Query 013167
Match_columns 448
No_of_seqs 183 out of 443
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 01:04:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013167.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013167hhsearch_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 4.9E-17 1.1E-21 132.4 6.7 74 137-210 2-76 (76)
2 smart00509 TFS2N Domain in the 99.6 8.1E-16 1.8E-20 125.4 6.0 70 141-210 3-74 (75)
3 TIGR01385 TFSII transcription 99.6 2.9E-15 6.4E-20 150.1 8.0 76 137-212 2-78 (299)
4 PF08711 Med26: TFIIS helical 99.4 2E-13 4.4E-18 103.6 4.0 52 159-210 1-53 (53)
5 KOG1105 Transcription elongati 99.3 1.3E-11 2.9E-16 123.5 8.6 77 136-212 3-81 (296)
6 KOG2821 RNA polymerase II tran 97.4 9.6E-05 2.1E-09 78.0 3.0 70 137-210 9-78 (433)
7 KOG1793 Uncharacterized conser 94.9 0.051 1.1E-06 57.3 6.1 52 158-209 236-290 (417)
8 PF11467 LEDGF: Lens epitheliu 94.0 0.14 3.1E-06 45.0 6.1 59 152-210 20-80 (106)
9 COG5139 Uncharacterized conser 90.4 0.33 7.2E-06 49.9 4.3 51 159-209 234-286 (397)
10 PLN02976 amine oxidase 85.5 1.5 3.4E-05 53.5 6.3 58 155-212 1301-1359(1713)
11 cd08815 Death_TNFRSF25_DR3 Dea 80.6 2.3 4.9E-05 35.8 3.8 40 6-54 9-48 (77)
12 cd08784 Death_DRs Death Domain 42.6 40 0.00087 27.7 4.1 40 6-54 9-48 (79)
13 PF06881 Elongin_A: RNA polyme 42.2 39 0.00084 29.3 4.1 34 385-418 74-107 (109)
14 cd08316 Death_FAS_TNFRSF6 Deat 33.9 58 0.0013 28.3 3.9 40 7-54 19-58 (97)
15 PF14726 RTTN_N: Rotatin, an a 28.8 67 0.0015 28.0 3.4 67 137-203 27-96 (98)
16 PF06936 Selenoprotein_S: Sele 25.0 64 0.0014 31.3 2.9 30 385-414 79-119 (190)
17 cd08313 Death_TNFR1 Death doma 24.8 1.2E+02 0.0025 25.6 4.0 40 6-54 9-48 (80)
18 cd08315 Death_TRAILR_DR4_DR5 D 23.9 97 0.0021 26.6 3.5 40 6-54 17-56 (96)
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=99.68 E-value=4.9e-17 Score=132.44 Aligned_cols=74 Identities=51% Similarity=0.749 Sum_probs=69.2
Q ss_pred HHHHHHHHHHhhcCC-CChHHHHHHHHHHhcCcCCHHHHhccCccccccccccCCCHHHHHHHHHHHHHHHHHHH
Q 013167 137 GEVLRIKEILHNSRD-ESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVD 210 (448)
Q Consensus 137 eEV~rIK~~Le~~~d-~se~~llelLr~L~~l~iT~dlLksT~IGkaVnkLRKH~s~eI~~LAk~LIkkWK~lV~ 210 (448)
+||.+++..|+.... .+.+.++++|+.|+.++||+++|++|+||++||+||||.+++|+.+|+.||++||++|+
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 689999999998753 57889999999999999999999999999999999999999999999999999999873
No 2
>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere).
