Query 008379
Match_columns 568
No_of_seqs 258 out of 631
Neff 6.6
Searched_HMMs 46136
Date Thu Mar 28 23:05:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008379.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008379hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2140 Uncharacterized conser 100.0 3E-170 6E-175 1322.5 39.0 539 1-539 144-683 (739)
2 KOG2141 Protein involved in hi 100.0 1.9E-82 4.2E-87 683.5 29.2 425 7-446 310-754 (822)
3 smart00543 MIF4G Middle domain 99.9 2.7E-26 5.8E-31 221.7 19.6 183 23-205 2-200 (200)
4 PF02854 MIF4G: MIF4G domain; 99.9 4.4E-26 9.6E-31 220.3 16.5 183 23-205 2-209 (209)
5 smart00544 MA3 Domain in DAP-5 99.8 7.3E-19 1.6E-23 156.4 8.7 106 310-416 1-113 (113)
6 PF02847 MA3: MA3 domain; Int 99.7 5.4E-17 1.2E-21 144.2 7.0 106 310-416 1-113 (113)
7 KOG0401 Translation initiation 99.4 9.9E-13 2.1E-17 154.7 10.7 199 9-207 337-575 (970)
8 KOG2051 Nonsense-mediated mRNA 99.4 1E-11 2.2E-16 141.3 16.0 183 21-203 423-615 (1128)
9 KOG1104 Nuclear cap-binding co 99.2 3.3E-08 7.2E-13 110.1 33.7 405 15-475 21-483 (759)
10 KOG2051 Nonsense-mediated mRNA 98.2 1.9E-05 4.2E-10 91.2 15.6 185 21-206 634-838 (1128)
11 PF02854 MIF4G: MIF4G domain; 96.6 0.0058 1.2E-07 58.7 7.5 99 320-418 12-122 (209)
12 smart00543 MIF4G Middle domain 95.4 0.051 1.1E-06 52.1 7.5 97 322-418 14-115 (200)
13 PHA03308 transcriptional regul 94.5 0.024 5.3E-07 63.6 3.0 16 484-499 1191-1206(1463)
14 PF09088 MIF4G_like: MIF4G lik 94.5 0.38 8.1E-06 47.1 10.7 87 361-447 91-178 (191)
15 PF10500 SR-25: Nuclear RNA-sp 94.5 0.025 5.4E-07 55.8 2.6 6 551-556 80-85 (225)
16 KOG3942 MIF4G domain-containin 94.3 0.42 9.2E-06 49.5 11.1 138 69-207 183-334 (348)
17 PF07817 GLE1: GLE1-like prote 93.5 1 2.2E-05 46.1 12.4 162 15-176 23-251 (256)
18 KOG2140 Uncharacterized conser 92.9 0.082 1.8E-06 58.1 3.3 36 132-170 316-351 (739)
19 KOG2297 Predicted translation 92.3 0.84 1.8E-05 47.6 9.5 140 362-502 110-249 (412)
20 KOG2130 Phosphatidylserine-spe 91.8 0.24 5.2E-06 51.4 5.0 14 97-110 64-77 (407)
21 KOG2412 Nuclear-export-signal 91.6 4.1 8.9E-05 45.4 14.3 180 20-199 337-579 (591)
22 PHA03308 transcriptional regul 90.0 0.2 4.3E-06 56.7 2.5 19 398-416 1019-1037(1463)
23 KOG2130 Phosphatidylserine-spe 87.4 0.29 6.4E-06 50.8 1.6 16 337-352 218-233 (407)
24 cd03567 VHS_GGA VHS domain fam 79.1 5.3 0.00011 37.2 6.2 97 114-212 20-124 (139)
25 PF05110 AF-4: AF-4 proto-onco 77.5 1.6 3.5E-05 53.4 2.9 9 187-195 47-55 (1191)
26 PF05110 AF-4: AF-4 proto-onco 72.9 3 6.5E-05 51.2 3.5 9 329-337 306-314 (1191)
27 cd03569 VHS_Hrs_Vps27p VHS dom 69.9 32 0.0007 32.0 9.0 94 114-210 23-120 (142)
28 cd03561 VHS VHS domain family; 69.7 30 0.00065 31.6 8.6 94 114-209 19-117 (133)
29 PF01602 Adaptin_N: Adaptin N 66.9 1.6E+02 0.0035 32.5 15.4 170 23-196 323-520 (526)
30 KOG3064 RNA-binding nuclear pr 65.3 3.3 7.2E-05 42.0 1.5 21 312-332 74-94 (303)
31 cd03568 VHS_STAM VHS domain fa 64.6 53 0.0012 30.6 9.3 94 114-210 19-116 (144)
32 smart00288 VHS Domain present 62.6 72 0.0016 29.1 9.7 95 114-210 19-117 (133)
33 KOG1824 TATA-binding protein-i 62.6 2.7E+02 0.0058 34.0 16.0 39 9-52 59-97 (1233)
34 PF02847 MA3: MA3 domain; Int 59.4 1.1E+02 0.0023 26.5 10.0 105 21-129 1-113 (113)
35 KOG2477 Uncharacterized conser 58.6 5.9 0.00013 43.9 2.0 24 544-567 46-69 (628)
36 PHA03325 nuclear-egress-membra 55.6 74 0.0016 34.2 9.3 131 313-453 68-235 (418)
37 smart00544 MA3 Domain in DAP-5 53.8 1.1E+02 0.0024 26.6 9.0 103 22-128 2-112 (113)
38 PF00790 VHS: VHS domain; Int 53.8 60 0.0013 29.8 7.6 94 114-210 24-124 (140)
39 KOG2812 Uncharacterized conser 51.5 11 0.00024 39.9 2.6 7 448-454 153-159 (426)
40 KOG4032 Uncharacterized conser 49.3 75 0.0016 30.9 7.6 59 439-510 63-121 (184)
41 PF09733 VEFS-Box: VEFS-Box of 44.6 48 0.001 30.9 5.4 31 110-140 110-140 (140)
42 PF05501 DUF755: Domain of unk 43.5 18 0.00039 33.0 2.3 19 433-451 36-54 (123)
43 COG5129 MAK16 Nuclear protein 43.2 14 0.0003 36.9 1.6 24 309-332 70-93 (303)
44 PF06112 Herpes_capsid: Gammah 42.6 31 0.00067 32.3 3.7 18 456-473 4-21 (147)
45 TIGR03209 P21_Cbot clostridium 42.2 31 0.00068 31.1 3.8 54 355-410 2-55 (142)
46 PRK08307 stage III sporulation 41.2 58 0.0013 31.3 5.6 70 319-407 47-119 (171)
47 KOG1877 Putative transmembrane 41.2 1.8E+02 0.0039 34.7 10.4 121 74-207 38-175 (819)
48 TIGR02833 spore_III_AB stage I 41.0 55 0.0012 31.4 5.4 69 320-407 47-118 (170)
49 COG5129 MAK16 Nuclear protein 40.7 14 0.00031 36.8 1.3 13 468-481 171-183 (303)
50 cd03565 VHS_Tom1 VHS domain fa 40.4 2.2E+02 0.0048 26.3 9.2 95 114-210 20-121 (141)
51 PF02724 CDC45: CDC45-like pro 38.3 20 0.00043 41.5 2.2 24 403-426 16-39 (622)
52 KOG2188 Predicted RNA-binding 37.8 2.3E+02 0.0049 32.8 10.2 26 116-141 486-511 (650)
53 PHA02664 hypothetical protein; 36.2 27 0.00059 36.6 2.6 16 540-555 484-499 (534)
54 PHA02664 hypothetical protein; 36.0 30 0.00065 36.3 2.9 8 496-503 410-417 (534)
55 PTZ00007 (NAP-L) nucleosome as 35.0 27 0.00059 37.3 2.4 7 481-487 270-276 (337)
56 PF09548 Spore_III_AB: Stage I 30.4 1.1E+02 0.0025 29.0 5.7 69 320-407 47-118 (170)
57 KOG2141 Protein involved in hi 30.4 5.7E+02 0.012 30.2 11.9 29 227-255 554-582 (822)
58 PF04542 Sigma70_r2: Sigma-70 29.9 78 0.0017 24.4 3.8 45 358-402 5-49 (71)
59 PF00619 CARD: Caspase recruit 28.0 3.3E+02 0.0071 22.1 9.1 73 18-98 1-73 (85)
60 PF11864 DUF3384: Domain of un 27.2 5E+02 0.011 28.8 10.9 155 9-163 227-410 (464)
61 PF12830 Nipped-B_C: Sister ch 26.9 2.6E+02 0.0055 27.0 7.6 73 90-162 3-75 (187)
62 PF12311 DUF3632: Protein of u 26.6 1E+02 0.0022 29.1 4.7 57 110-166 79-146 (184)
63 PF15370 DUF4598: Domain of un 25.8 42 0.00091 30.1 1.7 7 490-496 50-56 (112)
64 PF14303 NAM-associated: No ap 23.3 72 0.0016 29.4 2.9 8 501-508 11-18 (154)
65 PTZ00007 (NAP-L) nucleosome as 22.3 95 0.002 33.2 3.8 7 483-489 224-230 (337)
66 PF04388 Hamartin: Hamartin pr 21.2 1.4E+03 0.03 26.9 13.5 68 111-178 84-157 (668)
67 PF07034 ORC3_N: Origin recogn 20.9 9.1E+02 0.02 25.5 11.0 90 15-105 36-148 (330)
68 PF04147 Nop14: Nop14-like fam 20.9 1.5E+03 0.033 27.3 15.4 109 25-134 431-569 (840)
69 PTZ00429 beta-adaptin; Provisi 20.7 1.5E+03 0.032 27.1 17.2 57 114-175 461-517 (746)
70 PF09905 DUF2132: Uncharacteri 20.6 1.3E+02 0.0028 24.3 3.3 33 435-467 8-46 (64)
No 1
>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]
Probab=100.00 E-value=2.7e-170 Score=1322.53 Aligned_cols=539 Identities=65% Similarity=1.055 Sum_probs=505.0
Q ss_pred CCccccCCCCHHHHHHHHHHHHHHHHHHhhcCChhhHHHHHHHHHHhhhhhhhhHHHHHHhhhccCCCChHHHHHHHHHH
Q 008379 1 MMKDVEDKSSAEYQRLTWDALRKSINGLVNKVNATNIKNIIPELFAENLIRGRGLFCRSCMKSQMASPGFTDVFAALVAV 80 (568)
Q Consensus 1 ~~~~~~~~~s~e~qr~~w~~Lkk~I~gllNKLs~~Ni~~i~~eL~~~Ni~rgrgll~~si~~~q~~~~~f~~vyAaLva~ 80 (568)
||++|+|++|.+|||++|++|||+|+|+|||||.+||..|++|||++|++|||||+|++||++|+++|.|++|||||+|+
T Consensus 144 mq~qi~Dk~s~~yQRmnWEalkksInglInkvn~sNi~~ii~eLfqeNiirgRgl~crsv~~aq~asp~ft~vyaALvAv 223 (739)
T KOG2140|consen 144 MQAQITDKNSIEYQRMNWEALKKSINGLINKVNASNIQEIIRELFQENIIRGRGLLCRSVMQAQAASPGFTPVYAALVAV 223 (739)
T ss_pred HHHHhcccchHHHHHHHHHHHHHHhHHHHhhhhHHHHHHHHHHHHHHHHHhccchhHHHHHHHHhcCCCCcHHHHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhcCCchHHHHHHHHHHHHHHHHHHhCChhhhhhhHHHHHHHHhhhhccHHHHHHHHHHHhhCCCCCcHHHHHHHHHHHh
Q 008379 81 VNTKFTAVGELLLKRIVLQLKRAYKRNDKPQLLAAVKFIAHLVNQQVAHEIIALELLTILLENPTDDSVEVAVGFVKECG 160 (568)
Q Consensus 81 ln~~~pe~G~lll~rlv~~F~~~~~~~dk~~~~n~i~fIa~Lyn~~Vv~~~lildii~~LLe~~te~sVE~ll~lLr~~G 160 (568)
||++||+||++|++|++.+|+++|+|||+..|.|.++|||||+||+|+|++++++|+.+||+.||+++||+++.+|+.||
T Consensus 224 iNskfP~IgElLlkrLilqf~r~f~RnDk~~c~~~~kfiahLinq~VahEIv~Leil~lLLe~PTddSvevaI~flkecG 303 (739)
T KOG2140|consen 224 INSKFPQIGELLLKRLILQFKRSFRRNDKVSCLNASKFIAHLINQQVAHEIVALEILTLLLERPTDDSVEVAIAFLKECG 303 (739)
T ss_pred HccCCchHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhccCChhHHHHHHHHHHHHhhcCCCChhHHHHHHHHHHHHHhccCCCCCCCCCccccccccceeeeeeccCcCCcccc
Q 008379 161 SILQDLSPKGLHGIFERFRGILHEGEIDKRVQFLIEGLFAIRKAKFQGYPAVRPELDLVDIEDQLTHEISLQDEIDPEIT 240 (568)
Q Consensus 161 ~~Lr~~~p~~lk~I~~~l~~il~e~~is~R~~fmIE~l~~lr~nk~k~~~~i~~~ldlve~~~~~th~i~l~~~~~~e~~ 240 (568)
.+|..++|.+++.||++||.|||+|++++|+|||||+||++|+++|+++|++.++||+|+++||+||.+++++.++|++.
T Consensus 304 akL~~VSpr~~n~IfErlR~ILhe~Eld~rvqy~iEtlf~iRkdkfk~~p~v~~~LDlvee~dq~tH~l~l~de~dpe~~ 383 (739)
T KOG2140|consen 304 AKLAEVSPRALNGIFERLRYILHEGELDRRVQYMIETLFQIRKDKFKSHPAVLEELDLVEEEDQITHSLSLEDEDDPEKE 383 (739)
T ss_pred HHHHHhChHHHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHHhhccCCccccccCccchhhheeeeeecccccChhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcccCCcccccchHHHHhhhhcccCCCCC-CcCCCCCCCCCCCCchhhhhhhhHHHhhhhhhhhcchhhhhhhhhhhhh
Q 008379 241 LDIFKPDPNFLDNEKRYEDMKKDLLGETSE-DEEGSDAGSGDEDDSEEEEEEEDEEQMKIKDETETNLVNLRRTIYLTIM 319 (568)
Q Consensus 241 l~~f~~D~~~~~~e~~~~~~k~~ilG~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~d~t~~n~t~~RR~Ifl~IM 319 (568)
|++|++||+|.+||++|+++|++|+|.... ++++++.++++++++++++++++++.++|.|+|.+|++++||+||||||
T Consensus 384 L~vFk~dp~f~ene~kydaikkeiLgn~dsen~d~~~~s~E~~~eee~e~~ee~~e~~qI~D~T~~Nlv~frr~IYLti~ 463 (739)
T KOG2140|consen 384 LGVFKKDPNFEENEEKYDAIKKEILGNEDSENEDDEDGSSEDDDEEEDESVEEDEEKLQIIDMTETNLVNFRRTIYLTIQ 463 (739)
T ss_pred hcccccCccHHHHHHHHHHHHHHHhcCCcccccccccccccccccccccccccccccceeeccccchhHHhhhhheeeee
Confidence 999999999999999999999999997543 2333333333333333444456677899999999999999999999999
Q ss_pred cCCCHHHHHHHHHcccCCCCcchHHHHHHHHhhcccCcchhhHHHHHHHHhhccHhhHHHHHHHHHHHhhhhhcCchhhH
Q 008379 320 SSVDFEEAGHKLLKIKLEPGQEMELCIMLLECCSQERTYLRYYGLLGQRFCMINKVHQENFEKCFVQQYSMIHRLETNKL 399 (568)
Q Consensus 320 SS~d~~eA~hKLlkL~lk~~qe~EI~~vli~Cc~qEktYn~yY~llaerlC~~~~~~~~~f~~~f~~~y~~i~~le~~kl 399 (568)
||+||+||+||||||.|+++|+.|+|+|||+||+||+||.+|||+|++|||.+|+.||.+|+.||.++|.+||++|++||
T Consensus 464 SSldfeEaaHKLLKmkip~~q~~elc~mii~cc~QerTy~kFYglL~eRfc~l~r~~q~~fe~~f~q~YstIhr~EtnkL 543 (739)
T KOG2140|consen 464 SSLDFEEAAHKLLKMKIPESQEKELCNMIIDCCAQERTYEKFYGLLGERFCMLHREWQEAFEKCFKQQYSTIHRYETNKL 543 (739)
T ss_pred ccCcHHHHHHHHHhccCCchhhHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhcCCcCcccccccccCCcccCchHHHHHHHHHHHHHHHHchHHHHhhcCCcchhhhhhccCCCCCCCCc
Q 008379 400 RNVAKFFAHLLGTHALPWHVLAYIRLTEEDTTSSSRIFIKILFQELSEHLGIRLLNERLTDPTMQDSFESIFPRDNPKNT 479 (568)
Q Consensus 400 rNlakf~ahLl~~~~l~l~vLk~i~l~e~dttss~riFik~LfqeL~~~lg~~~l~~rl~d~~~~~~~~glfp~d~~~~~ 479 (568)
||+||||||||++|+|||.||++|+|||++|||++||||||||||||++|||++|++||+||++||+|+||||+|||+|+
T Consensus 544 RnlakffahLlstd~lpw~vl~~ikLTEEdTtsssRIfiKilFqELve~lGl~~L~~RL~dptl~~~l~glFP~dnp~n~ 623 (739)
T KOG2140|consen 544 RNLAKFFAHLLSTDALPWDVLACIKLTEEDTTSSSRIFIKILFQELVEALGLDKLNERLNDPTLQPKLEGLFPRDNPRNT 623 (739)
T ss_pred HHHHHHHHHHhcccccchHHHHHhhcccccCCccceehHHHHHHHHHHHhChHHHHHHhcCcchhhhhhccCcCCCcccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eehhhHHHhcCchhhhHHHHHHHHhCChhHHHhhhhccCCCCCCcccCCCCCCCCCCCCC
Q 008379 480 RFAINFFTSIGLGGITENLREYLKNMPRLIMQQQKQVSESEPDSEADNESESSDSSDSDT 539 (568)
Q Consensus 480 rfsinfft~IgLg~lt~~~R~~l~~~~~~~~~~~~~~~~~~s~~~~~~~s~~~~~~~~~~ 539 (568)
||||||||+||||+||++||++|++.|+.+++++.++..++|+++|+|+++|++.|+|++
T Consensus 624 RfsINfFTsIGLGgLTeelRe~L~~~pk~~~a~~eq~~~ses~~ss~sss~ses~s~s~~ 683 (739)
T KOG2140|consen 624 RFSINFFTSIGLGGLTEELREYLKNMPKVEDAEKEQVAESESGSSSSSSSDSESESDSGD 683 (739)
T ss_pred eeeeehhhhhccccchHHHHHHHHhcchhhhhhHHHHhhcccccccccccccccCCCCCC
Confidence 999999999999999999999999999998866665554444444444444443343333
No 2
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=100.00 E-value=1.9e-82 Score=683.45 Aligned_cols=425 Identities=25% Similarity=0.402 Sum_probs=349.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHhhcCChhhHHHHHHH---HHHhhhhhh-----hhHHHHHHhhhccCCCChHHHHHHHH
Q 008379 7 DKSSAEYQRLTWDALRKSINGLVNKVNATNIKNIIPE---LFAENLIRG-----RGLFCRSCMKSQMASPGFTDVFAALV 78 (568)
Q Consensus 7 ~~~s~e~qr~~w~~Lkk~I~gllNKLs~~Ni~~i~~e---L~~~Ni~rg-----rgll~~si~~~q~~~~~f~~vyAaLv 78 (568)
++.+++.| +|+|+|+|+||||+++||..|+.+ ||..|.... ..++..+++..+...+.++.+||||.
