Query psy10763
Match_columns 90
No_of_seqs 100 out of 184
Neff 5.5
Searched_HMMs 46136
Date Fri Aug 16 17:53:56 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10763.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10763hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd03774 MATH_SPOP Speckle-type 99.3 3.8E-12 8.2E-17 86.1 3.5 46 9-54 94-139 (139)
2 cd03776 MATH_TRAF6 Tumor Necro 98.9 3.4E-10 7.3E-15 77.5 2.1 32 17-50 116-147 (147)
3 cd03781 MATH_TRAF4 Tumor Necro 98.9 6.7E-10 1.4E-14 77.1 2.2 31 17-49 123-153 (154)
4 cd03772 MATH_HAUSP Herpesvirus 98.9 1.8E-09 3.9E-14 72.9 3.3 42 11-52 91-133 (137)
5 cd03779 MATH_TRAF1 Tumor Necro 98.8 1.5E-09 3.3E-14 76.0 2.4 32 16-49 113-146 (147)
6 cd00270 MATH_TRAF_C Tumor Necr 98.7 8E-09 1.7E-13 70.1 2.4 32 16-49 117-148 (149)
7 cd03773 MATH_TRIM37 Tripartite 98.6 1.9E-08 4E-13 67.0 2.2 38 11-50 91-130 (132)
8 cd03780 MATH_TRAF5 Tumor Necro 98.4 1.4E-07 3.1E-12 65.9 2.8 38 10-49 103-147 (148)
9 cd03777 MATH_TRAF3 Tumor Necro 98.4 1.7E-07 3.6E-12 67.8 2.7 32 17-50 153-184 (186)
10 cd03775 MATH_Ubp21p Ubiquitin- 98.4 2.8E-07 6E-12 62.2 2.6 42 9-50 88-134 (134)
11 PF00917 MATH: MATH domain; I 98.3 6E-07 1.3E-11 57.3 3.2 40 10-51 80-119 (119)
12 cd00121 MATH MATH (meprin and 97.9 5.6E-06 1.2E-10 52.3 2.0 33 16-50 94-126 (126)
13 cd03778 MATH_TRAF2 Tumor Necro 96.2 0.0049 1.1E-07 44.1 3.0 32 17-49 132-163 (164)
14 cd03771 MATH_Meprin Meprin fam 96.1 0.0055 1.2E-07 43.8 2.8 31 17-49 136-166 (167)
15 cd03783 MATH_Meprin_Alpha Mepr 94.2 0.035 7.7E-07 40.0 2.2 32 16-49 135-166 (167)
16 cd03782 MATH_Meprin_Beta Mepri 92.6 0.1 2.2E-06 37.7 2.4 31 16-48 135-165 (167)
17 COG5077 Ubiquitin carboxyl-ter 86.0 0.67 1.5E-05 41.0 2.8 47 10-56 125-175 (1089)
18 cd06406 PB1_P67 A PB1 domain i 81.4 0.51 1.1E-05 30.3 0.2 24 26-50 57-80 (80)
19 KOG1863|consensus 76.0 1.9 4E-05 38.7 2.1 46 9-54 108-154 (1093)
20 PF01022 HTH_5: Bacterial regu 54.2 5.2 0.00011 22.1 0.4 17 71-87 27-43 (47)
21 PF12840 HTH_20: Helix-turn-he 46.1 8.3 0.00018 22.3 0.4 17 71-87 36-52 (61)
22 PF12188 STAT2_C: Signal trans 32.7 19 0.00041 21.7 0.5 13 71-83 4-16 (56)
23 PF06565 DUF1126: Repeat of un 29.8 14 0.00031 19.6 -0.3 9 37-45 5-13 (33)
24 TIGR01552 phd_fam prevent-host 29.4 26 0.00055 19.4 0.7 16 71-86 2-17 (52)
25 cd04468 S1_eIF5A S1_eIF5A: Euk 27.9 46 0.00099 20.6 1.6 18 71-88 31-48 (69)
26 KOG2488|consensus 27.2 14 0.00029 27.7 -1.0 37 17-53 74-122 (202)
27 PRK10141 DNA-binding transcrip 26.8 35 0.00076 22.9 1.1 17 71-87 42-58 (117)
28 PF13601 HTH_34: Winged helix 26.4 26 0.00056 21.7 0.3 17 71-87 26-42 (80)
29 PF13895 Ig_2: Immunoglobulin 26.0 54 0.0012 18.2 1.7 14 37-50 11-24 (80)
30 PF05253 zf-U11-48K: U11-48K-l 25.2 26 0.00057 17.6 0.2 12 71-82 13-24 (27)
31 KOG4844|consensus 24.5 32 0.0007 22.9 0.5 18 72-89 49-66 (102)
32 cd06411 PB1_p51 The PB1 domain 20.5 1.8E+02 0.004 18.5 3.4 12 43-54 1-12 (78)
33 COG4259 Uncharacterized protei 20.1 70 0.0015 21.9 1.5 14 73-86 71-84 (121)
No 1
>cd03774 MATH_SPOP Speckle-type POZ protein (SPOP) family, MATH domain; composed of proteins with similarity to human SPOP. SPOP was isolated as a novel antigen recognized by serum from a scleroderma patient, whose overexpression in COS cells results in a discrete speckled pattern in the nuclei. It contains an N-terminal MATH domain and a C-terminal BTB (also called POZ) domain. Together with Cul3, SPOP constitutes an ubiquitin E3 ligase which is able to ubiquitinate the PcG protein BMI1, the variant histone macroH2A1 and the death domain-associated protein Daxx. Therefore, SPOP may be involved in the regulation of these proteins and may play a role in transcriptional regulation, apoptosis and X-chromosome inactivation. Cul3 binds to the BTB domain of SPOP whereas Daxx and the macroH2A1 nonhistone region have been shown to bind to the MATH domain. Both MATH and BTB domains are necessary for the nuclear speckled accumulation of SPOP. There are many proteins, mostly uncharacterized, conta
Probab=99.26 E-value=3.8e-12 Score=86.09 Aligned_cols=46 Identities=80% Similarity=1.375 Sum_probs=39.1
Q ss_pred ceeeeecCCccccccceecccccccccCCCCCCeEEEEEEEEEeee
Q psy10763 9 RAYRFVQGKDWGFKKFIRRDFLLDELNGLLPEDKLTIFCEQNPLIL 54 (90)
Q Consensus 9 ~~~~F~~~~~wG~~~Fi~R~~Le~e~s~~L~dD~ltI~C~VtVv~e 54 (90)
..+.|.....|||.+||+|++|+++.++||.||+|||+|+|+|+++
