Query 004059
Match_columns 776
No_of_seqs 301 out of 845
Neff 6.0
Searched_HMMs 46136
Date Thu Mar 28 16:49:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004059.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004059hhsearch_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 7.1E-70 1.5E-74 656.9 41.7 758 2-775 142-940 (970)
2 PF02854 MIF4G: MIF4G domain; 100.0 1.2E-31 2.6E-36 268.9 20.7 201 199-423 1-209 (209)
3 smart00543 MIF4G Middle domain 100.0 8.7E-27 1.9E-31 233.8 22.2 193 200-423 2-200 (200)
4 smart00544 MA3 Domain in DAP-5 99.9 8.1E-23 1.8E-27 189.5 13.3 113 611-723 1-113 (113)
5 PF02847 MA3: MA3 domain; Int 99.9 4.1E-23 8.9E-28 191.2 10.9 113 611-723 1-113 (113)
6 KOG0403 Neoplastic transformat 99.8 1E-20 2.2E-25 205.3 14.0 152 607-759 340-491 (645)
7 KOG0403 Neoplastic transformat 99.8 8.4E-19 1.8E-23 190.5 14.1 143 608-751 46-188 (645)
8 KOG2140 Uncharacterized conser 99.8 8.3E-18 1.8E-22 185.3 15.3 191 195-427 161-352 (739)
9 KOG2141 Protein involved in hi 99.4 4.4E-12 9.5E-17 145.1 19.0 199 195-427 316-524 (822)
10 KOG3942 MIF4G domain-containin 98.8 5.5E-08 1.2E-12 102.9 13.8 169 228-429 163-338 (348)
11 KOG2051 Nonsense-mediated mRNA 98.7 8E-08 1.7E-12 114.7 14.1 183 198-416 423-610 (1128)
12 KOG0401 Translation initiation 98.2 1.7E-07 3.6E-12 115.8 -1.0 271 173-446 588-892 (970)
13 KOG2051 Nonsense-mediated mRNA 97.6 0.0023 5E-08 77.7 17.8 183 208-421 641-835 (1128)
14 KOG1104 Nuclear cap-binding co 94.5 2.4 5.2E-05 51.0 19.2 201 190-428 19-248 (759)
15 PF12152 eIF_4G1: Eukaryotic t 89.9 0.17 3.7E-06 44.2 1.5 27 54-80 42-69 (75)
16 PF05918 API5: Apoptosis inhib 85.8 9 0.0002 45.5 12.8 155 196-378 177-346 (556)
17 PF02847 MA3: MA3 domain; Int 84.1 8.4 0.00018 35.3 9.5 63 199-263 2-66 (113)
18 smart00544 MA3 Domain in DAP-5 81.7 9.4 0.0002 35.1 8.8 62 200-263 3-66 (113)
19 PF02854 MIF4G: MIF4G domain; 64.7 39 0.00084 33.5 9.1 123 613-737 2-134 (209)
20 PLN00131 hypothetical protein; 56.0 1.6E+02 0.0034 29.5 10.9 68 597-675 117-185 (218)
21 PF05456 eIF_4EBP: Eukaryotic 53.4 4 8.7E-05 38.7 -0.3 18 61-78 44-61 (116)
22 PF07817 GLE1: GLE1-like prote 48.7 3.7E+02 0.008 28.8 13.8 166 197-381 28-240 (256)
23 PF04844 Ovate: Transcriptiona 48.3 47 0.001 28.0 5.2 46 608-653 5-52 (59)
24 PRK14703 glutaminyl-tRNA synth 47.5 3.4E+02 0.0074 34.0 14.7 86 662-759 663-761 (771)
25 PLN03081 pentatricopeptide (PP 45.4 1.7E+02 0.0036 35.7 11.7 62 616-681 263-324 (697)
26 KOG2140 Uncharacterized conser 44.6 69 0.0015 37.8 7.6 140 605-751 448-593 (739)
27 PRK05477 gatB aspartyl/glutamy 42.9 2.9E+02 0.0062 32.6 12.5 93 662-760 367-466 (474)
28 PLN03218 maturation of RBCL 1; 42.4 1.4E+02 0.003 38.7 10.7 69 615-684 582-651 (1060)
29 PF08044 DUF1707: Domain of un 39.6 42 0.0009 27.5 3.7 45 659-703 4-53 (53)
30 KOG2141 Protein involved in hi 39.2 1.1E+02 0.0023 37.6 8.2 105 207-346 627-731 (822)
31 TIGR01568 A_thal_3678 uncharac 38.8 98 0.0021 26.7 5.8 47 607-653 10-59 (66)
32 PF08876 DUF1836: Domain of un 35.3 1.1E+02 0.0024 28.7 6.2 48 661-708 57-104 (105)
33 PF10602 RPN7: 26S proteasome 35.0 1.2E+02 0.0027 30.5 7.1 56 605-660 29-88 (177)
34 PF04129 Vps52: Vps52 / Sac2 f 34.8 4.4E+02 0.0096 31.2 12.7 85 327-423 71-160 (508)
35 smart00543 MIF4G Middle domain 34.6 3.8E+02 0.0083 26.3 10.6 31 704-734 94-124 (200)
36 PLN03218 maturation of RBCL 1; 33.0 2.5E+02 0.0053 36.6 10.8 68 614-682 616-684 (1060)
37 PF12854 PPR_1: PPR repeat 32.9 59 0.0013 23.6 3.2 26 614-639 9-34 (34)
38 PF04286 DUF445: Protein of un 32.0 4.5E+02 0.0097 28.8 11.6 93 607-699 102-200 (367)
39 TIGR01446 DnaD_dom DnaD and ph 30.1 3.3E+02 0.0073 22.9 8.2 43 643-685 30-72 (73)
40 PTZ00009 heat shock 70 kDa pro 27.9 2.6E+02 0.0056 34.2 9.4 79 360-442 512-597 (653)
41 cd03567 VHS_GGA VHS domain fam 26.9 2.4E+02 0.0052 27.6 7.3 94 325-425 19-119 (139)
42 PF10363 DUF2435: Protein of u 26.5 4.8E+02 0.01 23.6 8.7 82 649-735 6-87 (92)
43 PLN03081 pentatricopeptide (PP 26.2 3.8E+02 0.0082 32.7 10.5 62 615-680 161-222 (697)
44 PLN03077 Protein ECB2; Provisi 26.1 3E+02 0.0066 34.4 9.9 64 614-681 325-388 (857)
45 COG5537 IRR1 Cohesin [Cell div 26.0 9.3E+02 0.02 29.4 12.8 135 609-752 328-468 (740)
46 TIGR00756 PPR pentatricopeptid 26.0 76 0.0016 21.6 2.8 26 615-640 3-28 (35)
47 KOG2050 Puf family RNA-binding 25.0 1.2E+02 0.0027 36.2 5.6 60 614-675 322-387 (652)
48 PF10884 DUF2683: Protein of u 24.3 1.9E+02 0.0041 25.9 5.3 45 612-656 12-61 (80)
49 PF01535 PPR: PPR repeat; Int 24.0 99 0.0022 20.7 3.0 25 616-640 4-28 (31)
50 COG1421 CRISPR system related 23.8 1.8E+02 0.0038 28.6 5.5 65 678-742 43-115 (137)
51 PF04147 Nop14: Nop14-like fam 23.6 1.3E+03 0.028 29.3 14.6 127 199-346 428-569 (840)
52 PRK09498 sifA secreted effecto 23.5 1.4E+02 0.0031 32.7 5.4 28 614-641 29-56 (336)
53 PF13041 PPR_2: PPR repeat fam 23.4 1.5E+02 0.0032 22.9 4.3 29 615-643 6-34 (50)
54 PF02650 HTH_WhiA: WhiA C-term 23.3 5.2E+02 0.011 23.3 8.1 64 323-400 21-84 (85)
55 PF08542 Rep_fac_C: Replicatio 23.1 4.1E+02 0.009 23.0 7.6 48 644-695 4-51 (89)
56 PF12612 TFCD_C: Tubulin foldi 22.0 2.5E+02 0.0054 28.6 6.7 37 641-677 2-38 (193)
57 PF09851 SHOCT: Short C-termin 21.9 1.3E+02 0.0028 21.7 3.3 26 667-692 5-30 (31)
58 PF10155 DUF2363: Uncharacteri 21.5 6.4E+02 0.014 24.3 8.9 32 661-692 77-108 (126)
59 PF05004 IFRD: Interferon-rela 21.2 1.1E+03 0.023 26.1 11.9 121 607-728 37-170 (309)
60 PF02284 COX5A: Cytochrome c o 20.9 6.1E+02 0.013 24.0 8.2 93 606-704 6-102 (108)
61 PLN03077 Protein ECB2; Provisi 20.7 5.8E+02 0.013 31.9 10.9 26 615-640 256-281 (857)
62 KOG1924 RhoA GTPase effector D 20.3 5.2E+02 0.011 32.4 9.5 71 623-699 204-281 (1102)
63 smart00139 MyTH4 Domain in Myo 20.3 1.2E+02 0.0026 29.8 3.8 35 229-263 41-76 (144)
64 cd07347 harmonin_N_like N-term 20.2 2E+02 0.0044 25.5 4.8 38 606-644 16-54 (78)
No 1
>KOG0401 consensus Translation initiation factor 4F, ribosome/mRNA-bridging subunit (eIF-4G) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.1e-70 Score=656.92 Aligned_cols=758 Identities=30% Similarity=0.423 Sum_probs=556.9
Q ss_pred CcCCcc---eeEeccCCCCCCCCCccccccCCCC--CCC--CCCCCCCCCCCCCCc---ccccCCCccCCCcccccCHHH
Q 004059 2 QAADQT---VISLRPGGGGGPRGTRLFTHRFDSS--STP--SSDSQTLPPHGGVAS---AFKMGDLRFEGHERVRYTREQ 71 (776)
Q Consensus 2 ~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~--~~~--~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~y~~~~ 71 (776)
+.+++. +++++|+|.. ...+.|+.....+ .+. ++....++.+++.+. .......++....+..|....
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 345556 9999999995 3445555553322 221 222222455666433 445567778888899999999
Q ss_pred HHHHHHHhhhcHHHHHhhhhhhccccCCCCCCCCCCCCCCchhhhhhhhhcccCccccccCCCC--Cccchhhhhhhhhh
Q 004059 72 LLQLKEVAQLTEDILKIKQEIESEFDGEGQSWGGRAENNNLQSQFQARYLEADNRDWRTRSTTS--GQEKSLEANQEKME 149 (776)
Q Consensus 72 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~--~~~~~~~~~~~~~~ 149 (776)
+++......++.+++..+......+..++.+|. ...+..+.....|..++.++||..+..+. ...+.|++.++.+.
T Consensus 220 ~~~~e~~~~~~d~~~~~~e~~~~~~~~e~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~ 297 (970)
T KOG0401|consen 220 LLEAENTPRSSDEYVRRIEAEQEPLRPEEPSGL--RAIQKIPEKATERRAEESGRDKPEHEDQTKPAGNRLLDEPRESQP 297 (970)
T ss_pred hhhhhhcCCcchHHHHHHHHHhhccCCccchhh--hcccccccccccccccccccccccccccccccccccccchhhhcc
Confidence 999988889999988888777788889999883 22224456777899999999998776664 33356666666654
Q ss_pred hcccccc---ccchhhhhhcccCCCCCCCcchhcccCCcccccCCCChHHHHHHHHHHHHhcCChhhHHHHHHHHHHccC
Q 004059 150 FGAHEGQ---LNSQFASAQISTNQGAGPAPALIKAEVPWSARRGNLSEKDRVLKTVKGILNKLTPEKFDVLKGQLIDSGI 226 (776)
Q Consensus 150 ~~~~~~~---~~~~~~~~~~~~~~~~~p~~~l~~~e~~w~~~~~~~~e~e~l~rkVk~ILNKLTpenFd~l~~qLl~l~I 226 (776)
++++-.+ -...+.........+..|.+...++..+|...+..++..+++.+.|++|||||||++|+.++.+++++.|
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 4332110 1223333333344566778888888999988887788899999999999999999999999999999999
Q ss_pred CCHHHHHHHHHHHHHHHhhCCCChHHHHHHHHHHhhhCCCCCCCCCCCchhhHHHHHHHHHHHHHhhhh-chHHHHhhcC
Q 004059 227 TTPDILKGVIELIFDKAVLEPTFCPMYALLCSDLNEKLPPFPSDEPGGKDITFKRILLNHCQEAFEGAD-NTRAEIRQMT 305 (776)
Q Consensus 227 ~t~e~Lk~VI~lIFeKAi~Ep~fs~mYA~LC~~L~~~lp~~~~~e~~gk~~~FR~~LLnrcQeeFe~~~-~~~~ei~~~~ 305 (776)
++.+.|++||.+||||||.||+||+|||+||..|.. .+.++..+..+..++||++||++||++|+... ...+++..+.
T Consensus 378 ~t~~~l~~vi~~vfdkAi~EP~f~~~yA~lc~~l~~-~~~~~~~~~~~~~~~fr~~lL~rcq~~fe~~~~~~~~~~~~~~ 456 (970)
T KOG0401|consen 378 DTDDALKEVIELVFDKAINEPTFCAMYARLCFDLEG-PPSEPELDMGGDEINFRRLLLNRCQKEFEGEDDKIADEYSEAE 456 (970)
T ss_pred CcHHHHhHHHHHHHHhhhcccccchhcchhcccccC-CccCCCcCCCCCcccHHHHHHHHhHHHhhcccHHHHHHhhhhc
Confidence 999999999999999999999999999999999998 55555555567789999999999999999987 5666777766
Q ss_pred ChHH-HHHHhHHHHHHHHhhhhHHHHHHHHHhcCCCCHHHHHHHHH-hhhcCCCCCCChhhHHHHHHHHHHHhhhhhcCC
Q 004059 306 APEQ-EMERMDQERLVKLRTLGNIRLIGELLKQKMVPEKIVHHIVQ-LLENDGKTCPAEENVEAICQFFNTIGKQLDENP 383 (776)
Q Consensus 306 ~~e~-E~E~~e~e~~~Krr~LGnIrFIGELfk~~mL~e~Im~~ci~-LL~~~~~~~p~Ee~IE~Lc~LL~tiGk~Ld~~~ 383 (776)
.+++ |.++++.++++++|+||||+|||+||+.+|++++|||.|++ ||..+. ++|++|||+|+|++|||+.||...
T Consensus 457 ~~~~~e~~le~~k~~~~~rtlgn~~~ig~l~~~~ml~e~i~~~~v~~Ll~~~~---~~ee~ie~lc~f~~tig~~lD~~~ 533 (970)
T KOG0401|consen 457 EPDELEEELEEEKYILRRRTLGNFRFIGELFKLKMLTEKIVHACVQKLLSDDQ---PSEESIECLCRFLTTIGKKLDFSK 533 (970)
T ss_pred CchhHHHHHHhccceecCCccchHHHHHHHHHHHHHHHHHHHHHHHHhhcccc---ccchhhhhHHhhhhcccccccccC
Confidence 6655 55666677788999999999999999999999999999999 888642 789999999999999999999754
Q ss_pred cchhhHHHHHHHHHHHhhCCCCChHHHHHHHHHHHHHhCCCCCcccccCCc-cHHHHHHHHHHhcCCCCchhhhhhcCCC
Q 004059 384 KSRRVNDVYFSRLKELTTNSQLVPRLRFMIHDVLDLRANNWVPRREEMKAK-TITEIHSEAEKNLGLRPGATAMMRNGRT 462 (776)
Q Consensus 384 k~~~~md~yF~rL~~l~~~~~lssRiRFmL~dvidLR~nnW~~r~~~~~pk-ti~eIh~eae~~~~~~~~~~~~~r~~r~ 462 (776)
.....||.||.+++.+...+++++|+|||++++||||.++|++|+.+.+++ +|++||.++.++....++....++..+.
T Consensus 534 ~s~r~md~~~~~~k~~~~~~~~s~r~RfM~~~~idlR~~~w~~rr~~~~~~~~ieei~~~~~~~~~~~p~~~~~~~~~~~ 613 (970)
T KOG0401|consen 534 ESPRNMDEYFNSMKNLKRKPQRSNRIRFMLQSVIDLRKSGWGPRRAEETNDKPIEEIAPEAPSANRWSPKSLSKKTEGRL 613 (970)
T ss_pred cccchhHHHHHHHHHhhhhhhhccchhhhhccccccccccccchhcccCCCCchhhcchhhhhhcccCcccccccccccc
Confidence 444449999999999999999999999999999999999999999988877 9999999998887655555444444432
Q ss_pred CCC---CC-C----CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCC--CCCCCCCCCCCCCCCCCCCCCC
Q 004059 463 GAT---GG-M----GPGGFPIARPGTGGMMPGMPGTQKMPGMPGFDTDNWEVPRSR--TMPRGDSKSPSQFPGRVQSPLI 532 (776)
Q Consensus 463 ~~~---g~-~----~~g~~~~~~~~~gg~~p~~~~~~~~p~~pg~~~d~~~~~~~~--s~~r~~~~~~~~~~~~~~~~~~ 532 (776)
+.. +. . .+.+....+...+.|+++++...-+..++.++.++|++.... ...+..+.. +++ ...+.+..
