Query 009767
Match_columns 526
No_of_seqs 267 out of 735
Neff 6.6
Searched_HMMs 46136
Date Thu Mar 28 17:05:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009767.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009767hhsearch_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 1.5E-53 3.2E-58 490.3 27.2 513 1-525 403-940 (970)
2 smart00544 MA3 Domain in DAP-5 99.9 1.1E-23 2.4E-28 185.3 13.4 113 361-473 1-113 (113)
3 PF02847 MA3: MA3 domain; Int 99.9 4.7E-24 1E-28 187.5 10.9 113 361-473 1-113 (113)
4 PF02854 MIF4G: MIF4G domain; 99.9 1.6E-22 3.4E-27 193.3 15.3 149 1-173 55-209 (209)
5 KOG0403 Neoplastic transformat 99.9 4.8E-21 1E-25 197.7 14.4 152 358-510 341-492 (645)
6 KOG0403 Neoplastic transformat 99.8 1.1E-20 2.4E-25 195.0 12.8 121 352-473 499-619 (645)
7 smart00543 MIF4G Middle domain 99.8 4.1E-19 8.9E-24 169.6 15.0 142 1-173 54-200 (200)
8 KOG2140 Uncharacterized conser 99.4 2.6E-13 5.7E-18 143.0 8.6 152 1-194 216-367 (739)
9 KOG2051 Nonsense-mediated mRNA 98.8 3.6E-08 7.8E-13 111.8 12.5 92 74-170 523-614 (1128)
10 KOG3942 MIF4G domain-containin 98.4 9.1E-07 2E-11 88.9 9.5 130 25-178 202-337 (348)
11 KOG2141 Protein involved in hi 97.9 4.2E-05 9.1E-10 84.6 10.4 99 72-177 423-524 (822)
12 KOG2051 Nonsense-mediated mRNA 96.8 0.006 1.3E-07 70.5 9.9 103 67-170 721-834 (1128)
13 KOG0401 Translation initiation 96.1 0.0043 9.4E-08 73.4 4.0 168 25-195 713-891 (970)
14 PLN00131 hypothetical protein; 65.1 1E+02 0.0023 28.8 10.9 68 347-425 117-185 (218)
15 PF02854 MIF4G: MIF4G domain; 64.9 45 0.00097 31.1 9.1 124 363-488 2-135 (209)
16 PLN03081 pentatricopeptide (PP 57.4 93 0.002 35.7 11.6 63 365-431 262-324 (697)
17 PLN03218 maturation of RBCL 1; 55.1 74 0.0016 38.8 10.6 64 364-428 544-610 (1060)
18 PF04844 Ovate: Transcriptiona 54.8 35 0.00076 26.8 5.2 45 358-402 5-51 (59)
19 PF08876 DUF1836: Domain of un 52.0 36 0.00078 29.8 5.5 51 408-458 54-104 (105)
20 COG5537 IRR1 Cohesin [Cell div 51.1 2.6E+02 0.0056 31.9 12.9 137 359-503 328-469 (740)
21 KOG2140 Uncharacterized conser 50.5 93 0.002 34.8 9.3 136 357-501 450-593 (739)
22 cd03567 VHS_GGA VHS domain fam 50.0 1.1E+02 0.0024 28.1 8.6 95 74-175 19-119 (139)
23 PRK14703 glutaminyl-tRNA synth 49.5 4.1E+02 0.0089 31.4 15.0 85 412-508 663-760 (771)
24 PRK05477 gatB aspartyl/glutamy 48.3 2.5E+02 0.0054 31.2 12.4 111 394-510 338-466 (474)
25 TIGR01568 A_thal_3678 uncharac 46.9 67 0.0014 25.8 5.7 46 357-402 10-58 (66)
26 PF08044 DUF1707: Domain of un 46.1 32 0.0007 26.2 3.7 45 409-453 4-53 (53)
27 PLN03218 maturation of RBCL 1; 46.1 1.3E+02 0.0028 36.8 10.7 26 365-390 582-607 (1060)
28 PLN03081 pentatricopeptide (PP 45.5 4.8E+02 0.01 29.9 15.0 75 365-440 90-166 (697)
29 PF12854 PPR_1: PPR repeat 41.0 40 0.00086 22.8 3.3 26 364-389 9-34 (34)
30 cd03569 VHS_Hrs_Vps27p VHS dom 39.4 1.3E+02 0.0029 27.5 7.5 94 74-175 22-117 (142)
31 PF10188 Oscp1: Organic solute 39.3 2.8E+02 0.006 26.5 9.7 116 75-196 31-148 (173)
32 TIGR01446 DnaD_dom DnaD and ph 39.1 1.1E+02 0.0023 24.2 6.0 43 393-435 30-72 (73)
33 KOG1104 Nuclear cap-binding co 39.0 1.6E+02 0.0034 34.3 9.2 105 71-177 122-247 (759)
34 PF04286 DUF445: Protein of un 37.1 4.3E+02 0.0093 27.2 11.9 93 357-449 102-200 (367)
35 PLN03077 Protein ECB2; Provisi 36.8 1.6E+02 0.0035 34.7 9.6 63 364-430 325-387 (857)
36 PLN03077 Protein ECB2; Provisi 36.3 2.8E+02 0.0062 32.7 11.5 73 365-438 357-430 (857)
37 TIGR00153 conserved hypothetic 35.6 4.2E+02 0.0091 25.7 13.4 80 365-453 30-112 (216)
38 COG1421 CRISPR system related 35.5 92 0.002 28.5 5.5 60 428-487 43-110 (137)
39 PF13041 PPR_2: PPR repeat fam 35.1 76 0.0017 22.9 4.3 41 365-405 6-47 (50)
40 PF10884 DUF2683: Protein of u 32.7 1.2E+02 0.0027 25.2 5.3 45 362-406 12-61 (80)
41 TIGR00756 PPR pentatricopeptid 32.7 53 0.0011 20.9 2.8 26 365-390 3-28 (35)
42 PF09851 SHOCT: Short C-termin 32.5 71 0.0015 21.5 3.3 25 418-442 6-30 (31)
43 PRK09498 sifA secreted effecto 32.2 88 0.0019 32.2 5.4 46 364-425 29-74 (336)
44 PF10363 DUF2435: Protein of u 31.4 3.2E+02 0.007 23.1 8.7 78 400-482 7-84 (92)
45 PF10602 RPN7: 26S proteasome 31.3 90 0.0019 29.6 5.1 57 354-410 28-88 (177)
46 PF08542 Rep_fac_C: Replicatio 31.0 2.8E+02 0.0061 22.5 7.6 48 394-445 4-51 (89)
47 PF01535 PPR: PPR repeat; Int 30.8 69 0.0015 20.0 3.1 25 366-390 4-28 (31)
48 smart00543 MIF4G Middle domain 29.4 4.5E+02 0.0098 24.2 11.2 32 454-485 94-125 (200)
49 PF08321 PPP5: PPP5 TPR repeat 28.7 34 0.00075 29.3 1.6 69 431-505 11-90 (95)
50 PF10155 DUF2363: Uncharacteri 28.4 4.4E+02 0.0096 23.7 8.8 32 411-442 77-108 (126)
51 PF09733 VEFS-Box: VEFS-Box of 28.1 99 0.0021 28.5 4.6 42 60-101 98-140 (140)
52 KOG2050 Puf family RNA-binding 27.6 1.1E+02 0.0024 34.5 5.6 62 364-425 322-387 (652)
53 cd03565 VHS_Tom1 VHS domain fa 27.0 2.6E+02 0.0057 25.5 7.3 95 74-175 19-118 (141)
54 PF12755 Vac14_Fab1_bd: Vacuol 26.9 1.8E+02 0.004 24.8 5.8 74 393-469 24-97 (97)
55 PF12612 TFCD_C: Tubulin foldi 26.6 2E+02 0.0043 27.5 6.7 37 391-427 2-38 (193)
56 PF02650 HTH_WhiA: WhiA C-term 26.1 3.6E+02 0.0078 22.6 7.3 64 72-150 21-84 (85)
57 KOG3785 Uncharacterized conser 25.1 3.7E+02 0.0081 28.9 8.6 104 367-477 290-400 (557)
58 cd07347 harmonin_N_like N-term 24.7 1.6E+02 0.0035 24.4 4.8 38 356-394 16-54 (78)
59 KOG4368 Predicted RNA binding 24.2 9.9E+02 0.022 27.3 11.9 71 397-474 87-157 (757)
60 cd03568 VHS_STAM VHS domain fa 24.1 5.6E+02 0.012 23.5 10.8 94 74-175 18-113 (144)
61 PRK14137 recX recombination re 24.1 6.7E+02 0.014 24.3 15.2 31 352-382 29-59 (195)
62 PTZ00009 heat shock 70 kDa pro 23.5 3.1E+02 0.0066 31.6 8.6 78 111-192 513-597 (653)
63 cd03561 VHS VHS domain family; 23.2 5.4E+02 0.012 22.9 11.0 92 75-175 19-115 (133)
64 PF14837 INTS5_N: Integrator c 22.6 6.8E+02 0.015 24.8 9.5 32 426-457 72-103 (213)
65 PF11867 DUF3387: Domain of un 22.1 5.9E+02 0.013 26.6 9.7 90 356-445 117-231 (335)
66 PF12295 Symplekin_C: Sympleki 21.7 3.2E+02 0.0069 26.2 7.0 80 364-446 75-160 (183)
67 PF01865 PhoU_div: Protein of 21.1 3.4E+02 0.0073 26.0 7.2 90 365-463 27-120 (214)
68 PF13311 DUF4080: Protein of u 20.4 5.1E+02 0.011 24.8 8.2 74 352-425 18-95 (190)
No 1
>KOG0401 consensus Translation initiation factor 4F, ribosome/mRNA-bridging subunit (eIF-4G) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.5e-53 Score=490.26 Aligned_cols=513 Identities=33% Similarity=0.477 Sum_probs=369.9
Q ss_pred CHHHHHHHHhhhCCCCCCCCCCCcchhHHHHHHHHHHHHHhccc-ccHHHHhcCCChHH-HHHHHHHHHHHHhhhhhhHH
Q 009767 1 MYALLCSDLNEKLPPFPSDEPGGKDITFKRILLNHCQEAFEGAD-NTRAEIRQMTAPEQ-EMERMDQERLVKLRTLGNIR 78 (526)
Q Consensus 1 mYA~LC~~L~~~~~~~~~~~~~~~~~~Fr~~LL~~cQ~eFe~~~-~~~~~~~~~~~~e~-e~e~~~~~~~~K~r~lGnir 78 (526)
|||+||..|.. .+.++.-+.++..++||+.||++||++|+... ...+++..+..+++ |.+.++.+.++++|++|||+
T Consensus 403 ~yA~lc~~l~~-~~~~~~~~~~~~~~~fr~~lL~rcq~~fe~~~~~~~~~~~~~~~~~~~e~~le~~k~~~~~rtlgn~~ 481 (970)
T KOG0401|consen 403 MYARLCFDLEG-PPSEPELDMGGDEINFRRLLLNRCQKEFEGEDDKIADEYSEAEEPDELEEELEEEKYILRRRTLGNFR 481 (970)
T ss_pred hcchhcccccC-CccCCCcCCCCCcccHHHHHHHHhHHHhhcccHHHHHHhhhhcCchhHHHHHHhccceecCCccchHH
Confidence 79999999988 55555445566789999999999999999987 56667776665554 55566667789999999999
Q ss_pred HHHHHhcCCCCCHHHHHHHHHHHHhcCCCCCCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHHhCCCCChh
Q 009767 79 LIGELLKQKMVPEKIVHHIVQELLENDGKTCPAEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTTNSQLVPR 158 (526)
Q Consensus 79 FIGELfk~~~l~e~ii~~ci~~Ll~~~~~~~p~ee~iE~lc~LL~tiG~~Ld~~~~~~~~~d~~f~~l~~l~~~~~ls~R 158 (526)
|||+||+.+|++++|||.|++.||.... ++|++|||+|.|++|||+.||........||.||.+++.++..+.+++|
T Consensus 482 ~ig~l~~~~ml~e~i~~~~v~~Ll~~~~---~~ee~ie~lc~f~~tig~~lD~~~~s~r~md~~~~~~k~~~~~~~~s~r 558 (970)
T KOG0401|consen 482 FIGELFKLKMLTEKIVHACVQKLLSDDQ---PSEESIECLCRFLTTIGKKLDFSKESPRNMDEYFNSMKNLKRKPQRSNR 558 (970)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcccc---ccchhhhhHHhhhhcccccccccCcccchhHHHHHHHHHhhhhhhhccc
Confidence 9999999999999999999999998742 6899999999999999999997544333399999999999999999999
Q ss_pred HHHHHHHHHHHHhCCCCccccccCCC-cHHHHHHHHHHhcCCCCchhhhhhcCCCCCC---CC-C----CCCCCCCCCCC
Q 009767 159 LRFMIHDVLDLRANNWVPRREEMKAK-TITEIHSEAEKNLGLRPGATAMMRNGRTGAT---GG-M----GPGGFPIARPG 229 (526)
Q Consensus 159 irfmi~dvidlR~~~W~~r~~~~~pk-ti~~i~~e~~~~~~~~~~~~~~~r~~~~~~~---~~-~----~~g~~~~~~~~ 229 (526)
+|||+++++|||.++|++|+.+.+++ +|++||.++.++....+.....++.++.+.- +. . .+.+....+..
T Consensus 559 ~RfM~~~~idlR~~~w~~rr~~~~~~~~ieei~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 638 (970)
T KOG0401|consen 559 IRFMLQSVIDLRKSGWGPRRAEETNDKPIEEIAPEAPSANRWSPKSLSKKTEGRLAEESDSGLLGKEVVERKGKSGLRKL 638 (970)
T ss_pred hhhhhccccccccccccchhcccCCCCchhhcchhhhhhcccCcccccccccccccccccccccCccccccccccccccC
Confidence 99999999999999999999987766 9999999998887654544333344332110 00 0 01111222333
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCcccCCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCC----CccCCCCCCCCcCC
Q 009767 230 TGGMMPGMPGTQKMPGMPGFDTDNWEVPRSR--TMPRGDSKSPSQFPGRVQSPLIGKSPSIN----SKFLPQGSGGIISG 303 (526)
Q Consensus 230 ~gg~~p~~~~~~~~~~~~g~~~~~~~~~~~~--s~~~~~~~~~~~~~~~~~~~~~~k~~~~~----~~~~p~~s~~~~~~ 303 (526)
.+.++++++........+..+.++|.+.... +.++...... +......+..++..... ....++|+.+....
T Consensus 639 ~~e~~~~i~~~~~~~~~~~~~e~~~~~~k~~~~~~~~k~~~~~--~~~~~~~~~~~~~~~~~s~~~~~~~~~g~~~~~~~ 716 (970)
T KOG0401|consen 639 TPEMFDKISDPILDIADQSMDEEDGEASKQKGEQGGRKASDEQ--HFSSMRAPALEKVVPSLSSDIDDKRNRGSNGELLS 716 (970)
T ss_pred ChhhcccccccccccchhhccccccchhhhcccccccccCccc--cccccCCccccccccccccccccccccCCcccccc
Confidence 3444444443323333445566666654322 1111111100 00011111111111101 12334444331111
Q ss_pred C--CccccC---CCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCC--CCCHHHHHHHHHHHHHHHhcCC
Q 009767 304 K--TSALLQ---GSPTPSARPSGIASGVEPLTQYTKPVAPAASVVASPEKPSAPVT--KLNLADLRKKTVSLLEEYFSIR 376 (526)
Q Consensus 304 k--~s~~~~---~~~~p~~r~~~~~~~~~~~~~~~~~~k~~~~~p~~~~~~~~~~~--~~s~eel~kk~~~il~EY~~~~ 376 (526)
. .++... ..+....++++....+ .+.-..+. -.++.+.+.++.+. .++.+.+..+++.|+.||++..
