Query 030929
Match_columns 169
No_of_seqs 104 out of 343
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 06:42:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030929.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030929hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08718 GLTP: Glycolipid tran 100.0 8.2E-39 1.8E-43 250.6 7.4 131 29-159 1-139 (149)
2 KOG4189 Uncharacterized conser 100.0 1.2E-32 2.6E-37 223.2 11.5 156 3-158 3-164 (209)
3 KOG3221 Glycolipid transfer pr 100.0 1.4E-32 3E-37 223.0 6.9 133 26-159 13-151 (199)
4 PF04711 ApoA-II: Apolipoprote 64.5 12 0.00027 26.4 3.8 55 10-64 15-71 (76)
5 PF08718 GLTP: Glycolipid tran 47.4 7.9 0.00017 30.1 0.6 59 103-164 73-138 (149)
6 PF07889 DUF1664: Protein of u 45.7 99 0.0021 23.8 6.4 77 35-119 40-116 (126)
7 PF00036 EF-hand_1: EF hand; 45.7 24 0.00052 20.0 2.3 28 13-43 2-29 (29)
8 PF06512 Na_trans_assoc: Sodiu 35.1 43 0.00092 27.5 3.2 22 99-120 9-30 (239)
9 PF03735 ENT: ENT domain; Int 31.4 1.2E+02 0.0027 21.1 4.5 49 37-86 10-60 (73)
10 cd08789 CARD_IPS-1_RIG-I Caspa 28.1 1.4E+02 0.0031 21.0 4.5 26 97-122 50-76 (84)
11 PF09373 PMBR: Pseudomurein-bi 26.1 77 0.0017 18.4 2.4 28 28-55 2-29 (33)
12 smart00054 EFh EF-hand, calciu 24.6 87 0.0019 15.1 2.2 26 14-42 3-28 (29)
13 cd08812 CARD_RIG-I_like Caspas 22.7 2.4E+02 0.0052 19.9 4.9 27 97-123 52-81 (88)
14 PF13405 EF-hand_6: EF-hand do 20.9 1.6E+02 0.0035 16.1 3.1 27 12-41 1-27 (31)
15 PF14788 EF-hand_10: EF hand; 20.7 1.5E+02 0.0032 19.4 3.1 31 11-44 21-51 (51)
No 1
>PF08718 GLTP: Glycolipid transfer protein (GLTP); InterPro: IPR014830 Glycolipid transfer protein (GLTP) is a cytosolic protein that catalyses the intermembrane transfer of glycolipids such as glycosphingolipids, glyceroglycolipids, and possibly glucosylceramides, but not of phospholipids. The GLTP protein consists of a single domain with a multi-helical structure consisting of two layers of orthogonally packed helices [, ]. The GLTP domain is also found in trans-Golgi network proteins involved in Golgi-to-cell-surface membrane traffic [].; GO: 0017089 glycolipid transporter activity, 0051861 glycolipid binding, 0046836 glycolipid transport, 0005737 cytoplasm; PDB: 2BV7_A 1TFJ_A 1WBE_A 3KV0_A 3RWV_B 2EVD_A 2EUK_A 3RZN_A 2EVL_A 3S0K_A ....
