Query psy7100
Match_columns 76
No_of_seqs 36 out of 38
Neff 3.9
Searched_HMMs 46136
Date Fri Aug 16 18:11:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7100.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7100hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1788|consensus 94.7 0.01 2.2E-07 54.5 0.4 71 2-75 84-159 (2799)
2 cd08818 CARD_MDA5_1 Caspase ac 80.7 2.8 6.1E-05 27.7 3.5 52 8-62 24-77 (88)
3 PF07271 Cytadhesin_P30: Cytad 62.5 11 0.00025 29.5 3.6 39 1-39 102-140 (279)
4 PF05184 SapB_1: Saposin-like 61.9 16 0.00035 19.0 3.2 22 14-35 5-26 (39)
5 smart00139 MyTH4 Domain in Myo 50.2 23 0.00051 24.1 3.2 60 2-62 23-93 (144)
6 COG3541 Predicted nucleotidylt 49.8 8.4 0.00018 29.6 1.0 39 33-74 47-85 (248)
7 PF12807 eIF3_p135: Translatio 48.3 48 0.001 22.7 4.5 35 11-45 46-80 (169)
8 PF10127 Nuc-transf: Predicted 45.5 10 0.00022 27.4 0.8 28 47-74 68-95 (247)
9 PF09496 CENP-O: Cenp-O kineto 37.4 56 0.0012 20.8 3.3 22 6-27 64-85 (90)
10 cd08816 CARD_RIG-I_1 Caspase a 37.1 1E+02 0.0022 20.5 4.5 44 14-62 31-76 (89)
11 cd08789 CARD_IPS-1_RIG-I Caspa 36.8 44 0.00096 21.0 2.7 37 8-44 23-59 (84)
12 PF12872 OST-HTH: OST-HTH/LOTU 35.7 21 0.00046 20.6 1.0 30 30-62 1-30 (74)
13 cd08812 CARD_RIG-I_like Caspas 34.9 1.2E+02 0.0026 19.1 4.7 45 14-62 31-77 (88)
14 PRK13798 putative OHCU decarbo 34.6 77 0.0017 22.4 3.9 29 17-45 126-154 (166)
15 TIGR03164 UHCUDC OHCU decarbox 33.9 82 0.0018 21.9 3.9 29 17-45 121-149 (157)
16 TIGR03180 UraD_2 OHCU decarbox 32.7 87 0.0019 21.9 3.9 29 17-45 121-149 (158)
17 PF15651 Tox-SGS: Salivary gla 32.7 20 0.00044 24.2 0.7 10 52-61 79-88 (100)
18 PF15400 TEX33: Testis-express 32.2 71 0.0015 22.8 3.4 30 9-48 9-38 (140)
19 KOG1058|consensus 32.2 86 0.0019 28.4 4.5 35 3-37 210-244 (948)
20 PF03299 TF_AP-2: Transcriptio 31.3 72 0.0016 23.4 3.4 39 18-59 23-61 (209)
21 KOG0812|consensus 30.3 2.2E+02 0.0048 22.7 6.2 49 9-63 244-298 (311)
22 TIGR02702 SufR_cyano iron-sulf 29.8 1.4E+02 0.003 20.8 4.6 39 7-45 94-132 (203)
23 PF07704 PSK_trans_fac: Rv0623 28.5 1.5E+02 0.0033 18.4 4.3 36 1-45 3-39 (82)
24 PF09349 OHCU_decarbox: OHCU d 27.4 88 0.0019 21.5 3.2 30 16-45 123-152 (159)
25 PF00616 RasGAP: GTPase-activa 25.8 1.3E+02 0.0028 20.2 3.7 30 14-43 126-155 (197)
26 KOG4077|consensus 24.9 95 0.0021 22.4 3.0 47 25-75 37-90 (149)
27 KOG4070|consensus 24.5 1.3E+02 0.0028 22.2 3.7 26 20-45 83-109 (180)
28 smart00337 BCL BCL (B-Cell lym 23.7 1.7E+02 0.0037 18.5 3.8 31 8-44 55-87 (100)
29 TIGR00179 murB UDP-N-acetyleno 23.5 45 0.00097 25.0 1.2 42 13-58 183-224 (284)
30 PF11978 MVP_shoulder: Shoulde 22.7 94 0.002 21.5 2.6 27 8-34 45-71 (118)
31 PF01602 Adaptin_N: Adaptin N 22.5 2.8E+02 0.0062 21.2 5.4 59 13-74 109-171 (526)
32 smart00288 VHS Domain present 22.4 2.4E+02 0.0052 18.6 4.7 24 16-39 35-58 (133)
33 PF11547 E3_UbLigase_EDD: E3 u 22.2 93 0.002 18.9 2.2 47 12-69 5-52 (53)
34 TIGR02135 phoU_full phosphate 22.0 2.5E+02 0.0053 18.5 5.5 57 7-71 87-143 (212)
35 PF11943 DUF3460: Protein of u 20.4 1.8E+02 0.004 17.9 3.3 37 19-56 7-43 (60)
36 PF14735 HAUS4: HAUS augmin-li 20.2 1.9E+02 0.0041 21.7 4.0 36 14-55 36-71 (238)
37 PF14669 Asp_Glu_race_2: Putat 20.0 89 0.0019 24.0 2.2 23 3-25 82-104 (233)
No 1
>KOG1788|consensus
Probab=94.69 E-value=0.01 Score=54.51 Aligned_cols=71 Identities=14% Similarity=0.079 Sum_probs=61.2
Q ss_pred chhhhhHHHHHHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHhhhhcccccchhHHHHHHHH-----HHhcCCcchhhcC
Q psy7100 2 TDKFRDVHQFCDHVSRLMVTKVCQRASNQSTEIASCAIAKFLEIENSEESSSGWMLLSTLN-----LLAAGDVSLVEEG 75 (76)
Q Consensus 2 v~~F~~i~~fa~~vs~~lv~EIr~ras~k~tE~A~~ai~~fL~~~~~e~~~~GwlLLksv~-----lLs~~d~~~v~~~ 75 (76)
.++|++...|++..|...+.|+|+|+....|-++.+.|.+|+.. .+.-.||..||++. |||+.+.-+++++
T Consensus 84 seeeKEaalnlTvlcfcrlvkvhanvdqlvTmlveqhIfsFvig---rafvkdyekLkagss~ganLLtaeevlmsgpa 159 (2799)
T KOG1788|consen 84 SEEEKEAALNLTVLCFCRLVKVHANVDQLVTMLVEQHIFSFVIG---RAFVKDYEKLKAGSSHGANLLTAEEVLMSGPA 159 (2799)
T ss_pred cHHHHHHHHhhhheeeeeeeHHhhhhhhhhhhhhHhhHHHHhcC---ccccccchhhhccccccchhhhhhHHHhhCch
