Query psy13110
Match_columns 183
No_of_seqs 147 out of 334
Neff 4.1
Searched_HMMs 46136
Date Fri Aug 16 19:52:07 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13110.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13110hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00786 PBD: P21-Rho-binding 99.9 4.7E-23 1E-27 142.8 4.4 59 107-165 1-59 (59)
2 KOG0578|consensus 99.8 2.3E-21 5E-26 182.2 4.5 78 101-179 21-98 (550)
3 cd01093 CRIB_PAK_like PAK (p21 99.8 4.5E-20 9.8E-25 122.8 4.9 46 106-151 1-46 (46)
4 smart00285 PBD P21-Rho-binding 99.6 2.3E-16 5.1E-21 100.4 3.5 35 108-142 1-35 (36)
5 cd00132 CRIB PAK (p21 activate 99.6 1.6E-15 3.5E-20 99.2 3.0 40 107-147 2-42 (42)
6 KOG3671|consensus 98.1 6.7E-07 1.4E-11 84.8 0.7 62 101-162 229-297 (569)
7 PF08671 SinI: Anti-repressor 93.4 0.083 1.8E-06 32.8 2.5 21 132-152 1-24 (30)
8 PF14229 DUF4332: Domain of un 69.2 8.4 0.00018 30.0 4.1 39 129-167 58-98 (122)
9 PF12096 DUF3572: Protein of u 59.9 16 0.00035 27.8 4.0 37 130-166 18-57 (88)
10 PF10126 Nit_Regul_Hom: Unchar 53.0 7.9 0.00017 30.7 1.4 30 128-166 35-65 (110)
11 cd08315 Death_TRAILR_DR4_DR5 D 51.7 30 0.00065 26.0 4.3 40 130-169 15-62 (96)
12 cd08815 Death_TNFRSF25_DR3 Dea 43.9 40 0.00087 25.1 3.8 39 130-168 7-53 (77)
13 PF00301 Rubredoxin: Rubredoxi 39.8 13 0.00027 25.0 0.6 16 122-137 11-36 (47)
14 COG0824 FcbC Predicted thioest 38.9 43 0.00093 26.0 3.5 30 114-143 105-134 (137)
15 PF13351 DUF4099: Protein of u 37.8 32 0.0007 25.3 2.5 30 135-166 7-36 (85)
16 PF13619 KTSC: KTSC domain 36.4 44 0.00094 22.7 2.9 14 128-141 29-43 (60)
17 cd08306 Death_FADD Fas-associa 35.9 51 0.0011 24.1 3.3 38 131-168 11-56 (86)
18 cd01670 Death Death Domain: a 33.8 77 0.0017 21.5 3.8 38 132-169 9-53 (79)
19 cd08316 Death_FAS_TNFRSF6 Deat 33.4 72 0.0016 24.3 3.9 39 131-169 17-64 (97)
20 cd08313 Death_TNFR1 Death doma 32.3 45 0.00099 24.5 2.5 37 130-166 7-51 (80)
21 PF04255 DUF433: Protein of un 32.1 1.1E+02 0.0024 20.5 4.3 33 131-164 18-56 (56)
22 cd08779 Death_PIDD Death Domai 30.8 83 0.0018 23.0 3.7 39 131-169 11-57 (86)
23 PF03868 Ribosomal_L6e_N: Ribo 30.6 21 0.00046 25.1 0.5 13 5-17 25-37 (59)
24 cd08784 Death_DRs Death Domain 29.3 1E+02 0.0022 22.0 4.0 35 133-167 11-52 (79)
25 smart00005 DEATH DEATH domain, 28.5 1.1E+02 0.0025 21.2 4.0 38 132-169 16-61 (88)
26 PF03562 MltA: MltA specific i 26.9 36 0.00078 28.2 1.4 42 116-161 96-148 (158)
27 PRK10800 acyl-CoA thioesterase 24.8 91 0.002 23.1 3.1 25 116-140 105-129 (130)
28 COG2441 Predicted butyrate kin 24.4 14 0.0003 34.3 -1.6 48 120-167 1-50 (374)
29 COG2442 Uncharacterized conser 23.5 1.5E+02 0.0033 21.8 4.0 49 119-168 12-72 (79)
30 cd04790 HTH_Cfa-like_unk Helix 22.9 1.3E+02 0.0027 24.7 3.8 35 134-168 119-161 (172)
31 PF00969 MHC_II_beta: Class II 21.8 80 0.0017 22.7 2.2 27 114-140 20-46 (75)
32 PF00531 Death: Death domain; 21.7 95 0.0021 21.1 2.5 36 132-167 11-53 (83)
33 cd08804 Death_ank2 Death domai 20.7 1.9E+02 0.0041 21.1 4.0 38 132-169 14-59 (84)
34 PRK04217 hypothetical protein; 20.6 2.7E+02 0.0059 21.6 5.1 33 130-162 41-80 (110)
35 PF00570 HRDC: HRDC domain Blo 20.4 70 0.0015 21.3 1.6 31 131-161 38-68 (68)
No 1
>PF00786 PBD: P21-Rho-binding domain; InterPro: IPR000095 The molecular bases of the versatile functions of Rho-like GTPases are still unknown. Small domains that bind Cdc42p- and/or Rho-like small GTPases. Also known as the Cdc42/Rac interactive binding (CRIB). The Cdc42/Rac interactive binding (CRIB) region has been shown to inhibit transcriptional activation and cell transformation mediated by the Ras-Rac pathway []. In fission yeast pak1+ encodes a protein kinase that interacts with Cdc42p and is involved in the control of cell polarity and mating [].; GO: 0005515 protein binding; PDB: 2OV2_O 1EES_B 2ODB_B 1E0A_B 2QME_I 1F3M_B 3PCS_H 1T84_A 2K42_A 1EJ5_A ....