Probab=100.00 E-value=8.2e-39 Score=250.65 Aligned_cols=131 Identities=24% Similarity=0.378 Sum_probs=116.9
Q ss_pred CCcChHHHHHHHhHHHHHHhhcCccchhhHhhHHhhHHHHH-----hccccchhHHHHHHHHHhcCCccCCCCcchhHHH
Q 030929 29 ADVELAAFSRACSYVSPLFGCLGIAFKFAEMDYVAKVDDLA-----EASKSILTLQSVIDRDIEGNCVRKAGSHTRNLLR 103 (169)
Q Consensus 29 ~~I~t~~FL~a~~~l~~lfd~LG~~F~fV~~Dv~~kI~~L~-----~~~~~y~TL~~mv~~E~~~~~~~k~~S~srtLLr 103 (169)
++|++++||+||++|++|||.||++|+||++||.+||++|+ .+|+.|.||++||++|+++|++++++||||+|||
T Consensus 1 n~i~~~~fl~a~~~l~~~~~~lG~~f~~v~~Dv~~ni~~l~~~~~~~~~~~~~tl~~~v~~E~~~~~~~~~~s~s~~LLw 80 (149)
T PF08718_consen 1 NDIDTEPFLEACRELVKFFDKLGTVFSFVKSDVQGNIKKLRKAYQEEDPEKYKTLESMVDYEVENGTHKKKGSGSRTLLW 80 (149)
T ss_dssp SEEBHHHHHHHHTTSHHHHCCSSGGGHHHHHHHHHHHHHHHHHH-HHSTTTTSBHHHHHHHHHHHHGGGTSSHHHHHHHH
T ss_pred CCCcHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhhcCChhhhccHHHHHHHHHHHhcccccccHHHHHHH
Confidence 47999999999999999999999999999999999999994 5678999999999999999999988999999999
Q ss_pred HhhHHHHHHHHHHHHHhCcchh---hhhhhhcccccccccccccchhhhhHHhhhcccC
Q 030929 104 VKRGLDMVRVLFEQILAAEYVY---QHGKFLKGSSIQGLHTSICSPSWMGYKKSCCRRD 159 (169)
Q Consensus 104 L~RaL~Fi~~fl~~l~~~~~~~---~~~~f~~~~~l~~~h~~~~~~~~~~~~~~~~~~~ 159 (169)
|||||+|+..||+++.++++++ ..+.-+|..||++||+|+||.+|.++++++|-++
T Consensus 81 L~RaL~Fi~~~l~~l~~~~~~~~~~~~~~~AY~~tL~~yH~w~vr~~~~~a~~~~P~R~ 139 (149)
T PF08718_consen 81 LHRALEFIVAFLENLLESPDDEKLSDAAREAYDKTLAPYHGWIVRKAFKLALKALPSRS 139 (149)
T ss_dssp HHHHHHHHHHHHHHHHTS--BTBHHHHHHHHHHHHTGGGB-HHHHHHHHHHHHT--BHH
T ss_pred HHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCHH
Confidence 9999999999999999986655 5556666789999999999999999999999763
No 2
>KOG4189 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.2e-32 Score=223.18 Aligned_cols=156 Identities=32% Similarity=0.419 Sum_probs=137.3
Q ss_pred CCCCCCChhHHHHHHHHhHhhhcCCCCCcChHHHHHHHhHHHHHHhhcCccchhhHhhHHhhHHHHHh-ccccchhHHHH
Q 030929 3 GTDNDKPLTKISESFKELAATVNSQAADVELAAFSRACSYVSPLFGCLGIAFKFAEMDYVAKVDDLAE-ASKSILTLQSV 81 (169)
Q Consensus 3 ~~~~~f~l~~v~~~F~~~~~~v~~~~~~I~t~~FL~a~~~l~~lfd~LG~~F~fV~~Dv~~kI~~L~~-~~~~y~TL~~m 81 (169)
+.+..-++.++...|+.+..++..++++|++++|+.||+++++||++||++|+||.+|+.+||++|.+ .+....|+..|
T Consensus 3 ~~~~~~~~~~i~~~~~~i~~~v~~e~~eV~L~~f~~a~e~v~~~f~~lG~iF~Fve~Dv~aKid~L~~l~ssd~et~rti 82 (209)
T KOG4189|consen 3 CMEQLGPLPKILQAFKTIEKSVIEEDNEVDLDQFLLAYEEVCKFFGCLGTIFSFVEKDVRAKIDDLVELRSSDPETYRTI 82 (209)
T ss_pred chhhccchHHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcChHHHHHH
Confidence 44556788899999999999999999999999999999999999999999999999999999999953 33337788888
Q ss_pred HHHHHhcCCccCCC--CcchhHHHHhhHHHHHHHHHHHHHhCcchh---hhhhhhcccccccccccccchhhhhHHhhhc
Q 030929 82 IDRDIEGNCVRKAG--SHTRNLLRVKRGLDMVRVLFEQILAAEYVY---QHGKFLKGSSIQGLHTSICSPSWMGYKKSCC 156 (169)
Q Consensus 82 v~~E~~~~~~~k~~--S~srtLLrL~RaL~Fi~~fl~~l~~~~~~~---~~~~f~~~~~l~~~h~~~~~~~~~~~~~~~~ 156 (169)
++.+.++..+.+++ ||||+||||+|||+|+..||+++.++++++ +.++-.|..++.+||+|+||..-.++|-+=|
T Consensus 83 ld~~~e~~~~~~~G~~Sgtr~Llrl~R~LefV~efl~~i~as~nD~s~~diakesYd~~lakhHsW~IRtAV~~amYtLP 162 (209)
T KOG4189|consen 83 LDLDTEESEVGTIGNQSGTRNLLRLNRALEFVIEFLDQIFASTNDESLKDIAKESYDKTLAKHHSWAIRTAVAAAMYTLP 162 (209)
T ss_pred HHHHHHHhHhcccCccccchHHHHHHhhHHHHHHHHHHHHcCCCcchhhHHHHHHHHHhhhccccHHHHHHHHHHHHhCC
Confidence 88888888888877 999999999999999999999999987665 4445566779999999999999999999888
Q ss_pred cc
Q 030929 157 RR 158 (169)
Q Consensus 157 ~~ 158 (169)
.+
T Consensus 163 TR 164 (209)
T KOG4189|consen 163 TR 164 (209)
T ss_pred Cc
Confidence 65
No 3
>KOG3221 consensus Glycolipid transfer protein [Carbohydrate transport and metabolism]
Probab=99.97 E-value=1.4e-32 Score=222.98 Aligned_cols=133 Identities=21% Similarity=0.293 Sum_probs=124.0
Q ss_pred CCCCCcChHHHHHHHhHHHHHHhhcCccchhhHhhHHhhHHHHH----hccccchhHHHHHHHHHhcCCccCCCCcchhH
Q 030929 26 SQAADVELAAFSRACSYVSPLFGCLGIAFKFAEMDYVAKVDDLA----EASKSILTLQSVIDRDIEGNCVRKAGSHTRNL 101 (169)
Q Consensus 26 ~~~~~I~t~~FL~a~~~l~~lfd~LG~~F~fV~~Dv~~kI~~L~----~~~~~y~TL~~mv~~E~~~~~~~k~~S~srtL 101 (169)
.++++|+|.+||+||.+|++|+|+||++|+||++||+|||+++. +++..|++||.+|+.|++....+ ++|||++|
T Consensus 13 ~~d~~i~T~~FL~ac~~i~pvid~lG~~ftpVk~Di~gNI~kv~~~y~~d~~k~~~Lq~~i~~eie~~~a~-~~sat~aL 91 (199)
T KOG3221|consen 13 PDDGKIETGPFLEACKHIVPVIDKLGAVFTPVKSDISGNITKVKKVYDTDKEKFKYLQKIVKVEIETDIAE-KVSATLAL 91 (199)
T ss_pred CcccCCccHHHHHHHhhhhhHHHHhhhhhHhHHHHhhccHHHHHHHHhcChHHHHHHHHHHHHHHHHhhcc-cchhhHHH
Confidence 67899999999999999999999999999999999999999994 79999999999999999998877 89999999
Q ss_pred HHHhhHHHHHHHHHHHHHhCcch--hhhhhhhcccccccccccccchhhhhHHhhhcccC
Q 030929 102 LRVKRGLDMVRVLFEQILAAEYV--YQHGKFLKGSSIQGLHTSICSPSWMGYKKSCCRRD 159 (169)
Q Consensus 102 LrL~RaL~Fi~~fl~~l~~~~~~--~~~~~f~~~~~l~~~h~~~~~~~~~~~~~~~~~~~ 159 (169)
|||+|||+|+..||++|.++++. ..+..-+|+.||++||+||++..|.++-++.|-++
T Consensus 92 LWLkRgldF~~~~l~~l~~~~~~~l~~av~daY~kTLK~~HGwI~q~~FkvaLklvP~r~ 151 (199)