Confidence 47899999999999999999999999999999999999999965 56668899888874 7777776666543
No 2
>cd08818 CARD_MDA5_1 Caspase activation and recruitment domain found in MDA5, first repeat. Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), first repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays 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, MDA5 recognizes different sets of viruses compared to RIG-I, a related RNA helicase. MDA5 associates 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 mechanisms. DDs are protein-
Probab=80.70 E-value=2.8 Score=27.66 Aligned_cols=52 Identities=15% Similarity=0.285 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHhhhhcccccchhHH--HHHHHH
Q psy7100 8 VHQFCDHVSRLMVTKVCQRASNQSTEIASCAIAKFLEIENSEESSSGWM--LLSTLN 62 (76)
Q Consensus 8 i~~fa~~vs~~lv~EIr~ras~k~tE~A~~ai~~fL~~~~~e~~~~Gwl--LLksv~ 62 (76)
|.+|-..+..-.+.+||+...+++.-+|...+.+.|+. ....-||- +|.+++
T Consensus 24 VL~~l~~L~~e~ke~I~a~~~~~Gn~~AA~~LL~~l~~---~~~~~GWf~~FldAL~ 77 (88)
T cd08818 24 VLDYLTFLEAEVKERIRAAAATRGNIAAAELLLSTLEK---GTWDPGWFREFVTALE 77 (88)
T ss_pred HhhhcccCCHHHHHHHHHHHHccCcHHHHHHHHHHHHH---hccCCchHHHHHHHHH
Confidence 66677777788899999999999998898888888875 23457994 555543
No 3
>PF07271 Cytadhesin_P30: Cytadhesin P30/P32; InterPro: IPR009896 This family consists of several Mycoplasma species specific Cytadhesin P32 and P30 proteins. P30 has been found to be membrane associated and localised on the tip organelle. It is thought that it is important in cytadherence and virulence [].; GO: 0007157 heterophilic cell-cell adhesion, 0009405 pathogenesis, 0016021 integral to membrane
Probab=62.49 E-value=11 Score=29.45 Aligned_cols=39 Identities=10% Similarity=0.205 Sum_probs=34.6
Q ss_pred CchhhhhHHHHHHHHHHHHHHHHHHHhhcCcHHHHHHHH
Q psy7100 1 MTDKFRDVHQFCDHVSRLMVTKVCQRASNQSTEIASCAI 39 (76)
Q Consensus 1 mv~~F~~i~~fa~~vs~~lv~EIr~ras~k~tE~A~~ai 39 (76)
|++.|-+....++++.++--||+++.+..++++||.+..
T Consensus 102 ~iee~e~~~q~~e~~~~i~qq~~~ea~e~~~~~e~~~~A 140 (279)
T PF07271_consen 102 MIEEKEEHEQLAEQLGRISQQEETEAIEKTPSAEANAQA 140 (279)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhcCchhhhhccc
Confidence 578899999999999999999999999999999887643
No 4
>PF05184 SapB_1: Saposin-like type B, region 1; InterPro: IPR007856 Synonym(s):cerebroside sulphate activator, CSAct Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity. Although the secondary structure of saposin B is similar to that of the known monomeric members of the saposin-like superfamily, the helices are repacked into a different tertiary arrangement to form the homodimer. A comparison of the two forms of the saposin B dimer suggests that extraction of target lipids from membranes involves a conformational change that facilitates access to the inner cavity [].; GO: 0006629 lipid metabolic process; PDB: 1N69_C 1QDM_C 4DDJ_A 2DOB_A 1OF9_A 2Z9A_A 1M12_A 2GTG_A 1SN6_A 2QYP_B ....
Probab=61.92 E-value=16 Score=18.96 Aligned_cols=22 Identities=18% Similarity=0.318 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHHhhcCcHHHH
Q psy7100 14 HVSRLMVTKVCQRASNQSTEIA 35 (76)
Q Consensus 14 ~vs~~lv~EIr~ras~k~tE~A 35 (76)
.+|..+|++|++.+.+..|++.
T Consensus 5 ~~C~~~v~~i~~~l~~~~t~~~ 26 (39)
T PF05184_consen 5 DICKFVVKEIEKLLKNNKTEEE 26 (39)
T ss_dssp HHHHHHHHHHHHHHHSTCHHHH
T ss_pred hHHHHHHHHHHHHHHcCccHHH
Confidence 4678889999999988777653
No 5
>smart00139 MyTH4 Domain in Myosin and Kinesin Tails. Domain present twice in myosin-VIIa, and also present in 3 other myosins.
Probab=50.21 E-value=23 Score=24.13 Aligned_cols=60 Identities=20% Similarity=0.339 Sum_probs=37.2
Q ss_pred chhhhhHHHHHHHH-------HHHHHHHHHHHhhcCcH--HHHHHHHHHHhhhhccc--ccchhHHHHHHHH
Q psy7100 2 TDKFRDVHQFCDHV-------SRLMVTKVCQRASNQST--EIASCAIAKFLEIENSE--ESSSGWMLLSTLN 62 (76)
Q Consensus 2 v~~F~~i~~fa~~v-------s~~lv~EIr~ras~k~t--E~A~~ai~~fL~~~~~e--~~~~GwlLLksv~ 62 (76)
+..|..|+.|.++. ...+++.|-+.+-+++. .|.=+=|.+-+.- ++. ..-+||.||.-..