T Consensus 94 ~~~~f~~~~~wG~~~fi~~~~L~~~~~g~l~dD~l~I~c~I~V~~~ 139 (139)
T cd03774 94 RAYRFVQGKDWGFKKFIRRDFLLDEANGLLPDDKLTLFCEVSVVQD 139 (139)
T ss_pred CcEeCCCCCccCHHHeeeHHHhhhhhcccccCCEEEEEEEEEEEcC
Confidence 3456665567999999999999766789999999999999999864
No 2
>cd03776 MATH_TRAF6 Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF6 subfamily, TRAF domain, C-terminal MATH subdomain; composed of proteins with similarity to human TRAF6, including the Drosophila protein DTRAF2. TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF6 is the most divergent in its TRAF domain among the mammalian TRAFs. In addition to mediating TNFR family signaling, it is also an essential signaling molecule of the interleukin-1/Toll-like receptor superfamily. Whereas other TRAF molecules display similar and overlapping TNFR-binding specificities, TRAF6 binds completely different sites on receptors such as CD40 and RANK. TRAF6 serves as a molecular bridge between innate and adaptive immunity and plays a central role in osteoimmunology. DTRAF2, as an activator of nuclear factor-kapp
Probab=98.95 E-value=3.4e-10 Score=77.54 Aligned_cols=32 Identities=31% Similarity=0.462 Sum_probs=29.2
Q ss_pred CccccccceecccccccccCCCCCCeEEEEEEEE
Q psy10763 17 KDWGFKKFIRRDFLLDELNGLLPEDKLTIFCEQN 50 (90)
Q Consensus 17 ~~wG~~~Fi~R~~Le~e~s~~L~dD~ltI~C~Vt 50 (90)
..||+.+||+|++| |.++||+||+|+|+|+|+
T Consensus 116 ~~~G~~~fi~~~~L--e~~~yl~dD~l~I~c~V~ 147 (147)
T cd03776 116 KGFGYVEFAHIEDL--LQRGFVKNDTLLIKIEVN 147 (147)
T ss_pred CCeeEceeeEHHHh--hhCCCccCCEEEEEEEEC
Confidence 56999999999999 567899999999999985
No 3
>cd03781 MATH_TRAF4 Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF4 subfamily, TRAF domain, C-terminal MATH subdomain; composed of proteins with similarity to human TRAF4, including the Drosophila protein DTRAF1. TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF4 is highly expressed during embryogenesis, especially in the central and peripheral nervous system. Studies using TRAF4-deficient mice show that TRAF4 is required for neurogenesis, as well as the development of the trachea and the axial skeleton. In addition, TRAF4 augments nuclear factor-kappaB activation triggered by GITR (glucocorticoid-induced TNFR), a receptor expressed in T-cells, B-cells and macrophages. It also participates in counteracting the signaling mediated by Toll-like receptors through its association with TRAF6 and TR
Probab=98.90 E-value=6.7e-10 Score=77.15 Aligned_cols=31 Identities=19% Similarity=0.409 Sum_probs=28.6
Q ss_pred CccccccceecccccccccCCCCCCeEEEEEEE
Q psy10763 17 KDWGFKKFIRRDFLLDELNGLLPEDKLTIFCEQ 49 (90)
Q Consensus 17 ~~wG~~~Fi~R~~Le~e~s~~L~dD~ltI~C~V 49 (90)
.+|||.+||+|++| |.++||+||+|+|+|+|
T Consensus 123 ~~~G~~~fi~~~~L--e~~~yl~dD~l~Irc~v 153 (154)
T cd03781 123 LGFGYPKFISHEDL--KKRNYIKDDAIFLRASV 153 (154)
T ss_pred CccchhHeeEHHHH--hhCCcccCCEEEEEEEe
Confidence 45999999999999 57889999999999997
No 4
>cd03772 MATH_HAUSP Herpesvirus-associated ubiquitin-specific protease (HAUSP, also known as USP7) family, N-terminal MATH (TRAF-like) domain; composed of proteins similar to human HAUSP, an enzyme that specifically catalyzes the deubiquitylation of p53 and MDM2, hence playing an important role in the p53-MDM2 pathway. It contains an N-terminal TRAF-like domain and a C-terminal catalytic protease (C19 family) domain. The tumor suppressor p53 protein is a transcription factor that responds to many cellular stress signals and is regulated primarily through ubiquitylation and subsequent degradation. MDM2 is a RING-finger E3 ubiquitin ligase that promotes p53 ubiquitinylation. p53 and MDM2 bind to the same site in the N-terminal TRAF-like domain of HAUSP in a mutually exclusive manner. HAUSP also interacts with the Epstein-Barr nuclear antigen 1 (EBNA1) protein of the Epstein-Barr virus (EBV), which efficiently immortalizes infected cells predisposing the host to a variety of cancers. EBNA1
Probab=98.86 E-value=1.8e-09 Score=72.91 Aligned_cols=42 Identities=24% Similarity=0.467 Sum_probs=35.8
Q ss_pred eeeec-CCccccccceecccccccccCCCCCCeEEEEEEEEEe
Q psy10763 11 YRFVQ-GKDWGFKKFIRRDFLLDELNGLLPEDKLTIFCEQNPL 52 (90)
Q Consensus 11 ~~F~~-~~~wG~~~Fi~R~~Le~e~s~~L~dD~ltI~C~VtVv 52 (90)
+.|.. ...||+.+||++++|+++.++||.||+|+|+|+|++=