Probab=99.87 E-value=4.7e-23 Score=142.81 Aligned_cols=59 Identities=58% Similarity=1.001 Sum_probs=52.4
Q ss_pred ccCCCCCCeeeeeeeeeCCCcccccCcHHHHHHHHHcCCCHHHHhhChHHHHHHHHhhc
Q psy13110 107 VISNPTNFEHTVHVGFDAHTGEFTGMPEAWARLLMSSNISKLEQKKNPQAVLDVLNWFD 165 (183)
Q Consensus 107 ~IS~PtNF~H~~HVg~D~~TGeftGLP~eW~~lL~~sGISk~E~k~NpqaVldVl~Fy~ 165 (183)
+||.|+||+|++|||||+++|.|.|||++|+.+|..+|||++|+++||+++++|++||+
T Consensus 1 ~Is~P~nf~H~~HVg~d~~~g~~~glp~ew~~~l~~~~it~~~~~~~~~~~~~v~~f~~ 59 (59)
T PF00786_consen 1 DISNPTNFKHVAHVGWDPNTGGFTGLPPEWEKLLKSSGITEEEIKDNPQAVFDVLQFYQ 59 (59)
T ss_dssp TB---EEEEEEEEEEEETTTTEEES--HHHHHHHHSCTTSHHHHCCHHHHHHHHHHHHH
T ss_pred CCCCCCCCcceeeeccCCCccccccCCHHHHhhccccCCCHHHhhcCCcceeeeeeecC
Confidence 59999999999999999999999999999999999999999999999999999999984
No 2
>KOG0578|consensus
Probab=99.83 E-value=2.3e-21 Score=182.24 Aligned_cols=78 Identities=50% Similarity=0.814 Sum_probs=70.0
Q ss_pred CCCCCCccCCCCCCeeeeeeeeeCCCcccccCcHHHHHHHHHcCCCHHHHhhChHHHHHHHHhhcccccccCCCccccc
Q psy13110 101 PEAEKPVISNPTNFEHTVHVGFDAHTGEFTGMPEAWARLLMSSNISKLEQKKNPQAVLDVLNWFDNSTKEAKGSKYMTT 179 (183)
Q Consensus 101 ~~~~k~~IS~PtNF~H~~HVg~D~~TGeftGLP~eW~~lL~~sGISk~E~k~NpqaVldVl~Fy~~~~~~~~~~K~m~~ 179 (183)
+...+++||.|+||+|.+|||||++||+|+|||++|++||+.++|++.|+..||+||+++|+||.........++ |.+
T Consensus 21 ~~~~~s~iS~P~nf~h~vHvGfd~~tg~ftGlP~~W~~Ll~~s~it~~e~~~~~~avi~~~~~y~~~t~~~~~~~-l~~ 98 (550)
T KOG0578|consen 21 KKSGKSEISSPSNFEHRVHVGFDPVTGEFTGLPKQWQRLLQSSEITKREQPLNPPAVITALQFYESKTLSRGISK-LRS 98 (550)
T ss_pred cccCCCccCCCCCccceeecccCCCcccccCCcHHHHHHhcchhhcccccccCChhheehhhhccccccccCccc-cCc
Confidence 335678999999999999999999999999999999999999999999999999999999999998876555566 443
No 3
>cd01093 CRIB_PAK_like PAK (p21 activated kinase) Binding Domain (PBD), binds Cdc42p- and/or Rho-like small GTPases; also known as the Cdc42/Rac interactive binding (CRIB) motif; has been shown to inhibit transcriptional activation and cell transformation mediated by the Ras-Rac pathway. This subgroup of CRIB/PBD-domains is found N-terminal of Serine/Threonine kinase domains in PAK and PAK-like proteins.
Probab=99.80 E-value=4.5e-20 Score=122.83 Aligned_cols=46 Identities=72% Similarity=1.170 Sum_probs=43.7
Q ss_pred CccCCCCCCeeeeeeeeeCCCcccccCcHHHHHHHHHcCCCHHHHh
Q psy13110 106 PVISNPTNFEHTVHVGFDAHTGEFTGMPEAWARLLMSSNISKLEQK 151 (183)
Q Consensus 106 ~~IS~PtNF~H~~HVg~D~~TGeftGLP~eW~~lL~~sGISk~E~k 151 (183)
+.||.|+||+|++|||||+++|+|+|||++|+++|+++|||++|++
T Consensus 1 ~~IS~P~n~~H~~Hv~~d~~~g~f~glP~eW~~ll~~sgis~~e~~ 46 (46)
T cd01093 1 PEISSPTNFKHRVHVGFDPQTGEFTGLPEEWQRLLKSSGITKEEQK 46 (46)
T ss_pred CccCCCCCceeeeEeeECCCCCcccCCCHHHHHHHHHcCCCHHHcC
Confidence 3699999999999999999999999999999999999999999974
No 4
>smart00285 PBD P21-Rho-binding domain. Small domains that bind Cdc42p- and/or Rho-like small GTPases. Also known as the Cdc42/Rac interactive binding (CRIB).
Probab=99.62 E-value=2.3e-16 Score=100.37 Aligned_cols=35 Identities=60% Similarity=1.173 Sum_probs=33.2
Q ss_pred cCCCCCCeeeeeeeeeCCCcccccCcHHHHHHHHH
Q psy13110 108 ISNPTNFEHTVHVGFDAHTGEFTGMPEAWARLLMS 142 (183)
Q Consensus 108 IS~PtNF~H~~HVg~D~~TGeftGLP~eW~~lL~~ 142 (183)
||.|+||+|++|||||+++|+|+|||++|+++|+.
T Consensus 1 IS~P~nf~H~~HVg~d~~~~~f~glp~ew~~~l~~ 35 (36)
T smart00285 1 ISTPTDFKHIAHVGFDGQTGEFTGLPTEWESLLKT 35 (36)
T ss_pred CCCCCCCcEEEEeeECCCCCccCCCCHHHHHHhcc
Confidence 89999999999999999888999999999999964
No 5
>cd00132 CRIB PAK (p21 activated kinase) Binding Domain (PBD), binds Cdc42p- and/or Rho-like small GTPases; also known as the Cdc42/Rac interactive binding (CRIB) motif; has been shown to inhibit transcriptional activation and cell transformation mediated by the Ras-Rac pathway. CRIB-containing effector proteins are functionally diverse and include serine/threonine kinases, tyrosine kinases, actin-binding proteins, and adapter molecules.