T Consensus 717 ~~~~~~~~~~~~~~~~~~~~~s~~~~~~-----~~e~~~~~-~~~~~~~~~~~~~~v~~~~~~~l~~~sk~l~ee~~~~~ 790 (970)
T KOG0401|consen 717 DSYLSARCHEEFENGWSRELPSGKDGER-----EPEMMSPE-YYAAKAAKRAGLGLVIALSSELLELLSKSLLEEFLSLR 790 (970)
T ss_pred ccccchhhhhhccccccccCCCCccccc-----chhhcCcc-cchhhhhhccCCcchhhhhHHHHHHHHHHHHHHHHHHh
Confidence 1 111111 0000000111110000 00000110 01111222333444 7899999999999999999999
Q ss_pred CHHHHHHHHHHhCCCCChHHHHHHHHHHHhcCCCcChHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcchhhhcCCCchh
Q 009767 377 ILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTGCLLYGSLLDDIGIDLPKAP 456 (526)
Q Consensus 377 D~~Ea~~~i~eL~~p~~~~~~V~~~I~~aLE~~~~~re~v~~LL~~L~~~~~ls~~q~~~Gf~~vl~~l~Dl~iDiP~a~ 456 (526)
+.+|++.|++++++|.+|+.+|..+|+..|++++..|+++++||..|+..+.++.+++..||..++..++|+.||+|++|
T Consensus 791 ~~~~~~~~ie~l~S~~~~~~~v~~~v~~~l~~~~~~~~~~~~ll~~l~~~~~~~~~~~~~~~~~~~~~~~d~~~d~pk~w 870 (970)
T KOG0401|consen 791 LEKEALKCIEELESPSLLLKTVGENIEPTLEKSPQAVEELLQLLDILVSKNPLSIETLEIGYREKFKLADDKELDLPKGW 870 (970)
T ss_pred hhhhhhhhhhcccchhhhHHHHHHhcCcccccChhHHHHHHHHHHHHHhcCcccHHHHhhhHHHHHhhhHHHhcccccch
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHcCCCCh-HHHHHHHHhhhchhHHHHHHHHHHHHHhcCCCchhhHHhhhhhHHHHhhhh
Q 009767 457 NNFGEMVGKLVVAKSLDF-IVLKEVLKKVEDNMFRRSIFTAAMKSIQSSPAGQEVLAVQGAEVQACESLL 525 (526)
Q Consensus 457 ~~la~~iar~i~~~~l~~-~~i~~~~~~~~~~~~~~~~l~~~l~~l~~~~~g~~~~~~~~~~~~~~~~~~ 525 (526)
.|+++|++..+..+++++ ..+..+...+.+.+++..|+.+++..+...-++.|+.+..+....+|..++
T Consensus 871 ~~~~e~~gp~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~ 940 (970)
T KOG0401|consen 871 NYIKEFLGPLIHQKILDESELVREILKNMRPNGRRSNVLFSVLEIVEKELGRADLGDIQRESFLSTKTLL 940 (970)
T ss_pred hHHHHhhhhHhhhccccHHHHHHHHhhcCCccccccchHHHHHHHHHHhhhHHHHHHHHHHhcccchhcc
Confidence 999999999999999999 445677778999999999999999999998888999999999999998764
No 2
>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=99.91 E-value=1.1e-23 Score=185.33 Aligned_cols=113 Identities=35% Similarity=0.472 Sum_probs=110.2
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhcCCCcChHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 009767 361 LRKKTVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTGCLL 440 (526)
Q Consensus 361 l~kk~~~il~EY~~~~D~~Ea~~~i~eL~~p~~~~~~V~~~I~~aLE~~~~~re~v~~LL~~L~~~~~ls~~q~~~Gf~~ 440 (526)
+++++..+|+||++++|.+||++||++|+.|++||+||+.+|..++|+++.+|+.+++||.+|++.+++++++|..||.+
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 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcchhhhcCCCchhHHHHHHHHHHHHcCCCC
Q 009767 441 YGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLD 473 (526)
Q Consensus 441 vl~~l~Dl~iDiP~a~~~la~~iar~i~~~~l~ 473 (526)
+++.++|+++|+|+++.++|+|+|++|.+|++|
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 3
>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=99.91 E-value=4.7e-24 Score=187.47 Aligned_cols=113 Identities=35% Similarity=0.537 Sum_probs=107.1
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhcCCCcChHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 009767 361 LRKKTVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTGCLL 440 (526)
Q Consensus 361 l~kk~~~il~EY~~~~D~~Ea~~~i~eL~~p~~~~~~V~~~I~~aLE~~~~~re~v~~LL~~L~~~~~ls~~q~~~Gf~~ 440 (526)
+++++..+|.|||+++|.+||+.||+||+.|.+|++||..+|..+||+++.+|+.++.||.+|++.++++.++|.+||.+
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 58999999999999999999999999999998899999999999999999999999999999999999999999999999
Q ss_pred HhhcchhhhcCCCchhHHHHHHHHHHHHcCCCC
Q 009767 441 YGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLD 473 (526)
Q Consensus 441 vl~~l~Dl~iDiP~a~~~la~~iar~i~~~~l~ 473 (526)
+++.++|+.+|+|++|+++|+|++++|.+|+||
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 4
>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=99.89 E-value=1.6e-22 Score=193.34 Aligned_cols=149 Identities=38% Similarity=0.711 Sum_probs=125.5
Q ss_pred CHHHHHHHHhhhCCCCCCCCCCCcchhHHHHHHHHHHHHHhcccccHHHHhcCCChHHHHHHHHHHHHHHhhhhhhHHHH
Q 009767 1 MYALLCSDLNEKLPPFPSDEPGGKDITFKRILLNHCQEAFEGADNTRAEIRQMTAPEQEMERMDQERLVKLRTLGNIRLI 80 (526)
Q Consensus 1 mYA~LC~~L~~~~~~~~~~~~~~~~~~Fr~~LL~~cQ~eFe~~~~~~~~~~~~~~~e~e~e~~~~~~~~K~r~lGnirFI 80 (526)
+||+||..|....+ ..|+..||++||++|+... ... +.++.....++|..|+++||
T Consensus 55 ~~a~l~~~l~~~~~-----------~~f~~~ll~~~~~~f~~~~-----------~~~--~~~~~~~~~~~~~~~~~~fl 110 (209)
T PF02854_consen 55 LYARLCAALNSRFP-----------SEFRSLLLNRCQEEFEERY-----------SNE--ELEENRQSSKQRRRGNIRFL 110 (209)
T ss_dssp HHHHHHHHHHHHCH-----------HHHHHHHHHHHHHHHHHHT------------HH--HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhccch-----------hhHHHHHHHHHHHHHHHhh-----------hhh--hHHHHHHHHHHHHhhhhhHH
Confidence 59999999999753 6899999999999999854 011 11122345678999999999
Q ss_pred HHHhcCCCCCHHHHHHHHHHHHhcCCC---CCCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHHhC---CC
Q 009767 81 GELLKQKMVPEKIVHHIVQELLENDGK---TCPAEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTTN---SQ 154 (526)
Q Consensus 81 GELfk~~~l~e~ii~~ci~~Ll~~~~~---~~p~ee~iE~lc~LL~tiG~~Ld~~~~~~~~~d~~f~~l~~l~~~---~~ 154 (526)
||||+.+++++++|+.|+..|+..... ..+++++|||+|.+|.+||+.|+.....+..|+.||..++.+..+ +.
T Consensus 111 ~eL~~~~vv~~~~i~~~l~~ll~~~~~~~~~~~~~~~ie~~~~lL~~~G~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 190 (209)
T PF02854_consen 111 AELFNFGVVSEKIIFDILRELLSDGTDECQPPPDEENIECLCTLLKTCGKKLENSEESPKALDEIFERLQKYANSKKDPN 190 (209)
T ss_dssp HHHHHTTSSCHHHHHHHHHHHHHHTSHHCCHHTCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCHSSS
T ss_pred HhhHhhccccchhHHHHHHHHHhcccccccCCCcHhHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHhhcccC
Confidence 999999999999999999999987421 125679999999999999999995455668899999999999887 79
Q ss_pred CChhHHHHHHHHHHHHhCC
Q 009767 155 LVPRLRFMIHDVLDLRANN 173 (526)
Q Consensus 155 ls~Rirfmi~dvidlR~~~ 173 (526)
+++|+||||+|++|+|+|+
T Consensus 191 ~~~r~~~~l~~l~~lr~~~ 209 (209)
T PF02854_consen 191 LSSRIRFMLEDLIELRNNK 209 (209)
T ss_dssp SSHHHHHHHHHHHHHHHTC
T ss_pred CCHHHHHHHHHHHHHhcCC
Confidence 9999999999999999986
No 5
>KOG0403 consensus Neoplastic transformation suppressor Pdcd4/MA-3, contains MA3 domain [Signal transduction mechanisms]
Probab=99.85 E-value=4.8e-21 Score=197.68 Aligned_cols=152 Identities=23% Similarity=0.354 Sum_probs=143.0
Q ss_pred HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhcCCCcChHHHHHHHHHHHhCCCCCHHHHHHH
Q 009767 358 LADLRKKTVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTG 437 (526)
Q Consensus 358 ~eel~kk~~~il~EY~~~~D~~Ea~~~i~eL~~p~~~~~~V~~~I~~aLE~~~~~re~v~~LL~~L~~~~~ls~~q~~~G 437 (526)
...|++.+..||+|||.++|+.|.++|+++|+.|.|.+.|++.+|++|||+++.++|+++.||+.|+- .++|++++..|
T Consensus 341 ~r~Fkk~~~~IIqEYFlsgDt~Evi~~L~DLn~~E~~~~f~k~lITLAldrK~~ekEMasvllS~L~~-e~fsteDv~~~ 419 (645)
T KOG0403|consen 341 LRAFKKDLTPIIQEYFLSGDTPEVIRSLRDLNLPEYNPGFLKLLITLALDRKNSEKEMASVLLSDLHG-EVFSTEDVEKG 419 (645)
T ss_pred HHHHHHhhHHHHHHHHhcCChHHHHHHHHHcCCccccchHHHHHHHHHhccchhHHHHHHHHHHHhhc-ccCCHHHHHHH
Confidence 56799999999999999999999999999999999999999999999999999999999999999988 79999999999
Q ss_pred HHHHhhcchhhhcCCCchhHHHHHHHHHHHHcCCCChHHHHHHHHhhhchhHHHHHHHHHHHHHhcCCCchhh
Q 009767 438 CLLYGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLDFIVLKEVLKKVEDNMFRRSIFTAAMKSIQSSPAGQEV 510 (526)
Q Consensus 438 f~~vl~~l~Dl~iDiP~a~~~la~~iar~i~~~~l~~~~i~~~~~~~~~~~~~~~~l~~~l~~l~~~~~g~~~ 510 (526)
|..+++.++|+++|+|.|.+.||.|+||||.|++|.+.+++++..++.+....++.+..|-..|+.+.+|+-+
T Consensus 420 F~mLLesaedtALD~p~a~~elalFlARAViDdVLap~~leei~~~lp~~s~g~et~~~ArsLlsar~aGeRl 492 (645)
T KOG0403|consen 420 FDMLLESAEDTALDIPRASQELALFLARAVIDDVLAPTNLEEISGTLPPVSQGRETLDKARSLLSARHAGERL 492 (645)
T ss_pred HHHHHhcchhhhccccccHHHHHHHHHHHHhhcccccCcHHHHcCCCCCchhhHHHHHHHHHHHHHhhcccch
Confidence 9999999999999999999999999999999999999999999999988877888888888888877655433
No 6
>KOG0403 consensus Neoplastic transformation suppressor Pdcd4/MA-3, contains MA3 domain [Signal transduction mechanisms]
Probab=99.84 E-value=1.1e-20 Score=194.95 Aligned_cols=121 Identities=27% Similarity=0.383 Sum_probs=115.2
Q ss_pred CCCCCCHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhcCCCcChHHHHHHHHHHHhCCCCCH
Q 009767 352 PVTKLNLADLRKKTVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTT 431 (526)
Q Consensus 352 ~~~~~s~eel~kk~~~il~EY~~~~D~~Ea~~~i~eL~~p~~~~~~V~~~I~~aLE~~~~~re~v~~LL~~L~~~~~ls~ 431 (526)
++++++.++++++|..+|+||..+||+.||.+||+||..|+|||++|+++|.++||++.. .+++.+||..++++|+||.
T Consensus 499 GG~g~sVed~kdkI~~LLeEY~~~GdisEA~~CikeLgmPfFhHEvVkkAlVm~mEkk~d-~t~~ldLLk~cf~sglIT~ 577 (645)
T KOG0403|consen 499 GGGGWSVEDAKDKIDMLLEEYELSGDISEACHCIKELGMPFFHHEVVKKALVMVMEKKGD-STMILDLLKECFKSGLITT 577 (645)
T ss_pred CCCcchHHHHHHHHHHHHHHHHhccchHHHHHHHHHhCCCcchHHHHHHHHHHHHHhcCc-HHHHHHHHHHHHhcCceeH
Confidence 448999999999999999999999999999999999999999999999999999998753 3599999999999999999
Q ss_pred HHHHHHHHHHhhcchhhhcCCCchhHHHHHHHHHHHHcCCCC
Q 009767 432 RDIGTGCLLYGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLD 473 (526)
Q Consensus 432 ~q~~~Gf~~vl~~l~Dl~iDiP~a~~~la~~iar~i~~~~l~ 473 (526)
+|+.+||.+|.+.|+||.+|||+|++-+..++.++..+|++.
T Consensus 578 nQMtkGf~RV~dsl~DlsLDvPna~ekf~~~Ve~~~~~G~i~ 619 (645)
T KOG0403|consen 578 NQMTKGFERVYDSLPDLSLDVPNAYEKFERYVEECFQNGIIS 619 (645)
T ss_pred HHhhhhhhhhhccCcccccCCCcHHHHHHHHHHHHHHcCchh
Confidence 999999999999999999999999999999999999999654
No 7
>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=99.81 E-value=4.1e-19 Score=169.62 Aligned_cols=142 Identities=36% Similarity=0.562 Sum_probs=118.5
Q ss_pred CHHHHHHHHhhhCCCCCCCCCCCcchhHHHHHHHHHHHHHhcccccHHHHhcCCChHHHHHHHHHHHHHHhhhhhhHHHH
Q 009767 1 MYALLCSDLNEKLPPFPSDEPGGKDITFKRILLNHCQEAFEGADNTRAEIRQMTAPEQEMERMDQERLVKLRTLGNIRLI 80 (526)
Q Consensus 1 mYA~LC~~L~~~~~~~~~~~~~~~~~~Fr~~LL~~cQ~eFe~~~~~~~~~~~~~~~e~e~e~~~~~~~~K~r~lGnirFI 80 (526)
+||+||..|....+ .|+..+++.||++|++.- + +.+...++++.|+++||
T Consensus 54 ~ya~L~~~l~~~~~------------~f~~~ll~~~~~~f~~~~------------e------~~~~~~~~~~~~~i~fl 103 (200)
T smart00543 54 AYARLCALLNAKNP------------DFGSLLLERLQEEFEKGL------------E------SEEESDKQRRLGLVRFL 103 (200)
T ss_pred HHHHHHHHHHHHHH------------HHHHHHHHHHHHHHHHHH------------H------HHHHHhhhhHHhHHHHH
Confidence 59999999998742 799999999999998751 0 01123457889999999
Q ss_pred HHHhcCCCCCHHHHHHHHHHHHhcCCC--CCCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHHhCC---CC
Q 009767 81 GELLKQKMVPEKIVHHIVQELLENDGK--TCPAEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTTNS---QL 155 (526)
Q Consensus 81 GELfk~~~l~e~ii~~ci~~Ll~~~~~--~~p~ee~iE~lc~LL~tiG~~Ld~~~~~~~~~d~~f~~l~~l~~~~---~l 155 (526)
||||+.++++..++..|+..|+..... ..++++++||+|.+|.+||+.|+. +..+..|+.+|+.++....+. .+
T Consensus 104 ~eL~~~~~i~~~~i~~~l~~ll~~~~~~~~~~~~~~ve~l~~lL~~~G~~l~~-~~~~~~~~~~l~~l~~~~~~~~~~~~ 182 (200)
T smart00543 104 GELYNFQVLTSKIILELLKELLNDLTKLDPPRSDFSVECLLSLLPTCGKDLER-EKSPKLLDEILERLQDYLLKKDKTEL 182 (200)
T ss_pred HHHHHcccCcHHHHHHHHHHHHhccCCCCCCCcHHHHHHHHHHHHHhhHHHcC-cccHHHHHHHHHHHHHHHhcccccCC
Confidence 999999999999999999999987311 113568999999999999999994 234577999999999988776 79
Q ss_pred ChhHHHHHHHHHHHHhCC
Q 009767 156 VPRLRFMIHDVLDLRANN 173 (526)
Q Consensus 156 s~Rirfmi~dvidlR~~~ 173 (526)
++|+||||++++++|++.
