Query psy6618
Match_columns 109
No_of_seqs 139 out of 1142
Neff 8.6
Searched_HMMs 46136
Date Fri Aug 16 22:44:33 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6618.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6618hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0085|consensus 99.7 3.9E-17 8.5E-22 113.6 6.0 88 1-94 61-149 (359)
2 KOG0082|consensus 99.6 1.3E-15 2.9E-20 111.2 3.9 90 1-95 55-146 (354)
3 cd00066 G-alpha G protein alph 99.5 2.2E-14 4.8E-19 104.1 3.7 88 1-93 22-110 (317)
4 smart00275 G_alpha G protein a 99.4 2.1E-13 4.6E-18 99.9 3.9 87 1-92 43-132 (342)
5 KOG0099|consensus 99.3 3E-12 6.4E-17 90.7 4.0 87 1-93 62-151 (379)
6 PF00503 G-alpha: G-protein al 98.9 7.3E-10 1.6E-14 82.4 3.4 86 1-91 80-182 (389)
7 KOG0085|consensus 98.9 2.7E-09 5.9E-14 74.8 4.6 73 27-99 40-116 (359)
8 KOG0099|consensus 98.9 1.9E-09 4.2E-14 76.5 3.5 65 36-100 54-120 (379)
9 KOG0082|consensus 98.8 1.2E-08 2.6E-13 75.0 4.7 64 36-99 47-110 (354)
10 cd00066 G-alpha G protein alph 98.7 2E-08 4.4E-13 73.0 5.3 64 36-99 14-77 (317)
11 smart00275 G_alpha G protein a 98.6 5.4E-08 1.2E-12 71.6 5.2 73 27-99 22-98 (342)
12 PF00503 G-alpha: G-protein al 97.8 1.9E-05 4.2E-10 58.8 3.6 64 36-99 72-142 (389)
13 PF02216 B: B domain; InterPr 71.0 2.4 5.2E-05 22.9 1.0 34 1-34 16-49 (54)
14 PF11212 DUF2999: Protein of u 51.2 33 0.00071 19.9 3.3 62 5-85 11-72 (82)
15 PHA02652 hypothetical protein; 51.2 22 0.00047 19.5 2.5 34 18-56 31-64 (70)
16 cd08804 Death_ank2 Death domai 40.0 40 0.00086 19.7 2.7 30 5-34 25-54 (84)
17 PF09836 DUF2063: Uncharacteri 39.3 25 0.00053 20.7 1.7 28 6-33 26-54 (94)
18 PF08132 AdoMetDC_leader: S-ad 39.3 9.7 0.00021 20.3 -0.0 19 6-24 26-50 (54)
19 PF05261 Tra_M: TraM protein, 38.5 1.1E+02 0.0023 19.7 6.5 25 4-31 58-82 (127)
20 PRK12277 50S ribosomal protein 37.2 20 0.00044 21.2 1.1 11 4-14 31-41 (83)
21 COG0114 FumC Fumarase [Energy 35.0 37 0.0008 26.2 2.4 24 11-34 356-379 (462)
22 PF12488 DUF3704: Protein of u 32.3 18 0.00039 16.8 0.3 11 99-109 5-15 (27)
23 PF13373 DUF2407_C: DUF2407 C- 32.0 31 0.00067 22.4 1.4 17 4-20 8-24 (140)
24 TIGR02058 lin0512_fam conserve 29.9 34 0.00074 21.6 1.3 31 2-32 13-43 (116)
25 KOG1317|consensus 26.2 39 0.00085 25.5 1.3 24 11-34 381-404 (487)
26 smart00309 PAH Pancreatic horm 25.0 83 0.0018 15.6 1.9 16 4-19 9-24 (36)
27 PF00627 UBA: UBA/TS-N domain; 24.9 94 0.002 14.8 2.3 9 6-14 13-21 (37)
28 PF07553 Lipoprotein_Ltp: Host 23.0 1.3E+02 0.0028 15.8 3.5 18 40-57 26-43 (48)
29 cd00194 UBA Ubiquitin Associat 22.3 1.1E+02 0.0023 14.5 2.5 21 6-26 12-32 (38)
30 cd08803 Death_ank3 Death domai 21.7 1.2E+02 0.0025 17.8 2.5 27 6-32 26-52 (84)
31 PF08671 SinI: Anti-repressor 21.5 46 0.001 15.8 0.6 13 5-17 15-27 (30)
32 cd08318 Death_NMPP84 Death dom 21.4 1.2E+02 0.0025 17.7 2.5 25 6-31 29-53 (86)
33 smart00165 UBA Ubiquitin assoc 21.4 1E+02 0.0022 14.5 1.9 8 6-13 12-19 (37)
34 PF09585 Lin0512_fam: Conserve 21.2 73 0.0016 20.0 1.6 41 2-46 13-53 (113)
35 PF01517 HDV_ag: Hepatitis del 20.3 34 0.00074 23.0 0.0 15 3-17 89-103 (194)
No 1
>KOG0085|consensus
Probab=99.69 E-value=3.9e-17 Score=113.63 Aligned_cols=88 Identities=19% Similarity=0.213 Sum_probs=73.1
Q ss_pred CccCCCCCHHHHhcchhHhHhhHHHHHHHHHHhhhhhhhhhhhhhccCCCCHHHhhchhhhhhhchhHhH-HHHHHHhhh
Q psy6618 1 IIHESGFTSEDFKQYRPVVYSNTIQSTVRILGTFLLSKWLELRIIHESGFTSEDFKQYRPVVYSNTIQSL-VAILRAMPN 79 (109)
Q Consensus 1 iih~~gfs~ee~~~~~~~I~~Nii~~~~~li~a~~~~~~kql~I~~~~~~~~~e~~~~~~~i~~n~~~~~-~~i~~ai~~ 79 (109)
|||+.|||+||++.|+++||+||..+|+++|+|| +.++|++..+.+++.+..++...... +..+ ..++.||+.
