Query 018587
Match_columns 353
No_of_seqs 161 out of 433
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 10:15:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018587.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018587hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00183 TFIIS_I N-terminal dom 99.7 1E-17 2.2E-22 132.4 6.8 73 121-193 2-76 (76)
2 smart00509 TFS2N Domain in the 99.6 1.9E-16 4E-21 125.3 5.1 59 135-193 16-74 (75)
3 TIGR01385 TFSII transcription 99.6 3.5E-15 7.6E-20 145.1 8.0 78 121-198 2-81 (299)
4 PF08711 Med26: TFIIS helical 99.4 6E-14 1.3E-18 103.2 4.1 52 142-193 1-53 (53)
5 KOG1105 Transcription elongati 99.2 4.1E-11 8.9E-16 116.6 6.1 75 121-195 4-81 (296)
6 KOG2821 RNA polymerase II tran 97.3 0.00013 2.8E-09 74.7 2.7 72 121-195 9-80 (433)
7 PF11467 LEDGF: Lens epitheliu 95.2 0.03 6.6E-07 47.7 4.7 69 125-193 10-80 (106)
8 KOG1793 Uncharacterized conser 94.3 0.05 1.1E-06 55.7 4.3 52 141-192 236-290 (417)
9 COG5139 Uncharacterized conser 90.0 0.36 7.9E-06 48.3 4.1 51 142-192 234-286 (397)
10 PLN02976 amine oxidase 87.0 1.1 2.3E-05 53.2 5.9 60 139-198 1302-1362(1713)
11 cd08815 Death_TNFRSF25_DR3 Dea 79.3 2 4.4E-05 35.0 3.0 39 2-49 10-48 (77)
12 PF06881 Elongin_A: RNA polyme 54.3 16 0.00035 30.5 3.6 32 297-328 76-107 (109)
13 cd08784 Death_DRs Death Domain 49.4 22 0.00048 28.3 3.4 40 1-49 9-48 (79)
14 cd08316 Death_FAS_TNFRSF6 Deat 46.9 21 0.00045 30.0 3.0 42 1-50 18-59 (97)
15 PF14726 RTTN_N: Rotatin, an a 38.9 40 0.00086 28.5 3.5 52 135-186 45-96 (98)
16 cd08313 Death_TNFR1 Death doma 38.2 36 0.00079 27.6 3.1 40 1-49 9-48 (80)
17 PF11471 Sugarporin_N: Maltopo 32.6 66 0.0014 24.9 3.6 27 295-321 28-54 (60)
18 PF12054 DUF3535: Domain of un 29.1 25 0.00053 36.6 0.9 45 299-343 265-317 (441)
19 PF06936 Selenoprotein_S: Sele 28.6 49 0.0011 31.1 2.7 29 296-324 80-119 (190)
20 PF08735 DUF1786: Putative pyr 21.8 27 0.00059 34.2 -0.3 28 2-32 61-88 (254)
21 KOG1087 Cytosolic sorting prot 20.9 1.3E+02 0.0027 32.2 4.3 30 165-194 86-116 (470)
22 PF07149 Pes-10: Pes-10; Inte 20.6 1.9E+02 0.004 30.1 5.3 54 136-191 19-72 (370)
23 PF10588 NADH-G_4Fe-4S_3: NADH 20.4 64 0.0014 22.8 1.4 22 40-62 1-22 (41)
No 1
>cd00183 TFIIS_I N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme
Probab=99.72 E-value=1e-17 Score=132.38 Aligned_cols=73 Identities=45% Similarity=0.766 Sum_probs=69.0
Q ss_pred HHHHHHHHHhCCCCC--CHHHHHHHHHHhhcCCCCHHHhhccCcccccchhccCCCHHHHHHHHHHHHHHHHhHH
Q 018587 121 KRILEIKEHLEDPDQ--SEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVRKWKDIVD 193 (353)
Q Consensus 121 ~EV~rIKk~Le~~~~--see~llelLr~L~~l~iT~dlLk~T~IGkaVn~LRKH~s~~I~~LAk~LVkkWK~~V~ 193 (353)
+|+.++++.|+...+ +.+.++++|+.|+.+|||+++|++|+||++||.||||.+++|+.+|+.||++||++|+
T Consensus 2 ~ev~r~~~~l~~~~~~~~~~~~~~~L~~L~~~~it~~~L~~T~iG~~V~~Lrkh~~~~i~~~A~~Lv~~Wk~~v~ 76 (76)
T cd00183 2 EEVLRAKKKLEKKDSNEEVSRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHSNEKIRKLAKALIKSWKKLVD 76 (76)
T ss_pred hHHHHHHHHhhccccCCCHHHHHHHHHHHhcCCCCHHHHHHCCHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhcC
Confidence 479999999998764 8889999999999999999999999999999999999999999999999999999873
No 2
>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere).
