Query 028441
Match_columns 209
No_of_seqs 102 out of 153
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 11:34:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028441.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028441hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3284 Vacuolar sorting prote 100.0 5.4E-89 1.2E-93 575.9 18.5 203 1-204 10-213 (213)
2 PF03997 VPS28: VPS28 protein; 100.0 4.5E-86 9.6E-91 559.8 14.4 187 18-205 1-188 (188)
3 PF09454 Vps23_core: Vps23 cor 92.1 0.72 1.6E-05 33.2 6.3 49 5-53 5-53 (65)
4 PF09851 SHOCT: Short C-termin 89.0 0.54 1.2E-05 29.0 2.9 29 25-53 2-30 (31)
5 PF14056 DUF4250: Domain of un 67.2 9.4 0.0002 26.9 3.6 32 62-93 15-46 (55)
6 cd08323 CARD_APAF1 Caspase act 60.1 10 0.00022 28.6 3.0 26 182-207 43-72 (86)
7 PF06464 DMAP_binding: DMAP1-b 56.0 23 0.00049 27.8 4.4 35 24-58 9-43 (111)
8 cd08325 CARD_CASP1-like Caspas 52.2 29 0.00063 25.7 4.3 59 133-207 13-75 (83)
9 PF14361 RsbRD_N: RsbT co-anta 51.9 28 0.0006 26.4 4.2 62 134-197 37-98 (105)
10 cd08819 CARD_MDA5_2 Caspase ac 47.4 14 0.0003 28.5 1.9 28 180-207 49-79 (88)
11 cd08326 CARD_CASP9 Caspase act 45.0 22 0.00048 26.5 2.7 27 182-208 45-75 (84)
12 PF08969 USP8_dimer: USP8 dime 44.0 35 0.00076 26.3 3.7 55 143-204 9-65 (115)
13 cd08330 CARD_ASC_NALP1 Caspase 43.3 23 0.0005 26.2 2.5 26 181-206 43-72 (82)
14 PF13543 KSR1-SAM: SAM like do 41.1 40 0.00086 27.6 3.7 71 114-193 25-111 (129)
15 PF05120 GvpG: Gas vesicle pro 40.7 1E+02 0.0022 23.1 5.6 49 9-61 22-70 (79)
16 PRK05467 Fe(II)-dependent oxyg 39.8 36 0.00077 30.0 3.6 37 162-206 169-205 (226)
17 COG3462 Predicted membrane pro 37.5 44 0.00096 26.9 3.4 27 26-52 89-115 (117)
18 COG1725 Predicted transcriptio 36.4 2E+02 0.0044 23.3 7.1 96 45-147 13-121 (125)
19 KOG3046 Transcription factor, 33.9 1.4E+02 0.0029 25.1 5.8 34 18-53 63-97 (147)
20 COG5150 Class 2 transcription 33.3 60 0.0013 26.9 3.6 29 24-61 71-99 (148)
21 COG3882 FkbH Predicted enzyme 33.2 36 0.00079 33.9 2.8 108 80-192 335-455 (574)
22 PF08044 DUF1707: Domain of un 32.8 79 0.0017 21.7 3.7 27 27-53 11-37 (53)
23 PF11237 DUF3038: Protein of u 31.6 79 0.0017 27.0 4.2 96 73-193 43-153 (171)
24 cd08810 CARD_BCL10 Caspase act 31.5 47 0.001 25.1 2.6 30 179-208 42-74 (84)
25 cd00672 CysRS_core catalytic c 31.4 50 0.0011 28.5 3.1 64 32-102 73-136 (213)
26 COG5126 FRQ1 Ca2+-binding prot 31.2 78 0.0017 26.7 4.1 78 119-208 75-158 (160)
27 PF11740 KfrA_N: Plasmid repli 30.8 49 0.0011 25.1 2.6 59 40-99 1-65 (120)
28 PRK08719 ribonuclease H; Revie 30.5 58 0.0012 26.4 3.2 43 14-58 48-91 (147)
29 cd01145 TroA_c Periplasmic bin 30.1 1.7E+02 0.0037 24.5 6.1 54 43-98 137-202 (203)
30 cd08329 CARD_BIRC2_BIRC3 Caspa 27.4 69 0.0015 24.3 2.9 26 182-207 52-81 (94)
31 PF03909 BSD: BSD domain ; I 26.5 1.6E+02 0.0035 20.2 4.5 40 40-79 8-50 (62)
32 smart00345 HTH_GNTR helix_turn 26.4 96 0.0021 19.7 3.2 28 66-93 19-49 (60)
33 COG4496 Uncharacterized protei 26.3 1.1E+02 0.0023 24.0 3.8 40 12-51 5-46 (100)
34 PF06757 Ins_allergen_rp: Inse 26.3 2.8E+02 0.0061 22.9 6.7 84 12-97 2-90 (179)
35 PF12462 Helicase_IV_N: DNA he 25.8 1.4E+02 0.003 24.8 4.7 60 134-194 96-155 (166)
36 PF03206 NifW: Nitrogen fixati 25.6 1.7E+02 0.0036 23.1 4.8 36 168-203 41-77 (105)
37 PF14090 HTH_39: Helix-turn-he 24.9 1.1E+02 0.0023 21.7 3.4 44 55-99 2-48 (70)
38 PRK10280 dipeptidyl carboxypep 24.9 7.6E+02 0.016 25.2 11.6 38 38-75 21-60 (681)
39 PF14425 Imm3: Immunity protei 24.4 1.1E+02 0.0025 24.6 3.7 75 111-196 28-102 (117)
40 cd08327 CARD_RAIDD Caspase act 23.9 86 0.0019 24.0 2.9 25 181-205 49-77 (94)
41 cd08332 CARD_CASP2 Caspase act 22.9 94 0.002 23.3 2.9 26 182-207 49-78 (90)
42 COG2257 Uncharacterized homolo 22.8 88 0.0019 24.3 2.7 18 12-29 69-86 (92)
43 PF05816 TelA: Toxic anion res 22.6 1.9E+02 0.004 26.6 5.3 65 70-159 2-66 (333)
44 PF08365 IGF2_C: Insulin-like 22.3 37 0.00081 24.1 0.5 16 83-99 11-26 (56)
45 PLN02618 tryptophan synthase, 22.0 1.1E+02 0.0024 29.3 3.8 34 23-57 30-63 (410)
46 PF14426 Imm2: Immunity protei 21.8 70 0.0015 23.0 1.8 32 161-194 22-55 (60)
47 cd08785 CARD_CARD9-like Caspas 21.2 92 0.002 23.5 2.5 27 179-205 45-75 (86)
48 PF12668 DUF3791: Protein of u 21.1 86 0.0019 21.7 2.2 24 70-93 8-31 (62)
49 cd07977 TFIIE_beta_winged_heli 21.1 1E+02 0.0022 22.6 2.6 36 132-175 18-54 (75)
50 PF01756 ACOX: Acyl-CoA oxidas 20.9 4.5E+02 0.0098 21.6 6.9 52 6-57 72-123 (187)
51 KOG0869 CCAAT-binding factor, 20.5 87 0.0019 26.8 2.4 75 83-174 36-117 (168)
52 PRK04346 tryptophan synthase s 20.5 1.2E+02 0.0027 28.7 3.8 34 23-57 22-55 (397)
53 PF12719 Cnd3: Nuclear condens 20.3 2.7E+02 0.0059 24.6 5.8 152 25-186 132-296 (298)
54 PF08828 DSX_dimer: Doublesex 20.1 85 0.0018 22.7 2.0 42 42-95 3-51 (62)
55 smart00544 MA3 Domain in DAP-5 20.1 83 0.0018 23.4 2.1 45 44-88 51-99 (113)
No 1
>KOG3284 consensus Vacuolar sorting protein VPS28 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=5.4e-89 Score=575.89 Aligned_cols=203 Identities=62% Similarity=0.939 Sum_probs=198.7
Q ss_pred CcccccCChhHHHHHHhHHHHHHHHHHHHHHHHhhhcCCCChhhHHHHHHHHHHHHHHHHHHHhc-ccCCHHHHHHHhcC
Q 028441 1 MEVKLWNDKREREMYENFAELYAIIKATEKLEKAYVRDIISSSEYETECQKLIAHFKTLSSTLKD-IVPSIERFADTYKM 79 (209)
Q Consensus 1 ~EV~L~~~~~eRe~~e~lAelYSII~tle~LEkAyirD~I~~~eYt~~c~rLl~Qyk~~~~~v~~-~~~~l~~F~~~y~l 79 (209)
+||+||.|++|||+|||||+|||||+|+|+|||||+||+|++.|||++|.|||.|||++++.+++ .||+||.|+++|+|
T Consensus 10 ~Evkl~~N~rerE~~enlseLyaIi~ale~LEKAyirD~is~sey~s~c~kLi~Q~k~~~~~~~~~~f~SiE~Fc~kyrl 89 (213)
T KOG3284|consen 10 EEVKLFNNAREREVYENLSELYAIIKALEQLEKAYIRDCISPSEYTSECSKLIVQYKVAFRSVQGTEFPSIEDFCKKYRL 89 (213)
T ss_pred HHHHHhhchhHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHhcccccCcHHHHHHHHcc
Confidence 48999999999999999999999999999999999999999999999999999999999999954 89999999999999
Q ss_pred CchHHhhhhhhcCCCceeecccccccCCCcchhHHHHhhhhhhhHhhhhccccchhhhhcchHHHHHHhcccCCCCCCCC
Q 028441 80 DCPAALNRLVTSGVPATVEHRAAAVASTTTSAAIVAECVQNFITAMDSLKLNMVAVDQVHPLLSDLLGSLNKLTILPPDF 159 (209)
Q Consensus 80 ~cp~A~~RL~~~G~PaTveh~~~~~~~~~~~a~~Iae~t~~FIT~MDaLKLn~~a~DqLhPlL~dL~~slnk~~~lp~dF 159 (209)
+||+|++|| ++|+|+|++|+..++.++++++|+|||+||||||+|||||||++|||||||+|+||+.|||+++.+|+||
T Consensus 90 ~cp~Ai~Ri-~~~~piT~e~~ia~s~dk~~~ak~IAe~v~nFIT~mDaLrLn~~A~Dql~PlL~dL~~smnrls~~p~df 168 (213)
T KOG3284|consen 90 DCPAAIERI-REGRPITVEDRIAPSADKGNSAKCIAEIVQNFITVMDALRLNINAVDQLYPLLSDLSASMNRLSRLPPDF 168 (213)
T ss_pred CChHHHHHH-HcCCCCcccccccccCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhhcchHHHHHHHHHhhccCCccc
Confidence 999999999 9999999999888777899999999999999999999999999999999999999999999999999999
Q ss_pred cchhhHHHHHHHHhcCCcccCCCHHHHHHHHHhHHHHHHHHHhhc
Q 028441 160 EGKTKMKDWISRLSKMGAADELTEQQSRQLHFDLESSYNSFMAAL 204 (209)
Q Consensus 160 egk~kl~~Wl~kLn~M~asdeL~eeq~RqllfDle~aY~~F~~~L 204 (209)
+||.|+++||++||+|.|||||+|.|+|||+||||+||++|++.|
T Consensus 169 e~r~Kv~~Wl~rls~M~asDeL~e~q~RqllfDLEsAY~~f~~lL 213 (213)
T KOG3284|consen 169 EGRTKVKQWLIRLSKMSASDELTEQQVRQLLFDLESAYNSFNALL 213 (213)
T ss_pred hhHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHHhhC
Confidence 999999999999999999999999999999999999999999986
No 2
>PF03997 VPS28: VPS28 protein; InterPro: IPR007143 The Endosomal Sorting Complex Required for Transport (ESCRT) complexes form the machinery driving protein sorting from endosomes to lysosomes. ESCRT complexes are central to receptor down-regulation, lysosome biogenesis, and budding of HIV. Yeast ESCRT-I consists of three protein subunits, VPS23, VPS28, and VPS37. In humans, ESCRT-I comprises TSG101, VPS28, and one of four potential human VPS37 homologues. The main role of ESCRT-I is to recognise ubiquitinated cargo via the UEV domain of the VPS23/TSG101 subunit. The assembly of the ESCRT-I complex is directed by the C-terminal steadiness box (SB) of VPS23, the N-terminal half of VPS28, and the C-terminal half of VPS37. The structure is primarily composed of three long, parallel helical hairpins, each corresponding to a different subunit. The additional domains and motifs extending beyond the core serve as gripping tools for ESCRT-I critical functions [, ].; PDB: 2J9W_B 2J9U_C 2G3K_A 2F66_E 2F6M_D 2J9V_A 2CAZ_E 2P22_B.