T Consensus 23 ~~iF~~Il~ymgd~~~~~~~~~~~l~~~i~~~~~~~~~LrDEiy~QLiKQtt~-Np~~~s~~rgW~Ll~l~~ 93 (144)
T smart00139 23 VKIFKAILKFMGDLPLPKPDSHLDLVQFILQKGLAHPELRDEIYCQLIKQLTD-NPSRQSEERGWELLYLCT 93 (144)
T ss_pred HHHHHHHHHHhcCCCCCCcchHHHHHHHHHHHHhccHHHHHHHHHHHHHHHhC-CCCchHHHHHHHHHHHHH
Confidence 35699999999762 13477777777666653 4555555555532 332 2246999997554
No 6
>COG3541 Predicted nucleotidyltransferase [General function prediction only]
Probab=49.75 E-value=8.4 Score=29.64 Aligned_cols=39 Identities=28% Similarity=0.325 Sum_probs=30.7
Q ss_pred HHHHHHHHHHhhhhcccccchhHHHHHHHHHHhcCCcchhhc
Q psy7100 33 EIASCAIAKFLEIENSEESSSGWMLLSTLNLLAAGDVSLVEE 74 (76)
Q Consensus 33 E~A~~ai~~fL~~~~~e~~~~GwlLLksv~lLs~~d~~~v~~ 74 (76)
|+-+..|.+.+ .++.|-.||-|=|+++||...++.+++-
T Consensus 47 ~~~rdviE~pl---~~~~D~~gweLrK~L~Ll~k~Np~~lEw 85 (248)
T COG3541 47 EQPRDVIEEPL---DGEIDTVGWELRKFLLLLLKANANCLEW 85 (248)
T ss_pred cccccchheec---cCccchhHHHHHHHHHHHhcCCchHHHH
Confidence 44455555554 5688889999999999999999988763
No 7
>PF12807 eIF3_p135: Translation initiation factor eIF3 subunit 135
Probab=48.31 E-value=48 Score=22.74 Aligned_cols=35 Identities=14% Similarity=0.177 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHhhh
Q psy7100 11 FCDHVSRLMVTKVCQRASNQSTEIASCAIAKFLEI 45 (76)
Q Consensus 11 fa~~vs~~lv~EIr~ras~k~tE~A~~ai~~fL~~ 45 (76)
..+=|+|.+-+.+|..+.+.+.+..+.+|++||..
T Consensus 46 ~~EmiaR~~K~i~r~~l~~~~~~~~~~~v~~~lN~ 80 (169)
T PF12807_consen 46 LQEMIARAAKHILREYLRSVPQSELSSAVSHFLNC 80 (169)
T ss_pred HHHHHHHHHHHHHHHHHHccchhhHHHHHHHHHHH
Confidence 35667888888889999999999999999999965
No 8
>PF10127 Nuc-transf: Predicted nucleotidyltransferase; InterPro: IPR018775 Proteins in this entry are predicted to catalyse the transfer of nucleotide residues from nucleoside diphosphates or triphosphates into dimer or polymer forms.
Probab=45.47 E-value=10 Score=27.36 Aligned_cols=28 Identities=32% Similarity=0.518 Sum_probs=24.4
Q ss_pred cccccchhHHHHHHHHHHhcCCcchhhc
Q psy7100 47 NSEESSSGWMLLSTLNLLAAGDVSLVEE 74 (76)
Q Consensus 47 ~~e~~~~GwlLLksv~lLs~~d~~~v~~ 74 (76)
+++.|-.||-|=|.+.||..+|+.+++.
T Consensus 68 ~~~~D~~~~dl~k~l~L~~k~Np~~lE~ 95 (247)
T PF10127_consen 68 DDDLDINGWDLRKFLRLLLKGNPNLLEW 95 (247)
T ss_pred CCCCCeeEeeHHHHHHHHHcCCCceEee
Confidence 4567888999999999999999988764
No 9
>PF09496 CENP-O: Cenp-O kinetochore centromere component; InterPro: IPR018464 Chromosome segregation in eukaryotes requires the kinetochore, a multi-protein structure that assembles on centromeric DNA, and which acts to link chromosomes to spindle microtubules. Kinetochore structure and composition is highly conserved among vertebrates. The inner kinetochore is essential for kinetochore assembly, and is involved in chromosome segregation via regulation of the spindle. Inner kinetochore components include the multi-subunit CENP-H/I complex, which may function, in part, in directing centromere protein A (CENP-A) deposition to centromeres, where CENP-A is a centromere-specific histone H3 variant required for the organisation of centromeric chromatin during interphase. The CENP-H/I complex contains three functional classes of proteins [, ]: CENP-H class (includes CENP-H, -I, -K, -L) CENP-M class (includes CENP-M) CENP-O class (includes CENP-O, -P, -Q, -R, -50) The CENP-O class proteins form a stable complex and are required for proper kinetochore function. They are involved in the prevention of premature sister chromatid separation during recovery from spindle damage []. CENP-O mediates the attachment of the centromere to the mitotic spindle by forming essential interactions between the microtubule-associated outer kinetochore proteins and the centromere-associated inner kinetochore proteins. It has been shown to be involved in chromosome segregation via regulation of the spindle in both yeast [] and human [].; GO: 0007059 chromosome segregation, 0051301 cell division, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 3ZXU_C.
Probab=37.38 E-value=56 Score=20.81 Aligned_cols=22 Identities=23% Similarity=0.383 Sum_probs=18.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHHh
Q psy7100 6 RDVHQFCDHVSRLMVTKVCQRA 27 (76)
Q Consensus 6 ~~i~~fa~~vs~~lv~EIr~ra 27 (76)
.||..|+.+|.++|+.-.-|+.
T Consensus 64 ~dl~~F~~~l~~~L~~~~~R~~ 85 (90)
T PF09496_consen 64 QDLYRFARELRRELVAYHNRRD 85 (90)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHH
Confidence 4899999999999998777764
No 10
>cd08816 CARD_RIG-I_1 Caspase activation and recruitment domain found in RIG-I, first repeat. Caspase activation and recruitment domain (CARD) found in RIG-I (Retinoic acid Inducible Gene I, also known as Ddx58), first repeat. RIG-I is a cytoplasmic RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. RIG-I contains two N-terminal CARD domains and a C-terminal RNA helicase. 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 recognizes different sets of viruses compared to MDA5, a related RNA helicase. RIG-I associates 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 mechanisms. DDs are protein-protein interaction doma
Probab=37.12 E-value=1e+02 Score=20.50 Aligned_cols=44 Identities=14% Similarity=0.286 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHhhcCcHHHHHHHHHHHhhhhcccccchhHH--HHHHHH
Q psy7100 14 HVSRLMVTKVCQRASNQSTEIASCAIAKFLEIENSEESSSGWM--LLSTLN 62 (76)
Q Consensus 14 ~vs~~lv~EIr~ras~k~tE~A~~ai~~fL~~~~~e~~~~Gwl--LLksv~ 62 (76)
..-+-+|+-|+.- -||+.-+|.+-..++|.- -+..||- +|.|++
T Consensus 31 ~~~~e~v~~I~aE-e~kg~~~AaqlfL~~l~~----lee~GWFqafLDaL~ 76 (89)
T cd08816 31 WLEDEEVERILSE-EEKGVTSAAQLFLDYVLK----LEEEGWFQAFLDALY 76 (89)
T ss_pred hcCHHHHHHHHHH-hccChHHHHHHHHHHHHH----HccccHHHHHHHHHH
Confidence 3334456666663 346655555555555542 2557994 555543
No 11
>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=36.77 E-value=44 Score=21.05 Aligned_cols=37 Identities=11% Similarity=0.069 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHhh
Q psy7100 8 VHQFCDHVSRLMVTKVCQRASNQSTEIASCAIAKFLE 44 (76)
Q Consensus 8 i~~fa~~vs~~lv~EIr~ras~k~tE~A~~ai~~fL~ 44 (76)
|.++..-+...+..+|+..-.+++...|..-+.+.|+
T Consensus 23 il~~L~~Lt~~d~e~I~a~~~~~G~~~aa~~Ll~~L~ 59 (84)
T cd08789 23 VLPYLTCLTAEDKERIQAAENNSGNIKAAWTLLDTLV 59 (84)
T ss_pred HHhhCCcCCHHHHHHHHHHHhcCChHHHHHHHHHHHh
Confidence 3333334556688899999888999888888888886
No 12
>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A.