T KOG3221|consen 92 LWLKRGLDFTLAFLQELVNGESDCLIQAVADAYEKTLKKYHGWIVQSTFKVALKLVPDRK 151 (199)
T ss_pred HHHHhHHHHHHHHHHHHHcchhhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCcHH
Confidence 99999999999999999999876 46667777899999999999999999999988653
No 4
>PF04711 ApoA-II: Apolipoprotein A-II (ApoA-II); InterPro: IPR006801 Apolipoprotein A-II (ApoA-II) is the second major apolipoprotein of high density lipoprotein in human plasma. Mature ApoA-II is present as a dimer of two 77-amino acid chains joined by a disulphide bridge []. ApoA-II regulates many steps in HDL metabolism, and its role in coronary heart disease is unclear []. In bovine serum, the ApoA-II homologue is present in almost free form. Bovine ApoA-II shows antimicrobial activity against Escherichia coli and yeasts in phosphate buffered saline (PBS) [].; GO: 0008289 lipid binding, 0006869 lipid transport, 0042157 lipoprotein metabolic process, 0005576 extracellular region; PDB: 1L6L_W 2OU1_E.
Probab=64.53 E-value=12 Score=26.42 Aligned_cols=55 Identities=16% Similarity=0.205 Sum_probs=42.1
Q ss_pred hhHHHHHHHHhHhhhcCCCCCcChHHHHH-HHhHHHHHHhhcCc-cchhhHhhHHhh
Q 030929 10 LTKISESFKELAATVNSQAADVELAAFSR-ACSYVSPLFGCLGI-AFKFAEMDYVAK 64 (169)
Q Consensus 10 l~~v~~~F~~~~~~v~~~~~~I~t~~FL~-a~~~l~~lfd~LG~-~F~fV~~Dv~~k 64 (169)
+..|++.++++.++|+.++=.-....|.+ .-++++|+..+.|+ +|.|.++=|.-+
T Consensus 15 ~qt~TdYgKDL~Ekvk~pElqsQakaYfektqeQltPlvkKagtdl~nflS~~v~~~ 71 (76)
T PF04711_consen 15 FQTVTDYGKDLVEKVKGPELQSQAKAYFEKTQEQLTPLVKKAGTDLMNFLSSFVELK 71 (76)
T ss_dssp HHHHHHHHHHHHHHHHSHHTSSTCHHHHHHHHHHHHHHHHGGHHTHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHHhHHHHHHhHHHHHHHHHhhccc
Confidence 56788999999988877655555666665 55679999999998 789987766544
No 5
>PF08718 GLTP: Glycolipid transfer protein (GLTP); InterPro: IPR014830 Glycolipid transfer protein (GLTP) is a cytosolic protein that catalyses the intermembrane transfer of glycolipids such as glycosphingolipids, glyceroglycolipids, and possibly glucosylceramides, but not of phospholipids. The GLTP protein consists of a single domain with a multi-helical structure consisting of two layers of orthogonally packed helices [, ]. The GLTP domain is also found in trans-Golgi network proteins involved in Golgi-to-cell-surface membrane traffic [].; GO: 0017089 glycolipid transporter activity, 0051861 glycolipid binding, 0046836 glycolipid transport, 0005737 cytoplasm; PDB: 2BV7_A 1TFJ_A 1WBE_A 3KV0_A 3RWV_B 2EVD_A 2EUK_A 3RZN_A 2EVL_A 3S0K_A ....