T Consensus 183 ~~r~~~~l~~l~~l~~~~ 200 (200)
T smart00543 183 SSRLRFMLELLIELRKNK 200 (200)
T ss_pred ChHHHHHHHHHHHHhhCc
Confidence 999999999999999863
No 8
>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]
Probab=99.43 E-value=2.6e-13 Score=142.96 Aligned_cols=152 Identities=25% Similarity=0.466 Sum_probs=125.1
Q ss_pred CHHHHHHHHhhhCCCCCCCCCCCcchhHHHHHHHHHHHHHhcccccHHHHhcCCChHHHHHHHHHHHHHHhhhhhhHHHH
Q 009767 1 MYALLCSDLNEKLPPFPSDEPGGKDITFKRILLNHCQEAFEGADNTRAEIRQMTAPEQEMERMDQERLVKLRTLGNIRLI 80 (526)
Q Consensus 1 mYA~LC~~L~~~~~~~~~~~~~~~~~~Fr~~LL~~cQ~eFe~~~~~~~~~~~~~~~e~e~e~~~~~~~~K~r~lGnirFI 80 (526)
+||.|...|+..+|.+ .....++++|+ |.+..+ +.-|.-++..++||
T Consensus 216 vyaALvAviNskfP~I-------gElLlkrLilq-----f~r~f~---------------------RnDk~~c~~~~kfi 262 (739)
T KOG2140|consen 216 VYAALVAVINSKFPQI-------GELLLKRLILQ-----FKRSFR---------------------RNDKVSCLNASKFI 262 (739)
T ss_pred HHHHHHHHHccCCchH-------HHHHHHHHHHH-----HHHHhc---------------------ccchHHHHHHHHHH
Confidence 4888888888887754 35778888887 554322 12244677889999
Q ss_pred HHHhcCCCCCHHHHHHHHHHHHhcCCCCCCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHHhCCCCChhHH
Q 009767 81 GELLKQKMVPEKIVHHIVQELLENDGKTCPAEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTTNSQLVPRLR 160 (526)
Q Consensus 81 GELfk~~~l~e~ii~~ci~~Ll~~~~~~~p~ee~iE~lc~LL~tiG~~Ld~~~~~~~~~d~~f~~l~~l~~~~~ls~Rir 160 (526)
++|++++|.+|-|.++++..||+. |++++||.++.+|+.||.+|-.-. +..+|.+|+||+.++....++.|++
T Consensus 263 ahLinq~VahEIv~Leil~lLLe~-----PTddSvevaI~flkecGakL~~VS--pr~~n~IfErlR~ILhe~Eld~rvq 335 (739)
T KOG2140|consen 263 AHLINQQVAHEIVALEILTLLLER-----PTDDSVEVAIAFLKECGAKLAEVS--PRALNGIFERLRYILHEGELDRRVQ 335 (739)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcC-----CCCchHHHHHHHHHHHHHHHHHhC--hHHHhHHHHHHHHHHhHhhHHHHHH
Confidence 999999999999999999999986 899999999999999999998642 2457999999999999999999999
Q ss_pred HHHHHHHHHHhCCCCccccccCCCcHHHHHHHHH
Q 009767 161 FMIHDVLDLRANNWVPRREEMKAKTITEIHSEAE 194 (526)
Q Consensus 161 fmi~dvidlR~~~W~~r~~~~~pkti~~i~~e~~ 194 (526)
|||+-+++.|+.+|+.. ..++.-++.|.++++
T Consensus 336 y~iEtlf~iRkdkfk~~--p~v~~~LDlvee~dq 367 (739)
T KOG2140|consen 336 YMIETLFQIRKDKFKSH--PAVLEELDLVEEEDQ 367 (739)
T ss_pred HHHHHHHHHHHHhhccC--CccccccCccchhhh
Confidence 99999999999999876 345666777776653
No 9
>KOG2051 consensus Nonsense-mediated mRNA decay 2 protein [RNA processing and modification]
Probab=98.79 E-value=3.6e-08 Score=111.79 Aligned_cols=92 Identities=25% Similarity=0.398 Sum_probs=84.6
Q ss_pred hhhHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCCCCCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHHhCC
Q 009767 74 LGNIRLIGELLKQKMVPEKIVHHIVQELLENDGKTCPAEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTTNS 153 (526)
Q Consensus 74 lGnirFIGELfk~~~l~e~ii~~ci~~Ll~~~~~~~p~ee~iE~lc~LL~tiG~~Ld~~~~~~~~~d~~f~~l~~l~~~~ 153 (526)
+-+|+|||||.|.++++..-++.|++.||.+. ...+||.+|.||++||+.|-.++.++..|..++++|+......
T Consensus 523 ~~~VrfIsEL~KF~lv~~~~if~cLk~ll~dF-----~~hnIEm~c~lLE~~GrfLlr~pEt~lrM~~~Le~i~rkK~a~ 597 (1128)
T KOG2051|consen 523 LKIVRFISELCKFQLVPKFEIFSCLKMLLNDF-----THHNIEMACVLLESCGRFLLRSPETKLRMRVFLEQIKRKKRAS 597 (1128)
T ss_pred hhhhhhHHhhhhhCccChHHHHHHHHHHHHhc-----ccccHHHHHHHHHhcchhhhcChhHHHHHHHHHHHHHHHHHHh
Confidence 34799999999999999999999999999875 6678999999999999999999998899999999999887788
Q ss_pred CCChhHHHHHHHHHHHH
Q 009767 154 QLVPRLRFMIHDVLDLR 170 (526)
Q Consensus 154 ~ls~Rirfmi~dvidlR 170 (526)
.+.+|..-+|.|++-+=
T Consensus 598 ~lDsr~~~~iENay~~~ 614 (1128)
T KOG2051|consen 598 ALDSRQATLIENAYYLC 614 (1128)
T ss_pred hhchHHHHHHHHhHHhc
Confidence 99999999999999873
No 10
>KOG3942 consensus MIF4G domain-containing protein [Translation, ribosomal structure and biogenesis]
Probab=98.43 E-value=9.1e-07 Score=88.86 Aligned_cols=130 Identities=18% Similarity=0.147 Sum_probs=99.3
Q ss_pred chhHHHHHHHHHHHHHhcccccHHHHhcCCChHHHHHHHHHHHHHHhhhhhhHHHHHHHhcCC-----CCCHHHHHHHHH
Q 009767 25 DITFKRILLNHCQEAFEGADNTRAEIRQMTAPEQEMERMDQERLVKLRTLGNIRLIGELLKQK-----MVPEKIVHHIVQ 99 (526)
Q Consensus 25 ~~~Fr~~LL~~cQ~eFe~~~~~~~~~~~~~~~e~e~e~~~~~~~~K~r~lGnirFIGELfk~~-----~l~e~ii~~ci~ 99 (526)
.+.|+..|||.||+.|+-+..++ . ....|+++.|.|++|||-.- ++=..++..|+.
T Consensus 202 gt~f~~~Lln~lrq~f~~r~gl~-------s------------~~~~rw~~fisfltelf~nlgs~p~~vL~~~l~~cl~ 262 (348)
T KOG3942|consen 202 GTQFMDELLNLLRQGFLLRTGLS-------S------------LASCRWWRFISFLTELFDNLGSCPQVVLQRSLRLCLQ 262 (348)
T ss_pred cchHHHHHHHHHHHhhccchhcc-------c------------hhHHHHHHHHHHHHHHHhhcCCCChhhHHHHHHHHHH
Confidence 35699999999999999764321 1 23468999999999999863 455678899999
Q ss_pred HHHhcCCCCCCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHHhCCCCC-hhHHHHHHHHHHHHhCCCCccc
Q 009767 100 ELLENDGKTCPAEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTTNSQLV-PRLRFMIHDVLDLRANNWVPRR 178 (526)
Q Consensus 100 ~Ll~~~~~~~p~ee~iE~lc~LL~tiG~~Ld~~~~~~~~~d~~f~~l~~l~~~~~ls-~Rirfmi~dvidlR~~~W~~r~ 178 (526)
.|+..- +..+..+||+.-.|...|..|++.- ...|..+|.-.++..-...-| .-+|.+|..+|||-++.|..+.
T Consensus 263 ~llrsp---d~~~~e~ecl~~~L~~~g~dle~ql--P~ql~lL~~s~rDafL~~sep~a~~r~~lllliel~As~wqlpt 337 (348)
T KOG3942|consen 263 ILLRSP---DWPEFEYECLSMKLAVEGLDLEKQL--PFQLLLLFPSRRDAFLVRSEPLAPWRCPLLLLIELPASAWQLPT 337 (348)
T ss_pred HHccCC---CcchHHHHHHHHHHHHcCccchhhh--hHHHHHHHHHHHHhhhccccccccccchhhhccccCccccCCCC
Confidence 999862 2357899999999999999999632 245666777666544444333 4469999999999999999773
No 11
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=97.94 E-value=4.2e-05 Score=84.56 Aligned_cols=99 Identities=21% Similarity=0.326 Sum_probs=81.2
Q ss_pred hhhhhHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCCCCCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHHh
Q 009767 72 RTLGNIRLIGELLKQKMVPEKIVHHIVQELLENDGKTCPAEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTT 151 (526)
Q Consensus 72 r~lGnirFIGELfk~~~l~e~ii~~ci~~Ll~~~~~~~p~ee~iE~lc~LL~tiG~~Ld~~~~~~~~~d~~f~~l~~l~~ 151 (526)
.+-+.+.|+++||+.++++-.+|.++|..|..+ ++|-++|||..++..||..|-.... ..+..+..-+.....
T Consensus 423 ~~~Nl~~~l~ylynF~ivs~~LiydiI~kl~~~-----l~e~~ve~ll~ii~~~G~~LRkDDp--~alk~~i~eiq~~a~ 495 (822)
T KOG2141|consen 423 SLNNIVLFLSYLYNFGIVSCSLIYDIIRKLAEN-----LNETNVEALLTIIANCGFSLRKDDP--LALKDIITEIQSKAA 495 (822)
T ss_pred hhhhHHHHHHHHHHhhcccHHHHHHHHHHHHhc-----hhhhhHHHHHHHHHHccchhcCCCh--HHHHHHHHHHHHHhh
Confidence 567889999999999999999999999999987 5899999999999999999986432 345556666655444
Q ss_pred CCC---CChhHHHHHHHHHHHHhCCCCcc
Q 009767 152 NSQ---LVPRLRFMIHDVLDLRANNWVPR 177 (526)
Q Consensus 152 ~~~---ls~Rirfmi~dvidlR~~~W~~r 177 (526)
+.. .++|+|||+..++.|.+|+-++-
T Consensus 496 ~a~~s~~~pR~rFmleti~aLKnN~~kki 524 (822)
T KOG2141|consen 496 SAKISAISPRLRFMLETISALKNNKLKKI 524 (822)
T ss_pred cCCccccchHHHHHHHHHHHHhcCCCcCC
Confidence 432 47999999999999998876643
No 12
>KOG2051 consensus Nonsense-mediated mRNA decay 2 protein [RNA processing and modification]
Probab=96.77 E-value=0.006 Score=70.53 Aligned_cols=103 Identities=17% Similarity=0.313 Sum_probs=79.6
Q ss_pred HHHHhhhhhhHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCCCC-------CCh--hhHHHHHHHHHHHhhhhhcCCcchh
Q 009767 67 RLVKLRTLGNIRLIGELLKQKMVPEKIVHHIVQELLENDGKTC-------PAE--ENVEAICQFFNTIGKQLDENPKSRR 137 (526)
Q Consensus 67 ~~~K~r~lGnirFIGELfk~~~l~e~ii~~ci~~Ll~~~~~~~-------p~e--e~iE~lc~LL~tiG~~Ld~~~~~~~ 137 (526)
...++|.+.++||+||||...|+...+|...+-.++.-..... |.+ --|-.+|.||.|||..++. .+++.
T Consensus 721 ~~~nQrriA~aryL~ELynfemvds~vIl~tLy~~i~~g~~~~~~~~~ldppddlFRirlV~~lL~tc~~yf~r-gs~kk 799 (1128)
T KOG2051|consen 721 YVSNQRRIALARYLGELYNFEMVDSDVILNTLYHLISLGHFENLTPSALDPPDDLFRIRLVCMLLQTCGPYFTR-GSTKK 799 (1128)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHhcccccCCCCcccCCChHHHHHHHHHHHHHHHccccccc-chhHH
Confidence 4577889999999999999999999999999988875321111 222 3478899999999999996 45667
Q ss_pred hHHHHHHHHHHHHhCC--CCChhHHHHHHHHHHHH
Q 009767 138 VNDVYFSRLKELTTNS--QLVPRLRFMIHDVLDLR 170 (526)
Q Consensus 138 ~~d~~f~~l~~l~~~~--~ls~Rirfmi~dvidlR 170 (526)
.|+.|+--++.+.--+ ..|--+.++++|++.+-
T Consensus 800 kl~~fL~~fq~Y~~iKk~~~Pld~~~~f~d~~~~~ 834 (1128)
T KOG2051|consen 800 KLDQFLVAFQRYILIKKSQQPLDMEYEFEDFLELV 834 (1128)
T ss_pred HHHHHHHHHHHHhhcccccCCCchhhhHHhhhhhc
Confidence 7888766666544322 48889999999999884
No 13
>KOG0401 consensus Translation initiation factor 4F, ribosome/mRNA-bridging subunit (eIF-4G) [Translation, ribosomal structure and biogenesis]
Probab=96.13 E-value=0.0043 Score=73.42 Aligned_cols=168 Identities=15% Similarity=0.193 Sum_probs=106.9
Q ss_pred chhHHHHHHHHHHHHHhcccccHHHHhcCCCh--HHHHHHHHHHHHHHhhhhhhHHHHHHHhcCCCCCHHHHHHHHHHHH
Q 009767 25 DITFKRILLNHCQEAFEGADNTRAEIRQMTAP--EQEMERMDQERLVKLRTLGNIRLIGELLKQKMVPEKIVHHIVQELL 102 (526)
Q Consensus 25 ~~~Fr~~LL~~cQ~eFe~~~~~~~~~~~~~~~--e~e~e~~~~~~~~K~r~lGnirFIGELfk~~~l~e~ii~~ci~~Ll 102 (526)
..++.+.+..+||.+|.+.|...--....... +.-.+..+.....+++++|+| +......+.+.+..|++.|+...+
T Consensus 713 ~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~e~~~~~~~~~~~~~~~~~~~v-~~~~~~~l~~~sk~l~ee~~~~~~ 791 (970)
T KOG0401|consen 713 ELLSDSYLSARCHEEFENGWSRELPSGKDGEREPEMMSPEYYAAKAAKRAGLGLV-IALSSELLELLSKSLLEEFLSLRL 791 (970)
T ss_pred ccccccccchhhhhhccccccccCCCCcccccchhhcCcccchhhhhhccCCcch-hhhhHHHHHHHHHHHHHHHHHHhh
Confidence 46789999999999999987431000000011 100112234456789999999 777778888999999999998877
Q ss_pred hcCCCCCCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHH-Hh-------CCCCChhHHHHHHHHHHHH-hCC
Q 009767 103 ENDGKTCPAEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKEL-TT-------NSQLVPRLRFMIHDVLDLR-ANN 173 (526)
Q Consensus 103 ~~~~~~~p~ee~iE~lc~LL~tiG~~Ld~~~~~~~~~d~~f~~l~~l-~~-------~~~ls~Rirfmi~dvidlR-~~~ 173 (526)
.+. ..+..+.++..|.++++||..++..-.-...+..+..+|..+ +. .-..+.++.|-+.|.+.++ -++
T Consensus 792 ~~~--~~~~ie~l~S~~~~~~~v~~~v~~~l~~~~~~~~~~~~ll~~l~~~~~~~~~~~~~~~~~~~~~~~d~~~d~pk~ 869 (970)
T KOG0401|consen 792 EKE--ALKCIEELESPSLLLKTVGENIEPTLEKSPQAVEELLQLLDILVSKNPLSIETLEIGYREKFKLADDKELDLPKG 869 (970)
T ss_pred hhh--hhhhhhcccchhhhHHHHHHhcCcccccChhHHHHHHHHHHHHHhcCcccHHHHhhhHHHHHhhhHHHhcccccc
Confidence 653 346889999999999999999986332222223333333221 11 1234556666666666655 467
Q ss_pred CCccccccCCCcHHHHHHHHHH
Q 009767 174 WVPRREEMKAKTITEIHSEAEK 195 (526)
Q Consensus 174 W~~r~~~~~pkti~~i~~e~~~ 195 (526)
|.--....+|.+++.++.+.+.