Probab=100.00 E-value=4.5e-86 Score=559.84 Aligned_cols=187 Identities=56% Similarity=0.927 Sum_probs=159.5
Q ss_pred HHHHHHHHHHHHHHHHhhhcCCCChhhHHHHHHHHHHHHHHHHHHHhc-ccCCHHHHHHHhcCCchHHhhhhhhcCCCce
Q 028441 18 FAELYAIIKATEKLEKAYVRDIISSSEYETECQKLIAHFKTLSSTLKD-IVPSIERFADTYKMDCPAALNRLVTSGVPAT 96 (209)
Q Consensus 18 lAelYSII~tle~LEkAyirD~I~~~eYt~~c~rLl~Qyk~~~~~v~~-~~~~l~~F~~~y~l~cp~A~~RL~~~G~PaT 96 (209)
||+|||||+|||+||||||||+|+++|||++|+|||+|||++++.+.. .|+||++|+++|+|+||+|++|| ++|+|+|
T Consensus 1 LAeLysII~tle~LEkayikD~It~~eYt~~c~kLl~Qyk~~~~~~~~~~~~~le~F~~~y~l~cp~A~~Rl-~~G~P~T 79 (188)
T PF03997_consen 1 LAELYSIIKTLEHLEKAYIKDSITEKEYTTACNKLLNQYKTILKQLKDDEFPDLEEFMKKYNLDCPAALERL-REGVPAT 79 (188)
T ss_dssp HHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHTSTTHHHHHHHHHHHHHTTS-HHHHHHHH-HCTSS--
T ss_pred ChHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHHcccccCCCHHHHHHHhcccCChHHHHH-HcCCCCc
Confidence 799999999999999999999999999999999999999999998865 89999999999999999999999 9999999
Q ss_pred eecccccccCCCcchhHHHHhhhhhhhHhhhhccccchhhhhcchHHHHHHhcccCCCCCCCCcchhhHHHHHHHHhcCC
Q 028441 97 VEHRAAAVASTTTSAAIVAECVQNFITAMDSLKLNMVAVDQVHPLLSDLLGSLNKLTILPPDFEGKTKMKDWISRLSKMG 176 (209)
Q Consensus 97 veh~~~~~~~~~~~a~~Iae~t~~FIT~MDaLKLn~~a~DqLhPlL~dL~~slnk~~~lp~dFegk~kl~~Wl~kLn~M~ 176 (209)
|+|+++++++++++||+|||+||||||+||||||||+|||||||+|+||+.|||||+.+|+||+||+||++|+++||+|+
T Consensus 80 ie~~~~~~~~~~~~ak~Vae~t~~FIT~mDaLKLn~~a~DqLhPlL~dL~~slnr~~~~~~dfe~r~kl~~Wl~~Ln~m~ 159 (188)
T PF03997_consen 80 IEHRISSSSDKGNSAKLVAEATQNFITLMDALKLNYRAKDQLHPLLSDLMQSLNRVTDLPPDFEGRSKLVEWLIKLNGMK 159 (188)
T ss_dssp ------------CHHHHHHHHHHHHHHHHHHHHTT--BHHHHHHHHHHHHHHHHHCTTS-TT-CCHHHHHHHHHHHHTS-
T ss_pred hhhhcccccCCchHHHHHHHHhChhhhhhHHHhccchhHhhHhhHHHHHHHHHhccCCCCCCCccHHHHHHHHHHHhCCC
Confidence 99987665577889999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCHHHHHHHHHhHHHHHHHHHhhcC
Q 028441 177 AADELTEQQSRQLHFDLESSYNSFMAALP 205 (209)
Q Consensus 177 asdeL~eeq~RqllfDle~aY~~F~~~L~ 205 (209)
|+|||+|+|+|||+||||+||++|+++|+
T Consensus 160 asdeL~e~q~rqllfDle~aY~~F~~~L~ 188 (188)
T PF03997_consen 160 ASDELSEEQARQLLFDLESAYNAFYRSLH 188 (188)
T ss_dssp TT-B--HHHHHHHHHHHHHHHHHHHHCH-
T ss_pred cccccCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 99999999999999999999999999984
No 3
>PF09454 Vps23_core: Vps23 core domain; InterPro: IPR017916 The Endosomal Sorting Complex Required for Transport (ESCRT) complexes form the machinery driving protein sorting from endosomes to lysosomes. ESCRT complexes are central to receptor down-regulation, lysosome biogenesis, and budding of HIV. Yeast ESCRT-I consists of three protein subunits, VPS23, VPS28, and VPS37. In humans, ESCRT-I comprises TSG101, VPS28, and one of four potential human VPS37 homologues. The main role of ESCRT-I is to recognise ubiquitinated cargo via the UEV domain of the VPS23/TSG101 subunit. The assembly of the ESCRT-I complex is directed by the C-terminal steadiness box (SB) of VPS23, the N-terminal half of VPS28, and the C-terminal half of VPS37. The structure is primarily composed of three long, parallel helical hairpins, each corresponding to a different subunit. The additional domains and motifs extending beyond the core serve as gripping tools for ESCRT-I critical functions [, ]. This entry represents the Steadiness box domain.; PDB: 2CAZ_A 2F66_D 2F6M_A 2P22_A.
Probab=92.06 E-value=0.72 Score=33.22 Aligned_cols=49 Identities=24% Similarity=0.265 Sum_probs=42.6
Q ss_pred ccCChhHHHHHHhHHHHHHHHHHHHHHHHhhhcCCCChhhHHHHHHHHH
Q 028441 5 LWNDKREREMYENFAELYAIIKATEKLEKAYVRDIISSSEYETECQKLI 53 (209)
Q Consensus 5 L~~~~~eRe~~e~lAelYSII~tle~LEkAyirD~I~~~eYt~~c~rLl 53 (209)
.-.++..++.||-.|+-.+|==|+.+|.+|+-++.|+-+.|-.....|=
T Consensus 5 ~~~~~l~~Ql~el~Aed~AieDtiy~L~~al~~g~I~~d~~lK~vR~La 53 (65)
T PF09454_consen 5 VAEDPLSNQLYELVAEDHAIEDTIYYLDRALQRGSIDLDTFLKQVRSLA 53 (65)
T ss_dssp E-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHH
T ss_pred ccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence 3468899999999999999999999999999999999998988876653
No 4
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=88.96 E-value=0.54 Score=29.03 Aligned_cols=29 Identities=34% Similarity=0.486 Sum_probs=25.9
Q ss_pred HHHHHHHHHhhhcCCCChhhHHHHHHHHH
Q 028441 25 IKATEKLEKAYVRDIISSSEYETECQKLI 53 (209)
Q Consensus 25 I~tle~LEkAyirD~I~~~eYt~~c~rLl 53 (209)
.-.|+.|...|-++.||++||...=.+||
T Consensus 2 ~~~L~~L~~l~~~G~IseeEy~~~k~~ll 30 (31)
T PF09851_consen 2 EDRLEKLKELYDKGEISEEEYEQKKARLL 30 (31)
T ss_pred hHHHHHHHHHHHcCCCCHHHHHHHHHHHh
Confidence 45688999999999999999999888876
No 5
>PF14056 DUF4250: Domain of unknown function (DUF4250)
Probab=67.19 E-value=9.4 Score=26.88 Aligned_cols=32 Identities=22% Similarity=0.387 Sum_probs=27.0
Q ss_pred HHhcccCCHHHHHHHhcCCchHHhhhhhhcCC
Q 028441 62 TLKDIVPSIERFADTYKMDCPAALNRLVTSGV 93 (209)
Q Consensus 62 ~v~~~~~~l~~F~~~y~l~cp~A~~RL~~~G~ 93 (209)
.+++.++|+++||..|+++...=.+||-..|.
T Consensus 15 kLRD~~~sLd~Lc~~~~id~~~l~~kL~~~Gy 46 (55)
T PF14056_consen 15 KLRDEYSSLDELCYDYDIDKEELEEKLASIGY 46 (55)
T ss_pred HHHhccCCHHHHHHHhCCCHHHHHHHHHHcCC
Confidence 46799999999999999999999999933343
No 6
>cd08323 CARD_APAF1 Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1. Caspase activation and recruitment domain (CARD) similar to that found in apoptotic protease-activating factor 1 (APAF-1), which is an activator of caspase-9. APAF-1 contains WD-40 repeats, a CARD, and an ATPase domain. Upon stimulation, APAF-1, together with caspase-9, forms the heptameric 'apoptosome', which leads to the processing and activation of caspase-9, starting a caspase cascade which leads to apoptosis. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effect
Probab=60.14 E-value=10 Score=28.62 Aligned_cols=26 Identities=23% Similarity=0.241 Sum_probs=22.5
Q ss_pred CHHHHHHHHHhHH----HHHHHHHhhcCCC
Q 028441 182 TEQQSRQLHFDLE----SSYNSFMAALPNA 207 (209)
Q Consensus 182 ~eeq~RqllfDle----~aY~~F~~~L~~~ 207 (209)
..+|+|+|+.+|. .||..|+.+|...
T Consensus 43 ~~~qa~~Lld~L~trG~~Af~~F~~aL~~~ 72 (86)
T cd08323 43 QKEKAVMLINMILTKDNHAYVSFYNALLHE 72 (86)
T ss_pred hHHHHHHHHHHHHhcCHHHHHHHHHHHHhc
Confidence 4799999999996 6999999999643
No 7
>PF06464 DMAP_binding: DMAP1-binding Domain; InterPro: IPR010506 This domain binds DMAP1, a transcriptional co-repressor.; GO: 0008134 transcription factor binding, 0005634 nucleus
Probab=56.04 E-value=23 Score=27.80 Aligned_cols=35 Identities=20% Similarity=0.311 Sum_probs=31.9
Q ss_pred HHHHHHHHHHhhhcCCCChhhHHHHHHHHHHHHHH
Q 028441 24 IIKATEKLEKAYVRDIISSSEYETECQKLIAHFKT 58 (209)
Q Consensus 24 II~tle~LEkAyirD~I~~~eYt~~c~rLl~Qyk~ 58 (209)
+-..|..||.-|-.+.||.+.|...-.+||.+|-.
T Consensus 9 vq~~L~~L~~el~~GdiT~KGY~kkr~~LL~~yl~ 43 (111)
T PF06464_consen 9 VQNRLQELDLELEEGDITQKGYEKKRSKLLAPYLP 43 (111)
T ss_pred HHHHHHHHHHhhhcCcchHHHHHHHHHHHHHHHHh
Confidence 44578899999999999999999999999999985
No 8
>cd08325 CARD_CASP1-like Caspase activation and recruitment domain found in Caspase-1 and related proteins. Caspase activation and recruitment domain (CARD) similar to those found in Caspase-1 (CASP1, ICE) and related proteins, including CARD-only proteins such as ICEBERG or CARD18, INCA (CARD17), CARD16 (COP1, PSEUDO-ICE), CARD8 (DACAR, NDPP1, TUCAN), and CARD12 (NLRC4), as well as ICE-like caspases such as CASP12, CASP5 (ICH-3) and CASP4 (TX, ICH-2). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. CASP1 plays a central role in the cellular response to a wide variety of microbial and non-microbial stimuli, being activated by the inflammasome or the pyroptosome. CARD8 binds itself and the initiator caspase-9, interfering with the binding of APAF-1 and suppressing caspase-9 activation. CARD12 is a Nod-like receptor (NLR) that plays an important role in the innate immune response to Gram-negative bacteria. Caspase-4 (CASP4), -5 (CASP5),
Probab=52.15 E-value=29 Score=25.68 Aligned_cols=59 Identities=24% Similarity=0.286 Sum_probs=40.6
Q ss_pred chhhhhcchHHHHHHhcccCCCCCCCCcchhhHHHHHHHHhcCCcccCCCHHHHHHHHHhHH----HHHHHHHhhcCCC
Q 028441 133 VAVDQVHPLLSDLLGSLNKLTILPPDFEGKTKMKDWISRLSKMGAADELTEQQSRQLHFDLE----SSYNSFMAALPNA 207 (209)
Q Consensus 133 ~a~DqLhPlL~dL~~slnk~~~lp~dFegk~kl~~Wl~kLn~M~asdeL~eeq~RqllfDle----~aY~~F~~~L~~~ 207 (209)
.+++.+.|+|-+|+.. |-++. . -++.++....-..++||+|+-++. .|.+.|..+|.+.