Probab=99.56 E-value=1.6e-15 Score=99.23 Aligned_cols=40 Identities=38% Similarity=0.603 Sum_probs=37.6
Q ss_pred ccCCCCCCeeeeeeeeeCCCcccc-cCcHHHHHHHHHcCCCH
Q psy13110 107 VISNPTNFEHTVHVGFDAHTGEFT-GMPEAWARLLMSSNISK 147 (183)
Q Consensus 107 ~IS~PtNF~H~~HVg~D~~TGeft-GLP~eW~~lL~~sGISk 147 (183)
+||.|+||+|++|||||+. |.+. |||++|+++|+.+|||.
T Consensus 2 ~IS~Ptnf~H~~HvG~d~~-g~~~~~~p~~w~~l~~~~~is~ 42 (42)
T cd00132 2 EISTPTDFKHISHVGWDGV-GFDGANLPPDLQSLFQTAGISA 42 (42)
T ss_pred cccCCCCcCcccccCCCCC-CccccCCCHHHHHHHHHccCCC
Confidence 6999999999999999999 9777 99999999999999983
No 6
>KOG3671|consensus
Probab=98.12 E-value=6.7e-07 Score=84.83 Aligned_cols=62 Identities=29% Similarity=0.457 Sum_probs=52.1
Q ss_pred CCCCCCccCCCCCCeeeeeeeeeCCCc-cc----ccCcHHHHHHHHHcCCCHHHHhh--ChHHHHHHHH
Q psy13110 101 PEAEKPVISNPTNFEHTVHVGFDAHTG-EF----TGMPEAWARLLMSSNISKLEQKK--NPQAVLDVLN 162 (183)
Q Consensus 101 ~~~~k~~IS~PtNF~H~~HVg~D~~TG-ef----tGLP~eW~~lL~~sGISk~E~k~--NpqaVldVl~ 162 (183)
+..++.+||+|+||.|+.|||||+++| .. ..+++....+|..+||++.++.+ ...+|+|+|+
T Consensus 229 sk~tk~disaPtnf~h~~hVgwd~~~gf~~~~~p~~~dp~~nn~~s~agise~~l~~~~t~~fi~~fi~ 297 (569)
T KOG3671|consen 229 SKITKADISAPTNFPHIPHVGWDEQVGFDSAPAPNNNDPPLNNLFSSAGISEAQLTERDTMKFIYDFIQ 297 (569)
T ss_pred cccccccCCCCCCCccccccCCCcCCCcccCCCCCCCChhhhcccccCCCCcccccchhhccccccchh
Confidence 446889999999999999999999999 44 35889999999999999999875 5566666653
No 7
>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=93.37 E-value=0.083 Score=32.79 Aligned_cols=21 Identities=33% Similarity=0.629 Sum_probs=14.8
Q ss_pred CcHHHHHHHH---HcCCCHHHHhh
Q psy13110 132 MPEAWARLLM---SSNISKLEQKK 152 (183)
Q Consensus 132 LP~eW~~lL~---~sGISk~E~k~ 152 (183)
|++||..|++ .+|||++|+++
T Consensus 1 LD~EW~~Li~eA~~~Gls~eeir~ 24 (30)
T PF08671_consen 1 LDEEWVELIKEAKESGLSKEEIRE 24 (30)
T ss_dssp --HHHHHHHHHHHHTT--HHHHHH
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHH
Confidence 6899999998 68999999874
No 8
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=69.20 E-value=8.4 Score=29.95 Aligned_cols=39 Identities=23% Similarity=0.391 Sum_probs=32.1
Q ss_pred cccCcHHHHHHHHHcCC-CHHHHhh-ChHHHHHHHHhhccc
Q psy13110 129 FTGMPEAWARLLMSSNI-SKLEQKK-NPQAVLDVLNWFDNS 167 (183)
Q Consensus 129 ftGLP~eW~~lL~~sGI-Sk~E~k~-NpqaVldVl~Fy~~~ 167 (183)
..||.++|..||..+|| |-.|+.+ ||+.+.+-|.=++..
T Consensus 58 i~gi~~~~a~LL~~AGv~Tv~~LA~~~p~~L~~~l~~~n~~ 98 (122)
T PF14229_consen 58 IPGIGPQYAELLEHAGVDTVEELAQRNPQNLHQKLGRLNRK 98 (122)
T ss_pred cCCCCHHHHHHHHHhCcCcHHHHHhCCHHHHHHHHHHHHHH
Confidence 45999999999999999 7888886 999988777665443
No 9
>PF12096 DUF3572: Protein of unknown function (DUF3572); InterPro: IPR021955 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 100 amino acids in length.
Probab=59.95 E-value=16 Score=27.75 Aligned_cols=37 Identities=24% Similarity=0.403 Sum_probs=32.7
Q ss_pred ccCcHHHHHHHHHcCCCHHHHhh---ChHHHHHHHHhhcc
Q psy13110 130 TGMPEAWARLLMSSNISKLEQKK---NPQAVLDVLNWFDN 166 (183)
Q Consensus 130 tGLP~eW~~lL~~sGISk~E~k~---NpqaVldVl~Fy~~ 166 (183)
.|=|+-..++|..+|++.++++. .|++..-||+|+-.
T Consensus 18 a~d~e~l~rFLa~TG~~p~~LR~~a~dp~FL~~VLdFl~~ 57 (88)
T PF12096_consen 18 AGDPERLPRFLALTGLSPDDLRAAAGDPAFLAAVLDFLLM 57 (88)
T ss_pred hCCHHHHHHHHHHhCCCHHHHHHHccChHHHHHHHHHHHc
Confidence 35588899999999999999996 99999999999854
No 10
>PF10126 Nit_Regul_Hom: Uncharacterized protein, homolog of nitrogen regulatory protein PII; InterPro: IPR019296 This family consists of various hypothetical archaeal proteins. It includes a putative nitrogen regulatory protein PII homolog.