T Consensus 614 ~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~i~~~~~~~~~~~~~e~~~~~~k~~~~~~~~k~~~~-~~~-~~~~~~~~ 691 (970)
T KOG0401|consen 614 AEESDSGLLGKEVVERKGKSGLRKLTPEMFDKISDPILDIADQSMDEEDGEASKQKGEQGGRKASDE-QHF-SSMRAPAL 691 (970)
T ss_pred cccccccccCccccccccccccccCChhhcccccccccccchhhccccccchhhhcccccccccCcc-ccc-cccCCccc
Confidence 110 00 0 011122223344555665554433445556667777765332 121211111 011 01112222
Q ss_pred CCCCCCC----CCcCCCCCCCCcCC--CcccccC---CCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCC
Q 004059 533 GKSPSIN----SKFLPQGSGGIISG--KTSALLQ---GSPTPSARPSGIASGVEPLTQYTKPVAPAASVVASPEKPSAPV 603 (776)
Q Consensus 533 ~k~~~~n----~~~~p~gs~~~~sg--k~s~ll~---~~~~p~~r~~~~~~~~~~~~~~~~~~k~~~~~p~~~~~~~~~~ 603 (776)
++..... ....++|+.+.... ..++... ..+....++++....+ .+.-+.+.. .++.+.+.+...
T Consensus 692 ~~~~~~~s~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~-----~~e~~~~~~-~~~~~~~~~~~~ 765 (970)
T KOG0401|consen 692 EKVVPSLSSDIDDKRNRGSNGELLSDSYLSARCHEEFENGWSRELPSGKDGER-----EPEMMSPEY-YAAKAAKRAGLG 765 (970)
T ss_pred cccccccccccccccccCCccccccccccchhhhhhccccccccCCCCccccc-----chhhcCccc-chhhhhhccCCc
Confidence 2211111 12334444431111 1111111 1111111111111000 001011100 011112222333
Q ss_pred C--CCCHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCCCH
Q 004059 604 T--KLNLADLRKKTVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTT 681 (776)
Q Consensus 604 ~--~~s~eel~kki~~ll~EY~~~~D~~EA~~clkEL~~p~~~~e~V~~~I~~aLEk~~~~re~v~~LL~~L~~~~~ls~ 681 (776)
. .++.+.+..+++.|++||++..+.+|++.|+++|++|.+|+.+|...|+..|++++..++++++||..|+..+.++.
T Consensus 766 ~v~~~~~~~l~~~sk~l~ee~~~~~~~~~~~~~ie~l~S~~~~~~~v~~~v~~~l~~~~~~~~~~~~ll~~l~~~~~~~~ 845 (970)
T KOG0401|consen 766 LVIALSSELLELLSKSLLEEFLSLRLEKEALKCIEELESPSLLLKTVGENIEPTLEKSPQAVEELLQLLDILVSKNPLSI 845 (970)
T ss_pred chhhhhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcccchhhhHHHHHHhcCcccccChhHHHHHHHHHHHHHhcCcccH
Confidence 3 78899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhcchhhhcCCCchhHHHHHHHHHHHHcCCCCh-HHHHHHHhhhcchhHHHHHHHHHHHHHhcCCCchhh
Q 004059 682 RDIGTGCLLYGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLDF-IVLKEVLKKVEDNMFRRSIFTAAMKSIQSSPAGQEV 760 (776)
Q Consensus 682 ~q~~~Gf~~vle~LdDl~iDiP~A~~~La~~iaraI~d~~l~~-~~v~~~~~~~~~~~~~~~~~~a~l~~l~~~~~g~~v 760 (776)
+++..||..++..++|+.||+|++|.|+++|++.++..+++++ ..+..+...+.+.+++..|+.+++..+...-+..++
T Consensus 846 ~~~~~~~~~~~~~~~d~~~d~pk~w~~~~e~~gp~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 925 (970)
T KOG0401|consen 846 ETLEIGYREKFKLADDKELDLPKGWNYIKEFLGPLIHQKILDESELVREILKNMRPNGRRSNVLFSVLEIVEKELGRADL 925 (970)
T ss_pred HHHhhhHHHHHhhhHHHhcccccchhHHHHhhhhHhhhccccHHHHHHHHhhcCCccccccchHHHHHHHHHHhhhHHHH
Confidence 9999999999999999999999999999999999999999999 456788888999999999999999999988899999
Q ss_pred HhhhhhhHHHHhhhh
Q 004059 761 LAVQGAEVQACESLL 775 (776)
Q Consensus 761 ~~~~~~~~~~~~~~~ 775 (776)
.+..+....+|+.++
T Consensus 926 ~~~~~~~~~s~~~~~ 940 (970)
T KOG0401|consen 926 GDIQRESFLSTKTLL 940 (970)
T ss_pred HHHHHHhcccchhcc
Confidence 999999999988764
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=1.2e-31 Score=268.92 Aligned_cols=201 Identities=41% Similarity=0.774 Sum_probs=173.2
Q ss_pred HHHHHHHHhcCChhhHHHHHHHHHHccCC-CHHHHHHHHHHHHHHHhhCCCChHHHHHHHHHHhhhCCCCCCCCCCCchh
Q 004059 199 LKTVKGILNKLTPEKFDVLKGQLIDSGIT-TPDILKGVIELIFDKAVLEPTFCPMYALLCSDLNEKLPPFPSDEPGGKDI 277 (776)
Q Consensus 199 ~rkVk~ILNKLTpenFd~l~~qLl~l~I~-t~e~Lk~VI~lIFeKAi~Ep~fs~mYA~LC~~L~~~lp~~~~~e~~gk~~ 277 (776)
.|+|++||||||++||+.++++|..+... +.+.++.+++.||++|+.+|+|+.+||+||..|+...+ .
T Consensus 1 ~r~v~~~lnklt~~n~~~~~~~l~~~~~~~~~~~~~~i~~~i~~~a~~~~~~~~~~a~l~~~l~~~~~-----------~ 69 (209)
T PF02854_consen 1 LRKVRGILNKLTPSNFESIIDELIKLNWSDDPETLKEIVKLIFEKAVEEPNFSPLYARLCAALNSRFP-----------S 69 (209)
T ss_dssp HHHHHHHHHHCSSTTHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHSGGGHHHHHHHHHHHHHHCH-----------H
T ss_pred CchHHHHHHHCCHHHHHHHHHHHHHHHhhccHHHHHHHHHHHhhhhhcCchHHHHHHHHHHHHhccch-----------h
Confidence 48999999999999999999999998765 59999999999999999999999999999999999753 5
Q ss_pred hHHHHHHHHHHHHHhhhhchHHHHhhcCChHHHHHHhHHHHHHHHhhhhHHHHHHHHHhcCCCCHHHHHHHHH-hhhcCC
Q 004059 278 TFKRILLNHCQEAFEGADNTRAEIRQMTAPEQEMERMDQERLVKLRTLGNIRLIGELLKQKMVPEKIVHHIVQ-LLENDG 356 (776)
Q Consensus 278 ~FR~~LLnrcQeeFe~~~~~~~ei~~~~~~e~E~E~~e~e~~~Krr~LGnIrFIGELfk~~mL~e~Im~~ci~-LL~~~~ 356 (776)
.|+..||++||++|+.... ..+.+ +.....+++..|+++||||||+.++++++++++|+. ||....
T Consensus 70 ~f~~~ll~~~~~~f~~~~~-----------~~~~~--~~~~~~~~~~~~~~~fl~eL~~~~vv~~~~i~~~l~~ll~~~~ 136 (209)
T PF02854_consen 70 EFRSLLLNRCQEEFEERYS-----------NEELE--ENRQSSKQRRRGNIRFLAELFNFGVVSEKIIFDILRELLSDGT 136 (209)
T ss_dssp HHHHHHHHHHHHHHHHHT------------HHHHH--HHHHHHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHTS
T ss_pred hHHHHHHHHHHHHHHHhhh-----------hhhHH--HHHHHHHHHHhhhhhHHHhhHhhccccchhHHHHHHHHHhccc
Confidence 8999999999999998541 00111 122345678999999999999999999999999999 988632
Q ss_pred C---CCCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHhhC---CCCChHHHHHHHHHHHHHhCC
Q 004059 357 K---TCPAEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTTN---SQLVPRLRFMIHDVLDLRANN 423 (776)
Q Consensus 357 ~---~~p~Ee~IE~Lc~LL~tiGk~Ld~~~k~~~~md~yF~rL~~l~~~---~~lssRiRFmL~dvidLR~nn 423 (776)
. ..+++++|||+|.+|.+||+.|+.+...+..|+.||..++....+ +.+++|+||||++++|+|+||
T Consensus 137 ~~~~~~~~~~~ie~~~~lL~~~G~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~r~~~~l~~l~~lr~~~ 209 (209)
T PF02854_consen 137 DECQPPPDEENIECLCTLLKTCGKKLENSEESPKALDEIFERLQKYANSKKDPNLSSRIRFMLEDLIELRNNK 209 (209)
T ss_dssp HHCCHHTCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCHSSSSSHHHHHHHHHHHHHHHTC
T ss_pred ccccCCCcHhHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHHHHHhcCC
Confidence 1 125679999999999999999994445567899999999999887 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=8.7e-27 Score=233.82 Aligned_cols=193 Identities=37% Similarity=0.604 Sum_probs=166.8
Q ss_pred HHHHHHHhcCChhhHHHHHHHHHHccCCCHHHHHHHHHHHHHHHhhCCCChHHHHHHHHHHhhhCCCCCCCCCCCchhhH
Q 004059 200 KTVKGILNKLTPEKFDVLKGQLIDSGITTPDILKGVIELIFDKAVLEPTFCPMYALLCSDLNEKLPPFPSDEPGGKDITF 279 (776)
Q Consensus 200 rkVk~ILNKLTpenFd~l~~qLl~l~I~t~e~Lk~VI~lIFeKAi~Ep~fs~mYA~LC~~L~~~lp~~~~~e~~gk~~~F 279 (776)
++|+++|||||++||+.++.+|..+.+.+++..+.+++.||++|+.+|+|+.+||+||..|+...+ .|
T Consensus 2 ~~v~~~lnkLs~~n~~~~~~~l~~~~~~~~~~~~~l~~~i~~~~~~~~~~~~~ya~L~~~l~~~~~------------~f 69 (200)
T smart00543 2 KKVKGLINKLSPSNFESIIKELLKLNNSDKNLRKYILELIFEKAVEEPNFIPAYARLCALLNAKNP------------DF 69 (200)
T ss_pred hHHHHHHhhCCHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHHHH------------HH
Confidence 689999999999999999999999988888999999999999999999999999999999998642 69
Q ss_pred HHHHHHHHHHHHhhhhchHHHHhhcCChHHHHHHhHHHHHHHHhhhhHHHHHHHHHhcCCCCHHHHHHHHH-hhhcCCC-
Q 004059 280 KRILLNHCQEAFEGADNTRAEIRQMTAPEQEMERMDQERLVKLRTLGNIRLIGELLKQKMVPEKIVHHIVQ-LLENDGK- 357 (776)
Q Consensus 280 R~~LLnrcQeeFe~~~~~~~ei~~~~~~e~E~E~~e~e~~~Krr~LGnIrFIGELfk~~mL~e~Im~~ci~-LL~~~~~- 357 (776)
+..|++.|+++|+..-. . .+...++++.|+++||||||+.++++..++.+|+. |+.....
T Consensus 70 ~~~ll~~~~~~f~~~~e----------------~--~~~~~~~~~~~~i~fl~eL~~~~~i~~~~i~~~l~~ll~~~~~~ 131 (200)
T smart00543 70 GSLLLERLQEEFEKGLE----------------S--EEESDKQRRLGLVRFLGELYNFQVLTSKIILELLKELLNDLTKL 131 (200)
T ss_pred HHHHHHHHHHHHHHHHH----------------H--HHHHhhhhHHhHHHHHHHHHHcccCcHHHHHHHHHHHHhccCCC
Confidence 99999999999987411 0 01224567899999999999999999999999999 8875311
Q ss_pred -CCCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHhhCC---CCChHHHHHHHHHHHHHhCC
Q 004059 358 -TCPAEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTTNS---QLVPRLRFMIHDVLDLRANN 423 (776)
Q Consensus 358 -~~p~Ee~IE~Lc~LL~tiGk~Ld~~~k~~~~md~yF~rL~~l~~~~---~lssRiRFmL~dvidLR~nn 423 (776)
...++.+|||+|.+|.+||+.|+. +..+..|+.+|..++....+. .+++|+|||++++++||+++
T Consensus 132 ~~~~~~~~ve~l~~lL~~~G~~l~~-~~~~~~~~~~l~~l~~~~~~~~~~~~~~r~~~~l~~l~~l~~~~ 200 (200)
T smart00543 132 DPPRSDFSVECLLSLLPTCGKDLER-EKSPKLLDEILERLQDYLLKKDKTELSSRLRFMLELLIELRKNK 200 (200)
T ss_pred CCCCcHHHHHHHHHHHHHhhHHHcC-cccHHHHHHHHHHHHHHHhcccccCCChHHHHHHHHHHHHhhCc
Confidence 113568999999999999999994 234567999999999998876 79999999999999999864
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=99.89 E-value=8.1e-23 Score=189.47 Aligned_cols=113 Identities=35% Similarity=0.472 Sum_probs=110.4
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 004059 611 LRKKTVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTGCLL 690 (776)
Q Consensus 611 l~kki~~ll~EY~~~~D~~EA~~clkEL~~p~~~~e~V~~~I~~aLEk~~~~re~v~~LL~~L~~~~~ls~~q~~~Gf~~ 690 (776)
++|++..+|+||++++|.+||++||++|+.|++||+||+.+|+.+||+++.+++.+++||.+|++.+++++++|..||.+
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 47899999999999999999999999999999999999999999999998999999999999999999999999999999
Q ss_pred HhhcchhhhcCCCchhHHHHHHHHHHHHcCCCC
Q 004059 691 YGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLD 723 (776)
Q Consensus 691 vle~LdDl~iDiP~A~~~La~~iaraI~d~~l~ 723 (776)
+++.++|+++|+|+|+.++|+|+|++|.+|+||
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=99.89 E-value=4.1e-23 Score=191.16 Aligned_cols=113 Identities=35% Similarity=0.537 Sum_probs=107.2
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 004059 611 LRKKTVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTGCLL 690 (776)
Q Consensus 611 l~kki~~ll~EY~~~~D~~EA~~clkEL~~p~~~~e~V~~~I~~aLEk~~~~re~v~~LL~~L~~~~~ls~~q~~~Gf~~ 690 (776)
++|++..+|.|||+++|.+||+.||+||+.|.+|++||..+|..+||+++.+|+.++.||.+|+..++++.++|..||.+
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 004059 691 YGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLD 723 (776)
Q Consensus 691 vle~LdDl~iDiP~A~~~La~~iaraI~d~~l~ 723 (776)
+++.++|+.+|+|++|+++|+|++++|.+|+||
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=99.84 E-value=1e-20 Score=205.26 Aligned_cols=152 Identities=24% Similarity=0.359 Sum_probs=143.2
Q ss_pred CHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCCCHHHHHH
Q 004059 607 NLADLRKKTVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGT 686 (776)
Q Consensus 607 s~eel~kki~~ll~EY~~~~D~~EA~~clkEL~~p~~~~e~V~~~I~~aLEk~~~~re~v~~LL~~L~~~~~ls~~q~~~ 686 (776)
+...+++.+..||+|||.++|+.|.++|+++|+.|.|.+-|++.+|++|||+++.++||++.||+.|+- .++|++++..
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 6999999999
Q ss_pred HHHHHhhcchhhhcCCCchhHHHHHHHHHHHHcCCCChHHHHHHHhhhcchhHHHHHHHHHHHHHhcCCCchh
Q 004059 687 GCLLYGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLDFIVLKEVLKKVEDNMFRRSIFTAAMKSIQSSPAGQE 759 (776)
Q Consensus 687 Gf~~vle~LdDl~iDiP~A~~~La~~iaraI~d~~l~~~~v~~~~~~~~~~~~~~~~~~a~l~~l~~~~~g~~ 759 (776)
||..+++.++|+++|+|.|++.||.|+||||.|++|-+.+|+++...+.+.....+.+..|-..|+...+|+.