Probab=47.36 E-value=7.9 Score=30.11 Aligned_cols=59 Identities=19% Similarity=0.094 Sum_probs=38.8
Q ss_pred HHhhHHHHHHHHHHHH---HhCcchh-hhhhhhc---ccccccccccccchhhhhHHhhhcccCCCCCC
Q 030929 103 RVKRGLDMVRVLFEQI---LAAEYVY-QHGKFLK---GSSIQGLHTSICSPSWMGYKKSCCRRDVCPSH 164 (169)
Q Consensus 103 rL~RaL~Fi~~fl~~l---~~~~~~~-~~~~f~~---~~~l~~~h~~~~~~~~~~~~~~~~~~~~~p~~ 164 (169)
=--|+|-|+...|+=+ +..-.+. ...+... .+|-+.+.+ ||+|++++.+-..-.+||+-
T Consensus 73 s~s~~LLwL~RaL~Fi~~~l~~l~~~~~~~~~~~~~~~AY~~tL~~---yH~w~vr~~~~~a~~~~P~R 138 (149)
T PF08718_consen 73 SGSRTLLWLHRALEFIVAFLENLLESPDDEKLSDAAREAYDKTLAP---YHGWIVRKAFKLALKALPSR 138 (149)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHTS--BTBHHHHHHHHHHHHTGG---GB-HHHHHHHHHHHHT--BH
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHh---CCCHHHHHHHHHHHHHCCCH
Confidence 3457788877665544 4433333 3332333 679999999 99999999999999999974
No 6
>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=45.69 E-value=99 Score=23.82 Aligned_cols=77 Identities=12% Similarity=0.195 Sum_probs=58.1
Q ss_pred HHHHHHhHHHHHHhhcCccchhhHhhHHhhHHHHHhccccchhHHHHHHHHHhcCCccCCCCcchhHHHHhhHHHHHHHH
Q 030929 35 AFSRACSYVSPLFGCLGIAFKFAEMDYVAKVDDLAEASKSILTLQSVIDRDIEGNCVRKAGSHTRNLLRVKRGLDMVRVL 114 (169)
Q Consensus 35 ~FL~a~~~l~~lfd~LG~~F~fV~~Dv~~kI~~L~~~~~~y~TL~~mv~~E~~~~~~~k~~S~srtLLrL~RaL~Fi~~f 114 (169)
..-+||..+.+=++.+....+=.+..+.++|+.|...-+...-+++.++.|+.. .-+.+=+++.-++.++..
T Consensus 40 ~m~~A~~~v~kql~~vs~~l~~tKkhLsqRId~vd~klDe~~ei~~~i~~eV~~--------v~~dv~~i~~dv~~v~~~ 111 (126)
T PF07889_consen 40 SMSDAVASVSKQLEQVSESLSSTKKHLSQRIDRVDDKLDEQKEISKQIKDEVTE--------VREDVSQIGDDVDSVQQM 111 (126)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHH--------HHhhHHHHHHHHHHHHHH
Confidence 456899999999999999999999999999999976666666677888888754 344555566666666665
Q ss_pred HHHHH
Q 030929 115 FEQIL 119 (169)
Q Consensus 115 l~~l~ 119 (169)
.+.|-
T Consensus 112 V~~Le 116 (126)
T PF07889_consen 112 VEGLE 116 (126)
T ss_pred HHHHH
Confidence 55553
No 7
>PF00036 EF-hand_1: EF hand; InterPro: IPR018248 Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both sides by a twelve residue alpha-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration. The six residues involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12 provides two oxygens for liganding Ca (bidentate ligand).; PDB: 1BJF_A 1XFW_R 1XFV_O 2K0J_A 2F3Z_A 3BYA_A 1XFU_Q 2R28_B 1ZOT_B 3G43_D ....