T Consensus 870 w~~~~e~~gp~~~~~~~~~~e~ 891 (970)
T KOG0401|consen 870 WNYIKEFLGPLIHQKILDESEL 891 (970)
T ss_pred hhHHHHhhhhHhhhccccHHHH
Confidence 7755555667777777665543
No 14
>PLN00131 hypothetical protein; Provisional
Probab=65.05 E-value=1e+02 Score=28.82 Aligned_cols=68 Identities=19% Similarity=0.251 Sum_probs=38.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHH-HHhcCCCcChHHHHHHHHHHHh
Q 009767 347 EKPSAPVTKLNLADLRKKTVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIA-LALEKIPPCVEPVIQLLEFLLN 425 (526)
Q Consensus 347 ~~~~~~~~~~s~eel~kk~~~il~EY~~~~D~~Ea~~~i~eL~~p~~~~~~V~~~I~-~aLE~~~~~re~v~~LL~~L~~ 425 (526)
++.+.++|.+.+.++..|-+..-+| ++.+-.+.+-.....+..+++. +.|| ++.+|.++-+|..||+.
T Consensus 117 eqepepapplddqdlltkrkrvsee----------lrlllqigavkrknkiadqlldwmgld-netdrtllddlynhlyd 185 (218)
T PLN00131 117 EQEPEPAPPLDDQDLLTKRKRVSEE----------LRLLLQIGAVKRKNKIADQLLDWMGLD-NETDRTLLDDLYNHLYD 185 (218)
T ss_pred ccCCCCCCCCCcHHHHHHHHHHHHH----------HHHHHHHhhhhhhhHHHHHHHHHhccC-ccchHHHHHHHHHHHhh
Confidence 3334456778887776665554333 2222222222223344444444 3444 45688899999999987
No 15
>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=64.85 E-value=45 Score=31.10 Aligned_cols=124 Identities=11% Similarity=0.028 Sum_probs=70.6
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHhCCCC---ChHHHHHHHHHHHhcCCCcChHHHHHHHHHHHhCCC-CCHHHHHHHH
Q 009767 363 KKTVSLLEEYFSIRILDEALQCVEELRAPT---YHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNV-LTTRDIGTGC 438 (526)
Q Consensus 363 kk~~~il~EY~~~~D~~Ea~~~i~eL~~p~---~~~~~V~~~I~~aLE~~~~~re~v~~LL~~L~~~~~-ls~~q~~~Gf 438 (526)
++++.+|...- .++.++.+..+..+.... ....+|..++..+.+.. ......+.|...|....- -=...+...+
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 45556665543 677777777777765443 33455555555555443 445677777777665322 1112233333
Q ss_pred HHHhhc------chhhhcCCCchhHHHHHHHHHHHHcCCCChHHHHHHHHhhhchh
Q 009767 439 LLYGSL------LDDIGIDLPKAPNNFGEMVGKLVVAKSLDFIVLKEVLKKVEDNM 488 (526)
Q Consensus 439 ~~vl~~------l~Dl~iDiP~a~~~la~~iar~i~~~~l~~~~i~~~~~~~~~~~ 488 (526)
...+.. +++..--.-.-..-+..|+|.+..-+.++...+.+++..+-...
T Consensus 80 ~~~f~~~~~~~~~~~~~~~~~~~~~~~~~fl~eL~~~~vv~~~~i~~~l~~ll~~~ 135 (209)
T PF02854_consen 80 QEEFEERYSNEELEENRQSSKQRRRGNIRFLAELFNFGVVSEKIIFDILRELLSDG 135 (209)
T ss_dssp HHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHT
T ss_pred HHHHHHhhhhhhHHHHHHHHHHHHhhhhhHHHhhHhhccccchhHHHHHHHHHhcc
Confidence 333332 22222222233455778999999999999998888777664443
No 16
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=57.41 E-value=93 Score=35.74 Aligned_cols=63 Identities=13% Similarity=0.114 Sum_probs=41.7
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhcCCCcChHHHHHHHHHHHhCCCCCH
Q 009767 365 TVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTT 431 (526)
Q Consensus 365 ~~~il~EY~~~~D~~Ea~~~i~eL~~p~~~~~~V~~~I~~aLE~~~~~re~v~~LL~~L~~~~~ls~ 431 (526)
...+|+-|...|++++|...+.++..+. .++...+..++-+.. ..+.+..+|..+...|+-..
T Consensus 262 ~n~Li~~y~k~g~~~~A~~vf~~m~~~~---~vt~n~li~~y~~~g-~~~eA~~lf~~M~~~g~~pd 324 (697)
T PLN03081 262 SCALIDMYSKCGDIEDARCVFDGMPEKT---TVAWNSMLAGYALHG-YSEEALCLYYEMRDSGVSID 324 (697)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHhCCCCC---hhHHHHHHHHHHhCC-CHHHHHHHHHHHHHcCCCCC
Confidence 3567888888888888888888886543 345555555554432 34567777777777665433
No 17
>PLN03218 maturation of RBCL 1; Provisional
Probab=55.13 E-value=74 Score=38.84 Aligned_cols=64 Identities=14% Similarity=0.168 Sum_probs=35.6
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhCC--CCC-hHHHHHHHHHHHhcCCCcChHHHHHHHHHHHhCCC
Q 009767 364 KTVSLLEEYFSIRILDEALQCVEELRA--PTY-HPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNV 428 (526)
Q Consensus 364 k~~~il~EY~~~~D~~Ea~~~i~eL~~--p~~-~~~~V~~~I~~aLE~~~~~re~v~~LL~~L~~~~~ 428 (526)
....+|.-|...+++++|...+.++.. ... ...++...+..++-+. ...+.+.+++..+...++
T Consensus 544 TYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~-G~ldeA~elf~~M~e~gi 610 (1060)
T PLN03218 544 VFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANA-GQVDRAKEVYQMIHEYNI 610 (1060)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHcCC
Confidence 367777778888888888887777742 111 1234444444444332 233455555555555554
No 18
>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=54.84 E-value=35 Score=26.77 Aligned_cols=45 Identities=29% Similarity=0.430 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHHh--cCCCHHHHHHHHHHhCCCCChHHHHHHHH
Q 009767 358 LADLRKKTVSLLEEYF--SIRILDEALQCVEELRAPTYHPEVVKEAI 402 (526)
Q Consensus 358 ~eel~kk~~~il~EY~--~~~D~~Ea~~~i~eL~~p~~~~~~V~~~I 402 (526)
-++|++.+..+|.|-- .-.+++|-+.|.-.||.|.+|..+|.-..
T Consensus 5 ~~DFr~SM~EMI~~~~i~~~~~LeeLL~cYL~LN~~~~H~~Iv~aF~ 51 (59)
T PF04844_consen 5 YEDFRESMVEMIEENGIRDWDDLEELLACYLSLNSPEHHKFIVEAFV 51 (59)
T ss_pred HHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCChhhhhHHHHHHH
Confidence 4688888888877753 33589999999999999988766555443
No 19
>PF08876 DUF1836: Domain of unknown function (DUF1836); InterPro: IPR014975 This group of proteins are functionally uncharacterised.
Probab=52.05 E-value=36 Score=29.78 Aligned_cols=51 Identities=27% Similarity=0.129 Sum_probs=41.0
Q ss_pred CCCcChHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcchhhhcCCCchhHH
Q 009767 408 KIPPCVEPVIQLLEFLLNKNVLTTRDIGTGCLLYGSLLDDIGIDLPKAPNN 458 (526)
Q Consensus 408 ~~~~~re~v~~LL~~L~~~~~ls~~q~~~Gf~~vl~~l~Dl~iDiP~a~~~ 458 (526)
++-=.|++++.|+.--.-+.++|-+++.++|..+.....+-..+...||++
T Consensus 54 kKkYsr~qla~li~I~~lK~vlsi~dI~~ll~~~~~~~~~~~~~~~~~Y~~ 104 (105)
T PF08876_consen 54 KKKYSREQLAYLIVISILKQVLSIDDIKKLLDLQFNNYEDDEISLEDAYNY 104 (105)
T ss_pred cCccCHHHHHHHHHHHHHHccCCHHHHHHHHHHHHhcccccCCCHHHHHhc
Confidence 344478999999886666799999999999999999887777666666654
No 20
>COG5537 IRR1 Cohesin [Cell division and chromosome partitioning]
Probab=51.11 E-value=2.6e+02 Score=31.95 Aligned_cols=137 Identities=14% Similarity=0.092 Sum_probs=90.3
Q ss_pred HHHHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhcCCCcChHHHHHHHHHHHhCCCCCHHHHHHHH
Q 009767 359 ADLRKKTVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTGC 438 (526)
Q Consensus 359 eel~kk~~~il~EY~~~~D~~Ea~~~i~eL~~p~~~~~~V~~~I~~aLE~~~~~re~v~~LL~~L~~~~~ls~~q~~~Gf 438 (526)
+.++..+-.++.-+++..--..|++-+-| .|-..+++.+.--.+..|-...+++.+|...|+|+...+..--
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 45666666677666655433434433222 3334444443333455677788999999999999999888777
Q ss_pred HHHhhcchhhhcCCCchhHHHHHHHHHHHHcCC---CChHHHHHHHHhhhchhH--HHHHHHHHHHHHhc
Q 009767 439 LLYGSLLDDIGIDLPKAPNNFGEMVGKLVVAKS---LDFIVLKEVLKKVEDNMF--RRSIFTAAMKSIQS 503 (526)
Q Consensus 439 ~~vl~~l~Dl~iDiP~a~~~la~~iar~i~~~~---l~~~~i~~~~~~~~~~~~--~~~~l~~~l~~l~~ 503 (526)
.-+++..+|--+-+-.+.+.++++.|+.|.+.+ +-.+.+..++.+.-..++ ...+|..+++.++.
T Consensus 400 scmlDi~pd~r~~~~E~v~~icK~~aevikEKipl~~k~n~lL~a~~qgse~~f~v~~~iFsr~~~llk~ 469 (740)
T COG5537 400 SCMLDIIPDSRENIVESVESICKIDAEVIKEKIPLATKTNRLLEAMKQGSERYFVVCEEIFSRFVHLLKK 469 (740)
T ss_pred HHHhcCCCcchHHHHHHHHHHHHHHHHHHHhhcchhhhhhhHHHHHHhhhhccchhHHHHHHHHHHHHHH
Confidence 778887777555577789999999999999543 222344445555555565 66677887777654
No 21
>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]
Probab=50.49 E-value=93 Score=34.79 Aligned_cols=136 Identities=16% Similarity=0.167 Sum_probs=86.5
Q ss_pred CHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCCC-hHHHHHHHHHHHhcCCCcChHHH-HHHHHHHHhCCCCCHHHH
Q 009767 357 NLADLRKKTVSLLEEYFSIRILDEALQCVEELRAPTY-HPEVVKEAIALALEKIPPCVEPV-IQLLEFLLNKNVLTTRDI 434 (526)
Q Consensus 357 s~eel~kk~~~il~EY~~~~D~~Ea~~~i~eL~~p~~-~~~~V~~~I~~aLE~~~~~re~v-~~LL~~L~~~~~ls~~q~ 434 (526)
+.-+|+++|=-.| .++-|.+||..-+-.++.|.- ..+++..+|........ -+.. +-|-..++.-+..=.+.|
T Consensus 450 Nlv~frr~IYLti---~SSldfeEaaHKLLKmkip~~q~~elc~mii~cc~QerT--y~kFYglL~eRfc~l~r~~q~~f 524 (739)
T KOG2140|consen 450 NLVNFRRTIYLTI---QSSLDFEEAAHKLLKMKIPESQEKELCNMIIDCCAQERT--YEKFYGLLGERFCMLHREWQEAF 524 (739)
T ss_pred hhHHhhhhheeee---eccCcHHHHHHHHHhccCCchhhHHHHHHHHHHhhhHHH--HHHHHHHHHHHHHHHHHHHHHHH
Confidence 4445665553322 256799999999988888765 46777777776543221 1122 222222333233456788
Q ss_pred HHHHHHHhhcchhhhcCCCchhHHHHHHHHHHHHcCCCChHHHHHHHHhhhc-h-----hHHHHHHHHHHHHH
Q 009767 435 GTGCLLYGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLDFIVLKEVLKKVED-N-----MFRRSIFTAAMKSI 501 (526)
Q Consensus 435 ~~Gf~~vl~~l~Dl~iDiP~a~~~la~~iar~i~~~~l~~~~i~~~~~~~~~-~-----~~~~~~l~~~l~~l 501 (526)
.+-|+...+++.+++.+- --.||+|+|+++.-+.||...+. .++..++ + -|-+-+|.++.+.|
T Consensus 525 e~~f~q~YstIhr~Etnk---LRnlakffahLlstd~lpw~vl~-~ikLTEEdTtsssRIfiKilFqELve~l 593 (739)
T KOG2140|consen 525 EKCFKQQYSTIHRYETNK---LRNLAKFFAHLLSTDALPWDVLA-CIKLTEEDTTSSSRIFIKILFQELVEAL 593 (739)
T ss_pred HHHHHHHHHHHHHHhHHH---HHHHHHHHHHHhcccccchHHHH-HhhcccccCCccceehHHHHHHHHHHHh
Confidence 999999999999988653 34689999999999999999776 4444333 2 34444555554443
No 22
>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=50.05 E-value=1.1e+02 Score=28.07 Aligned_cols=95 Identities=9% Similarity=0.116 Sum_probs=59.2
Q ss_pred hhhHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCCCCCC--hhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHHh
Q 009767 74 LGNIRLIGELLKQKMVPEKIVHHIVQELLENDGKTCPA--EENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTT 151 (526)
Q Consensus 74 lGnirFIGELfk~~~l~e~ii~~ci~~Ll~~~~~~~p~--ee~iE~lc~LL~tiG~~Ld~~~~~~~~~d~~f~~l~~l~~ 151 (526)
.+.|--|+++.+.+--..+.....|+.-|... +|. =-.|.-|=.+++.||..+...-..+.+++. |..++.
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 35677788888877665555555555555432 111 123444455667788888754333445554 444443
Q ss_pred C----CCCChhHHHHHHHHHHHHhCCCC
Q 009767 152 N----SQLVPRLRFMIHDVLDLRANNWV 175 (526)
Q Consensus 152 ~----~~ls~Rirfmi~dvidlR~~~W~ 175 (526)
. +..+..|+-.|..+|+.+...+.
T Consensus 92 ~k~~~~~~~~~Vk~kil~li~~W~~~f~ 119 (139)
T cd03567 92 PKYLGSRTSEKVKTKIIELLYSWTLELP 119 (139)
T ss_pred cccCCCCCCHHHHHHHHHHHHHHHHHhc
Confidence 2 46789999999999998876664
No 23
>PRK14703 glutaminyl-tRNA synthetase/YqeY domain fusion protein; Provisional
Probab=49.45 E-value=4.1e+02 Score=31.40 Aligned_cols=85 Identities=14% Similarity=0.106 Sum_probs=48.5
Q ss_pred ChHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcchhhhcCCCchhHHHHHHHHHHHHcCCCChHHHHHHHHhhh------
Q 009767 412 CVEPVIQLLEFLLNKNVLTTRDIGTGCLLYGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLDFIVLKEVLKKVE------ 485 (526)
Q Consensus 412 ~re~v~~LL~~L~~~~~ls~~q~~~Gf~~vl~~l~Dl~iDiP~a~~~la~~iar~i~~~~l~~~~i~~~~~~~~------ 485 (526)
.-+.++.|+ .|+..|.||..+..+-|..+++.=. + | ..+|...=...+.+...|..+++++.