T Consensus 419 ~F~mLLesaedtALD~p~a~~elalFlARAViDdVLap~~leei~~~lp~~s~g~et~~~ArsLlsar~aGeR 491 (645)
T KOG0403|consen 419 GFDMLLESAEDTALDIPRASQELALFLARAVIDDVLAPTNLEEISGTLPPVSQGRETLDKARSLLSARHAGER 491 (645)
T ss_pred HHHHHHhcchhhhccccccHHHHHHHHHHHHhhcccccCcHHHHcCCCCCchhhHHHHHHHHHHHHHhhcccc
Confidence 9999999999999999999999999999999999999999999999998887788888888888887766543
No 7
>KOG0403 consensus Neoplastic transformation suppressor Pdcd4/MA-3, contains MA3 domain [Signal transduction mechanisms]
Probab=99.79 E-value=8.4e-19 Score=190.48 Aligned_cols=143 Identities=29% Similarity=0.389 Sum_probs=130.7
Q ss_pred HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCCCHHHHHHH
Q 004059 608 LADLRKKTVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTG 687 (776)
Q Consensus 608 ~eel~kki~~ll~EY~~~~D~~EA~~clkEL~~p~~~~e~V~~~I~~aLEk~~~~re~v~~LL~~L~~~~~ls~~q~~~G 687 (776)
.++++|+..+||+|||+++|+.-|+.-++||....|||.||+++|.+||||.++++|+++-||+.||. -+|+++|+..|
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 57999999999999999999999999999999999999999999999999999999999999999999 79999999999
Q ss_pred HHHHhhcchhhhcCCCchhHHHHHHHHHHHHcCCCChHHHHHHHhhhcchhHHHHHHHHHHHHH
Q 004059 688 CLLYGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLDFIVLKEVLKKVEDNMFRRSIFTAAMKSI 751 (776)
Q Consensus 688 f~~vle~LdDl~iDiP~A~~~La~~iaraI~d~~l~~~~v~~~~~~~~~~~~~~~~~~a~l~~l 751 (776)
|.+++++.+|+++|||+|-+.||-||||||.|++||+.|+....+-+.++.-.-.|+..+-+.+
T Consensus 125 f~~ll~s~ddl~vdipdavnvlalfiaraivddilpp~fl~r~~k~lp~~skg~qV~~~aeksy 188 (645)
T KOG0403|consen 125 FIRLLESADDLAVDIPDAVNVLALFIARAIVDDILPPAFLKRAKKLLPDSSKGFQVINTAEKSY 188 (645)
T ss_pred HHHHHHhcccceecCchHHHHHHHHHHHHHHHhccChHHHHHHHhhCCCcccchhHHHHHHhhc
Confidence 9999999999999999999999999999999999999999998887765543334444444433
No 8
>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]
Probab=99.75 E-value=8.3e-18 Score=185.34 Aligned_cols=191 Identities=24% Similarity=0.443 Sum_probs=163.6
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHHccCCCHHHHHHHHHHHHHHHhhCCCChHHHHHHHHHHhhhCCCCCCCCCCC
Q 004059 195 KDRVLKTVKGILNKLTPEKFDVLKGQLIDSGITTPDILKGVIELIFDKAVLEPTFCPMYALLCSDLNEKLPPFPSDEPGG 274 (776)
Q Consensus 195 ~e~l~rkVk~ILNKLTpenFd~l~~qLl~l~I~t~e~Lk~VI~lIFeKAi~Ep~fs~mYA~LC~~L~~~lp~~~~~e~~g 274 (776)
+|.+.+.|.+|+|||+..|+..++.+|+..+|..+..| +...|++-....|.|+.+||.|...|+.++|.+.
T Consensus 161 WEalkksInglInkvn~sNi~~ii~eLfqeNiirgRgl--~crsv~~aq~asp~ft~vyaALvAviNskfP~Ig------ 232 (739)
T KOG2140|consen 161 WEALKKSINGLINKVNASNIQEIIRELFQENIIRGRGL--LCRSVMQAQAASPGFTPVYAALVAVINSKFPQIG------ 232 (739)
T ss_pred HHHHHHHhHHHHhhhhHHHHHHHHHHHHHHHHHhccch--hHHHHHHHHhcCCCCcHHHHHHHHHHccCCchHH------
Confidence 47899999999999999999999999999998777766 7888888888899999999999999999998763
Q ss_pred chhhHHHHHHHHHHHHHhhhhchHHHHhhcCChHHHHHHhHHHHHHHHhhhhHHHHHHHHHhcCCCCHHHHHHHHH-hhh
Q 004059 275 KDITFKRILLNHCQEAFEGADNTRAEIRQMTAPEQEMERMDQERLVKLRTLGNIRLIGELLKQKMVPEKIVHHIVQ-LLE 353 (776)
Q Consensus 275 k~~~FR~~LLnrcQeeFe~~~~~~~ei~~~~~~e~E~E~~e~e~~~Krr~LGnIrFIGELfk~~mL~e~Im~~ci~-LL~ 353 (776)
. +||.+..-.|.+..+ +.-|..|+..++||++|+++++.+|-+..+++. ||+
T Consensus 233 E------lLlkrLilqf~r~f~---------------------RnDk~~c~~~~kfiahLinq~VahEIv~Leil~lLLe 285 (739)
T KOG2140|consen 233 E------LLLKRLILQFKRSFR---------------------RNDKVSCLNASKFIAHLINQQVAHEIVALEILTLLLE 285 (739)
T ss_pred H------HHHHHHHHHHHHHhc---------------------ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 2 555555556665432 122346889999999999999999999999999 887
Q ss_pred cCCCCCCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHhhCCCCChHHHHHHHHHHHHHhCCCCCc
Q 004059 354 NDGKTCPAEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTTNSQLVPRLRFMIHDVLDLRANNWVPR 427 (776)
Q Consensus 354 ~~~~~~p~Ee~IE~Lc~LL~tiGk~Ld~~~k~~~~md~yF~rL~~l~~~~~lssRiRFmL~dvidLR~nnW~~r 427 (776)
. |++++||.++.+|+.||..|-... +..++.+|++|+.+.....++.|++|||+-++..|+.++..-
T Consensus 286 ~-----PTddSvevaI~flkecGakL~~VS--pr~~n~IfErlR~ILhe~Eld~rvqy~iEtlf~iRkdkfk~~ 352 (739)
T KOG2140|consen 286 R-----PTDDSVEVAIAFLKECGAKLAEVS--PRALNGIFERLRYILHEGELDRRVQYMIETLFQIRKDKFKSH 352 (739)
T ss_pred C-----CCCchHHHHHHHHHHHHHHHHHhC--hHHHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHHhhccC
Confidence 4 899999999999999999998643 346899999999999888999999999999999999888743
No 9
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=99.43 E-value=4.4e-12 Score=145.12 Aligned_cols=199 Identities=20% Similarity=0.266 Sum_probs=148.8
Q ss_pred HHHHHHHHHHHHhcCChhhHHHHHHHHHHccCCC-HHHHHHHHHHHHHHHhhC-----CCChHHHHHHHHHHhhhCCCCC
Q 004059 195 KDRVLKTVKGILNKLTPEKFDVLKGQLIDSGITT-PDILKGVIELIFDKAVLE-----PTFCPMYALLCSDLNEKLPPFP 268 (776)
Q Consensus 195 ~e~l~rkVk~ILNKLTpenFd~l~~qLl~l~I~t-~e~Lk~VI~lIFeKAi~E-----p~fs~mYA~LC~~L~~~lp~~~ 268 (776)
..++.|+|+|+||||+..|+.+|+..|..++..+ ....+.-+.-...+|+.- -.++..||-|...|+....
T Consensus 316 l~rl~rkv~g~LNKLSdaNi~~I~~~i~~Ly~~~sr~~v~~sLtk~l~~~~~~~~~~ld~~~~~y~AL~~~l~~~vg--- 392 (822)
T KOG2141|consen 316 LQRLRRKVNGSLNKLSDANIIKIIAGIAELYMNNSRYDVTSSLTKLLLKALLGPFRLLDSLLTTYAALAAMLHTMVG--- 392 (822)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHh---
Confidence 3579999999999999999999999999987643 222333333333344443 3578899999999988642
Q ss_pred CCCCCCchhhHHHHHHHHHHHHHhhhhchHHHHhhcCChHHHHHHhHHHHHHHHhhhhHHHHHHHHHhcCCCCHHHHHHH
Q 004059 269 SDEPGGKDITFKRILLNHCQEAFEGADNTRAEIRQMTAPEQEMERMDQERLVKLRTLGNIRLIGELLKQKMVPEKIVHHI 348 (776)
Q Consensus 269 ~~e~~gk~~~FR~~LLnrcQeeFe~~~~~~~ei~~~~~~e~E~E~~e~e~~~Krr~LGnIrFIGELfk~~mL~e~Im~~c 348 (776)
..|-..++....+.|-...+.. +++... -+.+-+.+.|+++||..+++...+|+++
T Consensus 393 --------~eigahf~q~~ve~f~~~~~~~----------~~~~~~------~K~~~Nl~~~l~ylynF~ivs~~Liydi 448 (822)
T KOG2141|consen 393 --------NEIGAHFLQTFVEDFLKSYKEE----------EEMDLK------DKSLNNIVLFLSYLYNFGIVSCSLIYDI 448 (822)
T ss_pred --------hHHHHHHHHHHHHHHHHHHHHH----------Hhcccc------cchhhhHHHHHHHHHHhhcccHHHHHHH
Confidence 3455566766677777654311 111111 1357799999999999999999999999
Q ss_pred HH-hhhcCCCCCCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHhhCCC---CChHHHHHHHHHHHHHhCCC
Q 004059 349 VQ-LLENDGKTCPAEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTTNSQ---LVPRLRFMIHDVLDLRANNW 424 (776)
Q Consensus 349 i~-LL~~~~~~~p~Ee~IE~Lc~LL~tiGk~Ld~~~k~~~~md~yF~rL~~l~~~~~---lssRiRFmL~dvidLR~nnW 424 (776)
|. |+.+ ++|-++|||..++..||..|..++. ..+.+++..|+..+.+.. .++|+|||+..++.|++|+-
T Consensus 449 I~kl~~~-----l~e~~ve~ll~ii~~~G~~LRkDDp--~alk~~i~eiq~~a~~a~~s~~~pR~rFmleti~aLKnN~~ 521 (822)
T KOG2141|consen 449 IRKLAEN-----LNETNVEALLTIIANCGFSLRKDDP--LALKDIITEIQSKAASAKISAISPRLRFMLETISALKNNKL 521 (822)
T ss_pred HHHHHhc-----hhhhhHHHHHHHHHHccchhcCCCh--HHHHHHHHHHHHHhhcCCccccchHHHHHHHHHHHHhcCCC
Confidence 99 8775 7899999999999999999987543 356777777777665433 37999999999999999877
Q ss_pred CCc
Q 004059 425 VPR 427 (776)
Q Consensus 425 ~~r 427 (776)
.+-
T Consensus 522 kki 524 (822)
T KOG2141|consen 522 KKI 524 (822)
T ss_pred cCC
Confidence 644
No 10
>KOG3942 consensus MIF4G domain-containing protein [Translation, ribosomal structure and biogenesis]
Probab=98.81 E-value=5.5e-08 Score=102.87 Aligned_cols=169 Identities=18% Similarity=0.143 Sum_probs=133.0
Q ss_pred CHHHHHHHHHHHHHHHhhCCCChHHHHHHHHHHhhhCCCCCCCCCCCchhhHHHHHHHHHHHHHhhhhchHHHHhhcCCh
Q 004059 228 TPDILKGVIELIFDKAVLEPTFCPMYALLCSDLNEKLPPFPSDEPGGKDITFKRILLNHCQEAFEGADNTRAEIRQMTAP 307 (776)
Q Consensus 228 t~e~Lk~VI~lIFeKAi~Ep~fs~mYA~LC~~L~~~lp~~~~~e~~gk~~~FR~~LLnrcQeeFe~~~~~~~ei~~~~~~ 307 (776)
+.+.|-.++-.|+.+||..-.|.-.-++||..|..... +.+.|+..||+.|++.|+-+..++ +
T Consensus 163 ~de~l~rc~~~~~r~avegg~ggl~v~klC~n~~~~~~---------~gt~f~~~Lln~lrq~f~~r~gl~----s---- 225 (348)
T KOG3942|consen 163 DDEMLFRCGPTIARQAVEGGGGGLFVCKLCTNLGSSWR---------NGTQFMDELLNLLRQGFLLRTGLS----S---- 225 (348)
T ss_pred hHHHHHHHHHHHHHHHHhcCCCchhHHHHhhhhhhhhh---------ccchHHHHHHHHHHHhhccchhcc----c----
Confidence 35788899999999999999999999999998876532 345699999999999998764322 1
Q ss_pred HHHHHHhHHHHHHHHhhhhHHHHHHHHHhcC-----CCCHHHHHHHHH-hhhcCCCCCCChhhHHHHHHHHHHHhhhhhc
Q 004059 308 EQEMERMDQERLVKLRTLGNIRLIGELLKQK-----MVPEKIVHHIVQ-LLENDGKTCPAEENVEAICQFFNTIGKQLDE 381 (776)
Q Consensus 308 e~E~E~~e~e~~~Krr~LGnIrFIGELfk~~-----mL~e~Im~~ci~-LL~~~~~~~p~Ee~IE~Lc~LL~tiGk~Ld~ 381 (776)
....|++++|.|++|||-+- +|=..++..|++ ||..- ...+..+|||.-.|..+|..|++
T Consensus 226 -----------~~~~rw~~fisfltelf~nlgs~p~~vL~~~l~~cl~~llrsp---d~~~~e~ecl~~~L~~~g~dle~ 291 (348)
T KOG3942|consen 226 -----------LASCRWWRFISFLTELFDNLGSCPQVVLQRSLRLCLQILLRSP---DWPEFEYECLSMKLAVEGLDLEK 291 (348)
T ss_pred -----------hhHHHHHHHHHHHHHHHhhcCCCChhhHHHHHHHHHHHHccCC---CcchHHHHHHHHHHHHcCccchh
Confidence 12358999999999999874 555778999999 88752 23578999999999999999986
Q ss_pred CCcchhhHHHHHHHHHHHhhCCCCC-hHHHHHHHHHHHHHhCCCCCccc
Q 004059 382 NPKSRRVNDVYFSRLKELTTNSQLV-PRLRFMIHDVLDLRANNWVPRRE 429 (776)
Q Consensus 382 ~~k~~~~md~yF~rL~~l~~~~~ls-sRiRFmL~dvidLR~nnW~~r~~ 429 (776)
. -...|..+|.-.++..-+..-| .-+|.||..+|||-++.|.++..
T Consensus 292 q--lP~ql~lL~~s~rDafL~~sep~a~~r~~lllliel~As~wqlpt~ 338 (348)
T KOG3942|consen 292 Q--LPFQLLLLFPSRRDAFLVRSEPLAPWRCPLLLLIELPASAWQLPTT 338 (348)
T ss_pred h--hhHHHHHHHHHHHHhhhccccccccccchhhhccccCccccCCCCC
Confidence 3 2345667777777655444444 34699999999999999998753
No 11
>KOG2051 consensus Nonsense-mediated mRNA decay 2 protein [RNA processing and modification]
Probab=98.74 E-value=8e-08 Score=114.69 Aligned_cols=183 Identities=22% Similarity=0.356 Sum_probs=129.8
Q ss_pred HHHHHHHHHhcCC----hhhHHHHHHHHHHccCCCHHHHHHHHHHHHHHHhhCCCChHHHHHHHHHHhhhCCCCCCCCCC
Q 004059 198 VLKTVKGILNKLT----PEKFDVLKGQLIDSGITTPDILKGVIELIFDKAVLEPTFCPMYALLCSDLNEKLPPFPSDEPG 273 (776)
Q Consensus 198 l~rkVk~ILNKLT----penFd~l~~qLl~l~I~t~e~Lk~VI~lIFeKAi~Ep~fs~mYA~LC~~L~~~lp~~~~~e~~ 273 (776)
+..+|...|-+|- -+-+|.++.++... ++|...=+.+|..+|.---+.-...+.|++|...|...+|.+.