Probab=99.64 E-value=1.9e-16 Score=125.31 Aligned_cols=59 Identities=41% Similarity=0.734 Sum_probs=56.3
Q ss_pred CCHHHHHHHHHHhhcCCCCHHHhhccCcccccchhccCCCHHHHHHHHHHHHHHHHhHH
Q 018587 135 QSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVRKWKDIVD 193 (353)
Q Consensus 135 ~see~llelLr~L~~l~iT~dlLk~T~IGkaVn~LRKH~s~~I~~LAk~LVkkWK~~V~ 193 (353)
.+++.++++|+.|+.++||+++|+.|+||++||+||||++++|+.+|+.||+.||++|+
T Consensus 16 ~~~~~~l~~L~~L~~~~~t~~~L~~T~iG~~v~~Lrkh~~~~I~~~A~~Li~~WK~~v~ 74 (75)
T smart00509 16 KEVSRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHKNEEIRKLAKKLIKSWKKLVY 74 (75)
T ss_pred CCHHHHHHHHHHHhcCCCCHHHHHHCcHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHhc
Confidence 34788999999999999999999999999999999999999999999999999999985
No 3
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=99.57 E-value=3.5e-15 Score=145.08 Aligned_cols=78 Identities=29% Similarity=0.534 Sum_probs=71.6
Q ss_pred HHHHHHHHHhCCCC--CCHHHHHHHHHHhhcCCCCHHHhhccCcccccchhccCCCHHHHHHHHHHHHHHHHhHHHHhhc
Q 018587 121 KRILEIKEHLEDPD--QSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVRKWKDIVDEWVKL 198 (353)
Q Consensus 121 ~EV~rIKk~Le~~~--~see~llelLr~L~~l~iT~dlLk~T~IGkaVn~LRKH~s~~I~~LAk~LVkkWK~~V~e~~~~ 198 (353)
+||.++.+.|+++. .+++.+|++|+.|+.++||+++|++|+||++||+||||++++|+.||+.||++||++|+.+...
T Consensus 2 ~ei~~~~k~L~k~~~~~~~~~~l~~L~~L~~~~~t~~lL~~T~IG~~Vn~lrkh~~~~I~~lAk~li~~WK~~v~~~k~~ 81 (299)
T TIGR01385 2 AEVASHAKALDKNKSSKNVEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDISKLAKKIIKSWKKVVDKNKSD 81 (299)
T ss_pred hHHHHHHHHhhhhccCCCHHHHHHHHHHHhcCCCcHHHHhhCchhHHHHHHHcCCcHHHHHHHHHHHHHHHHHHhhhccc
Confidence 37999999998854 4778999999999999999999999999999999999999999999999999999999987443
No 4
>PF08711 Med26: TFIIS helical bundle-like domain; InterPro: IPR017923 Transcription factor IIS (TFIIS) is a transcription elongation factor that increases the overall transcription rate of RNA polymerase II by reactivating transcription elongation complexes that have arrested transcription. The three structural domains of TFIIS are conserved from yeast to human. The 80 or so N-terminal residues form a protein interaction domain containing a conserved motif, which has been called the LW motif because of the invariant leucine and tryptophan residues it contains. Although the N-terminal domain is not needed for transcriptional activity, a similar sequence has been identified in other transcription factors and proteins that are predominantly nuclear localized [, ]: MED26 (also known as CRSP70 and ARC70), a subunit of the Mediator complex, which is required for the activity of the enhancer-binding protein Sp1. Elongin A, a subunit of a transcription elongation factor previously known as SIII. It increases the rate of transcription by suppressing transient pausing of the elongation complex. PPP1R10, a nuclear regulatory subunit of protein phosphatase 1 that was previously known as p99, FB19 or PNUTS. PIBP, a small hypothetical protein that could be a phosphoinositide binding protein. IWS1, which is thought to function in both transcription initiation and elongation. The TFIIS N-terminal domain is a compact four-helix bundle. The hydrophobic core residues of helices 2, 3, and 4 are well conserved among TFIIS domains, although helix 1 is less conserved []. ; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 1EO0_A 3OAK_A 3NFQ_B 3O8Z_A 1WJT_A 2XPL_A 2XPO_A 2XPP_A 2XPN_A.