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 346788886 4677799999999888888775411 1 1 12222221111223344444444332
Q ss_pred -------chhHHHHHHHHHHHHHhcCCCch
Q 009767 486 -------DNMFRRSIFTAAMKSIQSSPAGQ 508 (526)
Q Consensus 486 -------~~~~~~~~l~~~l~~l~~~~~g~ 508 (526)
......-++|.||+..+..=.++
T Consensus 731 Ve~yk~GK~kalgfLVGqVMK~tkGKAdP~ 760 (771)
T PRK14703 731 VAAYRAGKTKLLGFFVGQVMRETGGKANPQ 760 (771)
T ss_pred HHHHhcchHHHHHHHHHHHHHHhCCCCCHH
Confidence 24555778999999887663333
No 24
>PRK05477 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated
Probab=48.26 E-value=2.5e+02 Score=31.18 Aligned_cols=111 Identities=11% Similarity=0.071 Sum_probs=58.3
Q ss_pred hHHHHHHHHHHHh----cCCC-------cChHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcchh---hh--cCCCch--
Q 009767 394 HPEVVKEAIALAL----EKIP-------PCVEPVIQLLEFLLNKNVLTTRDIGTGCLLYGSLLDD---IG--IDLPKA-- 455 (526)
Q Consensus 394 ~~~~V~~~I~~aL----E~~~-------~~re~v~~LL~~L~~~~~ls~~q~~~Gf~~vl~~l~D---l~--iDiP~a-- 455 (526)
.+.++..||..-+ .+.. -.-+.++.|+. |+..|.||..+..+-|..+++.=.| +. .++-.+
T Consensus 338 ~~k~~anwl~~el~~~l~~~~~~~~~~~i~~~~l~~Li~-lv~~g~Is~~~ak~vl~~~~~~~~~~~~ii~~~gl~~isd 416 (474)
T PRK05477 338 DAKLAANWLMGELLGLLNEEGIEIEESPITPEQLAELIK-LIDDGTISGKIAKEVFEEMLETGGDPDEIVEEKGLKQISD 416 (474)
T ss_pred CHHHHHHHHHHHHHHHHHHCCCChhhcCCCHHHHHHHHH-HHHcCCccHHHHHHHHHHHHhcCCCHHHHHHHcCCcccCC
Confidence 4567777766544 2221 23467788875 7777999999999999988765111 00 000000
Q ss_pred hHHHHHHHHHHHHcCCCChHHHHHHHHhhhchhHHHHHHHHHHHHHhcCCCchhh
Q 009767 456 PNNFGEMVGKLVVAKSLDFIVLKEVLKKVEDNMFRRSIFTAAMKSIQSSPAGQEV 510 (526)
Q Consensus 456 ~~~la~~iar~i~~~~l~~~~i~~~~~~~~~~~~~~~~l~~~l~~l~~~~~g~~~ 510 (526)
...|..+|...|.+ .++.|++... .......-++|.+++..+..-.++.|
T Consensus 417 ~~~l~~iv~evi~~---np~~v~~~~~--Gk~~~~~~lvG~vMk~t~GkAdp~~v 466 (474)
T PRK05477 417 EGALEAIVDEVLAA---NPKAVEDYKA--GKEKALGFLVGQVMKATKGKANPKLV 466 (474)
T ss_pred HHHHHHHHHHHHHH---CHHHHHHHHc--ccHHHHHHHHHHHHHHhcCCCCHHHH
Confidence 01122222222222 1222221111 12456677899999998777445444
No 25
>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=46.95 E-value=67 Score=25.81 Aligned_cols=46 Identities=24% Similarity=0.355 Sum_probs=34.8
Q ss_pred CHHHHHHHHHHHHHHHhc--C-CCHHHHHHHHHHhCCCCChHHHHHHHH
Q 009767 357 NLADLRKKTVSLLEEYFS--I-RILDEALQCVEELRAPTYHPEVVKEAI 402 (526)
Q Consensus 357 s~eel~kk~~~il~EY~~--~-~D~~Ea~~~i~eL~~p~~~~~~V~~~I 402 (526)
+-++|++.+..+|.|-=- . .+++|-+.|.-.||.+.+|+.+|.-..
T Consensus 10 Py~DFr~SM~EMI~~~~i~~~w~~LeeLL~cYL~LN~~~~H~~Iv~AF~ 58 (66)
T TIGR01568 10 PYEDFRRSMEEMIEERELEADWKELEELLACYLDLNPKKSHRFIVRAFV 58 (66)
T ss_pred hHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCchhhhHHHHHHH
Confidence 357899988888887632 2 468999999999999888765555443
No 26
>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=46.11 E-value=32 Score=26.22 Aligned_cols=45 Identities=20% Similarity=0.138 Sum_probs=36.1
Q ss_pred CCcChHHHHHHHHHHHhCCCCCHHHHHHHHHHHh-----hcchhhhcCCC
Q 009767 409 IPPCVEPVIQLLEFLLNKNVLTTRDIGTGCLLYG-----SLLDDIGIDLP 453 (526)
Q Consensus 409 ~~~~re~v~~LL~~L~~~~~ls~~q~~~Gf~~vl-----~~l~Dl~iDiP 453 (526)
++.+|+.+..+|..-+..|-|+.+.|..=...++ ..|..+.-|+|
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 5679999999999999999999999998777654 34555555555
No 27
>PLN03218 maturation of RBCL 1; Provisional
Probab=46.06 E-value=1.3e+02 Score=36.84 Aligned_cols=26 Identities=12% Similarity=0.144 Sum_probs=15.7
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHhCC
Q 009767 365 TVSLLEEYFSIRILDEALQCVEELRA 390 (526)
Q Consensus 365 ~~~il~EY~~~~D~~Ea~~~i~eL~~ 390 (526)
...+|.-|...|++++|...++++..
T Consensus 582 ynaLI~ay~k~G~ldeA~elf~~M~e 607 (1060)
T PLN03218 582 VGALMKACANAGQVDRAKEVYQMIHE 607 (1060)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45566666666666666666666543
No 28
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=45.51 E-value=4.8e+02 Score=29.93 Aligned_cols=75 Identities=19% Similarity=0.107 Sum_probs=48.8
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHhCCC--CChHHHHHHHHHHHhcCCCcChHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q 009767 365 TVSLLEEYFSIRILDEALQCVEELRAP--TYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTGCLL 440 (526)
Q Consensus 365 ~~~il~EY~~~~D~~Ea~~~i~eL~~p--~~~~~~V~~~I~~aLE~~~~~re~v~~LL~~L~~~~~ls~~q~~~Gf~~ 440 (526)
...+|..|...++.+||+..++.+... .....++...+..++-+.. ..+.+.+++..+...|+.+.......+-.
T Consensus 90 ~~~~i~~l~~~g~~~~Al~~f~~m~~~~~~~~~~~t~~~ll~a~~~~~-~~~~a~~l~~~m~~~g~~~~~~~~n~Li~ 166 (697)
T PLN03081 90 LCSQIEKLVACGRHREALELFEILEAGCPFTLPASTYDALVEACIALK-SIRCVKAVYWHVESSGFEPDQYMMNRVLL 166 (697)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhCC-CHHHHHHHHHHHHHhCCCcchHHHHHHHH
Confidence 567788999999999999999998542 2234556666666655432 34556677777777676554443333333
No 29
>PF12854 PPR_1: PPR repeat
Probab=41.05 E-value=40 Score=22.82 Aligned_cols=26 Identities=23% Similarity=0.459 Sum_probs=22.9
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhC
Q 009767 364 KTVSLLEEYFSIRILDEALQCVEELR 389 (526)
Q Consensus 364 k~~~il~EY~~~~D~~Ea~~~i~eL~ 389 (526)
....+|+-|...|+++||.+.++++.
T Consensus 9 ty~~lI~~~Ck~G~~~~A~~l~~~M~ 34 (34)
T PF12854_consen 9 TYNTLIDGYCKAGRVDEAFELFDEMK 34 (34)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence 35789999999999999999998863
No 30
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=39.38 E-value=1.3e+02 Score=27.47 Aligned_cols=94 Identities=18% Similarity=0.243 Sum_probs=62.8
Q ss_pred hhhHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCCCCCC--hhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHHh
Q 009767 74 LGNIRLIGELLKQKMVPEKIVHHIVQELLENDGKTCPA--EENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTT 151 (526)
Q Consensus 74 lGnirFIGELfk~~~l~e~ii~~ci~~Ll~~~~~~~p~--ee~iE~lc~LL~tiG~~Ld~~~~~~~~~d~~f~~l~~l~~ 151 (526)
.+.|..|+++.+.+=...+-...+|++-|... +|. =-.++-|=.+++.||..+...-..+ .+.+.|..++.
T Consensus 22 w~~ileicD~In~~~~~~k~a~ral~krl~~~---n~~vql~AL~LLe~~vkNCG~~fh~evas~----~fl~~l~~l~~ 94 (142)
T cd03569 22 LASILEICDMIRSKDVQPKYAMRALKKRLLSK---NPNVQLYALLLLESCVKNCGTHFHDEVASR----EFMDELKDLIK 94 (142)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHHHcCC---ChHHHHHHHHHHHHHHHHCCHHHHHHHhhH----HHHHHHHHHHc
Confidence 46788899999987666666666666655542 122 1334555566677888887533333 45566776665
Q ss_pred CCCCChhHHHHHHHHHHHHhCCCC
Q 009767 152 NSQLVPRLRFMIHDVLDLRANNWV 175 (526)
Q Consensus 152 ~~~ls~Rirfmi~dvidlR~~~W~ 175 (526)
+ ..+.+|+-.|..+|+-....+.
T Consensus 95 ~-~~~~~Vk~kil~li~~W~~~f~ 117 (142)
T cd03569 95 T-TKNEEVRQKILELIQAWALAFR 117 (142)
T ss_pred c-cCCHHHHHHHHHHHHHHHHHhC
Confidence 4 7889999999999998776654
No 31
>PF10188 Oscp1: Organic solute transport protein 1; InterPro: IPR019332 Organic solute carrier protein 1, or Oscp1, is a family of proteins conserved from plants to humans. It is called organic solute transport protein or oxido-red-nitro domain-containing protein 1, however no reference could be find to confirm the function of the protein.
Probab=39.34 E-value=2.8e+02 Score=26.55 Aligned_cols=116 Identities=14% Similarity=0.179 Sum_probs=77.6
Q ss_pred hhHHHHHHHhc-CCCCCHHHHHHHHHHHHhcCCCCCCChhhHHHHHHHHHHHhh-hhhcCCcchhhHHHHHHHHHHHHhC
Q 009767 75 GNIRLIGELLK-QKMVPEKIVHHIVQELLENDGKTCPAEENVEAICQFFNTIGK-QLDENPKSRRVNDVYFSRLKELTTN 152 (526)
Q Consensus 75 GnirFIGELfk-~~~l~e~ii~~ci~~Ll~~~~~~~p~ee~iE~lc~LL~tiG~-~Ld~~~~~~~~~d~~f~~l~~l~~~ 152 (526)
=|=+|+.|||+ +.|.+.+-+...+..|-... ---.++.+.+-|-.|+..+=| ++-..+.+++.++.-++.|+.+..-
T Consensus 31 f~~~fl~eLfkPq~lys~~~~r~~f~~lah~S-IMRLn~~SMdKL~DLM~M~~KyQl~~~~~p~ell~vTlnHld~i~~~ 109 (173)
T PF10188_consen 31 FNPKFLDELFKPQPLYSKKALRTVFEKLAHSS-IMRLNENSMDKLFDLMTMAFKYQLFLCRHPKELLLVTLNHLDAIRDL 109 (173)
T ss_pred cCHHHHHHHcCCccccCHHHHHHHHHHHHhhh-hhhcCHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 37799999999 67889988888888876542 111489999999999987654 4555566678888888888776431
Q ss_pred CCCChhHHHHHHHHHHHHhCCCCccccccCCCcHHHHHHHHHHh
Q 009767 153 SQLVPRLRFMIHDVLDLRANNWVPRREEMKAKTITEIHSEAEKN 196 (526)
Q Consensus 153 ~~ls~Rirfmi~dvidlR~~~W~~r~~~~~pkti~~i~~e~~~~ 196 (526)
-. ..-++..+..+...=..-|. ...+-....||+.--.-
T Consensus 110 v~-~~~~~~~v~~~~~~~~~~y~----~ls~~~~~~iR~~ll~f 148 (173)
T PF10188_consen 110 VP-DPEVQALVDEVFNRLIEFYG----KLSPGEFQLIRQTLLNF 148 (173)
T ss_pred cc-CHHHHHHHHHHHHHHHHHHh----CCCHHHHHHHHHHHHHH
Confidence 00 15666666666655444443 34555666677654443
No 32
>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=39.14 E-value=1.1e+02 Score=24.25 Aligned_cols=43 Identities=23% Similarity=0.292 Sum_probs=35.5
Q ss_pred ChHHHHHHHHHHHhcCCCcChHHHHHHHHHHHhCCCCCHHHHH
Q 009767 393 YHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIG 435 (526)
Q Consensus 393 ~~~~~V~~~I~~aLE~~~~~re~v~~LL~~L~~~~~ls~~q~~ 435 (526)
+.+++|..+|..+++++.....-+-..|..-.++|+-|.+|+.
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 3489999999999987655567888888899999999988864
No 33
>KOG1104 consensus Nuclear cap-binding complex, subunit NCBP1/CBP80 [RNA processing and modification]
Probab=39.04 E-value=1.6e+02 Score=34.27 Aligned_cols=105 Identities=13% Similarity=0.247 Sum_probs=77.9
Q ss_pred hhhhhhHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCC-CCC---ChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHH
Q 009767 71 LRTLGNIRLIGELLKQKMVPEKIVHHIVQELLENDGK-TCP---AEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRL 146 (526)
Q Consensus 71 ~r~lGnirFIGELfk~~~l~e~ii~~ci~~Ll~~~~~-~~p---~ee~iE~lc~LL~tiG~~Ld~~~~~~~~~d~~f~~l 146 (526)
.+.-+.+||+.-|+.-+|+...-|...+..|+..... ..| .+--+-|+..-|--+|+.|.+. .+..|+.++..+
T Consensus 122 n~ar~llrfL~dL~~~~vl~~~sli~l~esl~~~~~e~~~Pqvr~D~~v~~vLs~lPw~g~el~e~--~~~~~e~ll~~i 199 (759)
T KOG1104|consen 122 NEARYLLRFLSDLSNCHVLQADSLINLFESLLDAAIEENVPQVRRDYYVYCVLSSLPWFGRELNEK--KPTEMEELLVYI 199 (759)
T ss_pred HHHHHHHHHHHHHhcCCccChHHHHHHHHHHHHHHHhhcCcchhhhHHHHHHHhccchhhhhhccc--chHHHHHHHHHH
Confidence 3455789999999999999999999999888875311 112 4566777777788899999864 346688888888
Q ss_pred HHHHhCCC---------CC--------hhHHHHHHHHHHHHhCCCCcc
Q 009767 147 KELTTNSQ---------LV--------PRLRFMIHDVLDLRANNWVPR 177 (526)
Q Consensus 147 ~~l~~~~~---------ls--------~Rirfmi~dvidlR~~~W~~r 177 (526)
+..++.++ .+ -=++.+...+.-+|.|+|+..
T Consensus 200 e~Yl~~R~~shi~lL~vw~~~~~~~qeeyle~L~~qI~~lr~n~w~e~ 247 (759)
T KOG1104|consen 200 EIYLKKRKKSHINLLNVWSGEPDHPQEEYLELLWAQIQKLRQNDWAEN 247 (759)
T ss_pred HHHHHHhcccccchhhcCCCCCCchHHHHHHHHHHHHHHHHhcCcccc
Confidence 86654322 11 236778888999999999974
No 34
>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=37.13 E-value=4.3e+02 Score=27.18 Aligned_cols=93 Identities=18% Similarity=0.153 Sum_probs=50.5
Q ss_pred CHHHHHHHHHHHHHHHhcCCCHHHHHHHH-HHhCCCCChHHHHHHHHHHHhc--CCCcChHHHHHHHHHHHhCCCCC--H
Q 009767 357 NLADLRKKTVSLLEEYFSIRILDEALQCV-EELRAPTYHPEVVKEAIALALE--KIPPCVEPVIQLLEFLLNKNVLT--T 431 (526)
Q Consensus 357 s~eel~kk~~~il~EY~~~~D~~Ea~~~i-~eL~~p~~~~~~V~~~I~~aLE--~~~~~re~v~~LL~~L~~~~~ls--~ 431 (526)
..+.+.+.+...+..++..-+.......+ ..+-...+|..++..++....+ .++..++.+.+++.....+..-+ .