T Consensus 91 ~~f~~~~~~~G~~~fi~~~~L~~~~sgyl~~D~l~Ie~~V~~~ 133 (137)
T cd03772 91 HLFFSKENDWGFSNFMTWSEVTDPEKGFIEDDTITLEVYVQAD 133 (137)
T ss_pred eEEcCCCCCccchheeEHHHhcCCCCCcEECCEEEEEEEEEee
Confidence 46754 4679999999999997667899999999999999874
No 5
>cd03779 MATH_TRAF1 Tumor Necrosis Factor Receptor (TNFR) Associated Factor (TRAF) family, TRAF1 subfamily, TRAF domain, C-terminal MATH subdomain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF1 expression is the most restricted among the TRAFs. It is found exclusively in activated lymphocytes, dendritic cells and certain epithelia. TRAF1 associates, directly or indirectly through heterodimerization with TRAF2, with the TNFR family receptors TNFR-2, CD30, RANK, CD40 and LMP1, among others. It also binds the intracellular proteins TRADD, TANK, TRIP, RIP1, RIP2 and FLIP. TRAF1 is unique among the TRAFs in that it lacks a RING domain, which is critical for the activation of nuclear factor-kappaB and Jun NH2-terminal kinase. Studies on TRAF1-deficient mice suggest that TRAF1 has a negative regulatory role in TNFR-mediat
Probab=98.84 E-value=1.5e-09 Score=76.03 Aligned_cols=32 Identities=19% Similarity=0.161 Sum_probs=28.5
Q ss_pred CCccccccceeccccccccc--CCCCCCeEEEEEEE
Q psy10763 16 GKDWGFKKFIRRDFLLDELN--GLLPEDKLTIFCEQ 49 (90)
Q Consensus 16 ~~~wG~~~Fi~R~~Le~e~s--~~L~dD~ltI~C~V 49 (90)
+..|||.+||+|++|| +| +||+||+|+|+|+|
T Consensus 113 n~~~G~~~Fi~~~~Le--~s~~~ylkDD~~~Irc~V 146 (147)
T cd03779 113 NVASGCPLFFPLKKLQ--SPKHAYCKDDTIYIKCVV 146 (147)
T ss_pred CCCcchhheeEHHHhc--ccCCCcEeCCEEEEEEEE
Confidence 3469999999999994 65 89999999999997
No 6
>cd00270 MATH_TRAF_C Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF domain, C-terminal MATH subdomain; TRAF molecules serve as adapter proteins that link cell surface TNFRs and receptors of the interleukin-1/Toll-like family to downstream kinase signaling cascades which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. There are at least six mammalian and three Drosophila proteins containing TRAF domains. The mammalian TRAFs display varying expression profiles, indicating independent and cell type-specific regulation. They display distinct, as well as overlapping functions and interactions with receptors. Most TRAFs, except TRAF1, share N-terminal homology and contain a RING domain, multiple zinc finger domains, and a TRAF domain. TRAFs form homo- and heterotrimers through its TRAF domain. The TRAF domain can be divided into a more divergent N-ter
Probab=98.70 E-value=8e-09 Score=70.13 Aligned_cols=32 Identities=25% Similarity=0.418 Sum_probs=28.8
Q ss_pred CCccccccceecccccccccCCCCCCeEEEEEEE
Q psy10763 16 GKDWGFKKFIRRDFLLDELNGLLPEDKLTIFCEQ 49 (90)
Q Consensus 16 ~~~wG~~~Fi~R~~Le~e~s~~L~dD~ltI~C~V 49 (90)
...|||.+||++++|+ .++||+||+|+|+|+|
T Consensus 117 ~~~~G~~~fi~~~~L~--~~gfl~dD~l~I~~~v 148 (149)
T cd00270 117 NIGFGYPEFVPLEKLE--SRGYVKDDTLFIKVEV 148 (149)
T ss_pred CCCcCcceEeEHHHhc--cCCCEeCCEEEEEEEE
Confidence 4569999999999994 5689999999999997
No 7
>cd03773 MATH_TRIM37 Tripartite motif containing protein 37 (TRIM37) family, MATH domain; TRIM37 is a peroxisomal protein and is a member of the tripartite motif (TRIM) protein subfamily, also known as the RING-B-box-coiled-coil (RBCC) subfamily of zinc-finger proteins. Mutations in the human TRIM37 gene (also known as MUL) cause Mulibrey (muscle-liver-brain-eye) nanism, a rare growth disorder of prenatal onset characterized by dysmorphic features, pericardial constriction and hepatomegaly. TRIM37, similar to other TRIMs, contains a cysteine-rich, zinc-binding RING-finger domain followed by another cysteine-rich zinc-binding domain, the B-box, and a coiled-coil domain. TRIM37 is autoubiquitinated in a RING domain-dependent manner, indicating that it functions as an ubiquitin E3 ligase. In addition to the tripartite motif, TRIM37 also contains a MATH domain C-terminal to the coiled-coil domain. The MATH domain of TRIM37 has been shown to interact with the TRAF domain of six known TRAFs i
Probab=98.62 E-value=1.9e-08 Score=66.95 Aligned_cols=38 Identities=32% Similarity=0.624 Sum_probs=31.8
Q ss_pred eeeecCCccccccceecccccccccCCCCC--CeEEEEEEEE
Q psy10763 11 YRFVQGKDWGFKKFIRRDFLLDELNGLLPE--DKLTIFCEQN 50 (90)
Q Consensus 11 ~~F~~~~~wG~~~Fi~R~~Le~e~s~~L~d--D~ltI~C~Vt 50 (90)
+.|..+..|||.+||+|++|+ .++||+| |+|+|+|+|.