Probab=99.45 E-value=6e-14 Score=103.24 Aligned_cols=52 Identities=50% Similarity=0.872 Sum_probs=47.5
Q ss_pred HHHHHhhcCCCCHHHhhccCcccccchhccC-CCHHHHHHHHHHHHHHHHhHH
Q 018587 142 DLLQSLADMDITFKALKETDIGRHVNQLRKH-SSNDVRKLVKHLVRKWKDIVD 193 (353)
Q Consensus 142 elLr~L~~l~iT~dlLk~T~IGkaVn~LRKH-~s~~I~~LAk~LVkkWK~~V~ 193 (353)
++|+.|..+|||.++|++|+||++||.|||| .+++|+++|+.||++||.+|+
T Consensus 1 ~iL~~L~~l~it~~~L~~T~IGk~V~~l~k~~~~~~i~~~A~~Li~~Wk~~v~ 53 (53)
T PF08711_consen 1 EILKVLEKLPITVELLKSTGIGKAVNKLRKHSENPEIRKLAKELIKKWKRIVD 53 (53)
T ss_dssp HHHHHHHCSS-SHHHHHHHSHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHH-
T ss_pred CHHHHhhcCCCCHHHHHhCChhHHHHHHHcCCCCHHHHHHHHHHHHHHhHhcC
Confidence 5899999999999999999999999999999 889999999999999999985
No 5
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=99.15 E-value=4.1e-11 Score=116.61 Aligned_cols=75 Identities=37% Similarity=0.628 Sum_probs=68.3
Q ss_pred HHHHHHHHHhCCCCC--CHHHHHHHHHHhhcCCCCHHHhhccCcccccc-hhccCCCHHHHHHHHHHHHHHHHhHHHH
Q 018587 121 KRILEIKEHLEDPDQ--SEDALIDLLQSLADMDITFKALKETDIGRHVN-QLRKHSSNDVRKLVKHLVRKWKDIVDEW 195 (353)
Q Consensus 121 ~EV~rIKk~Le~~~~--see~llelLr~L~~l~iT~dlLk~T~IGkaVn-~LRKH~s~~I~~LAk~LVkkWK~~V~e~ 195 (353)
+|++++.+.|+...+ +.+.++++|.+|..+|||+++|++|+||+.|| .|++|++++|+.+|+.||+.||++|+..
T Consensus 4 e~~~r~ak~l~~~~~~~n~~~~ld~l~~L~~~pvt~ell~~Tr~g~~vn~~~Kk~~n~ev~~~ak~Lik~Wkk~~~~~ 81 (296)
T KOG1105|consen 4 EEALRAAKALEKDKQSKNVEAALDLLKRLKKIPVTLELLQETRTGMGVNEVLKKHKNEEVRSLAKKLIKSWKKLVDKS 81 (296)
T ss_pred HHHHHHHHHHHhhcccccHHHHHHHHHHHHhcccHHHHHHHhhHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhhcc
Confidence 579999999988644 56789999999999999999999999999999 5667889999999999999999999986
No 6
>KOG2821 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin A [Transcription]
Probab=97.30 E-value=0.00013 Score=74.75 Aligned_cols=72 Identities=35% Similarity=0.464 Sum_probs=64.5
Q ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHHhhcCCCCHHHhhccCcccccchhccCCCHHHHHHHHHHHHHHHHhHHHH
Q 018587 121 KRILEIKEHLEDPDQSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVRKWKDIVDEW 195 (353)
Q Consensus 121 ~EV~rIKk~Le~~~~see~llelLr~L~~l~iT~dlLk~T~IGkaVn~LRKH~s~~I~~LAk~LVkkWK~~V~e~ 195 (353)
.-|.++...|++. .....++..|..|..+|++++.|.+|.||++|+.||||. .|..++..|+..||+.|...