Probab=52.98 E-value=7.9 Score=30.67 Aligned_cols=30 Identities=27% Similarity=0.790 Sum_probs=23.7
Q ss_pred ccccC-cHHHHHHHHHcCCCHHHHhhChHHHHHHHHhhcc
Q psy13110 128 EFTGM-PEAWARLLMSSNISKLEQKKNPQAVLDVLNWFDN 166 (183)
Q Consensus 128 eftGL-P~eW~~lL~~sGISk~E~k~NpqaVldVl~Fy~~ 166 (183)
+|.|| |.+|+-++. +++|+-++.+++=+.+
T Consensus 35 eYkGmSP~~wkgf~l---------~EDpe~ai~~I~d~s~ 65 (110)
T PF10126_consen 35 EYKGMSPQDWKGFLL---------DEDPEMAIKAINDLSE 65 (110)
T ss_pred eecCCChHHhcCccc---------ccCHHHHHHHHHHhcc
Confidence 57788 899998863 3789999998887743
No 11
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. 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=51.71 E-value=30 Score=26.01 Aligned_cols=40 Identities=23% Similarity=0.394 Sum_probs=30.7
Q ss_pred ccCc-HHHHHHHHHcCCCHHHHhh-------ChHHHHHHHHhhccccc
Q psy13110 130 TGMP-EAWARLLMSSNISKLEQKK-------NPQAVLDVLNWFDNSTK 169 (183)
Q Consensus 130 tGLP-~eW~~lL~~sGISk~E~k~-------NpqaVldVl~Fy~~~~~ 169 (183)
..+| .+|.++....|+|+.+|.. |.+.+++.|....+...
T Consensus 15 ~~V~~~~Wk~laR~LGLse~~I~~i~~~~~~~~eq~~qmL~~W~~~~G 62 (96)
T cd08315 15 KEVPFDSWNRLMRQLGLSENEIDVAKANERVTREQLYQMLLTWVNKTG 62 (96)
T ss_pred HHCCHHHHHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHhhC
Confidence 4577 7899999999999999874 45677888876655443
No 12
>cd08815 Death_TNFRSF25_DR3 Death domain of Tumor Necrosis Factor Receptor superfamily 25. Death Domain (DD) found in Tumor Necrosis Factor (TNF) receptor superfamily 25 (TNFRSF25), also known as TRAMP (TNF receptor-related apoptosis-mediating protein), LARD, APO-3, WSL-1, or DR3 (Death Receptor-3). TNFRSF25 is primarily expressed in T cells, is activated by binding to its ligand TL1A, and plays an important role in T-cell function. 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=43.90 E-value=40 Score=25.10 Aligned_cols=39 Identities=10% Similarity=0.323 Sum_probs=29.5
Q ss_pred ccCc-HHHHHHHHHcCCCHHHHhh-------ChHHHHHHHHhhcccc
Q psy13110 130 TGMP-EAWARLLMSSNISKLEQKK-------NPQAVLDVLNWFDNST 168 (183)
Q Consensus 130 tGLP-~eW~~lL~~sGISk~E~k~-------NpqaVldVl~Fy~~~~ 168 (183)
..+| +.|.+++..-|+|+.+++. ..++.++.|+-.-+.+
T Consensus 7 D~VP~~~wk~F~R~LGLsdn~Ie~~E~~~~~~rda~y~ML~~W~~q~ 53 (77)
T cd08815 7 DAVPARRWKEFVRTLGLREAEIEAVELEIGRFRDQQYEMLKRWRQQQ 53 (77)
T ss_pred ccCChHHHHHHHHHcCCcHhHHHHHHhcccchHHHHHHHHHHHHHcC
Confidence 4454 8999999999999998873 4578888876654433
No 13
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=39.82 E-value=13 Score=25.03 Aligned_cols=16 Identities=31% Similarity=1.057 Sum_probs=9.9
Q ss_pred eeCCCc----------ccccCcHHHH
Q psy13110 122 FDAHTG----------EFTGMPEAWA 137 (183)
Q Consensus 122 ~D~~TG----------eftGLP~eW~ 137 (183)
||+..| .|..||+.|.
T Consensus 11 Yd~~~Gd~~~~i~pGt~F~~Lp~~w~ 36 (47)
T PF00301_consen 11 YDPEKGDPENGIPPGTPFEDLPDDWV 36 (47)
T ss_dssp EETTTBBGGGTB-TT--GGGS-TT-B
T ss_pred EcCCcCCcccCcCCCCCHHHCCCCCc
Confidence 677666 3888999885
No 14
>COG0824 FcbC Predicted thioesterase [General function prediction only]
Probab=38.94 E-value=43 Score=26.05 Aligned_cols=30 Identities=23% Similarity=0.194 Sum_probs=26.2
Q ss_pred CeeeeeeeeeCCCcccccCcHHHHHHHHHc
Q psy13110 114 FEHTVHVGFDAHTGEFTGMPEAWARLLMSS 143 (183)
Q Consensus 114 F~H~~HVg~D~~TGeftGLP~eW~~lL~~s 143 (183)
--+++||-+|+.+|.-.-+|++|...|...
T Consensus 105 ~~~~~~V~v~~~~~kp~~~P~~~~~~l~~~ 134 (137)
T COG0824 105 TGETTLVCVDLKTGKPVPLPPELREALEAL 134 (137)
T ss_pred EEEEEEEEEECCCCCcccCCHHHHHHHHHh
Confidence 348899999999999999999999998653
No 15
>PF13351 DUF4099: Protein of unknown function (DUF4099)
Probab=37.75 E-value=32 Score=25.29 Aligned_cols=30 Identities=30% Similarity=0.431 Sum_probs=22.6
Q ss_pred HHHHHHHHcCCCHHHHhhChHHHHHHHHhhcc
Q psy13110 135 AWARLLMSSNISKLEQKKNPQAVLDVLNWFDN 166 (183)
Q Consensus 135 eW~~lL~~sGISk~E~k~NpqaVldVl~Fy~~ 166 (183)
.|.. |++-|||++.+.+ +..+-..|+.|..