T Consensus 310 ~~~sE~l~-----rl~rkv~g~LNKLSdaNi~~I~~~i~~Ly~~~sr~~v~~sLtk~l~~~~~~~~~~ld~~~~~y~AL~ 384 (822)
T KOG2141|consen 310 SSESEQLQ-----RLRRKVNGSLNKLSDANIIKIIAGIAELYMNNSRYDVTSSLTKLLLKALLGPFRLLDSLLTTYAALA 384 (822)
T ss_pred ccchHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Confidence 34555555 589999999999999999999765 576665432 24556677777777788999999999
Q ss_pred HHHhc-CCchHHHHHHHHHHHHHHHHHHhCC-----hhhhhhhHHHHHHHHhhhhccHHHHHHHHHHHhhCCCCCcHHHH
Q 008379 79 AVVNT-KFTAVGELLLKRIVLQLKRAYKRND-----KPQLLAAVKFIAHLVNQQVAHEIIALELLTILLENPTDDSVEVA 152 (568)
Q Consensus 79 a~ln~-~~pe~G~lll~rlv~~F~~~~~~~d-----k~~~~n~i~fIa~Lyn~~Vv~~~lildii~~LLe~~te~sVE~l 152 (568)
+.+++ .+.+||++|++..|+.|.+.|+... .+.|.|++.|+||||||++|+|.+|||||+.|.+++|+.+||++
T Consensus 385 ~~l~~~vg~eigahf~q~~ve~f~~~~~~~~~~~~~~K~~~Nl~~~l~ylynF~ivs~~LiydiI~kl~~~l~e~~ve~l 464 (822)
T KOG2141|consen 385 AMLHTMVGNEIGAHFLQTFVEDFLKSYKEEEEMDLKDKSLNNIVLFLSYLYNFGIVSCSLIYDIIRKLAENLNETNVEAL 464 (822)
T ss_pred HHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHhhcccHHHHHHHHHHHHhchhhhhHHHH
Confidence 99997 6889999999999999999998532 46799999999999999999999999999999999999999999
Q ss_pred HHHHHHHhHhhccCChhHHHHHHHHHHHHhhcCC---CChhHHHHHHHHHHHHHhccCCCCCCCCCccccccccceeeee
Q 008379 153 VGFVKECGSILQDLSPKGLHGIFERFRGILHEGE---IDKRVQFLIEGLFAIRKAKFQGYPAVRPELDLVDIEDQLTHEI 229 (568)
Q Consensus 153 l~lLr~~G~~Lr~~~p~~lk~I~~~l~~il~e~~---is~R~~fmIE~l~~lr~nk~k~~~~i~~~ldlve~~~~~th~i 229 (568)
+.++..||+.||++||.++++|+..++..+.... ++.|++||+|++.+|+||+.++.|...++. |+...+++.-+
T Consensus 465 l~ii~~~G~~LRkDDp~alk~~i~eiq~~a~~a~~s~~~pR~rFmleti~aLKnN~~kki~~~d~e~--ve~lrk~~k~l 542 (822)
T KOG2141|consen 465 LTIIANCGFSLRKDDPLALKDIITEIQSKAASAKISAISPRLRFMLETISALKNNKLKKIPYADPER--VENLRKLKKAL 542 (822)
T ss_pred HHHHHHccchhcCCChHHHHHHHHHHHHHhhcCCccccchHHHHHHHHHHHHhcCCCcCCCcCChHH--HHHHHHHHHHH
Confidence 9999999999999999999999999998776543 478999999999999999999888776653 44333333222
Q ss_pred eccCcCCccccCCcccCCcccccchHHHHhhhhcccCCCCCCcCCCC--C-CCCCCCCchhhhhhhhHHHhhhhhhhhcc
Q 008379 230 SLQDEIDPEITLDIFKPDPNFLDNEKRYEDMKKDLLGETSEDEEGSD--A-GSGDEDDSEEEEEEEDEEQMKIKDETETN 306 (568)
Q Consensus 230 ~l~~~~~~e~~l~~f~~D~~~~~~e~~~~~~k~~ilG~~~~~~~~~~--~-~~~~~~~~~~~~~~~~~~~~~i~d~t~~n 306 (568)
.-.....+..+|.|..-|. ...-+.|||||||++|.+..... . ...+............++++++|++|+||
T Consensus 543 ~~~~~s~~~~~l~vTledl-----l~ae~kGrWWlVGsaw~g~~~~~~s~~~~~d~~~~k~~~gs~~~kmL~lArkqrMN 617 (822)
T KOG2141|consen 543 GSSASSSVSLPLSVTLEDL-----LHAEQKGRWWLVGSAWRGNEQFMGSINTASDSAKSKKAEGSFADKMLELARKQRMN 617 (822)
T ss_pred HhccchhhhccccccHHHh-----hChHhcCceEEecchhcCCcccccccchHhHHhhhhcccCCccHHHHHHHHHhhcc
Confidence 1111233334444543332 22335799999999998643211 0 00000000011122456788999999999
Q ss_pred hhhhhhhhhhhhhcCCCHHHHHHHHHcccCCCCcchHHHHHHHHhhcccCcchhhHHHHHHHHhhccHhhHHHHHHHHHH
Q 008379 307 LVNLRRTIYLTIMSSVDFEEAGHKLLKIKLEPGQEMELCIMLLECCSQERTYLRYYGLLGQRFCMINKVHQENFEKCFVQ 386 (568)
Q Consensus 307 ~t~~RR~Ifl~IMSS~d~~eA~hKLlkL~lk~~qe~EI~~vli~Cc~qEktYn~yY~llaerlC~~~~~~~~~f~~~f~~ 386 (568)
|++||+|||+||||.||.|||+|||||.||++|+|||++||||||++|++||||||+||.|||.+++.|+.+||++|||
T Consensus 618 -TdiRr~IFcsImsaeDyiDAFEklLkL~LK~~Q~rEI~~VllhC~l~EK~yNpfYa~lA~KfCe~~~~~~~tfQF~~WD 696 (822)
T KOG2141|consen 618 -TDIRRAIFCSIMSAEDYIDAFEKLLKLSLKGKQEREIARVLLHCCLNEKTYNPFYALLALKFCEFNKNLKKTFQFALWD 696 (822)
T ss_pred -hHhhhhheeeeecchHHHHHHHHHHhccCCCcchHHHHHHHHHHHhhhcccchHHHHHHHHHHHHhhhhHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhhhcCchhhHHHHHHHHHHHHhcCCcCcccccccccCCcccCchHHHHHHHHHHHHH
Q 008379 387 QYSMIHRLETNKLRNVAKFFAHLLGTHALPWHVLAYIRLTEEDTTSSSRIFIKILFQELS 446 (568)
Q Consensus 387 ~y~~i~~le~~klrNlakf~ahLl~~~~l~l~vLk~i~l~e~dttss~riFik~LfqeL~ 446 (568)
.|+.++.+.+.+++|+|+|||||+.+.++|++|||+|+|.+. ++....|++.+|..|+
T Consensus 697 ~f~ele~ls~~ri~nLa~l~a~Li~~~~lsLtVLK~Vdfm~l--~~~~~~fl~~~l~~l~ 754 (822)
T KOG2141|consen 697 RFKELEQLSLFRISNLAKLLASLISNAVLSLTVLKHVDFMEL--NARRTTFLKKLLFGLI 754 (822)
T ss_pred HHHHhhhcchhhHhHHHHHHHHHHHhcccceeeeeeccHhhc--ChHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999965 4566778887776663
No 3
>smart00543 MIF4G Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)
Probab=99.94 E-value=2.7e-26 Score=221.71 Aligned_cols=183 Identities=34% Similarity=0.530 Sum_probs=168.3
Q ss_pred HHHHHHhhcCChhhHHHHHHHHHHhhhhhh--hhHHHHHHhhhccCCCChHHHHHHHHHHHhcCCchHHHHHHHHHHHHH
Q 008379 23 KSINGLVNKVNATNIKNIIPELFAENLIRG--RGLFCRSCMKSQMASPGFTDVFAALVAVVNTKFTAVGELLLKRIVLQL 100 (568)
Q Consensus 23 k~I~gllNKLs~~Ni~~i~~eL~~~Ni~rg--rgll~~si~~~q~~~~~f~~vyAaLva~ln~~~pe~G~lll~rlv~~F 100 (568)
++++|++||||++|+..++.+|...+...+ +..+++.+++.+...|.++++||+||+.+|...|+||+.++++++..|
T Consensus 2 ~~v~~~lnkLs~~n~~~~~~~l~~~~~~~~~~~~~l~~~i~~~~~~~~~~~~~ya~L~~~l~~~~~~f~~~ll~~~~~~f 81 (200)
T smart00543 2 KKVKGLINKLSPSNFESIIKELLKLNNSDKNLRKYILELIFEKAVEEPNFIPAYARLCALLNAKNPDFGSLLLERLQEEF 81 (200)
T ss_pred hHHHHHHhhCCHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 689999999999999999999987765433 567888899988889999999999999999999999999999999999
Q ss_pred HH---HHHhCChhhhhhhHHHHHHHHhhhhccHHHHHHHHHHHhhCCCC-------CcHHHHHHHHHHHhHhhc-cCChh
Q 008379 101 KR---AYKRNDKPQLLAAVKFIAHLVNQQVAHEIIALELLTILLENPTD-------DSVEVAVGFVKECGSILQ-DLSPK 169 (568)
Q Consensus 101 ~~---~~~~~dk~~~~n~i~fIa~Lyn~~Vv~~~lildii~~LLe~~te-------~sVE~ll~lLr~~G~~Lr-~~~p~ 169 (568)
+. .....++.++.++++|||+||+++|+++.++++++..|+..+++ .+||+++.+|++||..|. .++|.
T Consensus 82 ~~~~e~~~~~~~~~~~~~i~fl~eL~~~~~i~~~~i~~~l~~ll~~~~~~~~~~~~~~ve~l~~lL~~~G~~l~~~~~~~ 161 (200)
T smart00543 82 EKGLESEEESDKQRRLGLVRFLGELYNFQVLTSKIILELLKELLNDLTKLDPPRSDFSVECLLSLLPTCGKDLEREKSPK 161 (200)
T ss_pred HHHHHHHHHHhhhhHHhHHHHHHHHHHcccCcHHHHHHHHHHHHhccCCCCCCCcHHHHHHHHHHHHHhhHHHcCcccHH
Confidence 98 55556778899999999999999999999999999999998776 799999999999999999 89999
Q ss_pred HHHHHHHHHHHHhhcC---CCChhHHHHHHHHHHHHHhc
Q 008379 170 GLHGIFERFRGILHEG---EIDKRVQFLIEGLFAIRKAK 205 (568)
Q Consensus 170 ~lk~I~~~l~~il~e~---~is~R~~fmIE~l~~lr~nk 205 (568)
.++.+++.++.....+ .++.|++||+++++++|+++
T Consensus 162 ~~~~~l~~l~~~~~~~~~~~~~~r~~~~l~~l~~l~~~~ 200 (200)
T smart00543 162 LLDEILERLQDYLLKKDKTELSSRLRFMLELLIELRKNK 200 (200)
T ss_pred HHHHHHHHHHHHHhcccccCCChHHHHHHHHHHHHhhCc
Confidence 9999999999988776 68999999999999999874
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=99.94 E-value=4.4e-26 Score=220.30 Aligned_cols=183 Identities=28% Similarity=0.530 Sum_probs=167.2
Q ss_pred HHHHHHhhcCChhhHHHHHHHHHHhhhhh---hhhHHHHHHhhhccCCCChHHHHHHHHHHHhcCCc-hHHHHHHHHHHH
Q 008379 23 KSINGLVNKVNATNIKNIIPELFAENLIR---GRGLFCRSCMKSQMASPGFTDVFAALVAVVNTKFT-AVGELLLKRIVL 98 (568)
Q Consensus 23 k~I~gllNKLs~~Ni~~i~~eL~~~Ni~r---grgll~~si~~~q~~~~~f~~vyAaLva~ln~~~p-e~G~lll~rlv~ 98 (568)
|+|+|++||||++|+..++.++...+... ....+++.|+..+...|.++++||+||+.|+...| +||..++++++.
T Consensus 2 r~v~~~lnklt~~n~~~~~~~l~~~~~~~~~~~~~~i~~~i~~~a~~~~~~~~~~a~l~~~l~~~~~~~f~~~ll~~~~~ 81 (209)
T PF02854_consen 2 RKVRGILNKLTPSNFESIIDELIKLNWSDDPETLKEIVKLIFEKAVEEPNFSPLYARLCAALNSRFPSEFRSLLLNRCQE 81 (209)
T ss_dssp HHHHHHHHHCSSTTHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHSGGGHHHHHHHHHHHHHHCHHHHHHHHHHHHHH
T ss_pred chHHHHHHHCCHHHHHHHHHHHHHHHhhccHHHHHHHHHHHhhhhhcCchHHHHHHHHHHHHhccchhhHHHHHHHHHHH
Confidence 78999999999999999999997665543 45678888998888899999999999999999999 999999999999
Q ss_pred HHHH--------HHHhCChhhhhhhHHHHHHHHhhhhccHHHHHHHHHHHhhCCCC--------CcHHHHHHHHHHHhHh
Q 008379 99 QLKR--------AYKRNDKPQLLAAVKFIAHLVNQQVAHEIIALELLTILLENPTD--------DSVEVAVGFVKECGSI 162 (568)
Q Consensus 99 ~F~~--------~~~~~dk~~~~n~i~fIa~Lyn~~Vv~~~lildii~~LLe~~te--------~sVE~ll~lLr~~G~~ 162 (568)
.|.. ......+.+..+.++|||+||+++|+++.++++++..|+...++ .+||++|.+|++||+.
T Consensus 82 ~f~~~~~~~~~~~~~~~~~~~~~~~~~fl~eL~~~~vv~~~~i~~~l~~ll~~~~~~~~~~~~~~~ie~~~~lL~~~G~~ 161 (209)
T PF02854_consen 82 EFEERYSNEELEENRQSSKQRRRGNIRFLAELFNFGVVSEKIIFDILRELLSDGTDECQPPPDEENIECLCTLLKTCGKK 161 (209)
T ss_dssp HHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHTSHHCCHHTCHHHHHHHHHHHHHHHHH
T ss_pred HHHHhhhhhhHHHHHHHHHHHHhhhhhHHHhhHhhccccchhHHHHHHHHHhcccccccCCCcHhHHHHHHHHHHHHHHH
Confidence 9999 33444567899999999999999999999999999999987766 8999999999999999
Q ss_pred hc--cCChhHHHHHHHHHHHHhhc---CCCChhHHHHHHHHHHHHHhc
Q 008379 163 LQ--DLSPKGLHGIFERFRGILHE---GEIDKRVQFLIEGLFAIRKAK 205 (568)
Q Consensus 163 Lr--~~~p~~lk~I~~~l~~il~e---~~is~R~~fmIE~l~~lr~nk 205 (568)
|+ ...|..++.+|+.++..... +.++.|++||+++++++|+||
T Consensus 162 l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~r~~~~l~~l~~lr~~~ 209 (209)
T PF02854_consen 162 LENSEESPKALDEIFERLQKYANSKKDPNLSSRIRFMLEDLIELRNNK 209 (209)
T ss_dssp HHHCHHHHHHHHHHHHHHHHHHHHCHSSSSSHHHHHHHHHHHHHHHTC
T ss_pred HhcCCCchhHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHHHHHhcCC
Confidence 99 88999999999999998877 789999999999999999986
No 5
>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=99.77 E-value=7.3e-19 Score=156.40 Aligned_cols=106 Identities=39% Similarity=0.610 Sum_probs=101.4
Q ss_pred hhhhhhhhhhcCC---CHHHHHHHHHcccCCCCcchHHHHHHHHhhcccC-cchhhHHHHHHHHhhccHhhHHHHHHHHH
Q 008379 310 LRRTIYLTIMSSV---DFEEAGHKLLKIKLEPGQEMELCIMLLECCSQER-TYLRYYGLLGQRFCMINKVHQENFEKCFV 385 (568)
Q Consensus 310 ~RR~Ifl~IMSS~---d~~eA~hKLlkL~lk~~qe~EI~~vli~Cc~qEk-tYn~yY~llaerlC~~~~~~~~~f~~~f~ 385 (568)
+||+||.+||++. |++||+++|.+|+++ .+.+++|.++|+||++++ +|++||+.|+++||+.+..++..|+.+||
T Consensus 1 ~~k~i~~~l~ey~~~~D~~ea~~~l~~L~~~-~~~~~vv~~~i~~~le~~~~~~~~~~~Ll~~L~~~~~~~~~~~~~~f~ 79 (113)
T smart00544 1 LKKKIFLIIEEYLSSGDTDEAVHCLLELKLP-EQHHEVVKVLLTCALEEKRTYREMYSVLLSRLCQANVISTKQFEKGFW 79 (113)
T ss_pred ChhHHHHHHHHHHHcCCHHHHHHHHHHhCCC-cchHHHHHHHHHHHHcCCccHHHHHHHHHHHHHHcCCcCHHHHHHHHH
Confidence 5899999998877 999999999999998 799999999999999995 89999999999999999999999999999
Q ss_pred HHhhhhhcCch---hhHHHHHHHHHHHHhcCCcC
Q 008379 386 QQYSMIHRLET---NKLRNVAKFFAHLLGTHALP 416 (568)
Q Consensus 386 ~~y~~i~~le~---~klrNlakf~ahLl~~~~l~ 416 (568)
+.++.++.++. +...|+|+|+|++++.|.||
T Consensus 80 ~~~~~l~dl~~D~P~a~~~la~~~a~~v~~~~l~ 113 (113)
T smart00544 80 RLLEDIEDLELDIPNAWRNLAEFVARLISDGILP 113 (113)
T ss_pred HHHhhChhhhcccccHHHHHHHHHHHHHHcCCCC
Confidence 99999999986 89999999999999999987
No 6
>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=99.68 E-value=5.4e-17 Score=144.17 Aligned_cols=106 Identities=31% Similarity=0.545 Sum_probs=98.6
Q ss_pred hhhhhhhhhhcCC---CHHHHHHHHHcccCCCCcchHHHHHHHHhhccc-CcchhhHHHHHHHHhhccHhhHHHHHHHHH
Q 008379 310 LRRTIYLTIMSSV---DFEEAGHKLLKIKLEPGQEMELCIMLLECCSQE-RTYLRYYGLLGQRFCMINKVHQENFEKCFV 385 (568)
Q Consensus 310 ~RR~Ifl~IMSS~---d~~eA~hKLlkL~lk~~qe~EI~~vli~Cc~qE-ktYn~yY~llaerlC~~~~~~~~~f~~~f~ 385 (568)
+||+||.+||+.. |++||++.|.+|+++ .+.+++|.++|+||+++ ++|++||+.|+.+||..+...+..|+.+||
T Consensus 1 ~rk~i~~~l~ey~~~~d~~ea~~~l~el~~~-~~~~~vv~~~l~~~le~~~~~r~~~~~Ll~~L~~~~~~~~~~~~~gf~ 79 (113)
T PF02847_consen 1 LRKKIFSILMEYFSSGDVDEAVECLKELKLP-SQHHEVVKVILECALEEKKSYREYYSKLLSHLCKRKLISKEQFQEGFE 79 (113)
T ss_dssp HHHHHHHHHHHHHHHT-HHHHHHHHHHTT-G-GGHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHTTSS-HHHHHHHHH
T ss_pred ChHHHHHHHHHHhcCCCHHHHHHHHHHhCCC-ccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHhcCCCCHHHHHHHHH
Confidence 6899999999999 999999999999999 99999999999999999 899999999999999999999999999999
Q ss_pred HHhhhhhcCchh---hHHHHHHHHHHHHhcCCcC
Q 008379 386 QQYSMIHRLETN---KLRNVAKFFAHLLGTHALP 416 (568)
Q Consensus 386 ~~y~~i~~le~~---klrNlakf~ahLl~~~~l~ 416 (568)
+.++.++.+... ...|+|+|+||++..|+||
T Consensus 80 ~~l~~l~Dl~~D~P~~~~~la~~~~~~i~~~~lp 113 (113)
T PF02847_consen 80 DLLESLEDLELDIPKAPEYLAKFLARLIADGILP 113 (113)
T ss_dssp HHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTSS-
T ss_pred HHHhHhhhccccchHHHHHHHHHHHHHHHcCCcC
Confidence 999999988765 9999999999999999997
No 7
>KOG0401 consensus Translation initiation factor 4F, ribosome/mRNA-bridging subunit (eIF-4G) [Translation, ribosomal structure and biogenesis]
Probab=99.38 E-value=9.9e-13 Score=154.74 Aligned_cols=199 Identities=19% Similarity=0.327 Sum_probs=162.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHhhcCChhhHHHHHHHHHHhhhhhh--hhHHHHHHhhhccCCCChHHHHHHHHHHHhc--C
Q 008379 9 SSAEYQRLTWDALRKSINGLVNKVNATNIKNIIPELFAENLIRG--RGLFCRSCMKSQMASPGFTDVFAALVAVVNT--K 84 (568)
Q Consensus 9 ~s~e~qr~~w~~Lkk~I~gllNKLs~~Ni~~i~~eL~~~Ni~rg--rgll~~si~~~q~~~~~f~~vyAaLva~ln~--~ 84 (568)
..+..+-..=+.+.++|++++||+++.++...+.++...++... -+-.+..|+..+..+|+|+..||.||..++. .