Probab=99.61 E-value=8.1e-16 Score=125.40 Aligned_cols=70 Identities=43% Similarity=0.681 Sum_probs=61.3
Q ss_pred HHHHHHhhcCC--CChHHHHHHHHHHhcCcCCHHHHhccCccccccccccCCCHHHHHHHHHHHHHHHHHHH
Q 013167 141 RIKEILHNSRD--ESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVD 210 (448)
Q Consensus 141 rIK~~Le~~~d--~se~~llelLr~L~~l~iT~dlLksT~IGkaVnkLRKH~s~eI~~LAk~LIkkWK~lV~ 210 (448)
++.+.|+++.. ..++.++++|++|+.++||+++|++|+||++||+||||++++|+.+|+.||++||++|+
T Consensus 3 ~~~k~~~k~~~~~~~~~~~l~~L~~L~~~~~t~~~L~~T~iG~~v~~Lrkh~~~~I~~~A~~Li~~WK~~v~ 74 (75)
T smart00509 3 RAAKKLDKVANNGKEVSRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHKNEEIRKLAKKLIKSWKKLVY 74 (75)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhcCCCCHHHHHHCcHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHhc
Confidence 34455555432 34678999999999999999999999999999999999999999999999999999985
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=99.58 E-value=2.9e-15 Score=150.10 Aligned_cols=76 Identities=30% Similarity=0.494 Sum_probs=71.4
Q ss_pred HHHHHHHHHHhhcCC-CChHHHHHHHHHHhcCcCCHHHHhccCccccccccccCCCHHHHHHHHHHHHHHHHHHHHH
Q 013167 137 GEVLRIKEILHNSRD-ESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDEW 212 (448)
Q Consensus 137 eEV~rIK~~Le~~~d-~se~~llelLr~L~~l~iT~dlLksT~IGkaVnkLRKH~s~eI~~LAk~LIkkWK~lV~e~ 212 (448)
+||.++.+.|+++.. .+++.+|++|++|+.++||+++|++|+||++||+||||++++|+.||+.||++||++|..+
T Consensus 2 ~ei~~~~k~L~k~~~~~~~~~~l~~L~~L~~~~~t~~lL~~T~IG~~Vn~lrkh~~~~I~~lAk~li~~WK~~v~~~ 78 (299)
T TIGR01385 2 AEVASHAKALDKNKSSKNVEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDISKLAKKIIKSWKKVVDKN 78 (299)
T ss_pred hHHHHHHHHhhhhccCCCHHHHHHHHHHHhcCCCcHHHHhhCchhHHHHHHHcCCcHHHHHHHHHHHHHHHHHHhhh
Confidence 589999999998764 5678999999999999999999999999999999999999999999999999999999876
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=99.40 E-value=2e-13 Score=103.60 Aligned_cols=52 Identities=54% Similarity=0.827 Sum_probs=47.4
Q ss_pred HHHHHHhcCcCCHHHHhccCccccccccccC-CCHHHHHHHHHHHHHHHHHHH
Q 013167 159 ESLRRLQLMALTVDTLKATEIGKAVNGLRKH-GSKQIRHLARTLIEGWKDLVD 210 (448)
Q Consensus 159 elLr~L~~l~iT~dlLksT~IGkaVnkLRKH-~s~eI~~LAk~LIkkWK~lV~ 210 (448)
++|+.|+.+|||.++|++|+||++|+.|+|| .+++|+.+|+.||++||.+|+
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 888999999999999999985
No 5
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=99.25 E-value=1.3e-11 Score=123.51 Aligned_cols=77 Identities=34% Similarity=0.583 Sum_probs=70.6
Q ss_pred HHHHHHHHHHHhhcCC-CChHHHHHHHHHHhcCcCCHHHHhccCcccccc-ccccCCCHHHHHHHHHHHHHHHHHHHHH
Q 013167 136 VGEVLRIKEILHNSRD-ESDSVLFESLRRLQLMALTVDTLKATEIGKAVN-GLRKHGSKQIRHLARTLIEGWKDLVDEW 212 (448)
Q Consensus 136 ~eEV~rIK~~Le~~~d-~se~~llelLr~L~~l~iT~dlLksT~IGkaVn-kLRKH~s~eI~~LAk~LIkkWK~lV~e~ 212 (448)
.+|++++.+.|+++.. .+.+.++++|.+|+.+|||+++|++|+||+.|| .|++|.+++|+++|+.||+.||++|+..