T Consensus 423 ~~~~~d~Fl~~L~~~vsrdliD~~a~ef~~n-lNtKa~RkrLvKal~~vprt~ldllPyYsRlVAtl~~~M~dva----- 496 (1128)
T KOG2051|consen 423 VVSNVDCFLLDLPNCVSRDLIDQAAIEFCSN-LNTKANRKRLVKALFVVPRTRLDLLPYYSRLVATLSKCMPDVA----- 496 (1128)
T ss_pred HHHHHHHHHccCcchHHHHHHHHHHHHHHHH-hccHHHHHHHHHhhhcccchhhhhhhHHHHHHHHHHhhhhHHH-----
Confidence 4445555555554 34455555555443 7788888899999998766777889999999999999987653
Q ss_pred CchhhHHHHHHHHHHHHHhhhhchHHHHhhcCChHHHHHHhHHHHHHHHhhhhHHHHHHHHHhcCCCCHHHHHHHHH-hh
Q 004059 274 GKDITFKRILLNHCQEAFEGADNTRAEIRQMTAPEQEMERMDQERLVKLRTLGNIRLIGELLKQKMVPEKIVHHIVQ-LL 352 (776)
Q Consensus 274 gk~~~FR~~LLnrcQeeFe~~~~~~~ei~~~~~~e~E~E~~e~e~~~Krr~LGnIrFIGELfk~~mL~e~Im~~ci~-LL 352 (776)
.-|++..-++|...-.....+ +.| ..+-+|+|||||.|.++++..-+..|++ ||
T Consensus 497 -------t~lv~~L~~eFr~~~hkK~q~--------~ie----------tk~~~VrfIsEL~KF~lv~~~~if~cLk~ll 551 (1128)
T KOG2051|consen 497 -------TELVTMLRKEFRSHLHKKAQI--------NIE----------TKLKIVRFISELCKFQLVPKFEIFSCLKMLL 551 (1128)
T ss_pred -------HHHHHHHHHHHHHHHhhhhhh--------hhh----------hhhhhhhhHHhhhhhCccChHHHHHHHHHHH
Confidence 357777777787642111000 011 1245899999999999999999999999 87
Q ss_pred hcCCCCCCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHhhCCCCChHHHHHHHHH
Q 004059 353 ENDGKTCPAEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTTNSQLVPRLRFMIHDV 416 (776)
Q Consensus 353 ~~~~~~~p~Ee~IE~Lc~LL~tiGk~Ld~~~k~~~~md~yF~rL~~l~~~~~lssRiRFmL~dv 416 (776)
.. ..-.+||.+|.||++||+.|-.++..+..|..++++|+.......+.+|-.-+|.++
T Consensus 552 ~d-----F~~hnIEm~c~lLE~~GrfLlr~pEt~lrM~~~Le~i~rkK~a~~lDsr~~~~iENa 610 (1128)
T KOG2051|consen 552 ND-----FTHHNIEMACVLLESCGRFLLRSPETKLRMRVFLEQIKRKKRASALDSRQATLIENA 610 (1128)
T ss_pred Hh-----cccccHHHHHHHHHhcchhhhcChhHHHHHHHHHHHHHHHHHHhhhchHHHHHHHHh
Confidence 64 345679999999999999999888777778888888875444444444444444443
No 12
>KOG0401 consensus Translation initiation factor 4F, ribosome/mRNA-bridging subunit (eIF-4G) [Translation, ribosomal structure and biogenesis]
Probab=98.23 E-value=1.7e-07 Score=115.77 Aligned_cols=271 Identities=20% Similarity=0.221 Sum_probs=181.2
Q ss_pred CCCcchhcccCCccccc------CCC---Ch-----HHHHHHHHHHHHhcCChhhHHHHHHHHHHcc-----CCCHHHHH
Q 004059 173 GPAPALIKAEVPWSARR------GNL---SE-----KDRVLKTVKGILNKLTPEKFDVLKGQLIDSG-----ITTPDILK 233 (776)
Q Consensus 173 ~p~~~l~~~e~~w~~~~------~~~---~e-----~e~l~rkVk~ILNKLTpenFd~l~~qLl~l~-----I~t~e~Lk 233 (776)
...++...+.+.|.+.. ..+ ++ .+.+.+.+.+.+|++++++|+.+...++... -.+.+.++
T Consensus 588 eei~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~i~~~~~~~~~~~~~e~~~~~~k 667 (970)
T KOG0401|consen 588 EEIAPEAPSANRWSPKSLSKKTEGRLAEESDSGLLGKEVVERKGKSGLRKLTPEMFDKISDPILDIADQSMDEEDGEASK 667 (970)
T ss_pred hhcchhhhhhcccCcccccccccccccccccccccCccccccccccccccCChhhcccccccccccchhhccccccchhh
Confidence 44567777888898742 111 11 2345788999999999999999999987542 25688999
Q ss_pred HHHHHHHHHHhhCCCChHHHHHHHHHHhhhCCCCCC---CCCCCchhhHHHHHHHHHHHHHhhhhchHHHHhhcCChH-H
Q 004059 234 GVIELIFDKAVLEPTFCPMYALLCSDLNEKLPPFPS---DEPGGKDITFKRILLNHCQEAFEGADNTRAEIRQMTAPE-Q 309 (776)
Q Consensus 234 ~VI~lIFeKAi~Ep~fs~mYA~LC~~L~~~lp~~~~---~e~~gk~~~FR~~LLnrcQeeFe~~~~~~~ei~~~~~~e-~ 309 (776)
.++..++.|+..+++|+.||+..|.........-.. .........+.+.+..+|+.+|.+.+.-.--........ +
T Consensus 668 ~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~e 747 (970)
T KOG0401|consen 668 QKGEQGGRKASDEQHFSSMRAPALEKVVPSLSSDIDDKRNRGSNGELLSDSYLSARCHEEFENGWSRELPSGKDGEREPE 747 (970)
T ss_pred hcccccccccCccccccccCCccccccccccccccccccccCCccccccccccchhhhhhccccccccCCCCcccccchh
Confidence 999999999999999999999999987665432100 011122346788999999999998764210000000000 0
Q ss_pred HH-HHhHHHHHHHHhhhhHHHHHHHHHhcCCCCHHHHHHHHH-hhhcCCCCCCChhhHHHHHHHHHHHhhhhhcCCcchh
Q 004059 310 EM-ERMDQERLVKLRTLGNIRLIGELLKQKMVPEKIVHHIVQ-LLENDGKTCPAEENVEAICQFFNTIGKQLDENPKSRR 387 (776)
Q Consensus 310 E~-E~~e~e~~~Krr~LGnIrFIGELfk~~mL~e~Im~~ci~-LL~~~~~~~p~Ee~IE~Lc~LL~tiGk~Ld~~~k~~~ 387 (776)
.+ +........+++.+|+| +......+.+.+..|++.|+. .+... ..+..+.+++.|.++++||..++..-....
T Consensus 748 ~~~~~~~~~~~~~~~~~~~v-~~~~~~~l~~~sk~l~ee~~~~~~~~~--~~~~ie~l~S~~~~~~~v~~~v~~~l~~~~ 824 (970)
T KOG0401|consen 748 MMSPEYYAAKAAKRAGLGLV-IALSSELLELLSKSLLEEFLSLRLEKE--ALKCIEELESPSLLLKTVGENIEPTLEKSP 824 (970)
T ss_pred hcCcccchhhhhhccCCcch-hhhhHHHHHHHHHHHHHHHHHHhhhhh--hhhhhhcccchhhhHHHHHHhcCcccccCh
Confidence 00 11223345688999999 777777778999999999998 44431 346788999999999999999985332212
Q ss_pred hHHHHHHHHHH-Hh-hC------CCCChHHHHHHHHHHHHH-hCCCCCcccccCCccHHHHHHHHHHh
Q 004059 388 VNDVYFSRLKE-LT-TN------SQLVPRLRFMIHDVLDLR-ANNWVPRREEMKAKTITEIHSEAEKN 446 (776)
Q Consensus 388 ~md~yF~rL~~-l~-~~------~~lssRiRFmL~dvidLR-~nnW~~r~~~~~pkti~eIh~eae~~ 446 (776)
.+..+..+|-. ++ ++ -..+.+..|-+.|.+.++ -++|.--.+..+|.+++.++.+.+..
T Consensus 825 ~~~~~~~~ll~~l~~~~~~~~~~~~~~~~~~~~~~~d~~~d~pk~w~~~~e~~gp~~~~~~~~~~e~~ 892 (970)
T KOG0401|consen 825 QAVEELLQLLDILVSKNPLSIETLEIGYREKFKLADDKELDLPKGWNYIKEFLGPLIHQKILDESELV 892 (970)
T ss_pred hHHHHHHHHHHHHHhcCcccHHHHhhhHHHHHhhhHHHhcccccchhHHHHhhhhHhhhccccHHHHH
Confidence 22333333322 11 11 124667777777777776 47888877778888888888776543
No 13
>KOG2051 consensus Nonsense-mediated mRNA decay 2 protein [RNA processing and modification]
Probab=97.56 E-value=0.0023 Score=77.71 Aligned_cols=183 Identities=17% Similarity=0.271 Sum_probs=114.1
Q ss_pred cCChhhHHHHHHHHHHccCCCHHHHHHHHHHHHHHHhhCCCChHHHHHHHHHHhhhCCCCCCCCCCCchhhHHHHHHHHH
Q 004059 208 KLTPEKFDVLKGQLIDSGITTPDILKGVIELIFDKAVLEPTFCPMYALLCSDLNEKLPPFPSDEPGGKDITFKRILLNHC 287 (776)
Q Consensus 208 KLTpenFd~l~~qLl~l~I~t~e~Lk~VI~lIFeKAi~Ep~fs~mYA~LC~~L~~~lp~~~~~e~~gk~~~FR~~LLnrc 287 (776)
.|+..+|+.++.++-.+.-.++++=+.+|..+..-=.-.-+--..-|.|..-|+...|.|.. ..+.
T Consensus 641 dL~k~tvd~~lkllRkl~W~D~e~~~yli~~~~k~w~iky~~i~~lA~llaGL~~y~~~fvi------------~VID-- 706 (1128)
T KOG2051|consen 641 DLSKDTVDRVLKLLRKLDWSDPEVKQYLISCFSKPWKIKYQNIHALASLLAGLSSYHPEFVI------------HVID-- 706 (1128)
T ss_pred HhccccHHHHHHHHHhcccccHHHHHHHHHHhhhhhccccccHHHHHHHHHHHHhhchhhhh------------hhHH--
Confidence 45556677777777766666677777777776643333333334446666666655443321 1111
Q ss_pred HHHHhhhhchHHHHhhcCChHHHHHHhHHHHHHHHhhhhHHHHHHHHHhcCCCCHHHHHHHHH-hhh--cCCC-----CC
Q 004059 288 QEAFEGADNTRAEIRQMTAPEQEMERMDQERLVKLRTLGNIRLIGELLKQKMVPEKIVHHIVQ-LLE--NDGK-----TC 359 (776)
Q Consensus 288 QeeFe~~~~~~~ei~~~~~~e~E~E~~e~e~~~Krr~LGnIrFIGELfk~~mL~e~Im~~ci~-LL~--~~~~-----~~ 359 (776)
..+|.. .. -+|..+ ...+.|++.++|||||||...|+...+|...+= ++. .... ..
T Consensus 707 -~vlE~I-------r~------glEin~--~~~nQrriA~aryL~ELynfemvds~vIl~tLy~~i~~g~~~~~~~~~ld 770 (1128)
T KOG2051|consen 707 -HVLEDI-------RP------GLEIND--YVSNQRRIALARYLGELYNFEMVDSDVILNTLYHLISLGHFENLTPSALD 770 (1128)
T ss_pred -HHHHHH-------Hh------hhhcCc--HHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHhcccccCCCCcccCC
Confidence 122221 10 011111 345678899999999999999999988887776 443 2111 01
Q ss_pred CChh--hHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHhhCC--CCChHHHHHHHHHHHHHh
Q 004059 360 PAEE--NVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTTNS--QLVPRLRFMIHDVLDLRA 421 (776)
Q Consensus 360 p~Ee--~IE~Lc~LL~tiGk~Ld~~~k~~~~md~yF~rL~~l~~~~--~lssRiRFmL~dvidLR~ 421 (776)
|.++ -|--+|.||.|||..++. .+.+..|+.|+-..+...--+ ..|--+.++++|++.+-.
T Consensus 771 ppddlFRirlV~~lL~tc~~yf~r-gs~kkkl~~fL~~fq~Y~~iKk~~~Pld~~~~f~d~~~~~r 835 (1128)
T KOG2051|consen 771 PPDDLFRIRLVCMLLQTCGPYFTR-GSTKKKLDQFLVAFQRYILIKKSQQPLDMEYEFEDFLELVR 835 (1128)
T ss_pred ChHHHHHHHHHHHHHHHccccccc-chhHHHHHHHHHHHHHHhhcccccCCCchhhhHHhhhhhcc
Confidence 2222 688899999999999985 345567888777777644322 478889999999998743
No 14
>KOG1104 consensus Nuclear cap-binding complex, subunit NCBP1/CBP80 [RNA processing and modification]
Probab=94.48 E-value=2.4 Score=51.00 Aligned_cols=201 Identities=14% Similarity=0.233 Sum_probs=134.0
Q ss_pred CCCChHHHHHHHHHHHHhcCCh-------hhHHHHHHHHHHccCCCHHHHHHHHHHHHHHHhhCCCChHHHHHHHHHHhh
Q 004059 190 GNLSEKDRVLKTVKGILNKLTP-------EKFDVLKGQLIDSGITTPDILKGVIELIFDKAVLEPTFCPMYALLCSDLNE 262 (776)
Q Consensus 190 ~~~~e~e~l~rkVk~ILNKLTp-------enFd~l~~qLl~l~I~t~e~Lk~VI~lIFeKAi~Ep~fs~mYA~LC~~L~~ 262 (776)
...++.+.+.+++.+..-++.. .|.+.+..-|.+ .+ +..-..+++.|-.=|+.-|.=+..||-|...|+.
T Consensus 19 ~r~~~~e~l~krl~~~i~~vg~~s~ss~e~~l~~l~~~l~~-~~--~~~~~~iL~~L~~ca~~lP~K~~~yaTLvgllN~ 95 (759)
T KOG1104|consen 19 RRISPAETLEKRLESLIREVGEPSGSSVEDNLENLVAVLEA-DL--ENFKSKILDILNTCAVYLPEKITAYATLVGLLNL 95 (759)
T ss_pred ccCCcHHHHHHHHHHHHHhhcCCCCCcHHHhHHHHHHHHHh-hH--HHHHHHHHHHHHHHHHHcccchhHHHHHHHHHhc
Confidence 3456678888889888888882 344444433332 11 2244567888888899999999999999999987
Q ss_pred hCCCCCCCCCCCchhhHHHHHHHHHHHHHhhhhchHHHHhhcCChHHHHHHhHHHHHHHHhhhhHHHHHHHHHhcCCCCH
Q 004059 263 KLPPFPSDEPGGKDITFKRILLNHCQEAFEGADNTRAEIRQMTAPEQEMERMDQERLVKLRTLGNIRLIGELLKQKMVPE 342 (776)
Q Consensus 263 ~lp~~~~~e~~gk~~~FR~~LLnrcQeeFe~~~~~~~ei~~~~~~e~E~E~~e~e~~~Krr~LGnIrFIGELfk~~mL~e 342 (776)
+-.. |-.-+++..-.+|... ++... -.+.-+.+||+..|+.-+|+..
T Consensus 96 kn~~------------fg~~~v~~~~~~~q~s------l~~~~---------------~n~ar~llrfL~dL~~~~vl~~ 142 (759)
T KOG1104|consen 96 KNFN------------FGGEFVEYMIEELQES------LKSGN---------------WNEARYLLRFLSDLSNCHVLQA 142 (759)
T ss_pred cchh------------hHHHHHHHHHHHHHHH------hhcCC---------------hHHHHHHHHHHHHHhcCCccCh
Confidence 6433 3333444433333321 11100 0123478999999999999999
Q ss_pred HHHHHHHH-hhhcCCC-CCC---ChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHhhCCC-------------
Q 004059 343 KIVHHIVQ-LLENDGK-TCP---AEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTTNSQ------------- 404 (776)
Q Consensus 343 ~Im~~ci~-LL~~~~~-~~p---~Ee~IE~Lc~LL~tiGk~Ld~~~k~~~~md~yF~rL~~l~~~~~------------- 404 (776)
.-|..++. |+..... ..| .+--+-|+..-|--+|+.|.+. .+..|+.++..++...+.++
T Consensus 143 ~sli~l~esl~~~~~e~~~Pqvr~D~~v~~vLs~lPw~g~el~e~--~~~~~e~ll~~ie~Yl~~R~~shi~lL~vw~~~ 220 (759)
T KOG1104|consen 143 DSLINLFESLLDAAIEENVPQVRRDYYVYCVLSSLPWFGRELNEK--KPTEMEELLVYIEIYLKKRKKSHINLLNVWSGE 220 (759)
T ss_pred HHHHHHHHHHHHHHHhhcCcchhhhHHHHHHHhccchhhhhhccc--chHHHHHHHHHHHHHHHHhcccccchhhcCCCC
Confidence 88888888 7764211 123 3456778888888899999753 34678988888876443221
Q ss_pred --CChH--HHHHHHHHHHHHhCCCCCcc
Q 004059 405 --LVPR--LRFMIHDVLDLRANNWVPRR 428 (776)
Q Consensus 405 --lssR--iRFmL~dvidLR~nnW~~r~ 428 (776)
..++ ++.+...|..||.|+|....
T Consensus 221 ~~~~qeeyle~L~~qI~~lr~n~w~e~h 248 (759)
T KOG1104|consen 221 PDHPQEEYLELLWAQIQKLRQNDWAENH 248 (759)
T ss_pred CCchHHHHHHHHHHHHHHHHhcCccccc
Confidence 2222 77899999999999999744
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=89.85 E-value=0.17 Score=44.22 Aligned_cols=27 Identities=26% Similarity=0.433 Sum_probs=15.9
Q ss_pred cCCCccCCC-cccccCHHHHHHHHHHhh
Q 004059 54 MGDLRFEGH-ERVRYTREQLLQLKEVAQ 80 (776)
Q Consensus 54 ~~~~~~~~~-~~~~y~~~~l~~~~~~~~ 80 (776)
.-+++++.. -+.||.++|||||+.+|.
T Consensus 42 ~P~~~ln~~~~kf~Yd~~FLLQF~~v~~ 69 (75)
T PF12152_consen 42 SPDPALNKAAKKFRYDPDFLLQFQDVFK 69 (75)
T ss_dssp -SSTTGGGSS-SS---HHHHHHHHHHH-
T ss_pred CCCHHHccccCccccCHHHHHHHHHHhc
Confidence 334444443 588999999999999993
No 16
>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=85.80 E-value=9 Score=45.50 Aligned_cols=155 Identities=24% Similarity=0.350 Sum_probs=90.6
Q ss_pred HHHHHHHHHHHhcCChhhHHHHHHHHHHccC----CCHHHHHHHHHHHHHHHhhC----CCChHHHHHHHHHHhhhCCCC
Q 004059 196 DRVLKTVKGILNKLTPEKFDVLKGQLIDSGI----TTPDILKGVIELIFDKAVLE----PTFCPMYALLCSDLNEKLPPF 267 (776)
Q Consensus 196 e~l~rkVk~ILNKLTpenFd~l~~qLl~l~I----~t~e~Lk~VI~lIFeKAi~E----p~fs~mYA~LC~~L~~~lp~~ 267 (776)
+-|...++.+|..+|.+.|+.++.=|-.+.+ .+.+..+.++++|++.|--+ +.....+.+|...+...+|-|
T Consensus 177 ~~i~~~ikkvL~DVTaeEF~l~m~lL~~lk~~~~~~t~~g~qeLv~ii~eQa~Ld~~f~~sD~e~Idrli~C~~~Alp~f 256 (556)
T PF05918_consen 177 EFIVDEIKKVLQDVTAEEFELFMSLLKSLKIYGGKQTIEGRQELVDIIEEQADLDQPFDPSDPESIDRLISCLRQALPFF 256 (556)
T ss_dssp HHHHHHHHHHCTT--HHHHHHHHHHHHTSGG---GSSHHHHHHHHHHHHHHHTTTS---SSSHHHHHHHHHHHHHHGGG-
T ss_pred HHHHHHHHHHHHhccHHHHHHHHHHHHhCccccccCChHHHHHHHHHHHHHhccCCCCCCcCHHHHHHHHHHHHHhhHHh
Confidence 4477889999999999999999955555665 68999999999999999533 344578888988888888765
Q ss_pred CCCCCCCchhhHHHHHHHHHHHHHhhhhchHHHHhhcCChHHHHHHhHHHHHHHHhhhhHHHHHHHHHhcC--CCCHHHH
Q 004059 268 PSDEPGGKDITFKRILLNHCQEAFEGADNTRAEIRQMTAPEQEMERMDQERLVKLRTLGNIRLIGELLKQK--MVPEKIV 345 (776)
Q Consensus 268 ~~~e~~gk~~~FR~~LLnrcQeeFe~~~~~~~ei~~~~~~e~E~E~~e~e~~~Krr~LGnIrFIGELfk~~--mL~e~Im 345 (776)
.. +...+.|-.++..+.-=.|+. + ++ + +.+-.++.++|+--.- +-...++
T Consensus 257 s~---~v~Sskfv~y~~~kvlP~l~~----------l--~e-~------------~kl~lLk~lAE~s~~~~~~d~~~~L 308 (556)
T PF05918_consen 257 SR---GVSSSKFVNYMCEKVLPKLSD----------L--PE-D------------RKLDLLKLLAELSPFCGAQDARQLL 308 (556)
T ss_dssp BT---TB--HHHHHHHHHHTCCCTT------------------------------HHHHHHHHHHHHHTT----THHHHH
T ss_pred cC---CCChHHHHHHHHHHhcCChhh----------C--Ch-H------------HHHHHHHHHHHHcCCCCcccHHHHH
Confidence 32 233445555554322111111 1 00 0 1134667777776542 2223344
Q ss_pred HHHHHhhhcC-C--CCCC--ChhhHHHHHHHHHHHhhh
Q 004059 346 HHIVQLLEND-G--KTCP--AEENVEAICQFFNTIGKQ 378 (776)
Q Consensus 346 ~~ci~LL~~~-~--~~~p--~Ee~IE~Lc~LL~tiGk~ 378 (776)
-.++.+|... + ...| .--.||||...+..+|+.