Probab=45.68 E-value=24 Score=19.96 Aligned_cols=28 Identities=14% Similarity=0.428 Sum_probs=21.0
Q ss_pred HHHHHHHhHhhhcCCCCCcChHHHHHHHhHH
Q 030929 13 ISESFKELAATVNSQAADVELAAFSRACSYV 43 (169)
Q Consensus 13 v~~~F~~~~~~v~~~~~~I~t~~FL~a~~~l 43 (169)
+...|+.... ..++.|+.++|..++..+
T Consensus 2 ~~~~F~~~D~---d~dG~I~~~Ef~~~~~~L 29 (29)
T PF00036_consen 2 LKEAFREFDK---DGDGKIDFEEFKEMMKKL 29 (29)
T ss_dssp HHHHHHHHST---TSSSEEEHHHHHHHHHHT
T ss_pred HHHHHHHHCC---CCCCcCCHHHHHHHHHhC
Confidence 4567777663 557889999999988653
No 8
>PF06512 Na_trans_assoc: Sodium ion transport-associated; InterPro: IPR010526 Members of this entry contain a region found exclusively in eukaryotic sodium channels or their subunits, many of which are voltage-gated. Members very often also contain between one and four copies of IPR005821 from INTERPRO and, less often, one copy of IPR000048 from INTERPRO.; GO: 0005248 voltage-gated sodium channel activity, 0006814 sodium ion transport, 0001518 voltage-gated sodium channel complex
Probab=35.13 E-value=43 Score=27.50 Aligned_cols=22 Identities=18% Similarity=0.350 Sum_probs=17.9
Q ss_pred hhHHHHhhHHHHHHHHHHHHHh
Q 030929 99 RNLLRVKRGLDMVRVLFEQILA 120 (169)
Q Consensus 99 rtLLrL~RaL~Fi~~fl~~l~~ 120 (169)
-|+-|++||+.|++..+..+..
T Consensus 9 iAi~RI~Rgi~~vK~~i~~~~~ 30 (239)
T PF06512_consen 9 IAIARIQRGIAWVKRAILDFCC 30 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4788999999999987776654
No 9
>PF03735 ENT: ENT domain; InterPro: IPR005491 This entry represents a protein regulator which is able to repress transcription, possibly via its interaction with a multi protein chromatin re-modeling complex that modifies the chromatin. Its interaction with BRCA2 suggests that it may play a central role in the DNA repair function of BRCA2 []. ; PDB: 1UZ3_B 1UTU_B 2FMM_E.
Probab=31.36 E-value=1.2e+02 Score=21.10 Aligned_cols=49 Identities=12% Similarity=0.147 Sum_probs=33.4
Q ss_pred HHHHhHHHHHHhhcCccchhhHhhHHhhHHHH--HhccccchhHHHHHHHHH
Q 030929 37 SRACSYVSPLFGCLGIAFKFAEMDYVAKVDDL--AEASKSILTLQSVIDRDI 86 (169)
Q Consensus 37 L~a~~~l~~lfd~LG~~F~fV~~Dv~~kI~~L--~~~~~~y~TL~~mv~~E~ 86 (169)
++||..++..|..=|+ ++.=+..+-.++.+. .++..+-.-+..++..|.