T Consensus 337 ~~~~~~~~~~~el~~~vrsilnkltp~~~~~l~~q~~~~~i~t~~~l~~vi~~vfdkAi~EP~f~~~yA~lc~~l~~~~~ 416 (970)
T KOG0401|consen 337 GAERKDVELKEELAKRVRSLLNKLTPERKELLIEQLIELNVDTDDALKEVIELVFDKAINEPTFCAMYARLCFDLEGPPS 416 (970)
T ss_pred ccccchhHHHHHHHHHHhhhcCCCchHHHHHHHHHHHhhccCcHHHHhHHHHHHHHhhhcccccchhcchhcccccCCcc
Confidence 34445556677899999999999999999999998875554332 1234445666677899999999999987766 1
Q ss_pred C---------chHHHHHHHHHHHHHHHHH--H-----h----CC------------hhhhhhhHHHHHHHHhhhhccHHH
Q 008379 85 F---------TAVGELLLKRIVLQLKRAY--K-----R----ND------------KPQLLAAVKFIAHLVNQQVAHEII 132 (568)
Q Consensus 85 ~---------pe~G~lll~rlv~~F~~~~--~-----~----~d------------k~~~~n~i~fIa~Lyn~~Vv~~~l 132 (568)
. +.|-.++|.+|...|...- . . .+ +++.++.++||++||..+|+.+.+
T Consensus 417 ~~~~~~~~~~~~fr~~lL~rcq~~fe~~~~~~~~~~~~~~~~~~~e~~le~~k~~~~~rtlgn~~~ig~l~~~~ml~e~i 496 (970)
T KOG0401|consen 417 EPELDMGGDEINFRRLLLNRCQKEFEGEDDKIADEYSEAEEPDELEEELEEEKYILRRRTLGNFRFIGELFKLKMLTEKI 496 (970)
T ss_pred CCCcCCCCCcccHHHHHHHHhHHHhhcccHHHHHHhhhhcCchhHHHHHHhccceecCCccchHHHHHHHHHHHHHHHHH
Confidence 2 3577899999999887543 1 0 11 257789999999999999999999
Q ss_pred HHHHHHHHhhC--CCCCcHHHHHHHHHHHhHhhcc--CChhHHHHHHHHHHHHhhcCCCChhHHHHHHHHHHHHHhccC
Q 008379 133 ALELLTILLEN--PTDDSVEVAVGFVKECGSILQD--LSPKGLHGIFERFRGILHEGEIDKRVQFLIEGLFAIRKAKFQ 207 (568)
Q Consensus 133 ildii~~LLe~--~te~sVE~ll~lLr~~G~~Lr~--~~p~~lk~I~~~l~~il~e~~is~R~~fmIE~l~~lr~nk~k 207 (568)
++.|+..||.. +.+.++||+|.|+.++|..|.. .+|..+..+|...+.......++.|++||+..++++|.++|.
T Consensus 497 ~~~~v~~Ll~~~~~~ee~ie~lc~f~~tig~~lD~~~~s~r~md~~~~~~k~~~~~~~~s~r~RfM~~~~idlR~~~w~ 575 (970)
T KOG0401|consen 497 VHACVQKLLSDDQPSEESIECLCRFLTTIGKKLDFSKESPRNMDEYFNSMKNLKRKPQRSNRIRFMLQSVIDLRKSGWG 575 (970)
T ss_pred HHHHHHHhhccccccchhhhhHHhhhhcccccccccCcccchhHHHHHHHHHhhhhhhhccchhhhhcccccccccccc
Confidence 99999999998 7899999999999999999975 455667888899988888888999999999999999999993
No 8
>KOG2051 consensus Nonsense-mediated mRNA decay 2 protein [RNA processing and modification]
Probab=99.36 E-value=1e-11 Score=141.27 Aligned_cols=183 Identities=17% Similarity=0.261 Sum_probs=146.2
Q ss_pred HHHHHHHHhhcCChhh----HHHHHHHHHH-hhhhhhhhHHHHHHhhhccCCCChHHHHHHHHHHHhcCCchHHHHHHHH
Q 008379 21 LRKSINGLVNKVNATN----IKNIIPELFA-ENLIRGRGLFCRSCMKSQMASPGFTDVFAALVAVVNTKFTAVGELLLKR 95 (568)
Q Consensus 21 Lkk~I~gllNKLs~~N----i~~i~~eL~~-~Ni~rgrgll~~si~~~q~~~~~f~~vyAaLva~ln~~~pe~G~lll~r 95 (568)
++-++.+.+-+|...= |.....+.+. .|-...|.-+++.++..++.+-.+.|.|+.|||.|+...|+|...|+..
T Consensus 423 ~~~~~d~Fl~~L~~~vsrdliD~~a~ef~~nlNtKa~RkrLvKal~~vprt~ldllPyYsRlVAtl~~~M~dvat~lv~~ 502 (1128)
T KOG2051|consen 423 VVSNVDCFLLDLPNCVSRDLIDQAAIEFCSNLNTKANRKRLVKALFVVPRTRLDLLPYYSRLVATLSKCMPDVATELVTM 502 (1128)
T ss_pred HHHHHHHHHccCcchHHHHHHHHHHHHHHHHhccHHHHHHHHHhhhcccchhhhhhhHHHHHHHHHHhhhhHHHHHHHHH
Confidence 3445555555554433 4444445544 5555567788888888877777899999999999999999999999999
Q ss_pred HHHHHHHHHHhCChhh---hhhhHHHHHHHHhhhhccHHHHHHHHHHHhhCCCCCcHHHHHHHHHHHhHhhccCChhHH-
Q 008379 96 IVLQLKRAYKRNDKPQ---LLAAVKFIAHLVNQQVAHEIIALELLTILLENPTDDSVEVAVGFVKECGSILQDLSPKGL- 171 (568)
Q Consensus 96 lv~~F~~~~~~~dk~~---~~n~i~fIa~Lyn~~Vv~~~lildii~~LLe~~te~sVE~ll~lLr~~G~~Lr~~~p~~l- 171 (568)
+-..|+.+..+++... -.-+++|||+|++||+++.-.+|.|++.|+..++.++||++|.+|..||.+|-....+.+
T Consensus 503 L~~eFr~~~hkK~q~~ietk~~~VrfIsEL~KF~lv~~~~if~cLk~ll~dF~~hnIEm~c~lLE~~GrfLlr~pEt~lr 582 (1128)
T KOG2051|consen 503 LRKEFRSHLHKKAQINIETKLKIVRFISELCKFQLVPKFEIFSCLKMLLNDFTHHNIEMACVLLESCGRFLLRSPETKLR 582 (1128)
T ss_pred HHHHHHHHHhhhhhhhhhhhhhhhhhHHhhhhhCccChHHHHHHHHHHHHhcccccHHHHHHHHHhcchhhhcChhHHHH
Confidence 9999999988776543 234589999999999999999999999999999999999999999999999866544443
Q ss_pred -HHHHHHHHHHhhcCCCChhHHHHHHHHHHHHH
Q 008379 172 -HGIFERFRGILHEGEIDKRVQFLIEGLFAIRK 203 (568)
Q Consensus 172 -k~I~~~l~~il~e~~is~R~~fmIE~l~~lr~ 203 (568)
+..++.++..-....+++|.+-+||..+-+.+
T Consensus 583 M~~~Le~i~rkK~a~~lDsr~~~~iENay~~~~ 615 (1128)
T KOG2051|consen 583 MRVFLEQIKRKKRASALDSRQATLIENAYYLCN 615 (1128)
T ss_pred HHHHHHHHHHHHHHhhhchHHHHHHHHhHHhcc
Confidence 34778887665666789999999999887765
No 9
>KOG1104 consensus Nuclear cap-binding complex, subunit NCBP1/CBP80 [RNA processing and modification]
Probab=99.22 E-value=3.3e-08 Score=110.15 Aligned_cols=405 Identities=19% Similarity=0.283 Sum_probs=259.8
Q ss_pred HHHHHHHHHHHHHHhhcCC-------hhhHHHHHHHHHH--hhhhhhhhHHHHHHhhhccCCCChHHHHHHHHHHHhcCC
Q 008379 15 RLTWDALRKSINGLVNKVN-------ATNIKNIIPELFA--ENLIRGRGLFCRSCMKSQMASPGFTDVFAALVAVVNTKF 85 (568)
Q Consensus 15 r~~w~~Lkk~I~gllNKLs-------~~Ni~~i~~eL~~--~Ni~rgrgll~~si~~~q~~~~~f~~vyAaLva~ln~~~ 85 (568)
--.|+.+.+.|.+.+-++. ++|++..+.-|-. .| -+.-+.+.+.......|.-.++||.||.++|.+-
T Consensus 21 ~~~~e~l~krl~~~i~~vg~~s~ss~e~~l~~l~~~l~~~~~~---~~~~iL~~L~~ca~~lP~K~~~yaTLvgllN~kn 97 (759)
T KOG1104|consen 21 ISPAETLEKRLESLIREVGEPSGSSVEDNLENLVAVLEADLEN---FKSKILDILNTCAVYLPEKITAYATLVGLLNLKN 97 (759)
T ss_pred CCcHHHHHHHHHHHHHhhcCCCCCcHHHhHHHHHHHHHhhHHH---HHHHHHHHHHHHHHHcccchhHHHHHHHHHhccc
Confidence 3468999999999999999 4566666554321 11 1112223333334457899999999999999999
Q ss_pred chHHHHHHHHHHHHHHHHHHhCChhhhhhhHHHHHHHHhhhhccHHHHHHHHHHHhhCCCCC---------cHHHHHHHH
Q 008379 86 TAVGELLLKRIVLQLKRAYKRNDKPQLLAAVKFIAHLVNQQVAHEIIALELLTILLENPTDD---------SVEVAVGFV 156 (568)
Q Consensus 86 pe~G~lll~rlv~~F~~~~~~~dk~~~~n~i~fIa~Lyn~~Vv~~~lildii~~LLe~~te~---------sVE~ll~lL 156 (568)
++||+.++...+.+|....+..++..|.++++|++-|+|.+|+...-+..++..|++...+. -+-+++.-|
T Consensus 98 ~~fg~~~v~~~~~~~q~sl~~~~~n~ar~llrfL~dL~~~~vl~~~sli~l~esl~~~~~e~~~Pqvr~D~~v~~vLs~l 177 (759)
T KOG1104|consen 98 FNFGGEFVEYMIEELQESLKSGNWNEARYLLRFLSDLSNCHVLQADSLINLFESLLDAAIEENVPQVRRDYYVYCVLSSL 177 (759)
T ss_pred hhhHHHHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHhcCCccChHHHHHHHHHHHHHHHhhcCcchhhhHHHHHHHhcc
Confidence 99999999999999999999999999999999999999999999999999999999753333 356888889
Q ss_pred HHHhHhhccCChhHHHHHHHHHHHHhhc-------------CCCC----hhHHHHHHHHHHHHHhccCCCCCCCCCcccc
Q 008379 157 KECGSILQDLSPKGLHGIFERFRGILHE-------------GEID----KRVQFLIEGLFAIRKAKFQGYPAVRPELDLV 219 (568)
Q Consensus 157 r~~G~~Lr~~~p~~lk~I~~~l~~il~e-------------~~is----~R~~fmIE~l~~lr~nk~k~~~~i~~~ldlv 219 (568)
.+.|+.|.+.-|++++.|+..++.-+.- |.-+ .=+.-+...|-.+|.|+|...-.-.|.+..
T Consensus 178 Pw~g~el~e~~~~~~e~ll~~ie~Yl~~R~~shi~lL~vw~~~~~~~qeeyle~L~~qI~~lr~n~w~e~hIprPy~~F- 256 (759)
T KOG1104|consen 178 PWFGRELNEKKPTEMEELLVYIEIYLKKRKKSHINLLNVWSGEPDHPQEEYLELLWAQIQKLRQNDWAENHIPRPYLGF- 256 (759)
T ss_pred chhhhhhcccchHHHHHHHHHHHHHHHHhcccccchhhcCCCCCCchHHHHHHHHHHHHHHHHhcCcccccCCCchhhH-
Confidence 9999999999999999998877643211 1111 224456666777899999853222233321
Q ss_pred ccccceeeeee--ccC-cCCccc-------c---CCcccCCcccccchHHHHhhhhcccCCCCCCcCCCCCCCCCCCCch
Q 008379 220 DIEDQLTHEIS--LQD-EIDPEI-------T---LDIFKPDPNFLDNEKRYEDMKKDLLGETSEDEEGSDAGSGDEDDSE 286 (568)
Q Consensus 220 e~~~~~th~i~--l~~-~~~~e~-------~---l~~f~~D~~~~~~e~~~~~~k~~ilG~~~~~~~~~~~~~~~~~~~~ 286 (568)
++..+|... |-. ...|.+ + -++|.++. .| .+...-.++ ..
T Consensus 257 --es~L~~~~~h~Lp~~~~pph~~~~~yp~p~v~fR~f~~~~----------------~~--~e~p~mp~~-------ss 309 (759)
T KOG1104|consen 257 --ESTLVHALQHNLPSFVSPPHTEDSEYPMPRVVFRMFQYTD----------------CG--FEIPTMPGA-------SS 309 (759)
T ss_pred --HHHHHHhcccCCCCCCCCCCcccccCCcchhhhhcccccc----------------cC--CCCCCCCCc-------hh
Confidence 222233210 100 001111 0 11111110 01 000000000 00
Q ss_pred hhhhhhhHHHhhhhhhhhcchhhhhhhhhhhhhcCCCHHHHHHHHHcccCCCC---cchHHHHHHHHhh--cccCcchh-
Q 008379 287 EEEEEEDEEQMKIKDETETNLVNLRRTIYLTIMSSVDFEEAGHKLLKIKLEPG---QEMELCIMLLECC--SQERTYLR- 360 (568)
Q Consensus 287 ~~~~~~~~~~~~i~d~t~~n~t~~RR~Ifl~IMSS~d~~eA~hKLlkL~lk~~---qe~EI~~vli~Cc--~qEktYn~- 360 (568)
.+-.-.++....|....+-| =.||+.-|+-+..+.. -|-=|+.+|+-=. +.-.+|.+
T Consensus 310 i~rflfe~~i~dii~sl~fn-----------------RKecA~~l~~l~~~f~~~p~eylivEtIfgell~LP~~~~~~i 372 (759)
T KOG1104|consen 310 IERFLFEEIILDIIESLEFN-----------------RKECARQLLSLPVKFKAIPIEYLIVETIFGELLRLPTPPYKTI 372 (759)
T ss_pred HHHHHHHHHHHHHHHHhhhh-----------------HHHHHHHHHcCcccccCccHHHHHHHHHHHHHhcCCCCCCchH
Confidence 01111112223333333333 2578888888877655 2333555554322 34567877
Q ss_pred hHHHHHHHHhhcc-HhhHHHHHHHHHHHhhhhhcCchhhHHHHHHHHHHHHhcCCcCc--ccccc-cccCCcccCchHHH
Q 008379 361 YYGLLGQRFCMIN-KVHQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLLGTHALPW--HVLAY-IRLTEEDTTSSSRI 436 (568)
Q Consensus 361 yY~llaerlC~~~-~~~~~~f~~~f~~~y~~i~~le~~klrNlakf~ahLl~~~~l~l--~vLk~-i~l~e~dttss~ri 436 (568)
||+.|.--||+.. +.+-..|-.++.-.|..++.+++.-+.-+---|.|-++.--..| +-|.. +.+ +--++.+.
T Consensus 373 yy~slLiElCK~~P~~lpqV~aqa~r~lY~rldsm~~~c~dR~idWFShHLSNF~F~w~W~eW~~~l~~---d~~~pk~~ 449 (759)
T KOG1104|consen 373 YYTSLLIELCKLQPKALPQVLAQAVRILYMRLDSMDTECFDRFIDWFSHHLSNFQFRWKWNEWADCLGL---DFEHPKPN 449 (759)
T ss_pred HHHHHHHHHHHhCccchhHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHhccCcceechhhhhhhcCC---CCcCcchh
Confidence 9999999999997 56899999999999999999999877777778899998877755 44533 333 23356799
Q ss_pred HHHHHHHHHHHHHchHHHHhhcCCcchhhhhhccCCCCC
Q 008379 437 FIKILFQELSEHLGIRLLNERLTDPTMQDSFESIFPRDN 475 (568)
Q Consensus 437 Fik~LfqeL~~~lg~~~l~~rl~d~~~~~~~~glfp~d~ 475 (568)
|++-++|.=.. +.. ..|..| .+-..+..+-|.+.
T Consensus 450 Fvreviqkelr---Lsy-~~rI~d-slP~~~~~l~P~~~ 483 (759)
T KOG1104|consen 450 FVREVIQKELR---LSY-YQRIKD-SLPTLLAKLLPPPP 483 (759)
T ss_pred HHHHHHHHHHH---HHH-HHHHHH-hhhHHHHHhCCCCC
Confidence 99888774221 222 334433 12256777777554
No 10
>KOG2051 consensus Nonsense-mediated mRNA decay 2 protein [RNA processing and modification]
Probab=98.24 E-value=1.9e-05 Score=91.19 Aligned_cols=185 Identities=12% Similarity=0.204 Sum_probs=126.1
Q ss_pred HHHHHHHHhhcCChhhHHHHHHHHHHhhhhhhhhHHHHHHhhhccCCCChHHHHHHHHHHHhcCCchHHHHHHHHHHHHH
Q 008379 21 LRKSINGLVNKVNATNIKNIIPELFAENLIRGRGLFCRSCMKSQMASPGFTDVFAALVAVVNTKFTAVGELLLKRIVLQL 100 (568)
Q Consensus 21 Lkk~I~gllNKLs~~Ni~~i~~eL~~~Ni~rgrgll~~si~~~q~~~~~f~~vyAaLva~ln~~~pe~G~lll~rlv~~F 100 (568)
+|.-|..=|+|.|..++...++-|--..+ --...+.+.+++.-...-+-.+..|.|+|.|...-|+||-++|..+.+..
T Consensus 634 iR~Li~~dL~k~tvd~~lkllRkl~W~D~-e~~~yli~~~~k~w~iky~~i~~lA~llaGL~~y~~~fvi~VID~vlE~I 712 (1128)
T KOG2051|consen 634 IRYLIRSDLSKDTVDRVLKLLRKLDWSDP-EVKQYLISCFSKPWKIKYQNIHALASLLAGLSSYHPEFVIHVIDHVLEDI 712 (1128)
T ss_pred HHHHHHHHhccccHHHHHHHHHhcccccH-HHHHHHHHHhhhhhccccccHHHHHHHHHHHHhhchhhhhhhHHHHHHHH
Confidence 66666666667666665555554410000 01244555555554444455677889999999999999999999999999
Q ss_pred HHHHHhCC---hhhhhhhHHHHHHHHhhhhccHHHHHHHHHHHhh--CCCC------------CcHHHHHHHHHHHhHhh
Q 008379 101 KRAYKRND---KPQLLAAVKFIAHLVNQQVAHEIIALELLTILLE--NPTD------------DSVEVAVGFVKECGSIL 163 (568)
Q Consensus 101 ~~~~~~~d---k~~~~n~i~fIa~Lyn~~Vv~~~lildii~~LLe--~~te------------~sVE~ll~lLr~~G~~L 163 (568)
+.+..-|+ +..+.+.++|||+||||.++++.+|+..|-.++- .+++ .-|-++|.+|.+||++.
T Consensus 713 r~glEin~~~~nQrriA~aryL~ELynfemvds~vIl~tLy~~i~~g~~~~~~~~~ldppddlFRirlV~~lL~tc~~yf 792 (1128)
T KOG2051|consen 713 RPGLEINDYVSNQRRIALARYLGELYNFEMVDSDVILNTLYHLISLGHFENLTPSALDPPDDLFRIRLVCMLLQTCGPYF 792 (1128)
T ss_pred HhhhhcCcHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHhcccccCCCCcccCCChHHHHHHHHHHHHHHHccccc
Confidence 99988776 3578999999999999999999999999987763 2222 14779999999999976
Q ss_pred -ccCChhHHHHHHHHHHHHhh-cC-CCChhHHHHHHHHHHHHHhcc
Q 008379 164 -QDLSPKGLHGIFERFRGILH-EG-EIDKRVQFLIEGLFAIRKAKF 206 (568)
Q Consensus 164 -r~~~p~~lk~I~~~l~~il~-e~-~is~R~~fmIE~l~~lr~nk~ 206 (568)
+.....-++.++--++.-.- .+ ..+--..|+.++.+...+-+.
T Consensus 793 ~rgs~kkkl~~fL~~fq~Y~~iKk~~~Pld~~~~f~d~~~~~rp~~ 838 (1128)
T KOG2051|consen 793 TRGSTKKKLDQFLVAFQRYILIKKSQQPLDMEYEFEDFLELVRPEM 838 (1128)
T ss_pred ccchhHHHHHHHHHHHHHHhhcccccCCCchhhhHHhhhhhccccc
Confidence 44455666666665654321 11 134445566666665544433
No 11
>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=96.62 E-value=0.0058 Score=58.68 Aligned_cols=99 Identities=13% Similarity=0.178 Sum_probs=79.1
Q ss_pred cCCCHHHHHHHHHcccCCC--CcchHHHHHHHHhhcccCcchhhHHHHHHHHhhccH-hhHHHHHHHHHHHhhh------
Q 008379 320 SSVDFEEAGHKLLKIKLEP--GQEMELCIMLLECCSQERTYLRYYGLLGQRFCMINK-VHQENFEKCFVQQYSM------ 390 (568)
Q Consensus 320 SS~d~~eA~hKLlkL~lk~--~qe~EI~~vli~Cc~qEktYn~yY~llaerlC~~~~-~~~~~f~~~f~~~y~~------ 390 (568)
|..+++....-|.++.... ..-..|++.|++|+..+..|.|+||.+...++.... .|...+-..+...|..