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 34455555555555555554444444333 3333345566666665554443 24556667777777777644333 6
Q ss_pred HHHHHHHHHH-hhcchhhh
Q 009767 432 RDIGTGCLLY-GSLLDDIG 449 (526)
Q Consensus 432 ~q~~~Gf~~v-l~~l~Dl~ 449 (526)
+.+...|... ...++++.
T Consensus 182 ~~l~~~i~~~l~~~l~~l~ 200 (367)
T PF04286_consen 182 DKLAEKIQDELDSLLEKLQ 200 (367)
T ss_pred hHHHHHHHHHHHHHHHHHH
Confidence 6666666654 44566665
No 35
>PLN03077 Protein ECB2; Provisional
Probab=36.85 E-value=1.6e+02 Score=34.70 Aligned_cols=63 Identities=19% Similarity=0.194 Sum_probs=42.6
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhcCCCcChHHHHHHHHHHHhCCCCC
Q 009767 364 KTVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLT 430 (526)
Q Consensus 364 k~~~il~EY~~~~D~~Ea~~~i~eL~~p~~~~~~V~~~I~~aLE~~~~~re~v~~LL~~L~~~~~ls 430 (526)
....+|.-|...|++++|...++++..|.. +....+..++-+.. ..+.+..+|..+...|+-.
T Consensus 325 ~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~---~s~n~li~~~~~~g-~~~~A~~lf~~M~~~g~~P 387 (857)
T PLN03077 325 VCNSLIQMYLSLGSWGEAEKVFSRMETKDA---VSWTAMISGYEKNG-LPDKALETYALMEQDNVSP 387 (857)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHhhCCCCCe---eeHHHHHHHHHhCC-CHHHHHHHHHHHHHhCCCC
Confidence 357788889999999999999999876642 33444444554433 3456677777776665443
No 36
>PLN03077 Protein ECB2; Provisional
Probab=36.30 E-value=2.8e+02 Score=32.65 Aligned_cols=73 Identities=14% Similarity=0.174 Sum_probs=44.9
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHhCCCCChH-HHHHHHHHHHhcCCCcChHHHHHHHHHHHhCCCCCHHHHHHHH
Q 009767 365 TVSLLEEYFSIRILDEALQCVEELRAPTYHP-EVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTGC 438 (526)
Q Consensus 365 ~~~il~EY~~~~D~~Ea~~~i~eL~~p~~~~-~~V~~~I~~aLE~~~~~re~v~~LL~~L~~~~~ls~~q~~~Gf 438 (526)
...+|.-|...|+.+||...++++......| .+....+..++-+. ...+...+++..+.+.|+.+...+...+
T Consensus 357 ~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~-g~~~~a~~l~~~~~~~g~~~~~~~~n~L 430 (857)
T PLN03077 357 WTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACL-GDLDVGVKLHELAERKGLISYVVVANAL 430 (857)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhcc-chHHHHHHHHHHHHHhCCCcchHHHHHH
Confidence 5778999999999999999999884322221 23333333344332 2345666777777776665544443333
No 37
>TIGR00153 conserved hypothetical protein TIGR00153. An apparent homolog with a suggested function is Pit accessory protein from Sinorhizobium meliloti, which may be involved in phosphate (Pi) transport.
Probab=35.56 E-value=4.2e+02 Score=25.66 Aligned_cols=80 Identities=19% Similarity=0.157 Sum_probs=47.6
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhcCC---CcChHHHHHHHHHHHhCCCCCHHHHHHHHHHH
Q 009767 365 TVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKI---PPCVEPVIQLLEFLLNKNVLTTRDIGTGCLLY 441 (526)
Q Consensus 365 ~~~il~EY~~~~D~~Ea~~~i~eL~~p~~~~~~V~~~I~~aLE~~---~~~re~v~~LL~~L~~~~~ls~~q~~~Gf~~v 441 (526)
...+++.|. .+|.+++....+++..-.....-++.-|...|.++ +-+|+-+..|+..+ +++....+.+
T Consensus 30 L~~~~~~~~-~~~~~~~~~~~~~I~~lE~eaD~i~~~i~~~L~~~fitP~dReDi~~L~~~l--------D~I~D~i~~~ 100 (216)
T TIGR00153 30 LIKSFELLK-SGNNEKDEELRKEIIEIEHEADEIKREIRLNLEKGAFLPNDRRDLLELAELL--------DEILDSLEHA 100 (216)
T ss_pred HHHHHHHHH-hCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcccccCcCcHHHHHHHHHHH--------HHHHHHHHHH
Confidence 444556665 45555544444444332334445555555667664 88999999988876 4466666666
Q ss_pred hhcchhhhcCCC
Q 009767 442 GSLLDDIGIDLP 453 (526)
Q Consensus 442 l~~l~Dl~iDiP 453 (526)
...+.=..++.|
T Consensus 101 a~~l~l~~~~~~ 112 (216)
T TIGR00153 101 AMLYELRKFEFP 112 (216)
T ss_pred HHHHhcccCCCC
Confidence 655554555566
No 38
>COG1421 CRISPR system related protein [Defense mechanisms]
Probab=35.48 E-value=92 Score=28.54 Aligned_cols=60 Identities=25% Similarity=0.270 Sum_probs=44.0
Q ss_pred CCCHHHHHHHHHHH-------hhcchhhhcCCCchhHHHHHHHHHHHHcCC-CChHHHHHHHHhhhch
Q 009767 428 VLTTRDIGTGCLLY-------GSLLDDIGIDLPKAPNNFGEMVGKLVVAKS-LDFIVLKEVLKKVEDN 487 (526)
Q Consensus 428 ~ls~~q~~~Gf~~v-------l~~l~Dl~iDiP~a~~~la~~iar~i~~~~-l~~~~i~~~~~~~~~~ 487 (526)
-+++.|+-+=+..+ .....++.+|+|+..-.||.-++|.+..-. =-..+++.++.++.++
T Consensus 43 ~l~~~q~R~fy~~~~r~~~~~~~~~k~i~~~l~~m~~~lay~~gR~~~~~~e~lyevle~~idkid~D 110 (137)
T COG1421 43 NLTTTQLRKFYDYILRIDEENENSWKEIVLDLPKMKPQLAYAVGRDGKEALEGLYEVLEEMIDKIDDD 110 (137)
T ss_pred cCcHHHHHHHHHHHHHHhHhccCcHHHHHHHHHHHHHHHHHHHhhcchhhHHHHHHHHHHHHHHhhhh
Confidence 58888888777766 456789999999999888888888776641 1235567788888433
No 39
>PF13041 PPR_2: PPR repeat family
Probab=35.07 E-value=76 Score=22.88 Aligned_cols=41 Identities=17% Similarity=0.275 Sum_probs=29.7
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHhCCCCChH-HHHHHHHHHH
Q 009767 365 TVSLLEEYFSIRILDEALQCVEELRAPTYHP-EVVKEAIALA 405 (526)
Q Consensus 365 ~~~il~EY~~~~D~~Ea~~~i~eL~~p~~~~-~~V~~~I~~a 405 (526)
...+|.-|...+++++|...++++..-...| .+....+..+
T Consensus 6 yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~ 47 (50)
T PF13041_consen 6 YNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILING 47 (50)
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence 4678999999999999999999986544432 4444444443
No 40
>PF10884 DUF2683: Protein of unknown function (DUF2683); InterPro: IPR020271 This entry contains proteins with no known function.
Probab=32.75 E-value=1.2e+02 Score=25.16 Aligned_cols=45 Identities=11% Similarity=0.316 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHH-----HhCCCCChHHHHHHHHHHHh
Q 009767 362 RKKTVSLLEEYFSIRILDEALQCVE-----ELRAPTYHPEVVKEAIALAL 406 (526)
Q Consensus 362 ~kk~~~il~EY~~~~D~~Ea~~~i~-----eL~~p~~~~~~V~~~I~~aL 406 (526)
.+++-.|++-=|+..|..+|+.-+- ++-.|.+.|+||+++....=
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 4578899999999999999986543 45568999999999988543
No 41
>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=32.70 E-value=53 Score=20.90 Aligned_cols=26 Identities=19% Similarity=0.276 Sum_probs=22.4
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHhCC
Q 009767 365 TVSLLEEYFSIRILDEALQCVEELRA 390 (526)
Q Consensus 365 ~~~il~EY~~~~D~~Ea~~~i~eL~~ 390 (526)
...+|.-|...++.++|...+.++..
T Consensus 3 ~n~li~~~~~~~~~~~a~~~~~~M~~ 28 (35)
T TIGR00756 3 YNTLIDGLCKAGRVEEALELFKEMLE 28 (35)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35788999999999999999998854
No 42
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=32.48 E-value=71 Score=21.46 Aligned_cols=25 Identities=12% Similarity=0.041 Sum_probs=21.0
Q ss_pred HHHHHHHhCCCCCHHHHHHHHHHHh
Q 009767 418 QLLEFLLNKNVLTTRDIGTGCLLYG 442 (526)
Q Consensus 418 ~LL~~L~~~~~ls~~q~~~Gf~~vl 442 (526)
.-|..|+..|+||.+.|.+--..++
T Consensus 6 ~~L~~l~~~G~IseeEy~~~k~~ll 30 (31)
T PF09851_consen 6 EKLKELYDKGEISEEEYEQKKARLL 30 (31)
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHHh
Confidence 4577899999999999998877665
No 43
>PRK09498 sifA secreted effector protein SifA; Reviewed
Probab=32.21 E-value=88 Score=32.21 Aligned_cols=46 Identities=15% Similarity=0.183 Sum_probs=32.4
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhcCCCcChHHHHHHHHHHHh
Q 009767 364 KTVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLN 425 (526)
Q Consensus 364 k~~~il~EY~~~~D~~Ea~~~i~eL~~p~~~~~~V~~~I~~aLE~~~~~re~v~~LL~~L~~ 425 (526)
.+=+-|++||.+.--.||.+||.||--|. .+..||.+..+|..|..
T Consensus 29 ~LWEKIKdFFcSThqaeA~~CI~eLchp~----------------~~~trE~i~~~F~~Lk~ 74 (336)
T PRK09498 29 VLWEKIKDFFFSTGKAKADRCLHEMLFAD----------------RAPTRERLTEIFFELKE 74 (336)
T ss_pred HHHHHHHHHhhcccHHHHHHHHHHHhCCC----------------CCCCHHHHHHHHHHHHH
Confidence 34455789999999999999999995442 23455666666665543
No 44
>PF10363 DUF2435: Protein of unknown function (DUF2435)
Probab=31.44 E-value=3.2e+02 Score=23.09 Aligned_cols=78 Identities=23% Similarity=0.182 Sum_probs=51.5
Q ss_pred HHHHHHhcCCCcChHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcchhhhcCCCchhHHHHHHHHHHHHcCCCChHHHHH
Q 009767 400 EAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTGCLLYGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLDFIVLKE 479 (526)
Q Consensus 400 ~~I~~aLE~~~~~re~v~~LL~~L~~~~~ls~~q~~~Gf~~vl~~l~Dl~iDiP~a~~~la~~iar~i~~~~l~~~~i~~ 479 (526)
+++...-|.-..-|-+-..+|..|+.++-.+..++..-+.-+++.|.| |.-|-||+-+=+-+...+..|-..+..
T Consensus 7 ~al~~L~dp~~PvRa~gL~~L~~Li~~~~~~~~~~~~il~l~l~~L~d-----~DsyVYL~aI~~L~~La~~~p~~vl~~ 81 (92)
T PF10363_consen 7 EALSDLNDPLPPVRAHGLVLLRKLIESKSEPVIDIPKILDLFLSQLKD-----EDSYVYLNAIKGLAALADRHPDEVLPI 81 (92)
T ss_pred HHHHHccCCCcchHHHHHHHHHHHHHcCCcchhhHHHHHHHHHHHcCC-----CCchHHHHHHHHHHHHHHHChHHHHHH
Confidence 333333333455677778888888887766777777778888888888 677878877766555555555444444
Q ss_pred HHH
Q 009767 480 VLK 482 (526)
Q Consensus 480 ~~~ 482 (526)
+++
T Consensus 82 L~~ 84 (92)
T PF10363_consen 82 LLD 84 (92)
T ss_pred HHH
Confidence 443
No 45
>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=31.31 E-value=90 Score=29.61 Aligned_cols=57 Identities=21% Similarity=0.204 Sum_probs=41.8
Q ss_pred CCCCHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhCCC----CChHHHHHHHHHHHhcCCC
Q 009767 354 TKLNLADLRKKTVSLLEEYFSIRILDEALQCVEELRAP----TYHPEVVKEAIALALEKIP 410 (526)
Q Consensus 354 ~~~s~eel~kk~~~il~EY~~~~D~~Ea~~~i~eL~~p----~~~~~~V~~~I~~aLE~~~ 410 (526)
..+-+++++.....+-+-|+..||.++|++|+...... ...-.+.-.+|..++...+
T Consensus 28 ~n~~kesir~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d 88 (177)
T PF10602_consen 28 SNLGKESIRMALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGD 88 (177)
T ss_pred hccchHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCC
Confidence 34567888888889999999999999999999986432 2223556666666666553
No 46
>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=31.04 E-value=2.8e+02 Score=22.48 Aligned_cols=48 Identities=21% Similarity=0.065 Sum_probs=30.3
Q ss_pred hHHHHHHHHHHHhcCCCcChHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcc
Q 009767 394 HPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTGCLLYGSLL 445 (526)
Q Consensus 394 ~~~~V~~~I~~aLE~~~~~re~v~~LL~~L~~~~~ls~~q~~~Gf~~vl~~l 445 (526)
+++.|..++...+.+ .-+.+...+..|... -++..++.+.+.+++-..
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 356777777766654 345566666777776 678888888887766544
No 47
>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=30.82 E-value=69 Score=20.01 Aligned_cols=25 Identities=32% Similarity=0.577 Sum_probs=21.9
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHhCC
Q 009767 366 VSLLEEYFSIRILDEALQCVEELRA 390 (526)
Q Consensus 366 ~~il~EY~~~~D~~Ea~~~i~eL~~ 390 (526)
..+|+-|...++.++|...++++..
T Consensus 4 ~~li~~~~~~~~~~~a~~~~~~M~~ 28 (31)
T PF01535_consen 4 NSLISGYCKMGQFEEALEVFDEMRE 28 (31)
T ss_pred HHHHHHHHccchHHHHHHHHHHHhH
Confidence 5788999999999999999998753
No 48
>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=29.44 E-value=4.5e+02 Score=24.18 Aligned_cols=32 Identities=19% Similarity=0.234 Sum_probs=26.0
Q ss_pred chhHHHHHHHHHHHHcCCCChHHHHHHHHhhh
Q 009767 454 KAPNNFGEMVGKLVVAKSLDFIVLKEVLKKVE 485 (526)
Q Consensus 454 ~a~~~la~~iar~i~~~~l~~~~i~~~~~~~~ 485 (526)
..+..+..|++.+..-+.++...+-+++..+-
T Consensus 94 ~~~~~~i~fl~eL~~~~~i~~~~i~~~l~~ll 125 (200)
T smart00543 94 QRRLGLVRFLGELYNFQVLTSKIILELLKELL 125 (200)
T ss_pred hhHHhHHHHHHHHHHcccCcHHHHHHHHHHHH
Confidence 55677889999999999999888877777653
No 49
>PF08321 PPP5: PPP5 TPR repeat region; InterPro: IPR013235 This domain is specific to the PPP5 subfamily of serine/threonine phosphatases.; GO: 0004722 protein serine/threonine phosphatase activity, 0046872 metal ion binding; PDB: 3ICF_B 3H60_B 3H63_A 3H66_A 3H62_B 1A17_A 1S95_B 3H69_A 3H68_D 3H64_D ....
