
Q 003543 468 AKTITEIHSE 477 (811)
Q Consensus 468 pkti~eIh~E 477 (811)
..+++++.+.
T Consensus 588 ~~~~~~~~~k 597 (653)
T PTZ00009 588 LAEKEEFEHK 597 (653)
T ss_pred chhHHHHHHH
Confidence 2345555443
No 56
>PF13041 PPR_2: PPR repeat family
Probab=22.28 E-value=1.6e+02 Score=22.92 Aligned_cols=41 Identities=17% Similarity=0.275 Sum_probs=29.1
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHhCCCCChH-HHHHHHHHHH
Q 003543 650 TVSLLEEYFSIRILDEALQCVEELRAPTYHP-EVVKEAIALA 690 (811)
Q Consensus 650 i~sil~EY~~~~D~~EA~~cikEL~~p~~~~-evV~~~I~~a 690 (811)
...+|.-|...+++++|...++++..-...| .+...++..+
T Consensus 6 yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~ 47 (50)
T PF13041_consen 6 YNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILING 47 (50)
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence 4678999999999999999999986544432 3444444333
No 57
>COG5538 SEC66 Endoplasmic reticulum translocation complex, subunit SEC66 [Cell motility and secretion]
Probab=22.26 E-value=8.4e+02 Score=24.85 Aligned_cols=119 Identities=21% Similarity=0.191 Sum_probs=65.2
Q ss_pred hcCCCchHHHHHHHHHHhhhCCCCCCCCCCCcchhHHHHHHHHHHHHHhhhhhhHHHHhhcCChHHHHHHHHHHHHHHHh
Q 003543 278 VLEPTFCPMYALLCSDLNEKLPPFPSDEPGGKDITFKRILLNHCQEAFEGADNTRAEIRQMTAPEQEMERMDQERLVKLR 357 (811)
Q Consensus 278 i~Ep~fs~mYA~LC~~L~~~l~~~~~~e~~gk~~~FRrlLLnrcQeeFe~~~~~~~ei~~l~~~e~E~E~~e~e~~~KrR 357 (811)
.+|.-|++-|+.=..-+.... .++...++.+..|+++.-+--++.-++ |.
T Consensus 36 ~~eewF~eN~~~~vyF~~k~~------Np~a~~~~LkaaLv~raae~~rR~mKL-----------------------k~- 85 (180)
T COG5538 36 GDEEWFSENLELEVYFLQKSE------NPGASSSTLKAALVKRAAEFKRRVMKL-----------------------KK- 85 (180)
T ss_pred CCccccCCchhHHHHHHHHhh------CCCchHHHHHHHHHHHHHHHHHHHHHH-----------------------HH-
Confidence 456677877776555544432 223345788888888765533332222 11
Q ss_pred hhhhHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHhhC
Q 003543 358 TLGNIRLIGELLKQKMVPEKIVHHIVQELLENDGKTCPAEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTTN 437 (811)
Q Consensus 358 ~LGnIrFIGELfk~~mL~e~Ii~~cI~~LL~~~~~~~p~Ee~IEcLc~LL~tiGk~Ld~~~k~~~~mD~yF~rL~~l~~~ 437 (811)
.+--|+-||+.++|.+......= .+-+. -++|-.|.+= -...|. | -+...+|..-.++..|
T Consensus 86 ---~~~~ln~Ly~~g~igee~w~rf~-~e~K~--------~ElE~~di~~--eAn~lq--P---Gw~q~if~~c~eI~eN 146 (180)
T COG5538 86 ---DMEVLNTLYEDGMIGEEHWERFN-EESKN--------CELERIDIES--EANILQ--P---GWGQEIFKDCSEISEN 146 (180)
T ss_pred ---HHHHHHHHHHcCCccHHHHHHHH-HHhhh--------hhHHHHHHHH--HHhhcC--C---chhHHHHHHHHHHHhh
Confidence 22347789999999998665422 22221 1233333211 111121 1 3556777777788777
Q ss_pred CCCChHHH
Q 003543 438 SQLVPRLR 445 (811)
Q Consensus 438 ~~lSsRIR 445 (811)
..+++|+.