T Consensus 12 t~~n~~~~~~~l~~~~~~~~~~~~~~i~~~i~~~a~~~~~~~~~~a~l~~~l~~~~~~~f~~~ll~~~~~~f~~~~~~~~ 91 (209)
T PF02854_consen 12 TPSNFESIIDELIKLNWSDDPETLKEIVKLIFEKAVEEPNFSPLYARLCAALNSRFPSEFRSLLLNRCQEEFEERYSNEE 91 (209)
T ss_dssp SSTTHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHSGGGHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHT-HHH
T ss_pred CHHHHHHHHHHHHHHHhhccHHHHHHHHHHHhhhhhcCchHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHhhhhhh
Confidence 4677888888888876654 345689999999999999999999999999998888 7877776666666655
Q ss_pred ---hhcCchhhHHHHHHHHHHHHhcCCcCcc
Q 008379 391 ---IHRLETNKLRNVAKFFAHLLGTHALPWH 418 (568)
Q Consensus 391 ---i~~le~~klrNlakf~ahLl~~~~l~l~ 418 (568)
-.....++.++..+|+|+|+..+.++-.
T Consensus 92 ~~~~~~~~~~~~~~~~~fl~eL~~~~vv~~~ 122 (209)
T PF02854_consen 92 LEENRQSSKQRRRGNIRFLAELFNFGVVSEK 122 (209)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHTTSSCHH
T ss_pred HHHHHHHHHHHHhhhhhHHHhhHhhccccch
Confidence 2233446899999999999999976654
No 12
>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=95.36 E-value=0.051 Score=52.08 Aligned_cols=97 Identities=13% Similarity=0.188 Sum_probs=75.0
Q ss_pred CCHHHHHHHHHcccCCC-CcchHHHHHHHHhhcccCcchhhHHHHHHHHhhccHhhHHHHHHHHHHHhhh----hhcCch
Q 008379 322 VDFEEAGHKLLKIKLEP-GQEMELCIMLLECCSQERTYLRYYGLLGQRFCMINKVHQENFEKCFVQQYSM----IHRLET 396 (568)
Q Consensus 322 ~d~~eA~hKLlkL~lk~-~qe~EI~~vli~Cc~qEktYn~yY~llaerlC~~~~~~~~~f~~~f~~~y~~----i~~le~ 396 (568)
.+++..+.-|.++.... ..-..++..+++|+..+..|-|+||.++..+......|...+-..+...|.. -+.-..
T Consensus 14 ~n~~~~~~~l~~~~~~~~~~~~~l~~~i~~~~~~~~~~~~~ya~L~~~l~~~~~~f~~~ll~~~~~~f~~~~e~~~~~~~ 93 (200)
T smart00543 14 SNFESIIKELLKLNNSDKNLRKYILELIFEKAVEEPNFIPAYARLCALLNAKNPDFGSLLLERLQEEFEKGLESEEESDK 93 (200)
T ss_pred HHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 45666667777766553 3446799999999999999999999999999988877776666666665544 233445
Q ss_pred hhHHHHHHHHHHHHhcCCcCcc
Q 008379 397 NKLRNVAKFFAHLLGTHALPWH 418 (568)
Q Consensus 397 ~klrNlakf~ahLl~~~~l~l~ 418 (568)
++.+++.+|+|+|+..+.++-.
T Consensus 94 ~~~~~~i~fl~eL~~~~~i~~~ 115 (200)
T smart00543 94 QRRLGLVRFLGELYNFQVLTSK 115 (200)
T ss_pred hhHHhHHHHHHHHHHcccCcHH
Confidence 7899999999999999987754
No 13
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=94.55 E-value=0.024 Score=63.62 Aligned_cols=16 Identities=25% Similarity=0.438 Sum_probs=8.7
Q ss_pred hHHHhcCchhhhHHHH
Q 008379 484 NFFTSIGLGGITENLR 499 (568)
Q Consensus 484 nfft~IgLg~lt~~~R 499 (568)
-|.|-+-|-.|.+-.|
T Consensus 1191 pflthvtlrrlrdvar 1206 (1463)
T PHA03308 1191 PFLTHVTLRRLRDVAR 1206 (1463)
T ss_pred chhhhhhHHHHHHHHH
Confidence 3555555655555444
No 14
>PF09088 MIF4G_like: MIF4G like; InterPro: IPR015172 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 1", and is found in nuclear cap-binding proteins and eIF4G. 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.; GO: 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A.
Probab=94.48 E-value=0.38 Score=47.06 Aligned_cols=87 Identities=15% Similarity=0.315 Sum_probs=67.8
Q ss_pred hHHHHHHHHhhccH-hhHHHHHHHHHHHhhhhhcCchhhHHHHHHHHHHHHhcCCcCcccccccccCCcccCchHHHHHH
Q 008379 361 YYGLLGQRFCMINK-VHQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLLGTHALPWHVLAYIRLTEEDTTSSSRIFIK 439 (568)
Q Consensus 361 yY~llaerlC~~~~-~~~~~f~~~f~~~y~~i~~le~~klrNlakf~ahLl~~~~l~l~vLk~i~l~e~dttss~riFik 439 (568)
||+-|.--+|+..+ .+-..|..++.-.|+.++.++..-.+.++-.|+|-++.-...|.==..++-.+.+...+.++|++
T Consensus 91 yY~sllielCk~~P~~i~pv~~~air~ly~~l~~md~e~~~Rf~dWfS~hLSNF~f~W~W~eW~~~~~l~~~~pk~~Fi~ 170 (191)
T PF09088_consen 91 YYHSLLIELCKLSPSAIPPVLGRAIRFLYRNLDSMDFELRDRFVDWFSHHLSNFGFQWKWDEWVDDLELPPLHPKRVFIR 170 (191)
T ss_dssp HHHHHHHHHHHHSTTTHHHHHHHHHHHHHHGGGGB-HHHHHHHHHHHHHHHHTTTT---GGGGGGGTTS-TTSHHHHHHH
T ss_pred HHHHHHHHHHHhCHHHHHHHHHHHHHHHHHhhhhcCHHHHHHHHHHHHHHHhcCCceeeHHHhhhhhhCCccCCHHHHHH
Confidence 99999999999984 68899999999999999999999999999999999999888775212233334444467899999
Q ss_pred HHHHHHHH
Q 008379 440 ILFQELSE 447 (568)
Q Consensus 440 ~LfqeL~~ 447 (568)
-++...+.
T Consensus 171 ~~l~k~iR 178 (191)
T PF09088_consen 171 EVLEKEIR 178 (191)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHh
Confidence 99876544
No 15
>PF10500 SR-25: Nuclear RNA-splicing-associated protein; InterPro: IPR019532 SR-25, otherwise known as ADP-ribosylation factor-like factor 6-interacting protein 4, is expressed in virtually all tissue types. At the N terminus there is a repeat of serine-arginine (SR repeat), and towards the middle of the protein there are clusters of both serines and of basic amino acids. The presence of many nuclear localisation signals strongly implies that this is a nuclear protein that may contribute to RNA splicing []. SR-25 is also implicated, along with heat-shock-protein-27, as a mediator in the Rac1 (GTPase ras-related C3 botulinum toxin substrate 1; also see IPR019093 from INTERPRO) signalling pathway [].
Probab=94.48 E-value=0.025 Score=55.80 Aligned_cols=6 Identities=50% Similarity=0.495 Sum_probs=2.2
Q ss_pred Ccccch
Q 008379 551 SSDESN 556 (568)
Q Consensus 551 ~~~~~~ 556 (568)
+.++..
T Consensus 80 ~~~~k~ 85 (225)
T PF10500_consen 80 SSKEKR 85 (225)
T ss_pred ccchhh
Confidence 333333
No 16
>KOG3942 consensus MIF4G domain-containing protein [Translation, ribosomal structure and biogenesis]
Probab=94.33 E-value=0.42 Score=49.46 Aligned_cols=138 Identities=16% Similarity=0.109 Sum_probs=86.6
Q ss_pred ChHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHh------CChhhhhhhHHHHHHHHhhh-----hccHHHHHHHH
Q 008379 69 GFTDVFAALVAVVNTKFTAVGELLLKRIVLQLKRAYKR------NDKPQLLAAVKFIAHLVNQQ-----VAHEIIALELL 137 (568)
Q Consensus 69 ~f~~vyAaLva~ln~~~pe~G~lll~rlv~~F~~~~~~------~dk~~~~n~i~fIa~Lyn~~-----Vv~~~lildii 137 (568)
.|.-.-+.||+-+.. .+..|..|+..++...++.|.- .+...+...+.|+++||-.- ++=..+++.|+
T Consensus 183 ~ggl~v~klC~n~~~-~~~~gt~f~~~Lln~lrq~f~~r~gl~s~~~~rw~~fisfltelf~nlgs~p~~vL~~~l~~cl 261 (348)
T KOG3942|consen 183 GGGLFVCKLCTNLGS-SWRNGTQFMDELLNLLRQGFLLRTGLSSLASCRWWRFISFLTELFDNLGSCPQVVLQRSLRLCL 261 (348)
T ss_pred CCchhHHHHhhhhhh-hhhccchHHHHHHHHHHHhhccchhccchhHHHHHHHHHHHHHHHhhcCCCChhhHHHHHHHHH
Confidence 343334556655543 2344555555555555555542 23467889999999999753 44455688899
Q ss_pred HHHhhCCC--CCcHHHHHHHHHHHhHhhccCChhHHHHHHHHHHHHh-hcCCCChhHHHHHHHHHHHHHhccC
Q 008379 138 TILLENPT--DDSVEVAVGFVKECGSILQDLSPKGLHGIFERFRGIL-HEGEIDKRVQFLIEGLFAIRKAKFQ 207 (568)
Q Consensus 138 ~~LLe~~t--e~sVE~ll~lLr~~G~~Lr~~~p~~lk~I~~~l~~il-~e~~is~R~~fmIE~l~~lr~nk~k 207 (568)
+.|+..|. ++.+||+.-.|...|.-|.+--|..+-.++...++.+ .-++----.+-|+=.++.+..+.|+
T Consensus 262 ~~llrspd~~~~e~ecl~~~L~~~g~dle~qlP~ql~lL~~s~rDafL~~sep~a~~r~~lllliel~As~wq 334 (348)
T KOG3942|consen 262 QILLRSPDWPEFEYECLSMKLAVEGLDLEKQLPFQLLLLFPSRRDAFLVRSEPLAPWRCPLLLLIELPASAWQ 334 (348)
T ss_pred HHHccCCCcchHHHHHHHHHHHHcCccchhhhhHHHHHHHHHHHHhhhccccccccccchhhhccccCccccC
Confidence 99998764 5688888889999998888877777777776666543 2222111123344455555555554
No 17
>PF07817 GLE1: GLE1-like protein; InterPro: IPR012476 The members of this family are sequences that are similar to the human protein GLE1 (O75458 from SWISSPROT). This protein is localised at the nuclear pore complexes and functions in poly(A)+ RNA export to the cytoplasm []. ; GO: 0016973 poly(A)+ mRNA export from nucleus, 0005643 nuclear pore; PDB: 3PEV_B 3RRN_B 3PEU_B 3RRM_B.
Probab=93.53 E-value=1 Score=46.07 Aligned_cols=162 Identities=15% Similarity=0.261 Sum_probs=96.2
Q ss_pred HHHHHHHHHHHHHHhhcCChhh--HHHHHHHHHHh------------hhhh----h----hhHHHHHHhhhc----cCCC
Q 008379 15 RLTWDALRKSINGLVNKVNATN--IKNIIPELFAE------------NLIR----G----RGLFCRSCMKSQ----MASP 68 (568)
Q Consensus 15 r~~w~~Lkk~I~gllNKLs~~N--i~~i~~eL~~~------------Ni~r----g----rgll~~si~~~q----~~~~ 68 (568)
+..+..+||.|+..+|.||.++ +..++.+|... .... + -..|++.++... ...|
T Consensus 23 Kk~~~~~kr~I~~~vgQls~~~~qi~~i~~~i~~ll~~~~~~~~~~~~~~~~~~~~~~~~l~~lAk~iv~Q~e~ev~~~~ 102 (256)
T PF07817_consen 23 KKLRFDLKRKINPKVGQLSNSSSQINRIINQISNLLSGQPVKSNDLQQSKNDHPLAYKYLLNFLAKKIVSQAETEVSANP 102 (256)
T ss_dssp HHHHHHHHHHHCCHHHC--SBHHHHHHHHHHHHHH----------HHTTTT-SHHHHHHHHHHHHHHHHHHHHHHHHH-G
T ss_pred HHHHHHhhhhCcCcHhhccCcHHHHHHHHHHHHHHhhhhhhchhhhhhhccCCchHHHHHHHHHHHHHHHHHHHHhccCC
Confidence 4567899999999999999876 45555555322 0011 1 124455554321 1245
Q ss_pred ChHHHHHHHHHHHhcCCchHHHHHHHHHHHH----------HH---------H--HHHhCCh---------hhhhhhHHH
Q 008379 69 GFTDVFAALVAVVNTKFTAVGELLLKRIVLQ----------LK---------R--AYKRNDK---------PQLLAAVKF 118 (568)
Q Consensus 69 ~f~~vyAaLva~ln~~~pe~G~lll~rlv~~----------F~---------~--~~~~~dk---------~~~~n~i~f 118 (568)
...-.+|.+++.|-..+|+||.+|+.+++.. |. + +|++++. ++..+++++
T Consensus 103 ~~A~PlA~v~~~l~~~~p~~~dillA~l~k~Cp~~vP~~~~~~~~~~~e~~~k~lGyk~~~~~~E~~~~y~~Rm~Gi~~l 182 (256)
T PF07817_consen 103 ESAFPLARVAVQLWSQHPEFGDILLARLHKKCPYLVPKYPGFTCDQSTEEYRKRLGYKRDDGGWESEDQYLKRMTGIIRL 182 (256)
T ss_dssp GGHHHHHHHHHHHHHHSTCHHHHHHHHHHHH-GGGG----T-----SSHHHHHHTT--B-TTSB--HHHHHHHHHHHHHH
T ss_pred chhhhHHHHHHHHHHcCCcHHHHHHHHHHHcCceeEeecCcccCCCCHHHHHHHcCCccCCCCccchHHHHHHHHHHHHH
Confidence 5666789988888888999999998887633 11 1 1333321 467788888
Q ss_pred HHHHHhhhh---------ccHHHHHHHHHHHhhCCC--CCcHHHHHHHHHHHhHhhccCChhHHHHHHH
Q 008379 119 IAHLVNQQV---------AHEIIALELLTILLENPT--DDSVEVAVGFVKECGSILQDLSPKGLHGIFE 176 (568)
Q Consensus 119 Ia~Lyn~~V---------v~~~lildii~~LLe~~t--e~sVE~ll~lLr~~G~~Lr~~~p~~lk~I~~ 176 (568)
-|.+.--.. ..-...-..+..++..+. +-...++..+|+.+|..|...=......++.
T Consensus 183 yaAi~~~~~~~~~~~~~p~~~~~~W~wlAr~lN~~p~~~~~~~lL~~~Le~ag~~l~~~Yg~Qf~Kll~ 251 (256)
T PF07817_consen 183 YAAIIQTPPPKGQKTSNPHGLEHGWRWLARILNLPPAPNITATLLHSFLEVAGFRLLQIYGRQFVKLLQ 251 (256)
T ss_dssp HHHHHHS---CCCCTT-SS-THHHHHHHHHHHCS-CC-HHHHHHHHHHHHHHHHHHHHHHTHHHHHHHH
T ss_pred HHHHHhccCCcCCCCCCCCCcHHHHHHHHHHhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 777764322 222334666777776544 3456788999999999987654444444433
No 18
>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]
Probab=92.88 E-value=0.082 Score=58.11 Aligned_cols=36 Identities=17% Similarity=0.141 Sum_probs=20.5
Q ss_pred HHHHHHHHHhhCCCCCcHHHHHHHHHHHhHhhccCChhH
Q 008379 132 IALELLTILLENPTDDSVEVAVGFVKECGSILQDLSPKG 170 (568)
Q Consensus 132 lildii~~LLe~~te~sVE~ll~lLr~~G~~Lr~~~p~~ 170 (568)
.|++=++..|. +..++--+..+-++-++.|++.-.+
T Consensus 316 ~IfErlR~ILh---e~Eld~rvqy~iEtlf~iRkdkfk~ 351 (739)
T KOG2140|consen 316 GIFERLRYILH---EGELDRRVQYMIETLFQIRKDKFKS 351 (739)
T ss_pred HHHHHHHHHHh---HhhHHHHHHHHHHHHHHHHHHhhcc
Confidence 36666665554 2335556666666666666654333
No 19
>KOG2297 consensus Predicted translation factor, contains W2 domain [Translation, ribosomal structure and biogenesis]
Probab=92.29 E-value=0.84 Score=47.58 Aligned_cols=140 Identities=24% Similarity=0.249 Sum_probs=94.8
Q ss_pred HHHHHHHHhhccHhhHHHHHHHHHHHhhhhhcCchhhHHHHHHHHHHHHhcCCcCcccccccccCCcccCchHHHHHHHH
Q 008379 362 YGLLGQRFCMINKVHQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLLGTHALPWHVLAYIRLTEEDTTSSSRIFIKIL 441 (568)
Q Consensus 362 Y~llaerlC~~~~~~~~~f~~~f~~~y~~i~~le~~klrNlakf~ahLl~~~~l~l~vLk~i~l~e~dttss~riFik~L 441 (568)
|+.+.++|....+-.-..|+.-.+...--+..|+++--.-||.|-|-|++.|.+|=+||..+.=...-.---.--|.--|
T Consensus 110 ~~qvf~KliRRykyLeK~fE~e~~k~Llflk~F~e~Er~KLA~~Tal~l~nGt~~~tvl~~L~~d~LVkeGi~l~F~~~l 189 (412)
T KOG2297|consen 110 SVQVFQKLIRRYKYLEKNFENEMRKFLLFLKLFEENERKKLAMLTALLLSNGTLPATVLQSLLNDNLVKEGIALSFAVKL 189 (412)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHhhHHHHhHHHHHHHHH
Confidence 34444555443333334566656666666788999988999999999999999999999775322111111123488889
Q ss_pred HHHHHHHHchHHHHhhcCCcchhhhhhccCCCCCCCCceehhhHHHhcCchhhhHHHHHHH
Q 008379 442 FQELSEHLGIRLLNERLTDPTMQDSFESIFPRDNPKNTRFAINFFTSIGLGGITENLREYL 502 (568)
Q Consensus 442 fqeL~~~lg~~~l~~rl~d~~~~~~~~glfp~d~~~~~rfsinfft~IgLg~lt~~~R~~l 502 (568)
|++...+=+|..|-.-|.--.+-.-+--+||- |......---|||--||-.|.+=.|...
T Consensus 190 Fk~~~~Ek~i~~lis~Lrkg~md~rLmeffPp-nkrs~E~Fak~Ft~agL~elvey~~~q~ 249 (412)
T KOG2297|consen 190 FKEWLVEKDINDLISSLRKGKMDDRLMEFFPP-NKRSVEHFAKYFTDAGLKELVEYHRNQQ 249 (412)
T ss_pred HHHHHhhccHHHHHHHHHhcChHhHHHHhcCC-cchhHHHHHHHHhHhhHHHHHHHHHHHH
Confidence 99999888888877766555555555577884 3333445557899999999988666543
No 20
>KOG2130 consensus Phosphatidylserine-specific receptor PtdSerR, contains JmjC domain [Chromatin structure and dynamics; Signal transduction mechanisms]
Probab=91.85 E-value=0.24 Score=51.40 Aligned_cols=14 Identities=29% Similarity=0.479 Sum_probs=8.0
Q ss_pred HHHHHHHHHhCChh
Q 008379 97 VLQLKRAYKRNDKP 110 (568)
Q Consensus 97 v~~F~~~~~~~dk~ 110 (568)
|++|.+.|.+..|.
