Query 016860
Match_columns 381
No_of_seqs 225 out of 603
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 03:27:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016860.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016860hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2297 Predicted translation 100.0 6E-104 1E-108 753.1 25.1 349 29-381 62-411 (412)
2 KOG1461 Translation initiation 99.9 8.6E-24 1.9E-28 218.3 16.5 164 218-381 504-669 (673)
3 smart00515 eIF5C Domain at the 99.9 4.1E-22 9E-27 159.9 8.4 83 295-377 1-83 (83)
4 PF02020 W2: eIF4-gamma/eIF5/e 99.8 2.6E-21 5.6E-26 155.8 7.9 76 306-381 2-80 (84)
5 KOG2767 Translation initiation 99.5 8.3E-14 1.8E-18 135.8 14.6 96 286-381 292-393 (400)
6 PF09090 MIF4G_like_2: MIF4G l 97.2 0.0056 1.2E-07 59.0 12.9 121 224-354 11-136 (253)
7 KOG1104 Nuclear cap-binding co 94.6 0.61 1.3E-05 50.9 13.4 174 152-355 448-623 (759)
8 KOG2140 Uncharacterized conser 93.9 0.53 1.2E-05 49.8 10.9 134 74-212 504-640 (739)
9 KOG0401 Translation initiation 87.3 0.7 1.5E-05 52.8 4.7 75 114-193 871-945 (970)
10 smart00544 MA3 Domain in DAP-5 83.1 3.4 7.4E-05 34.1 5.9 59 72-133 52-113 (113)
11 PF02847 MA3: MA3 domain; Int 82.8 3.9 8.5E-05 33.7 6.1 59 72-133 52-113 (113)
12 PF02847 MA3: MA3 domain; Int 71.2 55 0.0012 26.7 11.2 103 223-342 2-112 (113)
13 PF11517 Nab2: Nuclear abundan 57.0 49 0.0011 27.7 6.6 71 98-175 16-90 (107)
14 PF10193 Telomere_reg-2: Telom 41.1 89 0.0019 26.4 6.1 67 69-141 18-90 (114)
15 PF02583 Trns_repr_metal: Meta 40.5 54 0.0012 26.3 4.5 43 227-273 18-60 (85)
16 PF08362 TetR_C_3: YcdC-like p 40.0 83 0.0018 27.8 6.0 65 67-134 19-87 (143)
17 PF13972 TetR: Bacterial trans 37.6 1.3E+02 0.0028 25.9 6.8 63 69-134 20-85 (146)
18 PRK11352 regulator protein Frm 35.9 1.6E+02 0.0034 24.1 6.5 29 227-255 22-50 (91)
19 PF07528 DZF: DZF domain; Int 33.5 31 0.00066 33.4 2.3 69 19-87 161-234 (248)
20 KOG2141 Protein involved in hi 33.4 2.3E+02 0.005 31.7 9.0 97 76-177 672-768 (822)
21 KOG3811 Transcription factor A 31.9 6.2E+02 0.013 26.5 12.9 163 151-342 240-414 (434)
22 PF09733 VEFS-Box: VEFS-Box of 30.7 1.9E+02 0.0042 25.5 6.7 61 286-348 67-134 (140)
23 PF14026 DUF4242: Protein of u 29.9 30 0.00065 27.3 1.4 27 51-78 39-65 (77)
24 TIGR02923 AhaC ATP synthase A1 29.8 5.4E+02 0.012 25.1 13.1 112 144-266 121-232 (343)
25 PF09851 SHOCT: Short C-termin 29.0 55 0.0012 21.2 2.2 19 330-348 5-23 (31)
26 cd00620 Methyltransferase_Sun 28.5 2.6E+02 0.0057 23.4 7.1 85 73-165 37-125 (126)
27 PRK15039 transcriptional repre 28.4 2E+02 0.0044 23.5 6.0 29 227-255 22-50 (90)
28 PF03299 TF_AP-2: Transcriptio 27.9 5.2E+02 0.011 24.3 14.2 83 147-252 35-120 (209)
29 KOG2213 Apoptosis inhibitor 5/ 27.5 7.4E+02 0.016 26.0 13.6 116 147-274 89-226 (460)
30 KOG1241 Karyopherin (importin) 25.7 5.9E+02 0.013 28.9 10.5 127 247-376 500-645 (859)
31 PRK10167 hypothetical protein; 25.2 1.8E+02 0.0038 26.6 5.6 74 71-149 70-144 (169)
32 PF08006 DUF1700: Protein of u 24.1 65 0.0014 29.1 2.6 20 188-207 17-38 (181)
33 PF12952 DUF3841: Domain of un 23.8 1.2E+02 0.0026 27.7 4.3 49 186-234 106-154 (178)
34 PF12825 DUF3818: Domain of un 23.7 7.5E+02 0.016 25.1 10.4 72 116-187 156-243 (341)
35 PF03542 Tuberin: Tuberin; In 23.4 5.3E+02 0.012 26.3 9.3 100 223-336 181-281 (356)
36 PF02671 PAH: Paired amphipath 23.3 2.2E+02 0.0047 19.7 4.7 41 291-331 4-44 (47)
37 TIGR03147 cyt_nit_nrfF cytochr 23.2 1.2E+02 0.0026 26.5 3.9 33 218-250 54-86 (126)
38 PRK10144 formate-dependent nit 22.2 1.3E+02 0.0028 26.3 3.9 33 218-250 54-86 (126)
39 PF04286 DUF445: Protein of un 22.1 7.4E+02 0.016 24.1 15.0 218 110-336 36-256 (367)
40 TIGR03652 FeS_repair_RIC iron- 21.8 3.8E+02 0.0083 24.9 7.5 45 229-273 29-75 (216)
41 PF15069 FAM163: FAM163 family 21.6 28 0.00061 30.9 -0.2 8 39-46 6-13 (143)
42 COG1937 Uncharacterized protei 21.5 4.3E+02 0.0092 21.6 6.6 29 227-255 22-50 (89)
43 smart00544 MA3 Domain in DAP-5 21.3 4.4E+02 0.0096 21.3 10.4 100 225-341 4-111 (113)
44 cd08323 CARD_APAF1 Caspase act 21.2 1.9E+02 0.0042 23.3 4.6 48 329-376 16-71 (86)
45 PF13551 HTH_29: Winged helix- 20.8 2.5E+02 0.0053 22.3 5.3 72 192-263 26-106 (112)
46 cd08330 CARD_ASC_NALP1 Caspase 20.7 2.8E+02 0.006 22.0 5.4 50 329-378 17-74 (82)
47 PF10083 DUF2321: Uncharacteri 20.0 3.4E+02 0.0074 24.6 6.2 74 85-164 76-151 (158)
No 1
>KOG2297 consensus Predicted translation factor, contains W2 domain [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.7e-104 Score=753.06 Aligned_cols=349 Identities=47% Similarity=0.798 Sum_probs=343.2
Q ss_pred ccccccceeeeeeecCcCCCCcccCCCCC-CCCceeeccCcchhhhhhHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhc
Q 016860 29 QDTVTPFLRQVVFTGGRTQPGTTKPDEGE-RHSYSIIDCEPQREAILPSVIYIQKILRRRPFLIKNLENVTRRFMQSLEL 107 (381)
Q Consensus 29 ~~~~~~~lf~il~~Gg~l~pgg~~~~d~~-~~~~~if~~~~~~~~~~~~~~~~~kl~rrykyL~k~~e~~~~~~l~~l~~ 107 (381)
-.+|+|.||||+|+||+++|||+.+|||+ +|+||||+|++++|+|++|+|||||||||||||+|+|||+|+|+|+||++
T Consensus 62 ~~rYgd~~fdil~~gg~~~pg~~~sddge~~t~~cvfda~e~~E~i~~~~qvf~KliRRykyLeK~fE~e~~k~Llflk~ 141 (412)
T KOG2297|consen 62 YRRYGDILFDILFAGGRLQPGGVKSDDGERHTSYCVFDAEEKREAIRNSVQVFQKLIRRYKYLEKNFENEMRKFLLFLKL 141 (412)
T ss_pred HHHHHHHHHHHHHHhcccCCCCccccccCccCceeEeecCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 35799999999999999999999999997 56799999999999999999999999999999999999999999999999
Q ss_pred cChhhhHHHHHHHHHHHhhhcCCCCCccchhhhhhhcccCCCchHHHHHHHHHHHHHhCChhHHHHHHHhCCCchhhhhh
Q 016860 108 FEENERKKLAIFTALAFSQKLSGLPPETVFQPLLKDNLVGKGLVLSFITDFFKEYLVDNSLDDLIAILKRGKMEDNLLDF 187 (381)
Q Consensus 108 f~~~~r~kLA~~~a~~~~~~~~g~~~~~~l~~l~~~~Lv~~G~a~~fl~~i~~~~~~~~~~~~l~~~lr~sgl~~~l~~f 187 (381)
|++++|+|||++||++++ +|++|+++|++|+|||||++|++++|++++|++|+.|+|++.|+++||+++|++||++|
T Consensus 142 F~e~Er~KLA~~Tal~l~---nGt~~~tvl~~L~~d~LVkeGi~l~F~~~lFk~~~~Ek~i~~lis~Lrkg~md~rLmef 218 (412)
T KOG2297|consen 142 FEENERKKLAMLTALLLS---NGTLPATVLQSLLNDNLVKEGIALSFAVKLFKEWLVEKDINDLISSLRKGKMDDRLMEF 218 (412)
T ss_pred cCHHHHHHHHHHHHHHHh---CCCCCHHHHHHHHHhhHHHHhHHHHHHHHHHHHHHhhccHHHHHHHHHhcChHhHHHHh
Confidence 999999999999999999 99999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCChhhHHHHHHhcCCCccccchhhhhhHhHHHHHHHHHHHHHhhcCChhHHHHHHHHHhhhcCCCHHHHHHHHHH
Q 016860 188 FPSSKRSAEGFSEHFTKEGLIPLVEYNEKKIFEVKLKDMKSTLTTQIAEETEMSEVIESVKQRVKDAKLPDIEVVRILWD 267 (381)
Q Consensus 188 ~P~~kr~~e~~~~~~~~~gL~~l~~~~~~~~~~~~~~El~~~L~~~l~e~~~~~~ii~eIk~~~~~~n~s~~evi~~l~~ 267 (381)
||||+||.|+|.+||.++||.++++|++.|+++..++|+++.|+..+.++.|.++|+..||+.+...|+|+++||+++|+
T Consensus 219 fPpnkrs~E~Fak~Ft~agL~elvey~~~q~~~~a~kElq~~L~~q~s~e~p~~evi~~VKee~k~~nlPe~eVi~ivWs 298 (412)
T KOG2297|consen 219 FPPNKRSVEHFAKYFTDAGLKELVEYHRNQQSEGARKELQKELQEQVSEEDPVKEVILYVKEEMKRNNLPETEVIGIVWS 298 (412)
T ss_pred cCCcchhHHHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhcCCCCceEEeeeHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhhcccchhhHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHHhccchHHHhHHHHHHHHhhhccccchhhH
Q 016860 268 ILMDAVQWSGKNQQQNANAALRQVKTWAQLLNTFCTNAKLELELMYKVQMQCYEDAKLMKLFPEIVRSLYDQDVLAEDTI 347 (381)
Q Consensus 268 alm~~v~~s~k~~~~~~~~~~~~lk~~~pLL~~f~~~~~~Ql~lL~AlQ~~c~e~~~~~k~f~~Il~~LYd~DVVsEeaI 347 (381)
+||+.++||++ ++++++++++++++|+|||.+||+++++++.+|+.+|.|||+|.++|+.|++|+..||..||++||+|
T Consensus 299 ~iMsaveWnKk-eelva~qalrhlK~yaPLL~af~s~g~sEL~Ll~KvQe~CYen~~fMKaFqkiV~lfYk~dVLsEe~I 377 (412)
T KOG2297|consen 299 GIMSAVEWNKK-EELVAEQALRHLKQYAPLLAAFCSQGQSELELLLKVQEYCYENIHFMKAFQKIVVLFYKADVLSEETI 377 (412)
T ss_pred hhhHHHhhchH-HHHHHHHHHHHHHhhhHHHHHHhcCChHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhhHHH
Confidence 99999999955 88999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhcCCCcchhHHHHHhHHHHHHHHhhcccCC
Q 016860 348 LYWFRKGTNPKGRQTFVKALEPFVKWLEEAEEEE 381 (381)
Q Consensus 348 lkW~~~~~~~~Gk~~~lk~~~~Fv~WLeEAEEEs 381 (381)
++||++++.++||++|++|++|||+||++|||||
T Consensus 378 L~Wyk~gh~~KGk~~FleqmkkFVeWL~~AEEEs 411 (412)
T KOG2297|consen 378 LKWYKEGHVAKGKSVFLEQMKKFVEWLQNAEEES 411 (412)
T ss_pred HHHHHhccccccHHHHHHHHHHHHHHHHhhhhcc
Confidence 9999999999999999999999999999999996
No 2
>KOG1461 consensus Translation initiation factor 2B, epsilon subunit (eIF-2Bepsilon/GCD6) [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=8.6e-24 Score=218.28 Aligned_cols=164 Identities=23% Similarity=0.409 Sum_probs=143.7
Q ss_pred hhHhHHHHHHHHHHHHHhhcCChhHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHhhhhcccc-hhhHHHHHHHHHHHHH
Q 016860 218 IFEVKLKDMKSTLTTQIAEETEMSEVIESVKQRVKDAKLPDIEVVRILWDILMDAVQWSGKNQ-QQNANAALRQVKTWAQ 296 (381)
Q Consensus 218 ~~~~~~~El~~~L~~~l~e~~~~~~ii~eIk~~~~~~n~s~~evi~~l~~alm~~v~~s~k~~-~~~~~~~~~~lk~~~p 296 (381)
....|.+|+..+++|++++++.+|++++|||++|+++|++.+||+++++.|+|+.+.....+. .....++.+.+++|+|
T Consensus 504 d~~~F~~Ev~~s~~ra~Een~~~D~~vlEINslRla~N~s~~ev~~av~~all~~~~~~~~~~~~~~~~~~~~~~~~w~~ 583 (673)
T KOG1461|consen 504 DTKDFEKEVLGSLQRAFEENSDMDNLVLEINSLRLAYNVSLKEVAGAVFMALLKLILHQDHSSMNEVKRAALKVFTQWGP 583 (673)
T ss_pred hhHHHHHHHHHHHHHHHHhccchHHHHHHHhhhHHhhcCCHHHHHHHHHHHHHHHHhcCCCccchhHHHHHHHHHHHhhH
Confidence 345789999999999999999999999999999999999999999999999999976432211 1145578899999999
Q ss_pred HHHHHhcChHHHHHHHHHHHHHhccchHHHhHHHHHHHHhhhccccchhhHhhhhhcCCCcch-hHHHHHhHHHHHHHHh
Q 016860 297 LLNTFCTNAKLELELMYKVQMQCYEDAKLMKLFPEIVRSLYDQDVLAEDTILYWFRKGTNPKG-RQTFVKALEPFVKWLE 375 (381)
Q Consensus 297 LL~~f~~~~~~Ql~lL~AlQ~~c~e~~~~~k~f~~Il~~LYd~DVVsEeaIlkW~~~~~~~~G-k~~~lk~~~~Fv~WLe 375 (381)
++.+|+++.+.|+++|.+++.+|.++..+...+.++++.||+.||++||+|++|++..+...+ ..+.++++++||+||+
T Consensus 584 l~~~y~ks~deqid~l~~led~~~e~~~~~~~~~~~v~~lY~~dil~EdaI~~W~~~~~~~~~~~~~~~~~~k~fv~WL~ 663 (673)
T KOG1461|consen 584 LLGNYIKSEDEQIDLLLALEDKCVESEELGPKAAKLVHYLYDYDILQEDAILSWSSQKAGDDEEDAVYNQQLKKFVDWLK 663 (673)
T ss_pred HhhhhhhhHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHhHhhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999986667788999999999999999999999988443332 3678899999999999
Q ss_pred hcccCC
Q 016860 376 EAEEEE 381 (381)
Q Consensus 376 EAEEEs 381 (381)
||+|||
T Consensus 664 easeE~ 669 (673)
T KOG1461|consen 664 EASEEE 669 (673)
T ss_pred hccccc
Confidence 999885
No 3
>smart00515 eIF5C Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5.