T Consensus 61 iihg~gyseedrkgf~~lvyqnif~amqaMIrAM-----etL~I~y~~e~nk~~A~~vrevd~ek-Vttfe~~yv~aik~ 134 (359)
T KOG0085|consen 61 IIHGAGYSEEDRKGFTKLVYQNIFTAMQAMIRAM-----ETLKIPYKREENKAHASLVREVDVEK-VTTFEKRYVSAIKW 134 (359)
T ss_pred hhhcCCCChhhhccchHHHHHHHHHHHHHHHHHH-----HHhccccccccchhhhhHhhhcchHH-hhhhhHHHHHHHHH
Confidence 7999999999999999999999999999999999 99999998776666554444433322 2345 789999999
Q ss_pred hCCCCCChhhHHhhh
Q psy6618 80 LSISFSNNERETAGL 94 (109)
Q Consensus 80 Lw~d~~~~~~~~~~~ 94 (109)
||-|+|++++-++.+
T Consensus 135 LW~D~GIqeCYdRRR 149 (359)
T KOG0085|consen 135 LWRDPGIQECYDRRR 149 (359)
T ss_pred HHhCcchHHHHHHHH
Confidence 999999999877553
No 2
>KOG0082|consensus
Probab=99.58 E-value=1.3e-15 Score=111.18 Aligned_cols=90 Identities=23% Similarity=0.287 Sum_probs=72.9
Q ss_pred CccCCCCCHHHHhcchhHhHhhHHHHHHHHHHhhhhhhhhhhhhhccCCCCHHHhhchhhhhhhchh-HhH-HHHHHHhh
Q psy6618 1 IIHESGFTSEDFKQYRPVVYSNTIQSTVRILGTFLLSKWLELRIIHESGFTSEDFKQYRPVVYSNTI-QSL-VAILRAMP 78 (109)
Q Consensus 1 iih~~gfs~ee~~~~~~~I~~Nii~~~~~li~a~~~~~~kql~I~~~~~~~~~e~~~~~~~i~~n~~-~~~-~~i~~ai~ 78 (109)
|||++|||++|+++||++||+|++++|..|++|| ..+++.+.++..+.+...+......... ..+ ++++++|+
T Consensus 55 ilh~~gfs~ee~~~~r~~I~~N~~~~~~~ll~a~-----~~~~i~~~~~~~~~d~~~~~~~~~~~~~~~~~~~e~~~~i~ 129 (354)
T KOG0082|consen 55 ILHGDGFSEEELLEYRPVIYSNIIQSLKALLRAM-----ETLGINLDDPERENDAQKLTLLADAAEELGVFSPELAEAIK 129 (354)
T ss_pred HHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHhcCCCCChhhhhHHHHHHHhhhcccccccCCHHHHHHHH
Confidence 6899999999999999999999999999999999 8999999887666665555432222222 234 99999999
Q ss_pred hhCCCCCChhhHHhhhh
Q psy6618 79 NLSISFSNNERETAGLS 95 (109)
Q Consensus 79 ~Lw~d~~~~~~~~~~~~ 95 (109)
.||.|++++..-.++..
T Consensus 130 ~lW~d~~Iq~~~~r~~e 146 (354)
T KOG0082|consen 130 ELWKDPGIQACYERRRE 146 (354)
T ss_pred HHHcCHHHHHHHHcCCc
Confidence 99999999988776543
No 3
>cd00066 G-alpha G protein alpha subunit. The alpha subunit of G proteins contains the guanine nucleotide binding site. The heterotrimeric GNP-binding proteins are signal transducers that communicate signals from many hormones, neurotransmitters, chemokines, and autocrine and paracrine factors. Extracellular signals are received by receptors, which activate the G proteins, which in turn route the signals to several distinct intracellular signaling pathways. The alpha subunit of G proteins is a weak GTPase. In the resting state, heterotrimeric G proteins are associated at the cytosolic face of the plasma membrane and the alpha subunit binds to GDP. Upon activation by a receptor GDP is replaced with GTP, and the G-alpha/GTP complex dissociates from the beta and gamma subunits. This results in activation of downstream signaling pathways, such as cAMP synthesis by adenylyl cyclase, which is terminated when GTP is hydrolized and the heterotrimers reconstitute.
Probab=99.48 E-value=2.2e-14 Score=104.08 Aligned_cols=88 Identities=25% Similarity=0.321 Sum_probs=67.4
Q ss_pred CccCCCCCHHHHhcchhHhHhhHHHHHHHHHHhhhhhhhhhhhhhccCCCCHHHhhchhhhhhhchhHhH-HHHHHHhhh
Q psy6618 1 IIHESGFTSEDFKQYRPVVYSNTIQSTVRILGTFLLSKWLELRIIHESGFTSEDFKQYRPVVYSNTIQSL-VAILRAMPN 79 (109)
Q Consensus 1 iih~~gfs~ee~~~~~~~I~~Nii~~~~~li~a~~~~~~kql~I~~~~~~~~~e~~~~~~~i~~n~~~~~-~~i~~ai~~ 79 (109)
|||++|||++|+++|+++||.|++++|+.|++|| +++++++..+.+......+...........+ +++++++..
T Consensus 22 il~~~gfs~~Er~~~~~~I~~Ni~~~~~~ll~a~-----~~~~i~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~i~~ 96 (317)
T cd00066 22 ILHGDGFSEEELREYRPVIYSNILQSMKALLEAM-----ERLNIPFGDPENEKDAKKILSFAPELEEGELPPELAEAIKE 96 (317)
T ss_pred HhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHcCCCCCChhhHHHHHHHHhccccccccCCCHHHHHHHHH
Confidence 5899999999999999999999999999999999 8999987765544433332221111111234 789999999
Q ss_pred hCCCCCChhhHHhh
Q psy6618 80 LSISFSNNERETAG 93 (109)
Q Consensus 80 Lw~d~~~~~~~~~~ 93 (109)
||.|++++..-.+.
T Consensus 97 lW~d~~iq~~~~~r 110 (317)
T cd00066 97 LWKDPGIQACYDRR 110 (317)
T ss_pred HhCCHHHHHHHHhc
Confidence 99999999875544
No 4
>smart00275 G_alpha G protein alpha subunit. Subunit of G proteins that contains the guanine nucleotide binding site
Probab=99.40 E-value=2.1e-13 Score=99.91 Aligned_cols=87 Identities=26% Similarity=0.356 Sum_probs=66.3
Q ss_pred CccCCCCCHHHHhcchhHhHhhHHHHHHHHHHhhhhhhhhhhhhhccCCCCHHHhhchhhhhh--hchhHhH-HHHHHHh
Q psy6618 1 IIHESGFTSEDFKQYRPVVYSNTIQSTVRILGTFLLSKWLELRIIHESGFTSEDFKQYRPVVY--SNTIQSL-VAILRAM 77 (109)
Q Consensus 1 iih~~gfs~ee~~~~~~~I~~Nii~~~~~li~a~~~~~~kql~I~~~~~~~~~e~~~~~~~i~--~n~~~~~-~~i~~ai 77 (109)
|+|++||+++|+.+|+++||.|++++|+.|++|| ++++|.+.++.+......+..... ......+ +++++++
T Consensus 43 il~~~gfs~~E~~~~~~~I~~Nii~~~~~ll~a~-----~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~i 117 (342)
T smart00275 43 ILHGDGFSQEERREYRPLIYSNILESMKALVDAM-----EELNIPFEDPESILDIRIITEQFNKTDETENVLPKEIAKAI 117 (342)
T ss_pred HhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHcCCCCCChhhHHHHHHHhccccccccccccCCHHHHHHH
Confidence 6899999999999999999999999999999999 999999876655333322222110 1111124 7899999
Q ss_pred hhhCCCCCChhhHHh
Q psy6618 78 PNLSISFSNNERETA 92 (109)
Q Consensus 78 ~~Lw~d~~~~~~~~~ 92 (109)
..||.|++++..-.+
T Consensus 118 ~~LW~D~~iq~~~~~ 132 (342)
T smart00275 118 KALWKDEGIQECYRR 132 (342)
T ss_pred HHHHCCHHHHHHHHh
Confidence 999999999986543
No 5
>KOG0099|consensus
Probab=99.28 E-value=3e-12 Score=90.65 Aligned_cols=87 Identities=13% Similarity=0.086 Sum_probs=68.4
Q ss_pred CccCCCCCHHHHhcchhHhHhhHHHHHHHHHHhhhhhhhhhhh--hhccCCCCHHHhhchhhhhhhchhHhH-HHHHHHh
Q psy6618 1 IIHESGFTSEDFKQYRPVVYSNTIQSTVRILGTFLLSKWLELR--IIHESGFTSEDFKQYRPVVYSNTIQSL-VAILRAM 77 (109)
Q Consensus 1 iih~~gfs~ee~~~~~~~I~~Nii~~~~~li~a~~~~~~kql~--I~~~~~~~~~e~~~~~~~i~~n~~~~~-~~i~~ai 77 (109)
|+|.+||+++|+++..+.|+.||-+||.+|+.|| ..+. +.++++.++........ +.......+ +++.+++
T Consensus 62 ILHvnGF~~~EkreKI~dI~~Ni~eai~~iv~aM-----~~l~p~v~l~~~~~~~~~dYIls-~~~~~~~~~~~Ef~dHv 135 (379)
T KOG0099|consen 62 ILHVNGFNDEEKREKIQDIKNNIKEAILTIVGAM-----SNLVPPVELANPENQFRVDYILS-VMNSPDFDYPPEFYDHV 135 (379)
T ss_pred eeeecCCChHHHHHhhHHHHHHHHHHHHHHHHHH-----hccCCCcccCCcccchhHHHHHh-cCCCCcccCCHHHHHHH
Confidence 7999999999999999999999999999999999 6776 77777766544333322 222222345 8999999
Q ss_pred hhhCCCCCChhhHHhh
Q psy6618 78 PNLSISFSNNERETAG 93 (109)
Q Consensus 78 ~~Lw~d~~~~~~~~~~ 93 (109)
.+||.|.|+..+-++.