T Consensus 3 ~e~~~r~ak~l~~~~~~~n~~~~ld~l~~L~~~pvt~ell~~Tr~g~~vn~~~Kk~~n~ev~~~ak~Lik~Wkk~~~~~ 81 (296)
T KOG1105|consen 3 EEEALRAAKALEKDKQSKNVEAALDLLKRLKKIPVTLELLQETRTGMGVNEVLKKHKNEEVRSLAKKLIKSWKKLVDKS 81 (296)
T ss_pred cHHHHHHHHHHHhhcccccHHHHHHHHHHHHhcccHHHHHHHhhHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhhcc
Confidence 4799999999999876 466899999999999999999999999999999 6678889999999999999999999864
No 6
>KOG2821 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin A [Transcription]
Probab=97.39 E-value=9.6e-05 Score=77.96 Aligned_cols=70 Identities=31% Similarity=0.451 Sum_probs=64.0
Q ss_pred HHHHHHHHHHhhcCCCChHHHHHHHHHHhcCcCCHHHHhccCccccccccccCCCHHHHHHHHHHHHHHHHHHH
Q 013167 137 GEVLRIKEILHNSRDESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVD 210 (448)
Q Consensus 137 eEV~rIK~~Le~~~d~se~~llelLr~L~~l~iT~dlLksT~IGkaVnkLRKH~s~eI~~LAk~LIkkWK~lV~ 210 (448)
.-|.++...|++.. ....++..|..|..+|++++.|.+|.||++|+.||||. .|..+|.+|+..||++|.
T Consensus 9 ~~Vr~lQ~~l~~~~--dpkR~lk~I~~ls~lP~~~k~l~Et~~~k~l~~L~k~~--~~g~~~~Dl~~~WK~~v~ 78 (433)
T KOG2821|consen 9 GAVRKLQARLENRI--DPKRLLKRIQKLSNLPHLFKHLLETGKGKTLNSLRKIS--HVGKLAFDLVALWKDLVL 78 (433)
T ss_pred HHHHHHHHHHHhCc--cHHHHHHHHHHhccchHHHHHHHHhhhhHHHHHHHHhh--cccccccchHHHHHHhcc
Confidence 56788888888763 46899999999999999999999999999999999997 799999999999999995
No 7
>KOG1793 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.88 E-value=0.051 Score=57.34 Aligned_cols=52 Identities=27% Similarity=0.376 Sum_probs=46.5
Q ss_pred HHHHHHHhcCcCCH-HHHhccCccccccccccCCCH--HHHHHHHHHHHHHHHHH
Q 013167 158 FESLRRLQLMALTV-DTLKATEIGKAVNGLRKHGSK--QIRHLARTLIEGWKDLV 209 (448)
Q Consensus 158 lelLr~L~~l~iT~-dlLksT~IGkaVnkLRKH~s~--eI~~LAk~LIkkWK~lV 209 (448)
..+|.-|..+||-. +.|+.++||++|==|-||+.+ +++.||..||..|-.-+
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 45788888899998 999999999999999999754 99999999999998766
No 8
>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=94.01 E-value=0.14 Score=45.01 Aligned_cols=59 Identities=24% Similarity=0.272 Sum_probs=47.7
Q ss_pred CChHHHHHHHHHHhcCcCCHHHHh-ccCccccccccccCC-CHHHHHHHHHHHHHHHHHHH
Q 013167 152 ESDSVLFESLRRLQLMALTVDTLK-ATEIGKAVNGLRKHG-SKQIRHLARTLIEGWKDLVD 210 (448)
Q Consensus 152 ~se~~llelLr~L~~l~iT~dlLk-sT~IGkaVnkLRKH~-s~eI~~LAk~LIkkWK~lV~ 210 (448)
.+...+|++|..|..|+||..+|+ .+.+--++.+||+.. |..|++.|..|..+.|.++.