T Consensus 91 ~~f~~~~~wG~~~Fi~~~~L~--~~gfl~~~~D~l~i~~~v~ 130 (132)
T cd03773 91 SDFEVGECWGYNRFFRLDLLI--NEGYLLPENDTLILRFSVR 130 (132)
T ss_pred ccccCCCCcCHHHhccHHHHh--hCCCcCCCCCEEEEEEEEe
Confidence 455545669999999999994 5789999 9999999974
No 8
>cd03780 MATH_TRAF5 Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF5 subfamily, TRAF domain, C-terminal MATH subdomain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF5 was identified as an activator of nuclear factor-kappaB and a regulator of lymphotoxin-beta receptor and CD40 signaling. Its interaction with CD40 is indirect, involving hetero-oligomerization with TRAF3. In addition, TRAF5 has been shown to associate with other TNFRs including CD27, CD30, OX40 and GITR (glucocorticoid-induced TNFR). It plays a role in modulating Th2 immune responses (driven by OX40 costimulation) and T-cell activation (triggered by GITR). It is also involved in osteoclastogenesis. TRAF5 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more dive
Probab=98.43 E-value=1.4e-07 Score=65.87 Aligned_cols=38 Identities=16% Similarity=0.224 Sum_probs=30.8
Q ss_pred eeeeec-----CCccccccceeccccccccc--CCCCCCeEEEEEEE
Q psy10763 10 AYRFVQ-----GKDWGFKKFIRRDFLLDELN--GLLPEDKLTIFCEQ 49 (90)
Q Consensus 10 ~~~F~~-----~~~wG~~~Fi~R~~Le~e~s--~~L~dD~ltI~C~V 49 (90)
...|.. +..|||.+||+|+.|| .| .||+||+|+|+|.|
T Consensus 103 ~~~F~rp~~~~n~~~G~~~Fi~~~~Le--~s~~~ylkdD~~~Ik~~v 147 (148)
T cd03780 103 SSSFKRPDGEMNIASGCPRFVAHSVLE--NAKNTYIKDDTLFLKVAV 147 (148)
T ss_pred cccccCCCCCCCCCcChhheeEHHHhh--cccCCcCcCCEEEEEEEE
Confidence 355743 3359999999999994 54 89999999999976
No 9
>cd03777 MATH_TRAF3 Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF3 subfamily, TRAF domain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF3 was first described as a molecule that binds the cytoplasmic tail of CD40. However, it is not required for CD40 signaling. More recently, TRAF3 has been identified as a key regulator of type I interferon (IFN) production and the mammalian innate antiviral immunity. It mediates IFN responses in Toll-like receptor (TLR)-dependent as well as TLR-independent viral recognition pathways. It is also a key element in immunological homeostasis through its regulation of the anti-inflammatory cytokine interleukin-10. TRAF3 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more divergent N-terminal al
Probab=98.41 E-value=1.7e-07 Score=67.84 Aligned_cols=32 Identities=19% Similarity=0.229 Sum_probs=29.1
Q ss_pred CccccccceecccccccccCCCCCCeEEEEEEEE
Q psy10763 17 KDWGFKKFIRRDFLLDELNGLLPEDKLTIFCEQN 50 (90)
Q Consensus 17 ~~wG~~~Fi~R~~Le~e~s~~L~dD~ltI~C~Vt 50 (90)
..|||.+||+|+.| |.+.||+||+|+|+|+|.
T Consensus 153 ~~~G~~~Fi~~~~L--e~~~ylkdD~l~Irv~v~ 184 (186)
T cd03777 153 IASGCPVFVAQTVL--ENGTYIKDDTIFIKVIVD 184 (186)
T ss_pred CCCCchheeEHHHh--ccCCcEeCCEEEEEEEEe
Confidence 35999999999999 578899999999999886
No 10
>cd03775 MATH_Ubp21p Ubiquitin-specific protease 21 (Ubp21p) family, MATH domain; composed of fungal proteins with similarity to Ubp21p of fission yeast. Ubp21p is a deubiquitinating enzyme that may be involved in the regulation of the protein kinase Prp4p, which controls the formation of active spliceosomes. Members of this family are similar to human HAUSP (Herpesvirus-associated ubiquitin-specific protease) in that they contain an N-terminal MATH domain and a C-terminal catalytic protease (C19 family) domain. HAUSP is also an ubiquitin-specific protease that specifically catalyzes the deubiquitylation of p53 and MDM2. The MATH domain of HAUSP contains the binding site for p53 and MDM2. Similarly, the MATH domain of members in this family may be involved in substrate binding.
Probab=98.35 E-value=2.8e-07 Score=62.20 Aligned_cols=42 Identities=31% Similarity=0.488 Sum_probs=34.0
Q ss_pred ceeeeec-CCccccccceecccccc----cccCCCCCCeEEEEEEEE
Q psy10763 9 RAYRFVQ-GKDWGFKKFIRRDFLLD----ELNGLLPEDKLTIFCEQN 50 (90)
Q Consensus 9 ~~~~F~~-~~~wG~~~Fi~R~~Le~----e~s~~L~dD~ltI~C~Vt 50 (90)
..+.|.. ...|||.+||+|++|++ ..++||.||+|+|.+.|.
T Consensus 88 ~~~~F~~~~~~wG~~~fi~~~~L~~~~~~~~~g~l~nD~l~I~~~~~ 134 (134)
T cd03775 88 AHHRFNAEDKDWGFTRFIELRKLAHRTPDKPSPFLENGELNITVYVR 134 (134)
T ss_pred ceeEeCCCCCCCChhHcccHHHHcccccCCCCceeECCEEEEEEEEC
Confidence 3567775 46799999999999962 257999999999998863
No 11
>PF00917 MATH: MATH domain; InterPro: IPR002083 Although apparently functionally unrelated, intracellular TRAFs and extracellular meprins share a conserved region of about 180 residues, the meprin and TRAF homology (MATH) domain []. Meprins are mammalian tissue-specific metalloendopeptidases of the astacin family implicated in developmental, normal and pathological processes by hydrolysing a variety of proteins. Various growth factors, cytokines, and extracellular matrix proteins are substrates for meprins. They are composed of five structural domains: an N-terminal endopeptidase domain, a MAM domain (see PDOC00604 from PROSITEDOC), a MATH domain, an EGF-like domain (see PDOC00021 from PROSITEDOC) and a C-terminal transmembrane region. Meprin A and B form membrane bound homotetramer whereas homooligomers of meprin A are secreted. A proteolitic site adjacent to the MATH domain, only present in meprin A, allows the release of the protein from the membrane []. TRAF proteins were first isolated by their ability to interact with TNF receptors []. They promote cell survival by the activation of downstream protein kinases and, finally, transcription factors of the NF-kB and AP-1 family. The TRAF proteins are composed of 3 structural domains: a RING finger (see PDOC00449 from PROSITEDOC) in the N-terminal part of the protein, one to seven TRAF zinc fingers (see PDOC50145 from PROSITEDOC) in the middle and the MATH domain in the C-terminal part []. The MATH domain is necessary and sufficient for self-association and receptor interaction. From the structural analysis two consensus sequence recognised by the TRAF domain have been defined: a major one, [PSAT]x[QE]E and a minor one, PxQxxD []. The structure of the TRAF2 protein reveals a trimeric self-association of the MATH domain []. The domain forms a new, light-stranded antiparallel beta sandwich structure. A coiled-coil region adjacent to the MATH domain is also important for the trimerisation. The oligomerisation is essential for establishing appropriate connections to form signalling complexes with TNF receptor-1. The ligand binding surface of TRAF proteins is located in beta-strands 6 and 7 [].; GO: 0005515 protein binding; PDB: 1D00_E 1CZY_A 1D01_F 1CA9_A 1D0J_D 1F3V_B 1CA4_C 1D0A_A 1QSC_C 1CZZ_C ....