T Consensus 13 l~~~~i~~llD~Ll~~-~Vl~~--~-------------E~e~i~~~~~t~~dkar~Lid~v~~KG~~A~~iF~~~L~~~ 75 (83)
T cd08325 13 VGKGVINGLLDDLLEK-NVLNE--E-------------EMEKIKEENNTIMDKARVLVDSVTEKGQEAGQIFIKHLLNR 75 (83)
T ss_pred hhHhhHHHHHHHHHHc-CCCCH--H-------------HHHHHHhccCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc
Confidence 4678899999999987 33332 1 122233322334699999999997 7899999888643
No 9
>PF14361 RsbRD_N: RsbT co-antagonist protein rsbRD N-terminal domain
Probab=51.92 E-value=28 Score=26.41 Aligned_cols=62 Identities=16% Similarity=0.224 Sum_probs=50.5
Q ss_pred hhhhhcchHHHHHHhcccCCCCCCCCcchhhHHHHHHHHhcCCcccCCCHHHHHHHHHhHHHHH
Q 028441 134 AVDQVHPLLSDLLGSLNKLTILPPDFEGKTKMKDWISRLSKMGAADELTEQQSRQLHFDLESSY 197 (209)
Q Consensus 134 a~DqLhPlL~dL~~slnk~~~lp~dFegk~kl~~Wl~kLn~M~asdeL~eeq~RqllfDle~aY 197 (209)
...|..|++..|..++....+ ...++-..+..+|..+...+|....|..|+=.|.|-|-.+-
T Consensus 37 l~~~~~~v~~~l~~~l~~~~d--~~~~~~~~l~~~L~~lsr~RA~Qgftpseta~fvf~LK~~l 98 (105)
T PF14361_consen 37 LRQFANPVLDALAAALESGLD--LAAPEWEELREALEELSRIRAVQGFTPSETASFVFALKRPL 98 (105)
T ss_pred HHHHHHHHHHHHHHHHHHhhh--ccccchHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHH
Confidence 346788888888888877733 34445589999999999999999999999999999887653
No 10
>cd08819 CARD_MDA5_2 Caspase activation and recruitment domain found in MDA5, second repeat. Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), second 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 protei
Probab=47.38 E-value=14 Score=28.46 Aligned_cols=28 Identities=21% Similarity=0.311 Sum_probs=23.1
Q ss_pred CCCHHHHHHHHHhHH---HHHHHHHhhcCCC
Q 028441 180 ELTEQQSRQLHFDLE---SSYNSFMAALPNA 207 (209)
Q Consensus 180 eL~eeq~RqllfDle---~aY~~F~~~L~~~ 207 (209)
.=..+++|||+.+|+ .||..|...|+..
T Consensus 49 ~g~~~~ar~LL~~L~rg~~aF~~Fl~aLreT 79 (88)
T cd08819 49 HGNESGARELLKRIVQKEGWFSKFLQALRET 79 (88)
T ss_pred cCcHHHHHHHHHHhccCCcHHHHHHHHHHHc
Confidence 356899999999997 6888888888754
No 11
>cd08326 CARD_CASP9 Caspase activation and recruitment domain of Caspase-9. Caspase activation and recruitment domain (CARD) similar to that found in caspase-9 (CASP9, MCH6, APAF3), which interacts with the CARD of apoptotic protease-activating factor 1 (APAF-1). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-9 is the initiator caspase associated with the intrinsic or mitochondrial pathway of apoptosis, induced by many pro-apoptotic signals. Together with APAF-1, it forms the heptameric 'apoptosome' in response to the release of cytochrome c from mitochondria. Activated caspase-9 cleaves and activates downstream effector caspases, like caspase-3, caspase-6, and caspase-7, resulting in apoptosis. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apopt
Probab=44.97 E-value=22 Score=26.55 Aligned_cols=27 Identities=41% Similarity=0.726 Sum_probs=22.8
Q ss_pred CHHHHHHHHHhHH----HHHHHHHhhcCCCC
Q 028441 182 TEQQSRQLHFDLE----SSYNSFMAALPNAG 208 (209)
Q Consensus 182 ~eeq~RqllfDle----~aY~~F~~~L~~~~ 208 (209)
..+++++|+-.|. .||..|+..|...|
T Consensus 45 r~~q~~~LLd~L~~RG~~AF~~F~~aL~~~~ 75 (84)
T cd08326 45 RRDQARQLLIDLETRGKQAFPAFLSALRETG 75 (84)
T ss_pred HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC
Confidence 4789999999996 69999999997543
No 12
>PF08969 USP8_dimer: USP8 dimerisation domain; InterPro: IPR015063 This domain is predominantly found in the amino terminal region of Ubiquitin carboxyl-terminal hydrolase 8 (USP8). It has no known function. ; PDB: 2XZE_B 2A9U_A.
Probab=43.95 E-value=35 Score=26.26 Aligned_cols=55 Identities=25% Similarity=0.410 Sum_probs=39.1
Q ss_pred HHHHHhcccCCCCCCCCcchhhHHHHHHHHhcCCcccCCCHHHHHHHH--HhHHHHHHHHHhhc
Q 028441 143 SDLLGSLNKLTILPPDFEGKTKMKDWISRLSKMGAADELTEQQSRQLH--FDLESSYNSFMAAL 204 (209)
Q Consensus 143 ~dL~~slnk~~~lp~dFegk~kl~~Wl~kLn~M~asdeL~eeq~Rqll--fDle~aY~~F~~~L 204 (209)
++=+..|++....-++|.+...+..|+...+.|- .+|.+.. .|+|.||--|++++
T Consensus 9 ~~s~~~L~~~a~~~~~~~~~~~l~~y~rsa~~l~-------~~A~~~~~egd~E~AYvl~~R~~ 65 (115)
T PF08969_consen 9 ASSLEELNKLADVFPEFDKNIPLKRYLRSANKLL-------REAEEYRQEGDEEQAYVLYMRYL 65 (115)
T ss_dssp -CCHHHHHHCCCT-GGGSTTS-HHHHHHHHHHHH-------HHHHHHHHCT-HHHHHHHHHHHH
T ss_pred HhhHHHHHHHHHHhcccccccCHHHHHHHHHHHH-------HHHHHHHHCCCHHHHHHHHHHHH
Confidence 4445666777652126667788999999999987 6777764 49999999998876
No 13
>cd08330 CARD_ASC_NALP1 Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins. Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They se
Probab=43.27 E-value=23 Score=26.18 Aligned_cols=26 Identities=19% Similarity=0.234 Sum_probs=22.2
Q ss_pred CCHHHHHHHHHhHH----HHHHHHHhhcCC
Q 028441 181 LTEQQSRQLHFDLE----SSYNSFMAALPN 206 (209)
Q Consensus 181 L~eeq~RqllfDle----~aY~~F~~~L~~ 206 (209)
=+.+++|+|+-.+. .||..|+..|..
T Consensus 43 T~~~kar~Lld~l~~kG~~A~~~F~~~L~e 72 (82)
T cd08330 43 TNQEKMRKLFSFVRSWGASCKDIFYQILRE 72 (82)
T ss_pred CcHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence 45799999999996 599999999964
No 14
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=41.11 E-value=40 Score=27.58 Aligned_cols=71 Identities=13% Similarity=0.269 Sum_probs=52.6
Q ss_pred HHHhhhhhhhHhhhhccccchhhhhcchHHHHHHhcccCCC--CCCCCcchhhHHHHHHHHh--------------cCCc
Q 028441 114 VAECVQNFITAMDSLKLNMVAVDQVHPLLSDLLGSLNKLTI--LPPDFEGKTKMKDWISRLS--------------KMGA 177 (209)
Q Consensus 114 Iae~t~~FIT~MDaLKLn~~a~DqLhPlL~dL~~slnk~~~--lp~dFegk~kl~~Wl~kLn--------------~M~a 177 (209)
-+|.||++|-.+-+ .|--+.+..+..-.++.. .|.++.+-.++.+||...| .+.+
T Consensus 25 s~eltqqeIr~lE~---------KLvK~fSkQL~~K~k~~~~~~~~~l~~yP~l~~WL~vVgl~~~~i~~i~~~~~tLe~ 95 (129)
T PF13543_consen 25 SSELTQQEIRTLEG---------KLVKYFSKQLQCKAKVAERERAAELNSYPSLRQWLRVVGLRPESIQAILSKVLTLEA 95 (129)
T ss_pred chHHHHHHHHHHHH---------HHHHHHHHHHHHHHhcCCccCchhcccCCcHHHHhhhcCCCHHHHHHHHHhhcCHHH
Confidence 38999999966543 456677778888788776 3557777799999997654 3334
Q ss_pred ccCCCHHHHHHHHHhH
Q 028441 178 ADELTEQQSRQLHFDL 193 (209)
Q Consensus 178 sdeL~eeq~RqllfDl 193 (209)
-=+++|+|.++++-+.
T Consensus 96 Llemsd~el~~~l~~~ 111 (129)
T PF13543_consen 96 LLEMSDEELKEILNRC 111 (129)
T ss_pred HHhCCHHHHHHHHHHh
Confidence 4478999999999873
No 15
>PF05120 GvpG: Gas vesicle protein G ; InterPro: IPR007804 Gas vesicles are intracellular, protein-coated, and hollow organelles found in cyanobacteria and halophilic archaea. They are permeable to ambient gases by diffusion and provide buoyancy, enabling cells to move upwards in water to access oxygen and/or light. Proteins containing this family are involved in the formation of gas vesicles [].
Probab=40.69 E-value=1e+02 Score=23.14 Aligned_cols=49 Identities=27% Similarity=0.413 Sum_probs=40.5
Q ss_pred hhHHHHHHhHHHHHHHHHHHHHHHHhhhcCCCChhhHHHHHHHHHHHHHHHHH
Q 028441 9 KREREMYENFAELYAIIKATEKLEKAYVRDIISSSEYETECQKLIAHFKTLSS 61 (209)
Q Consensus 9 ~~eRe~~e~lAelYSII~tle~LEkAyirD~I~~~eYt~~c~rLl~Qyk~~~~ 61 (209)
..||+.||- =.|=.-|..|+.+|-.+-||+++|...=..||.+...+..
T Consensus 22 ~Ae~E~~Dp----~~i~~~L~~L~~~~e~GEIseeEf~~~E~eLL~rL~~~~~ 70 (79)
T PF05120_consen 22 QAERELYDP----AAIRRELAELQEALEAGEISEEEFERREDELLDRLEEARR 70 (79)
T ss_pred HHHHHHcCH----HHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 456666643 2466778899999999999999999999999999987764
No 16
>PRK05467 Fe(II)-dependent oxygenase superfamily protein; Provisional
Probab=39.79 E-value=36 Score=30.02 Aligned_cols=37 Identities=27% Similarity=0.522 Sum_probs=28.9
Q ss_pred hhhHHHHHHHHhcCCcccCCCHHHHHHHHHhHHHHHHHHHhhcCC
Q 028441 162 KTKMKDWISRLSKMGAADELTEQQSRQLHFDLESSYNSFMAALPN 206 (209)
Q Consensus 162 k~kl~~Wl~kLn~M~asdeL~eeq~RqllfDle~aY~~F~~~L~~ 206 (209)
|--+..|+..+ +-+++-|++|||||++-.+-.+..+.
T Consensus 169 R~~~~~Wi~S~--------v~~~~~R~~lf~ld~~~~~l~~~~~~ 205 (226)
T PRK05467 169 RVASFFWIQSL--------VRDDSQRELLFDLDTAIQSLLARHGD 205 (226)
T ss_pred EEEEEecHHHH--------cCCHHHHHHHHhHHHHHHHHHHHcCC
Confidence 55677899876 56789999999999988877665543
No 17
>COG3462 Predicted membrane protein [Function unknown]
Probab=37.53 E-value=44 Score=26.93 Aligned_cols=27 Identities=26% Similarity=0.475 Sum_probs=22.3
Q ss_pred HHHHHHHHhhhcCCCChhhHHHHHHHH
Q 028441 26 KATEKLEKAYVRDIISSSEYETECQKL 52 (209)
Q Consensus 26 ~tle~LEkAyirD~I~~~eYt~~c~rL 52 (209)
.|.|-|-..|.|+-||++||+.--+.+
T Consensus 89 RA~eIlkER~AkGEItEEEY~r~~~~i 115 (117)
T COG3462 89 RAEEILKERYAKGEITEEEYRRIIRTI 115 (117)
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHh
Confidence 467888889999999999999865543
No 18
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=36.38 E-value=2e+02 Score=23.27 Aligned_cols=96 Identities=21% Similarity=0.354 Sum_probs=62.6
Q ss_pred HHHHHHHHHHHHHHHHH--HH--hcccCCHHHHHHHhcCCc---hHHhhhhhhcCCCceeecccccccCCC------cch
Q 028441 45 YETECQKLIAHFKTLSS--TL--KDIVPSIERFADTYKMDC---PAALNRLVTSGVPATVEHRAAAVASTT------TSA 111 (209)
Q Consensus 45 Yt~~c~rLl~Qyk~~~~--~v--~~~~~~l~~F~~~y~l~c---p~A~~RL~~~G~PaTveh~~~~~~~~~------~~a 111 (209)
|+..| +|.|.... .+ ++..||+-++....+++- .+|.+=|.+.|+=-|....+.-.++.+ ...