T Consensus 64 veeF~~~ferp~kP 77 (407)
T KOG2130|consen 64 VEEFIERFERPYKP 77 (407)
T ss_pred HHHHHHHhcccCCc
Confidence 45566666665554
No 21
>KOG2412 consensus Nuclear-export-signal (NES)-containing protein/polyadenylated-RNA export factor [RNA processing and modification]
Probab=91.62 E-value=4.1 Score=45.39 Aligned_cols=180 Identities=19% Similarity=0.328 Sum_probs=100.0
Q ss_pred HHHHHHHHHhhcCChhh---HHHHHHHHH---Hhhh--hhh--h----hHHHHHHhhhc----cCCCChHHHHHHHHHHH
Q 008379 20 ALRKSINGLVNKVNATN---IKNIIPELF---AENL--IRG--R----GLFCRSCMKSQ----MASPGFTDVFAALVAVV 81 (568)
Q Consensus 20 ~Lkk~I~gllNKLs~~N---i~~i~~eL~---~~Ni--~rg--r----gll~~si~~~q----~~~~~f~~vyAaLva~l 81 (568)
.++|.|+--++-+|.+| |..|...|. +.-. ... + ..||.+++... +..|.-.--+|.+|-.|
T Consensus 337 ~~kr~in~~~~qis~~~~q~L~qI~dkl~s~~~~~~~~~~pl~~~~~~~~iaka~V~Q~Etev~~~PeaAfPla~V~l~i 416 (591)
T KOG2412|consen 337 SLKRAINPPFSQISKSNGQVLRQIFDKLDSLFGGIPDIVDPLAYDWCLNFIAKAFVKQAETEVASKPEAAFPLAKVILYI 416 (591)
T ss_pred HHHhhcCCChhhhhhccHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHhCCcccchHHHHHHHH
Confidence 46666665555555554 555555553 2111 111 1 34555555332 22332222357788889
Q ss_pred hcCCchHHHHHHHHHHHH---------------HHH--HHHhCCh----------hhhhhhHHHHHHHHhhhh-------
Q 008379 82 NTKFTAVGELLLKRIVLQ---------------LKR--AYKRNDK----------PQLLAAVKFIAHLVNQQV------- 127 (568)
Q Consensus 82 n~~~pe~G~lll~rlv~~---------------F~~--~~~~~dk----------~~~~n~i~fIa~Lyn~~V------- 127 (568)
++.+|+||.+|+.+++.. +.+ +|+++|. .+..+++++-|-++..+.
T Consensus 417 ~~q~Pdv~dlllA~l~KkCP~~VPf~~~~~~Eq~~k~mGyk~~d~nk~Eqnd~YleRm~Gi~rLYAAIi~l~~p~~~~~~ 496 (591)
T KOG2412|consen 417 WSQFPDVGDLLLARLHKKCPYVVPFHIVNSTEQYQKMMGYKAWDSNKWEQNDAYLERMDGIMRLYAAIIQLDIPVGNATN 496 (591)
T ss_pred HHhCchHHHHHHHHHHhcCCccccccccCcHHHHHHhhcccccccccccccchHHHHhHhHHHHHHHHHHhcccccCCCC
Confidence 999999999999998632 222 3455443 467788888887766655
Q ss_pred ccH---HHHHHHHHHHhhC-CC-CCcHHHHHHHHHHHhHhhccC-ChhHHHHH---HHHHHHHhhcCCC--ChhHHHHHH
Q 008379 128 AHE---IIALELLTILLEN-PT-DDSVEVAVGFVKECGSILQDL-SPKGLHGI---FERFRGILHEGEI--DKRVQFLIE 196 (568)
Q Consensus 128 v~~---~lildii~~LLe~-~t-e~sVE~ll~lLr~~G~~Lr~~-~p~~lk~I---~~~l~~il~e~~i--s~R~~fmIE 196 (568)
+|+ .+-.-.+..++.. |. +-..-++-.+|.+||..|... -.+..|.+ .+.+-.-+..++- +.|++-+++
T Consensus 497 ~hpf~i~~gW~wLA~iln~~p~~~~tatll~s~Lq~aG~~L~q~Yg~Qf~Klli~i~E~y~~r~~a~~~~g~~rl~ill~ 576 (591)
T KOG2412|consen 497 VHPFGINHGWAWLARILNKIPLLDTTATLLNSFLQTAGFGLLQRYGSQFLKLLILIREHYLPRLAAKKDTGDLRLRILLE 576 (591)
T ss_pred CCcchhhcccHHHHHHhCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchHHHHHHH
Confidence 231 1122334444543 22 233446668999999998554 44555543 2222222333322 368888888
Q ss_pred HHH
Q 008379 197 GLF 199 (568)
Q Consensus 197 ~l~ 199 (568)
..+
T Consensus 577 ~~l 579 (591)
T KOG2412|consen 577 AWL 579 (591)
T ss_pred HHH
Confidence 876
No 22
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=89.99 E-value=0.2 Score=56.70 Aligned_cols=19 Identities=26% Similarity=0.415 Sum_probs=11.7
Q ss_pred hHHHHHHHHHHHHhcCCcC
Q 008379 398 KLRNVAKFFAHLLGTHALP 416 (568)
Q Consensus 398 klrNlakf~ahLl~~~~l~ 416 (568)
..+--|-.+|.|...-++|
T Consensus 1019 ~f~eraya~aal~grac~p 1037 (1463)
T PHA03308 1019 EFLERAYAYAALCGRACMP 1037 (1463)
T ss_pred hHHHHHHHHHHhhccccCC
Confidence 4555566666777666665
No 23
>KOG2130 consensus Phosphatidylserine-specific receptor PtdSerR, contains JmjC domain [Chromatin structure and dynamics; Signal transduction mechanisms]
Probab=87.35 E-value=0.29 Score=50.75 Aligned_cols=16 Identities=25% Similarity=0.337 Sum_probs=8.2
Q ss_pred CCCcchHHHHHHHHhh
Q 008379 337 EPGQEMELCIMLLECC 352 (568)
Q Consensus 337 k~~qe~EI~~vli~Cc 352 (568)
+++.-++.++|-.+--
T Consensus 218 Pp~~p~~lvkv~~~e~ 233 (407)
T KOG2130|consen 218 PPGTPPELVKVTVDEG 233 (407)
T ss_pred CCCCCCCceeeccccc
Confidence 4455555555555443
No 24
>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=79.08 E-value=5.3 Score=37.15 Aligned_cols=97 Identities=15% Similarity=0.295 Sum_probs=66.2
Q ss_pred hhHHHHHHHHhhhhccHHHHHHHHHHHhhCCCCC----cHHHHHHHHHHHhHhhccCChhHHHHHHHHHHHHhhc----C
Q 008379 114 AAVKFIAHLVNQQVAHEIIALELLTILLENPTDD----SVEVAVGFVKECGSILQDLSPKGLHGIFERFRGILHE----G 185 (568)
Q Consensus 114 n~i~fIa~Lyn~~Vv~~~lildii~~LLe~~te~----sVE~ll~lLr~~G~~Lr~~~p~~lk~I~~~l~~il~e----~ 185 (568)
..+.-||.++|.+-.....+...|..-|..++.. .+.++-.++++||...... -+-+.+++.+-+++.. +
T Consensus 20 ~~ileicD~In~~~~~~k~a~rai~krl~~~n~~v~l~AL~LLe~~vkNCG~~fh~e--vas~~Fl~el~kl~~~k~~~~ 97 (139)
T cd03567 20 EAIQAFCEQINKEPEGPQLAVRLLAHKIQSPQEKEALQALTVLEACMKNCGERFHSE--VGKFRFLNELIKLVSPKYLGS 97 (139)
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCHHHHHH--HHhHHHHHHHHHHhccccCCC
Confidence 4667788888888777777777777777666543 3556667788899987532 1223444444444432 3
Q ss_pred CCChhHHHHHHHHHHHHHhccCCCCCC
Q 008379 186 EIDKRVQFLIEGLFAIRKAKFQGYPAV 212 (568)
Q Consensus 186 ~is~R~~fmIE~l~~lr~nk~k~~~~i 212 (568)
..+..|+-.|=.|+......|++.|.+
T Consensus 98 ~~~~~Vk~kil~li~~W~~~f~~~p~~ 124 (139)
T cd03567 98 RTSEKVKTKIIELLYSWTLELPHEPKI 124 (139)
T ss_pred CCCHHHHHHHHHHHHHHHHHhcccchH
Confidence 567889988888888888888876654
No 25
>PF05110 AF-4: AF-4 proto-oncoprotein; InterPro: IPR007797 This family consist of family member 1 (proto-oncogene AF4), family member 2 or FMR2 (Fragile X E mental retardation syndrome), family member 3 or LAF4 (lymphoid nuclear protein related to AF4) and family member 4 (protein lilliputian). Lilliputian is a Drosophila AF4 protein homologue which contains an AT-hook domain. It represents a novel pair-rule gene that acts in cytoskeleton regulation, segmentation and morphogenesis in Drosophila []. These proteins have been linked to Homo sapiens diseases such as acute lymphoblastic leukemia and mental retardation [].
Probab=77.52 E-value=1.6 Score=53.41 Aligned_cols=9 Identities=22% Similarity=0.608 Sum_probs=5.1
Q ss_pred CChhHHHHH
Q 008379 187 IDKRVQFLI 195 (568)
Q Consensus 187 is~R~~fmI 195 (568)
++.|+|-||
T Consensus 47 LssriQ~mL 55 (1191)
T PF05110_consen 47 LSSRIQNML 55 (1191)
T ss_pred HHHHHHHHh
Confidence 455665555
No 26
>PF05110 AF-4: AF-4 proto-oncoprotein; InterPro: IPR007797 This family consist of family member 1 (proto-oncogene AF4), family member 2 or FMR2 (Fragile X E mental retardation syndrome), family member 3 or LAF4 (lymphoid nuclear protein related to AF4) and family member 4 (protein lilliputian). Lilliputian is a Drosophila AF4 protein homologue which contains an AT-hook domain. It represents a novel pair-rule gene that acts in cytoskeleton regulation, segmentation and morphogenesis in Drosophila []. These proteins have been linked to Homo sapiens diseases such as acute lymphoblastic leukemia and mental retardation [].
Probab=72.89 E-value=3 Score=51.21 Aligned_cols=9 Identities=44% Similarity=0.615 Sum_probs=4.3
Q ss_pred HHHHcccCC
Q 008379 329 HKLLKIKLE 337 (568)
Q Consensus 329 hKLlkL~lk 337 (568)
-||-||.|+
T Consensus 306 ~kl~kl~ip 314 (1191)
T PF05110_consen 306 AKLTKLKIP 314 (1191)
T ss_pred cccCccccc
Confidence 345555543
No 27
>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=69.91 E-value=32 Score=31.96 Aligned_cols=94 Identities=16% Similarity=0.267 Sum_probs=63.2
Q ss_pred hhHHHHHHHHhhhhccHHHHHHHHHHHhhCCCCC----cHHHHHHHHHHHhHhhccCChhHHHHHHHHHHHHhhcCCCCh
Q 008379 114 AAVKFIAHLVNQQVAHEIIALELLTILLENPTDD----SVEVAVGFVKECGSILQDLSPKGLHGIFERFRGILHEGEIDK 189 (568)
Q Consensus 114 n~i~fIa~Lyn~~Vv~~~lildii~~LLe~~te~----sVE~ll~lLr~~G~~Lr~~~p~~lk~I~~~l~~il~e~~is~ 189 (568)
..+.-||.++|.+=....-+...|+.-|..++.. .++++=.++++||..+... -+=+.+++.|.+++.. ..+.
T Consensus 23 ~~ileicD~In~~~~~~k~a~ral~krl~~~n~~vql~AL~LLe~~vkNCG~~fh~e--vas~~fl~~l~~l~~~-~~~~ 99 (142)
T cd03569 23 ASILEICDMIRSKDVQPKYAMRALKKRLLSKNPNVQLYALLLLESCVKNCGTHFHDE--VASREFMDELKDLIKT-TKNE 99 (142)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHCCHHHHHH--HhhHHHHHHHHHHHcc-cCCH
Confidence 5667788999988777777777777767665443 4566667888999987642 2235566777776654 5677
Q ss_pred hHHHHHHHHHHHHHhccCCCC
Q 008379 190 RVQFLIEGLFAIRKAKFQGYP 210 (568)
Q Consensus 190 R~~fmIE~l~~lr~nk~k~~~ 210 (568)
+++-.+=.++.-....|++.|
T Consensus 100 ~Vk~kil~li~~W~~~f~~~~ 120 (142)
T cd03569 100 EVRQKILELIQAWALAFRNKP 120 (142)
T ss_pred HHHHHHHHHHHHHHHHhCCCc
Confidence 777655556555556666544
No 28
>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=69.67 E-value=30 Score=31.58 Aligned_cols=94 Identities=15% Similarity=0.112 Sum_probs=65.5
Q ss_pred hhHHHHHHHHhhhhccHHHHHHHHHHHhhCCCCC----cHHHHHHHHHHHhHhhccCChhHHHHHHHHHHHHhhcC-CCC
Q 008379 114 AAVKFIAHLVNQQVAHEIIALELLTILLENPTDD----SVEVAVGFVKECGSILQDLSPKGLHGIFERFRGILHEG-EID 188 (568)
Q Consensus 114 n~i~fIa~Lyn~~Vv~~~lildii~~LLe~~te~----sVE~ll~lLr~~G~~Lr~~~p~~lk~I~~~l~~il~e~-~is 188 (568)
..+.-||.++|.+-.....+...|+.-|..++.. .+.++=.++++||..+... -+-+..++.+.+++... ..+
T Consensus 19 ~~il~icd~I~~~~~~~k~a~raL~krl~~~n~~vql~AL~lLd~~vkNcg~~f~~~--i~s~~fl~~l~~l~~~~~~~~ 96 (133)
T cd03561 19 ALNLELCDLINLKPNGPKEAARAIRKKIKYGNPHVQLLALTLLELLVKNCGKPFHLQ--VADKEFLLELVKIAKNSPKYD 96 (133)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCChHHHHH--HhhHHHHHHHHHHhCCCCCCC
Confidence 5677899999999888888999888888776543 4556667778889866432 11145555566666554 677
Q ss_pred hhHHHHHHHHHHHHHhccCCC
Q 008379 189 KRVQFLIEGLFAIRKAKFQGY 209 (568)
Q Consensus 189 ~R~~fmIE~l~~lr~nk~k~~ 209 (568)
..++-.+-.++.-....|++.
T Consensus 97 ~~Vk~kil~ll~~W~~~f~~~ 117 (133)
T cd03561 97 PKVREKALELILAWSESFGGH 117 (133)
T ss_pred HHHHHHHHHHHHHHHHHhcCC
Confidence 788877777766666677654
No 29
>PF01602 Adaptin_N: Adaptin N terminal region; InterPro: IPR002553 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the N-terminal domain of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and from the beta and gamma subunits of various coatomer (COP) adaptors. This domain has a 2-layer alpha/alpha fold that forms a right-handed superhelix, and is a member of the ARM repeat superfamily []. The N-terminal region of the various AP adaptor proteins share strong sequence identity; by contrast, the C-terminal domains of different adaptins share similar structural folds, but have little sequence identity []. It has been proposed that the N-terminal domain interacts with another uniform component of the coated vesicles. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 1W63_C 2JKR_A 2JKT_A 2XA7_A 2VGL_B 3TJZ_E.
Probab=66.85 E-value=1.6e+02 Score=32.51 Aligned_cols=170 Identities=18% Similarity=0.234 Sum_probs=89.8
Q ss_pred HHHHHHhhcCChhhHHHHHHHHHHh--hhhhh--hhHHHHHHhhh-ccCCCChHHHHHHHHHHHhcCC------------
Q 008379 23 KSINGLVNKVNATNIKNIIPELFAE--NLIRG--RGLFCRSCMKS-QMASPGFTDVFAALVAVVNTKF------------ 85 (568)
Q Consensus 23 k~I~gllNKLs~~Ni~~i~~eL~~~--Ni~rg--rgll~~si~~~-q~~~~~f~~vyAaLva~ln~~~------------ 85 (568)
+.+.-+.+=.++.|+..|+.+|... +.-.+ +.-+++.|... ....+....+.-.++.++....
T Consensus 323 ~~l~lL~~l~~~~n~~~Il~eL~~~l~~~~d~~~~~~~i~~I~~la~~~~~~~~~~v~~l~~ll~~~~~~~~~~~~~~i~ 402 (526)
T PF01602_consen 323 KALDLLYKLANESNVKEILDELLKYLSELSDPDFRRELIKAIGDLAEKFPPDAEWYVDTLLKLLEISGDYVSNEIINVIR 402 (526)
T ss_dssp HHHHHHHHH--HHHHHHHHHHHHHHHHHC--HHHHHHHHHHHHHHHHHHGSSHHHHHHHHHHHHHCTGGGCHCHHHHHHH
T ss_pred HHHHHHhhcccccchhhHHHHHHHHHHhccchhhhhhHHHHHHHHHhccCchHHHHHHHHHHhhhhccccccchHHHHHH
Confidence 4456566667889999999998531 11011 11222222111 1112333333334444444332
Q ss_pred ------chHHHHHHHHHHHHHHHHHHhCChhhhhhhHHHHHHHHhhhhccHHHHHHHHHHHhhCCCCCcHHHHHHHHHHH
Q 008379 86 ------TAVGELLLKRIVLQLKRAYKRNDKPQLLAAVKFIAHLVNQQVAHEIIALELLTILLENPTDDSVEVAVGFVKEC 159 (568)
Q Consensus 86 ------pe~G~lll~rlv~~F~~~~~~~dk~~~~n~i~fIa~Lyn~~Vv~~~lildii~~LLe~~te~sVE~ll~lLr~~ 159 (568)
|+..+..+..++..+.. -.+......++-.||+....-.-.. .+.++++.+.+.+.+.+.++=+.++..+
T Consensus 403 ~ll~~~~~~~~~~l~~L~~~l~~---~~~~~~~~~~~wilGEy~~~~~~~~-~~~~~~~~l~~~~~~~~~~vk~~ilt~~ 478 (526)
T PF01602_consen 403 DLLSNNPELREKILKKLIELLED---ISSPEALAAAIWILGEYGELIENTE-SAPDILRSLIENFIEESPEVKLQILTAL 478 (526)
T ss_dssp HHHHHSTTTHHHHHHHHHHHHTS---SSSHHHHHHHHHHHHHHCHHHTTTT-HHHHHHHHHHHHHTTSHHHHHHHHHHHH
T ss_pred HHhhcChhhhHHHHHHHHHHHHH---hhHHHHHHHHHhhhcccCCcccccc-cHHHHHHHHHHhhccccHHHHHHHHHHH
Confidence 33333444444333322 1223344556666776444333224 7888888888888888888888888888
Q ss_pred hHhhccCChhHH-HHHHHHHHHHhh--cCC--CChhHHHHHH
Q 008379 160 GSILQDLSPKGL-HGIFERFRGILH--EGE--IDKRVQFLIE 196 (568)
Q Consensus 160 G~~Lr~~~p~~l-k~I~~~l~~il~--e~~--is~R~~fmIE 196 (568)
.+......+... +.+++.+..... ..+ +..|..|...
T Consensus 479 ~Kl~~~~~~~~~~~~i~~~~~~~~~~~s~~~evr~Ra~~y~~ 520 (526)
T PF01602_consen 479 AKLFKRNPENEVQNEILQFLLSLATEDSSDPEVRDRAREYLR 520 (526)
T ss_dssp HHHHHHSCSTTHHHHHHHHHHCHHHHS-SSHHHHHHHHHHHH
T ss_pred HHHHhhCCchhhHHHHHHHHHHHhccCCCCHHHHHHHHHHHH
Confidence 887766554333 477777776665 333 3455555443
No 30
>KOG3064 consensus RNA-binding nuclear protein (MAK16) containing a distinct C4 Zn-finger [RNA processing and modification]
Probab=65.34 E-value=3.3 Score=41.96 Aligned_cols=21 Identities=24% Similarity=0.327 Sum_probs=12.9
Q ss_pred hhhhhhhhcCCCHHHHHHHHH
Q 008379 312 RTIYLTIMSSVDFEEAGHKLL 332 (568)
Q Consensus 312 R~Ifl~IMSS~d~~eA~hKLl 332 (568)
|..|=-|.=|.+|+.|.+.|-
T Consensus 74 ~klwErikLSkNyekALeQId 94 (303)
T KOG3064|consen 74 RKLWERIKLSKNYEKALEQID 94 (303)
T ss_pred HHHHHHHhcchhHHHHHHHHH
Confidence 344444555777888777664
No 31
>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=64.64 E-value=53 Score=30.61 Aligned_cols=94 Identities=9% Similarity=0.178 Sum_probs=64.4
Q ss_pred hhHHHHHHHHhhhhccHHHHHHHHHHHhhCCCCC----cHHHHHHHHHHHhHhhccCChhHHHHHHHHHHHHhhcCCCCh
Q 008379 114 AAVKFIAHLVNQQVAHEIIALELLTILLENPTDD----SVEVAVGFVKECGSILQDLSPKGLHGIFERFRGILHEGEIDK 189 (568)
Q Consensus 114 n~i~fIa~Lyn~~Vv~~~lildii~~LLe~~te~----sVE~ll~lLr~~G~~Lr~~~p~~lk~I~~~l~~il~e~~is~ 189 (568)
..+.=||.++|.+-....-+...|+.-|...+.. .+.++-.++++||......- +=+.+++.|.+++... .+.