Probab=98.30 E-value=6e-07 Score=57.29 Aligned_cols=40 Identities=33% Similarity=0.461 Sum_probs=33.7
Q ss_pred eeeeecCCccccccceecccccccccCCCCCCeEEEEEEEEE
Q psy10763 10 AYRFVQGKDWGFKKFIRRDFLLDELNGLLPEDKLTIFCEQNP 51 (90)
Q Consensus 10 ~~~F~~~~~wG~~~Fi~R~~Le~e~s~~L~dD~ltI~C~VtV 51 (90)
.+.|.....||+.+||.+++|+.+ .||.||+++|+|+|+|
T Consensus 80 ~~~F~~~~~~g~~~fi~~~~l~~~--~fl~dd~l~ie~~v~I 119 (119)
T PF00917_consen 80 SHSFNNPSSWGWSSFISWEDLEDP--YFLVDDSLTIEVEVKI 119 (119)
T ss_dssp CEEECTTSEEEEEEEEEHHHHTTC--TTSBTTEEEEEEEEEE
T ss_pred eeEEeeecccchhheeEHHHhCcc--CCeECCEEEEEEEEEC
Confidence 467776678999999999999533 3899999999999986
No 12
>cd00121 MATH MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins. Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane and are capable of cleaving growth factors, extracellular matrix proteins, and biologically active peptides. TRAF molecules serve as adapter proteins that link cell surface receptors of the Tumor Necrosis Factor and 1nterleukin-1/Toll-like families to downstream kinase cascades, which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. Other members include the ubiquitin ligases, TRIM37 and SPOP, and the ubiquitin-specific proteases, HAUSP and Ubp21p. A large number of uncharacterized members mostly from lineage-specific expansions in C. elegans and rice contain MATH and BTB domains, similar to SPOP. The MATH doma
Probab=97.93 E-value=5.6e-06 Score=52.31 Aligned_cols=33 Identities=45% Similarity=0.606 Sum_probs=27.8
Q ss_pred CCccccccceecccccccccCCCCCCeEEEEEEEE
Q psy10763 16 GKDWGFKKFIRRDFLLDELNGLLPEDKLTIFCEQN 50 (90)
Q Consensus 16 ~~~wG~~~Fi~R~~Le~e~s~~L~dD~ltI~C~Vt 50 (90)
..+||+.+||++++|+ ...++.||+|+|+|+|.
T Consensus 94 ~~~~G~~~fi~~~~l~--~~~~~~~d~l~i~~~v~ 126 (126)
T cd00121 94 GSGWGFPKFISWDDLE--DSYYLVDDSLTIEVEVK 126 (126)
T ss_pred CCCCChHHeeEHHHhc--cCCcEECCEEEEEEEEC
Confidence 4679999999999995 43349999999999984
No 13
>cd03778 MATH_TRAF2 Tumor Necrosis Factor Receptor (TNFR) Associated Factor (TRAF) family, TRAF2 subfamily, TRAF domain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF2 associates with the receptors TNFR-1, TNFR-2, RANK (which mediates differentiation and maturation of osteoclasts) and CD40 (which is important for the proliferation and activation of B cells), among others. It regulates distinct pathways that lead to the activation of nuclear factor-kappaB and Jun NH2-terminal kinases. TRAF2 also indirectly associates with death receptors through its interaction with TRADD (TNFR-associated death domain protein). It is involved in regulating oxidative stress or ROS-induced cell death and in the preconditioning of cells by sublethal stress for protection from subsequent injury. TRAF2 contains a RING finger domain, five z
Probab=96.18 E-value=0.0049 Score=44.12 Aligned_cols=32 Identities=16% Similarity=0.020 Sum_probs=27.4
Q ss_pred CccccccceecccccccccCCCCCCeEEEEEEE
Q psy10763 17 KDWGFKKFIRRDFLLDELNGLLPEDKLTIFCEQ 49 (90)
Q Consensus 17 ~~wG~~~Fi~R~~Le~e~s~~L~dD~ltI~C~V 49 (90)
..|||.+||.-++|+. +.+||+||.+-|+|.|
T Consensus 132 ~~~G~~~Fv~l~~l~~-~~~Yv~dDtlfIk~~V 163 (164)
T cd03778 132 IASGCPLFCPVSKXEA-KNSYVRDDAIFIKAIV 163 (164)
T ss_pred cCcCcceEEEhhHccc-cCCcccCCeEEEEEEE
Confidence 4599999999999952 2589999999999976
No 14
>cd03771 MATH_Meprin Meprin family, MATH domain; Meprins are multidomain, highly glycosylated extracellular metalloproteases, which are either anchored to the membrane or secreted into extracellular spaces. They are expressed in renal and intestinal brush border membranes, leukocytes, and cancer cells, and are capable of cleaving growth factors, cytokines, extracellular matrix proteins, and biologically active peptides. Meprin proteases are composed of two related subunits, alpha and beta, which form homo- or hetro-complexes where the basic unit is a disulfide-linked dimer. Despite their similarity, the two subunits differ in their ability to self-associate, in proteolytic processing during biosynthesis and in substrate specificity. Both subunits are synthesized as membrane spanning proteins, however, the alpha subunit is cleaved during biosynthesis and loses its transmembrane domain. Meprin beta forms homodimers or heterotetramers while meprin alpha oligomerizes into large complexes co
Probab=96.07 E-value=0.0055 Score=43.84 Aligned_cols=31 Identities=26% Similarity=0.436 Sum_probs=26.8
Q ss_pred CccccccceecccccccccCCCCCCeEEEEEEE
Q psy10763 17 KDWGFKKFIRRDFLLDELNGLLPEDKLTIFCEQ 49 (90)
Q Consensus 17 ~~wG~~~Fi~R~~Le~e~s~~L~dD~ltI~C~V 49 (90)
.+|||.+||.-+.|+ ...||+||.|-|+.++
T Consensus 136 ~g~G~~~Fis~~~L~--~r~ylk~dtl~i~~~~ 166 (167)
T cd03771 136 PGYGWSTFISHSRLR--RRDFLKGDDLIILLDF 166 (167)
T ss_pred CccccccceeHHHhc--cCCCCcCCEEEEEEEe