T Consensus 20 ~Dv~kcL~~LdeL~~l~vT~~mL~kn~e~V~TlkklRrY~gn~~Ir~KA~~lYnkfK~~f~ 80 (106)
T PF11467_consen 20 PDVKKCLKALDELKSLQVTSLMLQKNPECVETLKKLRRYKGNQQIRKKATELYNKFKSLFL 80 (106)
T ss_dssp E-HHHHHHHHHHHHTS---HHHHTTTHHHHHHHHHHTT-TT-HHHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHhccCCCHHHHHhCHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHhC
Confidence 467899999999999999999886 566888999999984 67999999999999999985
No 9
>COG5139 Uncharacterized conserved protein [Function unknown]
Probab=90.36 E-value=0.33 Score=49.94 Aligned_cols=51 Identities=22% Similarity=0.433 Sum_probs=42.4
Q ss_pred HHHHHHhcCcCCHHHHhccCccccccccc--cCCCHHHHHHHHHHHHHHHHHH
Q 013167 159 ESLRRLQLMALTVDTLKATEIGKAVNGLR--KHGSKQIRHLARTLIEGWKDLV 209 (448)
Q Consensus 159 elLr~L~~l~iT~dlLksT~IGkaVnkLR--KH~s~eI~~LAk~LIkkWK~lV 209 (448)
.+|-.|..|||-.+.|++++||+.|==.. |...++|+.+|+.||..|-.-|
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 36667788999999999999999986554 4456799999999999998655
No 10
>PLN02976 amine oxidase
Probab=85.46 E-value=1.5 Score=53.51 Aligned_cols=58 Identities=26% Similarity=0.423 Sum_probs=48.8
Q ss_pred HHHHHHHHHHhcCcCCHHHHhccCcccccc-ccccCCCHHHHHHHHHHHHHHHHHHHHH
Q 013167 155 SVLFESLRRLQLMALTVDTLKATEIGKAVN-GLRKHGSKQIRHLARTLIEGWKDLVDEW 212 (448)
Q Consensus 155 ~~llelLr~L~~l~iT~dlLksT~IGkaVn-kLRKH~s~eI~~LAk~LIkkWK~lV~e~ 212 (448)
.-+..+|+-|-.++..+..|+.++||++|. ++.-|.+.+|+.||+.|+..|-.++..+
T Consensus 1301 ~l~~~~~~ll~~~~~d~~a~r~sg~~~~~k~~~~~h~~~~~r~~a~~~~~~w~~~~~~~ 1359 (1713)
T PLN02976 1301 QLLRHCVRLLVLVSTDLLAVRLSGIGKTVKEKVCVHTSRDIRAIASQLVSVWLEVFRRE 1359 (1713)
T ss_pred HHHHHHHHHHhhcchhHHHHHhccchHHHHhhhhhcccHHHHHHHHHHHHHHHHHHHHh
Confidence 344557777777888888899999999994 6689999999999999999999998643
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=80.59 E-value=2.3 Score=35.80 Aligned_cols=40 Identities=18% Similarity=0.263 Sum_probs=31.9
Q ss_pred CChhhHHHHHhhcCCchHHHHHHHHHHHhcCCchHHHHhhhhHHHHHhh
Q 013167 6 GSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFT 54 (448)
Q Consensus 6 ~~ld~WR~~fr~ag~di~~~Id~AI~VAA~D~P~elr~RRD~IaErLf~ 54 (448)
..+++|++|||..|-. |+.|..|=.|+ +..||.+-++|-.