T Consensus 309 ~~i~~~L~~ymP~~~~~~~l~fs~vEcLL~afh~La~k 346 (556)
T PF05918_consen 309 PSIFQLLKKYMPSKKTEPKLQFSYVECLLYAFHQLARK 346 (556)
T ss_dssp HHHHHHHHTTS----------HHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHhCCCCCCCCcccchHhhHHHHHHHHHhhh
Confidence 3444433221 1 1112 224899999999888875
No 17
>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=84.14 E-value=8.4 Score=35.31 Aligned_cols=63 Identities=21% Similarity=0.241 Sum_probs=46.6
Q ss_pred HHHHHHHHhcCC-hhhHHHHHHHHHHccCCCHHHHHHHHHHHHHHHhhC-CCChHHHHHHHHHHhhh
Q 004059 199 LKTVKGILNKLT-PEKFDVLKGQLIDSGITTPDILKGVIELIFDKAVLE-PTFCPMYALLCSDLNEK 263 (776)
Q Consensus 199 ~rkVk~ILNKLT-penFd~l~~qLl~l~I~t~e~Lk~VI~lIFeKAi~E-p~fs~mYA~LC~~L~~~ 263 (776)
.|+++.+|.--- -..++..+..|.++.+. .....||..+++.++++ ..+..+|+.|..+|...
T Consensus 2 rk~i~~~l~ey~~~~d~~ea~~~l~el~~~--~~~~~vv~~~l~~~le~~~~~r~~~~~Ll~~L~~~ 66 (113)
T PF02847_consen 2 RKKIFSILMEYFSSGDVDEAVECLKELKLP--SQHHEVVKVILECALEEKKSYREYYSKLLSHLCKR 66 (113)
T ss_dssp HHHHHHHHHHHHHHT-HHHHHHHHHHTT-G--GGHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHT
T ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHhCCC--ccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHhc
Confidence 455555554221 23567777788887666 66778999999999999 99999999999999874
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=81.66 E-value=9.4 Score=35.12 Aligned_cols=62 Identities=21% Similarity=0.294 Sum_probs=47.8
Q ss_pred HHHHHHHhcC-ChhhHHHHHHHHHHccCCCHHHHHHHHHHHHHHHhhC-CCChHHHHHHHHHHhhh
Q 004059 200 KTVKGILNKL-TPEKFDVLKGQLIDSGITTPDILKGVIELIFDKAVLE-PTFCPMYALLCSDLNEK 263 (776)
Q Consensus 200 rkVk~ILNKL-TpenFd~l~~qLl~l~I~t~e~Lk~VI~lIFeKAi~E-p~fs~mYA~LC~~L~~~ 263 (776)
++|..+|+.- +...++..+.-|.++++. .....|+..++.-++++ .+|.++|+.|...|++.
T Consensus 3 k~i~~~l~ey~~~~D~~ea~~~l~~L~~~--~~~~~vv~~~i~~~le~~~~~~~~~~~Ll~~L~~~ 66 (113)
T smart00544 3 KKIFLIIEEYLSSGDTDEAVHCLLELKLP--EQHHEVVKVLLTCALEEKRTYREMYSVLLSRLCQA 66 (113)
T ss_pred hHHHHHHHHHHHcCCHHHHHHHHHHhCCC--cchHHHHHHHHHHHHcCCccHHHHHHHHHHHHHHc
Confidence 4455554432 245778888888888776 46778999999999988 58999999999999864
No 19
>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=64.71 E-value=39 Score=33.45 Aligned_cols=123 Identities=11% Similarity=0.038 Sum_probs=75.0
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHhCCCC---ChHHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCC-CCHHHHHHHH
Q 004059 613 KKTVSLLEEYFSIRILDEALQCVEELRAPT---YHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNV-LTTRDIGTGC 688 (776)
Q Consensus 613 kki~~ll~EY~~~~D~~EA~~clkEL~~p~---~~~e~V~~~I~~aLEk~~~~re~v~~LL~~L~~~~~-ls~~q~~~Gf 688 (776)
|+++.+|...- .+++++.+..+..+.... ....+|+.+++.+.+.. ......++|...|....- -=...+...+
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 56666666644 678888888887775543 34556666666655544 456788888887776332 1122233333
Q ss_pred HHHhhc------chhhhcCCCchhHHHHHHHHHHHHcCCCChHHHHHHHhhhcch
Q 004059 689 LLYGSL------LDDIGIDLPKAPNNFGEMVGKLVVAKSLDFIVLKEVLKKVEDN 737 (776)
Q Consensus 689 ~~vle~------LdDl~iDiP~A~~~La~~iaraI~d~~l~~~~v~~~~~~~~~~ 737 (776)
...+.. +++..--.=.-..-+..|+|.+..-+.++...+-+++..+...
T Consensus 80 ~~~f~~~~~~~~~~~~~~~~~~~~~~~~~fl~eL~~~~vv~~~~i~~~l~~ll~~ 134 (209)
T PF02854_consen 80 QEEFEERYSNEELEENRQSSKQRRRGNIRFLAELFNFGVVSEKIIFDILRELLSD 134 (209)
T ss_dssp HHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHH
T ss_pred HHHHHHhhhhhhHHHHHHHHHHHHhhhhhHHHhhHhhccccchhHHHHHHHHHhc
Confidence 333333 2222222223455677899999999999999888777765433
No 20
>PLN00131 hypothetical protein; Provisional
Probab=55.98 E-value=1.6e+02 Score=29.53 Aligned_cols=68 Identities=19% Similarity=0.251 Sum_probs=41.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHH-HHhccCCCChHHHHHHHHHHHh
Q 004059 597 EKPSAPVTKLNLADLRKKTVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIA-LALEKIPPCVEPVIQLLEFLLN 675 (776)
Q Consensus 597 ~~~~~~~~~~s~eel~kki~~ll~EY~~~~D~~EA~~clkEL~~p~~~~e~V~~~I~-~aLEk~~~~re~v~~LL~~L~~ 675 (776)
+..+.++|.+...++..|-+.+-+| ++.+-.+.+-.....+..+++. +.|| ++.+|.++-.|..||++
T Consensus 117 eqepepapplddqdlltkrkrvsee----------lrlllqigavkrknkiadqlldwmgld-netdrtllddlynhlyd 185 (218)
T PLN00131 117 EQEPEPAPPLDDQDLLTKRKRVSEE----------LRLLLQIGAVKRKNKIADQLLDWMGLD-NETDRTLLDDLYNHLYD 185 (218)
T ss_pred ccCCCCCCCCCcHHHHHHHHHHHHH----------HHHHHHHhhhhhhhHHHHHHHHHhccC-ccchHHHHHHHHHHHhh
Confidence 3344567778888877665554333 3333333333334455555555 4555 45678899999999987
No 21
>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=53.43 E-value=4 Score=38.72 Aligned_cols=18 Identities=33% Similarity=0.601 Sum_probs=8.6
Q ss_pred CCcccccCHHHHHHHHHH
Q 004059 61 GHERVRYTREQLLQLKEV 78 (776)
Q Consensus 61 ~~~~~~y~~~~l~~~~~~ 78 (776)
+|-||-|+|+|||++|--
T Consensus 44 GGTRIIYdR~FLL~~RnS 61 (116)
T PF05456_consen 44 GGTRIIYDRKFLLECRNS 61 (116)
T ss_dssp --------HHHHHCTCG-
T ss_pred CCcEEEEeHHHHHHhcCC
Confidence 467899999999999875
No 22
>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=48.74 E-value=3.7e+02 Score=28.83 Aligned_cols=166 Identities=17% Similarity=0.201 Sum_probs=87.9
Q ss_pred HHHHHHHHHHhcCCh--hhHHHHHHHHHHc-------------cCC-C----HHHHHHHHHHHHHHHhh----CCCChHH
Q 004059 197 RVLKTVKGILNKLTP--EKFDVLKGQLIDS-------------GIT-T----PDILKGVIELIFDKAVL----EPTFCPM 252 (776)
Q Consensus 197 ~l~rkVk~ILNKLTp--enFd~l~~qLl~l-------------~I~-t----~e~Lk~VI~lIFeKAi~----Ep~fs~m 252 (776)
.+.|+|+.-+|+||. +.+..++.+|.++ ... . .-.|..+++.|...|-. .|..+.-
T Consensus 28 ~~kr~I~~~vgQls~~~~qi~~i~~~i~~ll~~~~~~~~~~~~~~~~~~~~~~~~l~~lAk~iv~Q~e~ev~~~~~~A~P 107 (256)
T PF07817_consen 28 DLKRKINPKVGQLSNSSSQINRIINQISNLLSGQPVKSNDLQQSKNDHPLAYKYLLNFLAKKIVSQAETEVSANPESAFP 107 (256)
T ss_dssp HHHHHHCCHHHC--SBHHHHHHHHHHHHHH----------HHTTTT-SHHHHHHHHHHHHHHHHHHHHHHHHH-GGGHHH
T ss_pred HhhhhCcCcHhhccCcHHHHHHHHHHHHHHhhhhhhchhhhhhhccCCchHHHHHHHHHHHHHHHHHHHHhccCCchhhh
Confidence 466667777777774 3455555555554 111 2 23555666666666654 5888888
Q ss_pred HHHHHHHHhhhCCCCCCCCCCCchhhHHHHHHHHHHHH----H----hhh-hchHHHHhh-cC--ChHHHHHHhHHHHHH
Q 004059 253 YALLCSDLNEKLPPFPSDEPGGKDITFKRILLNHCQEA----F----EGA-DNTRAEIRQ-MT--APEQEMERMDQERLV 320 (776)
Q Consensus 253 YA~LC~~L~~~lp~~~~~e~~gk~~~FR~~LLnrcQee----F----e~~-~~~~~ei~~-~~--~~e~E~E~~e~e~~~ 320 (776)
||.++..|....|.| ..+|+.++... + ... ..-.++..+ |- ..+...| .+...
T Consensus 108 lA~v~~~l~~~~p~~------------~dillA~l~k~Cp~~vP~~~~~~~~~~~e~~~k~lGyk~~~~~~E---~~~~y 172 (256)
T PF07817_consen 108 LARVAVQLWSQHPEF------------GDILLARLHKKCPYLVPKYPGFTCDQSTEEYRKRLGYKRDDGGWE---SEDQY 172 (256)
T ss_dssp HHHHHHHHHHHSTCH------------HHHHHHHHHHH-GGGG----T-----SSHHHHHHTT--B-TTSB-----HHHH
T ss_pred HHHHHHHHHHcCCcH------------HHHHHHHHHHcCceeEeecCcccCCCCHHHHHHHcCCccCCCCcc---chHHH
Confidence 999999999887643 34555554433 1 000 000111111 00 0000011 11223
Q ss_pred HHhhhhHHHHHHHHHhcCCC---------CHHHHHHHHH-hhhcCCCCCC-ChhhHHHHHHHHHHHhhhhhc
Q 004059 321 KLRTLGNIRLIGELLKQKMV---------PEKIVHHIVQ-LLENDGKTCP-AEENVEAICQFFNTIGKQLDE 381 (776)
Q Consensus 321 Krr~LGnIrFIGELfk~~mL---------~e~Im~~ci~-LL~~~~~~~p-~Ee~IE~Lc~LL~tiGk~Ld~ 381 (776)
-.|+-|.+++-+-+.....- +-..-=..+. +|... | .+-....|..+|+.+|..|-.
T Consensus 173 ~~Rm~Gi~~lyaAi~~~~~~~~~~~~~p~~~~~~W~wlAr~lN~~----p~~~~~~~lL~~~Le~ag~~l~~ 240 (256)
T PF07817_consen 173 LKRMTGIIRLYAAIIQTPPPKGQKTSNPHGLEHGWRWLARILNLP----PAPNITATLLHSFLEVAGFRLLQ 240 (256)
T ss_dssp HHHHHHHHHHHHHHHHS---CCCCTT-SS-THHHHHHHHHHHCS-----CC-HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhccCCcCCCCCCCCCcHHHHHHHHHHhCCC----CCcccHHHHHHHHHHHHHHHHHH
Confidence 35889999999999875422 1222223344 55532 3 456788899999999999975
No 23
>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=48.30 E-value=47 Score=27.97 Aligned_cols=46 Identities=28% Similarity=0.418 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHHHHh--cCCCHHHHHHHHHHhCCCCChHHHHHHHHH
Q 004059 608 LADLRKKTVSLLEEYF--SIRILDEALQCVEELRAPTYHPEVVKEAIA 653 (776)
Q Consensus 608 ~eel~kki~~ll~EY~--~~~D~~EA~~clkEL~~p~~~~e~V~~~I~ 653 (776)
-+++++.+..+|.|-- .-.+++|-+.|.-.||.|.+|..+|.-...
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 4688888888887753 335899999999999999888766655444
No 24
>PRK14703 glutaminyl-tRNA synthetase/YqeY domain fusion protein; Provisional
Probab=47.54 E-value=3.4e+02 Score=34.02 Aligned_cols=86 Identities=14% Similarity=0.111 Sum_probs=48.8
Q ss_pred ChHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcchhhhcCCCchhHHHHHHHHHHHHcCCCChHHHHHHHhhhc------
Q 004059 662 CVEPVIQLLEFLLNKNVLTTRDIGTGCLLYGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLDFIVLKEVLKKVE------ 735 (776)
Q Consensus 662 ~re~v~~LL~~L~~~~~ls~~q~~~Gf~~vle~LdDl~iDiP~A~~~La~~iaraI~d~~l~~~~v~~~~~~~~------ 735 (776)
.-+.++.|+ .|+..|.||.....+-|..+++.=. + + ..+|...=...+-+...|+.++.++.
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----P---EAIVEAKGLEQVSDAGALEPIVEEVLAAHPDK 730 (771)
T ss_pred CHHHHHHHH-HHHHcCCccHHHHHHHHHHHHhcCC----C----H---HHHHHhcCCcccCCHHHHHHHHHHHHHHCHHH
Confidence 347888887 4667799999999888888775411 1 1 12222221111122244444444332
Q ss_pred -------chhHHHHHHHHHHHHHhcCCCchh
Q 004059 736 -------DNMFRRSIFTAAMKSIQSSPAGQE 759 (776)
Q Consensus 736 -------~~~~~~~~~~a~l~~l~~~~~g~~ 759 (776)
......-++|.||+..+..=.++-
T Consensus 731 Ve~yk~GK~kalgfLVGqVMK~tkGKAdP~~ 761 (771)
T PRK14703 731 VAAYRAGKTKLLGFFVGQVMRETGGKANPQQ 761 (771)
T ss_pred HHHHhcchHHHHHHHHHHHHHHhCCCCCHHH
Confidence 245567778999988876534433
No 25
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=45.36 E-value=1.7e+02 Score=35.75 Aligned_cols=62 Identities=13% Similarity=0.108 Sum_probs=37.6
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCCCH
Q 004059 616 VSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTT 681 (776)
Q Consensus 616 ~~ll~EY~~~~D~~EA~~clkEL~~p~~~~e~V~~~I~~aLEk~~~~re~v~~LL~~L~~~~~ls~ 681 (776)
..+|.-|...|++++|...++++..+. .++...+..++-+. ...+.+..+|..+...|+...