T Consensus 19 ~~il~icD~I~~~~~~~k~a~ral~KRl~~~n~~v~l~AL~LLe~~vkNCG~~fh~ev--ask~Fl~eL~kl~~~~-~~~ 95 (144)
T cd03568 19 GLILDVCDKVKSDENGAKDCLKAIMKRLNHKDPNVQLRALTLLDACAENCGKRFHQEV--ASRDFTQELKKLINDR-VHP 95 (144)
T ss_pred HHHHHHHHHHhcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHH--hhHHHHHHHHHHhccc-CCH
Confidence 4666788999988888887777777767665543 45566678888998765321 2346667777776654 566
Q ss_pred hHHHHHHHHHHHHHhccCCCC
Q 008379 190 RVQFLIEGLFAIRKAKFQGYP 210 (568)
Q Consensus 190 R~~fmIE~l~~lr~nk~k~~~ 210 (568)
.++-.|-.++.-....|++.|
T Consensus 96 ~Vk~kil~li~~W~~~f~~~~ 116 (144)
T cd03568 96 TVKEKLREVVKQWADEFKNDP 116 (144)
T ss_pred HHHHHHHHHHHHHHHHhCCCc
Confidence 777777777776666776544
No 32
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=62.62 E-value=72 Score=29.13 Aligned_cols=95 Identities=19% Similarity=0.164 Sum_probs=59.8
Q ss_pred hhHHHHHHHHhhhhccHHHHHHHHHHHhhCCCCC----cHHHHHHHHHHHhHhhccCChhHHHHHHHHHHHHhhcCCCCh
Q 008379 114 AAVKFIAHLVNQQVAHEIIALELLTILLENPTDD----SVEVAVGFVKECGSILQDLSPKGLHGIFERFRGILHEGEIDK 189 (568)
Q Consensus 114 n~i~fIa~Lyn~~Vv~~~lildii~~LLe~~te~----sVE~ll~lLr~~G~~Lr~~~p~~lk~I~~~l~~il~e~~is~ 189 (568)
..+.-||.++|.+-.....+...|+.=|..++.. .+.++=.++++||..+... -+-+.+++.|.+++.......
T Consensus 19 ~~~l~icD~i~~~~~~~k~a~r~l~krl~~~n~~v~l~AL~lLe~~vkNcg~~f~~e--v~s~~fl~~L~~l~~~~~~~~ 96 (133)
T smart00288 19 ELILEICDLINSTPDGPKDAVRLLKKRLNNKNPHVALLALTLLDACVKNCGSKFHLE--VASKEFLNELVKLIKPKYPLP 96 (133)
T ss_pred HHHHHHHHHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHH--HHhHHHHHHHHHHHcCCCCcH
Confidence 4667889999999888888888888777766654 4556667778889887532 123345566666655433333
Q ss_pred hHHHHHHHHHHHHHhccCCCC
Q 008379 190 RVQFLIEGLFAIRKAKFQGYP 210 (568)
Q Consensus 190 R~~fmIE~l~~lr~nk~k~~~ 210 (568)
.++-.+-.++.-....|++.|
T Consensus 97 ~Vk~kil~li~~W~~~f~~~~ 117 (133)
T smart00288 97 LVKKRILELIQEWADAFKNDP 117 (133)
T ss_pred HHHHHHHHHHHHHHHHHcCCC
Confidence 355444444444445555443
No 33
>KOG1824 consensus TATA-binding protein-interacting protein [General function prediction only]
Probab=62.62 E-value=2.7e+02 Score=33.95 Aligned_cols=39 Identities=31% Similarity=0.539 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHhhcCChhhHHHHHHHHHHhhhhhh
Q 008379 9 SSAEYQRLTWDALRKSINGLVNKVNATNIKNIIPELFAENLIRG 52 (568)
Q Consensus 9 ~s~e~qr~~w~~Lkk~I~gllNKLs~~Ni~~i~~eL~~~Ni~rg 52 (568)
.+.|.|-.+ -|-+--+++|+.+..++.++.+|.. |...|
T Consensus 59 ~ngEVQnlA----VKClg~lvsKvke~~le~~ve~L~~-~~~s~ 97 (1233)
T KOG1824|consen 59 KNGEVQNLA----VKCLGPLVSKVKEDQLETIVENLCS-NMLSG 97 (1233)
T ss_pred cCcHHHHHH----HHHHHHHHhhchHHHHHHHHHHHhh-hhccc
Confidence 445667542 3556668899999999999999863 43333
No 34
>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=59.45 E-value=1.1e+02 Score=26.49 Aligned_cols=105 Identities=11% Similarity=0.164 Sum_probs=52.8
Q ss_pred HHHHHHHHhhc-CChhhHHHHHHHHHHhhhhhhhhHHHHHHhhhccCC-CChHHHHHHHHHHHhcCCchHHHHHHHHHHH
Q 008379 21 LRKSINGLVNK-VNATNIKNIIPELFAENLIRGRGLFCRSCMKSQMAS-PGFTDVFAALVAVVNTKFTAVGELLLKRIVL 98 (568)
Q Consensus 21 Lkk~I~gllNK-Ls~~Ni~~i~~eL~~~Ni~rgrgll~~si~~~q~~~-~~f~~vyAaLva~ln~~~pe~G~lll~rlv~ 98 (568)
+||+++.+|.- ++..+....+..+-..+......-++..++...+.. +..-+.|+.|++.+.....--... +..
T Consensus 1 ~rk~i~~~l~ey~~~~d~~ea~~~l~el~~~~~~~~vv~~~l~~~le~~~~~r~~~~~Ll~~L~~~~~~~~~~----~~~ 76 (113)
T PF02847_consen 1 LRKKIFSILMEYFSSGDVDEAVECLKELKLPSQHHEVVKVILECALEEKKSYREYYSKLLSHLCKRKLISKEQ----FQE 76 (113)
T ss_dssp HHHHHHHHHHHHHHHT-HHHHHHHHHHTT-GGGHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHTTSS-HHH----HHH
T ss_pred ChHHHHHHHHHHhcCCCHHHHHHHHHHhCCCccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHhcCCCCHHH----HHH
Confidence 45666665543 333445555555543333323334555555554444 567778888887776432111111 111
Q ss_pred HHHHHHHh------CChhhhhhhHHHHHHHHhhhhcc
Q 008379 99 QLKRAYKR------NDKPQLLAAVKFIAHLVNQQVAH 129 (568)
Q Consensus 99 ~F~~~~~~------~dk~~~~n~i~fIa~Lyn~~Vv~ 129 (568)
-|.+-+.. .-.+...++..|+++++.-++++
T Consensus 77 gf~~~l~~l~Dl~~D~P~~~~~la~~~~~~i~~~~lp 113 (113)
T PF02847_consen 77 GFEDLLESLEDLELDIPKAPEYLAKFLARLIADGILP 113 (113)
T ss_dssp HHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTSS-
T ss_pred HHHHHHhHhhhccccchHHHHHHHHHHHHHHHcCCcC
Confidence 12222211 11346778899999998887763
No 35
>KOG2477 consensus Uncharacterized conserved protein [Function unknown]
Probab=58.63 E-value=5.9 Score=43.89 Aligned_cols=24 Identities=33% Similarity=0.435 Sum_probs=17.7
Q ss_pred CCCCCCCCcccchhHHhhhhhhcc
Q 008379 544 SESEDSSSSDESNRDKRHSKRRRR 567 (568)
Q Consensus 544 ~~~~~~~~~~~~~~~~~~~~~~~~ 567 (568)
+++.|+++++|+.|++|.||.||.
T Consensus 46 ~e~~ss~~egerer~~r~kk~~r~ 69 (628)
T KOG2477|consen 46 SERPSSREEGERERHERFKKEPRE 69 (628)
T ss_pred ccCCcccccchhhhhhccccccch
Confidence 445577788888888887777764
No 36
>PHA03325 nuclear-egress-membrane-like protein; Provisional
Probab=55.64 E-value=74 Score=34.19 Aligned_cols=131 Identities=16% Similarity=0.312 Sum_probs=75.0
Q ss_pred hhhhhhhcCCCHHHHHHHHHcccCCCCc--chHHHHHH--HHhhcccCc---------------------chh-hHHHHH
Q 008379 313 TIYLTIMSSVDFEEAGHKLLKIKLEPGQ--EMELCIML--LECCSQERT---------------------YLR-YYGLLG 366 (568)
Q Consensus 313 ~Ifl~IMSS~d~~eA~hKLlkL~lk~~q--e~EI~~vl--i~Cc~qEkt---------------------Yn~-yY~lla 366 (568)
=|||| +.||...-+-|.+|+=.+.. --+|..|+ |.|=.|-.. ||. -|.--.
T Consensus 68 FiFCt---~~D~~~~~~gI~qlkR~~~~vd~s~i~~v~~~i~CRlr~~~~~p~~~~~q~l~~tvr~vc~~FNrl~f~Ar~ 144 (418)
T PHA03325 68 FIFCT---SRDYRKFEQGIAQLKRQPDIVDPSRIDQVTQSIRCRLRKHPRSPPLPADQRLIRAVRRVCVLFNRLTFTARL 144 (418)
T ss_pred EEEEe---cchHHHHHHHHHHhccCcccCCHHHHHHHHhcceeeecCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 36764 88999888888887532211 13566665 556665443 222 111111
Q ss_pred HHHhhccHhhHHHHHHHHHH-----------HhhhhhcCchhhHHHHHHHHHHHHhcCCcCcccccccccCCcccCchHH
Q 008379 367 QRFCMINKVHQENFEKCFVQ-----------QYSMIHRLETNKLRNVAKFFAHLLGTHALPWHVLAYIRLTEEDTTSSSR 435 (568)
Q Consensus 367 erlC~~~~~~~~~f~~~f~~-----------~y~~i~~le~~klrNlakf~ahLl~~~~l~l~vLk~i~l~e~dttss~r 435 (568)
...|..+.+.+.-+-.-+.. .+..|+-++..+-+-|...+.-|+..--==|. +-|+|- .--+
T Consensus 145 rHYcd~dsr~v~YlRdeLtkRCge~S~Lg~~i~~li~lvd~erhrdLc~vLvGmlhQTPHMWa--RSIRLl-----~rLk 217 (418)
T PHA03325 145 RHYCDHDSRLVAYLRDELTKRCGEGSRLGEHIRQLISLVDHERHRDLCHVLVGMLHQTPHMWA--RSIRLL-----GRLK 217 (418)
T ss_pred hhhhcchHHHHHHHHHHHHHHhcccchhhhHHHHHHHhcChhhhhhHHHHHHHHhhcChHHHH--HHHHHH-----HHHH
Confidence 33344443333322222221 12234556778888888888877766543343 445553 3458
Q ss_pred HHHHHHHHHHHHHHchHH
Q 008379 436 IFIKILFQELSEHLGIRL 453 (568)
Q Consensus 436 iFik~LfqeL~~~lg~~~ 453 (568)
+|+..-|..|+..+||+-
T Consensus 218 ~f~Qn~fl~ll~d~~ldi 235 (418)
T PHA03325 218 IFYQNSFLKLLADSGLDI 235 (418)
T ss_pred HHHHHHHHHHHHHcCCCH
Confidence 899999999999888865
No 37
>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=53.85 E-value=1.1e+02 Score=26.55 Aligned_cols=103 Identities=10% Similarity=0.180 Sum_probs=52.7
Q ss_pred HHHHHHHhhc-CChhhHHHHHHHHHHhhhhhhhhHHHHHHhhhccCC-CChHHHHHHHHHHHhcCCchHHHHHHHHHHHH
Q 008379 22 RKSINGLVNK-VNATNIKNIIPELFAENLIRGRGLFCRSCMKSQMAS-PGFTDVFAALVAVVNTKFTAVGELLLKRIVLQ 99 (568)
Q Consensus 22 kk~I~gllNK-Ls~~Ni~~i~~eL~~~Ni~rgrgll~~si~~~q~~~-~~f~~vyAaLva~ln~~~pe~G~lll~rlv~~ 99 (568)
||+|..+|+- ++.......+.-+...++..-..-+++.++...+.. +..-+.|+.|...+.....-. -..+..-
T Consensus 2 ~k~i~~~l~ey~~~~D~~ea~~~l~~L~~~~~~~~vv~~~i~~~le~~~~~~~~~~~Ll~~L~~~~~~~----~~~~~~~ 77 (113)
T smart00544 2 KKKIFLIIEEYLSSGDTDEAVHCLLELKLPEQHHEVVKVLLTCALEEKRTYREMYSVLLSRLCQANVIS----TKQFEKG 77 (113)
T ss_pred hhHHHHHHHHHHHcCCHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCccHHHHHHHHHHHHHHcCCcC----HHHHHHH
Confidence 4445554443 233345555555544443322233444444443433 567788888888777543211 2222223
Q ss_pred HHHHHHhCC------hhhhhhhHHHHHHHHhhhhc
Q 008379 100 LKRAYKRND------KPQLLAAVKFIAHLVNQQVA 128 (568)
Q Consensus 100 F~~~~~~~d------k~~~~n~i~fIa~Lyn~~Vv 128 (568)
|.+-++.-+ .....++..|+|.++--+++
T Consensus 78 f~~~~~~l~dl~~D~P~a~~~la~~~a~~v~~~~l 112 (113)
T smart00544 78 FWRLLEDIEDLELDIPNAWRNLAEFVARLISDGIL 112 (113)
T ss_pred HHHHHhhChhhhcccccHHHHHHHHHHHHHHcCCC
Confidence 333333221 14667888899988877665
No 38
>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM. Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....
Probab=53.80 E-value=60 Score=29.83 Aligned_cols=94 Identities=17% Similarity=0.245 Sum_probs=61.0
Q ss_pred hhHHHHHHHHhhhhccHHHHHHHHHHHhhCCCCC----cHHHHHHHHHHHhHhhccC-ChhHHHHHHHHHHHHhhcCCCC
Q 008379 114 AAVKFIAHLVNQQVAHEIIALELLTILLENPTDD----SVEVAVGFVKECGSILQDL-SPKGLHGIFERFRGILHEGEID 188 (568)
Q Consensus 114 n~i~fIa~Lyn~~Vv~~~lildii~~LLe~~te~----sVE~ll~lLr~~G~~Lr~~-~p~~lk~I~~~l~~il~e~~is 188 (568)
..+.-||.++|.+-....-+...|+.=|..++.. .+.++=.++++||..++.. .. +.+++.+.+++......
T Consensus 24 ~~~l~icD~i~~~~~~~kea~~~l~krl~~~~~~vq~~aL~lld~lvkNcg~~f~~ev~~---~~fl~~l~~l~~~~~~~ 100 (140)
T PF00790_consen 24 SLILEICDLINSSPDGAKEAARALRKRLKHGNPNVQLLALTLLDALVKNCGPRFHREVAS---KEFLDELVKLIKSKKTD 100 (140)
T ss_dssp HHHHHHHHHHHTSTTHHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHSHHHHHHHHTS---HHHHHHHHHHHHHTTTH
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHcCCHHHHHHHhH---HHHHHHHHHHHccCCCC
Confidence 4555688999999777788888887777765543 3555667778899877542 22 23556666666554444
Q ss_pred hh--HHHHHHHHHHHHHhccCCCC
Q 008379 189 KR--VQFLIEGLFAIRKAKFQGYP 210 (568)
Q Consensus 189 ~R--~~fmIE~l~~lr~nk~k~~~ 210 (568)
.. |+-.+-.++.-....|+..|
T Consensus 101 ~~~~Vk~k~l~ll~~W~~~f~~~~ 124 (140)
T PF00790_consen 101 PETPVKEKILELLQEWAEAFKSDP 124 (140)
T ss_dssp HHSHHHHHHHHHHHHHHHHTTTST
T ss_pred chhHHHHHHHHHHHHHHHHHCCCC
Confidence 33 77666666666666665544
No 39
>KOG2812 consensus Uncharacterized conserved protein [Function unknown]
Probab=51.54 E-value=11 Score=39.94 Aligned_cols=7 Identities=29% Similarity=0.396 Sum_probs=3.8
Q ss_pred HHchHHH
Q 008379 448 HLGIRLL 454 (568)
Q Consensus 448 ~lg~~~l 454 (568)
++|++++
T Consensus 153 e~g~pev 159 (426)
T KOG2812|consen 153 ELGAPEV 159 (426)
T ss_pred hccchhh
Confidence 4566554
No 40
>KOG4032 consensus Uncharacterized conserved protein [Function unknown]
Probab=49.34 E-value=75 Score=30.90 Aligned_cols=59 Identities=20% Similarity=0.309 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHchHHHHhhcCCcchhhhhhccCCCCCCCCceehhhHHHhcCchhhhHHHHHHHHhCChhHH
Q 008379 439 KILFQELSEHLGIRLLNERLTDPTMQDSFESIFPRDNPKNTRFAINFFTSIGLGGITENLREYLKNMPRLIM 510 (568)
Q Consensus 439 k~LfqeL~~~lg~~~l~~rl~d~~~~~~~~glfp~d~~~~~rfsinfft~IgLg~lt~~~R~~l~~~~~~~~ 510 (568)
..-.-|++.++|..+++-...|.++-+. .++.+|+|-.|-=|- -..+|+.|..+|++..
T Consensus 63 ~~eieE~L~~~l~~EFnt~~eDDS~~~i------------a~~L~n~f~~~~~~N-~~~ieells~l~~q~~ 121 (184)
T KOG4032|consen 63 AREIEELLLELLGDEFNTKVEDDSLPEI------------AQLLLNLFHDIQNGN-YAIIEELLSKLPKQDL 121 (184)
T ss_pred HHHHHHHHHHHHHHHhhccccCCCHHHH------------HHHHHHHHHHHHccc-HHHHHHHHHHcchhhh
Confidence 3445667777888888777777665433 267788888775433 2456777777775433
No 41
>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=44.60 E-value=48 Score=30.91 Aligned_cols=31 Identities=13% Similarity=0.000 Sum_probs=27.0
Q ss_pred hhhhhhHHHHHHHHhhhhccHHHHHHHHHHH
Q 008379 110 PQLLAAVKFIAHLVNQQVAHEIIALELLTIL 140 (568)
Q Consensus 110 ~~~~n~i~fIa~Lyn~~Vv~~~lildii~~L 140 (568)
..+.+...+++.|+++|+++...|.+|++.|
T Consensus 110 ~l~~~f~lHl~~L~d~glLd~~~i~~c~~~l 140 (140)
T PF09733_consen 110 NLRREFLLHLINLWDFGLLDARTIDECMKIL 140 (140)
T ss_pred hHHHHHHHHHHHHHHcCCCCHHHHHHHHhhC
Confidence 4566788899999999999999999998764
No 42
>PF05501 DUF755: Domain of unknown function (DUF755) ; InterPro: IPR008474 This family is predominated by ORFs from Anelloviridae. The function of this family remains to be determined.
Probab=43.51 E-value=18 Score=33.01 Aligned_cols=19 Identities=16% Similarity=0.163 Sum_probs=10.3
Q ss_pred hHHHHHHHHHHHHHHHHch
Q 008379 433 SSRIFIKILFQELSEHLGI 451 (568)
Q Consensus 433 s~riFik~LfqeL~~~lg~ 451 (568)
......+-|+.|.....-|
T Consensus 36 d~~~L~~qLlKEC~kt~~L 54 (123)
T PF05501_consen 36 DVDSLQKQLLKECQKTSQL 54 (123)
T ss_pred hHHHHHHHHHHHHHHHHHH
Confidence 3455666666666543333
No 43
>COG5129 MAK16 Nuclear protein with HMG-like acidic region [General function prediction only]
Probab=43.18 E-value=14 Score=36.85 Aligned_cols=24 Identities=21% Similarity=0.318 Sum_probs=15.8
Q ss_pred hhhhhhhhhhhcCCCHHHHHHHHH
Q 008379 309 NLRRTIYLTIMSSVDFEEAGHKLL 332 (568)
Q Consensus 309 ~~RR~Ifl~IMSS~d~~eA~hKLl 332 (568)
.+-+..|--|.=|.+|+.|...|-
T Consensus 70 H~P~klwerIkLSkNY~kAL~QId 93 (303)
T COG5129 70 HVPRKLWERIKLSKNYEKALKQID 93 (303)
T ss_pred cCcHHHHHHHHhhhhHHHHHHHHH
Confidence 445555666666778888877663
No 44
>PF06112 Herpes_capsid: Gammaherpesvirus capsid protein; InterPro: IPR009299 This family consists of several Gammaherpesvirus capsid proteins. The exact function of this family is unknown.; GO: 0019028 viral capsid
Probab=42.59 E-value=31 Score=32.34 Aligned_cols=18 Identities=28% Similarity=0.560 Sum_probs=14.5
Q ss_pred hhcCCcchhhhhhccCCC
Q 008379 456 ERLTDPTMQDSFESIFPR 473 (568)
Q Consensus 456 ~rl~d~~~~~~~~glfp~ 473 (568)
.|+.+|.+|.-+|..||.