Probab=35.65 E-value=21 Score=20.64 Aligned_cols=30 Identities=30% Similarity=0.493 Sum_probs=16.9
Q ss_pred CcHHHHHHHHHHHhhhhcccccchhHHHHHHHH
Q psy7100 30 QSTEIASCAIAKFLEIENSEESSSGWMLLSTLN 62 (76)
Q Consensus 30 k~tE~A~~ai~~fL~~~~~e~~~~GwlLLksv~ 62 (76)
|+-++....|-+.|.- ..+.+||+.|..+.
T Consensus 1 ~~~~~~~~~l~~ll~~---~~~~~g~v~ls~l~ 30 (74)
T PF12872_consen 1 KSLEELKKLLRELLES---QKGEDGWVSLSQLG 30 (74)
T ss_dssp ---HHHHHHHHHHHHH---TCTTTSSEEHHHHH
T ss_pred ChHHHHHHHHHHHHHh---CcCCCceEEHHHHH
Confidence 3455666677777732 33446787777664
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=34.90 E-value=1.2e+02 Score=19.10 Aligned_cols=45 Identities=18% Similarity=0.271 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHhhcCcHHHHHHHHHHHhhhhcccccchhHH--HHHHHH
Q psy7100 14 HVSRLMVTKVCQRASNQSTEIASCAIAKFLEIENSEESSSGWM--LLSTLN 62 (76)
Q Consensus 14 ~vs~~lv~EIr~ras~k~tE~A~~ai~~fL~~~~~e~~~~Gwl--LLksv~ 62 (76)
.+...++.+|+.--.|++...|..-+...|+. ....||- ++.++.
T Consensus 31 ~L~~~~~e~I~a~~~~~g~~~aa~~Ll~~L~~----~r~~~wf~~Fl~AL~ 77 (88)
T cd08812 31 CLTDEDKEQILAEERNKGNIAAAEELLDRLER----CDKPGWFQAFLDALR 77 (88)
T ss_pred HcCHHHHHHHHHHHhccChHHHHHHHHHHHHH----hccCCcHHHHHHHHH
Confidence 56677889999988888888888888888863 1245773 555554
No 14
>PRK13798 putative OHCU decarboxylase; Provisional
Probab=34.62 E-value=77 Score=22.36 Aligned_cols=29 Identities=17% Similarity=0.177 Sum_probs=25.7
Q ss_pred HHHHHHHHHHhhcCcHHHHHHHHHHHhhh
Q psy7100 17 RLMVTKVCQRASNQSTEIASCAIAKFLEI 45 (76)
Q Consensus 17 ~~lv~EIr~ras~k~tE~A~~ai~~fL~~ 45 (76)
..+-.++++|+.|.+.+|-+.|+.+.-+|
T Consensus 126 ~~IL~~l~~Rl~n~~e~E~~~al~Ev~kI 154 (166)
T PRK13798 126 DEMLAALQQRLHNDPETERKVVREELAKI 154 (166)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Confidence 45668999999999999999999998877
No 15
>TIGR03164 UHCUDC OHCU decarboxylase. Previously thought to only proceed spontaneously, the decarboxylation of 2-oxo-4-hydroxy-4-carboxy--5-ureidoimidazoline (OHCU) has been recently been shown to be catalyzed by this enzyme in Mus musculus. Homologs of this enzyme are found adjacent to and fused with uricase in a number of prokaryotes and are represented by this model.
Probab=33.95 E-value=82 Score=21.94 Aligned_cols=29 Identities=14% Similarity=0.138 Sum_probs=25.6
Q ss_pred HHHHHHHHHHhhcCcHHHHHHHHHHHhhh
Q psy7100 17 RLMVTKVCQRASNQSTEIASCAIAKFLEI 45 (76)
Q Consensus 17 ~~lv~EIr~ras~k~tE~A~~ai~~fL~~ 45 (76)
..+-.++++|+.|-+.+|-+.|+.+.-+|
T Consensus 121 ~~Il~~l~~Rl~n~~~~E~~~a~~Ev~kI 149 (157)
T TIGR03164 121 QSILAAFEARLNNDRETEFARALREIERI 149 (157)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 45678999999999999999999998776
No 16
>TIGR03180 UraD_2 OHCU decarboxylase. Previously thought to only proceed spontaneously, the decarboxylation of 2-oxo-4-hydroxy-4-carboxy--5-ureidoimidazoline (OHCU) has been recently been shown to be catalyzed by this enzyme in Mus musculus. Homologs of this enzyme are found adjacent to and fused with uricase in a number of prokaryotes and are represented by this model. This model is a separate (but related) clade from that represented by TIGR3164. This model places a second homolog in streptomyces species which (are not in the vicinity of other urate catabolism associated genes) below the trusted cutoff.