T Consensus 263 n~Li~~y~k~g~~~~A~~vf~~m~~~~---~vt~n~li~~y~~~-g~~~eA~~lf~~M~~~g~~pd 324 (697)
T PLN03081 263 CALIDMYSKCGDIEDARCVFDGMPEKT---TVAWNSMLAGYALH-GYSEEALCLYYEMRDSGVSID 324 (697)
T ss_pred HHHHHHHHHCCCHHHHHHHHHhCCCCC---hhHHHHHHHHHHhC-CCHHHHHHHHHHHHHcCCCCC
Confidence 556777777788888888777776543 34444444444433 234556677777766555433
No 26
>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]
Probab=44.59 E-value=69 Score=37.84 Aligned_cols=140 Identities=15% Similarity=0.128 Sum_probs=91.0
Q ss_pred CCCHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCCC-hHHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCCCHHH
Q 004059 605 KLNLADLRKKTVSLLEEYFSIRILDEALQCVEELRAPTY-HPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRD 683 (776)
Q Consensus 605 ~~s~eel~kki~~ll~EY~~~~D~~EA~~clkEL~~p~~-~~e~V~~~I~~aLEk~~~~re~v~~LL~~L~~~~~ls~~q 683 (776)
..+.-+|+++|--.|. ++-|.+||..-+-.++.|.- ..+++..+|.....-..= -..-+-|...++.-+..=.+.
T Consensus 448 ~~Nlv~frr~IYLti~---SSldfeEaaHKLLKmkip~~q~~elc~mii~cc~QerTy-~kFYglL~eRfc~l~r~~q~~ 523 (739)
T KOG2140|consen 448 ETNLVNFRRTIYLTIQ---SSLDFEEAAHKLLKMKIPESQEKELCNMIIDCCAQERTY-EKFYGLLGERFCMLHREWQEA 523 (739)
T ss_pred cchhHHhhhhheeeee---ccCcHHHHHHHHHhccCCchhhHHHHHHHHHHhhhHHHH-HHHHHHHHHHHHHHHHHHHHH
Confidence 3455667766643332 57899999999999988765 477887777765433211 112222222333323345678
Q ss_pred HHHHHHHHhhcchhhhcCCCchhHHHHHHHHHHHHcCCCChHHHHHHHhhhcch-----hHHHHHHHHHHHHH
Q 004059 684 IGTGCLLYGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLDFIVLKEVLKKVEDN-----MFRRSIFTAAMKSI 751 (776)
Q Consensus 684 ~~~Gf~~vle~LdDl~iDiP~A~~~La~~iaraI~d~~l~~~~v~~~~~~~~~~-----~~~~~~~~a~l~~l 751 (776)
|++-|+..++.+.+++.+- --.||+|+|+++.-+.||...++.+---=+++ -|-+-+|.++.+.|
T Consensus 524 fe~~f~q~YstIhr~Etnk---LRnlakffahLlstd~lpw~vl~~ikLTEEdTtsssRIfiKilFqELve~l 593 (739)
T KOG2140|consen 524 FEKCFKQQYSTIHRYETNK---LRNLAKFFAHLLSTDALPWDVLACIKLTEEDTTSSSRIFIKILFQELVEAL 593 (739)
T ss_pred HHHHHHHHHHHHHHHhHHH---HHHHHHHHHHHhcccccchHHHHHhhcccccCCccceehHHHHHHHHHHHh
Confidence 8999999999999998653 45699999999999999999887553322333 34455555554443
No 27
>PRK05477 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated
Probab=42.91 E-value=2.9e+02 Score=32.63 Aligned_cols=93 Identities=12% Similarity=0.088 Sum_probs=49.3
Q ss_pred ChHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcchh---hhc--CCC--chhHHHHHHHHHHHHcCCCChHHHHHHHhhh
Q 004059 662 CVEPVIQLLEFLLNKNVLTTRDIGTGCLLYGSLLDD---IGI--DLP--KAPNNFGEMVGKLVVAKSLDFIVLKEVLKKV 734 (776)
Q Consensus 662 ~re~v~~LL~~L~~~~~ls~~q~~~Gf~~vle~LdD---l~i--DiP--~A~~~La~~iaraI~d~~l~~~~v~~~~~~~ 734 (776)
.-+.++.|+. |+..|.||..+..+-|..+++.-.| +.- ++- .-...|..+|...|.+ .++.|++...
T Consensus 367 ~~~~l~~Li~-lv~~g~Is~~~ak~vl~~~~~~~~~~~~ii~~~gl~~isd~~~l~~iv~evi~~---np~~v~~~~~-- 440 (474)
T PRK05477 367 TPEQLAELIK-LIDDGTISGKIAKEVFEEMLETGGDPDEIVEEKGLKQISDEGALEAIVDEVLAA---NPKAVEDYKA-- 440 (474)
T ss_pred CHHHHHHHHH-HHHcCCccHHHHHHHHHHHHhcCCCHHHHHHHcCCcccCCHHHHHHHHHHHHHH---CHHHHHHHHc--
Confidence 4578888875 6677999999999999988764111 000 000 0001122222222221 1222222111
Q ss_pred cchhHHHHHHHHHHHHHhcCCCchhh
Q 004059 735 EDNMFRRSIFTAAMKSIQSSPAGQEV 760 (776)
Q Consensus 735 ~~~~~~~~~~~a~l~~l~~~~~g~~v 760 (776)
........++|.||+..+..-.++.|
T Consensus 441 Gk~~~~~~lvG~vMk~t~GkAdp~~v 466 (474)
T PRK05477 441 GKEKALGFLVGQVMKATKGKANPKLV 466 (474)
T ss_pred ccHHHHHHHHHHHHHHhcCCCCHHHH
Confidence 13466677899999988776455444
No 28
>PLN03218 maturation of RBCL 1; Provisional
Probab=42.41 E-value=1.4e+02 Score=38.70 Aligned_cols=69 Identities=9% Similarity=0.015 Sum_probs=39.3
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHhCCCCCh-HHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCCCHHHH
Q 004059 615 TVSLLEEYFSIRILDEALQCVEELRAPTYH-PEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDI 684 (776)
Q Consensus 615 i~~ll~EY~~~~D~~EA~~clkEL~~p~~~-~e~V~~~I~~aLEk~~~~re~v~~LL~~L~~~~~ls~~q~ 684 (776)
...+|.-|...+++++|...++++...... ..++...+..++-+. ...+.+.+++..+...|+.+....
T Consensus 582 ynaLI~ay~k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~-G~~deAl~lf~eM~~~Gv~PD~~T 651 (1060)
T PLN03218 582 VGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQK-GDWDFALSIYDDMKKKGVKPDEVF 651 (1060)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhc-CCHHHHHHHHHHHHHcCCCCCHHH
Confidence 456777777777777777777777543332 223344444444432 235566667777766665544333
No 29
>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=39.63 E-value=42 Score=27.50 Aligned_cols=45 Identities=20% Similarity=0.138 Sum_probs=36.5
Q ss_pred CCCChHHHHHHHHHHHhCCCCCHHHHHHHHHHHh-----hcchhhhcCCC
Q 004059 659 IPPCVEPVIQLLEFLLNKNVLTTRDIGTGCLLYG-----SLLDDIGIDLP 703 (776)
Q Consensus 659 ~~~~re~v~~LL~~L~~~~~ls~~q~~~Gf~~vl-----e~LdDl~iDiP 703 (776)
++.+|+.+..+|...+..|-|+.+.|..=...++ ..|..+.-|+|
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 5678999999999999999999999998887754 34555555655
No 30
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=39.18 E-value=1.1e+02 Score=37.61 Aligned_cols=105 Identities=17% Similarity=0.289 Sum_probs=70.2
Q ss_pred hcCChhhHHHHHHHHHHccCCCHHHHHHHHHHHHHHHhhCCCChHHHHHHHHHHhhhCCCCCCCCCCCchhhHHHHHHHH
Q 004059 207 NKLTPEKFDVLKGQLIDSGITTPDILKGVIELIFDKAVLEPTFCPMYALLCSDLNEKLPPFPSDEPGGKDITFKRILLNH 286 (776)
Q Consensus 207 NKLTpenFd~l~~qLl~l~I~t~e~Lk~VI~lIFeKAi~Ep~fs~mYA~LC~~L~~~lp~~~~~e~~gk~~~FR~~LLnr 286 (776)
--++.+-|.--...|+.+.+.. +...+|+..|+.=+..|-.|-+.||-|..++|+.-..+ ..+|.-.|-.+
T Consensus 627 sImsaeDyiDAFEklLkL~LK~-~Q~rEI~~VllhC~l~EK~yNpfYa~lA~KfCe~~~~~--------~~tfQF~~WD~ 697 (822)
T KOG2141|consen 627 SIMSAEDYIDAFEKLLKLSLKG-KQEREIARVLLHCCLNEKTYNPFYALLALKFCEFNKNL--------KKTFQFALWDR 697 (822)
T ss_pred eeecchHHHHHHHHHHhccCCC-cchHHHHHHHHHHHhhhcccchHHHHHHHHHHHHhhhh--------HHHHHHHHHHH
Confidence 3456777777788888887754 33457889999999999999999999999998863221 23333322221
Q ss_pred HHHHHhhhhchHHHHhhcCChHHHHHHhHHHHHHHHhhhhHHHHHHHHHhcCCCCHHHHH
Q 004059 287 CQEAFEGADNTRAEIRQMTAPEQEMERMDQERLVKLRTLGNIRLIGELLKQKMVPEKIVH 346 (776)
Q Consensus 287 cQeeFe~~~~~~~ei~~~~~~e~E~E~~e~e~~~Krr~LGnIrFIGELfk~~mL~e~Im~ 346 (776)
. .++..+ ...|.....+|+++|.....++-.|+.
T Consensus 698 f-----------~ele~l---------------s~~ri~nLa~l~a~Li~~~~lsLtVLK 731 (822)
T KOG2141|consen 698 F-----------KELEQL---------------SLFRISNLAKLLASLISNAVLSLTVLK 731 (822)
T ss_pred H-----------HHhhhc---------------chhhHhHHHHHHHHHHHhcccceeeee
Confidence 1 112111 123566788999999988777665554
No 31
>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=38.84 E-value=98 Score=26.69 Aligned_cols=47 Identities=23% Similarity=0.345 Sum_probs=36.0
Q ss_pred CHHHHHHHHHHHHHHHhc--C-CCHHHHHHHHHHhCCCCChHHHHHHHHH
Q 004059 607 NLADLRKKTVSLLEEYFS--I-RILDEALQCVEELRAPTYHPEVVKEAIA 653 (776)
Q Consensus 607 s~eel~kki~~ll~EY~~--~-~D~~EA~~clkEL~~p~~~~e~V~~~I~ 653 (776)
+-++|++.+..+|.|-=- . .+++|-+.|.-.||.+.+|+.+|.-...
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 357899998888887632 2 4689999999999999888766655443
No 32
>PF08876 DUF1836: Domain of unknown function (DUF1836); InterPro: IPR014975 This group of proteins are functionally uncharacterised.
Probab=35.34 E-value=1.1e+02 Score=28.66 Aligned_cols=48 Identities=27% Similarity=0.134 Sum_probs=39.8
Q ss_pred CChHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcchhhhcCCCchhHH
Q 004059 661 PCVEPVIQLLEFLLNKNVLTTRDIGTGCLLYGSLLDDIGIDLPKAPNN 708 (776)
Q Consensus 661 ~~re~v~~LL~~L~~~~~ls~~q~~~Gf~~vle~LdDl~iDiP~A~~~ 708 (776)
=.|++++.|+.--.-+.++|-+++.++|..+.....+-.++...||++
T Consensus 57 Ysr~qla~li~I~~lK~vlsi~dI~~ll~~~~~~~~~~~~~~~~~Y~~ 104 (105)
T PF08876_consen 57 YSREQLAYLIVISILKQVLSIDDIKKLLDLQFNNYEDDEISLEDAYNY 104 (105)
T ss_pred cCHHHHHHHHHHHHHHccCCHHHHHHHHHHHHhcccccCCCHHHHHhc
Confidence 368999999886666799999999999999999887777776666654
No 33
>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=35.01 E-value=1.2e+02 Score=30.54 Aligned_cols=56 Identities=23% Similarity=0.262 Sum_probs=41.5
Q ss_pred CCCHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhCC----CCChHHHHHHHHHHHhccCC
Q 004059 605 KLNLADLRKKTVSLLEEYFSIRILDEALQCVEELRA----PTYHPEVVKEAIALALEKIP 660 (776)
Q Consensus 605 ~~s~eel~kki~~ll~EY~~~~D~~EA~~clkEL~~----p~~~~e~V~~~I~~aLEk~~ 660 (776)
.+-+++++.....+-+-|+..||+++|+.|+..... +...-.++-.+|..++..++
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 456788888888999999999999999999998642 22234555666666666553
No 34
>PF04129 Vps52: Vps52 / Sac2 family ; InterPro: IPR007258 Vps52 complexes with Vps53 and Vps54 to form a multi-subunit complex involved in regulating membrane trafficking events [].
Probab=34.81 E-value=4.4e+02 Score=31.21 Aligned_cols=85 Identities=15% Similarity=0.289 Sum_probs=55.5
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHhhhcCCCCCCChhhHHHHHHHHHHHhhhhhc----CCcchhhHHHHHHHHHHHhhC
Q 004059 327 NIRLIGELLKQKMVPEKIVHHIVQLLENDGKTCPAEENVEAICQFFNTIGKQLDE----NPKSRRVNDVYFSRLKELTTN 402 (776)
Q Consensus 327 nIrFIGELfk~~mL~e~Im~~ci~LL~~~~~~~p~Ee~IE~Lc~LL~tiGk~Ld~----~~k~~~~md~yF~rL~~l~~~ 402 (776)
...-|+.+...-+|+..+|..++. ..++|.-++++..+++..=..... ..++-..+...+++|+..+
T Consensus 71 ~~~~L~~~i~~i~ipP~lI~~I~~-------~~v~e~~~~~~~~~~~k~~~~~~~~~~~~~~a~~d~~~~Le~L~~ka-- 141 (508)
T PF04129_consen 71 VEEKLSPFIDDIVIPPDLIRSICE-------GPVNEQYIEELLELLKKKIFFSKDQSFKDSKAIKDVKPELEKLKNKA-- 141 (508)
T ss_pred HHHHHHHHHHHHcCCHHHHHhHhc-------CCCCHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHHH--
Confidence 345567777777899988888775 235778888888888754333221 1222233445666666544
Q ss_pred CCCChHHH-HHHHHHHHHHhCC
Q 004059 403 SQLVPRLR-FMIHDVLDLRANN 423 (776)
Q Consensus 403 ~~lssRiR-FmL~dvidLR~nn 423 (776)
..||| |++..+-.||..+
T Consensus 142 ---~~rir~fl~~kI~~lr~~~ 160 (508)
T PF04129_consen 142 ---VERIRDFLLKKIKSLRKPK 160 (508)
T ss_pred ---HHHHHHHHHHHHHHHcCCC
Confidence 47887 8889999999744
No 35
>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=34.56 E-value=3.8e+02 Score=26.32 Aligned_cols=31 Identities=19% Similarity=0.271 Sum_probs=25.2
Q ss_pred chhHHHHHHHHHHHHcCCCChHHHHHHHhhh
Q 004059 704 KAPNNFGEMVGKLVVAKSLDFIVLKEVLKKV 734 (776)
Q Consensus 704 ~A~~~La~~iaraI~d~~l~~~~v~~~~~~~ 734 (776)
..+..+..|++.+..-+.++...+-+++..+
T Consensus 94 ~~~~~~i~fl~eL~~~~~i~~~~i~~~l~~l 124 (200)
T smart00543 94 QRRLGLVRFLGELYNFQVLTSKIILELLKEL 124 (200)
T ss_pred hhHHhHHHHHHHHHHcccCcHHHHHHHHHHH
Confidence 5567788999999999999988777666654
No 36
>PLN03218 maturation of RBCL 1; Provisional
Probab=32.99 E-value=2.5e+02 Score=36.55 Aligned_cols=68 Identities=10% Similarity=0.028 Sum_probs=43.1
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhCCCCCh-HHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCCCHH
Q 004059 614 KTVSLLEEYFSIRILDEALQCVEELRAPTYH-PEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTR 682 (776)
Q Consensus 614 ki~~ll~EY~~~~D~~EA~~clkEL~~p~~~-~e~V~~~I~~aLEk~~~~re~v~~LL~~L~~~~~ls~~ 682 (776)
....+|.-|...|++++|...++++....+. ..++...+..++-+. ...+.+.+++..+.+.|+-...
T Consensus 616 tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~-G~~eeA~~l~~eM~k~G~~pd~ 684 (1060)
T PLN03218 616 VYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHA-GDLDKAFEILQDARKQGIKLGT 684 (1060)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhC-CCHHHHHHHHHHHHHcCCCCCH
Confidence 3467788888889999999888888654433 234444444444433 3456667777777776654433
No 37
>PF12854 PPR_1: PPR repeat
Probab=32.85 E-value=59 Score=23.64 Aligned_cols=26 Identities=23% Similarity=0.459 Sum_probs=22.8
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhC
Q 004059 614 KTVSLLEEYFSIRILDEALQCVEELR 639 (776)
Q Consensus 614 ki~~ll~EY~~~~D~~EA~~clkEL~ 639 (776)
....+|.-|...|.++||.+.++++.