T Consensus 136 ~~lW~D~Gv~acyeRS 151 (379)
T KOG0099|consen 136 KTLWEDEGVRACYERS 151 (379)
T ss_pred HHHhhhhhHHHHHhcc
Confidence 9999999999776654
No 6
>PF00503 G-alpha: G-protein alpha subunit; InterPro: IPR001019 Guanine nucleotide binding proteins (G proteins) are membrane-associated, heterotrimeric proteins composed of three subunits: alpha (IPR001019 from INTERPRO), beta (IPR001632 from INTERPRO) and gamma (IPR001770 from INTERPRO) []. G proteins and their receptors (GPCRs) form one of the most prevalent signalling systems in mammalian cells, regulating systems as diverse as sensory perception, cell growth and hormonal regulation []. At the cell surface, the binding of ligands such as hormones and neurotransmitters to a GPCR activates the receptor by causing a conformational change, which in turn activates the bound G protein on the intracellular-side of the membrane. The activated receptor promotes the exchange of bound GDP for GTP on the G protein alpha subunit. GTP binding changes the conformation of switch regions within the alpha subunit, which allows the bound trimeric G protein (inactive) to be released from the receptor, and to dissociate into active alpha subunit (GTP-bound) and beta/gamma dimer. The alpha subunit and the beta/gamma dimer go on to activate distinct downstream effectors, such as adenylyl cyclase, phosphodiesterases, phospholipase C, and ion channels. These effectors in turn regulate the intracellular concentrations of secondary messengers, such as cAMP, diacylglycerol, sodium or calcium cations, which ultimately lead to a physiological response, usually via the downstream regulation of gene transcription. The cycle is completed by the hydrolysis of alpha subunit-bound GTP to GDP, resulting in the re-association of the alpha and beta/gamma subunits and their binding to the receptor, which terminates the signal []. The length of the G protein signal is controlled by the duration of the GTP-bound alpha subunit, which can be regulated by RGS (regulator of G protein signalling) proteins (IPR000342 from INTERPRO) or by covalent modifications []. There are several isoforms of each subunit, many of which have splice variants, which together can make up hundreds of combinations of G proteins. The specific combination of subunits in heterotrimeric G proteins affects not only which receptor it can bind to, but also which downstream target is affected, providing the means to target specific physiological processes in response to specific external stimuli [, ]. G proteins carry lipid modifications on one or more of their subunits to target them to the plasma membrane and to contribute to protein interactions. This family consists of the G protein alpha subunit, which acts as a weak GTPase. G protein classes are defined based on the sequence and function of their alpha subunits, which in mammals fall into four main categories: G(S)alpha, G(Q)alpha, G(I)alpha and G(12)alpha; there are also fungal and plant classes of alpha subunits. The alpha subunit consists of two domains: a GTP-binding domain and a helical insertion domain (IPR011025 from INTERPRO). The GTP-binding domain is homologous to Ras-like small GTPases, and includes switch regions I and II, which change conformation during activation. The switch regions are loops of alpha-helices with conformations sensitive to guanine nucleotides. The helical insertion domain is inserted into the GTP-binding domain before switch region I and is unique to heterotrimeric G proteins. This helical insertion domain functions to sequester the guanine nucleotide at the interface with the GTP-binding domain and must be displaced to enable nucleotide dissociation.; GO: 0004871 signal transducer activity, 0019001 guanyl nucleotide binding, 0007186 G-protein coupled receptor protein signaling pathway; PDB: 3QI2_B 3QE0_A 2IK8_A 2OM2_A 2GTP_B 2XNS_B 3ONW_B 1KJY_A 2EBC_A 1Y3A_B ....
Probab=98.93 E-value=7.3e-10 Score=82.38 Aligned_cols=86 Identities=24% Similarity=0.303 Sum_probs=59.7
Q ss_pred CccCCCCCHHHHhcchhHhHhhHHHHHHHHHHhhhhhhhhhhhhhccC-------CCCHHHhhchhhhhhhchh------
Q psy6618 1 IIHESGFTSEDFKQYRPVVYSNTIQSTVRILGTFLLSKWLELRIIHES-------GFTSEDFKQYRPVVYSNTI------ 67 (109)
Q Consensus 1 iih~~gfs~ee~~~~~~~I~~Nii~~~~~li~a~~~~~~kql~I~~~~-------~~~~~e~~~~~~~i~~n~~------ 67 (109)
++|++||+++|+..|++.||.|++++|+.|+.++ ..+.+.... +........+.........
T Consensus 80 il~~~~~~~~E~~~~~~~I~~Nii~~~~~i~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 154 (389)
T PF00503_consen 80 ILYGPGFSEEERESYRPIIYSNIIQSMKQILEAL-----EELGIPFSFSESSQLNEENQEIAEKLKEILDPLDSSEFSLA 154 (389)
T ss_dssp HHHST---HHHHHHTHHHHHHHHHHHHHHHHHHH-----HHTTCH-SSS-TT--STTHHHHHHHHHHHHCTTSTTCTC--
T ss_pred HHhCCCCchhhhhcceeeEecCchhhHHHHHHHH-----HHcCCCccccccccCCHHHHHHHHHHHhhhccccccccccc
Confidence 4799999999999999999999999999999999 888888762 2222222222222211111
Q ss_pred ---HhH-HHHHHHhhhhCCCCCChhhHH
Q psy6618 68 ---QSL-VAILRAMPNLSISFSNNERET 91 (109)
Q Consensus 68 ---~~~-~~i~~ai~~Lw~d~~~~~~~~ 91 (109)
..+ .++++.+..||.|+++++.-.