Probab=99.87 E-value=4.1e-22 Score=159.89 Aligned_cols=83 Identities=39% Similarity=0.814 Sum_probs=77.7
Q ss_pred HHHHHHHhcChHHHHHHHHHHHHHhccchHHHhHHHHHHHHhhhccccchhhHhhhhhcCCCcchhHHHHHhHHHHHHHH
Q 016860 295 AQLLNTFCTNAKLELELMYKVQMQCYEDAKLMKLFPEIVRSLYDQDVLAEDTILYWFRKGTNPKGRQTFVKALEPFVKWL 374 (381)
Q Consensus 295 ~pLL~~f~~~~~~Ql~lL~AlQ~~c~e~~~~~k~f~~Il~~LYd~DVVsEeaIlkW~~~~~~~~Gk~~~lk~~~~Fv~WL 374 (381)
+|+|.+|+++.+.|+++|+++|.||+++....+.|+.|++.|||+|||+||+|++||+++++..|+++++++++|||+||
T Consensus 1 ~~ll~~~~~~~~~q~~~L~ale~~~~~~~~~~~~~~~il~~LYd~dileEe~il~W~~~~~~~~~~~~~~~~~~~fv~WL 80 (83)
T smart00515 1 GPLLKFLAKDEEEQIDLLYAIEEFCVELEKLIKLLPKILKSLYDADILEEEAILKWYEKAVSAEGKKKVRKNAKPFVTWL 80 (83)
T ss_pred ChHHHHHHCChHHHHHHHHHHHHHHHHcchHHHHHHHHHHHHhhhccccHHHHHHHHHcCCChHHHHHHHHHHhHHHHHH
Confidence 48999999999999999999999999866688999999999999999999999999999876678899999999999999
Q ss_pred hhc
Q 016860 375 EEA 377 (381)
Q Consensus 375 eEA 377 (381)
+||
T Consensus 81 ~eA 83 (83)
T smart00515 81 QEA 83 (83)
T ss_pred HcC
Confidence 987
No 4
>PF02020 W2: eIF4-gamma/eIF5/eIF2-epsilon; InterPro: IPR003307 This entry represents the W2 domain (two invariant tryptophans) and is a region of ~165 amino acids which is found in the C terminus of the following eIFs [, , , ]: Eukaryotic translation initiation factor 2B epsilon (eIF-2B-epsilon) Eukaryotic translation initiation factor 4 gamma (eIF-4-gamma) Eukaryotic translation initiation factor 5 (eIF-5), a GTPase-activating protein (GAP) specific for eIF2 Translation initiation is a sophisticated, well regulated and highly coordinated cellular process in eukaryotes, in which at least 11 eukayrotic initiation factors (eIFs) are included []. The W2 domain has a globular fold and is exclusively composed out of alpha-helices [, , ]. The structure can be divided into a structural C-terminal core onto which the two N-terminal helices are attached. The core contains two aromatic/acidic residue-rich regions (AA boxes), which are important for mediating protein-protein interactions. For example, the W2 domain of H. sapiens eIF5 binds eIF2-beta, eIF3 and eIF1 [], and therefore plays an important role in multifactor complex assembly. The entry covers the entire W2 domain.; GO: 0005488 binding; PDB: 3D3M_A 3L6A_A 1PAQ_A 2FUL_D 2IU1_A 1UG3_B 3JUI_A.
Probab=99.85 E-value=2.6e-21 Score=155.77 Aligned_cols=76 Identities=41% Similarity=0.846 Sum_probs=65.7
Q ss_pred HHHHHHHHHHHHHhccchHHHhHHHHHHHHhhhccccchhhHhhhhhcCC---CcchhHHHHHhHHHHHHHHhhcccCC
Q 016860 306 KLELELMYKVQMQCYEDAKLMKLFPEIVRSLYDQDVLAEDTILYWFRKGT---NPKGRQTFVKALEPFVKWLEEAEEEE 381 (381)
Q Consensus 306 ~~Ql~lL~AlQ~~c~e~~~~~k~f~~Il~~LYd~DVVsEeaIlkW~~~~~---~~~Gk~~~lk~~~~Fv~WLeEAEEEs 381 (381)
+.|+++|.|+|.||++++++++.|++||+.|||.|||+|++|++||++.. +..|+.+++++++|||+||++|||||
T Consensus 2 ~~Q~~~L~ale~~~~~~~~~~~~~~~il~~LYd~Dil~Eeail~W~~~~~~~~~~~~~~~~r~~~~~fi~WL~eaeeE~ 80 (84)
T PF02020_consen 2 DDQVDLLNALEEFCAENPNLMPLFPKILQQLYDEDILEEEAILEWYEDSKPAVDGEGRAKVRKQAQPFIEWLEEAEEES 80 (84)
T ss_dssp HHHHHHHHHHHHHHHHTCGHGGHHHHHHHHHHHTTSS-HHHHHHHHHC-SSSSCHHHHHHHHHHHHHHHHHHHHCC---
T ss_pred HHHHHHHHHHHHHHHhCccHHHHHHHHHHHHhhhhhccHHHHHHHHHcCCccccchhHHHHHHHHHHHHHHHhccCccC
Confidence 58999999999999999999999999999999999999999999999822 23466889999999999999999985
No 5
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=99.55 E-value=8.3e-14 Score=135.85 Aligned_cols=96 Identities=28% Similarity=0.549 Sum_probs=85.2
Q ss_pred HHHHHHHHHHHHHHHHhcC-hHHHHHHHHHHHHHhcc-chHHHhHHHHHHHHhhhccccchhhHhhhhhcCCCcc-h---
Q 016860 286 AALRQVKTWAQLLNTFCTN-AKLELELMYKVQMQCYE-DAKLMKLFPEIVRSLYDQDVLAEDTILYWFRKGTNPK-G--- 359 (381)
Q Consensus 286 ~~~~~lk~~~pLL~~f~~~-~~~Ql~lL~AlQ~~c~e-~~~~~k~f~~Il~~LYd~DVVsEeaIlkW~~~~~~~~-G--- 359 (381)
.+.+.+.++.++|.+||.+ ...|..+|..|+.+|.. +..+++..+.||+.|||+||++||.|++|+++++..+ +
T Consensus 292 ~ivkei~k~~~~l~k~~~~~~k~qr~LLggiE~~~~~~~~el~~kva~ilk~lYd~DI~~e~vi~~w~~K~skk~vsk~~ 371 (400)
T KOG2767|consen 292 KIVKEILKHRALLLKFCTNNEKAQRYLLGGIERFVEKHEAELISKVAGILKELYDEDILEEEVIIKWGEKPSKKYVSKEK 371 (400)
T ss_pred HHHHHHHHHHHHHHHHHhccHHHHHHHHhHHHHHHHhhHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHhcccccccchhh
Confidence 5678899999999999987 58999999999999996 5677889999999999999999999999999988743 2
Q ss_pred hHHHHHhHHHHHHHHhhcccCC
Q 016860 360 RQTFVKALEPFVKWLEEAEEEE 381 (381)
Q Consensus 360 k~~~lk~~~~Fv~WLeEAEEEs 381 (381)
....++.++||++||++||+||
T Consensus 372 sk~i~e~a~Pfi~WL~~AESe~ 393 (400)
T KOG2767|consen 372 SKKIRENAKPFIEWLKNAESED 393 (400)
T ss_pred hhhhHhhhhHHHHHHHhccccc
Confidence 3678999999999999998653
No 6
>PF09090 MIF4G_like_2: MIF4G like; InterPro: IPR015174 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 2", 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=97.22 E-value=0.0056 Score=58.96 Aligned_cols=121 Identities=12% Similarity=0.190 Sum_probs=85.6
Q ss_pred HHHHHHHHHHHhhcCChhHHHHHHHHHhhhcCCCH----HHHHHHHHHHHHHHhhhhcccchhhHHHHHHHHHHHHHHHH
Q 016860 224 KDMKSTLTTQIAEETEMSEVIESVKQRVKDAKLPD----IEVVRILWDILMDAVQWSGKNQQQNANAALRQVKTWAQLLN 299 (381)
Q Consensus 224 ~El~~~L~~~l~e~~~~~~ii~eIk~~~~~~n~s~----~evi~~l~~alm~~v~~s~k~~~~~~~~~~~~lk~~~pLL~ 299 (381)
+++.+.|.+.+..+.+++++..++++.....+-.. .-.+.++++|++.... |+-. =....|++|++.|+
T Consensus 11 ~~~a~~l~~~ir~k~~~eei~~~l~~i~~~~~~~~~~~~~~~i~v~~q~ll~~GS---kS~S----H~~~~lery~~~Lk 83 (253)
T PF09090_consen 11 HALAQKLLDLIRKKAPPEEISELLEEIEEPAEEHGSDFDKFVIDVFVQCLLHIGS---KSFS----HVLSALERYKEVLK 83 (253)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHHTTS------------HHHHHHHHHHHHHHTT---TSHH----HHHHHHHHTHHHHH
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHhccccccccccchhhHHHHHHHHHHHHhcC---chHH----HHHHHHHHHHHHHH
Confidence 35677888899889999999999888776555332 2355555666665431 2111 34578999999999
Q ss_pred HH-hcChHHHHHHHHHHHHHhccchHHHhHHHHHHHHhhhccccchhhHhhhhhcC
Q 016860 300 TF-CTNAKLELELMYKVQMQCYEDAKLMKLFPEIVRSLYDQDVLAEDTILYWFRKG 354 (381)
Q Consensus 300 ~f-~~~~~~Ql~lL~AlQ~~c~e~~~~~k~f~~Il~~LYd~DVVsEeaIlkW~~~~ 354 (381)
.+ +.+...|..+|.++-.|-..+|... .-+++.|=+.+||+-.+|..|-=+.