Probab=32.74 E-value=87 Score=21.87 Aligned_cols=29 Identities=17% Similarity=0.205 Sum_probs=25.9
Q ss_pred HHHHHHHHHHhhcCcHHHHHHHHHHHhhh
Q psy7100 17 RLMVTKVCQRASNQSTEIASCAIAKFLEI 45 (76)
Q Consensus 17 ~~lv~EIr~ras~k~tE~A~~ai~~fL~~ 45 (76)
..+-.++++|+.|-+.+|-+.|+.+.-+|
T Consensus 121 ~~IL~~l~~Rl~n~~e~E~~~al~Ev~kI 149 (158)
T TIGR03180 121 EEMLDALQARLPNDPEQELTIAAEQLRKI 149 (158)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 45678999999999999999999998877
No 17
>PF15651 Tox-SGS: Salivary glad secreted protein domain toxin
Probab=32.69 E-value=20 Score=24.15 Aligned_cols=10 Identities=30% Similarity=1.086 Sum_probs=7.6
Q ss_pred chhHHHHHHH
Q psy7100 52 SSGWMLLSTL 61 (76)
Q Consensus 52 ~~GwlLLksv 61 (76)
-|||+||-=|
T Consensus 79 vDGWLmLArV 88 (100)
T PF15651_consen 79 VDGWLMLARV 88 (100)
T ss_pred hhhhHHHHHH
Confidence 3899999644
No 18
>PF15400 TEX33: Testis-expressed sequence 33 protein family
Probab=32.23 E-value=71 Score=22.83 Aligned_cols=30 Identities=30% Similarity=0.411 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHhhhhcc
Q psy7100 9 HQFCDHVSRLMVTKVCQRASNQSTEIASCAIAKFLEIENS 48 (76)
Q Consensus 9 ~~fa~~vs~~lv~EIr~ras~k~tE~A~~ai~~fL~~~~~ 48 (76)
+.|-+.+++++|+| |+|+.||.+-++..++
T Consensus 9 hkfGs~~vdqlvse----------Eq~~r~~~~~~~~~~~ 38 (140)
T PF15400_consen 9 HKFGSNVVDQLVSE----------EQARRAIGEVFEGQKR 38 (140)
T ss_pred HHHhHHHHHHHHhH----------HHHHHhhhHHhhcCCC
Confidence 35778899999988 8899999999987554
No 19
>KOG1058|consensus
Probab=32.16 E-value=86 Score=28.38 Aligned_cols=35 Identities=14% Similarity=0.226 Sum_probs=29.3
Q ss_pred hhhhhHHHHHHHHHHHHHHHHHHHhhcCcHHHHHH
Q psy7100 3 DKFRDVHQFCDHVSRLMVTKVCQRASNQSTEIASC 37 (76)
Q Consensus 3 ~~F~~i~~fa~~vs~~lv~EIr~ras~k~tE~A~~ 37 (76)
.++-+|..|-..+.-.+|.-||+-.-+.|+|.++.
T Consensus 210 ~~idqi~~~~~~LqlViVE~Irkv~~~~p~~~~~~ 244 (948)
T KOG1058|consen 210 SNIDQIPSFNDSLQLVIVELIRKVCLANPAEKARY 244 (948)
T ss_pred hhHhhccCccHHHHHHHHHHHHHHHhcCHHHhhHH
Confidence 35666777888888899999999999999999883
No 20
>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=31.28 E-value=72 Score=23.44 Aligned_cols=39 Identities=15% Similarity=0.210 Sum_probs=25.5
Q ss_pred HHHHHHHHHhhcCcHHHHHHHHHHHhhhhcccccchhHHHHH
Q psy7100 18 LMVTKVCQRASNQSTEIASCAIAKFLEIENSEESSSGWMLLS 59 (76)
Q Consensus 18 ~lv~EIr~ras~k~tE~A~~ai~~fL~~~~~e~~~~GwlLLk 59 (76)
+-|-|||||+++ |-=.=++.++-+|+.. -..+.|-.|-+
T Consensus 23 VTv~Ei~RR~~~-PE~ln~S~lg~~LRra--K~k~~g~~lr~ 61 (209)
T PF03299_consen 23 VTVGEIRRRLSP-PECLNASLLGGVLRRA--KSKNGGRSLRE 61 (209)
T ss_pred eeHHHHHHHhcC-CccccHHHHHHHHHHh--cccchHHHHHH
Confidence 347899999954 4444566899999863 34444555544
No 21
>KOG0812|consensus
Probab=30.29 E-value=2.2e+02 Score=22.74 Aligned_cols=49 Identities=27% Similarity=0.426 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHHHHHHh-hcCc-----HHHHHHHHHHHhhhhcccccchhHHHHHHHHH
Q psy7100 9 HQFCDHVSRLMVTKVCQRA-SNQS-----TEIASCAIAKFLEIENSEESSSGWMLLSTLNL 63 (76)
Q Consensus 9 ~~fa~~vs~~lv~EIr~ra-s~k~-----tE~A~~ai~~fL~~~~~e~~~~GwlLLksv~l 63 (76)
+++|.+|+.+ .|+-+|+ .|-. -|.|...|.+|++. .+++-|++.|=.-+
T Consensus 244 ~QLA~mVseQ--~E~i~RID~nv~ds~lnI~gA~~ellKy~e~----vSSNRwLmvkiF~i 298 (311)
T KOG0812|consen 244 QQLASMVSEQ--EETIQRIDDNVDDSDLNIEGAHSELLKYFER----VSSNRWLMVKIFGI 298 (311)
T ss_pred HHHHHHHHHH--HHHHHHHHhcchhhhhhhHHHHHHHHHHHHH----hccchHHHHHHHHH
Confidence 4566777665 4555554 3333 27899999999984 47789999886543
No 22
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=29.79 E-value=1.4e+02 Score=20.82 Aligned_cols=39 Identities=3% Similarity=-0.078 Sum_probs=26.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHhhh
Q psy7100 7 DVHQFCDHVSRLMVTKVCQRASNQSTEIASCAIAKFLEI 45 (76)
Q Consensus 7 ~i~~fa~~vs~~lv~EIr~ras~k~tE~A~~ai~~fL~~ 45 (76)
++..+.+..-..+..+.++++...+.++.-.++++.+.-
T Consensus 94 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 132 (203)
T TIGR02702 94 QFEAVLQKQWQRKAEAYRRQLGQGSLAERLAQLVALRQQ 132 (203)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHh
Confidence 345555555566666666777557778888888888863
No 23
>PF07704 PSK_trans_fac: Rv0623-like transcription factor; InterPro: IPR011660 This entry represents the Rv0623 (P96913 from SWISSPROT)-like group of transcription factors associated with the PSK operon [].
Probab=28.47 E-value=1.5e+02 Score=18.42 Aligned_cols=36 Identities=25% Similarity=0.278 Sum_probs=24.6
Q ss_pred CchhhhhHHHHHHHHHHHHHHHHHHHhhcCc-HHHHHHHHHHHhhh
Q psy7100 1 MTDKFRDVHQFCDHVSRLMVTKVCQRASNQS-TEIASCAIAKFLEI 45 (76)
Q Consensus 1 mv~~F~~i~~fa~~vs~~lv~EIr~ras~k~-tE~A~~ai~~fL~~ 45 (76)
|.||-|++..+|.++.+ + .|.+ ||.-+.|+.+-|+.