T Consensus 155 ~~~~~~~~~~~~~i~~LW~D~~vq~~~~ 182 (389)
T PF00503_consen 155 SDDNKFPEELAEDIRSLWKDPGVQECYE 182 (389)
T ss_dssp ---HCHHHHHHHHHHHHHHSHHHHHHHG
T ss_pred cccccCCHHHHHHHHHHHCChhHHHHHH
Confidence 124 789999999999999987654
No 7
>KOG0085|consensus
Probab=98.88 E-value=2.7e-09 Score=74.80 Aligned_cols=73 Identities=26% Similarity=0.367 Sum_probs=64.5
Q ss_pred HHHHHHhhh----hhhhhhhhhhccCCCCHHHhhchhhhhhhchhHhHHHHHHHhhhhCCCCCChhhHHhhhhcccc
Q psy6618 27 TVRILGTFL----LSKWLELRIIHESGFTSEDFKQYRPVVYSNTIQSLVAILRAMPNLSISFSNNERETAGLSGLHC 99 (109)
Q Consensus 27 ~~~li~a~~----~~~~kql~I~~~~~~~~~e~~~~~~~i~~n~~~~~~~i~~ai~~Lw~d~~~~~~~~~~~~i~~~ 99 (109)
++.|+.+-| |||+|||+|+|+.|+++++++.+..++|.|+..+|..+++||++|-+.++-++|+.+|..+...
T Consensus 40 lkllllgtgesgkstfikqmriihg~gyseedrkgf~~lvyqnif~amqaMIrAMetL~I~y~~e~nk~~A~~vrev 116 (359)
T KOG0085|consen 40 LKLLLLGTGESGKSTFIKQMRIIHGAGYSEEDRKGFTKLVYQNIFTAMQAMIRAMETLKIPYKREENKAHASLVREV 116 (359)
T ss_pred heeeeecCCCcchhhHHHHHHhhhcCCCChhhhccchHHHHHHHHHHHHHHHHHHHHhccccccccchhhhhHhhhc
Confidence 444444444 9999999999999999999999999999999999999999999999999999999999887554
No 8
>KOG0099|consensus
Probab=98.86 E-value=1.9e-09 Score=76.54 Aligned_cols=65 Identities=23% Similarity=0.291 Sum_probs=61.9
Q ss_pred hhhhhhhhhhccCCCCHHHhhchhhhhhhchhHhHHHHHHHhhhhC--CCCCChhhHHhhhhccccC
Q psy6618 36 LSKWLELRIIHESGFTSEDFKQYRPVVYSNTIQSLVAILRAMPNLS--ISFSNNERETAGLSGLHCG 100 (109)
Q Consensus 36 ~~~~kql~I~~~~~~~~~e~~~~~~~i~~n~~~~~~~i~~ai~~Lw--~d~~~~~~~~~~~~i~~~~ 100 (109)
||.+|||+|+|-+||+.+|+.+-...|+.|+.+++..++.||..|- .+.++|+|+.++|+|++.+
T Consensus 54 sTIvKQMRILHvnGF~~~EkreKI~dI~~Ni~eai~~iv~aM~~l~p~v~l~~~~~~~~~dYIls~~ 120 (379)
T KOG0099|consen 54 STIVKQMRILHVNGFNDEEKREKIQDIKNNIKEAILTIVGAMSNLVPPVELANPENQFRVDYILSVM 120 (379)
T ss_pred hhhhhhhheeeecCCChHHHHHhhHHHHHHHHHHHHHHHHHHhccCCCcccCCcccchhHHHHHhcC
Confidence 8999999999999999999999888999999999999999999997 9999999999999999884
No 9
>KOG0082|consensus
Probab=98.75 E-value=1.2e-08 Score=75.00 Aligned_cols=64 Identities=41% Similarity=0.637 Sum_probs=60.2
Q ss_pred hhhhhhhhhhccCCCCHHHhhchhhhhhhchhHhHHHHHHHhhhhCCCCCChhhHHhhhhcccc
Q psy6618 36 LSKWLELRIIHESGFTSEDFKQYRPVVYSNTIQSLVAILRAMPNLSISFSNNERETAGLSGLHC 99 (109)
Q Consensus 36 ~~~~kql~I~~~~~~~~~e~~~~~~~i~~n~~~~~~~i~~ai~~Lw~d~~~~~~~~~~~~i~~~ 99 (109)
||++|||+|+|.+||+++|+..++..|+.|+.+++..+++|+..+.++++.|.++.++..++..
T Consensus 47 STI~KQmkilh~~gfs~ee~~~~r~~I~~N~~~~~~~ll~a~~~~~i~~~~~~~~~d~~~~~~~ 110 (354)
T KOG0082|consen 47 STIVKQMKILHGDGFSEEELLEYRPVIYSNIIQSLKALLRAMETLGINLDDPERENDAQKLTLL 110 (354)
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCChhhhhHHHHHHHh
Confidence 9999999999999999999999999999999999999999999999999999888888888543
No 10
>cd00066 G-alpha G protein alpha subunit. The alpha subunit of G proteins contains the guanine nucleotide binding site. The heterotrimeric GNP-binding proteins are signal transducers that communicate signals from many hormones, neurotransmitters, chemokines, and autocrine and paracrine factors. Extracellular signals are received by receptors, which activate the G proteins, which in turn route the signals to several distinct intracellular signaling pathways. The alpha subunit of G proteins is a weak GTPase. In the resting state, heterotrimeric G proteins are associated at the cytosolic face of the plasma membrane and the alpha subunit binds to GDP. Upon activation by a receptor GDP is replaced with GTP, and the G-alpha/GTP complex dissociates from the beta and gamma subunits. This results in activation of downstream signaling pathways, such as cAMP synthesis by adenylyl cyclase, which is terminated when GTP is hydrolized and the heterotrimers reconstitute.
Probab=98.73 E-value=2e-08 Score=73.03 Aligned_cols=64 Identities=38% Similarity=0.673 Sum_probs=59.7
Q ss_pred hhhhhhhhhhccCCCCHHHhhchhhhhhhchhHhHHHHHHHhhhhCCCCCChhhHHhhhhcccc
Q psy6618 36 LSKWLELRIIHESGFTSEDFKQYRPVVYSNTIQSLVAILRAMPNLSISFSNNERETAGLSGLHC 99 (109)
Q Consensus 36 ~~~~kql~I~~~~~~~~~e~~~~~~~i~~n~~~~~~~i~~ai~~Lw~d~~~~~~~~~~~~i~~~ 99 (109)
||++|||+|.|++|++++|+..++.+|+.|+..++..++++++.+.+++..+++...++.+...
T Consensus 14 STi~KQmril~~~gfs~~Er~~~~~~I~~Ni~~~~~~ll~a~~~~~i~~~~~~~~~~~~~i~~~ 77 (317)
T cd00066 14 STILKQMKILHGDGFSEEELREYRPVIYSNILQSMKALLEAMERLNIPFGDPENEKDAKKILSF 77 (317)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCChhhHHHHHHHHhc
Confidence 8999999999999999999999999999999999999999999999999989988888877665
No 11
>smart00275 G_alpha G protein alpha subunit. Subunit of G proteins that contains the guanine nucleotide binding site
Probab=98.63 E-value=5.4e-08 Score=71.55 Aligned_cols=73 Identities=29% Similarity=0.413 Sum_probs=63.8
Q ss_pred HHHHHHhhh----hhhhhhhhhhccCCCCHHHhhchhhhhhhchhHhHHHHHHHhhhhCCCCCChhhHHhhhhcccc
Q psy6618 27 TVRILGTFL----LSKWLELRIIHESGFTSEDFKQYRPVVYSNTIQSLVAILRAMPNLSISFSNNERETAGLSGLHC 99 (109)
Q Consensus 27 ~~~li~a~~----~~~~kql~I~~~~~~~~~e~~~~~~~i~~n~~~~~~~i~~ai~~Lw~d~~~~~~~~~~~~i~~~ 99 (109)
++.||-+.+ ||++|||++.|.+||+.+|+..++.+|+.|+..+|..++++++.+.+++..+++...++.+++.