T Consensus 84 ~l~~~~~~~q~~il~~v~~~W~~~~q~~---~li~dkll~~~ii~~~~Vv~w~f~~ 136 (253)
T PF09090_consen 84 ELEAESEEAQFWILDAVFRFWKNNPQMG---FLIIDKLLNYGIISPSAVVNWVFSP 136 (253)
T ss_dssp HH-TSSHHHHHHHHHHHHHHHTT-HHHH---HHHHHHHHHTTSS-HHHHHHHHTSG
T ss_pred HhccCChHHHHHHHHHHHHHHhcCCcee---hHHHHHHHhcCCCCHHHHHHHHcCc
Confidence 99 8888999999999999999888763 5678999999999999999998443
No 7
>KOG1104 consensus Nuclear cap-binding complex, subunit NCBP1/CBP80 [RNA processing and modification]
Probab=94.55 E-value=0.61 Score=50.93 Aligned_cols=174 Identities=9% Similarity=0.131 Sum_probs=114.4
Q ss_pred HHHHHHHHHHHHHhCChhHHHHHHHhCCCchhhhhhCCCCCCChhhHHHHHHhcCCCccccchhhhhhHhHHHHHHHHHH
Q 016860 152 LSFITDFFKEYLVDNSLDDLIAILKRGKMEDNLLDFFPSSKRSAEGFSEHFTKEGLIPLVEYNEKKIFEVKLKDMKSTLT 231 (381)
Q Consensus 152 ~~fl~~i~~~~~~~~~~~~l~~~lr~sgl~~~l~~f~P~~kr~~e~~~~~~~~~gL~~l~~~~~~~~~~~~~~El~~~L~ 231 (381)
-.|+-++++.=++......+..++- . -+.+++|+.. .+ +|. ++.++-..+. .+-+..++.
T Consensus 448 ~~FvreviqkelrLsy~~rI~dslP----~-~~~~l~P~~~-~p-ny~-----y~~Ee~~~~~--------~~~~~~~l~ 507 (759)
T KOG1104|consen 448 PNFVREVIQKELRLSYYQRIKDSLP----T-LLAKLLPPPP-LP-NYK-----YTDEEDPVLP--------QSLVAVQLI 507 (759)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHhhh----H-HHHHhCCCCC-CC-cee-----eecccCcccc--------chHHHHHHH
Confidence 3577777777666666666666664 2 1566677653 22 221 1111111111 111567888
Q ss_pred HHHhhcCChhHHHHHHHHHhhhcCCCHH-HHHHHHHHHHHHHhhhhcccchhhHHHHHHHHHHHHHHHHHHhcChH-HHH
Q 016860 232 TQIAEETEMSEVIESVKQRVKDAKLPDI-EVVRILWDILMDAVQWSGKNQQQNANAALRQVKTWAQLLNTFCTNAK-LEL 309 (381)
Q Consensus 232 ~~l~e~~~~~~ii~eIk~~~~~~n~s~~-evi~~l~~alm~~v~~s~k~~~~~~~~~~~~lk~~~pLL~~f~~~~~-~Ql 309 (381)
.++++..++++++.||++.-.....+.. =.+.++++++++... |+-+ -+...+.+|..+|.++|.+.. .|.
T Consensus 508 ~~~~~k~~~e~~~~iLk~~~~~~~~~~n~~~i~lfvq~~l~lGS---KSfS----H~f~~lek~~~vfk~l~~~~e~~q~ 580 (759)
T KOG1104|consen 508 VAFREKATAEEIVNILKSEDESEIGSFNRLKIILFVQTLLDLGS---KSFS----HAFSALEKYHTVFKKLCEDSETKQI 580 (759)
T ss_pred HHHhccCCHHHHHHHHhcCccccccCCcceehhhHHHHHHHhcc---chhh----hHHHHHHHHHHHHHHHhcCCchhHH
Confidence 9999999999999999932212222222 245667777777642 2222 235788999999999998875 599
Q ss_pred HHHHHHHHHhccchHHHhHHHHHHHHhhhccccchhhHhhhhhcCC
Q 016860 310 ELMYKVQMQCYEDAKLMKLFPEIVRSLYDQDVLAEDTILYWFRKGT 355 (381)
Q Consensus 310 ~lL~AlQ~~c~e~~~~~k~f~~Il~~LYd~DVVsEeaIlkW~~~~~ 355 (381)
.+|.++=.+...||... ..+.+.|-...||+=.+|..|-=+..
T Consensus 581 ~vl~~vft~Wk~n~Qm~---~v~~Dkml~~~ii~~~aVv~WiF~~~ 623 (759)
T KOG1104|consen 581 IVLEAVFTFWKANPQMG---FVLTDKMLKYQIIDCSAVVRWIFSEE 623 (759)
T ss_pred HHHHHHHHHHhcCchhh---HHHHHHHhccccccHHHHHHHhcCHH
Confidence 99999988888877643 44568888899999999999985443
No 8
>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]
Probab=93.89 E-value=0.53 Score=49.77 Aligned_cols=134 Identities=22% Similarity=0.262 Sum_probs=102.3
Q ss_pred hhHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhccChhhhHHHHHHHHHHHhhhcCCCCCccchhh--hhhhcccCCCch
Q 016860 74 LPSVIYIQKILRRRPFLIKNLENVTRRFMQSLELFEENERKKLAIFTALAFSQKLSGLPPETVFQP--LLKDNLVGKGLV 151 (381)
Q Consensus 74 ~~~~~~~~kl~rrykyL~k~~e~~~~~~l~~l~~f~~~~r~kLA~~~a~~~~~~~~g~~~~~~l~~--l~~~~Lv~~G~a 151 (381)
|=|--+-.++++=++-.+-.||+..+.--.-|+.++-+.-.-||.|.|.+++ ..-+|..||.- |.-+.=...|.
T Consensus 504 kFYglL~eRfc~l~r~~q~~fe~~f~q~YstIhr~EtnkLRnlakffahLls---td~lpw~vl~~ikLTEEdTtsssR- 579 (739)
T KOG2140|consen 504 KFYGLLGERFCMLHREWQEAFEKCFKQQYSTIHRYETNKLRNLAKFFAHLLS---TDALPWDVLACIKLTEEDTTSSSR- 579 (739)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhc---ccccchHHHHHhhcccccCCccce-
Confidence 3344455566666666777777766555555888888888999999999999 99999999975 33333333333
Q ss_pred HHHHHHHHHHHHHhCChhHHHHHHHhCCCchhhhhhCCCCCCChhhHH-HHHHhcCCCcccc
Q 016860 152 LSFITDFFKEYLVDNSLDDLIAILKRGKMEDNLLDFFPSSKRSAEGFS-EHFTKEGLIPLVE 212 (381)
Q Consensus 152 ~~fl~~i~~~~~~~~~~~~l~~~lr~sgl~~~l~~f~P~~kr~~e~~~-~~~~~~gL~~l~~ 212 (381)
-|+--+|+.++...|.+.|..-+....|...+..+||-....--.|. .+|+.-||+-+.+
T Consensus 580 -IfiKilFqELve~lGl~~L~~RL~dptl~~~l~glFP~dnp~n~RfsINfFTsIGLGgLTe 640 (739)
T KOG2140|consen 580 -IFIKILFQELVEALGLDKLNERLNDPTLQPKLEGLFPRDNPRNTRFSINFFTSIGLGGLTE 640 (739)
T ss_pred -ehHHHHHHHHHHHhChHHHHHHhcCcchhhhhhccCcCCCcccceeeeehhhhhccccchH
Confidence 38888999999999999999999999998889999998643333453 7899999987765
No 9
>KOG0401 consensus Translation initiation factor 4F, ribosome/mRNA-bridging subunit (eIF-4G) [Translation, ribosomal structure and biogenesis]
Probab=87.26 E-value=0.7 Score=52.76 Aligned_cols=75 Identities=9% Similarity=0.062 Sum_probs=72.1
Q ss_pred HHHHHHHHHHHhhhcCCCCCccchhhhhhhcccCCCchHHHHHHHHHHHHHhCChhHHHHHHHhCCCchhhhhhCCCCCC
Q 016860 114 KKLAIFTALAFSQKLSGLPPETVFQPLLKDNLVGKGLVLSFITDFFKEYLVDNSLDDLIAILKRGKMEDNLLDFFPSSKR 193 (381)
Q Consensus 114 ~kLA~~~a~~~~~~~~g~~~~~~l~~l~~~~Lv~~G~a~~fl~~i~~~~~~~~~~~~l~~~lr~sgl~~~l~~f~P~~kr 193 (381)
.+++.+.+..+. .|.+..+.+.+....+.-+.|.+..++-.++..++++.|.+++..+||++++. |.+|+|++..
T Consensus 871 ~~~~e~~gp~~~---~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s--~~~~~~~~~~ 945 (970)
T KOG0401|consen 871 NYIKEFLGPLIH---QKILDESELVREILKNMRPNGRRSNVLFSVLEIVEKELGRADLGDIQRESFLS--TKTLLQENSQ 945 (970)
T ss_pred hHHHHhhhhHhh---hccccHHHHHHHHhhcCCccccccchHHHHHHHHHHhhhHHHHHHHHHHhccc--chhcccccch
Confidence 899999999999 89999999999999999999999999999999999999999999999999999 8999999874
No 10
>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=83.14 E-value=3.4 Score=34.14 Aligned_cols=59 Identities=22% Similarity=0.278 Sum_probs=51.1
Q ss_pred hhhhHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhccCh---hhhHHHHHHHHHHHhhhcCCCCC
Q 016860 72 AILPSVIYIQKILRRRPFLIKNLENVTRRFMQSLELFEE---NERKKLAIFTALAFSQKLSGLPP 133 (381)
Q Consensus 72 ~~~~~~~~~~kl~rrykyL~k~~e~~~~~~l~~l~~f~~---~~r~kLA~~~a~~~~~~~~g~~~ 133 (381)
.-..|.+++..|..+...-...|++-+.+++..++-.+- .....+|.+.|++++ +|.+|
T Consensus 52 ~~~~~~~Ll~~L~~~~~~~~~~~~~~f~~~~~~l~dl~~D~P~a~~~la~~~a~~v~---~~~l~ 113 (113)
T smart00544 52 YREMYSVLLSRLCQANVISTKQFEKGFWRLLEDIEDLELDIPNAWRNLAEFVARLIS---DGILP 113 (113)
T ss_pred HHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHhhChhhhcccccHHHHHHHHHHHHHH---cCCCC
Confidence 566777899999989888888999988888888888755 578999999999999 99886
No 11
>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=82.80 E-value=3.9 Score=33.66 Aligned_cols=59 Identities=19% Similarity=0.210 Sum_probs=48.6
Q ss_pred hhhhHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhccChh---hhHHHHHHHHHHHhhhcCCCCC
Q 016860 72 AILPSVIYIQKILRRRPFLIKNLENVTRRFMQSLELFEEN---ERKKLAIFTALAFSQKLSGLPP 133 (381)
Q Consensus 72 ~~~~~~~~~~kl~rrykyL~k~~e~~~~~~l~~l~~f~~~---~r~kLA~~~a~~~~~~~~g~~~ 133 (381)
.-..|..++..|+.+...-...+++-+.+++..+.-..-. .-.++|.++|.+++ +|.+|
T Consensus 52 ~r~~~~~Ll~~L~~~~~~~~~~~~~gf~~~l~~l~Dl~~D~P~~~~~la~~~~~~i~---~~~lp 113 (113)
T PF02847_consen 52 YREYYSKLLSHLCKRKLISKEQFQEGFEDLLESLEDLELDIPKAPEYLAKFLARLIA---DGILP 113 (113)
T ss_dssp HHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHH---TTSS-
T ss_pred HHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHhHhhhccccchHHHHHHHHHHHHHHH---cCCcC
Confidence 4566788999999999888888888888888888776555 68999999999999 99887
No 12
>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=71.22 E-value=55 Score=26.69 Aligned_cols=103 Identities=16% Similarity=0.233 Sum_probs=62.4
Q ss_pred HHHHHHHHHHHHhhcCChhHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHhhhhcccchhhHHHHHHHHHHHHHHHHHHh
Q 016860 223 LKDMKSTLTTQIAEETEMSEVIESVKQRVKDAKLPDIEVVRILWDILMDAVQWSGKNQQQNANAALRQVKTWAQLLNTFC 302 (381)
Q Consensus 223 ~~El~~~L~~~l~e~~~~~~ii~eIk~~~~~~n~s~~evi~~l~~alm~~v~~s~k~~~~~~~~~~~~lk~~~pLL~~f~ 302 (381)
++.+...|...+.. .+.++++.-|+++..+ --.++|++.++...++.- + ..-+.+..++..++
T Consensus 2 rk~i~~~l~ey~~~-~d~~ea~~~l~el~~~--~~~~~vv~~~l~~~le~~----~----------~~r~~~~~Ll~~L~ 64 (113)
T PF02847_consen 2 RKKIFSILMEYFSS-GDVDEAVECLKELKLP--SQHHEVVKVILECALEEK----K----------SYREYYSKLLSHLC 64 (113)
T ss_dssp HHHHHHHHHHHHHH-T-HHHHHHHHHHTT-G--GGHHHHHHHHHHHHHTSS----H----------HHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHhcC-CCHHHHHHHHHHhCCC--ccHHHHHHHHHHHHhhcc----H----------HHHHHHHHHHHHHH
Confidence 34566666666654 5888888888886554 346677777777666641 1 12234556666666
Q ss_pred cCh-HHHHHHHHHHHHHh-------ccchHHHhHHHHHHHHhhhcccc
Q 016860 303 TNA-KLELELMYKVQMQC-------YEDAKLMKLFPEIVRSLYDQDVL 342 (381)
Q Consensus 303 ~~~-~~Ql~lL~AlQ~~c-------~e~~~~~k~f~~Il~~LYd~DVV 342 (381)
..+ -.+-++..+++.+. .+-|+....+..++-.+...|+|
T Consensus 65 ~~~~~~~~~~~~gf~~~l~~l~Dl~~D~P~~~~~la~~~~~~i~~~~l 112 (113)
T PF02847_consen 65 KRKLISKEQFQEGFEDLLESLEDLELDIPKAPEYLAKFLARLIADGIL 112 (113)
T ss_dssp HTTSS-HHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTSS
T ss_pred hcCCCCHHHHHHHHHHHHhHhhhccccchHHHHHHHHHHHHHHHcCCc
Confidence 443 34444444554443 34477777888888888888876
No 13
>PF11517 Nab2: Nuclear abundant poly(A) RNA-bind protein 2 (Nab2); InterPro: IPR021083 Nab2 is a yeast heterogeneous nuclear ribonucleoprotein that modulates poly(A) tail length and mRNA. This is the N-terminal domain of the protein which mediates interactions with the C-terminal globular domain, Myosin-like protein 1 and the mRNA export factor, Gfd1 []. The N-terminal domain of Nab2 shows a structure of a helical fold. The N-terminal domain of Nab2 is thought to mediate protein:protein interactions that facilitate the nuclear export of mRNA []. An essential hydrophobic Phe73 patch on the N-terminal domain is thought to be an important component of the interface between Nab2 and Mlp1 [].; PDB: 3LCN_B 2V75_A 2JPS_A.