T Consensus 9 ty~~lI~~~Ck~G~~~~A~~l~~~M~ 34 (34)
T PF12854_consen 9 TYNTLIDGYCKAGRVDEAFELFDEMK 34 (34)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence 35789999999999999999999873
No 38
>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=32.04 E-value=4.5e+02 Score=28.79 Aligned_cols=93 Identities=17% Similarity=0.134 Sum_probs=51.6
Q ss_pred CHHHHHHHHHHHHHHHhcCCCHHHHHHHH-HHhCCCCChHHHHHHHHHHHhcc--CCCChHHHHHHHHHHHhCCCCC--H
Q 004059 607 NLADLRKKTVSLLEEYFSIRILDEALQCV-EELRAPTYHPEVVKEAIALALEK--IPPCVEPVIQLLEFLLNKNVLT--T 681 (776)
Q Consensus 607 s~eel~kki~~ll~EY~~~~D~~EA~~cl-kEL~~p~~~~e~V~~~I~~aLEk--~~~~re~v~~LL~~L~~~~~ls--~ 681 (776)
..+.+.+.+...+..++...+.......+ ..+-...+|..++..++....+. ++..++.+.+++.....+..-+ .
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 34455555555555555555444444333 44444556666666666554442 3455667888888777644333 6
Q ss_pred HHHHHHHHHH-hhcchhhh
Q 004059 682 RDIGTGCLLY-GSLLDDIG 699 (776)
Q Consensus 682 ~q~~~Gf~~v-le~LdDl~ 699 (776)
+.+...|... ...++++.
T Consensus 182 ~~l~~~i~~~l~~~l~~l~ 200 (367)
T PF04286_consen 182 DKLAEKIQDELDSLLEKLQ 200 (367)
T ss_pred hHHHHHHHHHHHHHHHHHH
Confidence 6666666655 44566665
No 39
>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=30.12 E-value=3.3e+02 Score=22.87 Aligned_cols=43 Identities=23% Similarity=0.292 Sum_probs=36.3
Q ss_pred ChHHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCCCHHHHH
Q 004059 643 YHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIG 685 (776)
Q Consensus 643 ~~~e~V~~~I~~aLEk~~~~re~v~~LL~~L~~~~~ls~~q~~ 685 (776)
+.+++|..+|..+++++.....-+-..|..-.++|+-|.+|+.
T Consensus 30 ~~~evI~~ai~~a~~~~~~~~~Yi~~Il~~W~~~gi~T~e~~~ 72 (73)
T TIGR01446 30 NSPELIKEALKEAVSNNKANYKYIDAILNNWKNNGIKTVEDVE 72 (73)
T ss_pred CCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHcCCCCHHHHh
Confidence 4489999999999987655667888999999999999988864
No 40
>PTZ00009 heat shock 70 kDa protein; Provisional
Probab=27.89 E-value=2.6e+02 Score=34.21 Aligned_cols=79 Identities=9% Similarity=0.187 Sum_probs=38.8
Q ss_pred CChhhHHHHHHHHHHHhhhhhc---CCcchhhHHHHHHHHHHHhhC----CCCChHHHHHHHHHHHHHhCCCCCcccccC
Q 004059 360 PAEENVEAICQFFNTIGKQLDE---NPKSRRVNDVYFSRLKELTTN----SQLVPRLRFMIHDVLDLRANNWVPRREEMK 432 (776)
Q Consensus 360 p~Ee~IE~Lc~LL~tiGk~Ld~---~~k~~~~md~yF~rL~~l~~~----~~lssRiRFmL~dvidLR~nnW~~r~~~~~ 432 (776)
.++++++.+.+.+...-..-.. ....+..++.|+-.++..... ..++..-|--|.+.++--. +|.....
T Consensus 512 ls~~~i~~~~~~~~~~~~~d~~~~~~~eakN~lEs~Iy~~r~~L~~~~~~~~~t~ee~~~l~~~l~~~~-~wL~~~~--- 587 (653)
T PTZ00009 512 LSKADIDRMVNEAEKYKAEDEANRERVEAKNGLENYCYSMKNTLQDEKVKGKLSDSDKATIEKAIDEAL-EWLEKNQ--- 587 (653)
T ss_pred ccHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhhHHHHHHHHHHHhhhhhhccCCHHHHHHHHHHHHHHH-HHHhcCC---
Confidence 3566677766666543221110 001223466777777766542 2456555555555555433 5775322
Q ss_pred CccHHHHHHH
Q 004059 433 AKTITEIHSE 442 (776)
Q Consensus 433 pkti~eIh~e 442 (776)
..+++++.+.
T Consensus 588 ~~~~~~~~~k 597 (653)
T PTZ00009 588 LAEKEEFEHK 597 (653)
T ss_pred chhHHHHHHH
Confidence 2345555443
No 41
>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=26.85 E-value=2.4e+02 Score=27.60 Aligned_cols=94 Identities=11% Similarity=0.138 Sum_probs=56.1
Q ss_pred hhHHHHHHHHHhcCCCCHHHHHHHHH-hhhcCCCCCCCh--hhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHhh
Q 004059 325 LGNIRLIGELLKQKMVPEKIVHHIVQ-LLENDGKTCPAE--ENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTT 401 (776)
Q Consensus 325 LGnIrFIGELfk~~mL~e~Im~~ci~-LL~~~~~~~p~E--e~IE~Lc~LL~tiGk~Ld~~~k~~~~md~yF~rL~~l~~ 401 (776)
.+.|.-|+++.+.+-.+.+.....|+ -|.+. .|.. -.+..|=.+++.||..+...-..+.++++ |.+++.
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 45677788888877555544444444 44431 1211 24555556667788887643223344444 444443
Q ss_pred C----CCCChHHHHHHHHHHHHHhCCCC
Q 004059 402 N----SQLVPRLRFMIHDVLDLRANNWV 425 (776)
Q Consensus 402 ~----~~lssRiRFmL~dvidLR~nnW~ 425 (776)
. +..+..|+-+|..+|........
T Consensus 92 ~k~~~~~~~~~Vk~kil~li~~W~~~f~ 119 (139)
T cd03567 92 PKYLGSRTSEKVKTKIIELLYSWTLELP 119 (139)
T ss_pred cccCCCCCCHHHHHHHHHHHHHHHHHhc
Confidence 2 45789999999999998775553
No 42
>PF10363 DUF2435: Protein of unknown function (DUF2435)
Probab=26.47 E-value=4.8e+02 Score=23.63 Aligned_cols=82 Identities=22% Similarity=0.180 Sum_probs=56.8
Q ss_pred HHHHHHHhccCCCChHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcchhhhcCCCchhHHHHHHHHHHHHcCCCChHHHH
Q 004059 649 KEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTGCLLYGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLDFIVLK 728 (776)
Q Consensus 649 ~~~I~~aLEk~~~~re~v~~LL~~L~~~~~ls~~q~~~Gf~~vle~LdDl~iDiP~A~~~La~~iaraI~d~~l~~~~v~ 728 (776)
++++...-|.-..-|-+-..+|..|+.++-.+..++..-+.-+++.|.| |.-|-||+-+=+-+...+..|-..+.
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 3344443344455688888888888887766777777777777777777 57788888777776666666666666
Q ss_pred HHHhhhc
Q 004059 729 EVLKKVE 735 (776)
Q Consensus 729 ~~~~~~~ 735 (776)
.+++.+.
T Consensus 81 ~L~~~y~ 87 (92)
T PF10363_consen 81 ILLDEYA 87 (92)
T ss_pred HHHHHHh
Confidence 6665543
No 43
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=26.20 E-value=3.8e+02 Score=32.67 Aligned_cols=62 Identities=11% Similarity=0.014 Sum_probs=41.9
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCCC
Q 004059 615 TVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLT 680 (776)
Q Consensus 615 i~~ll~EY~~~~D~~EA~~clkEL~~p~~~~e~V~~~I~~aLEk~~~~re~v~~LL~~L~~~~~ls 680 (776)
...+|.=|...|++++|...+.++..|.. +....+..++-+. ..-+.+..+|..+...|+..
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 46778888999999999999999877642 3334444444433 23556777888777766543
No 44
>PLN03077 Protein ECB2; Provisional
Probab=26.11 E-value=3e+02 Score=34.39 Aligned_cols=64 Identities=19% Similarity=0.191 Sum_probs=42.5
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCCCH
Q 004059 614 KTVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTT 681 (776)
Q Consensus 614 ki~~ll~EY~~~~D~~EA~~clkEL~~p~~~~e~V~~~I~~aLEk~~~~re~v~~LL~~L~~~~~ls~ 681 (776)
....+|.=|...|++++|...++++..|.. +....+..++-+.. .-+.+..++..+...|+-+.
T Consensus 325 ~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~---~s~n~li~~~~~~g-~~~~A~~lf~~M~~~g~~Pd 388 (857)
T PLN03077 325 VCNSLIQMYLSLGSWGEAEKVFSRMETKDA---VSWTAMISGYEKNG-LPDKALETYALMEQDNVSPD 388 (857)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHhhCCCCCe---eeHHHHHHHHHhCC-CHHHHHHHHHHHHHhCCCCC
Confidence 347788889999999999999999876642 33444444444432 34666777777766665433
No 45
>COG5537 IRR1 Cohesin [Cell division and chromosome partitioning]
Probab=25.99 E-value=9.3e+02 Score=29.45 Aligned_cols=135 Identities=14% Similarity=0.104 Sum_probs=85.1
Q ss_pred HHHHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCCCHHHHHHHH
Q 004059 609 ADLRKKTVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTGC 688 (776)
Q Consensus 609 eel~kki~~ll~EY~~~~D~~EA~~clkEL~~p~~~~e~V~~~I~~aLEk~~~~re~v~~LL~~L~~~~~ls~~q~~~Gf 688 (776)
+.++..+..+|.-+++..--..|++-+-| .|-..+++.+.--.+..|-+..+++.+|...|+|+...+..=.
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 45666666666666655433334433222 3444444444333455677889999999999999999888777
Q ss_pred HHHhhcchhhhcCCCchhHHHHHHHHHHHHcCCCCh----HHHHHHHhhhcchhH--HHHHHHHHHHHHh
Q 004059 689 LLYGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLDF----IVLKEVLKKVEDNMF--RRSIFTAAMKSIQ 752 (776)
Q Consensus 689 ~~vle~LdDl~iDiP~A~~~La~~iaraI~d~~l~~----~~v~~~~~~~~~~~~--~~~~~~a~l~~l~ 752 (776)
.-+++..+|--+-+-.+.+.++++.|+.|.+.. |+ +.+-.++...-..++ .-.+|..+++.++
T Consensus 400 scmlDi~pd~r~~~~E~v~~icK~~aevikEKi-pl~~k~n~lL~a~~qgse~~f~v~~~iFsr~~~llk 468 (740)
T COG5537 400 SCMLDIIPDSRENIVESVESICKIDAEVIKEKI-PLATKTNRLLEAMKQGSERYFVVCEEIFSRFVHLLK 468 (740)
T ss_pred HHHhcCCCcchHHHHHHHHHHHHHHHHHHHhhc-chhhhhhhHHHHHHhhhhccchhHHHHHHHHHHHHH
Confidence 778888887666677889999999999988443 32 222223333323333 4555666666554
No 46
>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=25.99 E-value=76 Score=21.63 Aligned_cols=26 Identities=19% Similarity=0.276 Sum_probs=22.5
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHhCC
Q 004059 615 TVSLLEEYFSIRILDEALQCVEELRA 640 (776)
Q Consensus 615 i~~ll~EY~~~~D~~EA~~clkEL~~ 640 (776)
...+|.-|...++.++|...+.++..
T Consensus 3 ~n~li~~~~~~~~~~~a~~~~~~M~~ 28 (35)
T TIGR00756 3 YNTLIDGLCKAGRVEEALELFKEMLE 28 (35)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35788999999999999999999854
No 47
>KOG2050 consensus Puf family RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=25.00 E-value=1.2e+02 Score=36.25 Aligned_cols=60 Identities=22% Similarity=0.259 Sum_probs=39.8
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHH------HHHHHHHhccCCCChHHHHHHHHHHHh
Q 004059 614 KTVSLLEEYFSIRILDEALQCVEELRAPTYHPEVV------KEAIALALEKIPPCVEPVIQLLEFLLN 675 (776)
Q Consensus 614 ki~~ll~EY~~~~D~~EA~~clkEL~~p~~~~e~V------~~~I~~aLEk~~~~re~v~~LL~~L~~ 675 (776)
.+-.++-|||.+.|.+|+.+.+.-|. ...++|| +.+|.+.--..+.+|.++.+-+...+.
T Consensus 322 ivHk~mlEy~~~ade~e~~e~l~ll~--elv~e~vHT~dGS~vAm~li~~a~aKeRK~IiK~~K~h~~ 387 (652)
T KOG2050|consen 322 IVHKLMLEYLTIADEEEKSELLELLK--ELVPEMVHTRDGSRVAMKLIWHATAKERKLIIKNMKEHVE 387 (652)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHH--HHHHHHhcCCchHHHHHHHHhhCCHHHHHHHHHHHHHHHH
Confidence 34667889999999999998877764 2222332 334443333467888888888775544
No 48
>PF10884 DUF2683: Protein of unknown function (DUF2683); InterPro: IPR020271 This entry contains proteins with no known function.
Probab=24.29 E-value=1.9e+02 Score=25.85 Aligned_cols=45 Identities=13% Similarity=0.362 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHH-----HHhCCCCChHHHHHHHHHHHh
Q 004059 612 RKKTVSLLEEYFSIRILDEALQCV-----EELRAPTYHPEVVKEAIALAL 656 (776)
Q Consensus 612 ~kki~~ll~EY~~~~D~~EA~~cl-----kEL~~p~~~~e~V~~~I~~aL 656 (776)
.+++-.+++-=|+..|..+|+.-+ .++-.|.+.|+||+++....=
T Consensus 12 ~n~ilnIiKaky~lkdks~aId~~ieeye~~~lEpElkPEfVeki~~i~k 61 (80)
T PF10884_consen 12 TNQILNIIKAKYNLKDKSAAIDKIIEEYEEKILEPELKPEFVEKIKKIMK 61 (80)
T ss_pred chHHHHHHHHHhCCchHHHHHHHHHHHHHHHhcccccCHHHHHHHHHHHh
Confidence 467889999999999999998644 345678999999999988643
No 49
>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=24.02 E-value=99 Score=20.71 Aligned_cols=25 Identities=32% Similarity=0.577 Sum_probs=22.0
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHhCC
Q 004059 616 VSLLEEYFSIRILDEALQCVEELRA 640 (776)
Q Consensus 616 ~~ll~EY~~~~D~~EA~~clkEL~~ 640 (776)
..+|+-|...++.++|...++++..
T Consensus 4 ~~li~~~~~~~~~~~a~~~~~~M~~ 28 (31)
T PF01535_consen 4 NSLISGYCKMGQFEEALEVFDEMRE 28 (31)
T ss_pred HHHHHHHHccchHHHHHHHHHHHhH
Confidence 5789999999999999999999853
No 50
>COG1421 CRISPR system related protein [Defense mechanisms]
Probab=23.78 E-value=1.8e+02 Score=28.58 Aligned_cols=65 Identities=25% Similarity=0.275 Sum_probs=46.2
Q ss_pred CCCHHHHHHHHHHH-------hhcchhhhcCCCchhHHHHHHHHHHHHcCCCC-hHHHHHHHhhhcchhHHHH
Q 004059 678 VLTTRDIGTGCLLY-------GSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLD-FIVLKEVLKKVEDNMFRRS 742 (776)
Q Consensus 678 ~ls~~q~~~Gf~~v-------le~LdDl~iDiP~A~~~La~~iaraI~d~~l~-~~~v~~~~~~~~~~~~~~~ 742 (776)
-+++.|+.+=+..+ .....+|.+|+|+..-.||.-++|.+..-.=. -.++++++.++.++..+.+
T Consensus 43 ~l~~~q~R~fy~~~~r~~~~~~~~~k~i~~~l~~m~~~lay~~gR~~~~~~e~lyevle~~idkid~D~~~~~ 115 (137)
T COG1421 43 NLTTTQLRKFYDYILRIDEENENSWKEIVLDLPKMKPQLAYAVGRDGKEALEGLYEVLEEMIDKIDDDNDRNA 115 (137)
T ss_pred cCcHHHHHHHHHHHHHHhHhccCcHHHHHHHHHHHHHHHHHHHhhcchhhHHHHHHHHHHHHHHhhhhhhHHH
Confidence 57888887777666 34568899999999998888888877654211 2567888888844443333
No 51
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=23.57 E-value=1.3e+03 Score=29.28 Aligned_cols=127 Identities=15% Similarity=0.255 Sum_probs=78.3
Q ss_pred HHHHHHHHhcCChhhHHHHHHHHHHcc-----CCCHHHHHHHHHHHHHHH----hhC-CCChHHHHHHHHHHhhhCCCCC
Q 004059 199 LKTVKGILNKLTPEKFDVLKGQLIDSG-----ITTPDILKGVIELIFDKA----VLE-PTFCPMYALLCSDLNEKLPPFP 268 (776)
Q Consensus 199 ~rkVk~ILNKLTpenFd~l~~qLl~l~-----I~t~e~Lk~VI~lIFeKA----i~E-p~fs~mYA~LC~~L~~~lp~~~ 268 (776)
+..+..+|...+++....++..|..++ -.|.+.|..+...+++.. ... +..-.+.-.||.+|..-...+|
T Consensus 428 ~eel~~lL~~~~~~~~~~iI~RIrk~~hpsLa~~NK~Kl~~f~~vLlq~i~~la~~~~~~~~~~ld~L~~~L~~Laq~~p 507 (840)
T PF04147_consen 428 HEELLELLDGYSPEDQPTIIQRIRKCYHPSLAEGNKEKLQVFFGVLLQHILYLASQDSPPPFEVLDSLIPHLYDLAQKYP 507 (840)
T ss_pred HHHHHHHHhcCCHHHHhHHHHHHHHhCCCCCCcchHHHHHHHHHHHHHHHHHHhcccCCcCHHHHHHHHHHHHHHHHHHH
Confidence 455778888999999999999999874 246777766655555544 333 4555666788887766433222
Q ss_pred CCCCCCchhhHHHHHHHHHHHHHhhhhchHHHHhhcCChHHHHHHhHHHHHHHHhhhhHHHHHHHHHh-----cCCCCHH
Q 004059 269 SDEPGGKDITFKRILLNHCQEAFEGADNTRAEIRQMTAPEQEMERMDQERLVKLRTLGNIRLIGELLK-----QKMVPEK 343 (776)
Q Consensus 269 ~~e~~gk~~~FR~~LLnrcQeeFe~~~~~~~ei~~~~~~e~E~E~~e~e~~~Krr~LGnIrFIGELfk-----~~mL~e~ 343 (776)
. .-...||. .|..+|..|....-... ..+-| ....|=.++.||-||- +-|||..