T Consensus 147 e~i~~r~~ 154 (180)
T COG5538 147 ETIGPRKG 154 (180)
T ss_pred hccchhhc
Confidence 77777653
No 58
>KOG4699 consensus Preprotein translocase subunit Sec66 [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.26 E-value=8.4e+02 Score=24.85 Aligned_cols=119 Identities=21% Similarity=0.191 Sum_probs=65.2
Q ss_pred hcCCCchHHHHHHHHHHhhhCCCCCCCCCCCcchhHHHHHHHHHHHHHhhhhhhHHHHhhcCChHHHHHHHHHHHHHHHh
Q 003543 278 VLEPTFCPMYALLCSDLNEKLPPFPSDEPGGKDITFKRILLNHCQEAFEGADNTRAEIRQMTAPEQEMERMDQERLVKLR 357 (811)
Q Consensus 278 i~Ep~fs~mYA~LC~~L~~~l~~~~~~e~~gk~~~FRrlLLnrcQeeFe~~~~~~~ei~~l~~~e~E~E~~e~e~~~KrR 357 (811)
.+|.-|++-|+.=..-+.... .++...++.+..|+++.-+--++.-++ |.
T Consensus 36 ~~eewF~eN~~~~vyF~~k~~------Np~a~~~~LkaaLv~raae~~rR~mKL-----------------------k~- 85 (180)
T KOG4699|consen 36 GDEEWFSENLELEVYFLQKSE------NPGASSSTLKAALVKRAAEFKRRVMKL-----------------------KK- 85 (180)
T ss_pred CCccccCCchhHHHHHHHHhh------CCCchHHHHHHHHHHHHHHHHHHHHHH-----------------------HH-
Confidence 456677877776555544432 223345788888888765533332222 11
Q ss_pred hhhhHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHhhC
Q 003543 358 TLGNIRLIGELLKQKMVPEKIVHHIVQELLENDGKTCPAEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTTN 437 (811)
Q Consensus 358 ~LGnIrFIGELfk~~mL~e~Ii~~cI~~LL~~~~~~~p~Ee~IEcLc~LL~tiGk~Ld~~~k~~~~mD~yF~rL~~l~~~ 437 (811)
.+--|+-||+.++|.+......= .+-+. -++|-.|.+= -...|. | -+...+|..-.++..|
T Consensus 86 ---~~~~ln~Ly~~g~igee~w~rf~-~e~K~--------~ElE~~di~~--eAn~lq--P---Gw~q~if~~c~eI~eN 146 (180)
T KOG4699|consen 86 ---DMEVLNTLYEDGMIGEEHWERFN-EESKN--------CELERIDIES--EANILQ--P---GWGQEIFKDCSEISEN 146 (180)
T ss_pred ---HHHHHHHHHHcCCccHHHHHHHH-HHhhh--------hhHHHHHHHH--HHhhcC--C---chhHHHHHHHHHHHhh
Confidence 22347789999999998665422 22221 1233333211 111121 1 3556777777788777
Q ss_pred CCCChHHH
Q 003543 438 SQLVPRLR 445 (811)
Q Consensus 438 ~~lSsRIR 445 (811)
..+++|+.
T Consensus 147 e~i~~r~~ 154 (180)
T KOG4699|consen 147 ETIGPRKG 154 (180)
T ss_pred hccchhhc
Confidence 77777653
No 59
>PF12612 TFCD_C: Tubulin folding cofactor D C terminal; InterPro: IPR022577 This region is found in eukaryotes, and is typically between 182 and 199 amino acids in length. There is a single completely conserved residue R that may be functionally important. Tubulin folding cofactor D does not co-polymerise with microtubules either in vivo or in vitro, but instead modulates microtubule dynamics by sequestering beta-tubulin from GTP-bound alphabeta-heterodimers in microtubules [].
Probab=21.85 E-value=2.4e+02 Score=28.88 Aligned_cols=37 Identities=24% Similarity=0.263 Sum_probs=30.9
Q ss_pred CCChHHHHHHHHHHHhcCCCCChHHHHHHHHHHHhCC
Q 003543 676 PTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKN 712 (811)
Q Consensus 676 p~~~~evV~~~I~~aLEkk~~erElvs~LL~~L~~~~ 712 (811)
|...+.++..++-.+.||=+.-|+.+.+.|..+....