T Consensus 3 L~Ikd~ev~~LareLA~--------~-tG~s~TeAVr~AL~~~L~~ 39 (82)
T PF07704_consen 3 LNIKDPEVDRLARELAR--------L-TGESKTEAVRRALRERLER 39 (82)
T ss_pred CCcCCHHHHHHHHHHHH--------H-HCCCHHHHHHHHHHHHHHh
Confidence 35677887776655543 3 3445 88888999988874
No 24
>PF09349 OHCU_decarbox: OHCU decarboxylase; InterPro: IPR018020 The proteins in this entry are OHCU decarboxylase, an enzyme of the purine catabolism that catalyses the conversion of OHCU into S(+)-allantoin []; it is the third step of the conversion of uric acid (a purine derivative) to allantoin. Step one is catalysed by urate oxidase (IPR002042 from INTERPRO) and step two is catalysed by hydroxyisourate hydrolase (IPR000895 from INTERPRO). ; PDB: 3O7I_B 3O7H_B 3O7J_A 3O7K_A 2Q37_A 2O70_B 2O73_C 2O74_C 2O8I_A.
Probab=27.44 E-value=88 Score=21.54 Aligned_cols=30 Identities=17% Similarity=0.233 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHhhcCcHHHHHHHHHHHhhh
Q psy7100 16 SRLMVTKVCQRASNQSTEIASCAIAKFLEI 45 (76)
Q Consensus 16 s~~lv~EIr~ras~k~tE~A~~ai~~fL~~ 45 (76)
...+..++++|+.|.+.+|-+.|+.+.-+|
T Consensus 123 ~~~Il~~l~~Rl~n~~~~E~~~A~~Ev~kI 152 (159)
T PF09349_consen 123 AAEILAALERRLNNDPEEELRIALEEVAKI 152 (159)
T ss_dssp HHHHHHHHHHHTTS-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Confidence 356789999999999999999999987766
No 25
>PF00616 RasGAP: GTPase-activator protein for Ras-like GTPase; InterPro: IPR001936 Ras proteins are membrane-associated molecular switches that bind GTP and GDP and slowly hydrolyze GTP to GDP []. This intrinsic GTPase activity of ras is stimulated by a family of proteins collectively known as 'GAP' or GTPase-activating proteins [, ]. As it is the GTP bound form of ras which is active, these proteins are said to be down-regulators of ras. The Ras GTPase-activating proteins are quite large (from 765 residues for sar1 to 3079 residues for IRA2) but share only a limited (about 250 residues) region of sequence similarity, referred to as the 'catalytic domain' or rasGAP domain. Note: There are distinctly different GAPs for the rap and rho/rac subfamilies of ras-like proteins (reviewed in reference []) that do not share sequence similarity with ras GAPs.; GO: 0005096 GTPase activator activity, 0051056 regulation of small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3BXJ_B 1WQ1_G 1WER_A 1NF1_A 3FAY_A.
Probab=25.84 E-value=1.3e+02 Score=20.22 Aligned_cols=30 Identities=17% Similarity=0.255 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHhhcCcHHHHHHHHHHHh
Q psy7100 14 HVSRLMVTKVCQRASNQSTEIASCAIAKFL 43 (76)
Q Consensus 14 ~vs~~lv~EIr~ras~k~tE~A~~ai~~fL 43 (76)
.+|+.+-..++++.-+...+++..+|+.|+
T Consensus 126 ~i~~~i~~~~~~~fp~~~~~~~~~~v~~fi 155 (197)
T PF00616_consen 126 YICKQIYEAVEKKFPDASPEEILSAVGGFI 155 (197)
T ss_dssp HHHHHHHHHHHHHTTTSSHCHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhccCchHHHHHHHHHHHH
Confidence 456666677777776665678888898887
No 26
>KOG4077|consensus
Probab=24.91 E-value=95 Score=22.38 Aligned_cols=47 Identities=17% Similarity=0.334 Sum_probs=29.0
Q ss_pred HHhhcCcH---HHHHHHHHHHhhhhcccccchhHHHHHHHH-HHhcC---CcchhhcC
Q psy7100 25 QRASNQST---EIASCAIAKFLEIENSEESSSGWMLLSTLN-LLAAG---DVSLVEEG 75 (76)
Q Consensus 25 ~ras~k~t---E~A~~ai~~fL~~~~~e~~~~GwlLLksv~-lLs~~---d~~~v~~~ 75 (76)
++-.++.. ||=----.+||- -++-|||-+=|.+| +++.+ ++.+|++|
T Consensus 37 ~~~~~hg~et~EEfd~ry~~yf~----r~~iD~wEvrkglN~l~~yDlVP~pkvIEaa 90 (149)
T KOG4077|consen 37 KYSMEHGPETAEEFDARYEKYFN----RPEIDGWEVRKGLNNLFDYDLVPSPKVIEAA 90 (149)
T ss_pred hhHhhcCcccHHHHHHHHHHHcC----cccchHHHHHHHHHhhhccccCCChHHHHHH
Confidence 45555544 443333456664 24779999999999 55554 24477764
No 27
>KOG4070|consensus
Probab=24.46 E-value=1.3e+02 Score=22.23 Aligned_cols=26 Identities=27% Similarity=0.275 Sum_probs=22.8
Q ss_pred HHHHH-HHhhcCcHHHHHHHHHHHhhh
Q psy7100 20 VTKVC-QRASNQSTEIASCAIAKFLEI 45 (76)
Q Consensus 20 v~EIr-~ras~k~tE~A~~ai~~fL~~ 45 (76)
..|+. +|+.+||-|++-.+|-+.|.-
T Consensus 83 l~ela~~R~k~Ks~ee~l~~I~~llag 109 (180)
T KOG4070|consen 83 LEELATKRFKGKSKEEALDAICQLLAG 109 (180)
T ss_pred HHHHHHhhhcCCCHHHHHHHHHHHHhc
Confidence 45665 899999999999999999975
No 28
>smart00337 BCL BCL (B-Cell lymphoma); contains BH1, BH2 regions. (BH1, BH2, (BH3 (one helix only)) and not BH4(one helix only)). Involved in apoptosis regulation
Probab=23.71 E-value=1.7e+02 Score=18.47 Aligned_cols=31 Identities=16% Similarity=0.276 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCc--HHHHHHHHHHHhh
Q psy7100 8 VHQFCDHVSRLMVTKVCQRASNQS--TEIASCAIAKFLE 44 (76)
Q Consensus 8 i~~fa~~vs~~lv~EIr~ras~k~--tE~A~~ai~~fL~ 44 (76)
+..|+..++..+++. +.| .......+.+|+.