T Consensus 9 ~~Vr~lQ~~l~~~-~dpkR~lk~I~~ls~lP~~~k~l~Et~~~k~l~~L~k~~--~~g~~~~Dl~~~WK~~v~~d 80 (433)
T KOG2821|consen 9 GAVRKLQARLENR-IDPKRLLKRIQKLSNLPHLFKHLLETGKGKTLNSLRKIS--HVGKLAFDLVALWKDLVLVD 80 (433)
T ss_pred HHHHHHHHHHHhC-ccHHHHHHHHHHhccchHHHHHHHHhhhhHHHHHHHHhh--cccccccchHHHHHHhcccc
Confidence 3577888888865 567899999999999999999999999999999999996 79999999999999999633
No 7
>PF11467 LEDGF: Lens epithelium-derived growth factor (LEDGF) ; InterPro: IPR021567 LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis. It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alpha-helices. The residues essential for the interaction with the integrase are present in the inter-helical loop regions of the bundle structure. ; PDB: 3F9K_K 3HPG_G 3U88_C 3HPH_H 2B4J_D 1Z9E_A.
Probab=95.22 E-value=0.03 Score=47.71 Aligned_cols=69 Identities=22% Similarity=0.340 Sum_probs=51.8
Q ss_pred HHHHHhCCCCCCHHHHHHHHHHhhcCCCCHHHhhc-cCcccccchhccC-CCHHHHHHHHHHHHHHHHhHH
Q 018587 125 EIKEHLEDPDQSEDALIDLLQSLADMDITFKALKE-TDIGRHVNQLRKH-SSNDVRKLVKHLVRKWKDIVD 193 (353)
Q Consensus 125 rIKk~Le~~~~see~llelLr~L~~l~iT~dlLk~-T~IGkaVn~LRKH-~s~~I~~LAk~LVkkWK~~V~ 193 (353)
.|+..|--...+...+|++|..|..++||..+|+. +.+--++.+||+. +|..|+..|..|+.+.|.++.
T Consensus 10 ~Ik~~L~~~~~Dv~kcL~~LdeL~~l~vT~~mL~kn~e~V~TlkklRrY~gn~~Ir~KA~~lYnkfK~~f~ 80 (106)
T PF11467_consen 10 EIKSSLKVDNPDVKKCLKALDELKSLQVTSLMLQKNPECVETLKKLRRYKGNQQIRKKATELYNKFKSLFL 80 (106)
T ss_dssp HHHHTCETTEE-HHHHHHHHHHHHTS---HHHHTTTHHHHHHHHHHTT-TT-HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHcCCCCCHHHHHHHHHHHhccCCCHHHHHhCHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHhC
Confidence 34444532234788999999999999999998874 5688899999997 458999999999999999985
No 8
>KOG1793 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.25 E-value=0.05 Score=55.72 Aligned_cols=52 Identities=29% Similarity=0.519 Sum_probs=45.9
Q ss_pred HHHHHHhhcCCCCH-HHhhccCcccccchhccCCC--HHHHHHHHHHHHHHHHhH
Q 018587 141 IDLLQSLADMDITF-KALKETDIGRHVNQLRKHSS--NDVRKLVKHLVRKWKDIV 192 (353)
Q Consensus 141 lelLr~L~~l~iT~-dlLk~T~IGkaVn~LRKH~s--~~I~~LAk~LVkkWK~~V 192 (353)
..+|.-|..+||-. +.|+..+||++|==|-||+. ..++.+|..||..|-.-|
T Consensus 236 ~~ll~iL~dlpi~~~E~Lk~SGlGkvVmflsks~ket~~nkrlA~kLI~eWsRpI 290 (417)
T KOG1793|consen 236 KSLLDILNDLPIDKREHLKESGLGKVVMFLSKSPKETKENKRLANKLINEWSRPI 290 (417)
T ss_pred HHHHHHHhcCCcchHHHHHhcCCCeEEEEEecCCccchHHHHHHHHHHHHhhccc
Confidence 45677788889888 99999999999999999976 789999999999998755
No 9
>COG5139 Uncharacterized conserved protein [Function unknown]
Probab=89.95 E-value=0.36 Score=48.30 Aligned_cols=51 Identities=31% Similarity=0.513 Sum_probs=43.0
Q ss_pred HHHHHhhcCCCCHHHhhccCcccccchh--ccCCCHHHHHHHHHHHHHHHHhH
Q 018587 142 DLLQSLADMDITFKALKETDIGRHVNQL--RKHSSNDVRKLVKHLVRKWKDIV 192 (353)
Q Consensus 142 elLr~L~~l~iT~dlLk~T~IGkaVn~L--RKH~s~~I~~LAk~LVkkWK~~V 192 (353)
.||..|..|||-.+.|+..+||+.|==. .|...++|+.+|+.||..|-.-|
T Consensus 234 sL~dvL~~lpI~tEHL~eSgvGrIV~FYtiskk~e~~v~r~A~~LV~eWtrpI 286 (397)
T COG5139 234 SLLDVLKTLPIHTEHLVESGVGRIVYFYTISKKEEKEVRRSAKALVQEWTRPI 286 (397)
T ss_pred HHHHHHhhCCchHHHhhhcCCceEEEEEecCCcccHHHHHHHHHHHHHhhccc