T Consensus 22 ~klLLLG~geSGKSTi~KQmril~~~gfs~~E~~~~~~~I~~Nii~~~~~ll~a~~~~~i~~~~~~~~~~~~~~~~~ 98 (342)
T smart00275 22 VKLLLLGAGESGKSTILKQMRILHGDGFSQEERREYRPLIYSNILESMKALVDAMEELNIPFEDPESILDIRIITEQ 98 (342)
T ss_pred hheeeeecCCCcchhHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCChhhHHHHHHHhcc
Confidence 445554444 9999999999999999999999999999999999999999999999999988887777777664
No 12
>PF00503 G-alpha: G-protein alpha subunit; InterPro: IPR001019 Guanine nucleotide binding proteins (G proteins) are membrane-associated, heterotrimeric proteins composed of three subunits: alpha (IPR001019 from INTERPRO), beta (IPR001632 from INTERPRO) and gamma (IPR001770 from INTERPRO) []. G proteins and their receptors (GPCRs) form one of the most prevalent signalling systems in mammalian cells, regulating systems as diverse as sensory perception, cell growth and hormonal regulation []. At the cell surface, the binding of ligands such as hormones and neurotransmitters to a GPCR activates the receptor by causing a conformational change, which in turn activates the bound G protein on the intracellular-side of the membrane. The activated receptor promotes the exchange of bound GDP for GTP on the G protein alpha subunit. GTP binding changes the conformation of switch regions within the alpha subunit, which allows the bound trimeric G protein (inactive) to be released from the receptor, and to dissociate into active alpha subunit (GTP-bound) and beta/gamma dimer. The alpha subunit and the beta/gamma dimer go on to activate distinct downstream effectors, such as adenylyl cyclase, phosphodiesterases, phospholipase C, and ion channels. These effectors in turn regulate the intracellular concentrations of secondary messengers, such as cAMP, diacylglycerol, sodium or calcium cations, which ultimately lead to a physiological response, usually via the downstream regulation of gene transcription. The cycle is completed by the hydrolysis of alpha subunit-bound GTP to GDP, resulting in the re-association of the alpha and beta/gamma subunits and their binding to the receptor, which terminates the signal []. The length of the G protein signal is controlled by the duration of the GTP-bound alpha subunit, which can be regulated by RGS (regulator of G protein signalling) proteins (IPR000342 from INTERPRO) or by covalent modifications []. There are several isoforms of each subunit, many of which have splice variants, which together can make up hundreds of combinations of G proteins. The specific combination of subunits in heterotrimeric G proteins affects not only which receptor it can bind to, but also which downstream target is affected, providing the means to target specific physiological processes in response to specific external stimuli [, ]. G proteins carry lipid modifications on one or more of their subunits to target them to the plasma membrane and to contribute to protein interactions. This family consists of the G protein alpha subunit, which acts as a weak GTPase. G protein classes are defined based on the sequence and function of their alpha subunits, which in mammals fall into four main categories: G(S)alpha, G(Q)alpha, G(I)alpha and G(12)alpha; there are also fungal and plant classes of alpha subunits. The alpha subunit consists of two domains: a GTP-binding domain and a helical insertion domain (IPR011025 from INTERPRO). The GTP-binding domain is homologous to Ras-like small GTPases, and includes switch regions I and II, which change conformation during activation. The switch regions are loops of alpha-helices with conformations sensitive to guanine nucleotides. The helical insertion domain is inserted into the GTP-binding domain before switch region I and is unique to heterotrimeric G proteins. This helical insertion domain functions to sequester the guanine nucleotide at the interface with the GTP-binding domain and must be displaced to enable nucleotide dissociation.; GO: 0004871 signal transducer activity, 0019001 guanyl nucleotide binding, 0007186 G-protein coupled receptor protein signaling pathway; PDB: 3QI2_B 3QE0_A 2IK8_A 2OM2_A 2GTP_B 2XNS_B 3ONW_B 1KJY_A 2EBC_A 1Y3A_B ....
Probab=97.82 E-value=1.9e-05 Score=58.83 Aligned_cols=64 Identities=36% Similarity=0.568 Sum_probs=53.5
Q ss_pred hhhhhhhhhhccCCCCHHHhhchhhhhhhchhHhHHHHHHHhhhhCCCCC-------ChhhHHhhhhcccc
Q psy6618 36 LSKWLELRIIHESGFTSEDFKQYRPVVYSNTIQSLVAILRAMPNLSISFS-------NNERETAGLSGLHC 99 (109)
Q Consensus 36 ~~~~kql~I~~~~~~~~~e~~~~~~~i~~n~~~~~~~i~~ai~~Lw~d~~-------~~~~~~~~~~i~~~ 99 (109)
||++|||++.+.++++++|+..++..|+.|++.++..+++++..+-.+.. .++++..++.+...
T Consensus 72 STi~KQ~ril~~~~~~~~E~~~~~~~I~~Nii~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 142 (389)
T PF00503_consen 72 STILKQMRILYGPGFSEEERESYRPIIYSNIIQSMKQILEALEELGIPFSFSESSQLNEENQEIAEKLKEI 142 (389)
T ss_dssp HHHHHHHHHHHST---HHHHHHTHHHHHHHHHHHHHHHHHHHHHTTCH-SSS-TT--STTHHHHHHHHHHH
T ss_pred hhHHHHHHHHhCCCCchhhhhcceeeEecCchhhHHHHHHHHHHcCCCccccccccCCHHHHHHHHHHHhh
Confidence 89999999999999999999999999999999999999999999988887 57777777776554
No 13
>PF02216 B: B domain; InterPro: IPR003132 This entry represents the immunoglobulin-binding domain found in the Staphylococcus aureus virulence factor protein A (SpA). Protein A contains five highly homologous Ig-binding domains in tandem (designated domains E, D, A, B and C), which share a common structure consisting of three helices in a closed left-handed twist. Protein A can exist in both secreted and membrane-bound forms, and has two distinct Ig-binding activities: each domain can bind Fc-gamma (the constant region of IgG involved in effector functions) and Fab (the Ig fragment responsible for antigen recognition) [].; GO: 0019865 immunoglobulin binding, 0009405 pathogenesis; PDB: 1EDL_A 1EDI_A 1EDJ_A 1EDK_A 2B88_A 2B87_A 2B89_A 1FC2_C 1DEE_H 1ZXG_A ....
Probab=70.98 E-value=2.4 Score=22.94 Aligned_cols=34 Identities=15% Similarity=0.162 Sum_probs=24.2
Q ss_pred CccCCCCCHHHHhcchhHhHhhHHHHHHHHHHhh
Q psy6618 1 IIHESGFTSEDFKQYRPVVYSNTIQSTVRILGTF 34 (109)
Q Consensus 1 iih~~gfs~ee~~~~~~~I~~Nii~~~~~li~a~ 34 (109)
|+|..+.|+|+|..|...+..+==.|-..+.+|.