T Consensus 7 ~w~~-L~~~Gi~ke~Le~-~~~Le~ll~G~kT 36 (85)
T PF13351_consen 7 PWEE-LEKFGISKEMLEK-PGDLEALLNGYKT 36 (85)
T ss_pred CHHH-HHHcCCCHHHhhC-chhHHHHhCCCcc
Confidence 4777 6799999999998 6666666666643
No 16
>PF13619 KTSC: KTSC domain
Probab=36.44 E-value=44 Score=22.70 Aligned_cols=14 Identities=29% Similarity=0.667 Sum_probs=9.2
Q ss_pred ccccCcH-HHHHHHH
Q psy13110 128 EFTGMPE-AWARLLM 141 (183)
Q Consensus 128 eftGLP~-eW~~lL~ 141 (183)
++.|+|+ .|+.||.
T Consensus 29 ~Y~~Vp~~~~~~l~~ 43 (60)
T PF13619_consen 29 RYFGVPPEVYEALLN 43 (60)
T ss_pred EECCCCHHHHHHHHc
Confidence 4568875 5677664
No 17
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. 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),
Probab=35.91 E-value=51 Score=24.05 Aligned_cols=38 Identities=16% Similarity=0.321 Sum_probs=30.4
Q ss_pred cCcHHHHHHHHHcCCCHHHHhh----Ch----HHHHHHHHhhcccc
Q psy13110 131 GMPEAWARLLMSSNISKLEQKK----NP----QAVLDVLNWFDNST 168 (183)
Q Consensus 131 GLP~eW~~lL~~sGISk~E~k~----Np----qaVldVl~Fy~~~~ 168 (183)
.|-.+|..|....|+|+.++.. || +.+++.|....+..
T Consensus 11 ~lG~~Wk~laR~LGlse~~Id~i~~~~~~~~~eq~~~mL~~W~~~~ 56 (86)
T cd08306 11 NVGRDWRKLARKLGLSETKIESIEEAHPRNLREQVRQSLREWKKIK 56 (86)
T ss_pred HHhhhHHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHhH
Confidence 5678999999999999999873 65 67888887665543
No 18
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (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. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=33.80 E-value=77 Score=21.53 Aligned_cols=38 Identities=18% Similarity=0.369 Sum_probs=30.4
Q ss_pred CcHHHHHHHHHcCCCHHHHhh----Ch---HHHHHHHHhhccccc
Q psy13110 132 MPEAWARLLMSSNISKLEQKK----NP---QAVLDVLNWFDNSTK 169 (183)
Q Consensus 132 LP~eW~~lL~~sGISk~E~k~----Np---qaVldVl~Fy~~~~~ 169 (183)
|..+|++|-..-|++..++.. |+ +.++.+|........
T Consensus 9 lg~~W~~la~~Lgl~~~~I~~i~~~~~~~~~~~~~mL~~W~~~~~ 53 (79)
T cd01670 9 LGKDWKKLARKLGLSDGEIDQIEEDNPRVREQAYQLLLKWEEREG 53 (79)
T ss_pred HhhHHHHHHHHhCCCHHHHHHHHHhCCCHHHHHHHHHHHHHhccC
Confidence 458999999999999998874 64 778888888755543
No 19
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. 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 sign
Probab=33.37 E-value=72 Score=24.25 Aligned_cols=39 Identities=18% Similarity=0.259 Sum_probs=29.9
Q ss_pred cCc-HHHHHHHHHcCCCHHHHhh----Ch----HHHHHHHHhhccccc
Q psy13110 131 GMP-EAWARLLMSSNISKLEQKK----NP----QAVLDVLNWFDNSTK 169 (183)
Q Consensus 131 GLP-~eW~~lL~~sGISk~E~k~----Np----qaVldVl~Fy~~~~~ 169 (183)
.|| .+|.++....|||+.++.. || +.+++.|.-.-+...
T Consensus 17 ~~~~~~wK~faR~lglse~~Id~I~~~~~~d~~Eq~~qmL~~W~~~~G 64 (97)
T cd08316 17 VMTLKDVKKFVRKSGLSEPKIDEIKLDNPQDTAEQKVQLLRAWYQSHG 64 (97)
T ss_pred HcCHHHHHHHHHHcCCCHHHHHHHHHcCCCChHHHHHHHHHHHHHHhC
Confidence 455 7899999999999988874 55 778888876655443
No 20
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. 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 a
Probab=32.26 E-value=45 Score=24.52 Aligned_cols=37 Identities=16% Similarity=0.384 Sum_probs=26.6
Q ss_pred ccCc-HHHHHHHHHcCCCHHHHhh----Ch---HHHHHHHHhhcc
Q psy13110 130 TGMP-EAWARLLMSSNISKLEQKK----NP---QAVLDVLNWFDN 166 (183)
Q Consensus 130 tGLP-~eW~~lL~~sGISk~E~k~----Np---qaVldVl~Fy~~ 166 (183)
..+| .+|.++....|+|+.+|.. || +.+++.|.-..+
T Consensus 7 d~v~~~~wk~~~R~LGlse~~Id~ie~~~~~~~Eq~yqmL~~W~~ 51 (80)
T cd08313 7 DEVPPRRWKEFVRRLGLSDNEIERVELDHRRCRDAQYQMLKVWKE 51 (80)
T ss_pred HhCCHHHHHHHHHHcCCCHHHHHHHHHhCCChHHHHHHHHHHHHH
Confidence 3555 6999999999999988874 44 555666654433
No 21
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=32.14 E-value=1.1e+02 Score=20.47 Aligned_cols=33 Identities=18% Similarity=0.213 Sum_probs=21.5
Q ss_pred cCc-HHHHHHHHHcCCCHHHHhh-----ChHHHHHHHHhh
Q psy13110 131 GMP-EAWARLLMSSNISKLEQKK-----NPQAVLDVLNWF 164 (183)
Q Consensus 131 GLP-~eW~~lL~~sGISk~E~k~-----NpqaVldVl~Fy 164 (183)
++| ..-..++ .+|.|.+|+.+ +++.|.++|.||
T Consensus 18 RI~v~~i~~~~-~~G~s~eeI~~~yp~Lt~~~i~aAl~ya 56 (56)
T PF04255_consen 18 RIPVRDILDLL-AAGESPEEIAEDYPSLTLEDIRAALAYA 56 (56)
T ss_dssp S-BHHHHHHHH-HTT--HHHHHHHSTT--HHHHHHHHHHH
T ss_pred eecHHHHHHHH-HcCCCHHHHHHHCCCCCHHHHHHHHHhC
Confidence 344 3334445 89999999986 678999999986
No 22
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. 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
Probab=30.79 E-value=83 Score=23.00 Aligned_cols=39 Identities=15% Similarity=0.288 Sum_probs=31.3
Q ss_pred cCcHHHHHHHHHcCCCHHHHhh----Ch----HHHHHHHHhhccccc
Q psy13110 131 GMPEAWARLLMSSNISKLEQKK----NP----QAVLDVLNWFDNSTK 169 (183)
Q Consensus 131 GLP~eW~~lL~~sGISk~E~k~----Np----qaVldVl~Fy~~~~~ 169 (183)
.|-.+|..|-..-|||+.++.. || +.+++.|....+...