T Consensus 55 l~~F~~~la~~~~~~------~~~~~~~~i~~~~~~~l~ 87 (100)
T smart00337 55 LLSFGGALAVKLVQK------EDPDLVSRLASWLSEFLR 87 (100)
T ss_pred HHHHHHHHHHHHHHc------CCchHHHHHHHHHHHHHH
Confidence 456777777766541 121 2333445667775
No 29
>TIGR00179 murB UDP-N-acetylenolpyruvoylglucosamine reductase. This model describes MurB, UDP-N-acetylenolpyruvoylglucosamine reductase, which is also called UDP-N-acetylmuramate dehydrogenase. It is part of the pathway for the biosynthesis of the UDP-N-acetylmuramoyl-pentapeptide that is a precursor of bacterial peptidoglycan.
Probab=23.53 E-value=45 Score=25.01 Aligned_cols=42 Identities=12% Similarity=0.187 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHHhhcCcHHHHHHHHHHHhhhhcccccchhHHHH
Q psy7100 13 DHVSRLMVTKVCQRASNQSTEIASCAIAKFLEIENSEESSSGWMLL 58 (76)
Q Consensus 13 ~~vs~~lv~EIr~ras~k~tE~A~~ai~~fL~~~~~e~~~~GwlLL 58 (76)
+++...|....++|.+.||-... ..+.||. ++..+.-|||+=
T Consensus 183 ~~i~~~~~~~~~~r~~~~p~~~p--saGS~Fk--NP~~~~Ag~LIe 224 (284)
T TIGR00179 183 ETITAQQVFNKVCRMRTSHYPDP--NAGSFFK--NPSPNHAGRLIE 224 (284)
T ss_pred hhhhHHHHHHHHHHHHcCCCcCC--Ccccccc--CcCCchHHHHHH
Confidence 56677888888899999987664 6789996 566667899863
No 30
>PF11978 MVP_shoulder: Shoulder domain; InterPro: IPR021870 This domain is found in the Major Vault Protein and has been called the shoulder domain []. This family includes two bacterial proteins A6FXE2 from SWISSPROT and A1ZGE7 from SWISSPROT. This suggests that some bacteria may possess vault particles. ; PDB: 2ZUO_G 2QZV_B 2ZV5_c 2ZV4_Y.
Probab=22.72 E-value=94 Score=21.55 Aligned_cols=27 Identities=7% Similarity=0.215 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCcHHH
Q psy7100 8 VHQFCDHVSRLMVTKVCQRASNQSTEI 34 (76)
Q Consensus 8 i~~fa~~vs~~lv~EIr~ras~k~tE~ 34 (76)
|..|-.++|+.+++-||-.+++.+=++
T Consensus 45 VpDFVGd~Ck~iaSRIR~aVa~~~Fd~ 71 (118)
T PF11978_consen 45 VPDFVGDACKAIASRIRGAVASVTFDD 71 (118)
T ss_dssp STTHHHHHHHHHHHHHHHHHHTSHHHH
T ss_pred CcchHHHHHHHHHHHHHHHHhcCcHHH
Confidence 678999999999999999998877554
No 31
>PF01602 Adaptin_N: Adaptin N terminal region; InterPro: IPR002553 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the N-terminal domain of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and from the beta and gamma subunits of various coatomer (COP) adaptors. This domain has a 2-layer alpha/alpha fold that forms a right-handed superhelix, and is a member of the ARM repeat superfamily []. The N-terminal region of the various AP adaptor proteins share strong sequence identity; by contrast, the C-terminal domains of different adaptins share similar structural folds, but have little sequence identity []. It has been proposed that the N-terminal domain interacts with another uniform component of the coated vesicles. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 1W63_C 2JKR_A 2JKT_A 2XA7_A 2VGL_B 3TJZ_E.
Probab=22.47 E-value=2.8e+02 Score=21.15 Aligned_cols=59 Identities=22% Similarity=0.302 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHhhcCcH---HHHHHHHHHHhhhhcccccchhHHHHHHHH-HHhcCCcchhhc
Q psy7100 13 DHVSRLMVTKVCQRASNQST---EIASCAIAKFLEIENSEESSSGWMLLSTLN-LLAAGDVSLVEE 74 (76)
Q Consensus 13 ~~vs~~lv~EIr~ras~k~t---E~A~~ai~~fL~~~~~e~~~~GwlLLksv~-lLs~~d~~~v~~ 74 (76)
.++...+...|.+-+..... -.|..++.++.+. .++.-.++ ++.-+. +|...|+.++.+
T Consensus 109 ~~~~~~l~~~v~~ll~~~~~~VRk~A~~~l~~i~~~-~p~~~~~~--~~~~l~~lL~d~~~~V~~~ 171 (526)
T PF01602_consen 109 PEMAEPLIPDVIKLLSDPSPYVRKKAALALLKIYRK-DPDLVEDE--LIPKLKQLLSDKDPSVVSA 171 (526)
T ss_dssp HHHHHHHHHHHHHHHHSSSHHHHHHHHHHHHHHHHH-CHCCHHGG--HHHHHHHHTTHSSHHHHHH
T ss_pred cchhhHHHHHHHHHhcCCchHHHHHHHHHHHHHhcc-CHHHHHHH--HHHHHhhhccCCcchhHHH
Confidence 45667777888888887775 5677788888876 34443334 566665 776666665543
No 32
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=22.42 E-value=2.4e+02 Score=18.62 Aligned_cols=24 Identities=21% Similarity=0.254 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHhhcCcHHHHHHHH
Q psy7100 16 SRLMVTKVCQRASNQSTEIASCAI 39 (76)
Q Consensus 16 s~~lv~EIr~ras~k~tE~A~~ai 39 (76)
.+..++-||+|+.+...-++-.|+
T Consensus 35 ~k~a~r~l~krl~~~n~~v~l~AL 58 (133)
T smart00288 35 PKDAVRLLKKRLNNKNPHVALLAL 58 (133)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH
Confidence 677888999999988876666664
No 33
>PF11547 E3_UbLigase_EDD: E3 ubiquitin ligase EDD; InterPro: IPR024725 EDD, the ER ubiquitin ligase from the HECT ligases, contains an N-terminal ubiquitin-associated (UBA) domain which binds ubiquitin. Ubiquitin is recognised by helices alpha-1 and -3 in in the UBA domain. EDD is involved in DNA damage repair pathways and binds to mono-ubiquitinated proteins [].; GO: 0043130 ubiquitin binding; PDB: 2QHO_H.