Probab=28.70 E-value=34 Score=29.32 Aligned_cols=69 Identities=13% Similarity=0.206 Sum_probs=40.1
Q ss_pred HHHHHHHHHH------HhhcchhhhcCCCchhHHHHHHHHHHHHcCCCChHHHHHHHHhhhc-----hhHHHHHHHHHHH
Q 009767 431 TRDIGTGCLL------YGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLDFIVLKEVLKKVED-----NMFRRSIFTAAMK 499 (526)
Q Consensus 431 ~~q~~~Gf~~------vl~~l~Dl~iDiP~a~~~la~~iar~i~~~~l~~~~i~~~~~~~~~-----~~~~~~~l~~~l~ 499 (526)
...|++|+.. +.+.++=-.++||..|+ ++-+.++-++..|+..+++.+.+ -.++-.+|.++.+
T Consensus 11 ~~~FekAI~~d~~~~s~~e~~d~~~i~Ve~sY~------GP~l~~~~it~efv~~mie~FK~~K~Lhkkyv~~Il~~~~~ 84 (95)
T PF08321_consen 11 RIAFEKAIAVDEEKKSVSESIDLESIDVEDSYD------GPRLEDEPITLEFVKAMIEWFKNQKKLHKKYVYQILLEAKK 84 (95)
T ss_dssp HHHHSHHHHHHHHHHSTTTS-TTSTT---SS--------SS--BTTB--HHHHHHHHHHHHCT----HHHHHHHHHHHHH
T ss_pred HHHHHHHhccCCcccCHHHhcCccceecCCCCC------CCCCCCCCCCHHHHHHHHHHHHhCCCccHHHHHHHHHHHHH
Confidence 3455555553 44555444567887765 55566688999999999887654 3677788888888
Q ss_pred HHhcCC
Q 009767 500 SIQSSP 505 (526)
Q Consensus 500 ~l~~~~ 505 (526)
.++..|
T Consensus 85 llk~~P 90 (95)
T PF08321_consen 85 LLKQLP 90 (95)
T ss_dssp HHHTS-
T ss_pred HHHhCc
Confidence 888775
No 50
>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=28.43 E-value=4.4e+02 Score=23.74 Aligned_cols=32 Identities=16% Similarity=0.221 Sum_probs=25.4
Q ss_pred cChHHHHHHHHHHHhCCCCCHHHHHHHHHHHh
Q 009767 411 PCVEPVIQLLEFLLNKNVLTTRDIGTGCLLYG 442 (526)
Q Consensus 411 ~~re~v~~LL~~L~~~~~ls~~q~~~Gf~~vl 442 (526)
....+++.++..|+..++++.+++..-++.+.
T Consensus 77 R~VRlvcvfl~sLir~~i~~~~~l~~evq~FC 108 (126)
T PF10155_consen 77 RLVRLVCVFLQSLIRNKIIDVEDLFIEVQAFC 108 (126)
T ss_pred chhhhHHHHHHHHHHcCCCchHHHHhhHHHHH
Confidence 34579999999999999999988766555543
No 51
>PF09733 VEFS-Box: VEFS-Box of polycomb protein; InterPro: IPR019135 The VEFS-Box is found in the the C-terminal region of the VRN2, EMF2, FIS2, and Su(z)12 polycomb proteins. This domain is characterised by an acidic cluster and a tryptophan/methionine-rich sequence, the acidic-W/M domain []. In some proteins the VEFS-Box is associated with a zinc-finger domain located roughly 100 residues towards the N terminus. These proteins are part of the polycomb cluster of proteins which control HOX gene transcription as it functions in heterochromatin-mediated repression [].
Probab=28.07 E-value=99 Score=28.49 Aligned_cols=42 Identities=10% Similarity=0.004 Sum_probs=0.0
Q ss_pred HHHHHHHHHHH-hhhhhhHHHHHHHhcCCCCCHHHHHHHHHHH
Q 009767 60 MERMDQERLVK-LRTLGNIRLIGELLKQKMVPEKIVHHIVQEL 101 (526)
Q Consensus 60 ~e~~~~~~~~K-~r~lGnirFIGELfk~~~l~e~ii~~ci~~L 101 (526)
.+....+...+ .+....+.++..|+..|+|+...|..|++.|
T Consensus 98 v~~~~~~L~~~~~l~~~f~lHl~~L~d~glLd~~~i~~c~~~l 140 (140)
T PF09733_consen 98 VREHGQWLVEKPNLRREFLLHLINLWDFGLLDARTIDECMKIL 140 (140)
T ss_pred HHHhHHHHhhChhHHHHHHHHHHHHHHcCCCCHHHHHHHHhhC
No 52
>KOG2050 consensus Puf family RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=27.56 E-value=1.1e+02 Score=34.55 Aligned_cols=62 Identities=19% Similarity=0.233 Sum_probs=41.4
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhCC--CCC-h-HHHHHHHHHHHhcCCCcChHHHHHHHHHHHh
Q 009767 364 KTVSLLEEYFSIRILDEALQCVEELRA--PTY-H-PEVVKEAIALALEKIPPCVEPVIQLLEFLLN 425 (526)
Q Consensus 364 k~~~il~EY~~~~D~~Ea~~~i~eL~~--p~~-~-~~~V~~~I~~aLE~~~~~re~v~~LL~~L~~ 425 (526)
.+-.++-|||.+-|.+|+.+.+.-|.. |.+ | ++=-+.+|.+.--.++.+|.++.+-+...+.
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 IVHKLMLEYLTIADEEEKSELLELLKELVPEMVHTRDGSRVAMKLIWHATAKERKLIIKNMKEHVE 387 (652)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHhhCCHHHHHHHHHHHHHHHH
Confidence 466678899999999999888776641 222 1 1222344554444578899999888775554
No 53
>cd03565 VHS_Tom1 VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. The VHS domain of the Tom1 protein is essential for the negative regulation of Interleukin-1 and Tumor Necrosis Factor-induced signaling pathways.
Probab=26.96 E-value=2.6e+02 Score=25.48 Aligned_cols=95 Identities=8% Similarity=0.080 Sum_probs=59.9
Q ss_pred hhhHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCCCCCChh----hHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHH
Q 009767 74 LGNIRLIGELLKQKMVPEKIVHHIVQELLENDGKTCPAEE----NVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKEL 149 (526)
Q Consensus 74 lGnirFIGELfk~~~l~e~ii~~ci~~Ll~~~~~~~p~ee----~iE~lc~LL~tiG~~Ld~~~~~~~~~d~~f~~l~~l 149 (526)
.+.|-=|+++.+.+-...+-...+|++=|... ++.. .+.-|=.+++.||..+...-..+.+++.+ |..+
T Consensus 19 w~~ileicD~In~~~~~~k~a~ralkkRl~~~----~n~~v~l~aL~LLe~~vkNCG~~fh~eiask~Fl~e~---L~~~ 91 (141)
T cd03565 19 WGLNMEICDIINETEDGPKDAVRALKKRLNGN----KNHKEVMLTLTVLETCVKNCGHRFHVLVAKKDFIKDV---LVKL 91 (141)
T ss_pred HHHHHHHHHHHhCCCCcHHHHHHHHHHHHccC----CCHHHHHHHHHHHHHHHHHccHHHHHHHHHHHhhhHH---HHHH
Confidence 35667788888887776665555555544321 1222 45555667778898888544445555552 3333
Q ss_pred Hh-CCCCChhHHHHHHHHHHHHhCCCC
Q 009767 150 TT-NSQLVPRLRFMIHDVLDLRANNWV 175 (526)
Q Consensus 150 ~~-~~~ls~Rirfmi~dvidlR~~~W~ 175 (526)
+. ....+..|+-.|..+|+-....+.
T Consensus 92 i~~~~~~~~~Vk~kil~li~~W~~~f~ 118 (141)
T cd03565 92 INPKNNPPTIVQEKVLALIQAWADAFR 118 (141)
T ss_pred HcccCCCcHHHHHHHHHHHHHHHHHhC
Confidence 33 334677899999999988776664
No 54
>PF12755 Vac14_Fab1_bd: Vacuolar 14 Fab1-binding region
Probab=26.91 E-value=1.8e+02 Score=24.79 Aligned_cols=74 Identities=11% Similarity=0.019 Sum_probs=46.2
Q ss_pred ChHHHHHHHHHHHhcCCCcChHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcchhhhcCCCchhHHHHHHHHHHHHc
Q 009767 393 YHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTGCLLYGSLLDDIGIDLPKAPNNFGEMVGKLVVA 469 (526)
Q Consensus 393 ~~~~~V~~~I~~aLE~~~~~re~v~~LL~~L~~~~~ls~~q~~~Gf~~vl~~l~Dl~iDiP~a~~~la~~iar~i~~ 469 (526)
|..+++.-++...=|....-|...+.-|..+.+ +..+.+..=|.++++.|-.+.-|.=.--..-|+++.|++.|
T Consensus 24 ~l~~Il~pVL~~~~D~d~rVRy~AcEaL~ni~k---~~~~~~l~~f~~IF~~L~kl~~D~d~~Vr~~a~~Ld~llkd 97 (97)
T PF12755_consen 24 YLDEILPPVLKCFDDQDSRVRYYACEALYNISK---VARGEILPYFNEIFDALCKLSADPDENVRSAAELLDRLLKD 97 (97)
T ss_pred HHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhcC
Confidence 445566666655445556777888887777765 44556666666666666666666654445556666666543
No 55
>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=26.62 E-value=2e+02 Score=27.48 Aligned_cols=37 Identities=24% Similarity=0.263 Sum_probs=30.9
Q ss_pred CCChHHHHHHHHHHHhcCCCcChHHHHHHHHHHHhCC
Q 009767 391 PTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKN 427 (526)
Q Consensus 391 p~~~~~~V~~~I~~aLE~~~~~re~v~~LL~~L~~~~ 427 (526)
|...+.++..++-.+.||=|.-|+.+.+.|..+....
T Consensus 2 ~~~~~~~~~~llrqa~EKiDrvR~~A~~~l~~ll~~~ 38 (193)
T PF12612_consen 2 PELVQQIIGGLLRQAAEKIDRVREVAGKCLQRLLHSQ 38 (193)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 3455788899999999999999999999999988533
No 56
>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=26.11 E-value=3.6e+02 Score=22.62 Aligned_cols=64 Identities=17% Similarity=0.300 Sum_probs=42.3
Q ss_pred hhhhhHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCCCCCChhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHH
Q 009767 72 RTLGNIRLIGELLKQKMVPEKIVHHIVQELLENDGKTCPAEENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELT 150 (526)
Q Consensus 72 r~lGnirFIGELfk~~~l~e~ii~~ci~~Ll~~~~~~~p~ee~iE~lc~LL~tiG~~Ld~~~~~~~~~d~~f~~l~~l~ 150 (526)
+-+-+|.||=+-....-+++.....|-..|-. .|.++.-|+++|.. +-+|.-+..+|.+|+++.
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 45668999998888899999998877666553 35677766666655 445667788888888765
No 57
>KOG3785 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.10 E-value=3.7e+02 Score=28.94 Aligned_cols=104 Identities=14% Similarity=0.179 Sum_probs=64.0
Q ss_pred HHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhcCCCcChHHH--HHHHHHHHhC-----CCCCHHHHHHHHH
Q 009767 367 SLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPV--IQLLEFLLNK-----NVLTTRDIGTGCL 439 (526)
Q Consensus 367 ~il~EY~~~~D~~Ea~~~i~eL~~p~~~~~~V~~~I~~aLE~~~~~re~v--~~LL~~L~~~-----~~ls~~q~~~Gf~ 439 (526)
.++--|+.-+|++||..-++||..-.-|.-+++-++..++-..-..||++ ++-+-+|+.+ ..|+..|-.-..-
T Consensus 290 NL~iYyL~q~dVqeA~~L~Kdl~PttP~EyilKgvv~aalGQe~gSreHlKiAqqffqlVG~Sa~ecDTIpGRQsmAs~f 369 (557)
T KOG3785|consen 290 NLIIYYLNQNDVQEAISLCKDLDPTTPYEYILKGVVFAALGQETGSREHLKIAQQFFQLVGESALECDTIPGRQSMASYF 369 (557)
T ss_pred hheeeecccccHHHHHHHHhhcCCCChHHHHHHHHHHHHhhhhcCcHHHHHHHHHHHHHhcccccccccccchHHHHHHH
Confidence 45667889999999999999996433344455555555666555566654 5656667763 2344445444444
Q ss_pred HHhhcchhhhcCCCchhHHHHHHHHHHHHcCCCChHHH
Q 009767 440 LYGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLDFIVL 477 (526)
Q Consensus 440 ~vl~~l~Dl~iDiP~a~~~la~~iar~i~~~~l~~~~i 477 (526)
=+....||.. .||-.|-+-.+.|+.+.+++-
T Consensus 370 FL~~qFddVl-------~YlnSi~sYF~NdD~Fn~N~A 400 (557)
T KOG3785|consen 370 FLSFQFDDVL-------TYLNSIESYFTNDDDFNLNLA 400 (557)
T ss_pred HHHHHHHHHH-------HHHHHHHHHhcCcchhhhHHH
Confidence 4444455533 466666666677776666553
No 58
>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=24.68 E-value=1.6e+02 Score=24.37 Aligned_cols=38 Identities=24% Similarity=0.329 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHh-CCCCCh
Q 009767 356 LNLADLRKKTVSLLEEYFSIRILDEALQCVEEL-RAPTYH 394 (526)
Q Consensus 356 ~s~eel~kk~~~il~EY~~~~D~~Ea~~~i~eL-~~p~~~ 394 (526)
+++.| +..+...|++|...+++++.+..+..+ +.|..+
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 44555 456777899999999999999999985 677654
No 59
>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]
Probab=24.20 E-value=9.9e+02 Score=27.29 Aligned_cols=71 Identities=17% Similarity=0.143 Sum_probs=52.7
Q ss_pred HHHHHHHHHhcCCCcChHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcchhhhcCCCchhHHHHHHHHHHHHcCCCCh
Q 009767 397 VVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTGCLLYGSLLDDIGIDLPKAPNNFGEMVGKLVVAKSLDF 474 (526)
Q Consensus 397 ~V~~~I~~aLE~~~~~re~v~~LL~~L~~~~~ls~~q~~~Gf~~vl~~l~Dl~iDiP~a~~~la~~iar~i~~~~l~~ 474 (526)
-|..-|...|+...-+.+-+-.||..+++ .+|.+.|..|=.=+++.+- -|...+.++.|+---|.+++..+
T Consensus 87 ~~~~~~~k~l~~~~l~~~~~~~~l~~~~~--~c~kd~is~~k~w~f~~~~-----s~~~~e~~~~~l~n~~~~~~~~~ 157 (757)
T KOG4368|consen 87 AVEQQMQKLLEETQLDMNEFDNLLQPIID--TCTKDAISAGKNWMFSNAK-----SPPHCELMAGHLRNRITADGAHF 157 (757)
T ss_pred HHHHHHHHHHHhccCCHHHHHHHHHHHHH--HHhHHHHHHhhhhhhhcCC-----CchHHHHHHHHHHhhhcccccch
Confidence 34445555666677778888888888887 5889999999888888764 37777888888877777776544
No 60
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=24.12 E-value=5.6e+02 Score=23.46 Aligned_cols=94 Identities=17% Similarity=0.229 Sum_probs=61.5
Q ss_pred hhhHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCCCCCC--hhhHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHHh
Q 009767 74 LGNIRLIGELLKQKMVPEKIVHHIVQELLENDGKTCPA--EENVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELTT 151 (526)
Q Consensus 74 lGnirFIGELfk~~~l~e~ii~~ci~~Ll~~~~~~~p~--ee~iE~lc~LL~tiG~~Ld~~~~~~~~~d~~f~~l~~l~~ 151 (526)
.+.|-=|+++.+.+-...+-...+|++-|... +|. =-.|.-|=.+++.||..+...-..+ .+.+.|..++.