T Consensus 11 ~LG~~Wk~lar~LGlse~~Id~Ie~~~~~dl~eq~~~mL~~W~~~~~ 57 (86)
T cd08779 11 RLGLDWQAIGLHLGLSYRELQRIKYNNRDDLDEQIFDMLFSWAQRQA 57 (86)
T ss_pred HHhHHHHHHHHHcCCCHHHHHHHHHHCccCHHHHHHHHHHHHHHhcC
Confidence 4668999999999999998874 65 678888888866543
No 23
>PF03868 Ribosomal_L6e_N: Ribosomal protein L6, N-terminal domain; InterPro: IPR005568 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. L6 is a protein from the large (50S) subunit. In Escherichia coli, it is located in the aminoacyl-tRNA binding site of the peptidyltransferase centre, and is known to bind directly to 23S rRNA. It belongs to a family of ribosomal proteins, including L6 from bacteria, cyanelles (structures that perform similar functions to chloroplasts, but have structural and biochemical characteristics of Cyanobacteria) and mitochondria; and L9 from mammals, Drosophila, plants and yeast. L6 contains two domains with almost identical folds, suggesting that is was derived by the duplication of an ancient RNA-binding protein gene. Analysis reveals several sites on the protein surface where interactions with other ribosome components may occur, the N terminus being involved in protein-protein interactions and the C terminus containing possible RNA-binding sites [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_G.
Probab=30.58 E-value=21 Score=25.08 Aligned_cols=13 Identities=54% Similarity=0.813 Sum_probs=9.6
Q ss_pred hhhhhhhhhhhcC
Q psy13110 5 ISALYHQRALWCG 17 (183)
Q Consensus 5 ~~~~~~~~~~~~~ 17 (183)
-|++||.||||-.
T Consensus 25 rS~my~kralyk~ 37 (59)
T PF03868_consen 25 RSAMYHKRALYKR 37 (59)
T ss_dssp HHHHHHHHHH-S-
T ss_pred HHHHHHHHHHHHH
Confidence 4789999999964
No 24
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. 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=29.33 E-value=1e+02 Score=22.05 Aligned_cols=35 Identities=26% Similarity=0.362 Sum_probs=26.2
Q ss_pred cHHHHHHHHHcCCCHHHHhh----Ch---HHHHHHHHhhccc
Q psy13110 133 PEAWARLLMSSNISKLEQKK----NP---QAVLDVLNWFDNS 167 (183)
Q Consensus 133 P~eW~~lL~~sGISk~E~k~----Np---qaVldVl~Fy~~~ 167 (183)
+.+|..|....|++..++.. || +.+++.|.-..+.
T Consensus 11 ~~~Wk~laR~LGls~~~I~~ie~~~~~~~eq~~~mL~~W~~k 52 (79)
T cd08784 11 FDQHKRFFRKLGLSDNEIKVAELDNPQHRDRVYELLRIWRNK 52 (79)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHcCCchHHHHHHHHHHHHhc
Confidence 35699999999999999884 76 5666776555443
No 25
>smart00005 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
Probab=28.54 E-value=1.1e+02 Score=21.17 Aligned_cols=38 Identities=13% Similarity=0.360 Sum_probs=30.1
Q ss_pred CcHHHHHHHHHcCCCHHHHhh----Ch----HHHHHHHHhhccccc
Q psy13110 132 MPEAWARLLMSSNISKLEQKK----NP----QAVLDVLNWFDNSTK 169 (183)
Q Consensus 132 LP~eW~~lL~~sGISk~E~k~----Np----qaVldVl~Fy~~~~~ 169 (183)
+..+|+.|-..-|++..++.. |+ +.++.+|+.+.....
T Consensus 16 ~g~~W~~la~~Lg~~~~~i~~i~~~~~~~~~~~~~~lL~~W~~~~g 61 (88)
T smart00005 16 LGLDWRELARKLGLSEADIDQIRTEAPRDLAEQSVQLLRLWEQREG 61 (88)
T ss_pred cchHHHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHccc
Confidence 668999999999999988774 65 678888887755443
No 26
>PF03562 MltA: MltA specific insert domain; InterPro: IPR005300 This group of proteins includes MltA; a membrane-bound, murein degrading transglycosylase enzyme which plays an important role in the controlled growth of the stress-bearing sacculus of Escherichia coli [, ].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds; PDB: 2PI8_D 2AE0_X 2PIC_A 2GAE_A 2PJJ_A 3CZB_A 2G6G_A 2PNW_A 2G5D_A.