Probab=22.24 E-value=93 Score=18.88 Aligned_cols=47 Identities=19% Similarity=0.212 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHhhhhcccccchhHHHHHHHH-HHhcCCc
Q psy7100 12 CDHVSRLMVTKVCQRASNQSTEIASCAIAKFLEIENSEESSSGWMLLSTLN-LLAAGDV 69 (76)
Q Consensus 12 a~~vs~~lv~EIr~ras~k~tE~A~~ai~~fL~~~~~e~~~~GwlLLksv~-lLs~~d~ 69 (76)
+.+|-.-+..+.+..+.|||- ..|..=|+..+-+ .=-+|| |||.+|.
T Consensus 5 a~~vPedlI~q~q~VLqgksR----~vIirELqrTnLd-------VN~AvNNlLsRDde 52 (53)
T PF11547_consen 5 ASQVPEDLINQAQVVLQGKSR----NVIIRELQRTNLD-------VNLAVNNLLSRDDE 52 (53)
T ss_dssp GGGS-HHHHHHHHHHSTTS-H----HHHHHHHHHTTT--------HHHHHHHHHHHH--
T ss_pred cccCCHHHHHHHHHHHcCCcH----HHHHHHHHHhccc-------HHHHHHHHhccccC
Confidence 345566788899999999984 4566667663222 224565 7777664
No 34
>TIGR02135 phoU_full phosphate transport system regulatory protein PhoU. This model describes PhoU, a regulatory protein of unknown mechanism for high-affinity phosphate ABC transporter systems. The protein consists of two copies of the domain described by Pfam model pfam01895. Deletion of PhoU activates constitutive expression of the phosphate ABC transporter and allows phosphate transport, but causes a growth defect and so likely has some second function.
Probab=21.97 E-value=2.5e+02 Score=18.52 Aligned_cols=57 Identities=14% Similarity=0.166 Sum_probs=32.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHhhhhcccccchhHHHHHHHHHHhcCCcch
Q psy7100 7 DVHQFCDHVSRLMVTKVCQRASNQSTEIASCAIAKFLEIENSEESSSGWMLLSTLNLLAAGDVSL 71 (76)
Q Consensus 7 ~i~~fa~~vs~~lv~EIr~ras~k~tE~A~~ai~~fL~~~~~e~~~~GwlLLksv~lLs~~d~~~ 71 (76)
++-+.+.++.+ +++.+.+...++..++++..+.++.+. -.-++-.++..|...|+..
T Consensus 87 ~lErigD~~~~-ia~~~~~~~~~~~~~~~~~el~~m~~~-------v~~~l~~a~~al~~~d~~~ 143 (212)
T TIGR02135 87 DLERIGDYAVN-IAKRALRLKEEDAKPKHLEELEKMGKL-------ALKMLKDALDAFLNKDAEL 143 (212)
T ss_pred HHHHHHHHHHH-HHHHHHHhcccCCCCccHHHHHHHHHH-------HHHHHHHHHHHHHhCCHHH
Confidence 45566666444 566666666555445666666666543 2335555666666666543
No 35
>PF11943 DUF3460: Protein of unknown function (DUF3460); InterPro: IPR021853 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 70 amino acids in length. This protein has a conserved WDK sequence motif.
Probab=20.36 E-value=1.8e+02 Score=17.86 Aligned_cols=37 Identities=5% Similarity=-0.060 Sum_probs=29.5
Q ss_pred HHHHHHHHhhcCcHHHHHHHHHHHhhhhcccccchhHH
Q psy7100 19 MVTKVCQRASNQSTEIASCAIAKFLEIENSEESSSGWM 56 (76)
Q Consensus 19 lv~EIr~ras~k~tE~A~~ai~~fL~~~~~e~~~~Gwl 56 (76)
..+.|++-...+|..++.+--+.-|.|++ ..|.+.|-
T Consensus 7 ~TqFl~~lk~~~Pele~~Q~~GRallWDk-~~d~e~~~ 43 (60)
T PF11943_consen 7 ITQFLNQLKAKHPELEEEQRAGRALLWDK-PQDLEEQA 43 (60)
T ss_pred HHHHHHHHHHhCCchHHHHHHhhHHhcCC-CCCHHHHH
Confidence 35778888899999999999999999976 55555543
No 36
>PF14735 HAUS4: HAUS augmin-like complex subunit 4
Probab=20.22 E-value=1.9e+02 Score=21.74 Aligned_cols=36 Identities=17% Similarity=0.321 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHhhcCcHHHHHHHHHHHhhhhcccccchhH
Q psy7100 14 HVSRLMVTKVCQRASNQSTEIASCAIAKFLEIENSEESSSGW 55 (76)
Q Consensus 14 ~vs~~lv~EIr~ras~k~tE~A~~ai~~fL~~~~~e~~~~Gw 55 (76)
.+-..+..||-.++..|+ .++..|..+ +++.+++|=
T Consensus 36 ~~q~~L~~eiE~~Lk~KC-----~~Lls~~~p-~~~~~s~~l 71 (238)
T PF14735_consen 36 RMQQRLPREIEERLKKKC-----FSLLSYHQP-DSESSSEGL 71 (238)
T ss_pred HHHHHHHHHHHHHHHHHH-----HHHHHHhCC-CCccccchh
Confidence 677788999999998887 788999998 446666553
No 37
>PF14669 Asp_Glu_race_2: Putative aspartate racemase
Probab=20.05 E-value=89 Score=23.99 Aligned_cols=23 Identities=26% Similarity=0.618 Sum_probs=20.6
Q ss_pred hhhhhHHHHHHHHHHHHHHHHHH
Q psy7100 3 DKFRDVHQFCDHVSRLMVTKVCQ 25 (76)
Q Consensus 3 ~~F~~i~~fa~~vs~~lv~EIr~ 25 (76)
++|.|++.|+..|...|.++..-
T Consensus 82 e~~~dlq~~~~~va~~Ltkd~Kd 104 (233)
T PF14669_consen 82 EKFADLQRFCACVAEALTKDSKD 104 (233)
T ss_pred CCHHHHHHHHHHHHHHHHhcccc
Confidence 68999999999999999998854
Done!