Confidence 469999999999995 4559999999998875
No 15
>cd03783 MATH_Meprin_Alpha Meprin family, Alpha subunit, MATH domain; Meprins are multidomain extracellular metalloproteases capable of cleaving growth factors, cytokines, extracellular matrix proteins, and biologically active peptides. They are composed of two related subunits, alpha and beta, which form homo- or hetro-complexes where the basic unit is a disulfide-linked dimer. The alpha subunit is synthesized as a membrane spanning protein, however, it is cleaved during biosynthesis and loses its transmembrane domain. It oligomerizes into large complexes, containing 10-100 subunits (dimers that associate noncovalently), which are secreted as latent proteases and can move through extracellular spaces in a nondestructive manner. This allows delivery of the concentrated protease to sites containing activating enzymes, such as sites of inflammation, infection or cancerous growth. Meprin alpha shows preference for small or hydrophobic residues at the P1 and P1' sites of its substrate. Both
Probab=94.20 E-value=0.035 Score=39.99 Aligned_cols=32 Identities=34% Similarity=0.613 Sum_probs=26.9
Q ss_pred CCccccccceecccccccccCCCCCCeEEEEEEE
Q psy10763 16 GKDWGFKKFIRRDFLLDELNGLLPEDKLTIFCEQ 49 (90)
Q Consensus 16 ~~~wG~~~Fi~R~~Le~e~s~~L~dD~ltI~C~V 49 (90)
+.+|||.+||.-+.|+ ...||+||.+-|.-++
T Consensus 135 ~~gfG~~~Fish~~L~--~r~yikdDtlfI~~~~ 166 (167)
T cd03783 135 GIDFGWSTFISHSQLR--RRSFLKNDDLIIFVDF 166 (167)
T ss_pred CcccccccceeHHHHh--hCCcccCCeEEEEEec
Confidence 3469999999999994 6679999999997654
No 16
>cd03782 MATH_Meprin_Beta Meprin family, Beta subunit, MATH domain; Meprins are multidomain extracellular metalloproteases capable of cleaving growth factors, cytokines, extracellular matrix proteins, and biologically active peptides. They are composed of two related subunits, alpha and beta, which form homo- or hetro-complexes where the basic unit is a disulfide-linked dimer. The beta subunit is a type I membrane protein, which forms homodimers or heterotetramers (alpha2beta2 or alpha3beta). Meprin beta shows preference for acidic residues at the P1 and P1' sites of its substrate. Among its best substrates are growth factors and chemokines such as gastrin and osteopontin. Both alpha and beta subunits contain a catalytic astacin (M12 family) protease domain followed by the adhesion or interaction domains MAM, MATH and AM. The MATH and MAM domains provide symmetrical intersubunit disulfide bonds necessary for the dimerization of meprin subunits. The MATH domain may also be required for f
Probab=92.56 E-value=0.1 Score=37.68 Aligned_cols=31 Identities=19% Similarity=0.322 Sum_probs=26.1
Q ss_pred CCccccccceecccccccccCCCCCCeEEEEEE
Q psy10763 16 GKDWGFKKFIRRDFLLDELNGLLPEDKLTIFCE 48 (90)
Q Consensus 16 ~~~wG~~~Fi~R~~Le~e~s~~L~dD~ltI~C~ 48 (90)
+.+||+.+||.-+.|+ ...||+||.+-|--+
T Consensus 135 ~~~~G~~~Fish~~L~--~r~yikdD~ifi~~~ 165 (167)
T cd03782 135 GPGYGTSAFITHLRLR--SRDFIKGDDVIFLLT 165 (167)
T ss_pred ccccCccceeeHHHHh--hcCcccCCeEEEEEe
Confidence 4669999999999995 566999999888654
No 17
>COG5077 Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=85.98 E-value=0.67 Score=41.00 Aligned_cols=47 Identities=30% Similarity=0.411 Sum_probs=37.7
Q ss_pred eeeeec-CCccccccceeccccccc---ccCCCCCCeEEEEEEEEEeeeee
Q psy10763 10 AYRFVQ-GKDWGFKKFIRRDFLLDE---LNGLLPEDKLTIFCEQNPLILVV 56 (90)
Q Consensus 10 ~~~F~~-~~~wG~~~Fi~R~~Le~e---~s~~L~dD~ltI~C~VtVv~e~~ 56 (90)
-|+|+. ...|||.+||.-..|... ..++|.++.+.|.-.|.|.++|.
T Consensus 125 HhrFs~~~tDwGFt~f~dL~kl~~psp~~Ppfleeg~l~ItvyVRvlkdPT 175 (1089)
T COG5077 125 HHRFSMESTDWGFTNFIDLNKLIEPSPGRPPFLEEGTLVITVYVRVLKDPT 175 (1089)
T ss_pred cccccccccccchhhhhhhhhhcCCCCCCCCcccCCeEEEEEEEEEEeCCc
Confidence 478887 578999999998888621 12468899999999999999865
No 18
>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis. PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain
Probab=81.42 E-value=0.51 Score=30.34 Aligned_cols=24 Identities=13% Similarity=0.245 Sum_probs=18.1
Q ss_pred ecccccccccCCCCCCeEEEEEEEE
Q psy10763 26 RRDFLLDELNGLLPEDKLTIFCEQN 50 (90)
Q Consensus 26 ~R~~Le~e~s~~L~dD~ltI~C~Vt 50 (90)
.=++|+ ......+|.|||++|+.+
T Consensus 57 ~d~dle-~aws~~~~~~lTLwC~~~ 80 (80)
T cd06406 57 SDTNME-DVWSQAKDGCLTLWCTLT 80 (80)
T ss_pred ChHHHH-HHHHhhcCCeEEEEEecC
Confidence 445565 556789999999999853
No 19
>KOG1863|consensus
Probab=76.02 E-value=1.9 Score=38.73 Aligned_cols=46 Identities=15% Similarity=0.162 Sum_probs=39.5
Q ss_pred ceeeeec-CCccccccceecccccccccCCCCCCeEEEEEEEEEeee
Q psy10763 9 RAYRFVQ-GKDWGFKKFIRRDFLLDELNGLLPEDKLTIFCEQNPLIL 54 (90)
Q Consensus 9 ~~~~F~~-~~~wG~~~Fi~R~~Le~e~s~~L~dD~ltI~C~VtVv~e 54 (90)
..|.|.. ...|||..|+.++.+-..+.+|+.+|+..+++.|.|-+.