T Consensus 13 Y~QI~----~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~rg~G~fV~~~~~~~~~~~~~ 88 (125)
T COG1725 13 YEQIA----NQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVETKRGKGTFVTEDAKEILDQLKR 88 (125)
T ss_pred HHHHH----HHHHHHHHhCCcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCeeEEEcCCchhhHHHHHH
Confidence 66655 44444332 33 567899999999999874 577877866688766544332221111 124
Q ss_pred hHHHHhhhhhhhHhhhhccccchhhhhcchHHHHHH
Q 028441 112 AIVAECVQNFITAMDSLKLNMVAVDQVHPLLSDLLG 147 (209)
Q Consensus 112 ~~Iae~t~~FIT~MDaLKLn~~a~DqLhPlL~dL~~ 147 (209)
..+.+.+.+||.-|=++-+ ++++++.++.+...
T Consensus 89 ~~~~~~l~~~I~~~~~~G~---s~eei~~~~~~~~~ 121 (125)
T COG1725 89 ELAEEELEEFIEEAKALGL---SLEEILELLKEIYE 121 (125)
T ss_pred HHHHHHHHHHHHHHHHcCC---CHHHHHHHHHHHHh
Confidence 4677888899876666555 57888888887654
No 19
>KOG3046 consensus Transcription factor, subunit of SRB subcomplex of RNA polymerase II [Transcription]
Probab=33.88 E-value=1.4e+02 Score=25.13 Aligned_cols=34 Identities=24% Similarity=0.235 Sum_probs=25.7
Q ss_pred HHHHHH-HHHHHHHHHHhhhcCCCChhhHHHHHHHHH
Q 028441 18 FAELYA-IIKATEKLEKAYVRDIISSSEYETECQKLI 53 (209)
Q Consensus 18 lAelYS-II~tle~LEkAyirD~I~~~eYt~~c~rLl 53 (209)
+..=++ |-+-+|.|| ||-|.=.+..||..|....
T Consensus 63 ~s~k~n~i~IPleVl~--yIddGrNPd~ytke~le~~ 97 (147)
T KOG3046|consen 63 LSSKLNDIQIPLEVLE--YIDDGRNPDLYTKEFLEKC 97 (147)
T ss_pred HHHhhccccCcHHHHH--HHhcCCCccHHHHHHHHHH
Confidence 333344 556677776 9999999999999998764
No 20
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=33.27 E-value=60 Score=26.90 Aligned_cols=29 Identities=34% Similarity=0.548 Sum_probs=25.0
Q ss_pred HHHHHHHHHHhhhcCCCChhhHHHHHHHHHHHHHHHHH
Q 028441 24 IIKATEKLEKAYVRDIISSSEYETECQKLIAHFKTLSS 61 (209)
Q Consensus 24 II~tle~LEkAyirD~I~~~eYt~~c~rLl~Qyk~~~~ 61 (209)
||+||+-|| .++|.+.|.+....||...+
T Consensus 71 viKALenLe---------f~eyi~~~~e~~~n~k~~qK 99 (148)
T COG5150 71 VIKALENLE---------FEEYIESCMEEHENYKSYQK 99 (148)
T ss_pred HHHHHHhcc---------HHHHHHHHHHHHHHHHHHHh
Confidence 677777776 58999999999999999887
No 21
>COG3882 FkbH Predicted enzyme involved in methoxymalonyl-ACP biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=33.20 E-value=36 Score=33.92 Aligned_cols=108 Identities=17% Similarity=0.160 Sum_probs=79.1
Q ss_pred CchHHhhhhhhcCCCceeecccccccCCCcchhHHHHhhhhhhh----HhhhhccccchhhhhcchHHHHHHhcccC---
Q 028441 80 DCPAALNRLVTSGVPATVEHRAAAVASTTTSAAIVAECVQNFIT----AMDSLKLNMVAVDQVHPLLSDLLGSLNKL--- 152 (209)
Q Consensus 80 ~cp~A~~RL~~~G~PaTveh~~~~~~~~~~~a~~Iae~t~~FIT----~MDaLKLn~~a~DqLhPlL~dL~~slnk~--- 152 (209)
|-|+-+++. +.-+|++|..-.+. ..--.+-++ ..++|-+ .=|--|=++-+-.-.|+.|.+...|+...
T Consensus 335 D~p~ErE~v-k~~~~v~Vi~~~~D---ps~~~~~~~-~~~~f~~l~lt~ED~~ra~~y~~n~~rEelK~~s~sleEYlK~ 409 (574)
T COG3882 335 DNPAERELV-KRELPVSVIEFPED---PSFLRDPKN-SSGLFSHLPLTTEDLKRANSYGQNAKREELKEESGSLEEYLKN 409 (574)
T ss_pred CCHHHHHHH-HhcCceeeccCCCC---HHHHhhhhh-ccchhhccccchhhHhhhhhhhhhhhhHHHHHhcccHHHHHhh
Confidence 458889988 99999887664332 112223333 5566644 44888888888888999999998887652
Q ss_pred -----CCCCCCCcchhhHHHHHHHHhcCCccc-CCCHHHHHHHHHh
Q 028441 153 -----TILPPDFEGKTKMKDWISRLSKMGAAD-ELTEQQSRQLHFD 192 (209)
Q Consensus 153 -----~~lp~dFegk~kl~~Wl~kLn~M~asd-eL~eeq~RqllfD 192 (209)
+-.+.|=-+..++.+-..|=|+...+- .+++++++||..|
T Consensus 410 Lem~l~vs~~de~~i~RIsQLtqkTNQFnlTtkRy~e~dV~~~~~~ 455 (574)
T COG3882 410 LEMRLTVSKFDEVNIPRISQLTQKTNQFNLTTKRYNEEDVRQMQED 455 (574)
T ss_pred heEEEEEeeccccCcHHHHHHhhcccceeechhhhcHHHHHHHhhC
Confidence 222556668999999999999998876 5999999998765
No 22
>PF08044 DUF1707: Domain of unknown function (DUF1707); InterPro: IPR012551 This domain is found in a variety of actinomycetales proteins. All of the proteins containing this domain are hypothetical and probably membrane bound or associated. Currently, it is unclear to the function of this domain.
Probab=32.82 E-value=79 Score=21.71 Aligned_cols=27 Identities=19% Similarity=0.309 Sum_probs=24.3
Q ss_pred HHHHHHHhhhcCCCChhhHHHHHHHHH
Q 028441 27 ATEKLEKAYVRDIISSSEYETECQKLI 53 (209)
Q Consensus 27 tle~LEkAyirD~I~~~eYt~~c~rLl 53 (209)
+++.|-.||-.+-++..||..-|.+..
T Consensus 11 ~~~~L~~a~a~GrL~~~Ef~~R~~~a~ 37 (53)
T PF08044_consen 11 AVDLLRAAFAEGRLSLDEFDERLDAAY 37 (53)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHH
Confidence 688999999999999999999887654
No 23
>PF11237 DUF3038: Protein of unknown function (DUF3038); InterPro: IPR021399 This family of proteins with unknown function appear to be restricted to Cyanobacteria.
Probab=31.58 E-value=79 Score=27.03 Aligned_cols=96 Identities=22% Similarity=0.365 Sum_probs=59.2
Q ss_pred HHHHhcCCchHHhhhhhhcCCCceeecccccccCCCcchhHHHHhhhhhhhHhhhhccccchhhhhcchHHHHHHhcccC
Q 028441 73 FADTYKMDCPAALNRLVTSGVPATVEHRAAAVASTTTSAAIVAECVQNFITAMDSLKLNMVAVDQVHPLLSDLLGSLNKL 152 (209)
Q Consensus 73 F~~~y~l~cp~A~~RL~~~G~PaTveh~~~~~~~~~~~a~~Iae~t~~FIT~MDaLKLn~~a~DqLhPlL~dL~~slnk~ 152 (209)
=..-|++.|..-+.|- ..--|.|++. +++..-++.+-= +|++|+++.++..+..+
T Consensus 43 rV~LWrlR~~NPlRr~-~~r~~L~~ee-----------araLV~Iic~lA-------------~~~~~lIRqll~~~eQ~ 97 (171)
T PF11237_consen 43 RVELWRLRCTNPLRRS-SQRKPLTVEE-----------ARALVLIICYLA-------------KQLQPLIRQLLLLLEQM 97 (171)
T ss_pred HHHHHHHhcCCcCccc-ccCCCCCHHH-----------HHHHHHHHHHHH-------------HHhHHHHHHHHHHHHHH
Confidence 3456778888888877 4444555554 455554444432 89999999999888888
Q ss_pred CCCCCCCcchhhHHHHHHHH--------hcCCc-------ccCCCHHHHHHHHHhH
Q 028441 153 TILPPDFEGKTKMKDWISRL--------SKMGA-------ADELTEQQSRQLHFDL 193 (209)
Q Consensus 153 ~~lp~dFegk~kl~~Wl~kL--------n~M~a-------sdeL~eeq~RqllfDl 193 (209)
+.-.++......+...+.++ |.=+. +++-..+=+++++.||
T Consensus 98 ~~~~~~~~~~~ll~~Yl~rF~~~~~~Rmn~~r~~v~~~L~~~~~l~~La~kLL~~L 153 (171)
T PF11237_consen 98 SSQEPPPHQNQLLGDYLDRFRSLYQERMNPRRSAVKRLLNSPEKLNELALKLLIDL 153 (171)
T ss_pred HhcCCChhhHHHHHHHHHHHHHHHHHHcCCcchhhhhccCChhhhHHHHHHHHHHH
Confidence 86434444445555555544 33333 2333345667777776
No 24
>cd08810 CARD_BCL10 Caspase activation and recruitment domain of B-cell lymphoma 10. Caspase activation and recruitment domain (CARD) similar to that found in BCL10 (B-cell lymphoma 10). BCL10 and Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1) are the integral components of CBM signalosomes. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells) and with CARMA1 to form L-CBM (CBM complex in lymphoid immune cells), to mediate activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. Both CARMA1 and CARD9 associate with BCL10 via 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 domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by asso
Probab=31.49 E-value=47 Score=25.10 Aligned_cols=30 Identities=10% Similarity=0.162 Sum_probs=23.4
Q ss_pred cCCCHHHHHHHHHhHH---HHHHHHHhhcCCCC
Q 028441 179 DELTEQQSRQLHFDLE---SSYNSFMAALPNAG 208 (209)
Q Consensus 179 deL~eeq~RqllfDle---~aY~~F~~~L~~~~ 208 (209)
..-+.+++++|+.+|. .||.+|..+|+..+
T Consensus 42 ~~t~~~qa~~LLdiL~rGp~Af~~F~esL~~~~ 74 (84)
T cd08810 42 RTTSRKQAGKLLDILAENPKGLDALIESIRRER 74 (84)
T ss_pred cCCcHHHHHHHHHHHhhCchHHHHHHHHHHHcc
Confidence 3456789999999998 67888888887544
No 25
>cd00672 CysRS_core catalytic core domain of cysteinyl tRNA synthetase. Cysteinyl tRNA synthetase (CysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding.
Probab=31.39 E-value=50 Score=28.48 Aligned_cols=64 Identities=14% Similarity=0.160 Sum_probs=41.2
Q ss_pred HHhhhcCCCChhhHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHhcCCchHHhhhhhhcCCCceeecccc
Q 028441 32 EKAYVRDIISSSEYETECQKLIAHFKTLSSTLKDIVPSIERFADTYKMDCPAALNRLVTSGVPATVEHRAA 102 (209)
Q Consensus 32 EkAyirD~I~~~eYt~~c~rLl~Qyk~~~~~v~~~~~~l~~F~~~y~l~cp~A~~RL~~~G~PaTveh~~~ 102 (209)
+++=.+..+++.||+.. ...+|+..++.+.=.+| +.|...|++.|++...+. -|-|..|-.++.
T Consensus 73 ~~~A~~~g~~p~e~~~~---~~~~f~~~~~~l~i~~~--d~~~rtWh~ec~am~~~~--lg~~~dih~~G~ 136 (213)
T cd00672 73 IKRAREEGLSWKEVADY---YTKEFFEDMKALNVLPP--DVVPRVWHIECSAMAMKY--LGETFDIHGGGV 136 (213)
T ss_pred HHHHHHcCCCHHHHHHH---HHHHHHHHHHHcCCCCC--CcceeehhHHHHHHHHHH--cCCCccEEeecC
Confidence 33334456777776554 45677877776632222 557777999999877766 467777766543
No 26
>COG5126 FRQ1 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]
Probab=31.22 E-value=78 Score=26.65 Aligned_cols=78 Identities=14% Similarity=0.267 Sum_probs=51.7
Q ss_pred hhhhhHhhhhccccchhhhhcchHHHHHHhcccCCCCCCCCcchhhHHHHHHHHhcCCcccCCCHHHHHHHHHhHHH---
Q 028441 119 QNFITAMDSLKLNMVAVDQVHPLLSDLLGSLNKLTILPPDFEGKTKMKDWISRLSKMGAADELTEQQSRQLHFDLES--- 195 (209)
Q Consensus 119 ~~FIT~MDaLKLn~~a~DqLhPlL~dL~~slnk~~~lp~dFegk~kl~~Wl~kLn~M~asdeL~eeq~RqllfDle~--- 195 (209)
+.|+|+|=. ++... +.--+|..+..-+..-...+-+...|+.|+..| .++++++++..|+...+.