Probab=56.97 E-value=49 Score=27.71 Aligned_cols=71 Identities=21% Similarity=0.244 Sum_probs=44.3
Q ss_pred HHHHHHHhhccChhhhHHHHHHHHHHHhhhcCCCCCccchhhhhhhcccCCCchHHHHHH----HHHHHHHhCChhHHHH
Q 016860 98 TRRFMQSLELFEENERKKLAIFTALAFSQKLSGLPPETVFQPLLKDNLVGKGLVLSFITD----FFKEYLVDNSLDDLIA 173 (381)
Q Consensus 98 ~~~~l~~l~~f~~~~r~kLA~~~a~~~~~~~~g~~~~~~l~~l~~~~Lv~~G~a~~fl~~----i~~~~~~~~~~~~l~~ 173 (381)
+-.-|.-+.+|++ +-+|.|.++-++|+ ||.-+.++++.|. .|- |+++-..++. .|..+-..++-+.+..
T Consensus 16 VaEkL~~l~NFnE-Dv~YVAEyIvlLis---Nggs~esivqELs--sLF-D~vs~~~l~~VVQtaF~ale~Lq~Ge~~e~ 88 (107)
T PF11517_consen 16 VAEKLKTLPNFNE-DVNYVAEYIVLLIS---NGGSVESIVQELS--SLF-DSVSTEALTDVVQTAFFALEALQQGETVEN 88 (107)
T ss_dssp HHHHHTTSTT--S-SHHHHHHHHHHHHH---TT--HHHHHHHHH--HH--TTS-HHHHHHHHHHHHHHHHHHHTT--HHH
T ss_pred HHHHHccccCccc-cHHHHHHHhheeee---CCCCHHHHHHHHH--HHH-hccCHHHHHHHHHHHHHHHHHHhCCCcHHH
Confidence 4455677878875 46899999999999 9999999998764 233 7777777766 4555544444444444
Q ss_pred HH
Q 016860 174 IL 175 (381)
Q Consensus 174 ~l 175 (381)
+.
T Consensus 89 iv 90 (107)
T PF11517_consen 89 IV 90 (107)
T ss_dssp HH
T ss_pred HH
Confidence 43
No 14
>PF10193 Telomere_reg-2: Telomere length regulation protein; InterPro: IPR019337 This entry represents a conserved domain found in a group of proteins called telomere-length regulation, or clock abnormal protein-2, which are conserved from plants to humans. These proteins regulate telomere length and contribute to silencing of sub-telomeric regions []. In vitro the protein binds to telomeric DNA repeats. ; PDB: 3O4Z_B.
Probab=41.11 E-value=89 Score=26.40 Aligned_cols=67 Identities=21% Similarity=0.312 Sum_probs=38.4
Q ss_pred chhhhhhHHHHHHHHHhhhhH----HHHHHHHHHHHHHHHhhccChhh--hHHHHHHHHHHHhhhcCCCCCccchhhhh
Q 016860 69 QREAILPSVIYIQKILRRRPF----LIKNLENVTRRFMQSLELFEENE--RKKLAIFTALAFSQKLSGLPPETVFQPLL 141 (381)
Q Consensus 69 ~~~~~~~~~~~~~kl~rryky----L~k~~e~~~~~~l~~l~~f~~~~--r~kLA~~~a~~~~~~~~g~~~~~~l~~l~ 141 (381)
+.|.+..-.+...+||||.+= +...-++-++.++.-=+.|+.++ ..+...++|++++ .|..+..-|+
T Consensus 18 ~~e~~e~aL~~a~~LIR~k~~fg~el~~~a~eL~~~Ll~L~~~f~~~~Fe~~R~~alval~v~------~P~~~~~~L~ 90 (114)
T PF10193_consen 18 DYEKFEAALKSAEKLIRRKPDFGTELSEYAEELLKALLHLQNKFDIENFEELRQNALVALVVA------APEKVAPYLT 90 (114)
T ss_dssp --S-SHHHHHHHHHHHHS-----SSHHHHHHHHHHHHHH---TT--TTTTHHHHHHHHHHHHH------SGGGHHH-HH
T ss_pred CHHHHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHHHhhccccCCccCHHHHHHHHHHHHHHH------hhHHHHHHHH
Confidence 577788888899999999998 44444444444443333465443 7889999999998 5655555433
No 15
>PF02583 Trns_repr_metal: Metal-sensitive transcriptional repressor; InterPro: IPR003735 This entry describes proteins of unknown function.; PDB: 2HH7_A 3AAI_A 4ADZ_B.
Probab=40.51 E-value=54 Score=26.28 Aligned_cols=43 Identities=7% Similarity=0.221 Sum_probs=31.7
Q ss_pred HHHHHHHHhhcCChhHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHh
Q 016860 227 KSTLTTQIAEETEMSEVIESVKQRVKDAKLPDIEVVRILWDILMDAV 273 (381)
Q Consensus 227 ~~~L~~~l~e~~~~~~ii~eIk~~~~~~n~s~~evi~~l~~alm~~v 273 (381)
.+.+.++++++.++.+|...|.+.+.+-+ .+...++..-+..+
T Consensus 18 v~gI~~Miee~~~C~dIl~Qi~Av~~Al~----~~~~~vl~~hl~~c 60 (85)
T PF02583_consen 18 VRGIERMIEEDRDCEDILQQIAAVRSALD----KVGKLVLEDHLEHC 60 (85)
T ss_dssp HHHHHHHHHTTE-HHHHHHHHHHHHHHHH----HHHHHHHHHHHHHH
T ss_pred HHHHHHHHhCCCCHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHH
Confidence 45678899999999999999999888754 56666665555543
No 16
>PF08362 TetR_C_3: YcdC-like protein, C-terminal region; InterPro: IPR013573 This entry represents the C-terminal domain found in the hypothetical transcriptional regulators RutR and YcdC (P75899 from SWISSPROT) from Escherichia coli. Both of these proteins are member of the TetR (tetracycline resistance) transcriptional regulator family of proteins. RutR negatively controls the transcription of the rut operon involved in pyrimidine utilization. The C-terminal domains of RutR, YsiA and TetR share a multi-helical, interlocking structure. These proteins also contain helix-turn-helix (HTH) DNA-binding domains.; GO: 0045892 negative regulation of transcription, DNA-dependent; PDB: 3LOC_B.
Probab=40.00 E-value=83 Score=27.80 Aligned_cols=65 Identities=11% Similarity=-0.024 Sum_probs=45.5
Q ss_pred CcchhhhhhHHHHHHHHHhhhhHHHHHHHHHH----HHHHHHhhccChhhhHHHHHHHHHHHhhhcCCCCCc
Q 016860 67 EPQREAILPSVIYIQKILRRRPFLIKNLENVT----RRFMQSLELFEENERKKLAIFTALAFSQKLSGLPPE 134 (381)
Q Consensus 67 ~~~~~~~~~~~~~~~kl~rrykyL~k~~e~~~----~~~l~~l~~f~~~~r~kLA~~~a~~~~~~~~g~~~~ 134 (381)
.+..++++.|+.-.-.+-|+||..-|.|=.|+ +.+-.|++..-...-+..+..+..|+. .|.+.+
T Consensus 19 ~dP~~aL~~YI~~k~~~s~~~P~~Srlfa~Eii~Gap~L~~~l~~~l~~~~~~~~~~I~~Wi~---~G~i~~ 87 (143)
T PF08362_consen 19 DDPAEALRAYIRAKMEYSRDHPEASRLFANEIIQGAPHLKDYLRERLRPWVDRKVAVIERWIA---QGKIAP 87 (143)
T ss_dssp S-HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHTTSTTTHHHHHTHHHHHHHHHHHHHHHHHH---TTSS-S
T ss_pred CCHHHHHHHHHHHHHHHHHHCchhhHHHHHHHHcCchhhHHHHHHHHHHHHHHHHHHHHHHHH---CCCCCC
Confidence 34566999999999999999999999999986 345556543322222334557788889 898843
No 17
>PF13972 TetR: Bacterial transcriptional repressor; PDB: 3RH2_A 3NNR_A.
Probab=37.62 E-value=1.3e+02 Score=25.92 Aligned_cols=63 Identities=14% Similarity=0.276 Sum_probs=42.1
Q ss_pred chhhhhhHHHHHHHHHhhhhHHHHHHHHHHHH---HHHHhhccChhhhHHHHHHHHHHHhhhcCCCCCc
Q 016860 69 QREAILPSVIYIQKILRRRPFLIKNLENVTRR---FMQSLELFEENERKKLAIFTALAFSQKLSGLPPE 134 (381)
Q Consensus 69 ~~~~~~~~~~~~~kl~rrykyL~k~~e~~~~~---~l~~l~~f~~~~r~kLA~~~a~~~~~~~~g~~~~ 134 (381)
+.|.+-.|....-.+|.||+|+-+.+-+-+.+ +-.-...+...-+..+..+...++. .|.+.+
T Consensus 20 ~le~~~~~l~~~f~~~w~YRF~~~dl~~Ll~~~p~L~~~~~~~~~~~~~~~~~l~~~l~~---~g~l~~ 85 (146)
T PF13972_consen 20 SLEDLWNYLDSVFELMWRYRFFYRDLPDLLRRDPELKKRYRQLQQRRREQLRQLLQSLIE---AGILRI 85 (146)
T ss_dssp SHHHHHHHHHHHHHHHHHTHHHHHSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHH---TTSB--
T ss_pred CHHHHHHHHHHHHHHHHHhhhHHccHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHHHH---CCCCCC
Confidence 77899999999999999999999998886533 3332222333334455555555666 776653
No 18
>PRK11352 regulator protein FrmR; Provisional
Probab=35.85 E-value=1.6e+02 Score=24.09 Aligned_cols=29 Identities=10% Similarity=0.218 Sum_probs=24.6
Q ss_pred HHHHHHHHhhcCChhHHHHHHHHHhhhcC
Q 016860 227 KSTLTTQIAEETEMSEVIESVKQRVKDAK 255 (381)
Q Consensus 227 ~~~L~~~l~e~~~~~~ii~eIk~~~~~~n 255 (381)
.+.+.++++++.++.+|+..+.+.+.+-+
T Consensus 22 v~gi~~Mie~~~~C~dil~Ql~Avr~Al~ 50 (91)
T PRK11352 22 IDALERSLEGDAECRAILQQIAAVRGAAN 50 (91)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHH
Confidence 45678899999999999999999887754
No 19
>PF07528 DZF: DZF domain; InterPro: IPR006561 This domain is found in proteins containing the double-stranded RNA-binding motif, DSRM (IPR001159 from INTERPRO), or the zinc finger domain C2H2 (IPR007087 from INTERPRO). This domain is found exclusively in the metazoa.
Probab=33.48 E-value=31 Score=33.41 Aligned_cols=69 Identities=20% Similarity=0.235 Sum_probs=48.8
Q ss_pred hhhhccccccccccccceeee--eeecCcCCCCcccCCCC-CCCCceeecc--CcchhhhhhHHHHHHHHHhhh
Q 016860 19 SALNLLTLTSQDTVTPFLRQV--VFTGGRTQPGTTKPDEG-ERHSYSIIDC--EPQREAILPSVIYIQKILRRR 87 (381)
Q Consensus 19 ~~~~~~~~~~~~~~~~~lf~i--l~~Gg~l~pgg~~~~d~-~~~~~~if~~--~~~~~~~~~~~~~~~kl~rry 87 (381)
++++-.++....++++.|=-| ++|+|+|=|||.-+.|= ++.++.+.++ ..++|.|-..+|-+-|++--.