T Consensus 508 ~----~~a~~~r~-~L~~~~~~~~~~~l~~~---~~~~P-------------~l~~Lvllklv~~lFPTSD~~HpVVTPa 566 (840)
T PF04147_consen 508 E----EAAECFRE-VLKEMQKRFRKGALKPK---ERSWP-------------SLSDLVLLKLVGTLFPTSDFRHPVVTPA 566 (840)
T ss_pred H----HHHHHHHH-HHHHHHHHHhhhccccc---CCCCC-------------ChhHHHHHHHHHHhcCcccccCcchhHH
Confidence 1 12244554 56678888876310000 00001 1245778899999996 3477776
Q ss_pred HHH
Q 004059 344 IVH 346 (776)
Q Consensus 344 Im~ 346 (776)
++.
T Consensus 567 lll 569 (840)
T PF04147_consen 567 LLL 569 (840)
T ss_pred HHH
Confidence 665
No 52
>PRK09498 sifA secreted effector protein SifA; Reviewed
Probab=23.46 E-value=1.4e+02 Score=32.66 Aligned_cols=28 Identities=14% Similarity=0.199 Sum_probs=22.9
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhCCC
Q 004059 614 KTVSLLEEYFSIRILDEALQCVEELRAP 641 (776)
Q Consensus 614 ki~~ll~EY~~~~D~~EA~~clkEL~~p 641 (776)
.+=+-|++||.+.--.||.+||.||--|
T Consensus 29 ~LWEKIKdFFcSThqaeA~~CI~eLchp 56 (336)
T PRK09498 29 VLWEKIKDFFFSTGKAKADRCLHEMLFA 56 (336)
T ss_pred HHHHHHHHHhhcccHHHHHHHHHHHhCC
Confidence 3445578999999999999999999543
No 53
>PF13041 PPR_2: PPR repeat family
Probab=23.42 E-value=1.5e+02 Score=22.91 Aligned_cols=29 Identities=21% Similarity=0.332 Sum_probs=24.4
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHhCCCCC
Q 004059 615 TVSLLEEYFSIRILDEALQCVEELRAPTY 643 (776)
Q Consensus 615 i~~ll~EY~~~~D~~EA~~clkEL~~p~~ 643 (776)
...+|.-|...+++++|...++++..-..
T Consensus 6 yn~li~~~~~~~~~~~a~~l~~~M~~~g~ 34 (50)
T PF13041_consen 6 YNTLISGYCKAGKFEEALKLFKEMKKRGI 34 (50)
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHHHHcCC
Confidence 46789999999999999999999865443
No 54
>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=23.31 E-value=5.2e+02 Score=23.27 Aligned_cols=64 Identities=20% Similarity=0.335 Sum_probs=41.8
Q ss_pred hhhhHHHHHHHHHhcCCCCHHHHHHHHHhhhcCCCCCCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHh
Q 004059 323 RTLGNIRLIGELLKQKMVPEKIVHHIVQLLENDGKTCPAEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELT 400 (776)
Q Consensus 323 r~LGnIrFIGELfk~~mL~e~Im~~ci~LL~~~~~~~p~Ee~IE~Lc~LL~tiGk~Ld~~~k~~~~md~yF~rL~~l~ 400 (776)
+-+-+|.||=+-.....+++.....|---|.+ .|.++.-|+.+|.. +-+++-+.-+|.+|++++
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 44678999999888889999988766554554 35677777777765 445566778888888775
No 55
>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=23.07 E-value=4.1e+02 Score=23.01 Aligned_cols=48 Identities=21% Similarity=0.065 Sum_probs=29.1
Q ss_pred hHHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcc
Q 004059 644 HPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTGCLLYGSLL 695 (776)
Q Consensus 644 ~~e~V~~~I~~aLEk~~~~re~v~~LL~~L~~~~~ls~~q~~~Gf~~vle~L 695 (776)
++++|..++...+.+ .-+.+...+..|..+ -++..++.+.+.+++-..
T Consensus 4 ~~~~i~~i~~~~~~~---~~~~~~~~~~~l~~~-G~s~~~Il~~l~~~l~~~ 51 (89)
T PF08542_consen 4 PPEVIEEILESCLNG---DFKEARKKLYELLVE-GYSASDILKQLHEVLVES 51 (89)
T ss_dssp -HHHHHHHHHHHHHT---CHHHHHHHHHHHHHT-T--HHHHHHHHHHHHHTS
T ss_pred CHHHHHHHHHHHHhC---CHHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHHh
Confidence 356677777666654 344566666666665 577777777777766544
No 56
>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=22.02 E-value=2.5e+02 Score=28.61 Aligned_cols=37 Identities=24% Similarity=0.263 Sum_probs=31.0
Q ss_pred CCChHHHHHHHHHHHhccCCCChHHHHHHHHHHHhCC
Q 004059 641 PTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKN 677 (776)
Q Consensus 641 p~~~~e~V~~~I~~aLEk~~~~re~v~~LL~~L~~~~ 677 (776)
|...+.++..++-.+.||=|.-|+.+++.|..|....
T Consensus 2 ~~~~~~~~~~llrqa~EKiDrvR~~A~~~l~~ll~~~ 38 (193)
T PF12612_consen 2 PELVQQIIGGLLRQAAEKIDRVREVAGKCLQRLLHSQ 38 (193)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 3456788899999999999999999999999988533
No 57
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=21.91 E-value=1.3e+02 Score=21.75 Aligned_cols=26 Identities=12% Similarity=0.075 Sum_probs=21.5
Q ss_pred HHHHHHHHhCCCCCHHHHHHHHHHHh
Q 004059 667 IQLLEFLLNKNVLTTRDIGTGCLLYG 692 (776)
Q Consensus 667 ~~LL~~L~~~~~ls~~q~~~Gf~~vl 692 (776)
..-|..|+..|+||.+.|.+--..++
T Consensus 5 L~~L~~l~~~G~IseeEy~~~k~~ll 30 (31)
T PF09851_consen 5 LEKLKELYDKGEISEEEYEQKKARLL 30 (31)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHh
Confidence 34577899999999999998877665
No 58
>PF10155 DUF2363: Uncharacterized conserved protein (DUF2363); InterPro: IPR019312 This entry represents a region of 120 amino acids in proteins conserved from plants to humans. Their function is not known.
Probab=21.52 E-value=6.4e+02 Score=24.32 Aligned_cols=32 Identities=16% Similarity=0.221 Sum_probs=25.8
Q ss_pred CChHHHHHHHHHHHhCCCCCHHHHHHHHHHHh
Q 004059 661 PCVEPVIQLLEFLLNKNVLTTRDIGTGCLLYG 692 (776)
Q Consensus 661 ~~re~v~~LL~~L~~~~~ls~~q~~~Gf~~vl 692 (776)
.-..+++.+|..|+..+++..+++..-++.+.
T Consensus 77 R~VRlvcvfl~sLir~~i~~~~~l~~evq~FC 108 (126)
T PF10155_consen 77 RLVRLVCVFLQSLIRNKIIDVEDLFIEVQAFC 108 (126)
T ss_pred chhhhHHHHHHHHHHcCCCchHHHHhhHHHHH
Confidence 34579999999999999999988776666543
No 59
>PF05004 IFRD: Interferon-related developmental regulator (IFRD); InterPro: IPR007701 Interferon-related developmental regulator (IFRD1) is the human homologue of the Rattus norvegicus early response protein PC4 and its murine homologue TIS7 []. The exact function of IFRD1 is unknown but it has been shown that PC4 is necessary for muscle differentiation and that it might have a role in signal transduction. This entry also contains IFRD2 and its murine equivalent SKMc15, which are highly expressed soon after gastrulation and in the hepatic primordium, suggesting an involvement in early hematopoiesis [].
Probab=21.19 E-value=1.1e+03 Score=26.13 Aligned_cols=121 Identities=17% Similarity=0.079 Sum_probs=62.1
Q ss_pred CHHHHHHHHHHHHHHHhcCC--CHHHHHHHHHHhCCCCChHHHHHH-------HHHHHhccC-CCChHHHHHHHHHHHhC
Q 004059 607 NLADLRKKTVSLLEEYFSIR--ILDEALQCVEELRAPTYHPEVVKE-------AIALALEKI-PPCVEPVIQLLEFLLNK 676 (776)
Q Consensus 607 s~eel~kki~~ll~EY~~~~--D~~EA~~clkEL~~p~~~~e~V~~-------~I~~aLEk~-~~~re~v~~LL~~L~~~ 676 (776)
+.+++..++...|+.-..-. .=++|+..|..+-.-+|.+++|.. .+..++-+. ..++.++++++.-|+-+
T Consensus 37 ~~~~~e~~L~~~Id~l~eK~~~~Re~aL~~l~~~l~~~~~~d~v~~~~~tL~~~~~k~lkkg~~~E~~lA~~~l~Ll~lt 116 (309)
T PF05004_consen 37 SQEDLEDKLKEAIDLLTEKSSSTREAALEALIRALSSRYLPDFVEDRRETLLDALLKSLKKGKSEEQALAARALALLALT 116 (309)
T ss_pred chhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHhhh
Confidence 34566666666666665433 225566666665444555666633 233344443 24666777888877654
Q ss_pred -C-CCCHHHHHHHHHHHhhcc-hhhhcCCCchhHHHHHHHHHHHHcCCCChHHHH
Q 004059 677 -N-VLTTRDIGTGCLLYGSLL-DDIGIDLPKAPNNFGEMVGKLVVAKSLDFIVLK 728 (776)
Q Consensus 677 -~-~ls~~q~~~Gf~~vle~L-dDl~iDiP~A~~~La~~iaraI~d~~l~~~~v~ 728 (776)
| .-..+.+...+..+|..+ .|- -+.|++......-+|-+..=++-....+.
T Consensus 117 lg~g~~~~ei~~~~~~~L~~~l~d~-s~~~~~R~~~~~aLai~~fv~~~d~~~~~ 170 (309)
T PF05004_consen 117 LGAGEDSEEIFEELKPVLKRILTDS-SASPKARAACLEALAICTFVGGSDEEETE 170 (309)
T ss_pred cCCCccHHHHHHHHHHHHHHHHhCC-ccchHHHHHHHHHHHHHHHhhcCChhHHH
Confidence 2 234555555555544332 222 33445533333344444443444555555
No 60
>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=20.89 E-value=6.1e+02 Score=23.99 Aligned_cols=93 Identities=15% Similarity=0.116 Sum_probs=58.1
Q ss_pred CCHHHHHHHHHHHHHHHhcCC--CHHHHHHHHHHhCCCCCh--HHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCCCH
Q 004059 606 LNLADLRKKTVSLLEEYFSIR--ILDEALQCVEELRAPTYH--PEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTT 681 (776)
Q Consensus 606 ~s~eel~kki~~ll~EY~~~~--D~~EA~~clkEL~~p~~~--~e~V~~~I~~aLEk~~~~re~v~~LL~~L~~~~~ls~ 681 (776)
-|.||+..+. ..||+.. |.=|+.+.+.+|..=... |.+|..++-.+ |.-.+-.++...|..+..+---..
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 4667776554 4588755 555888899988654443 67777776543 233457788899998876444444
Q ss_pred HHHHHHHHHHhhcchhhhcCCCc
Q 004059 682 RDIGTGCLLYGSLLDDIGIDLPK 704 (776)
Q Consensus 682 ~q~~~Gf~~vle~LdDl~iDiP~ 704 (776)
+++..=++++=-.+++|.|+.|.
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 47777778888888999998874
No 61
>PLN03077 Protein ECB2; Provisional
Probab=20.69 E-value=5.8e+02 Score=31.90 Aligned_cols=26 Identities=19% Similarity=0.198 Sum_probs=22.1
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHhCC
Q 004059 615 TVSLLEEYFSIRILDEALQCVEELRA 640 (776)
Q Consensus 615 i~~ll~EY~~~~D~~EA~~clkEL~~ 640 (776)
...+|.-|...++.+||+..++++..
T Consensus 256 ~n~li~~~~~~g~~~eAl~lf~~M~~ 281 (857)
T PLN03077 256 WNAMISGYFENGECLEGLELFFTMRE 281 (857)
T ss_pred hHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 47788889999999999999998853
No 62
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=20.34 E-value=5.2e+02 Score=32.39 Aligned_cols=71 Identities=20% Similarity=0.269 Sum_probs=43.5
Q ss_pred hcCCCHHHHHHHHHHhCCCCChHHH------HHHHHHHHhccC-CCChHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcc
Q 004059 623 FSIRILDEALQCVEELRAPTYHPEV------VKEAIALALEKI-PPCVEPVIQLLEFLLNKNVLTTRDIGTGCLLYGSLL 695 (776)
Q Consensus 623 ~~~~D~~EA~~clkEL~~p~~~~e~------V~~~I~~aLEk~-~~~re~v~~LL~~L~~~~~ls~~q~~~Gf~~vle~L 695 (776)
+.+....|+++||+.+--.+|--.+ --.++..|||.. +.-+--+.+||++|+- +.. +.|.+.|++.|
T Consensus 204 ~~~k~~~eiIrClka~mNn~~Gl~~vL~~e~~lllla~aldpr~pnmm~dvvkllsalci---V~e---e~~~ekvl~ai 277 (1102)
T KOG1924|consen 204 LDIKNLQEIIRCLKAFMNNKFGLVLVLRRERSLLLLARALDPREPNMMTDVVKLLSALCI---VGE---ENGLEKVLEAI 277 (1102)
T ss_pred hHHHHHHHHHHHHHHHhccccceeeeecCCccHHHHHHhcCccCccHHHHHHHHHHHHhe---eeh---hhHHHHHHHHH
Confidence 4678889999999998544432111 123455678875 4444556667776654 443 66677776666
Q ss_pred hhhh
Q 004059 696 DDIG 699 (776)
Q Consensus 696 dDl~ 699 (776)
.-++
T Consensus 278 T~~a 281 (1102)
T KOG1924|consen 278 TTIA 281 (1102)
T ss_pred HHHH
Confidence 6554
No 63
>smart00139 MyTH4 Domain in Myosin and Kinesin Tails. Domain present twice in myosin-VIIa, and also present in 3 other myosins.
Probab=20.28 E-value=1.2e+02 Score=29.79 Aligned_cols=35 Identities=23% Similarity=0.512 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHHHHhhCCCC-hHHHHHHHHHHhhh
Q 004059 229 PDILKGVIELIFDKAVLEPTF-CPMYALLCSDLNEK 263 (776)
Q Consensus 229 ~e~Lk~VI~lIFeKAi~Ep~f-s~mYA~LC~~L~~~ 263 (776)
......++..|+.++++.|.. -++|.+||+.+..+
T Consensus 41 ~~~~~~l~~~i~~~~~~~~~LrDEiy~QLiKQtt~N 76 (144)
T smart00139 41 PDSHLDLVQFILQKGLAHPELRDEIYCQLIKQLTDN 76 (144)
T ss_pred cchHHHHHHHHHHHHhccHHHHHHHHHHHHHHHhCC
Confidence 455667899999999988887 58999999999875
No 64
>cd07347 harmonin_N_like N-terminal protein-binding module of harmonin and similar domains. This domain is found in harmonin, and similar proteins such as delphilin, and whirlin. These are postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold proteins. Harmonin and whirlin are organizers of the Usher protein network of the inner ear and the retina, delphilin is found at the cerebellar parallel fiber-Purkinje cell synapses. This harmonin_N_like domain is found in either one or two copies. Harmonin contains a single copy, which is found at its N-terminus and binds specifically to a short internal peptide fragment of the cadherin 23 cytoplasmic domain; cadherin 23 is a component of the Usher protein network. Whirlin contains two copies of the harmonin_N_like domain; the first of these has been assayed for interaction with the cytoplasmic domain of cadherin 23 and no interaction could be detected.
Probab=20.21 E-value=2e+02 Score=25.53 Aligned_cols=38 Identities=24% Similarity=0.329 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHh-CCCCCh
Q 004059 606 LNLADLRKKTVSLLEEYFSIRILDEALQCVEEL-RAPTYH 644 (776)
Q Consensus 606 ~s~eel~kki~~ll~EY~~~~D~~EA~~clkEL-~~p~~~ 644 (776)
+++.| +..+...|++|+..+++++.+..+.++ +.|..+
T Consensus 16 L~~~E-r~~~~~~L~~Y~~~~~Vd~LV~~L~~vLdtPaK~ 54 (78)
T cd07347 16 LTDAE-REQVTRALERYHQERNVDDLVRDLYLVLDTPAKL 54 (78)
T ss_pred CCHHH-HHHHHHHHHHHHhcCCHHHHHHHHHHHcCcHhHH
Confidence 45555 456677899999999999999999985 777654
Done!