T Consensus 75 ~~Fl~~ms~-~~~~~------~~~Eel~~aF~~fD~d~dG~Is~~eL~~vl~~l-----ge~~~deev~~ll~~~d~d~d 142 (160)
T COG5126 75 PEFLTVMSV-KLKRG------DKEEELREAFKLFDKDHDGYISIGELRRVLKSL-----GERLSDEEVEKLLKEYDEDGD 142 (160)
T ss_pred HHHHHHHHH-HhccC------CcHHHHHHHHHHhCCCCCceecHHHHHHHHHhh-----cccCCHHHHHHHHHhcCCCCC
Confidence 467777632 22211 224567777777765334466778888888833 589999999999998883
Q ss_pred ---HHHHHHhhcCCCC
Q 028441 196 ---SYNSFMAALPNAG 208 (209)
Q Consensus 196 ---aY~~F~~~L~~~~ 208 (209)
.|..|.+..-.++
T Consensus 143 G~i~~~eF~~~~~~~~ 158 (160)
T COG5126 143 GEIDYEEFKKLIKDSP 158 (160)
T ss_pred ceEeHHHHHHHHhccC
Confidence 5777776554433
No 27
>PF11740 KfrA_N: Plasmid replication region DNA-binding N-term; InterPro: IPR021104 The KfrA family of protiens are encoded on plasmids, generally in or near gene clusters invloved in stable inheritance functions. These proteins are thought to form an all-helical structure, consisting of an N-terminal helix-turn-helix DNA binding domain and an extended coiled-coil tail. The best-characterised KfrA protein, encoded on the broad host-range Plasmid RK2, is a site-specific DNA-binding protein whose operator overlaps its own promoter. The DNA-binding domain is essential for function, while the coiled-coil domain is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning []. This entry represents the N-terminal DNA-binding domain.
Probab=30.82 E-value=49 Score=25.14 Aligned_cols=59 Identities=14% Similarity=0.258 Sum_probs=40.9
Q ss_pred CChhhHHHHHHHHHHHHH-----HHHHHHh-cccCCHHHHHHHhcCCchHHhhhhhhcCCCceeec
Q 028441 40 ISSSEYETECQKLIAHFK-----TLSSTLK-DIVPSIERFADTYKMDCPAALNRLVTSGVPATVEH 99 (209)
Q Consensus 40 I~~~eYt~~c~rLl~Qyk-----~~~~~v~-~~~~~l~~F~~~y~l~cp~A~~RL~~~G~PaTveh 99 (209)
||.++...+|.+|+.+=+ .+...++ +..++|..+++.|+-.-+... +....++|..+..
T Consensus 1 IT~e~V~~Aa~~L~~~G~~pT~~~Vr~~lG~GS~~ti~~~l~~w~~~~~~~~-~~~~~~lP~~l~~ 65 (120)
T PF11740_consen 1 ITYEDVIEAADELLAAGKKPTVRAVRERLGGGSMSTISKHLKEWREEREAQV-SEAAPDLPEALQD 65 (120)
T ss_pred CcHHHHHHHHHHHHHcCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHhhhccc-cccccCCChhHHH
Confidence 788888899999997643 3344554 667789999999997777666 2214566655433
No 28
>PRK08719 ribonuclease H; Reviewed
Probab=30.51 E-value=58 Score=26.44 Aligned_cols=43 Identities=26% Similarity=0.244 Sum_probs=34.4
Q ss_pred HHHhHHHHHHHHHHHHHHHHhhhcCCCChhhHH-HHHHHHHHHHHH
Q 028441 14 MYENFAELYAIIKATEKLEKAYVRDIISSSEYE-TECQKLIAHFKT 58 (209)
Q Consensus 14 ~~e~lAelYSII~tle~LEkAyirD~I~~~eYt-~~c~rLl~Qyk~ 58 (209)
...+-|||-+|+.+|+.+.+.- -..|+++|. ..+++-+.+++.
T Consensus 48 ~Tnn~aEl~A~~~aL~~~~~~~--~i~tDS~yvi~~i~~~~~~W~~ 91 (147)
T PRK08719 48 TDNAELELLALIEALEYARDGD--VIYSDSDYCVRGFNEWLDTWKQ 91 (147)
T ss_pred ccHHHHHHHHHHHHHHHcCCCC--EEEechHHHHHHHHHHHHHHHh
Confidence 4678899999999999988763 477889998 566777777774
No 29
>cd01145 TroA_c Periplasmic binding protein TroA_c. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=30.10 E-value=1.7e+02 Score=24.46 Aligned_cols=54 Identities=24% Similarity=0.313 Sum_probs=32.9
Q ss_pred hhHHHHHHHHHHHHHHHHH-------HHhc-c----cCCHHHHHHHhcCCchHHhhhhhhcCCCceee
Q 028441 43 SEYETECQKLIAHFKTLSS-------TLKD-I----VPSIERFADTYKMDCPAALNRLVTSGVPATVE 98 (209)
Q Consensus 43 ~eYt~~c~rLl~Qyk~~~~-------~v~~-~----~~~l~~F~~~y~l~cp~A~~RL~~~G~PaTve 98 (209)
+.|..-..+++.|.+.+-+ .+++ . -+.+.-|++.|++.. .++-.+ .-|+|.+..
T Consensus 137 ~~y~~N~~~~~~~l~~l~~~~~~~l~~~~~~~~v~~H~af~Y~~~~yGl~~-~~~~~~-~~~~~p~~~ 202 (203)
T cd01145 137 EEYKENLRVFLAKLNKLLREWERQFEGLKGIQVVAYHPSYQYLADWLGIEV-VASLEP-LPELPPTSS 202 (203)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhccCCCeEEEecccHHHHHHHcCCce-eeeecc-CCCCCCCCC
Confidence 3366666666555554443 3321 1 256899999999985 455555 667776643
No 30
>cd08329 CARD_BIRC2_BIRC3 Caspase activation and recruitment domain found in Baculoviral IAP repeat-containing proteins, BIRC2 (c-IAP1) and BIRC3 (c-IAP2). Caspase activation and recruitment domain (CARD) similar to those found in Baculoviral IAP repeat (BIR)-containing protein 2 (BIRC2) or cellular Inhibitor of Apoptosis Protein 1 (c-IAP1), and BIRC3 (or c-IAP2). IAPs are anti-apoptotic proteins that contain at least one BIR domain. Most IAPs also contain a C-terminal RING domain. In addition, both BIRC2 and BIRC3 contain a CARD. BIRC2 and BIRC3, through their binding with TRAF (TNF receptor-associated factor) 2, are recruited to TNFR-1/2 signaling complexes, where they regulate caspase-8 activity. They also play important roles in pro-survival NF-kB signaling pathways. 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 interac
Probab=27.38 E-value=69 Score=24.31 Aligned_cols=26 Identities=23% Similarity=0.210 Sum_probs=22.1
Q ss_pred CHHHHHHHHHhHH----HHHHHHHhhcCCC
Q 028441 182 TEQQSRQLHFDLE----SSYNSFMAALPNA 207 (209)
Q Consensus 182 ~eeq~RqllfDle----~aY~~F~~~L~~~ 207 (209)
+.++||+|+-++. .|+..|+.+|.+.
T Consensus 52 ~~~qAr~Lld~l~~KG~~A~~~F~~~L~e~ 81 (94)
T cd08329 52 TPLQARELIDTVLVKGNAAAEVFRNCLKKN 81 (94)
T ss_pred hHHHHHHHHHHHHhhhHHHHHHHHHHHHhc
Confidence 4699999999986 7999999999743
No 31
>PF03909 BSD: BSD domain ; InterPro: IPR005607 The BSD domain is an about 60-residue long domain named after the BTF2-like transcription factors, Synapse-associated proteins and DOS2-like proteins in which it is found. Additionally, it is also found in several hypothetical proteins. The BSD domain occurs in one or two copies in a variety of species ranging from primal protozoan to human. It can be found associated with other domains such as the BTB domain (see PDOC50097 from PROSITEDOC) or the U-box in multidomain proteins. The function of the BSD domain is yet unknown []. Secondary structure prediction indicates the presence of three predicted alpha helices, which probably form a three-helical bundle in small domains. The third predicted helix contains neighbouring phenylalanine and tryptophan residues - less common amino acids that are invariant in all the BSD domains identified and that are the most striking sequence features of the domain []. Some proteins known to contain one or two BSD domains are listed below: Mammalian TFIIH basal transcription factor complex p62 subunit (GTF2H1). Yeast RNA polymerase II transcription factor B 73 kDa subunit (TFB1), the homologue of BTF2. Yeast DOS2 protein. It is involved in single-copy DNA replication and ubiquitination. Drosophila synapse-associated protein SAP47. Mammalian SYAP1. Various Arabidopsis thaliana (Mouse-ear cress) hypothetical proteins.; PDB: 1X3A_A 1PFJ_A 2RNR_B 2DII_A.
Probab=26.47 E-value=1.6e+02 Score=20.22 Aligned_cols=40 Identities=28% Similarity=0.360 Sum_probs=28.6
Q ss_pred CChhhHHHHHHHHHHHHHHHHHHHhcccCC---HHHHHHHhcC
Q 028441 40 ISSSEYETECQKLIAHFKTLSSTLKDIVPS---IERFADTYKM 79 (209)
Q Consensus 40 I~~~eYt~~c~rLl~Qyk~~~~~v~~~~~~---l~~F~~~y~l 79 (209)
.+-+.++....+||.++..+.+.-...+|+ =+.|+.+|=-
T Consensus 8 f~~~~~~e~i~~lL~~~p~l~~~~~~lVP~~~~e~~FW~rYf~ 50 (62)
T PF03909_consen 8 FDIDEQTEEIKKLLEEDPNLRKLYNELVPSKMSEEEFWKRYFY 50 (62)
T ss_dssp --CHHHHHHHHHHHHH-HHHHHHHHHCCTTTS-HHHHHHHHHC
T ss_pred ccccCCHHHHHHHHHhCHHHHHHHHHhCCCCCCHHHHHHHHHH
Confidence 345678999999999999977755555664 4889998853
No 32
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=26.35 E-value=96 Score=19.74 Aligned_cols=28 Identities=29% Similarity=0.405 Sum_probs=21.9
Q ss_pred ccCCHHHHHHHhcCCch---HHhhhhhhcCC
Q 028441 66 IVPSIERFADTYKMDCP---AALNRLVTSGV 93 (209)
Q Consensus 66 ~~~~l~~F~~~y~l~cp---~A~~RL~~~G~ 93 (209)
.+|++.+.++.|++..+ .|+++|.+.|+
T Consensus 19 ~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~ 49 (60)
T smart00345 19 KLPSERELAAQLGVSRTTVREALSRLEAEGL 49 (60)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence 45689999999999876 56677855587
No 33
>COG4496 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.29 E-value=1.1e+02 Score=24.02 Aligned_cols=40 Identities=25% Similarity=0.377 Sum_probs=30.4
Q ss_pred HHHHHhHHHHHHHHHHHHHHHH--hhhcCCCChhhHHHHHHH
Q 028441 12 REMYENFAELYAIIKATEKLEK--AYVRDIISSSEYETECQK 51 (209)
Q Consensus 12 Re~~e~lAelYSII~tle~LEk--AyirD~I~~~eYt~~c~r 51 (209)
|-.-..|.+||--|.+|+-+|. +|.+|..|.+|-.+...|
T Consensus 5 klr~~~Ld~l~dailtL~n~eecy~FfdDlcTinEiqslaqR 46 (100)
T COG4496 5 KLRGAALDELFDAILTLENLEECYAFFDDLCTINEIQSLAQR 46 (100)
T ss_pred chhhHHHHHHHHHHHHhccHHHHHHHHHhhcCHHHHHHHHHH
Confidence 3345678899999999999996 668888888776655543
No 34
>PF06757 Ins_allergen_rp: Insect allergen related repeat, nitrile-specifier detoxification; InterPro: IPR010629 This entry represents several insect specific allergen repeats. These repeats are commonly found in various proteins from cockroaches, fruit flies and mosquitos. It has been suggested that the repeat sequences have evolved by duplication of an ancestral amino acid domain, which may have arisen from the mitochondrial energy transfer proteins []. This family exemplifies a case of novel gene evolution. The case in point is the arms-race between plants and their infective insective herbivores in the area of the glucosinolate-myrosinase system. Brassicas have developed the glucosinolate-myrosinase system as chemical defence mechanism against the insects, and consequently the insects have adapted to produce a detoxifying molecule, nitrile-specifier protein (NSP). NSP is present in the Pieris rapae (Cabbage white butterfly). NSP is structurally different from and has no amino acid homology to any known detoxifying enzymes, and it appears to have arisen by a process of domain and gene duplication of a sequence of unknown function that is widespread in insect species and referred to as insect-allergen-repeat protein. Thus this family is found either as a single domain or as a multiple repeat-domain [].