T Consensus 108 ~~h~~~~~~~dwg~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~~~ 154 (1093)
T KOG1863|consen 108 IHHVFTADERDWGFSCFSTSSDIRKPEDGYVRNGLEKLEKRVRVEQP 154 (1093)
T ss_pred hhhcccccccchhhccchhHhhccCcccccccccceeeeeeeeeecC
Confidence 4567776 477999999999999888889999999999999999764
No 20
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=54.23 E-value=5.2 Score=22.14 Aligned_cols=17 Identities=18% Similarity=0.213 Sum_probs=14.4
Q ss_pred CCCCcHHHHHHHhhhcC
Q psy10763 71 SWNGKMPHQLKLVFQEN 87 (90)
Q Consensus 71 vPPSdL~~hLg~LL~~~ 87 (90)
+++|.+++||..|.+.|
T Consensus 27 ~s~~~vs~hL~~L~~~g 43 (47)
T PF01022_consen 27 LSQSTVSHHLKKLREAG 43 (47)
T ss_dssp S-HHHHHHHHHHHHHTT
T ss_pred ccchHHHHHHHHHHHCc
Confidence 58999999999999876
No 21
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=46.12 E-value=8.3 Score=22.29 Aligned_cols=17 Identities=12% Similarity=0.045 Sum_probs=14.0
Q ss_pred CCCCcHHHHHHHhhhcC
Q psy10763 71 SWNGKMPHQLKLVFQEN 87 (90)
Q Consensus 71 vPPSdL~~hLg~LL~~~ 87 (90)
+|++.+++||..|-+.|
T Consensus 36 ~~~~t~s~hL~~L~~aG 52 (61)
T PF12840_consen 36 ISQSTVSYHLKKLEEAG 52 (61)
T ss_dssp S-HHHHHHHHHHHHHTT
T ss_pred CCHHHHHHHHHHHHHCC
Confidence 59999999999998765
No 22
>PF12188 STAT2_C: Signal transducer and activator of transcription 2 C terminal; InterPro: IPR022756 This region is found in the mammalian signal transducer and activation of transcription (STAT) 2 protein, and is approximately 60 amino acids in length. The family is found in association with PF02865 from PFAM, PF00017 from PFAM, PF01017 from PFAM, PF02864 from PFAM. There is a conserved DLP sequence motif. STATs are involved in transcriptional regulation and are the only regulators known to be modulated by tyrosine phosphorylation. STAT2 forms a trimeric complex with STAT1 and IRF-9 (Interferon Regulatory Factor 9), on activation of the cell by interferon, which is called ISGF3 (Interferon-stimulated gene factor 3). The C-terminal domain of STAT2 contains a nuclear export signal (NES) which allows export of STAT2 into the cytoplasm along with any complexed molecules. ; PDB: 2KA4_B.
Probab=32.74 E-value=19 Score=21.70 Aligned_cols=13 Identities=23% Similarity=0.424 Sum_probs=5.2
Q ss_pred CCCCcHHHHHHHh
Q psy10763 71 SWNGKMPHQLKLV 83 (90)
Q Consensus 71 vPPSdL~~hLg~L 83 (90)
+|.|||.++|..|
T Consensus 4 ~pEpDLP~DL~hl 16 (56)
T PF12188_consen 4 VPEPDLPHDLQHL 16 (56)
T ss_dssp -------HHHHTS
T ss_pred CCCCCccHHHHHh
Confidence 4999999999876
No 23
>PF06565 DUF1126: Repeat of unknown function (DUF1126); InterPro: IPR010554 This group contains several eukaryote specific repeats of around 35 residues in length. The function of this family is unknown.; PDB: 2Z14_A 2Z13_A.
Probab=29.78 E-value=14 Score=19.64 Aligned_cols=9 Identities=33% Similarity=0.744 Sum_probs=6.7
Q ss_pred CCCCCeEEE
Q psy10763 37 LLPEDKLTI 45 (90)
Q Consensus 37 ~L~dD~ltI 45 (90)
||.||.+.|
T Consensus 5 ~L~DdTi~I 13 (33)
T PF06565_consen 5 YLADDTISI 13 (33)
T ss_dssp ETTTTEEEE
T ss_pred EccCCCEEE
Confidence 677888766
No 24
>TIGR01552 phd_fam prevent-host-death family protein. This model recognizes a region of about 55 amino acids toward the N-terminal end of bacterial proteins of about 85 amino acids in length. The best-characterized member is prevent-host-death (phd) of bacteriophage P1, the antidote partner of death-on-curing (doc) (TIGR01550) in an addiction module. Addiction modules prevent plasmid curing by killing the host cell as the longer-lived killing protein persists while the gene for the shorter-lived antidote is lost. Note, however, that relatively few members of this family appear to be plasmid or phage-encoded. Also, there is little overlap, except for phage P1 itself, of species with this family and with the doc family.
Probab=29.41 E-value=26 Score=19.42 Aligned_cols=16 Identities=6% Similarity=0.034 Sum_probs=13.4
Q ss_pred CCCCcHHHHHHHhhhc
Q psy10763 71 SWNGKMPHQLKLVFQE 86 (90)
Q Consensus 71 vPPSdL~~hLg~LL~~ 86 (90)
+|-+++..||+++|+.
T Consensus 2 v~~te~r~~~~~~l~~ 17 (52)
T TIGR01552 2 VSLSEAKNKLGELLKR 17 (52)
T ss_pred cCHHHHHHHHHHHHHH
Confidence 4788999999999853
No 25
>cd04468 S1_eIF5A S1_eIF5A: Eukaryotic translation Initiation Factor 5A (eIF5A), S1-like RNA-binding domain. eIF5A is an evolutionarily conserved protein found in eukaryotes. eIF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is essential for eIF5A function and is a post-translationally modified lysine. eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) in a hypusine-dependent manner. This C-terminal S1 domain resembles the oligonucleotides-binding fold (OB fold) which binds RNA. Moreover, eIF5A prefers binding to the actively translating ribosome. This evidence suggests that eIF5A plays a role in translation elongation instead of translation initiation as previously proposed.