Confidence 4566778899999999999999998654 45667899999999999998754
No 10
>PLN02976 amine oxidase
Probab=87.01 E-value=1.1 Score=53.24 Aligned_cols=60 Identities=22% Similarity=0.367 Sum_probs=50.3
Q ss_pred HHHHHHHHhhcCCCCHHHhhccCcccccch-hccCCCHHHHHHHHHHHHHHHHhHHHHhhc
Q 018587 139 ALIDLLQSLADMDITFKALKETDIGRHVNQ-LRKHSSNDVRKLVKHLVRKWKDIVDEWVKL 198 (353)
Q Consensus 139 ~llelLr~L~~l~iT~dlLk~T~IGkaVn~-LRKH~s~~I~~LAk~LVkkWK~~V~e~~~~ 198 (353)
-+...|+-|-.++..+-.|+..+|||+|.. +.-|.+.+|+.+|+.|+..|-+++..+..+
T Consensus 1302 l~~~~~~ll~~~~~d~~a~r~sg~~~~~k~~~~~h~~~~~r~~a~~~~~~w~~~~~~~~~~ 1362 (1713)
T PLN02976 1302 LLRHCVRLLVLVSTDLLAVRLSGIGKTVKEKVCVHTSRDIRAIASQLVSVWLEVFRREKAS 1362 (1713)
T ss_pred HHHHHHHHHhhcchhHHHHHhccchHHHHhhhhhcccHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 345566666678888888999999999965 789999999999999999999999766554
No 11
>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=79.33 E-value=2 Score=34.99 Aligned_cols=39 Identities=21% Similarity=0.302 Sum_probs=32.7
Q ss_pred ChhHHHHHHHhcCCchHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHh
Q 018587 2 DLDDFRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYA 49 (353)
Q Consensus 2 ~ld~wR~~f~~~g~di~~~ID~AI~VAA~D~p~elr~RRD~IvErLy~ 49 (353)
+.++|+.|||..| +=|+.|..+=.++ |..||.+-++|-.
T Consensus 10 P~~~wk~F~R~LG-----Lsdn~Ie~~E~~~----~~~rda~y~ML~~ 48 (77)
T cd08815 10 PARRWKEFVRTLG-----LREAEIEAVELEI----GRFRDQQYEMLKR 48 (77)
T ss_pred ChHHHHHHHHHcC-----CcHhHHHHHHhcc----cchHHHHHHHHHH
Confidence 4689999999999 8899999887776 5677888888876
No 12
>PF06881 Elongin_A: RNA polymerase II transcription factor SIII (Elongin) subunit A; InterPro: IPR010684 This family represents a conserved region within RNA polymerase II transcription factor SIII (Elongin) subunit A. In mammals, the Elongin complex activates elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites within transcription units. Elongin is a heterotrimer composed of A, B, and C subunits of 110, 18, and 15 kilodaltons, respectively. Subunit A has been shown to function as the transcriptionally active component of Elongin [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus, 0016021 integral to membrane
Probab=54.34 E-value=16 Score=30.54 Aligned_cols=32 Identities=25% Similarity=0.481 Sum_probs=28.0
Q ss_pred hhHHHHHHHHHHHHhHHHHHHhhhccceeeee
Q 018587 297 ADSRLASARKRLQENYKREENAKRQRTIQVMD 328 (353)
Q Consensus 297 ~~~kl~aakrkLqe~YqeAenAKkQRtIQvmd 328 (353)
.+.|+..+-.+|.+.|+.++..|.++++.++|
T Consensus 76 ~e~~~~~~~~~L~~~~~~~~~~K~~~~~~~v~ 107 (109)
T PF06881_consen 76 REEKLKEATERLRKKIKKLQQEKQSRRQKMVD 107 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCccCCceeec
Confidence 35689999999999999999999998887765
No 13
>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=49.43 E-value=22 Score=28.29 Aligned_cols=40 Identities=30% Similarity=0.484 Sum_probs=32.9
Q ss_pred CChhHHHHHHHhcCCchHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHh
Q 018587 1 MDLDDFRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYA 49 (353)
Q Consensus 1 m~ld~wR~~f~~~g~di~~~ID~AI~VAA~D~p~elr~RRD~IvErLy~ 49 (353)
|..++|+.|++..| +=++-|...-.|+|+ + ++.+.|+|..