Probab=26.26 E-value=2.8e+02 Score=22.92 Aligned_cols=84 Identities=20% Similarity=0.390 Sum_probs=57.5
Q ss_pred HHHHHhHHHHHHHHHHHHHHHHhhhcCCCChhhHHHHHHHHHHH-HHHHHHHHh--cccCCHHHHHHHhcCCchHHhhhh
Q 028441 12 REMYENFAELYAIIKATEKLEKAYVRDIISSSEYETECQKLIAH-FKTLSSTLK--DIVPSIERFADTYKMDCPAALNRL 88 (209)
Q Consensus 12 Re~~e~lAelYSII~tle~LEkAyirD~I~~~eYt~~c~rLl~Q-yk~~~~~v~--~~~~~l~~F~~~y~l~cp~A~~RL 88 (209)
|...+.+.++-.+|..-+ +..-..+=...+.|+-.+..=|-+. |+.++..+. .++..+-.|.+.-+++....++++
T Consensus 2 ~~L~~d~~dfl~lIp~~~-i~~i~~~Y~~~D~efq~~~~yl~s~~f~~l~~~l~~~pE~~~l~~yL~~~gldv~~~i~~i 80 (179)
T PF06757_consen 2 RSLQEDFQDFLDLIPMEE-IQDIVQRYYLEDAEFQAAVRYLNSSEFKQLWQQLEALPEVKALLDYLESAGLDVYYYINQI 80 (179)
T ss_pred hhHHHHHHHHHHhcCHHH-HHHHHHHHHHcCHHHHHHHHHHcChHHHHHHHHHHcCHHHHHHHHHHHHCCCCHHHHHHHH
Confidence 567788888888888554 4444433345566666655544433 566655552 456688999999999999999998
Q ss_pred hhc--CCCcee
Q 028441 89 VTS--GVPATV 97 (209)
Q Consensus 89 ~~~--G~PaTv 97 (209)
.. |+|.+.
T Consensus 81 -~~~l~~~~~~ 90 (179)
T PF06757_consen 81 -NDLLGLPPLN 90 (179)
T ss_pred -HHHHcCCcCC
Confidence 54 888663
No 35
>PF12462 Helicase_IV_N: DNA helicase IV / RNA helicase N terminal; InterPro: IPR022161 This domain family is found in bacteria and eukaryotes, and is approximately 170 amino acids in length. The family is found in association with PF00580 from PFAM. Nucleolin unwinds nucleic acid strands in the 5' to 3' direction with respect to the bound strand. It can unwind RNA-RNA duplexes, as well as DNA-DNA and DNA-RNA duplexes. Nucleolin is modulated by phosphorylation of serine and threonine residues in its N-terminal region.
Probab=25.80 E-value=1.4e+02 Score=24.79 Aligned_cols=60 Identities=12% Similarity=0.180 Sum_probs=49.7
Q ss_pred hhhhhcchHHHHHHhcccCCCCCCCCcchhhHHHHHHHHhcCCcccCCCHHHHHHHHHhHH
Q 028441 134 AVDQVHPLLSDLLGSLNKLTILPPDFEGKTKMKDWISRLSKMGAADELTEQQSRQLHFDLE 194 (209)
Q Consensus 134 a~DqLhPlL~dL~~slnk~~~lp~dFegk~kl~~Wl~kLn~M~asdeL~eeq~RqllfDle 194 (209)
..+++.+.|..+...+.++.. |+.|-.+..+..|+.+++..-.+=.++-+++.++.-+-+
T Consensus 96 ~~~~~~~~L~~~~~~i~~~~~-~~r~lt~~~~~~~~~~~r~~~~~l~~~l~~~~~~~~~r~ 155 (166)
T PF12462_consen 96 QSEQLAEVLPQWLQAIQRLSA-QDRWLTHSQVQPLLEKIRALFEALPLPLPELAQFDPCRD 155 (166)
T ss_pred HHHHHHHHHHHHHHHHHHHhc-CCCcCCHHHHHHHHHHHHHHHHcCCCCHHHHHhcchhHH
Confidence 347888999999999999997 778999999999999998876666777777777766654
No 36
>PF03206 NifW: Nitrogen fixation protein NifW; InterPro: IPR004893 Nitrogenase is a complex metalloenzyme composed of two proteins designated the Fe-protein and the MoFe-protein. Apart from these two proteins, a number of accessory proteins are essential for the maturation and assembly of nitrogenase. Even though experimental evidence suggests that these accessory proteins are required for nitrogenase activity, the exact roles played by many of these proteins in the functions of nitrogenase are unclear []. Using yeast two-hybrid screening it has been shown that NifW can interact with itself as well as NifZ. ; GO: 0009399 nitrogen fixation
Probab=25.57 E-value=1.7e+02 Score=23.05 Aligned_cols=36 Identities=22% Similarity=0.289 Sum_probs=26.6
Q ss_pred HHHHHhcCCcccCCCHHHHHHHHHh-HHHHHHHHHhh
Q 028441 168 WISRLSKMGAADELTEQQSRQLHFD-LESSYNSFMAA 203 (209)
Q Consensus 168 Wl~kLn~M~asdeL~eeq~RqllfD-le~aY~~F~~~ 203 (209)
.-.-|..-.....++|++.++..-. |..||..|..+
T Consensus 41 F~~yL~~~~~~~~~~e~~~~~~~R~~L~~AY~dFv~S 77 (105)
T PF03206_consen 41 FGQYLRAADFAPGLSEEEDWAAYRRALERAYQDFVTS 77 (105)
T ss_pred HHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHhcC
Confidence 4444444455578999998888877 78999999765
No 37
>PF14090 HTH_39: Helix-turn-helix domain
Probab=24.89 E-value=1.1e+02 Score=21.67 Aligned_cols=44 Identities=18% Similarity=0.205 Sum_probs=28.2
Q ss_pred HHHHHHHHHh--cccCCHHHHHHHhcCCchHHhh-hhhhcCCCceeec
Q 028441 55 HFKTLSSTLK--DIVPSIERFADTYKMDCPAALN-RLVTSGVPATVEH 99 (209)
Q Consensus 55 Qyk~~~~~v~--~~~~~l~~F~~~y~l~cp~A~~-RL~~~G~PaTveh 99 (209)
|.+.++..|. ..+.++ ++...|++-||+|.- .|-+.|.|+--..
T Consensus 2 Q~~rIL~~L~~~~~it~~-ea~~~~gi~~~~aRI~eLR~~G~~I~t~~ 48 (70)
T PF14090_consen 2 QCKRILAALRRGGSITTL-EARRELGIMRLAARISELRKKGYPIVTEW 48 (70)
T ss_pred HHHHHHHHHHcCCCcCHH-HHHHHcCCCCHHHHHHHHHHcCCeeeEEE
Confidence 6667777663 223333 455889988887754 6744499976444
No 38
>PRK10280 dipeptidyl carboxypeptidase II; Provisional
Probab=24.88 E-value=7.6e+02 Score=25.23 Aligned_cols=38 Identities=11% Similarity=0.129 Sum_probs=28.6
Q ss_pred CCCChhhHHHHHHHHHHHHHHHHHHHhc--ccCCHHHHHH
Q 028441 38 DIISSSEYETECQKLIAHFKTLSSTLKD--IVPSIERFAD 75 (209)
Q Consensus 38 D~I~~~eYt~~c~rLl~Qyk~~~~~v~~--~~~~l~~F~~ 75 (209)
+.|++++|.++|.++|.+.+..+..+.. .-++.+.++.
T Consensus 21 ~~i~~e~~~~a~~~~~~~~~~~i~~i~~~~~~~t~~n~i~ 60 (681)
T PRK10280 21 DQIADHHYRPAFDEGVRQKRAEIAAIALNPQAPDFNNTIL 60 (681)
T ss_pred CcCCHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHH
Confidence 5689999999999999999998887732 2345554444
No 39
>PF14425 Imm3: Immunity protein Imm3
Probab=24.44 E-value=1.1e+02 Score=24.59 Aligned_cols=75 Identities=17% Similarity=0.232 Sum_probs=55.1
Q ss_pred hhHHHHhhhhhhhHhhhhccccchhhhhcchHHHHHHhcccCCCCCCCCcchhhHHHHHHHHhcCCcccCCCHHHHHHHH
Q 028441 111 AAIVAECVQNFITAMDSLKLNMVAVDQVHPLLSDLLGSLNKLTILPPDFEGKTKMKDWISRLSKMGAADELTEQQSRQLH 190 (209)
Q Consensus 111 a~~Iae~t~~FIT~MDaLKLn~~a~DqLhPlL~dL~~slnk~~~lp~dFegk~kl~~Wl~kLn~M~asdeL~eeq~Rqll 190 (209)
..+||-+.--|. .|+-.-+=-++--+.+++.+=||+.. .+ +..+.+=|.++|-+.+.++||.+|-++|+
T Consensus 28 ~eaiar~~~eye------~lg~~EkiIv~~~igEi~l~~~~i~~---~~--~~~i~~~L~~~~~~~~~~eLt~eE~~dL~ 96 (117)
T PF14425_consen 28 SEAIARTFDEYE------NLGETEKIIVDTAIGEILLSHNKIFV---GQ--KEGITKRLSQFDFEEVKGELTQEEKEDLS 96 (117)
T ss_pred HHHHHHHHHHHH------ccCcHHHHHHHHHHHHHHhhcchHHh---hH--HHHHHHHHHhcChHHHHhHhhHHHHHHHH
Confidence 345666666663 34444555677788899999888774 32 46677889999999999999999999998
Q ss_pred HhHHHH
Q 028441 191 FDLESS 196 (209)
Q Consensus 191 fDle~a 196 (209)
.=.+.-
T Consensus 97 ~R~nkV 102 (117)
T PF14425_consen 97 QRINKV 102 (117)
T ss_pred HHHHHH
Confidence 765543
No 40
>cd08327 CARD_RAIDD Caspase activation and recruitment domain of RIP-associated ICH-1 homologous protein with a death domain. Caspase activation and recruitment domain (CARD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal CARD, which interacts with the caspase-2 CARD, and a C-terminal Death domain (DD), which interacts with the DD of PIDD. In general, CARDs are DDs associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodime
Probab=23.87 E-value=86 Score=24.00 Aligned_cols=25 Identities=16% Similarity=0.333 Sum_probs=21.4
Q ss_pred CCHHHHHHHHHhHH----HHHHHHHhhcC
Q 028441 181 LTEQQSRQLHFDLE----SSYNSFMAALP 205 (209)
Q Consensus 181 L~eeq~RqllfDle----~aY~~F~~~L~ 205 (209)
=+.+++++|+-.|. .||..|+..|.
T Consensus 49 T~~~k~~~LLdiLp~RG~~AF~~F~~aL~ 77 (94)
T cd08327 49 TSRRKTMKLLDILPSRGPKAFHAFLDSLE 77 (94)
T ss_pred ChHHHHHHHHHHHHhhChhHHHHHHHHHH
Confidence 34789999999996 79999999885
No 41
>cd08332 CARD_CASP2 Caspase activation and recruitment domain of Caspase-2. Caspase activation and recruitment domain (CARD) similar to that found in caspase-2. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Caspase-2 (also known as ICH1, NEDD2, or CASP2) is one of the most evolutionarily conserved caspases, and plays a role in apoptosis, DNA damage response, cell cycle regulation, and tumor suppression. It is localized in the nucleus and exhibits properties of both an initiator and an effector caspase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and
Probab=22.92 E-value=94 Score=23.29 Aligned_cols=26 Identities=23% Similarity=0.243 Sum_probs=21.1
Q ss_pred CHHHHHHHHHhHH----HHHHHHHhhcCCC
Q 028441 182 TEQQSRQLHFDLE----SSYNSFMAALPNA 207 (209)
Q Consensus 182 ~eeq~RqllfDle----~aY~~F~~~L~~~ 207 (209)
+.++++.|+-.|. .||..|+..|...