T Consensus 2 ~~~~~~~~~~llrqa~EKiDrvR~~A~~~l~~ll~~~ 38 (193)
T PF12612_consen 2 PELVQQIIGGLLRQAAEKIDRVREVAGKCLQRLLHSQ 38 (193)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 3456788899999999999999999999999988533
No 60
>PRK09498 sifA secreted effector protein SifA; Reviewed
Probab=21.20 E-value=1.7e+02 Score=32.41 Aligned_cols=28 Identities=14% Similarity=0.199 Sum_probs=22.9
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhCCC
Q 003543 649 KTVSLLEEYFSIRILDEALQCVEELRAP 676 (811)
Q Consensus 649 ki~sil~EY~~~~D~~EA~~cikEL~~p 676 (811)
.+=+-|++||.+.--.||.+||.||--|
T Consensus 29 ~LWEKIKdFFcSThqaeA~~CI~eLchp 56 (336)
T PRK09498 29 VLWEKIKDFFFSTGKAKADRCLHEMLFA 56 (336)
T ss_pred HHHHHHHHHhhcccHHHHHHHHHHHhCC
Confidence 3445578999999999999999999543
No 61
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=20.63 E-value=4.9e+02 Score=22.74 Aligned_cols=47 Identities=21% Similarity=0.075 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHhcCCCCChHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcc
Q 003543 680 PEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTGCLLYGSLL 730 (811)
Q Consensus 680 ~evV~~~I~~aLEkk~~erElvs~LL~~L~~~~lls~~q~~~Gf~~vle~L 730 (811)
+++|..++...+.+ .-+.+...+..|..+ -++..++.+.+.+++-..
T Consensus 5 ~~~i~~i~~~~~~~---~~~~~~~~~~~l~~~-G~s~~~Il~~l~~~l~~~ 51 (89)
T PF08542_consen 5 PEVIEEILESCLNG---DFKEARKKLYELLVE-GYSASDILKQLHEVLVES 51 (89)
T ss_dssp HHHHHHHHHHHHHT---CHHHHHHHHHHHHHT-T--HHHHHHHHHHHHHTS
T ss_pred HHHHHHHHHHHHhC---CHHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHHh
Confidence 56677777666655 345566666666666 577888877777766544
No 62
>PF10363 DUF2435: Protein of unknown function (DUF2435)
Probab=20.62 E-value=6.6e+02 Score=22.96 Aligned_cols=81 Identities=22% Similarity=0.182 Sum_probs=55.6
Q ss_pred HHHHHHHhcCCCCChHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcchhhhcCCCchhHHHHHHHHHHHHcCCCChHHHH
Q 003543 684 KEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTGCLLYGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLDFIVLK 763 (811)
Q Consensus 684 ~~~I~~aLEkk~~erElvs~LL~~L~~~~lls~~q~~~Gf~~vle~LdDl~iDiP~A~~~La~fiaraV~dg~l~~~~i~ 763 (811)
++++...-|.-...|-+-..+|..|+.++-.+..++..-+.-+++.|.| |.-|-||+-+=+-+...+..|-..+.
T Consensus 6 ~~al~~L~dp~~PvRa~gL~~L~~Li~~~~~~~~~~~~il~l~l~~L~d-----~DsyVYL~aI~~L~~La~~~p~~vl~ 80 (92)
T PF10363_consen 6 QEALSDLNDPLPPVRAHGLVLLRKLIESKSEPVIDIPKILDLFLSQLKD-----EDSYVYLNAIKGLAALADRHPDEVLP 80 (92)
T ss_pred HHHHHHccCCCcchHHHHHHHHHHHHHcCCcchhhHHHHHHHHHHHcCC-----CCchHHHHHHHHHHHHHHHChHHHHH
Confidence 3444444444456788888889999987766777777777778887877 46777887776666666666665565
Q ss_pred HHHhhh
Q 003543 764 EVLKKV 769 (811)
Q Consensus 764 ~~~~~~ 769 (811)
.+++..
T Consensus 81 ~L~~~y 86 (92)
T PF10363_consen 81 ILLDEY 86 (92)
T ss_pred HHHHHH
Confidence 555543
No 63
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=20.17 E-value=1.3e+02 Score=20.26 Aligned_cols=25 Identities=32% Similarity=0.577 Sum_probs=22.0
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHhCC
Q 003543 651 VSLLEEYFSIRILDEALQCVEELRA 675 (811)
Q Consensus 651 ~sil~EY~~~~D~~EA~~cikEL~~ 675 (811)
..+|+-|...++.++|...++++..
T Consensus 4 ~~li~~~~~~~~~~~a~~~~~~M~~ 28 (31)
T PF01535_consen 4 NSLISGYCKMGQFEEALEVFDEMRE 28 (31)
T ss_pred HHHHHHHHccchHHHHHHHHHHHhH
Confidence 5788999999999999999998853
Done!