T Consensus 9 VP~~~wk~F~R~LGLs-----dn~Ie~~E~~~----~~~rda~y~ML~~ 48 (77)
T cd08815 9 VPARRWKEFVRTLGLR-----EAEIEAVELEI----GRFRDQQYEMLKR 48 (77)
T ss_pred CChHHHHHHHHHcCCc-----HhHHHHHHhcc----cchHHHHHHHHHH
Confidence 5689999999999865 77788887766 5567888888764
No 12
>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=42.62 E-value=40 Score=27.72 Aligned_cols=40 Identities=35% Similarity=0.542 Sum_probs=31.4
Q ss_pred CChhhHHHHHhhcCCchHHHHHHHHHHHhcCCchHHHHhhhhHHHHHhh
Q 013167 6 GSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFT 54 (448)
Q Consensus 6 ~~ld~WR~~fr~ag~di~~~Id~AI~VAA~D~P~elr~RRD~IaErLf~ 54 (448)
.+.++|+.|+|.+|-. ++.|...-.|+|+ + ++.+.|.|..
T Consensus 9 v~~~~Wk~laR~LGls-----~~~I~~ie~~~~~-~---~eq~~~mL~~ 48 (79)
T cd08784 9 VPFDQHKRFFRKLGLS-----DNEIKVAELDNPQ-H---RDRVYELLRI 48 (79)
T ss_pred CCHHHHHHHHHHcCCC-----HHHHHHHHHcCCc-h---HHHHHHHHHH
Confidence 4789999999998865 7788888899996 3 5666776664
No 13
>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=42.16 E-value=39 Score=29.28 Aligned_cols=34 Identities=15% Similarity=0.316 Sum_probs=29.2
Q ss_pred HHHHHhHHHHHHHHHHHHHHHHHhhhcceeEEee
Q 013167 385 DAVQVKLEATKRKLQESYQLAENAKKQRTIQVME 418 (448)
Q Consensus 385 ~~~~~kleaaKRkLqe~YqeaenaKkqRtIQvmd 418 (448)
...+.|+..+-.+|.+.|+.++..|.++++.||+
T Consensus 74 ~e~e~~~~~~~~~L~~~~~~~~~~K~~~~~~~v~ 107 (109)
T PF06881_consen 74 KEREEKLKEATERLRKKIKKLQQEKQSRRQKMVD 107 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCccCCceeec
Confidence 3455599999999999999999999998887775
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=33.87 E-value=58 Score=28.26 Aligned_cols=40 Identities=15% Similarity=0.302 Sum_probs=31.7
Q ss_pred ChhhHHHHHhhcCCchHHHHHHHHHHHhcCCchHHHHhhhhHHHHHhh
Q 013167 7 SLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFT 54 (448)
Q Consensus 7 ~ld~WR~~fr~ag~di~~~Id~AI~VAA~D~P~elr~RRD~IaErLf~ 54 (448)
...+|+.|+|..|-. ++-|.-+-.|+|.. .++...+.|..