Probab=27.86 E-value=46 Score=20.64 Aligned_cols=18 Identities=22% Similarity=0.394 Sum_probs=15.7
Q ss_pred CCCCcHHHHHHHhhhcCC
Q psy10763 71 SWNGKMPHQLKLVFQENK 88 (90)
Q Consensus 71 vPPSdL~~hLg~LL~~~~ 88 (90)
+|+++|.+.+.+.++++|
T Consensus 31 lP~~elg~~I~~~f~~gk 48 (69)
T cd04468 31 LPEGELGKEIREKFDEGK 48 (69)
T ss_pred CCcHHHHHHHHHHHhCCC
Confidence 399999999999998775
No 26
>KOG2488|consensus
Probab=27.24 E-value=14 Score=27.65 Aligned_cols=37 Identities=14% Similarity=0.244 Sum_probs=27.9
Q ss_pred CccccccceecccccccccCCCC--CC----------eEEEEEEEEEee
Q psy10763 17 KDWGFKKFIRRDFLLDELNGLLP--ED----------KLTIFCEQNPLI 53 (90)
Q Consensus 17 ~~wG~~~Fi~R~~Le~e~s~~L~--dD----------~ltI~C~VtVv~ 53 (90)
+.||+..++++.+|....++||- |. +|++.|-+.|+-
T Consensus 74 s~~Gw~~~~K~~El~~~~~~Yi~a~~~~~~~vgf~~Frf~vd~g~~vlY 122 (202)
T KOG2488|consen 74 SSWGWDDNSKAKELRNRKLRYICAWNNKSKLVGFTMFRFTVDTGDPVLY 122 (202)
T ss_pred cccccCchhHHHHHhhccceEEEEEcCCCceeeEEEEEEEcccCCeEEE
Confidence 44999999999999877788863 33 466777767764
No 27
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=26.77 E-value=35 Score=22.91 Aligned_cols=17 Identities=18% Similarity=0.245 Sum_probs=14.8
Q ss_pred CCCCcHHHHHHHhhhcC
Q psy10763 71 SWNGKMPHQLKLVFQEN 87 (90)
Q Consensus 71 vPPSdL~~hLg~LL~~~ 87 (90)
+++|.+++||+.|-+.|
T Consensus 42 lsqstvS~HL~~L~~AG 58 (117)
T PRK10141 42 QSQPKISRHLALLRESG 58 (117)
T ss_pred cCHHHHHHHHHHHHHCC
Confidence 59999999999997765
No 28
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=26.44 E-value=26 Score=21.72 Aligned_cols=17 Identities=18% Similarity=0.278 Sum_probs=13.2
Q ss_pred CCCCcHHHHHHHhhhcC
Q psy10763 71 SWNGKMPHQLKLVFQEN 87 (90)
Q Consensus 71 vPPSdL~~hLg~LL~~~ 87 (90)
+++++|.+||..|=+.|
T Consensus 26 lt~g~Ls~hL~~Le~~G 42 (80)
T PF13601_consen 26 LTDGNLSKHLKKLEEAG 42 (80)
T ss_dssp --HHHHHHHHHHHHHTT
T ss_pred cCHHHHHHHHHHHHHCC
Confidence 58999999999987665
No 29
>PF13895 Ig_2: Immunoglobulin domain; PDB: 2V5R_B 2V5M_A 2V5S_B 2GI7_A 3LAF_A 4DEP_C 3O4O_B 2EC8_A 2E9W_A 1J87_A ....
Probab=25.95 E-value=54 Score=18.24 Aligned_cols=14 Identities=21% Similarity=0.442 Sum_probs=11.9
Q ss_pred CCCCCeEEEEEEEE
Q psy10763 37 LLPEDKLTIFCEQN 50 (90)
Q Consensus 37 ~L~dD~ltI~C~Vt 50 (90)
+...|.++|.|.+.
T Consensus 11 v~~g~~~~l~C~~~ 24 (80)
T PF13895_consen 11 VEEGDSVTLTCSVS 24 (80)
T ss_dssp EETTSEEEEEEEEE
T ss_pred EeCCCcEEEEEEEE
Confidence 45689999999987
No 30
>PF05253 zf-U11-48K: U11-48K-like CHHC zinc finger; InterPro: IPR022776 This zinc binding domain [] has four conserved zinc chelating residues in a CHHC pattern. This domain is predicted to have an RNA-binding function []. ; PDB: 2VY5_A 2VY4_A.
Probab=25.19 E-value=26 Score=17.55 Aligned_cols=12 Identities=8% Similarity=0.102 Sum_probs=10.0
Q ss_pred CCCCcHHHHHHH
Q psy10763 71 SWNGKMPHQLKL 82 (90)
Q Consensus 71 vPPSdL~~hLg~ 82 (90)
||.++|..|+..
T Consensus 13 v~~~~l~~Hi~~ 24 (27)
T PF05253_consen 13 VPASELQKHIKK 24 (27)
T ss_dssp EEGGGHHHHHHH
T ss_pred cCHHHHHHHHHH
Confidence 399999999864
No 31
>KOG4844|consensus
Probab=24.49 E-value=32 Score=22.92 Aligned_cols=18 Identities=11% Similarity=0.229 Sum_probs=17.1
Q ss_pred CCCcHHHHHHHhhhcCCC
Q psy10763 72 WNGKMPHQLKLVFQENKF 89 (90)
Q Consensus 72 PPSdL~~hLg~LL~~~~~ 89 (90)
||-+.-+||-.||.+++|
T Consensus 49 p~~~~~r~l~tll~d~ef 66 (102)
T KOG4844|consen 49 PPYDIKRELPTLLADEEF 66 (102)
T ss_pred chHHhhhhhhhhhccccc
Confidence 999999999999999988
No 32
>cd06411 PB1_p51 The PB1 domain is present in the p51 protein, a homolog of the p67 protein. p51 plays an important role in NADPH oxidase activation during phagosytosis. The PB1 domain is a modular domain mediating specific protein-protein interaction in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain mo
Probab=20.54 E-value=1.8e+02 Score=18.46 Aligned_cols=12 Identities=17% Similarity=0.329 Sum_probs=9.3
Q ss_pred EEEEEEEEEeee
Q psy10763 43 LTIFCEQNPLIL 54 (90)
Q Consensus 43 ltI~C~VtVv~e 54 (90)
+|++|..||.-.
T Consensus 1 ~~Vh~~fTVai~ 12 (78)
T cd06411 1 VTVQCAFTVALR 12 (78)
T ss_pred CEEEEEEEEEEE
Confidence 478999998743
No 33
>COG4259 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.07 E-value=70 Score=21.94 Aligned_cols=14 Identities=14% Similarity=0.249 Sum_probs=11.2
Q ss_pred CCcHHHHHHHhhhc
Q psy10763 73 NGKMPHQLKLVFQE 86 (90)
Q Consensus 73 PSdL~~hLg~LL~~ 86 (90)
|+..|.|||-|+++
T Consensus 71 pPG~HAhLGlLys~ 84 (121)
T COG4259 71 PPGYHAHLGLLYSN 84 (121)
T ss_pred CCcHHHHHHHHHhh
Confidence 34799999999864
Done!