T Consensus 16 vl~~~nLteeQrn~yI~~lKddPs~sq~v~~ea~ 49 (54)
T PF02216_consen 16 VLHMPNLTEEQRNGYIQSLKDDPSRSQNVFSEAK 49 (54)
T ss_dssp HHCSTTS-HHHHHHHHHHHHH-GCCHHHHHHHHH
T ss_pred HHcCCCcCHHHHHhHHHHHhhChHHHHHHHHHHH
Confidence 5789999999999998888776655555555554
No 14
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=51.25 E-value=33 Score=19.89 Aligned_cols=62 Identities=23% Similarity=0.316 Sum_probs=38.9
Q ss_pred CCCCHHHHhcchhHhHhhHHHHHHHHHHhhhhhhhhhhhhhccCCCCHHHhhchhhhhhhchhHhHHHHHHHhhhhCCCC
Q psy6618 5 SGFTSEDFKQYRPVVYSNTIQSTVRILGTFLLSKWLELRIIHESGFTSEDFKQYRPVVYSNTIQSLVAILRAMPNLSISF 84 (109)
Q Consensus 5 ~gfs~ee~~~~~~~I~~Nii~~~~~li~a~~~~~~kql~I~~~~~~~~~e~~~~~~~i~~n~~~~~~~i~~ai~~Lw~d~ 84 (109)
...|++...+.-+..-.|=+-+|.++ .|++|+. +-.+.+...+..| ..-+-+|+..|..|+
T Consensus 11 hnvsd~qi~elFq~lT~NPl~AMa~i---------~qLGip~------eKLQ~lm~~VMqn----P~LikeAv~ELgLDF 71 (82)
T PF11212_consen 11 HNVSDEQINELFQALTQNPLAAMATI---------QQLGIPQ------EKLQQLMAQVMQN----PALIKEAVEELGLDF 71 (82)
T ss_pred cCCCHHHHHHHHHHHhhCHHHHHHHH---------HHcCCCH------HHHHHHHHHHhcC----hHHHHHHHHHhCCcH
Confidence 34577777666667777777777554 5788774 3344444444333 344557888888888
Q ss_pred C
Q psy6618 85 S 85 (109)
Q Consensus 85 ~ 85 (109)
+
T Consensus 72 s 72 (82)
T PF11212_consen 72 S 72 (82)
T ss_pred H
Confidence 6
No 15
>PHA02652 hypothetical protein; Provisional
Probab=51.19 E-value=22 Score=19.50 Aligned_cols=34 Identities=9% Similarity=0.189 Sum_probs=22.1
Q ss_pred HhHhhHHHHHHHHHHhhhhhhhhhhhhhccCCCCHHHhh
Q psy6618 18 VVYSNTIQSTVRILGTFLLSKWLELRIIHESGFTSEDFK 56 (109)
Q Consensus 18 ~I~~Nii~~~~~li~a~~~~~~kql~I~~~~~~~~~e~~ 56 (109)
.--.||+..++++++-. +.|-+.-.--|.+.+.+
T Consensus 31 davmniiseikvlidll-----enmyllddllfdeaelq 64 (70)
T PHA02652 31 DAVMNIISEIKVLIDLL-----ENMYLLDDLLFDEAELQ 64 (70)
T ss_pred HHHHHHHHHHHHHHHHH-----HHHHHHHHHhcCHHHHH
Confidence 34468999999998877 67665543334444443
No 16
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, 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
Probab=40.02 E-value=40 Score=19.73 Aligned_cols=30 Identities=20% Similarity=0.187 Sum_probs=24.3
Q ss_pred CCCCHHHHhcchhHhHhhHHHHHHHHHHhh
Q psy6618 5 SGFTSEDFKQYRPVVYSNTIQSTVRILGTF 34 (109)
Q Consensus 5 ~gfs~ee~~~~~~~I~~Nii~~~~~li~a~ 34 (109)
-|||+.|+...+..-..|+-+....++..=
T Consensus 25 Lg~se~dI~~i~~~~~~~~~eq~~~mL~~W 54 (84)
T cd08804 25 LDFTEEQIHQIRIENPNSLQDQSHALLKYW 54 (84)
T ss_pred cCCCHHHHHHHHHHCcccHHHHHHHHHHHH
Confidence 489999999988887788888888877554
No 17
>PF09836 DUF2063: Uncharacterized protein conserved in bacteria (DUF2063); InterPro: IPR018640 This entry contains proteins that have no known function. ; PDB: 3DEE_A.
Probab=39.34 E-value=25 Score=20.75 Aligned_cols=28 Identities=14% Similarity=0.170 Sum_probs=14.7
Q ss_pred CCCHHHHhc-chhHhHhhHHHHHHHHHHh
Q psy6618 6 GFTSEDFKQ-YRPVVYSNTIQSTVRILGT 33 (109)
Q Consensus 6 gfs~ee~~~-~~~~I~~Nii~~~~~li~a 33 (109)
+.+.+++.. |+..++.|+++++...--+
T Consensus 26 ~~~~~~rl~iYr~~~~~~l~~~L~~~fP~ 54 (94)
T PF09836_consen 26 GLSPARRLAIYRNNYRARLIEALEATFPV 54 (94)
T ss_dssp ---------HHHHHHHHHHHHHHHHHTTT
T ss_pred cCChHHHHHHHHHHHHHHHHHHHHHHhHH
Confidence 455556655 8999999988888765533
No 18
>PF08132 AdoMetDC_leader: S-adenosyl-l-methionine decarboxylase leader peptide; InterPro: IPR012511 This family consists of the S-adenosyl-l-methionine decarboxylase (AdoMetDC) leader peptides. AdoMetDC is a key regulatory enzyme in the biosynthesis of polyamines. All expressed plant AdoMetDC mRNA 5, leader sequences contain a highly conserved pair of overlapping upstream ORFs (uORFs) that overlap by one base. Sequences of the small uORFs are highly conserved between monocot, dicot and gymnosperm AdoMetDC mRNA species, suggesting a translational regulatory mechanism [].
Probab=39.28 E-value=9.7 Score=20.27 Aligned_cols=19 Identities=42% Similarity=0.831 Sum_probs=14.6
Q ss_pred CCCHHHH------hcchhHhHhhHH
Q psy6618 6 GFTSEDF------KQYRPVVYSNTI 24 (109)
Q Consensus 6 gfs~ee~------~~~~~~I~~Nii 24 (109)
||+.||. +.||...|+|+.
T Consensus 26 gYsIEDvRP~GgikKfrsaaYSN~~ 50 (54)
T PF08132_consen 26 GYSIEDVRPNGGIKKFRSAAYSNCA 50 (54)
T ss_pred cceeeecccCCcHHHHHHHHhhhhc
Confidence 6777664 679999999974
No 19
>PF05261 Tra_M: TraM protein, DNA-binding; InterPro: IPR007925 The TraM protein is an essential part of the DNA transfer machinery of the conjugative resistance plasmid R1 (IncFII). On the basis of mutational analyses, it was shown that the essential transfer protein TraM has at least two functions. First, a functional TraM protein was found to be required for normal levels of transfer gene expression. Second, experimental evidence was obtained that TraM stimulates efficient site-specific single-stranded DNA cleavage at the oriT, in vivo. Furthermore, a specific interaction of the cytoplasmic TraM protein with the membrane protein TraD was demonstrated, suggesting that the TraM protein creates a physical link between the relaxosomal nucleoprotein complex and the membrane-bound DNA transfer apparatus [].; GO: 0003677 DNA binding, 0000746 conjugation; PDB: 3ON0_A 3OMY_B 1DP3_A 2G9E_A 3D8A_B 2G7O_A.