T Consensus 4 ~r~~~P~vQgRLE~d~p~ 21 (147)
T PF06112_consen 4 RRVRLPRVQGRLEADYPN 21 (147)
T ss_pred CCCCCCceeceecccCCC
Confidence 477888888888888884
No 45
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=42.21 E-value=31 Score=31.14 Aligned_cols=54 Identities=9% Similarity=0.209 Sum_probs=31.0
Q ss_pred cCcchhhHHHHHHHHhhccHhhHHHHHHHHHHHhhhhhcCchhhHHHHHHHHHHHH
Q 008379 355 ERTYLRYYGLLGQRFCMINKVHQENFEKCFVQQYSMIHRLETNKLRNVAKFFAHLL 410 (568)
Q Consensus 355 EktYn~yY~llaerlC~~~~~~~~~f~~~f~~~y~~i~~le~~klrNlakf~ahLl 410 (568)
+.-|+.||+.|....+.....- ..|.+|.+.|..++.++..++..-+.|-++|+
T Consensus 2 ~~~~~~y~~~l~~~~~~~~~~~--~~qdvf~~~w~~~~~~~~~~~~~~~~~~~wL~ 55 (142)
T TIGR03209 2 EEIYMNFKNTIDIFTRKYNLYY--DYNDILYHLWIILKKIDLNKFNTENDLEKYIS 55 (142)
T ss_pred hHHHHHHHHHHHHHHHHhcchh--hHHHHHHHHHHHHHHhhhhhcCchhHHHHHHH
Confidence 4568999998887777654322 23666666666554443333433344555543
No 46
>PRK08307 stage III sporulation protein SpoAB; Provisional
Probab=41.24 E-value=58 Score=31.25 Aligned_cols=70 Identities=13% Similarity=0.171 Sum_probs=49.3
Q ss_pred hcCCCHHHHHHHHHcccCCCCcchHHHHHHHHhhcccCcchhhHHHHHHHHhhcc-HhhHHHHHHHHHHHhhhh--hcCc
Q 008379 319 MSSVDFEEAGHKLLKIKLEPGQEMELCIMLLECCSQERTYLRYYGLLGQRFCMIN-KVHQENFEKCFVQQYSMI--HRLE 395 (568)
Q Consensus 319 MSS~d~~eA~hKLlkL~lk~~qe~EI~~vli~Cc~qEktYn~yY~llaerlC~~~-~~~~~~f~~~f~~~y~~i--~~le 395 (568)
-+...-.||++++-+- .+..|+.||..++++|++.. .++...++.+++..++.. .+=|
T Consensus 47 Y~~tpL~ea~~~i~~~-------------------~~~~~~~~f~~~a~~L~~~~g~s~~eaw~~~~~~~~~~~~L~~~d 107 (171)
T PRK08307 47 YGHTPLPEALENIAKQ-------------------SPKPISTLFQRFSERLESGEGETAYEAWEKALEENWKNTALKKED 107 (171)
T ss_pred hcCCcHHHHHHHHHHc-------------------cchhHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhhccCCCHHH
Confidence 3556677777777541 25679999999999999877 778888888887766542 3334
Q ss_pred hhhHHHHHHHHH
Q 008379 396 TNKLRNVAKFFA 407 (568)
Q Consensus 396 ~~klrNlakf~a 407 (568)
..-+.++|+-+|
T Consensus 108 ~eiL~~lg~~LG 119 (171)
T PRK08307 108 IEILLQFGKTLG 119 (171)
T ss_pred HHHHHHHHHHHC
Confidence 455666666655
No 47
>KOG1877 consensus Putative transmembrane protein cmp44E [General function prediction only]
Probab=41.19 E-value=1.8e+02 Score=34.67 Aligned_cols=121 Identities=21% Similarity=0.268 Sum_probs=69.8
Q ss_pred HHHHHHHHhc-CCchHHHHHHHHHHHHHHHHHHhCChhhhhhhHHHHHHHHhhhhccHH--------HHHHHHHHHhhCC
Q 008379 74 FAALVAVVNT-KFTAVGELLLKRIVLQLKRAYKRNDKPQLLAAVKFIAHLVNQQVAHEI--------IALELLTILLENP 144 (568)
Q Consensus 74 yAaLva~ln~-~~pe~G~lll~rlv~~F~~~~~~~dk~~~~n~i~fIa~Lyn~~Vv~~~--------lildii~~LLe~~ 144 (568)
|-..+|+=|. ++|-||..|.+||...+++. ..+ .+...-+.|++=+++|. -.+.+++.||++-
T Consensus 38 kL~~YAasnp~KL~KI~~yL~~R~~kdl~~~---r~~-----~v~Iamea~~kLL~~C~eq~n~F~ssfL~mv~~LLes~ 109 (819)
T KOG1877|consen 38 KLTFYAASNPSKLPKIGTYLEERCYKDLRRE---RFG-----SVKIAMEAYDKLLQACKEQINLFVSSFLRMVQKLLESN 109 (819)
T ss_pred HHHHHHhhChhhhhHHHHHHHHHHHHHHHhc---cCc-----chhhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcC
Confidence 5555566675 79999999999997666442 222 22222234444444433 2456778888865
Q ss_pred CCC----cHHHHHHHHHHHhHhhccCChhH---HHHHHHHHHHHhhc-CCCChhHHHHHHHHHHHHHhccC
Q 008379 145 TDD----SVEVAVGFVKECGSILQDLSPKG---LHGIFERFRGILHE-GEIDKRVQFLIEGLFAIRKAKFQ 207 (568)
Q Consensus 145 te~----sVE~ll~lLr~~G~~Lr~~~p~~---lk~I~~~l~~il~e-~~is~R~~fmIE~l~~lr~nk~k 207 (568)
.+. ..+..+.|... .++.|.. ++..+.++-.+.|+ |+-+.+..+-+..|..|+..-|+
T Consensus 110 ~~~~~ilg~~sf~~F~~i-----~~d~~sy~~~yd~Fi~kf~~l~he~~~~~~~~~lr~agl~gLsa~v~~ 175 (819)
T KOG1877|consen 110 NDEMQILGTNSFVKFANI-----EEDGPSYHRNYDFFISKFSSLCHERGDDDMKDCLRAAGLQGLSAVVWL 175 (819)
T ss_pred CCceeeehhhHHHHHHhh-----cccCchhhhhhHHHHHHHHHHhhcccchhhhhhccHhhhhhHHHHHHH
Confidence 222 22333444433 3345544 45577888888887 44455666666666666655554
No 48
>TIGR02833 spore_III_AB stage III sporulation protein AB. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is designated stage III sporulation protein AB.
Probab=41.04 E-value=55 Score=31.39 Aligned_cols=69 Identities=13% Similarity=0.099 Sum_probs=48.9
Q ss_pred cCCCHHHHHHHHHcccCCCCcchHHHHHHHHhhcccCcchhhHHHHHHHHhhcc-HhhHHHHHHHHHHHhhhh--hcCch
Q 008379 320 SSVDFEEAGHKLLKIKLEPGQEMELCIMLLECCSQERTYLRYYGLLGQRFCMIN-KVHQENFEKCFVQQYSMI--HRLET 396 (568)
Q Consensus 320 SS~d~~eA~hKLlkL~lk~~qe~EI~~vli~Cc~qEktYn~yY~llaerlC~~~-~~~~~~f~~~f~~~y~~i--~~le~ 396 (568)
+...-.||+.++-+- .+..|+.||..+|++|+... .++...++.+++..++.. .+=|.
T Consensus 47 ~~tpL~ea~~~i~~~-------------------~~~~~~~~f~~~a~~L~~~~g~s~~~~w~~~~~~~~~~~~L~~~d~ 107 (170)
T TIGR02833 47 GHTPLPEAFKKIALK-------------------SPKPVNLLFESASERLKEGEGLTVYEAWKKALNEVWKQTALQKSEK 107 (170)
T ss_pred cCCcHHHHHHHHHhh-------------------cchhHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhhccCCCHHHH
Confidence 456667777776441 26679999999999999887 678888888887766542 33344
Q ss_pred hhHHHHHHHHH
Q 008379 397 NKLRNVAKFFA 407 (568)
Q Consensus 397 ~klrNlakf~a 407 (568)
.-+.++|+-+|
T Consensus 108 eiL~~lG~~LG 118 (170)
T TIGR02833 108 EILLQFGKTLG 118 (170)
T ss_pred HHHHHHHHHHC
Confidence 56677666665
No 49
>COG5129 MAK16 Nuclear protein with HMG-like acidic region [General function prediction only]
Probab=40.72 E-value=14 Score=36.78 Aligned_cols=13 Identities=38% Similarity=0.600 Sum_probs=5.9
Q ss_pred hccCCCCCCCCcee
Q 008379 468 ESIFPRDNPKNTRF 481 (568)
Q Consensus 468 ~glfp~d~~~~~rf 481 (568)
.|++. |.|-|.||
T Consensus 171 SGiYG-d~pLnv~e 183 (303)
T COG5129 171 SGIYG-DTPLNVRE 183 (303)
T ss_pred ccccC-CCccchHH
Confidence 35553 44444443
No 50
>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=40.39 E-value=2.2e+02 Score=26.30 Aligned_cols=95 Identities=18% Similarity=0.214 Sum_probs=58.0
Q ss_pred hhHHHHHHHHhhhhccHHHHHHHHHHHhhC-CCCC----cHHHHHHHHHHHhHhhccCChhHHHHHHHH-HHHHhhc-CC
Q 008379 114 AAVKFIAHLVNQQVAHEIIALELLTILLEN-PTDD----SVEVAVGFVKECGSILQDLSPKGLHGIFER-FRGILHE-GE 186 (568)
Q Consensus 114 n~i~fIa~Lyn~~Vv~~~lildii~~LLe~-~te~----sVE~ll~lLr~~G~~Lr~~~p~~lk~I~~~-l~~il~e-~~ 186 (568)
..+.=||.++|.+-.+..-+...|+.=|.. ++.. .+.++-.++++||..+... -+-+.+++. |.+++.. +.
T Consensus 20 ~~ileicD~In~~~~~~k~a~ralkkRl~~~~n~~v~l~aL~LLe~~vkNCG~~fh~e--iask~Fl~e~L~~~i~~~~~ 97 (141)
T cd03565 20 GLNMEICDIINETEDGPKDAVRALKKRLNGNKNHKEVMLTLTVLETCVKNCGHRFHVL--VAKKDFIKDVLVKLINPKNN 97 (141)
T ss_pred HHHHHHHHHHhCCCCcHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHccHHHHHH--HHHHHhhhHHHHHHHcccCC
Confidence 466678888888888877777777655542 2222 4556667888999877532 133455555 5555542 23
Q ss_pred CChhHHHHHHHHHHHHHhccCCCC
Q 008379 187 IDKRVQFLIEGLFAIRKAKFQGYP 210 (568)
Q Consensus 187 is~R~~fmIE~l~~lr~nk~k~~~ 210 (568)
.+..++-.|-.++.-....|++.|
T Consensus 98 ~~~~Vk~kil~li~~W~~~f~~~~ 121 (141)
T cd03565 98 PPTIVQEKVLALIQAWADAFRGSP 121 (141)
T ss_pred CcHHHHHHHHHHHHHHHHHhCCCc
Confidence 455666656555555555666544
No 51
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=38.29 E-value=20 Score=41.52 Aligned_cols=24 Identities=13% Similarity=0.329 Sum_probs=18.0
Q ss_pred HHHHHHHHhcCCcCcccccccccC
Q 008379 403 AKFFAHLLGTHALPWHVLAYIRLT 426 (568)
Q Consensus 403 akf~ahLl~~~~l~l~vLk~i~l~ 426 (568)
+|.+.+||..|.||.++.=+-...
T Consensus 16 ~kiL~~Llk~d~I~~~l~PV~gy~ 39 (622)
T PF02724_consen 16 CKILTSLLKSDNIQYSLVPVSGYS 39 (622)
T ss_pred HHHHHHHHHhcCCCeeEEEeCCHH
Confidence 678889999999988876554443
No 52
>KOG2188 consensus Predicted RNA-binding protein, contains Pumilio domains [Translation, ribosomal structure and biogenesis]
Probab=37.75 E-value=2.3e+02 Score=32.77 Aligned_cols=26 Identities=23% Similarity=0.185 Sum_probs=17.4
Q ss_pred HHHHHHHHhhhhccHHHHHHHHHHHh
Q 008379 116 VKFIAHLVNQQVAHEIIALELLTILL 141 (568)
Q Consensus 116 i~fIa~Lyn~~Vv~~~lildii~~LL 141 (568)
..++-||++|.--|.....+.+..|.
T Consensus 486 a~lle~lv~f~k~~i~~litsll~L~ 511 (650)
T KOG2188|consen 486 AVLLEELVNFSKTHIQTLITSLLSLS 511 (650)
T ss_pred hHHHHHHHhhchhhhHHHHHHHHhhh
Confidence 45778888887777666655555443
No 53
>PHA02664 hypothetical protein; Provisional
Probab=36.24 E-value=27 Score=36.65 Aligned_cols=16 Identities=50% Similarity=0.557 Sum_probs=6.8
Q ss_pred CCCCCCCCCCCCcccc
Q 008379 540 SSSQSESEDSSSSDES 555 (568)
Q Consensus 540 ~~~~~~~~~~~~~~~~ 555 (568)
|++.++|.+++=+||+
T Consensus 484 s~de~ds~ddswgd~s 499 (534)
T PHA02664 484 SEDESDSADDSWGDES 499 (534)
T ss_pred cccccccccccccccc
Confidence 3334444444434443
No 54
>PHA02664 hypothetical protein; Provisional
Probab=36.00 E-value=30 Score=36.33 Aligned_cols=8 Identities=25% Similarity=0.044 Sum_probs=3.3
Q ss_pred HHHHHHHH
Q 008379 496 ENLREYLK 503 (568)
Q Consensus 496 ~~~R~~l~ 503 (568)
+++|....
T Consensus 410 ee~~aaa~ 417 (534)
T PHA02664 410 EEGRAAAA 417 (534)
T ss_pred hhhhhhhh
Confidence 34444433
No 55
>PTZ00007 (NAP-L) nucleosome assembly protein -L; Provisional
Probab=34.96 E-value=27 Score=37.26 Aligned_cols=7 Identities=29% Similarity=0.880 Sum_probs=6.3
Q ss_pred ehhhHHH
Q 008379 481 FAINFFT 487 (568)
Q Consensus 481 fsinfft 487 (568)
.|+.|||
T Consensus 270 ~AV~yft 276 (337)
T PTZ00007 270 YAVYWFL 276 (337)
T ss_pred ccHHhhC
Confidence 7899998
No 56
>PF09548 Spore_III_AB: Stage III sporulation protein AB (spore_III_AB); InterPro: IPR014198 This entry represents the stage III sporulation protein AB, which is encoded in a spore formation operon: spoIIIAABCDEFGH that is under sigma G regulation []. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
Probab=30.42 E-value=1.1e+02 Score=29.04 Aligned_cols=69 Identities=12% Similarity=0.168 Sum_probs=47.9
Q ss_pred cCCCHHHHHHHHHcccCCCCcchHHHHHHHHhhcccCcchhhHHHHHHHHhhcc-HhhHHHHHHHHHHHhhhh--hcCch
Q 008379 320 SSVDFEEAGHKLLKIKLEPGQEMELCIMLLECCSQERTYLRYYGLLGQRFCMIN-KVHQENFEKCFVQQYSMI--HRLET 396 (568)
Q Consensus 320 SS~d~~eA~hKLlkL~lk~~qe~EI~~vli~Cc~qEktYn~yY~llaerlC~~~-~~~~~~f~~~f~~~y~~i--~~le~ 396 (568)
++..-.||+.++-+- .+..|+.||..+|++|+... ..+...++.++....... .+=|.
T Consensus 47 ~~tpL~eal~~i~~~-------------------~~~~~~~~f~~~a~~L~~~~~~~~~~~w~~~~~~~~~~~~L~~~d~ 107 (170)
T PF09548_consen 47 GATPLPEALERISRR-------------------SEGPIGEFFERVAERLEKNEGESFAEAWEEAVEKLLKESALKKEDK 107 (170)
T ss_pred cCCCHHHHHHHHHhc-------------------ccchHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhhhcCCCCHHHH
Confidence 466667777777542 26789999999999999887 567777777776655432 23344
Q ss_pred hhHHHHHHHHH
Q 008379 397 NKLRNVAKFFA 407 (568)
Q Consensus 397 ~klrNlakf~a 407 (568)
.-+.++|+.+|
T Consensus 108 e~L~~lg~~LG 118 (170)
T PF09548_consen 108 EILLELGKSLG 118 (170)
T ss_pred HHHHHHHHHHc
Confidence 56777777665
No 57
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=30.41 E-value=5.7e+02 Score=30.23 Aligned_cols=29 Identities=17% Similarity=0.227 Sum_probs=24.9
Q ss_pred eeeeccCcCCccccCCcccCCcccccchH
Q 008379 227 HEISLQDEIDPEITLDIFKPDPNFLDNEK 255 (568)
Q Consensus 227 h~i~l~~~~~~e~~l~~f~~D~~~~~~e~ 255 (568)
..++|++.++++..++||.++..|.+++.
T Consensus 554 l~vTledll~ae~kGrWWlVGsaw~g~~~ 582 (822)
T KOG2141|consen 554 LSVTLEDLLHAEQKGRWWLVGSAWRGNEQ 582 (822)
T ss_pred ccccHHHhhChHhcCceEEecchhcCCcc
Confidence 35789999999999999999998887653
No 58
>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....
Probab=29.87 E-value=78 Score=24.42 Aligned_cols=45 Identities=9% Similarity=0.206 Sum_probs=32.8
Q ss_pred chhhHHHHHHHHhhccHhhHHHHHHHHHHHhhhhhcCchhhHHHH
Q 008379 358 YLRYYGLLGQRFCMINKVHQENFEKCFVQQYSMIHRLETNKLRNV 402 (568)
Q Consensus 358 Yn~yY~llaerlC~~~~~~~~~f~~~f~~~y~~i~~le~~klrNl 402 (568)
|.|..-.++.++|.......+.+|.+|...++.++++++.+-.++
T Consensus 5 ~~~~l~~~~~~~~~~~~~~eD~~qe~~~~l~~~~~~~~~~~~~~~ 49 (71)
T PF04542_consen 5 YYPLLYRYARRYTGDPEDAEDLVQEAFIKLWRAIDSYDPDRGDSF 49 (71)
T ss_dssp THHHHHHHHHTCTTCSSHHHHHHHHHHHHHHHHHHHTSTTSSSHH
T ss_pred HHHHHHHHHHHHhCCHhhHHHHhhHHHHHHHhhhhcccccccCCH
Confidence 455555566677766667889999999999999998886554343
No 59
>PF00619 CARD: Caspase recruitment domain; InterPro: IPR001315 The caspase recruitment domain domain (CARD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. CARD is related in sequence and structure to the death domain (DD, see IPR000488 from INTERPRO) and the death effector domain (DED, see IPR001875 from INTERPRO), which work in similar pathways and show similar interaction properties []. The CARD domain typically associates with other CARD-containing proteins, forming either dimers or trimers. CARD domains can be found in isolation, or in combination with other domains. Domains associated with CARD include: NACHT (IPR007111 from INTERPRO) (in Nal1 and Bir1), NB-ARC (IPR002182 from INTERPRO) (in Apaf-1), pyrin/dapin domains (IPR004020 from INTERPRO) (in Nal1), leucine-rich repeats () (in Nal1), WD repeats (IPR001680 from INTERPRO) (in Apaf1), Src homology domains (IPR001452 from INTERPRO), PDZ (IPR001478 from INTERPRO), RING, kinase and DD domains []. CARD-containing proteins are involved in apoptosis through their regulation of caspases that contain CARDs in their N-terminal pro-domains, including human caspases 1, 2, 9, 11 and 12 []. CARD-containing proteins are also involved in inflammation through their regulation of NF-kappaB []. The mechanisms by which CARDs activate caspases and NF-kappaB involve the assembly of multi-protein complexes, which can facilitate dimerisation or serve as scaffolds on which proteases and kinases are assembled and activated.; GO: 0005515 protein binding, 0042981 regulation of apoptosis, 0005622 intracellular; PDB: 2NSN_A 2NZ7_B 2DBD_A 4E9M_C 2B1W_A 3YGS_P 2KN6_A 3CRD_A 1DGN_A 3KAT_A ....
Probab=28.04 E-value=3.3e+02 Score=22.10 Aligned_cols=73 Identities=16% Similarity=0.290 Sum_probs=49.4
Q ss_pred HHHHHHHHHHHhhcCChhhHHHHHHHHHHhhhhhhhhHHHHHHhhhccCCCChHHHHHHHHHHHhcCCchHHHHHHHHHH
Q 008379 18 WDALRKSINGLVNKVNATNIKNIIPELFAENLIRGRGLFCRSCMKSQMASPGFTDVFAALVAVVNTKFTAVGELLLKRIV 97 (568)
Q Consensus 18 w~~Lkk~I~gllNKLs~~Ni~~i~~eL~~~Ni~rgrgll~~si~~~q~~~~~f~~vyAaLva~ln~~~pe~G~lll~rlv 97 (568)
|+.|++.=..++..++ ++..++..|+..++..... ...| .. .++-..-=..|+-+|-.++|.....|++-+.