T Consensus 10 ~eAY~svl~Af~Aqg~-lsweke~lLt~Lr~~L~IS~e~H~~~l~~~~~De~ 60 (73)
T PF03735_consen 10 LEAYSSVLRAFRAQGP-LSWEKEKLLTELRKELNISDEEHREELRRAVSDEQ 60 (73)
T ss_dssp HHHHHHHHHHHHHHSS---HHHHHHHHHHHHHTT--HHHHHHHHHHHHH-HH
T ss_pred HHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHhCCCcHHHHHHHHHHhccHH
Confidence 6899999999999999 888888887777766 244455555666655553
No 10
>cd08789 CARD_IPS-1_RIG-I Caspase activation and recruitment domains (CARDs) found in IPS-1 and RIG-I-like RNA helicases. Caspase activation and recruitment domains (CARDs) found in IPS-1 (Interferon beta promoter stimulator protein 1) and Retinoic acid Inducible Gene I (RIG-I)-like DEAD box helicases. RIG-I-like helicases and IPS-1 play important roles in the induction of interferons in response to viral infection. They are crucial in triggering innate immunity and in developing adaptive immunity against viral pathogens. RIG-I-like helicases, including MDA5 and RIG-I, contain two N-terminal CARD domains and a C-terminal DEAD box RNA helicase domain. They are cytoplasmic RNA helicases that play an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. MDA5 and RIG-I associate with IPS-1 through a CARD-CAR
Probab=28.15 E-value=1.4e+02 Score=21.03 Aligned_cols=26 Identities=12% Similarity=0.190 Sum_probs=19.0
Q ss_pred cchhHH-HHhhHHHHHHHHHHHHHhCc
Q 030929 97 HTRNLL-RVKRGLDMVRVLFEQILAAE 122 (169)
Q Consensus 97 ~srtLL-rL~RaL~Fi~~fl~~l~~~~ 122 (169)
+++.|| .|.|+-.|...|+..|....
T Consensus 50 aa~~Ll~~L~r~~~Wf~~Fl~AL~~~~ 76 (84)
T cd08789 50 AAWTLLDTLVRRDNWLEPFLDALRECG 76 (84)
T ss_pred HHHHHHHHHhccCChHHHHHHHHHHcC
Confidence 444443 35589999999999998764
No 11
>PF09373 PMBR: Pseudomurein-binding repeat; InterPro: IPR018975 Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) is a methanogenic Gram-positive microorganism with a cell wall consisting of pseudomurein. This repeat specifically binds to pseudomurein. This repeat is found at the N terminus of PeiW and PeiP which are pseudomurein binding phage proteins.
Probab=26.10 E-value=77 Score=18.44 Aligned_cols=28 Identities=11% Similarity=0.151 Sum_probs=23.9
Q ss_pred CCCcChHHHHHHHhHHHHHHhhcCccch
Q 030929 28 AADVELAAFSRACSYVSPLFGCLGIAFK 55 (169)
Q Consensus 28 ~~~I~t~~FL~a~~~l~~lfd~LG~~F~ 55 (169)
.+.|..++|++++..+..|.+.=|.+-.
T Consensus 2 ~~~i~~~~~~d~a~rv~~f~~~ngRlPn 29 (33)
T PF09373_consen 2 SGTISKEEYLDMASRVNNFYESNGRLPN 29 (33)
T ss_pred CceecHHHHHHHHHHHHHHHHHcCCCCC
Confidence 4678999999999999999998887643
No 12
>smart00054 EFh EF-hand, calcium binding motif. EF-hands are calcium-binding motifs that occur at least in pairs. Links between disease states and genes encoding EF-hands, particularly the S100 subclass, are emerging. Each motif consists of a 12 residue loop flanked on either side by a 12 residue alpha-helix. EF-hands undergo a conformational change unpon binding calcium ions.
Probab=24.55 E-value=87 Score=15.07 Aligned_cols=26 Identities=12% Similarity=0.296 Sum_probs=16.4
Q ss_pred HHHHHHhHhhhcCCCCCcChHHHHHHHhH
Q 030929 14 SESFKELAATVNSQAADVELAAFSRACSY 42 (169)
Q Consensus 14 ~~~F~~~~~~v~~~~~~I~t~~FL~a~~~ 42 (169)
...|+.+.. ..++.|+..+|......