Probab=38.52 E-value=1.1e+02 Score=19.68 Aligned_cols=25 Identities=28% Similarity=0.565 Sum_probs=17.5
Q ss_pred CCCCCHHHHhcchhHhHhhHHHHHHHHH
Q psy6618 4 ESGFTSEDFKQYRPVVYSNTIQSTVRIL 31 (109)
Q Consensus 4 ~~gfs~ee~~~~~~~I~~Nii~~~~~li 31 (109)
.+||.++| |+.++..|++.+-.++-
T Consensus 58 ~s~Fnq~e---Fnk~lLe~v~kt~~~~~ 82 (127)
T PF05261_consen 58 ESGFNQEE---FNKVLLENVSKTRFTVS 82 (127)
T ss_dssp SSS--HHH---HHHHHHHHHHHHHHHHH
T ss_pred cCCCCHHH---HHHHHHHHHHHHHHHHH
Confidence 46788877 89999999987765543
No 20
>PRK12277 50S ribosomal protein L13e; Provisional
Probab=37.16 E-value=20 Score=21.20 Aligned_cols=11 Identities=18% Similarity=0.522 Sum_probs=8.6
Q ss_pred CCCCCHHHHhc
Q psy6618 4 ESGFTSEDFKQ 14 (109)
Q Consensus 4 ~~gfs~ee~~~ 14 (109)
+.|||.+|++.
T Consensus 31 GRGFsl~ELka 41 (83)
T PRK12277 31 GRGFSIGELEA 41 (83)
T ss_pred cCCcCHHHHHH
Confidence 57899999853
No 21
>COG0114 FumC Fumarase [Energy production and conversion]
Probab=34.98 E-value=37 Score=26.25 Aligned_cols=24 Identities=21% Similarity=0.429 Sum_probs=22.7
Q ss_pred HHhcchhHhHhhHHHHHHHHHHhh
Q psy6618 11 DFKQYRPVVYSNTIQSTVRILGTF 34 (109)
Q Consensus 11 e~~~~~~~I~~Nii~~~~~li~a~ 34 (109)
|+.-|+|+|-.|+++|++.|-++|
T Consensus 356 ELNv~~Pvi~~N~LqS~~LLada~ 379 (462)
T COG0114 356 ELNVFKPVIAYNFLQSVRLLADAM 379 (462)
T ss_pred eeccccHHHHHHHHHHHHHHHHHH
Confidence 677899999999999999999999
No 22
>PF12488 DUF3704: Protein of unknown function (DUF3704) ; InterPro: IPR022173 This domain family is found in eukaryotes, and is approximately 30 amino acids in length.
Probab=32.29 E-value=18 Score=16.78 Aligned_cols=11 Identities=18% Similarity=0.190 Sum_probs=8.5
Q ss_pred cCCCCccccCC
Q psy6618 99 CGAPWFNSRRG 109 (109)
Q Consensus 99 ~~~~~~~~~~~ 109 (109)
.++.|||.|+|
T Consensus 5 gaS~gyMp~s~ 15 (27)
T PF12488_consen 5 GASFGYMPRSG 15 (27)
T ss_pred ecccceeeecc
Confidence 37788998875
No 23
>PF13373 DUF2407_C: DUF2407 C-terminal domain
Probab=31.97 E-value=31 Score=22.40 Aligned_cols=17 Identities=24% Similarity=0.550 Sum_probs=13.4
Q ss_pred CCCCCHHHHhcchhHhH
Q psy6618 4 ESGFTSEDFKQYRPVVY 20 (109)
Q Consensus 4 ~~gfs~ee~~~~~~~I~ 20 (109)
+-|||++|....|...|
T Consensus 8 ~~GFS~~eI~~LR~QF~ 24 (140)
T PF13373_consen 8 SAGFSPEEIQDLRSQFH 24 (140)
T ss_pred HcCCCHHHHHHHHHHHH
Confidence 46999999988777644
No 24
>TIGR02058 lin0512_fam conserved hypothetical protein. This family consists of few members, broadly distributed. It occurs so far in several Firmicutes (twice in Oceanobacillus), one Cyanobacterium, one alpha Proteobacterium, and (with a long prefix) in plants. The function is unknown. The alignment includes a perfectly conserved motif GxGxDxHG near the N-terminus.
Probab=29.87 E-value=34 Score=21.59 Aligned_cols=31 Identities=19% Similarity=0.249 Sum_probs=27.6
Q ss_pred ccCCCCCHHHHhcchhHhHhhHHHHHHHHHH
Q psy6618 2 IHESGFTSEDFKQYRPVVYSNTIQSTVRILG 32 (109)
Q Consensus 2 ih~~gfs~ee~~~~~~~I~~Nii~~~~~li~ 32 (109)
+|+.-||+.-.+--|..|..|.+-++..++.
T Consensus 13 lhGqD~TkAA~RAvrDAI~hnsipg~~~~~~ 43 (116)
T TIGR02058 13 QHGQNITKAAMRAVRNAIASNSMPGIWESLP 43 (116)
T ss_pred ccCccHHHHHHHHHHHHHhhccchhHHHhcC
Confidence 5888899999999999999999998888763
No 25
>KOG1317|consensus
Probab=26.15 E-value=39 Score=25.49 Aligned_cols=24 Identities=17% Similarity=0.404 Sum_probs=22.1
Q ss_pred HHhcchhHhHhhHHHHHHHHHHhh
Q psy6618 11 DFKQYRPVVYSNTIQSTVRILGTF 34 (109)
Q Consensus 11 e~~~~~~~I~~Nii~~~~~li~a~ 34 (109)
|+.-|+|+|-+|++.|++.|-++.
T Consensus 381 ELNVFKP~i~~nvL~SirLl~D~~ 404 (487)
T KOG1317|consen 381 ELNVFKPLIASNVLHSIRLLADAS 404 (487)
T ss_pred EEecchHHHHHHHHHHHHHhhhhh
Confidence 677899999999999999999887
No 26
>smart00309 PAH Pancreatic hormones / neuropeptide F / peptide YY family. Pancreatic hormone is a regulator of pancreatic and gastrointestinal functions.
Probab=25.00 E-value=83 Score=15.58 Aligned_cols=16 Identities=25% Similarity=0.478 Sum_probs=11.6
Q ss_pred CCCCCHHHHhcchhHh
Q psy6618 4 ESGFTSEDFKQYRPVV 19 (109)
Q Consensus 4 ~~gfs~ee~~~~~~~I 19 (109)
++..|.||+..|-..+
T Consensus 9 g~~a~~e~l~~Y~~~L 24 (36)
T smart00309 9 GDDASPEDLRQYLAAL 24 (36)
T ss_pred CCCCCHHHHHHHHHHH
Confidence 3557888888877665
No 27
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=24.91 E-value=94 Score=14.81 Aligned_cols=9 Identities=33% Similarity=0.796 Sum_probs=4.6
Q ss_pred CCCHHHHhc
Q psy6618 6 GFTSEDFKQ 14 (109)
Q Consensus 6 gfs~ee~~~ 14 (109)
||+.++.+.
T Consensus 13 Gf~~~~~~~ 21 (37)
T PF00627_consen 13 GFSREQARE 21 (37)
T ss_dssp TS-HHHHHH
T ss_pred CCCHHHHHH
Confidence 677665543
No 28
>PF07553 Lipoprotein_Ltp: Host cell surface-exposed lipoprotein; InterPro: IPR011434 This domain is found as 1-3 copies in a small family of proteins of unknown function.