T Consensus 1 ~~~L~~~r~~Lv~~l~--~~~~ild~L~~~~vlt~~e--~e~I-~~---~~t~~~k~~~LLd~l~~kg~~a~~~F~~~L~ 72 (85)
T PF00619_consen 1 QELLRKNRQELVEDLD--DLDDILDHLLSRGVLTEEE--YEEI-RS---EPTRQDKARKLLDILKRKGPEAFDIFCQALR 72 (85)
T ss_dssp HHHHHHTHHHHHHHSS--HHHHHHHHHHHTTSSSHHH--HHHH-HT---SSSHHHHHHHHHHHHHHCCHHHHHHHHHHHH
T ss_pred CHHHHHhHHHHHHHhC--cHHHHHHHHHHCCCCCHHH--HHHH-Hc---cCChHHHHHHHHHHHHHHCHHHHHHHHHHHH
Confidence 7788888899999999 8889999998877765422 1112 11 2332222345777788888887777777665
Q ss_pred H
Q 008379 98 L 98 (568)
Q Consensus 98 ~ 98 (568)
.
T Consensus 73 ~ 73 (85)
T PF00619_consen 73 E 73 (85)
T ss_dssp H
T ss_pred h
Confidence 4
No 60
>PF11864 DUF3384: Domain of unknown function (DUF3384); InterPro: IPR024584 This entry represents the N-terminal domain of tuberin which is functionally uncharacterised.
Probab=27.16 E-value=5e+02 Score=28.79 Aligned_cols=155 Identities=17% Similarity=0.242 Sum_probs=0.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHhhcCChhhHHHHH-----HHHHHhhhhhhhhHHHHHHhhhc----cCCCChHH--HHHHH
Q 008379 9 SSAEYQRLTWDALRKSINGLVNKVNATNIKNII-----PELFAENLIRGRGLFCRSCMKSQ----MASPGFTD--VFAAL 77 (568)
Q Consensus 9 ~s~e~qr~~w~~Lkk~I~gllNKLs~~Ni~~i~-----~eL~~~Ni~rgrgll~~si~~~q----~~~~~f~~--vyAaL 77 (568)
+.++++..+|..++.-+++-.-.-+...+..|+ ...=..|+.||---+.+..+-.. ...-.+++ +..+|
T Consensus 227 ~~~~l~~~~w~~m~nL~~S~~g~~~i~~L~~iL~~~~~~~~~~~~~lRGAv~~l~~ll~~~~~~~~~~l~~~~~~vl~sl 306 (464)
T PF11864_consen 227 NSVSLCKPSWRTMRNLLKSHLGHSAIRTLCDILRSPDPQNKRDINVLRGAVFFLRMLLWGSGEQGYPSLPFSPSSVLPSL 306 (464)
T ss_pred cccccchhHHHHHHHHHcCccHHHHHHHHHHHHcccCccccccHHHHhhHHHHHHHHHhccccCCcceecccHHHHHHHH
Q ss_pred HHHHhcCCchHHH---HHHHHHH-HHHHHHHHhCChhhhhhhHH-HHHHHHhhhhcc------------HHHHHHHHHHH
Q 008379 78 VAVVNTKFTAVGE---LLLKRIV-LQLKRAYKRNDKPQLLAAVK-FIAHLVNQQVAH------------EIIALELLTIL 140 (568)
Q Consensus 78 va~ln~~~pe~G~---lll~rlv-~~F~~~~~~~dk~~~~n~i~-fIa~Lyn~~Vv~------------~~lildii~~L 140 (568)
..+++..-+-+-. .++.+++ .+|.+.....++....+++. ....+.++..-. -.-++..|..|
T Consensus 307 ~~al~~~~~~v~~eIl~~i~~ll~~~~~~~l~~~~W~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ie~L 386 (464)
T PF11864_consen 307 LNALKSNSPRVDYEILLLINRLLDGKYGRELSEEDWDIILDIIEEIFDKIQPFDSWYSNSSSLDQLSSNLHSLLSSIESL 386 (464)
T ss_pred HHHHhCCCCeehHHHHHHHHHHHhHhhhhhhcccCchHHHHHHHHHHhhccccccccccccchHHHHHHHHHHHHHHHHH
Q ss_pred hhCCCCC-cHHHHHHHHHHHhHhh
Q 008379 141 LENPTDD-SVEVAVGFVKECGSIL 163 (568)
Q Consensus 141 Le~~te~-sVE~ll~lLr~~G~~L 163 (568)
.+...-. ..|-+..++..+...|
T Consensus 387 ~~~~~~~g~~~~~~~f~~~~~~~l 410 (464)
T PF11864_consen 387 YEQHDFNGPKDKLFNFFERVHSYL 410 (464)
T ss_pred HhCCCcCccHHHHHHHHHHHhccC
No 61
>PF12830 Nipped-B_C: Sister chromatid cohesion C-terminus
Probab=26.92 E-value=2.6e+02 Score=27.01 Aligned_cols=73 Identities=18% Similarity=0.195 Sum_probs=51.2
Q ss_pred HHHHHHHHHHHHHHHHhCChhhhhhhHHHHHHHHhhhhccHHHHHHHHHHHhhCCCCCcHHHHHHHHHHHhHh
Q 008379 90 ELLLKRIVLQLKRAYKRNDKPQLLAAVKFIAHLVNQQVAHEIIALELLTILLENPTDDSVEVAVGFVKECGSI 162 (568)
Q Consensus 90 ~lll~rlv~~F~~~~~~~dk~~~~n~i~fIa~Lyn~~Vv~~~lildii~~LLe~~te~sVE~ll~lLr~~G~~ 162 (568)
..++++-....-+.....+.......+.+|....+||.+|+....--+--|.-+|+..-=..+..+++....+
T Consensus 3 s~l~Qryl~~Il~~~~~~~~~vr~~Al~~l~~il~qGLvnP~~cvp~lIAL~ts~~~~ir~~A~~~l~~l~eK 75 (187)
T PF12830_consen 3 SALVQRYLKNILELCLSSDDSVRLAALQVLELILRQGLVNPKQCVPTLIALETSPNPSIRSRAYQLLKELHEK 75 (187)
T ss_pred HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhcCCCChHHHHhHhhhhhCCCChHHHHHHHHHHHHHHHH
Confidence 3455666655556666666667777889999999999999998777777766677665555566666554433
No 62
>PF12311 DUF3632: Protein of unknown function (DUF3632); InterPro: IPR022085 This domain family is found in eukaryotes, and is approximately 170 amino acids in length. There is a conserved ALE sequence motif.
Probab=26.63 E-value=1e+02 Score=29.14 Aligned_cols=57 Identities=25% Similarity=0.298 Sum_probs=46.0
Q ss_pred hhhhhhHHHHHHHHhhhhccH---HHHHHHHHHHhhC--------CCCCcHHHHHHHHHHHhHhhccC
Q 008379 110 PQLLAAVKFIAHLVNQQVAHE---IIALELLTILLEN--------PTDDSVEVAVGFVKECGSILQDL 166 (568)
Q Consensus 110 ~~~~n~i~fIa~Lyn~~Vv~~---~lildii~~LLe~--------~te~sVE~ll~lLr~~G~~Lr~~ 166 (568)
..-.|+..|+|.|..-++++. ..++-.|+.-||. ..+..|.+++..+..||.+|.+.
T Consensus 79 ~~w~Nl~aF~ArL~a~~~~~~~~~~~al~~lr~aLE~~~~~~~~~~~~~~v~aAa~Wi~~aG~~l~~~ 146 (184)
T PF12311_consen 79 QEWINLNAFLARLTAAGIIDWDLSLYALWALRDALEDSEEEPSGPELDARVPAAAQWIIHAGERLYEL 146 (184)
T ss_pred HHHHhHHHHHHHHHhccCCCCchhhhHHHHHHHHHhccccccccchhhhhHHHHHHHHHHHHHHHHHH
Confidence 567899999999999999996 6777788877881 12346888999999999998754
No 63
>PF15370 DUF4598: Domain of unknown function (DUF4598)
Probab=25.78 E-value=42 Score=30.12 Aligned_cols=7 Identities=57% Similarity=0.961 Sum_probs=4.8
Q ss_pred CchhhhH
Q 008379 490 GLGGITE 496 (568)
Q Consensus 490 gLg~lt~ 496 (568)
|||+|-+
T Consensus 50 ~LGVle~ 56 (112)
T PF15370_consen 50 GLGVLEE 56 (112)
T ss_pred hhchhhc
Confidence 7777654
No 64
>PF14303 NAM-associated: No apical meristem-associated C-terminal domain
Probab=23.28 E-value=72 Score=29.40 Aligned_cols=8 Identities=25% Similarity=0.659 Sum_probs=4.8
Q ss_pred HHHhCChh
Q 008379 501 YLKNMPRL 508 (568)
Q Consensus 501 ~l~~~~~~ 508 (568)
.|.+.||-
T Consensus 11 iLr~~pKW 18 (154)
T PF14303_consen 11 ILRDEPKW 18 (154)
T ss_pred HHcCCccc
Confidence 46666664
No 65
>PTZ00007 (NAP-L) nucleosome assembly protein -L; Provisional
Probab=22.30 E-value=95 Score=33.25 Aligned_cols=7 Identities=71% Similarity=1.013 Sum_probs=3.4
Q ss_pred hhHHHhc
Q 008379 483 INFFTSI 489 (568)
Q Consensus 483 infft~I 489 (568)
.|||+-.
T Consensus 224 FnfF~p~ 230 (337)
T PTZ00007 224 FNFFTSH 230 (337)
T ss_pred HHhcCCC
Confidence 3555543
No 66
>PF04388 Hamartin: Hamartin protein; InterPro: IPR007483 This family includes the hamartin protein which is thought to function as a tumour suppressor. The hamartin protein interacts with the tuberin protein IPR003913 from INTERPRO. Tuberous sclerosis complex (TSC) is an autosomal dominant disorder and is characterised by the presence of hamartomas in many organs, such as brain, skin, heart, lung, and kidney. It is caused by mutation in either TSC1 or TSC2 tumour suppressor genes. TSC1 encodes a protein, hamartin, containing two coiled-coil regions, which have been shown to mediate binding to tuberin. The TSC2 gene codes for tuberin IPR003913 from INTERPRO. These two proteins function within the same pathway(s) regulating cell cycle, cell growth, adhesion, and vesicular trafficking [].
Probab=21.16 E-value=1.4e+03 Score=26.90 Aligned_cols=68 Identities=18% Similarity=0.161 Sum_probs=34.0
Q ss_pred hhhhhHHHHHHHHhh------hhccHHHHHHHHHHHhhCCCCCcHHHHHHHHHHHhHhhccCChhHHHHHHHHH
Q 008379 111 QLLAAVKFIAHLVNQ------QVAHEIIALELLTILLENPTDDSVEVAVGFVKECGSILQDLSPKGLHGIFERF 178 (568)
Q Consensus 111 ~~~n~i~fIa~Lyn~------~Vv~~~lildii~~LLe~~te~sVE~ll~lLr~~G~~Lr~~~p~~lk~I~~~l 178 (568)
..+.++.++||++.- .++.-.++-.+++.|.-+.+.--|.+++.+|-.+=+.+-..-+..|.++|.-+
T Consensus 84 ~Rl~~L~Ll~~~v~~qp~~l~~i~~t~Lf~~LLk~L~~D~~~~~~~~al~~LimlLP~ip~~l~~~L~~Lf~If 157 (668)
T PF04388_consen 84 YRLQALTLLGHFVRSQPPWLYKILQTPLFKSLLKCLQFDTSITVVSSALLVLIMLLPHIPSSLGPHLPDLFNIF 157 (668)
T ss_pred hHHHHHHHHHHHHhcCCchHHHHhcChhHHHHHHHHhhcccHHHHHHHHHHHHHHhccccchhhHHHHHHHHHH
Confidence 344566677777664 34455555566666654444334444444444433333333344555544443
No 67
>PF07034 ORC3_N: Origin recognition complex (ORC) subunit 3 N-terminus; InterPro: IPR020795 The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded in yeast by ORC1-6 []. ORC is a central component for eukaryotic DNA replication, and binds chromatin at replication origins throughout the cell cycle []. ORC directs DNA replication throughout the genome and is required for its initiation [, , ]. ORC bound at replication origins serves as the foundation for assembly of the pre-replicative complex (pre-RC), which includes Cdc6, Tah11 (aka Cdt1), and the Mcm2-7 complex [, , ]. Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase [, , ]. Cell cycle-regulated phosphorylation of Orc2, Orc6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase [, , , ]. In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR) [, , ]. ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers [, , ]. Both Orc1 and Orc5 bind ATP, though only Orc1 has ATPase activity []. The binding of ATP by Orc1 is required for ORC binding to DNA and is essential for cell viability []. The ATPase activity of Orc1 is involved in formation of the pre-RC [, , ]. ATP binding by Orc5 is crucial for the stability of ORC as a whole. Only the Orc1-5 subunits are required for origin binding; Orc6 is essential for maintenance of pre-RCs once formed []. Interactions within ORC suggest that Orc2-3-6 may form a core complex []. ORC homologues have been found in various eukaryotes, including fission yeast, insects, amphibians, and humans []. ; GO: 0003677 DNA binding, 0006260 DNA replication, 0005664 nuclear origin of replication recognition complex
Probab=20.94 E-value=9.1e+02 Score=25.46 Aligned_cols=90 Identities=13% Similarity=0.208 Sum_probs=51.3
Q ss_pred HHHHHHHHHHHHHHhhcCChhhHHHHHHHH---HHhhhhh--------hhhHHHHHHhhhccCCCChHHHHHHHHHHHhc
Q 008379 15 RLTWDALRKSINGLVNKVNATNIKNIIPEL---FAENLIR--------GRGLFCRSCMKSQMASPGFTDVFAALVAVVNT 83 (568)
Q Consensus 15 r~~w~~Lkk~I~gllNKLs~~Ni~~i~~eL---~~~Ni~r--------grgll~~si~~~q~~~~~f~~vyAaLva~ln~ 83 (568)
+..|..+..+|+.+++.++..-+..|+.=+ +...... ..+-|--+++-.....|+-..+|..|...|..
T Consensus 36 ~~~W~~~~~~Iq~il~~~n~~~f~~l~~Fi~~~~~~~~~~~~~~~~~~~~~~IPtA~lltGvN~~dh~~~F~~L~~~L~~ 115 (330)
T PF07034_consen 36 QKLWSKIESRIQEILRELNSKLFDDLVDFIRNSHSSDESSARDWASQMNSREIPTALLLTGVNIPDHDLLFEQLSERLQS 115 (330)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccccccccccccccccchHHHHhCCCCccHHHHHHHHHHHHHh
Confidence 367999999999999999988777776533 2111000 00111112222233455556667777666644
Q ss_pred C-C-----------chHHHHHHHHHHHHHHHHHH
Q 008379 84 K-F-----------TAVGELLLKRIVLQLKRAYK 105 (568)
Q Consensus 84 ~-~-----------pe~G~lll~rlv~~F~~~~~ 105 (568)
. . |.++ ..++.++.+|.....
T Consensus 116 ~~~~~vv~L~S~dc~~lk-~~lk~iv~ql~~~~~ 148 (330)
T PF07034_consen 116 SVGPYVVRLNSKDCSNLK-SALKSIVRQLMSDKS 148 (330)
T ss_pred CCCcEEEEEecccchHHH-HHHHHHHHHHHhccc
Confidence 3 2 3443 457777777765544
No 68
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=20.92 E-value=1.5e+03 Score=27.32 Aligned_cols=109 Identities=14% Similarity=0.270 Sum_probs=57.0
Q ss_pred HHHHhhcCChhhHHHHHHHHHHhhhh---hh--------hhHHHHHHhh-hccC-CCChHHHHHHHHHHHhc---CCchH
Q 008379 25 INGLVNKVNATNIKNIIPELFAENLI---RG--------RGLFCRSCMK-SQMA-SPGFTDVFAALVAVVNT---KFTAV 88 (568)
Q Consensus 25 I~gllNKLs~~Ni~~i~~eL~~~Ni~---rg--------rgll~~si~~-~q~~-~~~f~~vyAaLva~ln~---~~pe~ 88 (568)
+..+|...+..+...||.-|-..|-. .| -++|.+-|.- +... .+.| .+.=.|+..|+. .+|+.
T Consensus 431 l~~lL~~~~~~~~~~iI~RIrk~~hpsLa~~NK~Kl~~f~~vLlq~i~~la~~~~~~~~-~~ld~L~~~L~~Laq~~p~~ 509 (840)
T PF04147_consen 431 LLELLDGYSPEDQPTIIQRIRKCYHPSLAEGNKEKLQVFFGVLLQHILYLASQDSPPPF-EVLDSLIPHLYDLAQKYPEE 509 (840)
T ss_pred HHHHHhcCCHHHHhHHHHHHHHhCCCCCCcchHHHHHHHHHHHHHHHHHHhcccCCcCH-HHHHHHHHHHHHHHHHHHHH
Confidence 44566777888888888777543322 12 1444443332 2112 2333 334556666553 35665
Q ss_pred HHHHHHHHHHHHHHHHHh-CC------h--hhhhhhHHHHHHHH-----hhhhccHHHHH
Q 008379 89 GELLLKRIVLQLKRAYKR-ND------K--PQLLAAVKFIAHLV-----NQQVAHEIIAL 134 (568)
Q Consensus 89 G~lll~rlv~~F~~~~~~-~d------k--~~~~n~i~fIa~Ly-----n~~Vv~~~lil 134 (568)
.+..+...+....+.|.+ .- + ...+-++++|+.|| .+.||++.+++
T Consensus 510 ~a~~~r~~L~~~~~~~~~~~l~~~~~~~P~l~~Lvllklv~~lFPTSD~~HpVVTPalll 569 (840)
T PF04147_consen 510 AAECFREVLKEMQKRFRKGALKPKERSWPSLSDLVLLKLVGTLFPTSDFRHPVVTPALLL 569 (840)
T ss_pred HHHHHHHHHHHHHHHHhhhcccccCCCCCChhHHHHHHHHHHhcCcccccCcchhHHHHH
Confidence 554444444444444443 11 1 15566677777776 45677776554
No 69
>PTZ00429 beta-adaptin; Provisional
Probab=20.69 E-value=1.5e+03 Score=27.09 Aligned_cols=57 Identities=5% Similarity=0.194 Sum_probs=38.9
Q ss_pred hhHHHHHHHHhhhhccHHHHHHHHHHHhhCCCCCcHHHHHHHHHHHhHhhccCChhHHHHHH
Q 008379 114 AAVKFIAHLVNQQVAHEIIALELLTILLENPTDDSVEVAVGFVKECGSILQDLSPKGLHGIF 175 (568)
Q Consensus 114 n~i~fIa~Lyn~~Vv~~~lildii~~LLe~~te~sVE~ll~lLr~~G~~Lr~~~p~~lk~I~ 175 (568)
+++=.|||...+ +. -..++|+.+++++.+++.++=+.+|..+.+.+-.. |...+..+
T Consensus 461 aiiWILGEy~~~--I~--~a~~~L~~~i~~f~~E~~~VqlqlLta~vKlfl~~-p~~~~~~l 517 (746)
T PTZ00429 461 SLLWMLGEYCDF--IE--NGKDIIQRFIDTIMEHEQRVQLAILSAAVKMFLRD-PQGMEPQL 517 (746)
T ss_pred HHHHHHHhhHhh--Hh--hHHHHHHHHHhhhccCCHHHHHHHHHHHHHHHhcC-cHHHHHHH
Confidence 445577776442 22 25678888888888899999999999988876654 44344433
No 70
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=20.57 E-value=1.3e+02 Score=24.28 Aligned_cols=33 Identities=30% Similarity=0.634 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHHchHHHHhhc------CCcchhhhh
Q 008379 435 RIFIKILFQELSEHLGIRLLNERL------TDPTMQDSF 467 (568)
Q Consensus 435 riFik~LfqeL~~~lg~~~l~~rl------~d~~~~~~~ 467 (568)
.+=++.++.+|+++.|-+.|-+|+ .||.++..+
T Consensus 8 GvtLe~il~~Lv~~yGW~~L~~~i~i~CF~~~PsikSSL 46 (64)
T PF09905_consen 8 GVTLETILTELVEHYGWEELGERININCFKNNPSIKSSL 46 (64)
T ss_dssp S--HHHHHHHHHHHT-HHHHHHHTTSSSTTSS--HHHHH
T ss_pred chhHHHHHHHHHHHhCHHHHHhhcccccCCCCCchHHHH
Confidence 455788999999999999999886 367776654
Done!