T Consensus 9 v~~~~Wk~laR~LG-----ls~~~I~~ie~~~~~-~---~eq~~~mL~~ 48 (79)
T cd08784 9 VPFDQHKRFFRKLG-----LSDNEIKVAELDNPQ-H---RDRVYELLRI 48 (79)
T ss_pred CCHHHHHHHHHHcC-----CCHHHHHHHHHcCCc-h---HHHHHHHHHH
Confidence 45789999999999 678899999999998 4 4667777765
No 14
>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=46.89 E-value=21 Score=30.00 Aligned_cols=42 Identities=24% Similarity=0.352 Sum_probs=35.1
Q ss_pred CChhHHHHHHHhcCCchHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHhh
Q 018587 1 MDLDDFRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYAT 50 (353)
Q Consensus 1 m~ld~wR~~f~~~g~di~~~ID~AI~VAA~D~p~elr~RRD~IvErLy~~ 50 (353)
|...+|+.|+|..| +=++-|.-.-.|||..+ ++..+++|..=
T Consensus 18 ~~~~~wK~faR~lg-----lse~~Id~I~~~~~~d~---~Eq~~qmL~~W 59 (97)
T cd08316 18 MTLKDVKKFVRKSG-----LSEPKIDEIKLDNPQDT---AEQKVQLLRAW 59 (97)
T ss_pred cCHHHHHHHHHHcC-----CCHHHHHHHHHcCCCCh---HHHHHHHHHHH
Confidence 45679999999999 77888888888999775 77888888874
No 15
>PF14726 RTTN_N: Rotatin, an armadillo repeat protein, centriole functioning
Probab=38.95 E-value=40 Score=28.45 Aligned_cols=52 Identities=13% Similarity=0.284 Sum_probs=42.3
Q ss_pred CCHHHHHHHHHHhhcCCCCHHHhhccCcccccchhccCCCHHHHHHHHHHHH
Q 018587 135 QSEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVR 186 (353)
Q Consensus 135 ~see~llelLr~L~~l~iT~dlLk~T~IGkaVn~LRKH~s~~I~~LAk~LVk 186 (353)
.-.+.++++|.+|-.-|-...+|..-+.-...++||++-++..+...-.|++
T Consensus 45 ~~~~~VL~Ll~~L~~~~~a~~~l~~iG~~~fL~klr~~~~~~~~~~id~il~ 96 (98)
T PF14726_consen 45 PMKEEVLALLLRLLKSPYAAQILRDIGAVRFLSKLRPNVEPNLQAEIDEILD 96 (98)
T ss_pred ccHHHHHHHHHHHHhCcHHHHHHHHccHHHHHHHHHhcCCHHHHHHHHHHHh
Confidence 4678899999999999999999998776677999999887777666655543
No 16
>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=38.20 E-value=36 Score=27.63 Aligned_cols=40 Identities=20% Similarity=0.276 Sum_probs=31.6
Q ss_pred CChhHHHHHHHhcCCchHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHh
Q 018587 1 MDLDDFRSILKTAGVDVWTFIDTAILVASLDYATELKERRDKIVERLYA 49 (353)
Q Consensus 1 m~ld~wR~~f~~~g~di~~~ID~AI~VAA~D~p~elr~RRD~IvErLy~ 49 (353)
|...+|+.|+|..| +=|+-|..+-.||| .+ |+...|+|..
T Consensus 9 v~~~~wk~~~R~LG-----lse~~Id~ie~~~~-~~---~Eq~yqmL~~ 48 (80)
T cd08313 9 VPPRRWKEFVRRLG-----LSDNEIERVELDHR-RC---RDAQYQMLKV 48 (80)
T ss_pred CCHHHHHHHHHHcC-----CCHHHHHHHHHhCC-Ch---HHHHHHHHHH
Confidence 55789999999999 77888888888998 54 4566666665
No 17
>PF11471 Sugarporin_N: Maltoporin periplasmic N-terminal extension; InterPro: IPR021570 This N-terminal domain is found in members of the sugar porin family 1.B.3 from TC, They are related to LamB - the well characterised maltoporin of Escherichia coli for which the three-dimensional structures with and without its substrate have been obtained by X-ray diffraction. The protein consists of an 18 beta-stranded beta-barrel in contrast to proteins of the general bacterial porin family (GBP) and the Rhodobacter PorCa Porin (RPP) family which consist of 16 beta-stranded beta-barrels. Although maltoporin contains a wider beta-barrel than the porins of the GBP and RPP families (1.B.1 from TC and 1.B.7 from TC), it exhibits a narrower channel, showing only 5% of the ionic conductance of the latter porins.