Probab=26.86 E-value=36 Score=28.19 Aligned_cols=42 Identities=31% Similarity=0.596 Sum_probs=22.2
Q ss_pred eeeeeeeeCCCc-ccccCcHHHHHHHHHcC-C-----CHHHHh----hChHHHHHHH
Q psy13110 116 HTVHVGFDAHTG-EFTGMPEAWARLLMSSN-I-----SKLEQK----KNPQAVLDVL 161 (183)
Q Consensus 116 H~~HVg~D~~TG-eftGLP~eW~~lL~~sG-I-----Sk~E~k----~NpqaVldVl 161 (183)
..++|||+..+| .|+.+ .++|.+.| | |-+-++ +||+.+-++|
T Consensus 96 ~~~rvgYAg~NG~pY~sI----Gr~Li~~G~i~~~~~Smq~Ir~wl~~~P~~~~~ll 148 (158)
T PF03562_consen 96 STVRVGYAGQNGHPYTSI----GRLLIDRGEIPREQMSMQAIRAWLRAHPEEADELL 148 (158)
T ss_dssp SEEEEEEEEE-SS----H----HHHHHHTTSS-TTS-SHHHHHHHHHHTGGGHHHHH
T ss_pred CEEEEEEcccCCCccccH----HHHHHHcCCcChhhCCHHHHHHHHHHCHHHHHHHH
Confidence 357999999999 78755 45566555 3 333333 3666655554
No 27
>PRK10800 acyl-CoA thioesterase YbgC; Provisional
Probab=24.83 E-value=91 Score=23.11 Aligned_cols=25 Identities=12% Similarity=0.116 Sum_probs=22.3
Q ss_pred eeeeeeeeCCCcccccCcHHHHHHH
Q psy13110 116 HTVHVGFDAHTGEFTGMPEAWARLL 140 (183)
Q Consensus 116 H~~HVg~D~~TGeftGLP~eW~~lL 140 (183)
+.++|-+|.+++.-.-+|++|.++|
T Consensus 105 ~~~~v~~d~~~~r~~~iP~~l~~~~ 129 (130)
T PRK10800 105 EVLIVCVDPLKMKPRALPKSIVAEF 129 (130)
T ss_pred EEEEEEEECCCCcCcCCCHHHHHhh
Confidence 6689999999998899999998876
No 28
>COG2441 Predicted butyrate kinase [Energy production and conversion]
Probab=24.44 E-value=14 Score=34.33 Aligned_cols=48 Identities=21% Similarity=0.472 Sum_probs=37.5
Q ss_pred eeeeCCCc--ccccCcHHHHHHHHHcCCCHHHHhhChHHHHHHHHhhccc
Q psy13110 120 VGFDAHTG--EFTGMPEAWARLLMSSNISKLEQKKNPQAVLDVLNWFDNS 167 (183)
Q Consensus 120 Vg~D~~TG--eftGLP~eW~~lL~~sGISk~E~k~NpqaVldVl~Fy~~~ 167 (183)
+|.||-|| ..-|..+|--.++..-.|..+|..+||..++++|.=++..
T Consensus 1 ~GIDpGT~smdvfgfdDEsg~vi~~~~I~rdeVtk~p~iiv~ii~e~~~e 50 (374)
T COG2441 1 IGIDPGTGSMDVFGFDDESGNVIVDVAIPRDEVTKSPRIIVDIIEEVQAE 50 (374)
T ss_pred CCcCCCCCceeEEEEecCCCCEEEEEecCHHHhccCchHHHHHHHHHhhh
Confidence 46777776 3446777766777788899999999999999999877543
No 29
>COG2442 Uncharacterized conserved protein [Function unknown]
Probab=23.50 E-value=1.5e+02 Score=21.80 Aligned_cols=49 Identities=14% Similarity=0.187 Sum_probs=34.5
Q ss_pred eeeeeCCC--c--cccc--CcH-HHHHHHHHcCCCHHHHhh-----ChHHHHHHHHhhcccc
Q psy13110 119 HVGFDAHT--G--EFTG--MPE-AWARLLMSSNISKLEQKK-----NPQAVLDVLNWFDNST 168 (183)
Q Consensus 119 HVg~D~~T--G--eftG--LP~-eW~~lL~~sGISk~E~k~-----NpqaVldVl~Fy~~~~ 168 (183)
++..+|.. | -+.| +|. .-...| ++|+|.+|+.. +.+.|.++|.|+.+..
T Consensus 12 ~I~~~P~i~gGkP~I~GtRI~V~~Il~~l-~~G~s~eeil~dyp~Lt~~dI~aal~ya~~~~ 72 (79)
T COG2442 12 RIVITPGICGGKPCIRGTRIPVWDILEML-AAGESIEEILADYPDLTLEDIRAALRYAADRE 72 (79)
T ss_pred eeEeCCcccCCcceEeCceecHHHHHHHH-HCCCCHHHHHHhCCCCCHHHHHHHHHHHHHHH
Confidence 66677764 3 2444 443 335556 59999999986 5689999999997763
No 30
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=22.90 E-value=1.3e+02 Score=24.66 Aligned_cols=35 Identities=17% Similarity=0.417 Sum_probs=28.2
Q ss_pred HHHHHHHHHcCCCHHHHh--------hChHHHHHHHHhhcccc
Q psy13110 134 EAWARLLMSSNISKLEQK--------KNPQAVLDVLNWFDNST 168 (183)
Q Consensus 134 ~eW~~lL~~sGISk~E~k--------~NpqaVldVl~Fy~~~~ 168 (183)
.+|..++..+|++++++. .+|++=.+.|+..+-+.
T Consensus 119 ~~w~~l~~~~g~~~~~m~~wh~~fe~~~p~~h~~~l~~~g~~~ 161 (172)
T cd04790 119 EKWVAILKAAGMDEADMRRWHIEFEKMEPEAHQEFLQSLGIPE 161 (172)
T ss_pred HHHHHHHHHcCCChHHHHHHHHHHHHhCcHHHHHHHHHcCCCH
Confidence 789999999999998854 39999888887765443
No 31
>PF00969 MHC_II_beta: Class II histocompatibility antigen, beta domain; InterPro: IPR000353 Major Histocompatibility Complex (MHC) glycoproteins are heterodimeric cell surface receptors that function to present antigen peptide fragments to T cells responsible for cell-mediated immune responses. MHC molecules can be subdivided into two groups on the basis of structure and function: class I molecules present intracellular antigen peptide fragments (~10 amino acids) on the surface of the host cells to cytotoxic T cells; class II molecules present exogenously derived antigenic peptides (~15 amino acids) to helper T cells. MHC class I and II molecules are assembled and loaded with their peptide ligands via different mechanisms. However, both present peptide fragments rather than entire proteins to T cells, and are required to mount an immune response. Class II MHC glycoproteins are expressed on the surface of antigen-presenting cells (APC), including macrophages, dendritic cells and B cells. MHC II proteins present peptide antigens that originate extracellularly from foreign bodies such as bacteria. Proteins from the pathogen are degraded into peptide fragments within the APC, which sequesters these fragments into the endosome so they can bind to MHC class II proteins, before being transported to the cell surface. MHC class II receptors display antigens for recognition by helper T cells (stimulate development of B cell clones) and inflammatory T cells (cause the release of lymphokines that attract other cells to site of infection) []. MHC class II molecules are comprised of two membrane-spanning chains, alpha and beta, of similar size. Both chains consist of two globular domains (N- and C-terminal), and a transmembrane segment to anchor them to the membrane []. A groove in the structure acts as the peptide-binding site. This entry represents the N-terminal domain (also called beta-1 domain) of the beta chain. More information about these proteins can be found at Protein of the Month: MHC [].; GO: 0006955 immune response, 0019882 antigen processing and presentation, 0016020 membrane, 0042613 MHC class II protein complex; PDB: 2WBJ_B 1BX2_E 1YMM_B 2Q6W_E 3C5J_B 2P24_B 2PXY_D 1K2D_B 1U3H_H 2Z31_D ....