T Consensus 19 ~~~~wK~faR~lgls-----e~~Id~I~~~~~~d---~~Eq~~qmL~~ 58 (97)
T cd08316 19 TLKDVKKFVRKSGLS-----EPKIDEIKLDNPQD---TAEQKVQLLRA 58 (97)
T ss_pred CHHHHHHHHHHcCCC-----HHHHHHHHHcCCCC---hHHHHHHHHHH
Confidence 457899999999864 67777777899944 48888888885
No 15
>PF14726 RTTN_N: Rotatin, an armadillo repeat protein, centriole functioning
Probab=28.78 E-value=67 Score=28.02 Aligned_cols=67 Identities=15% Similarity=0.165 Sum_probs=48.3
Q ss_pred HHHHHHHHHHhhcC--C-CChHHHHHHHHHHhcCcCCHHHHhccCccccccccccCCCHHHHHHHHHHHH
Q 013167 137 GEVLRIKEILHNSR--D-ESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIE 203 (448)
Q Consensus 137 eEV~rIK~~Le~~~--d-~se~~llelLr~L~~l~iT~dlLksT~IGkaVnkLRKH~s~eI~~LAk~LIk 203 (448)
.+..-++..|+=.- . .-.+.++++|.+|-.-|....+|..-+.-...++||++-++..+...-.|++
T Consensus 27 ~~~~Ll~~LleWFnf~~~~~~~~VL~Ll~~L~~~~~a~~~l~~iG~~~fL~klr~~~~~~~~~~id~il~ 96 (98)
T PF14726_consen 27 KERLLLKQLLEWFNFPPVPMKEEVLALLLRLLKSPYAAQILRDIGAVRFLSKLRPNVEPNLQAEIDEILD 96 (98)
T ss_pred cHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHhCcHHHHHHHHccHHHHHHHHHhcCCHHHHHHHHHHHh
Confidence 45555555555221 1 3567999999999999999999998776677999999877766665555543
No 16
>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=25.01 E-value=64 Score=31.32 Aligned_cols=30 Identities=30% Similarity=0.451 Sum_probs=22.2
Q ss_pred HHHHHhHHHHHHHHHHHHH-----------HHHHhhhccee
Q 013167 385 DAVQVKLEATKRKLQESYQ-----------LAENAKKQRTI 414 (448)
Q Consensus 385 ~~~~~kleaaKRkLqe~Yq-----------eaenaKkqRtI 414 (448)
+..+..+++|++||||-|. +.|..|++..|
T Consensus 79 ~~rqEa~eaAR~RmQEE~dakA~~~kEKq~q~EEEKRrqki 119 (190)
T PF06936_consen 79 VRRQEAMEAARRRMQEELDAKAEEYKEKQKQEEEEKRRQKI 119 (190)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456689999999999984 33446777777
No 17
>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=24.78 E-value=1.2e+02 Score=25.57 Aligned_cols=40 Identities=20% Similarity=0.289 Sum_probs=29.0
Q ss_pred CChhhHHHHHhhcCCchHHHHHHHHHHHhcCCchHHHHhhhhHHHHHhh
Q 013167 6 GSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFT 54 (448)
Q Consensus 6 ~~ld~WR~~fr~ag~di~~~Id~AI~VAA~D~P~elr~RRD~IaErLf~ 54 (448)
..+.+|+.|+|..|-. |+-|..+-.||| .+ |+...|.|..
T Consensus 9 v~~~~wk~~~R~LGls-----e~~Id~ie~~~~-~~---~Eq~yqmL~~ 48 (80)
T cd08313 9 VPPRRWKEFVRRLGLS-----DNEIERVELDHR-RC---RDAQYQMLKV 48 (80)
T ss_pred CCHHHHHHHHHHcCCC-----HHHHHHHHHhCC-Ch---HHHHHHHHHH
Confidence 4678999999999864 566667777888 44 4566666654
No 18
>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=23.85 E-value=97 Score=26.63 Aligned_cols=40 Identities=20% Similarity=0.360 Sum_probs=31.8
Q ss_pred CChhhHHHHHhhcCCchHHHHHHHHHHHhcCCchHHHHhhhhHHHHHhh
Q 013167 6 GSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFT 54 (448)
Q Consensus 6 ~~ld~WR~~fr~ag~di~~~Id~AI~VAA~D~P~elr~RRD~IaErLf~ 54 (448)
.+..+|+.|.|.+|-. ++-|..+-.|+|+ . ++.+.|.|..
T Consensus 17 V~~~~Wk~laR~LGLs-----e~~I~~i~~~~~~---~-~eq~~qmL~~ 56 (96)
T cd08315 17 VPFDSWNRLMRQLGLS-----ENEIDVAKANERV---T-REQLYQMLLT 56 (96)
T ss_pred CCHHHHHHHHHHcCCC-----HHHHHHHHHHCCC---C-HHHHHHHHHH
Confidence 4578999999998865 7888888889984 3 6778887765
Done!