T Consensus 161 ~~i~~~~~~~~l~~g~a~RRvle~lasGillp~~~gl~DPcE~~~~~~~~~lt~qq~e~it~sAQ~~LRllafg 234 (248)
T PF07528_consen 161 KAISNNSSRQPLSPGDAFRRVLECLASGILLPGSPGLRDPCEKDPVDVLDTLTLQQREDITSSAQTALRLLAFG 234 (248)
T ss_pred HHeeeCCCCCCCChHHHHHHHHHHHhCceecCCCCCCcCCCCCCCceeeccCCHHHHHHHHHHHHHHHHHHHhc
Confidence 344433455566777665433 37999999998877653 4678888885 668889999999888887433
No 20
>KOG2141 consensus Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms]
Probab=33.38 E-value=2.3e+02 Score=31.73 Aligned_cols=97 Identities=15% Similarity=0.135 Sum_probs=62.2
Q ss_pred HHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhccChhhhHHHHHHHHHHHhhhcCCCCCccchhhhhhhcccCCCchHHHH
Q 016860 76 SVIYIQKILRRRPFLIKNLENVTRRFMQSLELFEENERKKLAIFTALAFSQKLSGLPPETVFQPLLKDNLVGKGLVLSFI 155 (381)
Q Consensus 76 ~~~~~~kl~rrykyL~k~~e~~~~~~l~~l~~f~~~~r~kLA~~~a~~~~~~~~g~~~~~~l~~l~~~~Lv~~G~a~~fl 155 (381)
|+-+-+|+--+++-+++.|.=.+=-.+.=++..+...+.-||.++|-+|+ +-..|++||.+.==-.| +-...-|+
T Consensus 672 Ya~lA~KfCe~~~~~~~tfQF~~WD~f~ele~ls~~ri~nLa~l~a~Li~---~~~lsLtVLK~Vdfm~l--~~~~~~fl 746 (822)
T KOG2141|consen 672 YALLALKFCEFNKNLKKTFQFALWDRFKELEQLSLFRISNLAKLLASLIS---NAVLSLTVLKHVDFMEL--NARRTTFL 746 (822)
T ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHHHHhhhcchhhHhHHHHHHHHHHH---hcccceeeeeeccHhhc--ChHHHHHH
Confidence 45566667777777777776544444444555677788999999999999 99999999975210011 12223466
Q ss_pred HHHHHHHHHhCChhHHHHHHHh
Q 016860 156 TDFFKEYLVDNSLDDLIAILKR 177 (381)
Q Consensus 156 ~~i~~~~~~~~~~~~l~~~lr~ 177 (381)
..+|-.++.+...+.+..++.+
T Consensus 747 ~~~l~~l~l~~~~~~v~~~ftr 768 (822)
T KOG2141|consen 747 KKLLFGLILEPEEKDVFQLFTR 768 (822)
T ss_pred HHHHHHHHhcchHHHHHHHHHH
Confidence 6666666666555555555543
No 21
>KOG3811 consensus Transcription factor AP-2 [Transcription]
Probab=31.86 E-value=6.2e+02 Score=26.53 Aligned_cols=163 Identities=12% Similarity=0.083 Sum_probs=86.9
Q ss_pred hHHHHHHHHHHHHHhCChhHHHHHHHhCCCchhhhhhCCCCCCChhhHHHHHHhcCCCccccchhhhhhHhHHHHHHHHH
Q 016860 151 VLSFITDFFKEYLVDNSLDDLIAILKRGKMEDNLLDFFPSSKRSAEGFSEHFTKEGLIPLVEYNEKKIFEVKLKDMKSTL 230 (381)
Q Consensus 151 a~~fl~~i~~~~~~~~~~~~l~~~lr~sgl~~~l~~f~P~~kr~~e~~~~~~~~~gL~~l~~~~~~~~~~~~~~El~~~L 230 (381)
-.+++-=||+.-.+..|.+.|-+.|++-||+ +|.+.|...+. .- |..|+|-. .. -+-+.+
T Consensus 240 NaSlLggvLRRaKsKnGGr~lRe~L~k~Gln------lpagrRkaAnV-T~-----ltsLVE~E-------Av-HLArDf 299 (434)
T KOG3811|consen 240 NASLLGGVLRRAKSKNGGRLLREKLTKIGLN------LPAGRRKAANV-TL-----LTSLVEEE-------AV-HLARDF 299 (434)
T ss_pred hhHhhhhhhhhhhhcchHHHHHHHHHHcCCC------Ccccchhhccc-hh-----hhHHHHHH-------HH-HHHHhh
Confidence 3577888999999999999999999999998 68887743211 11 11222211 00 122233
Q ss_pred HHHHhhcCChhHHHHHHHHHhhhcCCCHHHHHHHHH--HHHHHHhhh------hcc----cchhhHHHHHHHHHHHHHHH
Q 016860 231 TTQIAEETEMSEVIESVKQRVKDAKLPDIEVVRILW--DILMDAVQW------SGK----NQQQNANAALRQVKTWAQLL 298 (381)
Q Consensus 231 ~~~l~e~~~~~~ii~eIk~~~~~~n~s~~evi~~l~--~alm~~v~~------s~k----~~~~~~~~~~~~lk~~~pLL 298 (381)
--..+++-+.+.|..++..-.++.+-......+++- +.+|+.... ..+ +.....-.+-..+..+. |
T Consensus 300 ~~vcE~efP~~~Iae~l~r~~l~~~~~~~~rk~ml~~t~q~~ke~~~lLsqdRtP~~~~rp~pll~~~lq~~lthFS--L 377 (434)
T KOG3811|consen 300 GYVCETEFPARAIAEELLRKHLAPENDLDDRKNMLLATTQICKELTDLLSQDRTPLTTSRPEPLLEPSLQNHLTHFS--L 377 (434)
T ss_pred hhhhhhhccHHHHHHHHHHHhhcCchhHHHHHHHHHHHHHHHHHHHHHHhcccCCCCCCCcccccCchhhhhhhhhh--h
Confidence 333456677788888877766655323333333322 444444321 111 11111112223444433 1
Q ss_pred HHHhcChHHHHHHHHHHHHHhccchHHHhHHHHHHHHhhhcccc
Q 016860 299 NTFCTNAKLELELMYKVQMQCYEDAKLMKLFPEIVRSLYDQDVL 342 (381)
Q Consensus 299 ~~f~~~~~~Ql~lL~AlQ~~c~e~~~~~k~f~~Il~~LYd~DVV 342 (381)
..--.+...+.+.|.++|.+..+-. ..+..+|.....
T Consensus 378 iTHGFG~pa~~a~l~s~q~il~eal-------~~leK~~~~~~~ 414 (434)
T KOG3811|consen 378 ITHGFGSPAICAALRSLQNILNEAL-------KYLEKLTEGNTL 414 (434)
T ss_pred hhccCCcHHHHHHHHHHHHHHHHHH-------HHHHHHccCCCC
Confidence 1111224788999999998877632 223555655544
No 22
>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=30.74 E-value=1.9e+02 Score=25.49 Aligned_cols=61 Identities=18% Similarity=0.179 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHHhcc-------chHHHhHHHHHHHHhhhccccchhhHh
Q 016860 286 AALRQVKTWAQLLNTFCTNAKLELELMYKVQMQCYE-------DAKLMKLFPEIVRSLYDQDVLAEDTIL 348 (381)
Q Consensus 286 ~~~~~lk~~~pLL~~f~~~~~~Ql~lL~AlQ~~c~e-------~~~~~k~f~~Il~~LYd~DVVsEeaIl 348 (381)
..++.++.|...+.+.--.++.| +=.|.+.|+.. ++++...|..-+-.||+.++|+..+|.
T Consensus 67 ~EKefM~lWN~fv~k~r~~aD~~--ip~ac~~Fv~~~~~~L~~~~~l~~~f~lHl~~L~d~glLd~~~i~ 134 (140)
T PF09733_consen 67 EEKEFMKLWNSFVMKQRVIADGH--IPWACEAFVREHGQWLVEKPNLRREFLLHLINLWDFGLLDARTID 134 (140)
T ss_pred HHHHHHHHHHHHHHHccCcchHH--HHHHHHHHHHHhHHHHhhChhHHHHHHHHHHHHHHcCCCCHHHHH
Confidence 45566777777774443323333 33345555542 467888899889999999999999885
No 23
>PF14026 DUF4242: Protein of unknown function (DUF4242)
Probab=29.85 E-value=30 Score=27.26 Aligned_cols=27 Identities=11% Similarity=0.218 Sum_probs=19.0
Q ss_pred ccCCCCCCCCceeeccCcchhhhhhHHH
Q 016860 51 TKPDEGERHSYSIIDCEPQREAILPSVI 78 (381)
Q Consensus 51 ~~~~d~~~~~~~if~~~~~~~~~~~~~~ 78 (381)
|++++++..-|||+.|| |.|+|+...+
T Consensus 39 s~v~~d~~k~~Cly~Ap-~~eaV~~~~~ 65 (77)
T PF14026_consen 39 SYVSEDDGKIFCLYEAP-DEEAVREHAR 65 (77)
T ss_pred EEEecCCCeEEEEEECC-CHHHHHHHHH
Confidence 45555456789999999 4577776554
No 24
>TIGR02923 AhaC ATP synthase A1, C subunit. The A1/A0 ATP synthase is homologous to the V-type (V1/V0, vacuolar) ATPase, but functions in the ATP synthetic direction as does the F1/F0 ATPase of bacteria. The C subunit is part of the hydrophilic A1 "stalk" complex (AhaABCDEFG) which is the site of ATP generation and is coupled to the membrane-embedded proton translocating A0 complex.
Probab=29.80 E-value=5.4e+02 Score=25.14 Aligned_cols=112 Identities=13% Similarity=0.195 Sum_probs=63.4
Q ss_pred cccCCCchHHHHHHHHHHHHHhCChhHHHHHHHhCCCchhhhhhCCCCCCChhhHHHHHHhcCCCccccchhhhhhHhHH
Q 016860 144 NLVGKGLVLSFITDFFKEYLVDNSLDDLIAILKRGKMEDNLLDFFPSSKRSAEGFSEHFTKEGLIPLVEYNEKKIFEVKL 223 (381)
Q Consensus 144 ~Lv~~G~a~~fl~~i~~~~~~~~~~~~l~~~lr~sgl~~~l~~f~P~~kr~~e~~~~~~~~~gL~~l~~~~~~~~~~~~~ 223 (381)
.|++.|. +-..-|+.++...+.+.+...++......-+.+++ +...+...++..+...-+..+....+ . ..
T Consensus 121 ~l~~~g~---~~~~~l~~l~~~~~~~e~~~~L~~t~y~~~l~~~~-~~~~~l~~~E~~Ld~~y~~~l~~~~~-~----~~ 191 (343)
T TIGR02923 121 LLIPAGE---FLEKRIKELAEAKTIEEIVEALEGTPYYGPLQEAL-AGNGDLSPIENELDRMYYEKLLKYVG-S----PS 191 (343)
T ss_pred Hhccccc---cCHHHHHHHHcCCCHHHHHHHcCCCccHHHHHHHH-hcCCCHHHHHHHHHHHHHHHHHHHhc-C----CC
Confidence 4566664 34566888888899999999998887765466666 33344545544443322222222111 0 00
Q ss_pred HHHHHHHHHHHhhcCChhHHHHHHHHHhhhcCCCHHHHHHHHH
Q 016860 224 KDMKSTLTTQIAEETEMSEVIESVKQRVKDAKLPDIEVVRILW 266 (381)
Q Consensus 224 ~El~~~L~~~l~e~~~~~~ii~eIk~~~~~~n~s~~evi~~l~ 266 (381)
..-...+...+....+..||...+++.+. +++..++...+.
T Consensus 192 ~~~~~~l~~~~~~eiD~~Nl~~ilr~k~~--~~~~e~i~~~li 232 (343)
T TIGR02923 192 DDETKLFTEFIKTEVDIRNLKTLLRLKAA--GLSPDEIMPYTI 232 (343)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHc--CCCHHHHHhhcc
Confidence 01123344555555677788777777654 666655555544
No 25
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=29.04 E-value=55 Score=21.24 Aligned_cols=19 Identities=26% Similarity=0.469 Sum_probs=16.1
Q ss_pred HHHHHHhhhccccchhhHh
Q 016860 330 PEIVRSLYDQDVLAEDTIL 348 (381)
Q Consensus 330 ~~Il~~LYd~DVVsEeaIl 348 (381)
...++.+|+.++|+|+-|-
T Consensus 5 L~~L~~l~~~G~IseeEy~ 23 (31)
T PF09851_consen 5 LEKLKELYDKGEISEEEYE 23 (31)
T ss_pred HHHHHHHHHcCCCCHHHHH
Confidence 3567999999999999875
No 26
>cd00620 Methyltransferase_Sun N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine transferase Sun, also known as RrmB or Fmu shares the RNA-binding non-catalytic domain with the transcription termination factor NusB. The precise biological role of this domain in Sun is unknown, although it is likely to be involved in sequence-specific RNA binding. The C-terminal methyltransferase domain of Sun has been shown to catalyze formation of m5C at position 967 of 16S rRNA in Escherichia coli.