T Consensus 49 ~~~k~~~Lld~L~~RG~~AF~~F~~aL~~~ 78 (90)
T cd08332 49 SFSQNVALLNLLPKRGPRAFSAFCEALRET 78 (90)
T ss_pred cHHHHHHHHHHHHHhChhHHHHHHHHHHhc
Confidence 4588888887775 7999999999753
No 42
>COG2257 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]
Probab=22.80 E-value=88 Score=24.34 Aligned_cols=18 Identities=39% Similarity=0.704 Sum_probs=15.7
Q ss_pred HHHHHhHHHHHHHHHHHH
Q 028441 12 REMYENFAELYAIIKATE 29 (209)
Q Consensus 12 Re~~e~lAelYSII~tle 29 (209)
-+.|+..||+|+.|..+|
T Consensus 69 eelY~vVAEifafi~~~~ 86 (92)
T COG2257 69 EELYEVVAEIFAFIYEVD 86 (92)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 378999999999998776
No 43
>PF05816 TelA: Toxic anion resistance protein (TelA); InterPro: IPR008863 This family consists of several prokaryotic TelA like proteins. TelA and KlA are associated with tellurite resistance [] and plasmid fertility inhibition [].
Probab=22.56 E-value=1.9e+02 Score=26.57 Aligned_cols=65 Identities=18% Similarity=0.384 Sum_probs=38.9
Q ss_pred HHHHHHHhcCCchHHhhhhhhcCCCceeecccccccCCCcchhHHHHhhhhhhhHhhhhccccchhhhhcchHHHHHHhc
Q 028441 70 IERFADTYKMDCPAALNRLVTSGVPATVEHRAAAVASTTTSAAIVAECVQNFITAMDSLKLNMVAVDQVHPLLSDLLGSL 149 (209)
Q Consensus 70 l~~F~~~y~l~cp~A~~RL~~~G~PaTveh~~~~~~~~~~~a~~Iae~t~~FIT~MDaLKLn~~a~DqLhPlL~dL~~sl 149 (209)
+++|.++..+.=|.++..+ +....+.+|..+. .+++.++-. ..+++--.|.+|+.-+
T Consensus 2 v~~~~~~id~~~~~~i~~~------------------G~~~~~~~a~~s~---~iL~~v~~~--d~~~vg~~L~~L~~~~ 58 (333)
T PF05816_consen 2 VEELAKQIDLTNPDAILSF------------------GAEAQEKIAQFSD---RILDRVRNK--DSGEVGELLNELRKEM 58 (333)
T ss_pred hHHHHhhhCcCChHHHHHH------------------HHHHHHHHHHHHH---HHHHHHHHh--ccchHhHHHHHHHHHH
Confidence 4566666666666666655 1122233443333 445554332 6678888999999999
Q ss_pred ccCCCCCCCC
Q 028441 150 NKLTILPPDF 159 (209)
Q Consensus 150 nk~~~lp~dF 159 (209)
+.+. |.+|
T Consensus 59 ~~~d--p~~~ 66 (333)
T PF05816_consen 59 DELD--PSEL 66 (333)
T ss_pred HhCC--hhhh
Confidence 9987 4554
No 44
>PF08365 IGF2_C: Insulin-like growth factor II E-peptide; InterPro: IPR013576 The insulin family of proteins groups together several evolutionarily related active peptides []: these include insulin [, ], relaxin [, ], insect prothoracicotropic hormone (bombyxin) [], insulin-like growth factors (IGF1 and IGF2) [, ], mammalian Leydig cell-specific insulin-like peptide (gene INSL3), early placenta insulin-like peptide (ELIP) (gene INSL4), locust insulin-related peptide (LIRP), molluscan insulin-related peptides (MIP), and Caenorhabditis elegans insulin-like peptides. The 3D structures of a number of family members have been determined [, , ]. The fold comprises two polypeptide chains (A and B) linked by two disulphide bonds: all share a conserved arrangement of 4 cysteines in their A chain, the first of which is linked by a disulphide bond to the third, while the second and fourth are linked by interchain disulphide bonds to cysteines in the B chain. Insulin is found in many animals, and is involved in the regulation of normal glucose homeostasis. It also has other specific physiological effects, such as increasing the permeability of cells to monosaccharides, amino acids and fatty acids, and accelerating glycolysis and glycogen synthesis in the liver []. Insulin exerts its effects by interaction with a cell-surface receptor, which may also result in the promotion of cell growth []. Insulin is synthesised as a prepropeptide from which an endoplasmic reticulum-targeting sequence is cleaved to yield proinsulin. The sequence of prosinsulin contains 2 well-conserved regions (designated A and B), separated by an intervening connecting region (C), which is variable between species []. The connecting region is cleaved, liberating the active protein, which contains the A and B chains, held together by 2 disulphide bonds []. Insulin-like Growth Factor Binding Proteins (IGFBP) are a group of vertebrate secreted proteins, which bind to IGF-I and IGF-II with high affinity and modulate the biological actions of IGFs. The IGFBP family has six distinct subgroups, IGFBP-1 through 6, based on conservation of gene (intron-exon) organisation, structural similarity, and binding affinity for IGFs. Across species, IGFBP-5 exhibits the most sequence conservation, while IGFBP-6 exhibits the least sequence conservation. The IGFBPs contain inhibitor domain homologues, which are related to MEROPS protease inhibitor family I31 (equistatin, clan IX). All IGFBPs share a common domain architecture (IPR000867 from INTERPRO:IPR000716 from INTERPRO). While the N-terminal (IPR000867 from INTERPRO, IGF binding protein domain), and the C-terminal (IPR000716 from INTERPRO, thyroglobulin type-1 repeat) domains are conserved across vertebrate species, the mid-region is highly variable with respect to protease cleavage sites and phosphorylation and glycosylation sites. IGFBPs contain 16-18 conserved cysteines located in the N-terminal and the C-terminal regions, which form 8-9 disulphide bonds []. As demonstrated for human IGFBP-5, the N terminus is the primary binding site for IGF. This region, comprised of Val49, Tyr50, Pro62 and Lys68-Leu75, forms a hydrophobic patch on the surface of the protein []. The C terminus is also required for high affinity IGF binding, as well as for binding to the extracellular matrix [] and for nuclear translocation [, ] of IGFBP-3 and -5. IGFBPs are unusually pleiotropic molecules. Like other binding proteins, IGFBP can prolong the half-life of IGFs via high affinity binding of the ligands. In addition to functioning as simple carrier proteins, serum IGFBPs also serve to regulate the endocrine and paracrine/autocrine actions of IGF by modulating the IGF available to bind to signalling IGF-I receptors [, ]. Furthermore, IGFBPs can function as growth modulators independent of IGFs. For example, IGFBP-5 stimulates markers of bone formation in osteoblasts lacking functional IGFs []. The binding of IGFBP to its putative receptor on the cell membrane may stimulate the signalling pathway independent of an IGF receptor, to mediate the effects of IGFBPs in certain target cell types. IGFBP-1 and -2, but not other IGFBPs, contain a C-terminal Arg-Gly-Asp integrin-binding motif. Thus, IGFBP-1 can also stimulate cell migration of CHO and human trophoblast cells through an action mediated by alpha 5 beta 1 integrin []. Finally, IGFBPs transported into the nucleus (via the nuclear localisation signal) may also exert IGF-independent effects by transcriptional activation of genes. This domain is the C-terminal domain of insulin-like growth factor II proteins (IGF-2, also see IPR004825 from INTERPRO) in vertebrates and seems to represent the E-peptide [, ].
Probab=22.34 E-value=37 Score=24.11 Aligned_cols=16 Identities=31% Similarity=0.578 Sum_probs=13.5
Q ss_pred HHhhhhhhcCCCceeec
Q 028441 83 AALNRLVTSGVPATVEH 99 (209)
Q Consensus 83 ~A~~RL~~~G~PaTveh 99 (209)
.|.+|| +.|+|+...-
T Consensus 11 ksaqRL-RRG~PaiLRa 26 (56)
T PF08365_consen 11 KSAQRL-RRGLPAILRA 26 (56)
T ss_pred HHHHHH-HccchHHHHh
Confidence 588999 9999998654
No 45
>PLN02618 tryptophan synthase, beta chain
Probab=22.04 E-value=1.1e+02 Score=29.26 Aligned_cols=34 Identities=18% Similarity=0.441 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHhhhcCCCChhhHHHHHHHHHHHHH
Q 028441 23 AIIKATEKLEKAYVRDIISSSEYETECQKLIAHFK 57 (209)
Q Consensus 23 SII~tle~LEkAyirD~I~~~eYt~~c~rLl~Qyk 57 (209)
.++.+|+.||++|.+ ...+.+|..+-..++.+|-
T Consensus 30 ~~~~~~~~~~~~~~~-~~~~~~f~~~~~~~l~~~v 63 (410)
T PLN02618 30 TLMTALSELEAAFNA-LATDPEFQEELAGILKDYV 63 (410)
T ss_pred HHHHHHHHHHHHHHH-HhcChhhHHHHHHHHHHhc
Confidence 468899999999987 7788899999999999884
No 46
>PF14426 Imm2: Immunity protein Imm2
Probab=21.79 E-value=70 Score=23.02 Aligned_cols=32 Identities=16% Similarity=0.420 Sum_probs=24.2
Q ss_pred chhhHHHHHHH--HhcCCcccCCCHHHHHHHHHhHH
Q 028441 161 GKTKMKDWISR--LSKMGAADELTEQQSRQLHFDLE 194 (209)
Q Consensus 161 gk~kl~~Wl~k--Ln~M~asdeL~eeq~RqllfDle 194 (209)
.|.++.+|+.. ||++= +++++||+..|.+|+-
T Consensus 22 h~~~I~~~l~~~~l~~Ll--~~ip~eEae~l~~D~r 55 (60)
T PF14426_consen 22 HRNWIHKLLSEIPLNNLL--DDIPSEEAEELRHDMR 55 (60)
T ss_pred HHHHHHHHHHhCCHHHHH--hhCCHHHHHHHHHHHH
Confidence 46677788754 44444 6899999999999974
No 47
>cd08785 CARD_CARD9-like Caspase activation and recruitment domain of CARD9 and related proteins. Caspase activation and recruitment domain (CARD) found in CARD9, CARD14 (CARMA2), CARD10 (CARMA3), CARD11 (CARMA1) and BCL10. BCL10 (B-cell lymphoma 10), together with Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1), are integral components of the CBM signalosome. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells), and with CARD11 to form L-CBM (CBM complex in lymphoid immune cells), which mediates activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. BCL10/Malt1 also associates with CARD10, which is more widely expressed and is not restricted to hematopoietic cells, to play a role in GPCR-induced NF-kB activation. CARD14 has also been shown to associate with BCL10. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inf
Probab=21.20 E-value=92 Score=23.49 Aligned_cols=27 Identities=19% Similarity=0.266 Sum_probs=22.7
Q ss_pred cCCCHHHHHHHHHhHH----HHHHHHHhhcC
Q 028441 179 DELTEQQSRQLHFDLE----SSYNSFMAALP 205 (209)
Q Consensus 179 deL~eeq~RqllfDle----~aY~~F~~~L~ 205 (209)
.....+++++|+.+|. .||.+|..+|+
T Consensus 45 ~~~r~~ka~~LLdiL~~rG~~Af~~F~~aL~ 75 (86)
T cd08785 45 LPIRANRTGRLLDILATRGKRGYVAFLESLE 75 (86)
T ss_pred cccHHHHHHHHHHHHHhcCcchHHHHHHHHH
Confidence 3445699999999998 69999999986
No 48
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=21.10 E-value=86 Score=21.73 Aligned_cols=24 Identities=38% Similarity=0.501 Sum_probs=20.2
Q ss_pred HHHHHHHhcCCchHHhhhhhhcCC
Q 028441 70 IERFADTYKMDCPAALNRLVTSGV 93 (209)
Q Consensus 70 l~~F~~~y~l~cp~A~~RL~~~G~ 93 (209)
|+.|++++++.-+.|.+++-+.|+
T Consensus 8 Ie~~A~~~~~s~~ea~~~~~~~~~ 31 (62)
T PF12668_consen 8 IEEFAKKLNISGEEAYNYFKRSGV 31 (62)
T ss_pred HHHHHHHHCcCHHHHHHHHHHcCc
Confidence 689999999999999999944344
No 49
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=21.06 E-value=1e+02 Score=22.61 Aligned_cols=36 Identities=36% Similarity=0.644 Sum_probs=25.5
Q ss_pred cchhhhhcch-HHHHHHhcccCCCCCCCCcchhhHHHHHHHHhcC
Q 028441 132 MVAVDQVHPL-LSDLLGSLNKLTILPPDFEGKTKMKDWISRLSKM 175 (209)
Q Consensus 132 ~~a~DqLhPl-L~dL~~slnk~~~lp~dFegk~kl~~Wl~kLn~M 175 (209)
|+.++| ||+ +.|++.-+|-+.. ..++++||......