Probab=32.55 E-value=66 Score=24.90 Aligned_cols=27 Identities=30% Similarity=0.464 Sum_probs=24.6
Q ss_pred cchhHHHHHHHHHHHHhHHHHHHhhhc
Q 018587 295 FDADSRLASARKRLQENYKREENAKRQ 321 (353)
Q Consensus 295 ~d~~~kl~aakrkLqe~YqeAenAKkQ 321 (353)
...|+||+.--.|||+.=|+|+.++++
T Consensus 28 ltiEqRLa~LE~rL~~ae~ra~~ae~~ 54 (60)
T PF11471_consen 28 LTIEQRLAALEQRLQAAEQRAQAAEAR 54 (60)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567889999999999999999999887
No 18
>PF12054 DUF3535: Domain of unknown function (DUF3535); InterPro: IPR022707 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 439 to 459 amino acids in length. This domain is found associated with PF00271 from PFAM, PF02985 from PFAM, and PF00176 from PFAM. This domain has two completely conserved residues (P and K) that may be functionally important.
Probab=29.07 E-value=25 Score=36.63 Aligned_cols=45 Identities=22% Similarity=0.389 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHhHHHHHHhhhccceee--------eecCCCCCCcccccCCC
Q 018587 299 SRLASARKRLQENYKREENAKRQRTIQV--------MDIHEIPKPKNAFFGKN 343 (353)
Q Consensus 299 ~kl~aakrkLqe~YqeAenAKkQRtIQv--------md~~~~pk~~~~~~~~~ 343 (353)
+-|+.+|++|+....+++.+|.++.++| +-++.||+..|..+.+-
T Consensus 265 ~~Le~~r~~l~~ai~~~~~~~~~~~~~V~Aa~A~A~v~l~~lP~KLnPiIrpL 317 (441)
T PF12054_consen 265 QALEDRRQRLQAAIEEAKEVQTSRDVRVLAAAASALVALGGLPKKLNPIIRPL 317 (441)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCccHHHHHH
Confidence 3799999999999999999999999998 56789999888776543
No 19
>PF06936 Selenoprotein_S: Selenoprotein S (SelS); InterPro: IPR009703 This family consists of several mammalian selenoprotein S (SelS) sequences. SelS is a plasma membrane protein and is present in a variety of tissues and cell types. These proteins are involved in the degradation process of misfolded endoplasmic reticulum (ER) luminal proteins which participate in the transfer of misfolded proteins from the ER to the cytosol, where they are destroyed by the proteasome in a ubiquitin-dependent manner []. They probably serve as a linker between DER1, which mediates the retro-translocation of misfolded proteins into the cytosol, and the ATPase complex VCP, which mediates the translocation and ubiquitination.; GO: 0008430 selenium binding, 0006886 intracellular protein transport, 0030176 integral to endoplasmic reticulum membrane; PDB: 2Q2F_A.
Probab=28.60 E-value=49 Score=31.07 Aligned_cols=29 Identities=34% Similarity=0.587 Sum_probs=21.3
Q ss_pred chhHHHHHHHHHHHHhHHH-----------HHHhhhccce
Q 018587 296 DADSRLASARKRLQENYKR-----------EENAKRQRTI 324 (353)
Q Consensus 296 d~~~kl~aakrkLqe~Yqe-----------AenAKkQRtI 324 (353)
.-.+.|++||+|+||-|.. .|.-|||..|
T Consensus 80 ~rqEa~eaAR~RmQEE~dakA~~~kEKq~q~EEEKRrqki 119 (190)
T PF06936_consen 80 RRQEAMEAARRRMQEELDAKAEEYKEKQKQEEEEKRRQKI 119 (190)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455899999999998853 3346777777
No 20
>PF08735 DUF1786: Putative pyruvate format-lyase activating enzyme (DUF1786); InterPro: IPR014846 This family is annotated as pyruvate formate-lyase activating enzyme (1.97.1.4 from EC) in UniProt. It is not clear where this annotation comes from.