Probab=28.54 E-value=2.6e+02 Score=23.41 Aligned_cols=85 Identities=7% Similarity=-0.101 Sum_probs=54.8
Q ss_pred hhhHHH-HHHHHHhhhhHHHHHHHHHHHHHHHHhhccChhhhHHHHHHHHHHHhhhcCCCCCccchhhhh---hhcccCC
Q 016860 73 ILPSVI-YIQKILRRRPFLIKNLENVTRRFMQSLELFEENERKKLAIFTALAFSQKLSGLPPETVFQPLL---KDNLVGK 148 (381)
Q Consensus 73 ~~~~~~-~~~kl~rrykyL~k~~e~~~~~~l~~l~~f~~~~r~kLA~~~a~~~~~~~~g~~~~~~l~~l~---~~~Lv~~ 148 (381)
-+.|++ ++.-.+|++.+|...++..+++- ...-.+..|.-|-+.++-++- .. +|+...-... .... ..
T Consensus 37 d~~~~~~lv~g~~r~~~~ld~~i~~~l~~~---~~~~~~~~~~iLr~a~~el~~---~~-~p~~avvneaVelak~~-~~ 108 (126)
T cd00620 37 DRGLATELVYGTLRWLALLDWIINPLLKKP---DVGKDPDVRNLLRLGLYQLLY---LD-VPPHAAVDETVEIAKIR-KD 108 (126)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHhCCC---ccccCHHHHHHHHHHHHHHHh---cC-CCchHHHHHHHHHHHHh-CC
Confidence 467776 99999999999999998876551 223456678777777777766 45 4544432211 1111 23
Q ss_pred CchHHHHHHHHHHHHHh
Q 016860 149 GLVLSFITDFFKEYLVD 165 (381)
Q Consensus 149 G~a~~fl~~i~~~~~~~ 165 (381)
..+..|+-.||+.+.++
T Consensus 109 ~~~~~fVNaVLr~i~r~ 125 (126)
T cd00620 109 LGRAGLVNAVLRRFERE 125 (126)
T ss_pred CchhhHHHHHHHHHhcc
Confidence 35566777777776654
No 27
>PRK15039 transcriptional repressor RcnR to maintain nickel and cobalt homeostasis; Provisional
Probab=28.40 E-value=2e+02 Score=23.47 Aligned_cols=29 Identities=14% Similarity=0.185 Sum_probs=24.7
Q ss_pred HHHHHHHHhhcCChhHHHHHHHHHhhhcC
Q 016860 227 KSTLTTQIAEETEMSEVIESVKQRVKDAK 255 (381)
Q Consensus 227 ~~~L~~~l~e~~~~~~ii~eIk~~~~~~n 255 (381)
.+.+.++++++.++.+|...+.+.+.+-+
T Consensus 22 v~gI~~Miee~~~C~dIl~Ql~Avr~Al~ 50 (90)
T PRK15039 22 VVALKKMLDEPHECAAVLQQIAAIRGAVN 50 (90)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHH
Confidence 46788899999999999999998887654
No 28
>PF03299 TF_AP-2: Transcription factor AP-2; InterPro: IPR013854 Activator protein-2 (AP-2) transcription factors constitute a family of closely related and evolutionarily conserved proteins that bind to the DNA consensus sequence GCCNNNGGC and stimulate target gene transcription [, ]. Four different isoforms of AP-2 have been identified in mammals, termed AP-2 alpha, beta, gamma and delta. Each family member shares a common structure, possessing a proline/glutamine-rich domain in the N-terminal region, which is responsible for transcriptional activation [], and a helix-span-helix domain in the C-terminal region, which mediates dimerisation and site-specific DNA binding []. The AP-2 family have been shown to be critical regulators of gene expression during embryogenesis. They regulate the development of facial prominence and limb buds, and are essential for cranial closure and development of the lens []; they have also been implicated in tumourigenesis. AP-2 protein expression levels have been found to affect cell transformation, tumour growth and metastasis, and may predict survival in some types of cancer [, ] This entry represents the C-terminal region of these proteins, including the helix-span-helix domain.
Probab=27.88 E-value=5.2e+02 Score=24.34 Aligned_cols=83 Identities=14% Similarity=0.170 Sum_probs=51.1
Q ss_pred CCCchHHHHHHHHHHHHHhCChhHHHHHHHhCCCchhhhhhCCCCCCChh---hHHHHHHhcCCCccccchhhhhhHhHH
Q 016860 147 GKGLVLSFITDFFKEYLVDNSLDDLIAILKRGKMEDNLLDFFPSSKRSAE---GFSEHFTKEGLIPLVEYNEKKIFEVKL 223 (381)
Q Consensus 147 ~~G~a~~fl~~i~~~~~~~~~~~~l~~~lr~sgl~~~l~~f~P~~kr~~e---~~~~~~~~~gL~~l~~~~~~~~~~~~~ 223 (381)
+...-.+.+--+|+.-.+..|.+.|-..|.+-||+ +|.+.|... .|...++++.+
T Consensus 35 PE~ln~S~lg~~LRraK~k~~g~~lr~~L~~~gi~------l~~~rrk~~~~t~~tsL~EgEAv---------------- 92 (209)
T PF03299_consen 35 PECLNASLLGGVLRRAKSKNGGRSLREKLEKHGIN------LPAGRRKAANVTLFTSLVEGEAV---------------- 92 (209)
T ss_pred CccccHHHHHHHHHHhcccchHHHHHHHHHHcCCC------CccccccccccchhHHHHHHHHH----------------
Confidence 45566778888888888888888888889888888 377766332 22222222111
Q ss_pred HHHHHHHHHHHhhcCChhHHHHHHHHHhh
Q 016860 224 KDMKSTLTTQIAEETEMSEVIESVKQRVK 252 (381)
Q Consensus 224 ~El~~~L~~~l~e~~~~~~ii~eIk~~~~ 252 (381)
.+...+.......-|...+..++.....
T Consensus 93 -hLA~D~~~~~~~~fP~~~lA~~l~~~~~ 120 (209)
T PF03299_consen 93 -HLARDFGYLCETEFPAKALAEYLVRQHL 120 (209)
T ss_pred -HHHHHHHHHHHhcCCHHHHHHHHHHHhh
Confidence 2334444455556677777766654433
No 29
>KOG2213 consensus Apoptosis inhibitor 5/fibroblast growth factor 2-interacting factor 2, and related proteins [Signal transduction mechanisms]
Probab=27.49 E-value=7.4e+02 Score=26.01 Aligned_cols=116 Identities=18% Similarity=0.173 Sum_probs=65.5
Q ss_pred CCCchHHHHHHHHHHHHHhCChhHHHHHHHhCCCchhhhhhCCCCCCChhhHHHHHHhcCCCccccchhhhhhHhHHHHH
Q 016860 147 GKGLVLSFITDFFKEYLVDNSLDDLIAILKRGKMEDNLLDFFPSSKRSAEGFSEHFTKEGLIPLVEYNEKKIFEVKLKDM 226 (381)
Q Consensus 147 ~~G~a~~fl~~i~~~~~~~~~~~~l~~~lr~sgl~~~l~~f~P~~kr~~e~~~~~~~~~gL~~l~~~~~~~~~~~~~~El 226 (381)
-.|-+++-+..++.+++. ...++.++.+++..| ....++-...+..+=++-..++..+..+.....|+
T Consensus 89 c~~d~~~rv~d~l~qLLn---k~sl~~Lf~~~~~~D---------~~irek~l~fi~tKl~~l~~e~L~kevE~~iv~ei 156 (460)
T KOG2213|consen 89 CKGDALSRVNDVLVQLLN---KASLTGLFGQIEVGD---------EQIREKVLKFIRTKLITLKGEVLTKEVERHIVDEI 156 (460)
T ss_pred ccCchhhhhHHHHHHHHH---HHHHHHHHhhhhhhh---------HHHHHHHHHHHHHHhhcccHHHhhhHHHHHHHHHH
Confidence 345667777777777777 456667776666531 11222333333333333344555544556666666
Q ss_pred HHHHHHHHhh-----------------cCCh---hHHHHHHHHHh--hhcCCCHHHHHHHHHHHHHHHhh
Q 016860 227 KSTLTTQIAE-----------------ETEM---SEVIESVKQRV--KDAKLPDIEVVRILWDILMDAVQ 274 (381)
Q Consensus 227 ~~~L~~~l~e-----------------~~~~---~~ii~eIk~~~--~~~n~s~~evi~~l~~alm~~v~ 274 (381)
++.|++--.+ ..+. .+++.++.+.. .+.|.++.+++.=+++|+.-++.
T Consensus 157 kkal~dVtgeef~lfm~~L~~lk~~~~k~~~a~lqeLa~~~e~~a~ldaf~~sD~d~VdRfisCl~~AvP 226 (460)
T KOG2213|consen 157 KKALEDVTGEEFTLFMDILASLKSLQTKAGEARLQELAEEQEGLADLDAFNVSDADYVDRFISCLLMAVP 226 (460)
T ss_pred HHHHHhccHHHHHHHHHHHHhhhcccCCCCHHHHHHHHHHHhhhhccCcccCCChHHHHHHHHHHHHhhh
Confidence 6666553211 1122 24444444443 33788999999888888887775
No 30
>KOG1241 consensus Karyopherin (importin) beta 1 [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=25.66 E-value=5.9e+02 Score=28.86 Aligned_cols=127 Identities=17% Similarity=0.198 Sum_probs=70.5
Q ss_pred HHHHhhhcCC---CHHHHHHHHHHHHHHHhhhhcccc-hhhHHHHHHHHHHHHHHHHHHhc--ChHHHH-----HHHHHH
Q 016860 247 VKQRVKDAKL---PDIEVVRILWDILMDAVQWSGKNQ-QQNANAALRQVKTWAQLLNTFCT--NAKLEL-----ELMYKV 315 (381)
Q Consensus 247 Ik~~~~~~n~---s~~evi~~l~~alm~~v~~s~k~~-~~~~~~~~~~lk~~~pLL~~f~~--~~~~Ql-----~lL~Al 315 (381)
|+++....+. .+.-.+.+.+.|+|+.|..+++.- +.......-.+++-...++.-.. .++.|+ -+...+
T Consensus 500 i~~Ll~~tdr~dgnqsNLR~AAYeALmElIk~st~~vy~~v~~~~l~il~kl~q~i~~~~l~~~dr~q~~eLQs~Lc~~L 579 (859)
T KOG1241|consen 500 IGSLLKVTDRADGNQSNLRSAAYEALMELIKNSTDDVYPMVQKLTLVILEKLDQTISSQILSLADRAQLNELQSLLCNTL 579 (859)
T ss_pred HHHHHhhccccccchhhHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHHHHhccHhhHHHHHHHHHHHHHHH
Confidence 4444444444 445678888888888886554310 00111112233444444541111 123333 333334
Q ss_pred HHHhcc--------chHHHhHHHHHHHHhhhccccchhhHhhhhhcCCCcchhHHHHHhHHHHHHHHhh
Q 016860 316 QMQCYE--------DAKLMKLFPEIVRSLYDQDVLAEDTILYWFRKGTNPKGRQTFVKALEPFVKWLEE 376 (381)
Q Consensus 316 Q~~c~e--------~~~~~k~f~~Il~~LYd~DVVsEeaIlkW~~~~~~~~Gk~~~lk~~~~Fv~WLeE 376 (381)
|.-... ...+|..|.+++.. =+..++.||||+.=+.-... -| +.|.+-+..|...|..
T Consensus 580 q~i~rk~~~~~~~~~d~iM~lflri~~s-~~s~~v~e~a~laV~tl~~~-Lg-~~F~kym~~f~pyL~~ 645 (859)
T KOG1241|consen 580 QSIIRKVGSDIREVSDQIMGLFLRIFES-KRSAVVHEEAFLAVSTLAES-LG-KGFAKYMPAFKPYLLM 645 (859)
T ss_pred HHHHHHccccchhHHHHHHHHHHHHHcC-CccccchHHHHHHHHHHHHH-Hh-HhHHHHHHHHHHHHHH
Confidence 444332 14568889999988 88999999999977643221 13 4566667777766654
No 31
>PRK10167 hypothetical protein; Provisional
Probab=25.18 E-value=1.8e+02 Score=26.62 Aligned_cols=74 Identities=14% Similarity=0.046 Sum_probs=54.4
Q ss_pred hhhhhHHHHHHHHHhhhhHHHHHHHHHHHHHHHHhhcc-ChhhhHHHHHHHHHHHhhhcCCCCCccchhhhhhhcccCCC
Q 016860 71 EAILPSVIYIQKILRRRPFLIKNLENVTRRFMQSLELF-EENERKKLAIFTALAFSQKLSGLPPETVFQPLLKDNLVGKG 149 (381)
Q Consensus 71 ~~~~~~~~~~~kl~rrykyL~k~~e~~~~~~l~~l~~f-~~~~r~kLA~~~a~~~~~~~~g~~~~~~l~~l~~~~Lv~~G 149 (381)
+-+..|.+.|.+.+++.+= .+..=|++..+..|+|.. +..||..+..++.-.- +|.+|..+.-.+++.++.+-+
T Consensus 70 ~~~~~Y~~~lm~al~~~~t-~~~~~NvL~Hi~GYFKk~Ls~~EKq~l~~lI~~Yr----~g~vpl~vpltlL~h~~~~y~ 144 (169)
T PRK10167 70 DFYNQYRQRVIVLLSHPAN-VRDHTNVLMHVQGYFRPHIDSTERQQLAALIDSYR----RGEQPLLAPLMRIKHYMALYP 144 (169)
T ss_pred HHHHHHHHHHHHHHcCCCC-cchhHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHH----cCCCCHHHHHHHHHHHHHHCC
Confidence 3577899999998887664 455668889999998874 8888999977777664 599997777665554444433
No 32
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=24.06 E-value=65 Score=29.08 Aligned_cols=20 Identities=30% Similarity=0.542 Sum_probs=11.4
Q ss_pred CCCCCCC--hhhHHHHHHhcCC
Q 016860 188 FPSSKRS--AEGFSEHFTKEGL 207 (381)
Q Consensus 188 ~P~~kr~--~e~~~~~~~~~gL 207 (381)
+|+++|. .+++.|||.+++-
T Consensus 17 lp~~e~~e~l~~Y~e~f~d~~~ 38 (181)
T PF08006_consen 17 LPEEEREEILEYYEEYFDDAGE 38 (181)
T ss_pred CCHHHHHHHHHHHHHHHHHhhh
Confidence 4655443 2566777776543
No 33
>PF12952 DUF3841: Domain of unknown function (DUF3841); InterPro: IPR024211 This family of proteins has no known function.