T Consensus 18 w~~il~icD~I~~~~~~~k~a~ral~KRl~~~---n~~v~l~AL~LLe~~vkNCG~~fh~evask----~Fl~eL~kl~~ 90 (144)
T cd03568 18 WGLILDVCDKVKSDENGAKDCLKAIMKRLNHK---DPNVQLRALTLLDACAENCGKRFHQEVASR----DFTQELKKLIN 90 (144)
T ss_pred HHHHHHHHHHHhcCCccHHHHHHHHHHHHcCC---CHHHHHHHHHHHHHHHHHCCHHHHHHHhhH----HHHHHHHHHhc
Confidence 35677789999887666666555555555442 121 1344555556667788877533333 45555777766
Q ss_pred CCCCChhHHHHHHHHHHHHhCCCC
Q 009767 152 NSQLVPRLRFMIHDVLDLRANNWV 175 (526)
Q Consensus 152 ~~~ls~Rirfmi~dvidlR~~~W~ 175 (526)
.+ ....|+-.|..+|......+.
T Consensus 91 ~~-~~~~Vk~kil~li~~W~~~f~ 113 (144)
T cd03568 91 DR-VHPTVKEKLREVVKQWADEFK 113 (144)
T ss_pred cc-CCHHHHHHHHHHHHHHHHHhC
Confidence 55 889999999999998766665
No 61
>PRK14137 recX recombination regulator RecX; Provisional
Probab=24.09 E-value=6.7e+02 Score=24.31 Aligned_cols=31 Identities=13% Similarity=0.055 Sum_probs=24.3
Q ss_pred CCCCCCHHHHHHHHHHHHHHHhcCCCHHHHH
Q 009767 352 PVTKLNLADLRKKTVSLLEEYFSIRILDEAL 382 (526)
Q Consensus 352 ~~~~~s~eel~kk~~~il~EY~~~~D~~Ea~ 382 (526)
..+.++.+|+..++....-.|++.++-.+..
T Consensus 29 ~~~~~~~~e~~~~~~~~Al~~Ls~R~rS~~E 59 (195)
T PRK14137 29 RRTPPTPDEAREALLAYAFRALAARAMTAAE 59 (195)
T ss_pred ccCCCCHHHHHHHHHHHHHHHHhcchhhHHH
Confidence 4556899999999999888888887766543
No 62
>PTZ00009 heat shock 70 kDa protein; Provisional
Probab=23.52 E-value=3.1e+02 Score=31.60 Aligned_cols=78 Identities=9% Similarity=0.191 Sum_probs=39.0
Q ss_pred ChhhHHHHHHHHHHHhhhhhc---CCcchhhHHHHHHHHHHHHhC----CCCChhHHHHHHHHHHHHhCCCCccccccCC
Q 009767 111 AEENVEAICQFFNTIGKQLDE---NPKSRRVNDVYFSRLKELTTN----SQLVPRLRFMIHDVLDLRANNWVPRREEMKA 183 (526)
Q Consensus 111 ~ee~iE~lc~LL~tiG~~Ld~---~~~~~~~~d~~f~~l~~l~~~----~~ls~Rirfmi~dvidlR~~~W~~r~~~~~p 183 (526)
++++++.+.+.+...-..=.. ....+..++.|.-.++..+.. ..++..-|--|.+.++-- ..|.... ..
T Consensus 513 s~~~i~~~~~~~~~~~~~d~~~~~~~eakN~lEs~Iy~~r~~L~~~~~~~~~t~ee~~~l~~~l~~~-~~wL~~~---~~ 588 (653)
T PTZ00009 513 SKADIDRMVNEAEKYKAEDEANRERVEAKNGLENYCYSMKNTLQDEKVKGKLSDSDKATIEKAIDEA-LEWLEKN---QL 588 (653)
T ss_pred cHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhhHHHHHHHHHHHhhhhhhccCCHHHHHHHHHHHHHH-HHHHhcC---Cc
Confidence 566677766666543221110 011233456777777776642 356666655555555432 3477431 12
Q ss_pred CcHHHHHHH
Q 009767 184 KTITEIHSE 192 (526)
Q Consensus 184 kti~~i~~e 192 (526)
.+++++.+.
T Consensus 589 ~~~~~~~~k 597 (653)
T PTZ00009 589 AEKEEFEHK 597 (653)
T ss_pred hhHHHHHHH
Confidence 345555543
No 63
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=23.20 E-value=5.4e+02 Score=22.93 Aligned_cols=92 Identities=11% Similarity=0.149 Sum_probs=61.0
Q ss_pred hhHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCCCCCChh----hHHHHHHHHHHHhhhhhcCCcchhhHHHHHHHHHHHH
Q 009767 75 GNIRLIGELLKQKMVPEKIVHHIVQELLENDGKTCPAEE----NVEAICQFFNTIGKQLDENPKSRRVNDVYFSRLKELT 150 (526)
Q Consensus 75 GnirFIGELfk~~~l~e~ii~~ci~~Ll~~~~~~~p~ee----~iE~lc~LL~tiG~~Ld~~~~~~~~~d~~f~~l~~l~ 150 (526)
..|..|+++.+.+-...+.....|+.-|... +.. .+..|=.+++.||+.+-..-..+ .++..|..++
T Consensus 19 ~~il~icd~I~~~~~~~k~a~raL~krl~~~-----n~~vql~AL~lLd~~vkNcg~~f~~~i~s~----~fl~~l~~l~ 89 (133)
T cd03561 19 ALNLELCDLINLKPNGPKEAARAIRKKIKYG-----NPHVQLLALTLLELLVKNCGKPFHLQVADK----EFLLELVKIA 89 (133)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHHHcCC-----CHHHHHHHHHHHHHHHHhCChHHHHHHhhH----HHHHHHHHHh
Confidence 5677889999888777777777777666542 332 34444455566677665422222 4555566666
Q ss_pred hCC-CCChhHHHHHHHHHHHHhCCCC
Q 009767 151 TNS-QLVPRLRFMIHDVLDLRANNWV 175 (526)
Q Consensus 151 ~~~-~ls~Rirfmi~dvidlR~~~W~ 175 (526)
..+ ..+..||-.|..+|.-....+.
T Consensus 90 ~~~~~~~~~Vk~kil~ll~~W~~~f~ 115 (133)
T cd03561 90 KNSPKYDPKVREKALELILAWSESFG 115 (133)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHhc
Confidence 654 8899999999999988765554
No 64
>PF14837 INTS5_N: Integrator complex subunit 5 N-terminus
Probab=22.65 E-value=6.8e+02 Score=24.77 Aligned_cols=32 Identities=19% Similarity=0.071 Sum_probs=26.0
Q ss_pred CCCCCHHHHHHHHHHHhhcchhhhcCCCchhH
Q 009767 426 KNVLTTRDIGTGCLLYGSLLDDIGIDLPKAPN 457 (526)
Q Consensus 426 ~~~ls~~q~~~Gf~~vl~~l~Dl~iDiP~a~~ 457 (526)
..--...++..++.++.+.|..+.-.-|+||.
T Consensus 72 ~~~~~~~~~~~ai~ei~~~L~~fv~~npkAWa 103 (213)
T PF14837_consen 72 KQQQDEADLDEAIQEIHDVLSRFVEANPKAWA 103 (213)
T ss_pred ccCCCCccHHHHHHHHHHHHHHHHhcCCcccH
Confidence 34456678888899999999999899999884
No 65
>PF11867 DUF3387: Domain of unknown function (DUF3387); InterPro: IPR021810 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is typically between 255 to 340 amino acids in length. This domain is found associated with PF04851 from PFAM, PF04313 from PFAM.
Probab=22.06 E-value=5.9e+02 Score=26.57 Aligned_cols=90 Identities=11% Similarity=0.223 Sum_probs=50.9
Q ss_pred CCHHHHHHHHHHHHHHHhcCCCHHH------------------HHHHHHHhCCCCChHHHHHHHHHHHhc----CCCcCh
Q 009767 356 LNLADLRKKTVSLLEEYFSIRILDE------------------ALQCVEELRAPTYHPEVVKEAIALALE----KIPPCV 413 (526)
Q Consensus 356 ~s~eel~kk~~~il~EY~~~~D~~E------------------a~~~i~eL~~p~~~~~~V~~~I~~aLE----~~~~~r 413 (526)
++.+++..++..+|+++..+..+.+ +..-|+++..|....+.++.+|..-+. .++...
T Consensus 117 ~~~~~~~~~i~~Lid~~I~s~~v~~i~~~~~~~~~disild~eFl~~v~~~~~k~~~~e~L~~~l~~~I~~~~~~N~~~~ 196 (335)
T PF11867_consen 117 PDIKEVEEKIRQLIDESIASEGVVDIFEAAGLKKPDISILDDEFLEEVKKMKSKNLKAELLEKLLRDEIKVRMKENPVRY 196 (335)
T ss_pred CCHHHHHHHHHHHHHHHHhcccchhHHhhcCCCCCChhhcCHHHHHHHHhccCchHHHHHHHHHHHHHHHHHHhcCHHHH
Confidence 5778999999999999987765543 333344444444334444444443332 222222
Q ss_pred HHHHHHHHHHHh---CCCCCHHHHHHHHHHHhhcc
Q 009767 414 EPVIQLLEFLLN---KNVLTTRDIGTGCLLYGSLL 445 (526)
Q Consensus 414 e~v~~LL~~L~~---~~~ls~~q~~~Gf~~vl~~l 445 (526)
...+..|..++. .+.++.+++.+-+..+...+
T Consensus 197 ~~fsErLe~iI~~Y~~~~i~~~e~~~eLi~la~el 231 (335)
T PF11867_consen 197 KKFSERLEEIIEKYNNRSISSEEVIEELIKLAKEL 231 (335)
T ss_pred HHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHH
Confidence 455555555554 46666666665555554443
No 66
>PF12295 Symplekin_C: Symplekin tight junction protein C terminal; InterPro: IPR022075 This domain family is found in eukaryotes, and is approximately 180 amino acids in length. There is a single completely conserved residue P that may be functionally important. Symplekn has been localized, by light and electron microscopy, to the plaque associated with the cytoplasmic face of the tight junction-containing zone (zonula occludens) of polar epithelial cells and of Sertoli cells of testis. However, both the mRNA and the protein can also be detected in a wide range of cell types that do not form tight junctions. Careful analyses have revealed that the protein occurs in all these diverse cells in the nucleoplasm, and only in those cells forming tight junctions is it recruited, partly but specifically, to the plaque structure of the zonula occludens.
Probab=21.70 E-value=3.2e+02 Score=26.20 Aligned_cols=80 Identities=28% Similarity=0.328 Sum_probs=55.4
Q ss_pred HHHHHHHHHhcCCC------HHHHHHHHHHhCCCCChHHHHHHHHHHHhcCCCcChHHHHHHHHHHHhCCCCCHHHHHHH
Q 009767 364 KTVSLLEEYFSIRI------LDEALQCVEELRAPTYHPEVVKEAIALALEKIPPCVEPVIQLLEFLLNKNVLTTRDIGTG 437 (526)
Q Consensus 364 k~~~il~EY~~~~D------~~Ea~~~i~eL~~p~~~~~~V~~~I~~aLE~~~~~re~v~~LL~~L~~~~~ls~~q~~~G 437 (526)
++...++--|+..+ +.-|++-+-|. .-.|.+.-+.+..++..-+.-+..++.+|..|+.+++.....+-+|
T Consensus 75 ~~~~a~~~Cf~~~~vf~~evla~~l~ql~~~---~~lP~LfmRTviq~~~~~p~L~~FV~~iL~rLi~kqvW~~~~lW~G 151 (183)
T PF12295_consen 75 KIIEALDLCFSMRDVFTQEVLASALQQLVEQ---PPLPLLFMRTVIQALQKYPSLRSFVSNILSRLIQKQVWKNKKLWEG 151 (183)
T ss_pred HHHHHHHHHHcccccCCHHHHHHHHHHHHCC---CCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcChhHHHH
Confidence 33555555555554 34444444443 2245555556666777777788999999999999999999999999
Q ss_pred HHHHhhcch
Q 009767 438 CLLYGSLLD 446 (526)
Q Consensus 438 f~~vl~~l~ 446 (526)
|-.-...+-
T Consensus 152 fi~C~~~~~ 160 (183)
T PF12295_consen 152 FIKCAKRLK 160 (183)
T ss_pred HHHHHHHhh
Confidence 998776554
No 67
>PF01865 PhoU_div: Protein of unknown function DUF47; InterPro: IPR018445 This family includes prokaryotic proteins of unknown function, as well as a protein annotated as the pit accessory protein from Rhizobium meliloti (Sinorhizobium meliloti) (O30498 from SWISSPROT). However, the function of this protein is also unknown (Pit stands for Phosphate transport) [].; PDB: 2OLT_C 2IIU_C 3L39_A.
Probab=21.10 E-value=3.4e+02 Score=26.03 Aligned_cols=90 Identities=22% Similarity=0.297 Sum_probs=46.3
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHhCCCCChHHHHHHHHHHHhcC---CCcChHHHHHHHHHHHhCCCCCHHHHHHHHHHH
Q 009767 365 TVSLLEEYFSIRILDEALQCVEELRAPTYHPEVVKEAIALALEK---IPPCVEPVIQLLEFLLNKNVLTTRDIGTGCLLY 441 (526)
Q Consensus 365 ~~~il~EY~~~~D~~Ea~~~i~eL~~p~~~~~~V~~~I~~aLE~---~~~~re~v~~LL~~L~~~~~ls~~q~~~Gf~~v 441 (526)
+..+++.|+. +|.++....++++..-.....-++.-|...|.+ .+-+|+-+..|+..+ +++..+++.+
T Consensus 27 ~~e~l~~~~~-~~~~~~~~~~~~i~~lE~~aD~i~~~i~~~L~~~fitP~dRedi~~L~~~l--------D~I~d~i~~~ 97 (214)
T PF01865_consen 27 LAELLEAYLE-GDYEDVEELLEEIKELEHEADEIKREIREELYKSFITPFDREDILRLISSL--------DDIADYIEDA 97 (214)
T ss_dssp HHHHHHHHCT-T-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS-SS-HHHHHHHHHHH--------HHHHHHHHHH
T ss_pred HHHHHHHHHh-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcHHHHHHHHHHH--------HHHHHHHHHH
Confidence 5556777776 554455444444432122344444455556665 378999999888876 4456666655
Q ss_pred hhcchhhhcCCC-chhHHHHHHH
Q 009767 442 GSLLDDIGIDLP-KAPNNFGEMV 463 (526)
Q Consensus 442 l~~l~Dl~iDiP-~a~~~la~~i 463 (526)
...+.=..+++| ..+..+..++
T Consensus 98 a~~l~~~~~~~~~~~~~~~~~l~ 120 (214)
T PF01865_consen 98 AKRLSLYKVEIPEELREEFQELA 120 (214)
T ss_dssp HHHHHHHT----CCGHHHHHHHH
T ss_pred HHHHHHhccCCCcchhHHHHHHH
Confidence 555544444444 3334344443
No 68
>PF13311 DUF4080: Protein of unknown function (DUF4080)
Probab=20.43 E-value=5.1e+02 Score=24.78 Aligned_cols=74 Identities=16% Similarity=0.247 Sum_probs=49.7
Q ss_pred CCCCCCHHHHH--HHHHHHHHHHhcCCCHHHHHHHHHHh-CCCC-ChHHHHHHHHHHHhcCCCcChHHHHHHHHHHHh
Q 009767 352 PVTKLNLADLR--KKTVSLLEEYFSIRILDEALQCVEEL-RAPT-YHPEVVKEAIALALEKIPPCVEPVIQLLEFLLN 425 (526)
Q Consensus 352 ~~~~~s~eel~--kk~~~il~EY~~~~D~~Ea~~~i~eL-~~p~-~~~~~V~~~I~~aLE~~~~~re~v~~LL~~L~~ 425 (526)
..+-+|-+|+. |.+..+++-|+++|-....+..|-.. .+|. +...|-.-+-..........++.+..+|...+.
T Consensus 18 ~t~~Ls~~ei~~Lk~~e~~le~yyNSgrF~~tl~~l~~~~~spF~ff~~l~~~~~~~g~~~~~~s~~~l~~~L~~F~~ 95 (190)
T PF13311_consen 18 STKWLSFDEIQRLKRFEDMLEKYYNSGRFDYTLEYLLKEFGSPFDFFEALADYWEEQGYFKRSHSLEDLFEILYDFLK 95 (190)
T ss_pred eCCCCCHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhcCCHHHHHHHHHHHHHHCCCcccCCCHHHHHHHHHHHHH
Confidence 34568889877 57999999999999999999998876 3332 233444444444454445555556665555554
Done!