Probab=23.02 E-value=1.3e+02 Score=15.75 Aligned_cols=18 Identities=28% Similarity=0.266 Sum_probs=12.4
Q ss_pred hhhhhhccCCCCHHHhhc
Q psy6618 40 LELRIIHESGFTSEDFKQ 57 (109)
Q Consensus 40 kql~I~~~~~~~~~e~~~ 57 (109)
.||.-.++++|+.+++..
T Consensus 26 ~QL~se~ge~Ft~e~A~Y 43 (48)
T PF07553_consen 26 DQLTSEYGEGFTEEEAQY 43 (48)
T ss_pred HHHHhhcccCCCHHHHHH
Confidence 566666777888877543
No 29
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=22.32 E-value=1.1e+02 Score=14.45 Aligned_cols=21 Identities=19% Similarity=0.336 Sum_probs=9.1
Q ss_pred CCCHHHHhcchhHhHhhHHHH
Q psy6618 6 GFTSEDFKQYRPVVYSNTIQS 26 (109)
Q Consensus 6 gfs~ee~~~~~~~I~~Nii~~ 26 (109)
||+.++...--..-..|+-.+
T Consensus 12 Gf~~~~~~~AL~~~~~d~~~A 32 (38)
T cd00194 12 GFSREEARKALRATNNNVERA 32 (38)
T ss_pred CCCHHHHHHHHHHhCCCHHHH
Confidence 666555443333333333333
No 30
>cd08803 Death_ank3 Death domain of Ankyrin-3. Death Domain (DD) of the human protein ankyrin-3 (ANK-3) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-3, also called anykyrin-G (for general or giant), is found in neurons and at least one splice variant has been shown to be essential for propagation of action potentials as a binding partner to neurofascin and voltage-gated sodium channels. It is required for maintaining axo-dendritic polarity, and may be a genetic risk factor associated with bipolar disorder. ANK-3 may also play roles in other cell types. Mutations affecting ANK-3 pathways for Na channel localization are associated with Brugada syndrome, a potentially fata arrythmia. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by se
Probab=21.68 E-value=1.2e+02 Score=17.80 Aligned_cols=27 Identities=19% Similarity=0.284 Sum_probs=20.1
Q ss_pred CCCHHHHhcchhHhHhhHHHHHHHHHH
Q psy6618 6 GFTSEDFKQYRPVVYSNTIQSTVRILG 32 (109)
Q Consensus 6 gfs~ee~~~~~~~I~~Nii~~~~~li~ 32 (109)
|||..|+..++..-..|+.+-...++.
T Consensus 26 g~s~~dI~~i~~e~p~~~~~q~~~lL~ 52 (84)
T cd08803 26 NFSVDEINQIRVENPNSLIAQSFMLLK 52 (84)
T ss_pred CCCHHHHHHHHHhCCCCHHHHHHHHHH
Confidence 789999888877767777666666653
No 31
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=21.47 E-value=46 Score=15.75 Aligned_cols=13 Identities=23% Similarity=0.680 Sum_probs=8.4
Q ss_pred CCCCHHHHhcchh
Q psy6618 5 SGFTSEDFKQYRP 17 (109)
Q Consensus 5 ~gfs~ee~~~~~~ 17 (109)
.|.|.+|.++|..
T Consensus 15 ~Gls~eeir~FL~ 27 (30)
T PF08671_consen 15 SGLSKEEIREFLE 27 (30)
T ss_dssp TT--HHHHHHHHH
T ss_pred cCCCHHHHHHHHH
Confidence 5889999888754
No 32
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, 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 CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=21.36 E-value=1.2e+02 Score=17.70 Aligned_cols=25 Identities=4% Similarity=0.138 Sum_probs=16.7
Q ss_pred CCCHHHHhcchhHhHhhHHHHHHHHH
Q psy6618 6 GFTSEDFKQYRPVVYSNTIQSTVRIL 31 (109)
Q Consensus 6 gfs~ee~~~~~~~I~~Nii~~~~~li 31 (109)
|||+.|+...+.. +.++-+....++
T Consensus 29 Gls~~dI~~i~~~-~~~~~eq~~~mL 53 (86)
T cd08318 29 EMKDKEIRAIESD-SEDIKMQAKQLL 53 (86)
T ss_pred CCCHHHHHHHHhc-CCCHHHHHHHHH
Confidence 7888888777765 566655555444
No 33
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=21.35 E-value=1e+02 Score=14.48 Aligned_cols=8 Identities=38% Similarity=0.700 Sum_probs=4.7
Q ss_pred CCCHHHHh
Q psy6618 6 GFTSEDFK 13 (109)
Q Consensus 6 gfs~ee~~ 13 (109)
||++++..
T Consensus 12 Gf~~~~a~ 19 (37)
T smart00165 12 GFSREEAL 19 (37)
T ss_pred CCCHHHHH
Confidence 66666543
No 34
>PF09585 Lin0512_fam: Conserved hypothetical protein (Lin0512_fam); InterPro: IPR011719 This family consists of few members, broadly distributed. It occurs so far in several Firmicutes (twice in Oceanobacillus), one Cyanobacterium, one alpha Proteobacterium, and (with a long prefix) in plants. The function is unknown. The alignment includes a perfectly conserved motif GxGxDxHG near the N terminus.
Probab=21.21 E-value=73 Score=20.01 Aligned_cols=41 Identities=20% Similarity=0.369 Sum_probs=31.1
Q ss_pred ccCCCCCHHHHhcchhHhHhhHHHHHHHHHHhhhhhhhhhhhhhc
Q psy6618 2 IHESGFTSEDFKQYRPVVYSNTIQSTVRILGTFLLSKWLELRIIH 46 (109)
Q Consensus 2 ih~~gfs~ee~~~~~~~I~~Nii~~~~~li~a~~~~~~kql~I~~ 46 (109)
+|+.-||+.-.+--|..|..|.+=++..++.--. ++|++.-
T Consensus 13 lhGqD~TkAA~RAv~DAI~~nslp~l~~~~~~~~----~~M~v~V 53 (113)
T PF09585_consen 13 LHGQDYTKAAVRAVRDAISHNSLPGLFEILGLDL----DDMKVEV 53 (113)
T ss_pred ccCCcHHHHHHHHHHHHHhhcchHHHHHHcCCCh----HHEEEEE
Confidence 5888899999999999999999977777664331 5555443
No 35
>PF01517 HDV_ag: Hepatitis delta virus delta antigen; InterPro: IPR002506 The Hepatitis delta virus (HDV) encodes a single protein, the hepatitis delta antigen (HDAg). The central region of this protein has been shown to bind RNA []. Several interactions are also mediated by a coiled-coil region at the N terminus of the protein [].; GO: 0003723 RNA binding, 0042025 host cell nucleus; PDB: 1A92_D 1BY0_A.
Probab=20.33 E-value=34 Score=22.97 Aligned_cols=15 Identities=33% Similarity=0.651 Sum_probs=0.0
Q ss_pred cCCCCCHHHHhcchh
Q psy6618 3 HESGFTSEDFKQYRP 17 (109)
Q Consensus 3 h~~gfs~ee~~~~~~ 17 (109)
|.+|||+.|+..+|.
T Consensus 89 ~~ggftdker~dhrr 103 (194)
T PF01517_consen 89 HRGGFTDKERRDHRR 103 (194)
T ss_dssp ---------------
T ss_pred CCCCCchHHHHHHHH
Confidence 568999999988765
Done!