Probab=23.77 E-value=1.2e+02 Score=27.74 Aligned_cols=49 Identities=10% Similarity=0.234 Sum_probs=39.9
Q ss_pred hhCCCCCCChhhHHHHHHhcCCCccccchhhhhhHhHHHHHHHHHHHHH
Q 016860 186 DFFPSSKRSAEGFSEHFTKEGLIPLVEYNEKKIFEVKLKDMKSTLTTQI 234 (381)
Q Consensus 186 ~f~P~~kr~~e~~~~~~~~~gL~~l~~~~~~~~~~~~~~El~~~L~~~l 234 (381)
-++|.++.+.+.|.+.++..|+..-.++..+......+++++++.+|.+
T Consensus 106 ~yi~~~e~D~~~~~~~l~~~Gi~~~~~~~~s~~yp~~k~~i~~SW~riF 154 (178)
T PF12952_consen 106 WYIPEDEEDERAFEEELKKYGISNDFDIFLSNFYPELKREIEKSWERIF 154 (178)
T ss_pred ccCCcccchHHHHHHHHHHcCCCchhhhhccccCHHHHHHHHHHHHHHh
Confidence 3679998888899999999999865566655566777889999999987
No 34
>PF12825 DUF3818: Domain of unknown function in PX-proteins (DUF3818); InterPro: IPR024554 The function of this domain is not known, but it is almost always found C-terminal to a PX-domain (IPR001683 from INTERPRO).
Probab=23.68 E-value=7.5e+02 Score=25.07 Aligned_cols=72 Identities=17% Similarity=0.227 Sum_probs=46.1
Q ss_pred HHHHHHHHHhhhcCCCCCccchhhhhh----------------hcccCCCchHHHHHHHHHHHHHhCChhHHHHHHHhCC
Q 016860 116 LAIFTALAFSQKLSGLPPETVFQPLLK----------------DNLVGKGLVLSFITDFFKEYLVDNSLDDLIAILKRGK 179 (381)
Q Consensus 116 LA~~~a~~~~~~~~g~~~~~~l~~l~~----------------~~Lv~~G~a~~fl~~i~~~~~~~~~~~~l~~~lr~sg 179 (381)
.-+.++.+-+.-+.+.++...+....+ .....++.-..-+-+.++.+++.++.+.+.++|.+.-
T Consensus 156 ~~iv~~IL~~~~~~p~L~~~~~~~v~~sy~~~~~~~~~~~~~~~~~~~~a~lf~~lk~yl~l~~r~RDk~~~~~l~~e~~ 235 (341)
T PF12825_consen 156 EDIVVAILRSSDIEPKLSPEQLQRVLESYKAWKNAVESVPDDDGEENEDAWLFSDLKEYLKLYLRKRDKEQMIQLWCEPE 235 (341)
T ss_pred CCchHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHhhhccccCCCccchhhHHHHHHHHHHHHHHHHhhHHHHHHHHcChh
Confidence 445666666622233455566655432 1123456667778899999999999999999998855
Q ss_pred Cchhhhhh
Q 016860 180 MEDNLLDF 187 (381)
Q Consensus 180 l~~~l~~f 187 (381)
+-.-+.++
T Consensus 236 ~~qllkd~ 243 (341)
T PF12825_consen 236 LTQLLKDL 243 (341)
T ss_pred HHHHHHHH
Confidence 54333443
No 35
>PF03542 Tuberin: Tuberin; InterPro: IPR018515 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This domain is found in Tuberin proteins. ; GO: 0005096 GTPase activator activity, 0043547 positive regulation of GTPase activity
Probab=23.41 E-value=5.3e+02 Score=26.33 Aligned_cols=100 Identities=15% Similarity=0.326 Sum_probs=56.2
Q ss_pred HHHHHHHHHHHHhhcCChhHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHhhhhcccchhhHHHHHHHHHHHHHHHHHHh
Q 016860 223 LKDMKSTLTTQIAEETEMSEVIESVKQRVKDAKLPDIEVVRILWDILMDAVQWSGKNQQQNANAALRQVKTWAQLLNTFC 302 (381)
Q Consensus 223 ~~El~~~L~~~l~e~~~~~~ii~eIk~~~~~~n~s~~evi~~l~~alm~~v~~s~k~~~~~~~~~~~~lk~~~pLL~~f~ 302 (381)
.+++.+.|.+++.++...+.+ .....+++..|+..+++.++-..+.--..-++...+...+.+.. -+
T Consensus 181 I~~L~~~Lc~~i~d~~~~~~l------~~~p~~~~~~D~~~~~~~~Ls~LisYh~~~~k~~qd~iV~~l~~-------GL 247 (356)
T PF03542_consen 181 IDQLRNALCSMICDRSFLESL------SNKPTGFKRADLQVCVFPVLSALISYHSHFSKQEQDEIVRALES-------GL 247 (356)
T ss_pred HHHHHHHHHHHHhcccccccc------cCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCHhHHHHHHHHHHH-------Hh
Confidence 345666677766554433222 12345778888888888766555432110011111122232211 11
Q ss_pred cChHHHHHHHHHHHHHhcc-chHHHhHHHHHHHHh
Q 016860 303 TNAKLELELMYKVQMQCYE-DAKLMKLFPEIVRSL 336 (381)
Q Consensus 303 ~~~~~Ql~lL~AlQ~~c~e-~~~~~k~f~~Il~~L 336 (381)
.+ +....|+.|+-..|+| +....|.++.|+..|
T Consensus 248 ~s-~~a~~CI~aLtic~~EmP~s~~k~L~~iL~kL 281 (356)
T PF03542_consen 248 GS-KTAKPCIHALTICCYEMPDSMKKLLPSILLKL 281 (356)
T ss_pred cc-CcHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence 11 4457799999999999 666678888887776
No 36
>PF02671 PAH: Paired amphipathic helix repeat; InterPro: IPR003822 This family contains the paired amphipathic helix (PAH) repeat. The family contains the eukaryotic Sin3 proteins, which have at least three PAH domains (PAH1, PAH2, and PAH3). Sin3 proteins are components of a co-repressor complex that silences transcription, playing important roles in the transition between proliferation and differentiation. Sin3 proteins are recruited to the DNA by various DNA-binding transcription factors such as the Mad family of repressors, Mnt/Rox, PLZF, MeCP2, p53, REST/NRSF, MNFbeta, Sp1, TGIF and Ume6 []. Sin3 acts as a scaffold protein that in turn recruits histone-binding proteins RbAp46/RbAp48 and histone deacetylases HDAC1/HDAC2, which deacetylate the core histones resulting in a repressed state of the chromatin []. The PAH domains are protein-protein interaction domains through which Sin3 fulfils its role as a scaffold. The PAH2 domain of Sin3 can interact with a wide range of unrelated and structurally diverse transcription factors that bind using different interaction motifs. For example, the Sin3 PAH2 domain can interact with the unrelated Mad and HBP1 factors using alternative interaction motifs that involve binding in opposite helical orientations [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1S5Q_B 2L9S_B 1G1E_B 1S5R_B 2CR7_A 2CZY_A 2LD7_B 2RMR_A 2RMS_A 1PD7_A ....
Probab=23.30 E-value=2.2e+02 Score=19.71 Aligned_cols=41 Identities=15% Similarity=0.210 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHhcChHHHHHHHHHHHHHhccchHHHhHHHH
Q 016860 291 VKTWAQLLNTFCTNAKLELELMYKVQMQCYEDAKLMKLFPE 331 (381)
Q Consensus 291 lk~~~pLL~~f~~~~~~Ql~lL~AlQ~~c~e~~~~~k~f~~ 331 (381)
-+.+-.++..|..+..+.-++...+..+..++|.++.-|..
T Consensus 4 Y~~FL~il~~y~~~~~~~~~v~~~v~~Ll~~hpdLl~~F~~ 44 (47)
T PF02671_consen 4 YNEFLKILNDYKKGRISRSEVIEEVSELLRGHPDLLEEFNR 44 (47)
T ss_dssp HHHHHHHHHHHHCTCSCHHHHHHHHHHHTTT-HHHHHHHHH
T ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHccCHHHHHHHHh
Confidence 34555677777776666667778888888888888766643
No 37
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=23.18 E-value=1.2e+02 Score=26.47 Aligned_cols=33 Identities=12% Similarity=0.176 Sum_probs=28.1
Q ss_pred hhHhHHHHHHHHHHHHHhhcCChhHHHHHHHHH
Q 016860 218 IFEVKLKDMKSTLTTQIAEETEMSEVIESVKQR 250 (381)
Q Consensus 218 ~~~~~~~El~~~L~~~l~e~~~~~~ii~eIk~~ 250 (381)
++....++++..+.+++++|.+.++|++++.+.
T Consensus 54 S~a~iA~dmR~~Vr~~i~~G~Sd~eI~~~~v~R 86 (126)
T TIGR03147 54 SNSPIAYDLRHEVYSMVNEGKSNQQIIDFMTAR 86 (126)
T ss_pred cCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 345677899999999999999999999988763
No 38
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=22.25 E-value=1.3e+02 Score=26.30 Aligned_cols=33 Identities=18% Similarity=0.171 Sum_probs=28.2
Q ss_pred hhHhHHHHHHHHHHHHHhhcCChhHHHHHHHHH
Q 016860 218 IFEVKLKDMKSTLTTQIAEETEMSEVIESVKQR 250 (381)
Q Consensus 218 ~~~~~~~El~~~L~~~l~e~~~~~~ii~eIk~~ 250 (381)
++....++++..+.+++.+|.+.++|++++.+.
T Consensus 54 Sna~iA~dmR~~Vr~~i~~G~sd~eI~~~~v~R 86 (126)
T PRK10144 54 SNAPVAVSMRHQVYSMVAEGKSEVEIIGWMTER 86 (126)
T ss_pred cCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 345667899999999999999999999998763
No 39
>PF04286 DUF445: Protein of unknown function (DUF445); InterPro: IPR007383 This entry contains proteins of unknown function. They are predicted to be transmembrane proteins with 2 or 3 TM domains.
Probab=22.09 E-value=7.4e+02 Score=24.10 Aligned_cols=218 Identities=14% Similarity=0.110 Sum_probs=0.0
Q ss_pred hhhhHHHHHHHHHHHhhhcCCCCCccchhhhhhhcccCCCchHHHHHHHHHHHHHhCChhHHHHHHHhCCCchhhhhhCC
Q 016860 110 ENERKKLAIFTALAFSQKLSGLPPETVFQPLLKDNLVGKGLVLSFITDFFKEYLVDNSLDDLIAILKRGKMEDNLLDFFP 189 (381)
Q Consensus 110 ~~~r~kLA~~~a~~~~~~~~g~~~~~~l~~l~~~~Lv~~G~a~~fl~~i~~~~~~~~~~~~l~~~lr~sgl~~~l~~f~P 189 (381)
|..|+++|..+|-++. +.++++..+..-+.+.=...-..--+-...-+..+...-...+...++.-.-+. +.+++
T Consensus 36 p~~r~~~~~~~~~~v~---~~ll~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~-i~~~i- 110 (367)
T PF04286_consen 36 PKNRERIAESIGEMVE---NELLTPETIRRKLESEDFSERLIEWLQDPENREKLRRILAELLEEILEKIDQEK-IAEFI- 110 (367)
T ss_pred cccHHHHHHHHHHHHH---HHCCCHHHHHHHHhcccHHHHHHHHHhchhhhHHHHHHHHHHHHHHhhhhhhHH-HHHHH-
Q ss_pred CCCCChhhHHHHHHhcCCCcc-ccchhhhhhHhHHHHHHHHHHHHHhhcCChhHHHHHHHHHhhhcCCC--HHHHHHHHH
Q 016860 190 SSKRSAEGFSEHFTKEGLIPL-VEYNEKKIFEVKLKDMKSTLTTQIAEETEMSEVIESVKQRVKDAKLP--DIEVVRILW 266 (381)
Q Consensus 190 ~~kr~~e~~~~~~~~~gL~~l-~~~~~~~~~~~~~~El~~~L~~~l~e~~~~~~ii~eIk~~~~~~n~s--~~evi~~l~ 266 (381)
.+.-...+.+..-..-++.+ -.+......+...+.+.+.+.+.+.+....+.|..-+......+.-. ...+...+.