Probab=21.85 E-value=27 Score=34.25 Aligned_cols=28 Identities=25% Similarity=0.323 Sum_probs=22.6
Q ss_pred ChhHHHHHHHhcCCchHHHHHHHHHHhhcCC
Q 018587 2 DLDDFRSILKTAGVDVWTFIDTAILVASLDY 32 (353)
Q Consensus 2 ~ld~wR~~f~~~g~di~~~ID~AI~VAA~D~ 32 (353)
|++.|+.+|.+||.+. -...|.||+-||
T Consensus 61 D~~~~~~~l~~fg~~~---p~~~vavAvQDH 88 (254)
T PF08735_consen 61 DPEALRGALSAFGLEL---PFDVVAVAVQDH 88 (254)
T ss_pred CHHHHHHHHHHcCCCC---CcceeEEEeccc
Confidence 5679999999999763 223688999999
No 21
>KOG1087 consensus Cytosolic sorting protein GGA2/TOM1 [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.93 E-value=1.3e+02 Score=32.15 Aligned_cols=30 Identities=17% Similarity=0.350 Sum_probs=25.9
Q ss_pred ccchhccC-CCHHHHHHHHHHHHHHHHhHHH
Q 018587 165 HVNQLRKH-SSNDVRKLVKHLVRKWKDIVDE 194 (353)
Q Consensus 165 aVn~LRKH-~s~~I~~LAk~LVkkWK~~V~e 194 (353)
.|...+++ .+..|+..+-.||+.|-..+.+
T Consensus 86 mVk~~k~~~~~~~Vr~kiL~LI~~W~~af~~ 116 (470)
T KOG1087|consen 86 MVKRPKNKPRDLKVREKILELIDTWQQAFCG 116 (470)
T ss_pred HHhccccCCcchhHHHHHHHHHHHHHHHccC
Confidence 66677888 7789999999999999998765
No 22
>PF07149 Pes-10: Pes-10; InterPro: IPR009819 This family consists of several Caenorhabditis elegans pes-10 and related proteins. Members of this family are typically around 400 residues in length. The function of this family is unknown.
Probab=20.59 E-value=1.9e+02 Score=30.12 Aligned_cols=54 Identities=13% Similarity=0.419 Sum_probs=43.4
Q ss_pred CHHHHHHHHHHhhcCCCCHHHhhccCcccccchhccCCCHHHHHHHHHHHHHHHHh
Q 018587 136 SEDALIDLLQSLADMDITFKALKETDIGRHVNQLRKHSSNDVRKLVKHLVRKWKDI 191 (353)
Q Consensus 136 see~llelLr~L~~l~iT~dlLk~T~IGkaVn~LRKH~s~~I~~LAk~LVkkWK~~ 191 (353)
.++.+..++..|..+++|+++|..+++--.|..--.| ++.-+.|++. +..||..
T Consensus 19 ~d~~IT~ai~qL~~~~~s~~ilDk~NlP~LI~~~ap~-N~aA~~L~~~-~~~~K~~ 72 (370)
T PF07149_consen 19 NDEMITKAINQLPNHPVSVEILDKCNLPYLIDRYAPN-NEAAQSLARI-HRQWKNI 72 (370)
T ss_pred chHhHHHHHHhCCCCCCcHHHHHHcCchHHHHHhCCC-cHHHHHHHHH-HHHHHHH
Confidence 3578899999999999999999999999999866666 3445555554 7889875
No 23
>PF10588 NADH-G_4Fe-4S_3: NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; InterPro: IPR019574 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry describes the G subunit (one of 14 subunits, A to N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This family does not contain related subunits from formate dehydrogenase complexes. This entry represents the iron-sulphur binding domain of the G subunit.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3M9S_C 2FUG_L 3IAS_L 2YBB_3 3IAM_3 3I9V_3.
Probab=20.40 E-value=64 Score=22.85 Aligned_cols=22 Identities=32% Similarity=0.587 Sum_probs=13.6
Q ss_pred HHHHHHHHHhhhcccccccCCCC
Q 018587 40 RDKIVERLYATCIASRCRNCDFG 62 (353)
Q Consensus 40 RD~IvErLy~~~~~~~c~~cd~~ 62 (353)
|-.|+|+|++-. ..-|..|+..
T Consensus 1 Rr~~lelll~~H-~~dC~~C~~~ 22 (41)
T PF10588_consen 1 RRTVLELLLANH-PLDCPTCDKN 22 (41)
T ss_dssp -HHHHHHHHTT-----TTT-TTG
T ss_pred CHHHHHHHHhCC-CCcCcCCCCC
Confidence 568999999976 6779999864
Done!