T Consensus 3 ~~~f~~~d~---~~~g~i~~~e~~~~~~~ 28 (29)
T smart00054 3 KEAFRLFDK---DGDGKIDFEEFKDLLKA 28 (29)
T ss_pred HHHHHHHCC---CCCCcEeHHHHHHHHHh
Confidence 445665542 33567998888877654
No 13
>cd08812 CARD_RIG-I_like Caspase activation and recruitment domains found in RIG-I-like DEAD box helicases. Caspase activation and recruitment domains (CARDs) found in Retinoic acid Inducible Gene I (RIG-I)-like DEAD box helicases. These helicases, including MDA5 and RIG-I, contain two N-terminal CARD domains and a C-terminal DEAD box RNA helicase domain. They are cytoplasmic RNA helicases that play an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, RIG-I and MDA5 have been shown to recognize different sets of viruses. MDA5 and RIG-I associate with IPS-1 through a CARD-CARD interaction. 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 mec
Probab=22.75 E-value=2.4e+02 Score=19.89 Aligned_cols=27 Identities=11% Similarity=0.234 Sum_probs=18.7
Q ss_pred cchhHH-HHh--hHHHHHHHHHHHHHhCcc
Q 030929 97 HTRNLL-RVK--RGLDMVRVLFEQILAAEY 123 (169)
Q Consensus 97 ~srtLL-rL~--RaL~Fi~~fl~~l~~~~~ 123 (169)
+++.|| +|. |+-.|...|+..|.....
T Consensus 52 aa~~Ll~~L~~~r~~~wf~~Fl~AL~~~g~ 81 (88)
T cd08812 52 AAEELLDRLERCDKPGWFQAFLDALRRTGN 81 (88)
T ss_pred HHHHHHHHHHHhccCCcHHHHHHHHHHcCC
Confidence 444443 344 688999999999987643
No 14
>PF13405 EF-hand_6: EF-hand domain; PDB: 2AMI_A 3QRX_A 1W7J_B 1OE9_B 1W7I_B 1KFU_S 1KFX_S 2BL0_B 1Y1X_B 3MSE_B ....
Probab=20.89 E-value=1.6e+02 Score=16.08 Aligned_cols=27 Identities=11% Similarity=0.263 Sum_probs=18.9
Q ss_pred HHHHHHHHhHhhhcCCCCCcChHHHHHHHh
Q 030929 12 KISESFKELAATVNSQAADVELAAFSRACS 41 (169)
Q Consensus 12 ~v~~~F~~~~~~v~~~~~~I~t~~FL~a~~ 41 (169)
++...|+.... ..++-|+.++|..+.+
T Consensus 1 ~l~~~F~~~D~---d~dG~I~~~el~~~l~ 27 (31)
T PF13405_consen 1 RLREAFKMFDK---DGDGFIDFEELRAILR 27 (31)
T ss_dssp HHHHHHHHH-T---TSSSEEEHHHHHHHHH
T ss_pred CHHHHHHHHCC---CCCCcCcHHHHHHHHH
Confidence 35677887763 4567899988887765
No 15
>PF14788 EF-hand_10: EF hand; PDB: 1DJW_B 1DJI_B 1DJG_B 1QAS_B 2ISD_B 1DJZ_B 1DJY_B 1DJX_B 1QAT_A 1DJH_A ....
Probab=20.71 E-value=1.5e+02 Score=19.42 Aligned_cols=31 Identities=19% Similarity=0.216 Sum_probs=24.0
Q ss_pred hHHHHHHHHhHhhhcCCCCCcChHHHHHHHhHHH
Q 030929 11 TKISESFKELAATVNSQAADVELAAFSRACSYVS 44 (169)
Q Consensus 11 ~~v~~~F~~~~~~v~~~~~~I~t~~FL~a~~~l~ 44 (169)
.....-|++|.. +.++.++-++|.+.|+.|+
T Consensus 21 ~yA~~LFq~~D~---s~~g~Le~~Ef~~Fy~~LT 51 (51)
T PF14788_consen 21 EYARQLFQECDK---SQSGRLEGEEFEEFYKRLT 51 (51)
T ss_dssp HHHHHHHHHH-S---SSSSEBEHHHHHHHHHHHS
T ss_pred HHHHHHHHHhcc---cCCCCccHHHHHHHHHHhC
Confidence 445568998874 6788999999999998763
Done!