T Consensus 111 -~~~~~~~l~~~~~~~~~~~~l~~ll~~~~~~~l~~~il~~i~~~l~~~e~~~~I~~~i~~~~~~~~~~~~~~~l~~~i~ 189 (367)
T PF04286_consen 111 -EKNLRKKLSEIILAPLLQKLLRSLLEEEQHQKLLDRILEKIKEYLKSEETRERIRDLIEEFLEEYLGKSFLDKLAEKIQ 189 (367)
T ss_pred -HHHHHHHHHHhccchhHHHHHHHHHhccchHHHHHHHHHHHHHHHcCchHHHHHHHHHHHHHHHhcccchhhHHHHHHH
Q ss_pred HHHHHHhhhhcccchhhHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHHhccchHHHhHHHHHHHHh
Q 016860 267 DILMDAVQWSGKNQQQNANAALRQVKTWAQLLNTFCTNAKLELELMYKVQMQCYEDAKLMKLFPEIVRSL 336 (381)
Q Consensus 267 ~alm~~v~~s~k~~~~~~~~~~~~lk~~~pLL~~f~~~~~~Ql~lL~AlQ~~c~e~~~~~k~f~~Il~~L 336 (381)
..+.+....-.. +.... .-....+.....+.+..+++..+ ..+..+......++........+...+
T Consensus 190 ~~l~~~l~~l~~-~~~~~-lr~~~~~~l~~~i~~L~~d~~~~-~~i~~~~~~~l~~~~~~~~~~~l~~~l 256 (367)
T PF04286_consen 190 DELDSLLEKLQE-DPDHP-LRQEIDQKLRELIERLLTDPELR-EKIEELKDKLLSELILEEFLEELWDSL 256 (367)
T ss_pred HHHHHHHHHHHh-CcccH-hHHHHHHHHHHHHHHHhcCHHHH-HHHHHHHHhhhhhhHHHHHHHHHHHHH
No 40
>TIGR03652 FeS_repair_RIC iron-sulfur cluster repair di-iron protein. Members of this protein family, designated variously as YftE, NorA, DrnN, and NipC, are di-iron proteins involved in the repair of iron-sulfur clusters. Previously assigned names reflect pleiotropic effects of damage from NO or other oxidative stress when this protein is mutated. The suggested name now is RIC, for Repair of Iron Centers.
Probab=21.81 E-value=3.8e+02 Score=24.91 Aligned_cols=45 Identities=9% Similarity=0.137 Sum_probs=23.2
Q ss_pred HHHHHH-hhcCChhHHHHHHHHHhhhc-CCCHHHHHHHHHHHHHHHh
Q 016860 229 TLTTQI-AEETEMSEVIESVKQRVKDA-KLPDIEVVRILWDILMDAV 273 (381)
Q Consensus 229 ~L~~~l-~e~~~~~~ii~eIk~~~~~~-n~s~~evi~~l~~alm~~v 273 (381)
+|.++. ..|.+++.++.++|...... +.+..++...-..++++++
T Consensus 29 ~l~~a~~~~g~d~~~~l~~ln~~~~~~~~~~~~~~~~~~~~~Lid~i 75 (216)
T TIGR03652 29 SLAEACKEKGLDPDEILAELNALQQEPENSGAKDWREAPLSELIDHI 75 (216)
T ss_pred hHHHHHHHcCCCHHHHHHHHHHHHhccccccccChhhCCHHHHHHHH
Confidence 444444 34567777777777665221 1122344444445556665
No 41
>PF15069 FAM163: FAM163 family
Probab=21.62 E-value=28 Score=30.92 Aligned_cols=8 Identities=63% Similarity=0.825 Sum_probs=3.9
Q ss_pred eeeecCcC
Q 016860 39 VVFTGGRT 46 (381)
Q Consensus 39 il~~Gg~l 46 (381)
|+|+||+|
T Consensus 6 vVItGgIL 13 (143)
T PF15069_consen 6 VVITGGIL 13 (143)
T ss_pred EEEechHH
Confidence 44555554
No 42
>COG1937 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.46 E-value=4.3e+02 Score=21.63 Aligned_cols=29 Identities=7% Similarity=0.173 Sum_probs=24.4
Q ss_pred HHHHHHHHhhcCChhHHHHHHHHHhhhcC
Q 016860 227 KSTLTTQIAEETEMSEVIESVKQRVKDAK 255 (381)
Q Consensus 227 ~~~L~~~l~e~~~~~~ii~eIk~~~~~~n 255 (381)
.+.+.+++++|.++.+|...|-+.+.+-|
T Consensus 22 v~gI~rMlEe~~~C~dVl~QIaAVr~Al~ 50 (89)
T COG1937 22 VRGIERMLEEDRDCIDVLQQIAAVRGALN 50 (89)
T ss_pred HHHHHHHHhCCCcHHHHHHHHHHHHHHHH
Confidence 45678999999999999999988777654
No 43
>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=21.29 E-value=4.4e+02 Score=21.26 Aligned_cols=100 Identities=11% Similarity=0.157 Sum_probs=56.6
Q ss_pred HHHHHHHHHHhhcCChhHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHhhhhcccchhhHHHHHHHHHHHHHHHHHHhcC
Q 016860 225 DMKSTLTTQIAEETEMSEVIESVKQRVKDAKLPDIEVVRILWDILMDAVQWSGKNQQQNANAALRQVKTWAQLLNTFCTN 304 (381)
Q Consensus 225 El~~~L~~~l~e~~~~~~ii~eIk~~~~~~n~s~~evi~~l~~alm~~v~~s~k~~~~~~~~~~~~lk~~~pLL~~f~~~ 304 (381)
.+...+.+.+.. .+.++.+.-+.++..+. -.+++++.++...++.- . +.-+.+..+++.+++.
T Consensus 4 ~i~~~l~ey~~~-~D~~ea~~~l~~L~~~~--~~~~vv~~~i~~~le~~----~----------~~~~~~~~Ll~~L~~~ 66 (113)
T smart00544 4 KIFLIIEEYLSS-GDTDEAVHCLLELKLPE--QHHEVVKVLLTCALEEK----R----------TYREMYSVLLSRLCQA 66 (113)
T ss_pred HHHHHHHHHHHc-CCHHHHHHHHHHhCCCc--chHHHHHHHHHHHHcCC----c----------cHHHHHHHHHHHHHHc
Confidence 444555555543 47778888888776552 46677777777666631 0 1234566677777744
Q ss_pred -hHHHHHHHHHHHHHhcc-------chHHHhHHHHHHHHhhhccc
Q 016860 305 -AKLELELMYKVQMQCYE-------DAKLMKLFPEIVRSLYDQDV 341 (381)
Q Consensus 305 -~~~Ql~lL~AlQ~~c~e-------~~~~~k~f~~Il~~LYd~DV 341 (381)
.-.+-++..+++.+... .|+....+..++-.+--.|+
T Consensus 67 ~~~~~~~~~~~f~~~~~~l~dl~~D~P~a~~~la~~~a~~v~~~~ 111 (113)
T smart00544 67 NVISTKQFEKGFWRLLEDIEDLELDIPNAWRNLAEFVARLISDGI 111 (113)
T ss_pred CCcCHHHHHHHHHHHHhhChhhhcccccHHHHHHHHHHHHHHcCC
Confidence 34555566666665542 24444444444444444443
No 44
>cd08323 CARD_APAF1 Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1. Caspase activation and recruitment domain (CARD) similar to that found in apoptotic protease-activating factor 1 (APAF-1), which is an activator of caspase-9. APAF-1 contains WD-40 repeats, a CARD, and an ATPase domain. Upon stimulation, APAF-1, together with caspase-9, forms the heptameric 'apoptosome', which leads to the processing and activation of caspase-9, starting a caspase cascade which leads to apoptosis. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effect
Probab=21.22 E-value=1.9e+02 Score=23.31 Aligned_cols=48 Identities=19% Similarity=0.072 Sum_probs=31.1
Q ss_pred HHHHHHHhhhccccchhhHhhhhhcCCCcchhHHH--------HHhHHHHHHHHhh
Q 016860 329 FPEIVRSLYDQDVLAEDTILYWFRKGTNPKGRQTF--------VKALEPFVKWLEE 376 (381)
Q Consensus 329 f~~Il~~LYd~DVVsEeaIlkW~~~~~~~~Gk~~~--------lk~~~~Fv~WLeE 376 (381)
...|+..||..+|++++-+-.=...++...--..+ -.....|.++|++
T Consensus 16 v~~ild~L~~~gvlt~~~~e~I~~~~t~~~qa~~Lld~L~trG~~Af~~F~~aL~~ 71 (86)
T cd08323 16 TSYIMDHMISDGVLTLDEEEKVKSKATQKEKAVMLINMILTKDNHAYVSFYNALLH 71 (86)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHcCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHh
Confidence 35688999999999999887666655543110111 1334458888875
No 45
>PF13551 HTH_29: Winged helix-turn helix
Probab=20.76 E-value=2.5e+02 Score=22.32 Aligned_cols=72 Identities=11% Similarity=0.157 Sum_probs=32.3
Q ss_pred CCChhhHHHHHHhcCCCcccc-chhhh-hhHhHHHHHHHHHHHHHhhcC-------ChhHHHHHHHHHhhhcCCCHHHHH
Q 016860 192 KRSAEGFSEHFTKEGLIPLVE-YNEKK-IFEVKLKDMKSTLTTQIAEET-------EMSEVIESVKQRVKDAKLPDIEVV 262 (381)
Q Consensus 192 kr~~e~~~~~~~~~gL~~l~~-~~~~~-~~~~~~~El~~~L~~~l~e~~-------~~~~ii~eIk~~~~~~n~s~~evi 262 (381)
.++.......|.+.|++.+.+ -.... +....-.+..+.|.+.+.+++ +.+.+..|+-+....-.++...+.
T Consensus 26 ~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~ 105 (112)
T PF13551_consen 26 RRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIR 105 (112)
T ss_pred HHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHH
Confidence 345555555566666555554 22211 111122344455555554432 345555555333333444554444
Q ss_pred H
Q 016860 263 R 263 (381)
Q Consensus 263 ~ 263 (381)
+
T Consensus 106 r 106 (112)
T PF13551_consen 106 R 106 (112)
T ss_pred H
Confidence 3
No 46
>cd08330 CARD_ASC_NALP1 Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins. Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They se
Probab=20.67 E-value=2.8e+02 Score=21.96 Aligned_cols=50 Identities=18% Similarity=0.214 Sum_probs=32.4
Q ss_pred HHHHHHHhhhccccchhhHhhhhhcCCCcchhHHH--------HHhHHHHHHHHhhcc
Q 016860 329 FPEIVRSLYDQDVLAEDTILYWFRKGTNPKGRQTF--------VKALEPFVKWLEEAE 378 (381)
Q Consensus 329 f~~Il~~LYd~DVVsEeaIlkW~~~~~~~~Gk~~~--------lk~~~~Fv~WLeEAE 378 (381)
.-.|++.||..+||+++..-.=..+++.+.-...+ ......|...|+|-+
T Consensus 17 v~~ilD~L~~~~Vit~e~~~~I~a~~T~~~kar~Lld~l~~kG~~A~~~F~~~L~e~~ 74 (82)
T cd08330 17 VDPILDKLHGKKVITQEQYSEVRAEKTNQEKMRKLFSFVRSWGASCKDIFYQILREEE 74 (82)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHcCCCcHHHHHHHHHHHHccCHHHHHHHHHHHHHhC
Confidence 46688999999999999877666666543211111 123345888887643
No 47
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=20.00 E-value=3.4e+02 Score=24.58 Aligned_cols=74 Identities=18% Similarity=0.191 Sum_probs=50.9
Q ss_pred hhhhHHHHHHHHHHHHHHHHhhccChhhhHHHHHHHHHHHhhhcCCCCCccchhh-hhhhcccCCCc-hHHHHHHHHHHH
Q 016860 85 RRRPFLIKNLENVTRRFMQSLELFEENERKKLAIFTALAFSQKLSGLPPETVFQP-LLKDNLVGKGL-VLSFITDFFKEY 162 (381)
Q Consensus 85 rrykyL~k~~e~~~~~~l~~l~~f~~~~r~kLA~~~a~~~~~~~~g~~~~~~l~~-l~~~~Lv~~G~-a~~fl~~i~~~~ 162 (381)
.+||.-++.||.- +.+..=+..+++.+++++..-+--++- +| |.+.++. .++.-+.|-|. ..+.+..|+-..
T Consensus 76 kpyPWt~~~L~aa-~el~ee~eeLs~deke~~~~sl~dL~~---d~--PkT~vA~~rfKk~~~K~g~~v~~~~~dIlVdv 149 (158)
T PF10083_consen 76 KPYPWTENALEAA-NELIEEDEELSPDEKEQFKESLPDLTK---DT--PKTKVAATRFKKILSKAGSIVGDAIRDILVDV 149 (158)
T ss_pred CCCchHHHHHHHH-HHHHHHhhcCCHHHHHHHHhhhHHHhh---cC--CccHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 3578888888773 356667889999999999988887877 65 8887777 46666666554 233444444433
Q ss_pred HH
Q 016860 163 LV 164 (381)
Q Consensus 163 ~~ 164 (381)
.+
T Consensus 150 ~S 151 (158)
T PF10083_consen 150 AS 151 (158)
T ss_pred HH
Confidence 33
Done!