Probab=21.78 E-value=80 Score=22.69 Aligned_cols=27 Identities=26% Similarity=0.474 Sum_probs=20.3
Q ss_pred CeeeeeeeeeCCCcccccCcHHHHHHH
Q psy13110 114 FEHTVHVGFDAHTGEFTGMPEAWARLL 140 (183)
Q Consensus 114 F~H~~HVg~D~~TGeftGLP~eW~~lL 140 (183)
|.-...|-||++.|.|.|..+-++..-
T Consensus 20 yNk~e~v~fdS~vG~~vg~Te~G~~~A 46 (75)
T PF00969_consen 20 YNKEEFVRFDSDVGKFVGYTELGEKNA 46 (75)
T ss_dssp ETTEEEEEEETTTTSEEESSGGGHHHH
T ss_pred cchheeeeeeccceEeeccccccccch
Confidence 344567999999999999887665444
No 32
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=21.66 E-value=95 Score=21.07 Aligned_cols=36 Identities=22% Similarity=0.473 Sum_probs=28.5
Q ss_pred CcHHHHHHHHHcCCCHHHHhh----Ch---HHHHHHHHhhccc
Q psy13110 132 MPEAWARLLMSSNISKLEQKK----NP---QAVLDVLNWFDNS 167 (183)
Q Consensus 132 LP~eW~~lL~~sGISk~E~k~----Np---qaVldVl~Fy~~~ 167 (183)
++.+|..|-..-||+..++.. |+ +.++.+|..+...
T Consensus 11 ~~~~Wk~La~~Lg~~~~~i~~i~~~~~~~~~~~~~~L~~W~~~ 53 (83)
T PF00531_consen 11 LGSDWKRLARKLGLSESEIENIEEENPDLREQTYEMLQRWRQR 53 (83)
T ss_dssp HSTCHHHHHHHTTS-HHHHHHHHHHSTSHHHHHHHHHHHHHHH
T ss_pred chhhHHHHHHHhCcCHHHHHHHHHhCCChHHHHHHHHHHHHHh
Confidence 467899999999999998874 65 6778888888665
No 33
>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=20.71 E-value=1.9e+02 Score=21.05 Aligned_cols=38 Identities=11% Similarity=0.254 Sum_probs=30.1
Q ss_pred CcHHHHHHHHHcCCCHHHHhh----C----hHHHHHHHHhhccccc
Q psy13110 132 MPEAWARLLMSSNISKLEQKK----N----PQAVLDVLNWFDNSTK 169 (183)
Q Consensus 132 LP~eW~~lL~~sGISk~E~k~----N----pqaVldVl~Fy~~~~~ 169 (183)
|=.+|.+|....|+|..++.. | .+.++..|........
T Consensus 14 LG~dWk~LAr~Lg~se~dI~~i~~~~~~~~~eq~~~mL~~W~~r~g 59 (84)
T cd08804 14 LGFSWTELARELDFTEEQIHQIRIENPNSLQDQSHALLKYWLERDG 59 (84)
T ss_pred HhhhHHHHHHHcCCCHHHHHHHHHHCcccHHHHHHHHHHHHHHccC
Confidence 345799999999999999986 4 4777888888866553
No 34
>PRK04217 hypothetical protein; Provisional
Probab=20.56 E-value=2.7e+02 Score=21.61 Aligned_cols=33 Identities=18% Similarity=0.049 Sum_probs=21.2
Q ss_pred ccCcHHHHHHHH---HcCCCHHHHhh----ChHHHHHHHH
Q psy13110 130 TGMPEAWARLLM---SSNISKLEQKK----NPQAVLDVLN 162 (183)
Q Consensus 130 tGLP~eW~~lL~---~sGISk~E~k~----NpqaVldVl~ 162 (183)
..|+++...+|. ..|+|.+|+.+ +..+|...|.
T Consensus 41 ~~Lt~eereai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~ 80 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALT 80 (110)
T ss_pred ccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 356666666554 46788888876 6666655543
No 35
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=20.40 E-value=70 Score=21.29 Aligned_cols=31 Identities=19% Similarity=0.411 Sum_probs=24.4
Q ss_pred cCcHHHHHHHHHcCCCHHHHhhChHHHHHHH
Q psy13110 131 GMPEAWARLLMSSNISKLEQKKNPQAVLDVL 161 (183)
Q Consensus 131 GLP~eW~~lL~~sGISk~E~k~NpqaVldVl 161 (183)
-+|.....|.+-.|+++..++++-+.++++|
T Consensus 38 ~~P~s~~~L~~i~g~~~~~~~~~g~~il~~I 68 (68)
T PF00570_consen 38 RLPTSIEELLQIPGMGKRKVRKYGDEILEII 68 (68)
T ss_dssp H--SSHHHHHTSTTCGHHHHHHCHHHHHHHH
T ss_pred hCCCCHHHHHHccCCCHHHHHHHHHHHHhhC
Confidence 4677788888778999999999999988875
Done!