T Consensus 18 mK~r~~-~Plt~~EIl~~ls~~d~-------~~~~~~~L~~~~~~ 54 (75)
T cd07977 18 MKKRHQ-HPLTLDEILDYLSLLDI-------GPKLKEWLKSEALV 54 (75)
T ss_pred HHhcCC-CCccHHHHHHHHhccCc-------cHHHHHHHHhhhhc
Confidence 467777 887 6677777765443 37889999876655
No 50
>PF01756 ACOX: Acyl-CoA oxidase; InterPro: IPR002655 Acyl-CoA oxidase (ACO) acts on CoA derivatives of fatty acids with chain lengths from 8 to 18. It catalyses the first and rate-determining step of the peroxisomal beta-oxidation of fatty acids []. Acyl-CoA oxidase is a homodimer and the polypeptide chain of the subunit is folded into the N-terminal alpha-domain, beta-domain, and C-terminal alpha-domain []. Functional differences between the peroxisomal acyl-CoA oxidases and the mitochondrial acyl-CoA dehydrogenases are attributed to structural differences in the FAD environments []. Experimental data indicate that, in the pumpkin, the expression pattern of ACOX is very similar to that of the glyoxysomal enzyme 3-ketoacyl-CoA thiolase []. In humans, defects in ACOX1 are the cause of pseudoneonatal adrenoleukodystrophy, also known as peroxisomal acyl-CoA oxidase deficiency. Pseudo-NALD is a peroxisomal single-enzyme disorder. Clinical features include mental retardation, leukodystrophy, seizures, mild hepatomegaly and hearing deficit. Pseudo-NALD is characterised by increased plasma levels of very-long chain fatty acids due to a decrease in, or absence of, peroxisome acyl-CoA oxidase activity, despite the peroxisomes being intact and functioning. This entry represents the Acyl-CoA oxidase C-terminal.; GO: 0003997 acyl-CoA oxidase activity, 0006635 fatty acid beta-oxidation, 0055114 oxidation-reduction process, 0005777 peroxisome; PDB: 2FON_A 1IS2_B 2DDH_A 1W07_B.
Probab=20.93 E-value=4.5e+02 Score=21.56 Aligned_cols=52 Identities=13% Similarity=0.175 Sum_probs=34.3
Q ss_pred cCChhHHHHHHhHHHHHHHHHHHHHHHHhhhcCCCChhhHHHHHHHHHHHHH
Q 028441 6 WNDKREREMYENFAELYAIIKATEKLEKAYVRDIISSSEYETECQKLIAHFK 57 (209)
Q Consensus 6 ~~~~~eRe~~e~lAelYSII~tle~LEkAyirD~I~~~eYt~~c~rLl~Qyk 57 (209)
..++..|.....|+.||++-.-.+++.--+--+++|+++-...-..+...+.
T Consensus 72 ~~~~~~~~vL~~L~~Lyal~~i~~~~g~fl~~g~ls~~~~~~l~~~i~~l~~ 123 (187)
T PF01756_consen 72 CADPEVRQVLRQLCQLYALSIIEENAGDFLEHGYLSPEQIKALRKAIEELCA 123 (187)
T ss_dssp -SSTTHHHHHHHHHHHHHHHHHHHTHHHHHHTTSS-HHHHHHHHHHHHHHHH
T ss_pred CCChHHHHHHHHHHHHHhHHHHHHHHHHHHhCCcCCHHHHHHHHHHHHHHHH
Confidence 4578899999999999987766666655566677888775444333333333
No 51
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=20.49 E-value=87 Score=26.76 Aligned_cols=75 Identities=23% Similarity=0.438 Sum_probs=44.8
Q ss_pred HHhhhhhhcCCCceeecccccccCCCcchh-HHHHhhhhhhhHhhhhccccchhhhhcch------HHHHHHhcccCCCC
Q 028441 83 AALNRLVTSGVPATVEHRAAAVASTTTSAA-IVAECVQNFITAMDSLKLNMVAVDQVHPL------LSDLLGSLNKLTIL 155 (209)
Q Consensus 83 ~A~~RL~~~G~PaTveh~~~~~~~~~~~a~-~Iae~t~~FIT~MDaLKLn~~a~DqLhPl------L~dL~~slnk~~~l 155 (209)
+-+-||.+..+|+.-+- +..|| +|-|||+-||.+.=. .|.|.-|-. =-||+-+|..|.=
T Consensus 36 ANV~RIMK~~lP~naKI--------sKDAKE~vQECVSEfISFvT~-----EAsekC~~EkRKTIngdDllwAm~tLGF- 101 (168)
T KOG0869|consen 36 ANVSRIMKKALPANAKI--------SKDAKETVQECVSEFISFVTG-----EASEKCQREKRKTINGDDLLWAMSTLGF- 101 (168)
T ss_pred HHHHHHHHhcCCccccc--------chHHHHHHHHHHHHHHHHHhh-----HHHHHHHHHhcCcccHHHHHHHHHHcCc-
Confidence 34678988899976443 23455 788999999988732 233332222 1367777777653
Q ss_pred CCCCcchhhHHHHHHHHhc
Q 028441 156 PPDFEGKTKMKDWISRLSK 174 (209)
Q Consensus 156 p~dFegk~kl~~Wl~kLn~ 174 (209)
.||- .-|+-+|.|-..
T Consensus 102 -e~Y~--eplkiyL~kYRe 117 (168)
T KOG0869|consen 102 -ENYA--EPLKIYLQKYRE 117 (168)
T ss_pred -HhHH--HHHHHHHHHHHH
Confidence 3443 445556666543
No 52
>PRK04346 tryptophan synthase subunit beta; Validated
Probab=20.45 E-value=1.2e+02 Score=28.70 Aligned_cols=34 Identities=26% Similarity=0.518 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHhhhcCCCChhhHHHHHHHHHHHHH
Q 028441 23 AIIKATEKLEKAYVRDIISSSEYETECQKLIAHFK 57 (209)
Q Consensus 23 SII~tle~LEkAyirD~I~~~eYt~~c~rLl~Qyk 57 (209)
.++.+|+.||++|.+ ...+.+|..+-..|+..|-
T Consensus 22 ~~~~~~~~~~~~~~~-~~~~~~f~~~~~~~~~~~~ 55 (397)
T PRK04346 22 TLMPALEELEEAYEK-AKNDPEFQAELDYLLKNYV 55 (397)
T ss_pred HHHHHHHHHHHHHHH-HhcCHHHHHHHHHHHHHhc
Confidence 468899999999987 7778889999999999983
No 53
>PF12719 Cnd3: Nuclear condensing complex subunits, C-term domain
Probab=20.33 E-value=2.7e+02 Score=24.64 Aligned_cols=152 Identities=20% Similarity=0.212 Sum_probs=94.4
Q ss_pred HHHHHHHHHhhhcCCCChhhHHHHHHHHHHHHHHHHH----HHhcccCCHHHHHHHhcCCchHHhhhhhhcCCCceeecc
Q 028441 25 IKATEKLEKAYVRDIISSSEYETECQKLIAHFKTLSS----TLKDIVPSIERFADTYKMDCPAALNRLVTSGVPATVEHR 100 (209)
Q Consensus 25 I~tle~LEkAyirD~I~~~eYt~~c~rLl~Qyk~~~~----~v~~~~~~l~~F~~~y~l~cp~A~~RL~~~G~PaTveh~ 100 (209)
.++.|-+=|-++.+.+++ +...-.+|+-.|=.-.. .++ .-+.-|...|.-..|..-.++ ..++--|+..-
T Consensus 132 ~~a~EGl~KLlL~~~i~~--~~~vL~~Lll~yF~p~t~~~~~Lr---Q~L~~Ffp~y~~s~~~~Q~~l-~~~f~~~l~~~ 205 (298)
T PF12719_consen 132 AIAVEGLCKLLLSGRISD--PPKVLSRLLLLYFNPSTEDNQRLR---QCLSVFFPVYASSSPENQERL-AEAFLPTLRTL 205 (298)
T ss_pred HHHHHHHHHHHhcCCCCc--HHHHHHHHHHHHcCcccCCcHHHH---HHHHHHHHHHHcCCHHHHHHH-HHHHHHHHHHH
Confidence 456778888888888887 44444455554432111 011 126789999999989888888 55544344332
Q ss_pred cccccC--CCcchhHHHHhhhhhhhHhhhhccccchhhh-----hcchHHHHHHhcccCCCCCCCCcchhhHHHHHHHHh
Q 028441 101 AAAVAS--TTTSAAIVAECVQNFITAMDSLKLNMVAVDQ-----VHPLLSDLLGSLNKLTILPPDFEGKTKMKDWISRLS 173 (209)
Q Consensus 101 ~~~~~~--~~~~a~~Iae~t~~FIT~MDaLKLn~~a~Dq-----LhPlL~dL~~slnk~~~lp~dFegk~kl~~Wl~kLn 173 (209)
.....+ +......+..+.+.||-.+|.-++.-..... .|..|. +.-++.+.. .....+...+-+..-|+
T Consensus 206 ~~~~~~~~~~~~~v~~~~v~~~lv~lt~~~~~~~~~~~~~~~~~~h~~La--~~il~~i~~--~~~~~~~~~k~~~~~L~ 281 (298)
T PF12719_consen 206 SNAPDELDSPLAMVSPSQVASFLVDLTDPSKLVKESNQEIQNESVHVDLA--IDILNEILS--DPEKEKEERKALCKALS 281 (298)
T ss_pred HhCcccccCchhhCCHHHHHHHHHHHCChhhccCccccccccccHHHHHH--HHHHHHHHh--ccccchHHHHHHHHHHh
Confidence 211111 2233345888899999999999998887755 777776 444455543 12223446667788888
Q ss_pred cCCcc--cCCCHHHH
Q 028441 174 KMGAA--DELTEQQS 186 (209)
Q Consensus 174 ~M~as--deL~eeq~ 186 (209)
++.-+ ++++.+..
T Consensus 282 ~L~i~~~~~~~~~~l 296 (298)
T PF12719_consen 282 KLEISLDEKLSSDKL 296 (298)
T ss_pred ccccCcCCCcchhhc
Confidence 88887 56665544
No 54
>PF08828 DSX_dimer: Doublesex dimerisation domain; InterPro: IPR014932 Doublesex (DSX) is a transcription factor that regulates somatic sexual differences in Drosophila. The structure has revealed a novel dimeric arrangement of ubiquitin-associated folds that has not previously been identified in a transcription factor []. ; PDB: 1ZV1_B 2JZ0_A 2JZ1_B.
Probab=20.13 E-value=85 Score=22.74 Aligned_cols=42 Identities=26% Similarity=0.345 Sum_probs=25.2
Q ss_pred hhhHHHHHHHHHHHHHHHHH-------HHhcccCCHHHHHHHhcCCchHHhhhhhhcCCCc
Q 028441 42 SSEYETECQKLIAHFKTLSS-------TLKDIVPSIERFADTYKMDCPAALNRLVTSGVPA 95 (209)
Q Consensus 42 ~~eYt~~c~rLl~Qyk~~~~-------~v~~~~~~l~~F~~~y~l~cp~A~~RL~~~G~Pa 95 (209)
.++...-|.|||.+|.--+. .+++.=.|+++ |..|| .+|.-.
T Consensus 3 ~e~Ll~~cqkLlEkf~YpWEmmpLmyVILK~A~~D~ee-----------A~rrI-~E~~~~ 51 (62)
T PF08828_consen 3 DEELLERCQKLLEKFRYPWEMMPLMYVILKYADADVEE-----------ASRRI-DEAKNV 51 (62)
T ss_dssp HHHHHHHHHHHHHHTT--GGGHHHHHHHHHHTTT-HHH-----------HHHHH-HH----
T ss_pred HHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCHHH-----------HHHHH-HHHHHH
Confidence 45577889999999985544 23555556665 78888 766543
No 55
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=20.09 E-value=83 Score=23.45 Aligned_cols=45 Identities=13% Similarity=0.178 Sum_probs=30.5
Q ss_pred hHHHHHHHHHHHHH----HHHHHHhcccCCHHHHHHHhcCCchHHhhhh
Q 028441 44 EYETECQKLIAHFK----TLSSTLKDIVPSIERFADTYKMDCPAALNRL 88 (209)
Q Consensus 44 eYt~~c~rLl~Qyk----~~~~~v~~~~~~l~~F~~~y~l~cp~A~~RL 88 (209)
.|.+.+.+|+.+.. ..-..+...|.++=..+....+|.|.|...+
T Consensus 51 ~~~~~~~~Ll~~L~~~~~~~~~~~~~~f~~~~~~l~dl~~D~P~a~~~l 99 (113)
T smart00544 51 TYREMYSVLLSRLCQANVISTKQFEKGFWRLLEDIEDLELDIPNAWRNL 99 (113)
T ss_pred cHHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHhhChhhhcccccHHHHH
Confidence 47777777777654 1222445556666677777888999888877
Done!