Query 021095
Match_columns 317
No_of_seqs 215 out of 466
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 07:33:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021095.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021095hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01385 TFSII transcription 99.9 7.7E-23 1.7E-27 195.8 14.7 137 137-277 2-155 (299)
2 KOG1105 Transcription elongati 99.8 4.6E-19 9.9E-24 169.1 12.0 156 136-294 3-169 (296)
3 cd00183 TFIIS_I N-terminal dom 99.7 9.7E-18 2.1E-22 130.7 6.4 74 137-210 2-76 (76)
4 smart00509 TFS2N Domain in the 99.7 7E-17 1.5E-21 125.9 5.1 70 141-210 3-74 (75)
5 PF08711 Med26: TFIIS helical 99.5 3.2E-14 7E-19 103.2 3.0 52 159-210 1-53 (53)
6 KOG2821 RNA polymerase II tran 97.2 0.00015 3.2E-09 73.2 2.4 70 137-210 9-78 (433)
7 KOG1793 Uncharacterized conser 95.4 0.017 3.7E-07 58.1 4.4 52 158-209 236-290 (417)
8 COG5139 Uncharacterized conser 93.9 0.069 1.5E-06 52.3 4.3 51 159-209 234-286 (397)
9 PF11467 LEDGF: Lens epitheliu 93.6 0.2 4.3E-06 42.0 5.9 59 152-210 20-80 (106)
10 cd08815 Death_TNFRSF25_DR3 Dea 90.4 0.35 7.6E-06 38.5 3.6 42 5-55 8-49 (77)
11 PLN02976 amine oxidase 82.5 2.1 4.5E-05 50.2 5.6 59 157-215 1303-1362(1713)
12 smart00510 TFS2M Domain in the 74.1 4.7 0.0001 33.3 3.9 22 256-279 1-22 (102)
13 PF07500 TFIIS_M: Transcriptio 62.1 13 0.00028 30.7 4.2 23 254-278 1-23 (115)
14 cd08784 Death_DRs Death Domain 47.8 30 0.00065 27.0 3.9 41 6-55 9-49 (79)
15 cd08316 Death_FAS_TNFRSF6 Deat 41.3 37 0.0008 28.0 3.6 41 7-55 19-59 (97)
16 cd08313 Death_TNFR1 Death doma 38.8 45 0.00097 26.6 3.6 40 6-54 9-48 (80)
17 PF14726 RTTN_N: Rotatin, an a 36.8 36 0.00077 28.2 2.9 67 137-203 27-96 (98)
18 cd08315 Death_TRAILR_DR4_DR5 D 29.5 63 0.0014 26.3 3.2 41 6-55 17-57 (96)
19 PRK15330 cell invasion protein 22.9 57 0.0012 32.7 2.1 55 263-317 78-132 (343)
No 1
>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=99.89 E-value=7.7e-23 Score=195.76 Aligned_cols=137 Identities=22% Similarity=0.287 Sum_probs=101.1
Q ss_pred HHHHHHHHHHhcCCC-CChHHHHHHHHHHhcCcCcHHhhccCCcceeccccccCCCHHHHHHHHHHHHHHHHHHHHhhhh
Q 021095 137 GEVLRIKEILHNSRD-ESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVDEWVNA 215 (317)
Q Consensus 137 ~EV~rIkk~Lek~~~-~s~e~llelL~~L~~v~iT~dlL~~T~IGk~VnkLRKh~s~eV~~LAk~LIkkWK~~V~~~~~~ 215 (317)
+||.++++.|+++.. .+++.++++|++|+.++||+++|++|+||++||+||||++++|++||+.||++||++|..++..
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 589999999999753 5667899999999999999999999999999999999999999999999999999999887443
Q ss_pred cccc----ccCCCCCCC---C--C---CCCcC-C---CCCCCCcccCcccCCCCCCcchhhHHHHHHHHHHHHHhcCC
Q 021095 216 TKAI----AEGTPDSVN---P--S---VVDEE-E---GLPSPPLDELAFFTGPSAGIELSQVFLMAWMILEILETVGN 277 (317)
Q Consensus 216 ~~a~----se~sp~ss~---~--s---~~~ee-~---~~P~~p~d~~af~~~~~T~d~vR~~~kc~emLy~AL~~~~~ 277 (317)
+.+. ....+.+++ . + ...+. . +.++++. ..+++.+.|+|.|| ++|++|||+||+.+.+
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~t~d~~R--dk~r~~L~~aL~~~~~ 155 (299)
T TIGR01385 82 HPGGNPEDKTTVGESVNSVKQEAKSQSDKIEQPKYVSSSPRNAK--NDFVPTAVTNDKVR--DKCRELLYDALAKDSD 155 (299)
T ss_pred CcccccccccccCCCCCCCCccccCCcccccCCCCCCCcccccC--CCCCCCccCCcHHH--HHHHHHHHHHHhhcCC
Confidence 2211 000000000 0 0 00000 1 1222222 33456678999999 9999999999998753
No 2
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=99.79 E-value=4.6e-19 Score=169.09 Aligned_cols=156 Identities=24% Similarity=0.275 Sum_probs=112.5
Q ss_pred HHHHHHHHHHHhcCCC-CChHHHHHHHHHHhcCcCcHHhhccCCcceecc-ccccCCCHHHHHHHHHHHHHHHHHHHHhh
Q 021095 136 VGEVLRIKEILHNSRD-ESDSVLFESLRRLQLMALTVDTLKATEIGKAVN-GLRKHGSKQIRHLARTLIEGWKDLVDEWV 213 (317)
Q Consensus 136 ~~EV~rIkk~Lek~~~-~s~e~llelL~~L~~v~iT~dlL~~T~IGk~Vn-kLRKh~s~eV~~LAk~LIkkWK~~V~~~~ 213 (317)
.+|+.++.++|+++.+ .+.+.++++|.+|+++|||+++|++|+||+.|| .|+||++++|+++||.||+.||++|....
T Consensus 3 ~e~~~r~ak~l~~~~~~~n~~~~ld~l~~L~~~pvt~ell~~Tr~g~~vn~~~Kk~~n~ev~~~ak~Lik~Wkk~~~~~~ 82 (296)
T KOG1105|consen 3 EEEALRAAKALEKDKQSKNVEAALDLLKRLKKIPVTLELLQETRTGMGVNEVLKKHKNEEVRSLAKKLIKSWKKLVDKSP 82 (296)
T ss_pred cHHHHHHHHHHHhhcccccHHHHHHHHHHHHhcccHHHHHHHhhHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhhccc
Confidence 3789999999999865 467899999999999999999999999999999 55678888999999999999999998641
Q ss_pred hhcccc--ccCCCCCC--C-CCCCC--cC--CCCCCCCcccCcccCCCCCCcchhhHHHHHHHHHHHHHhcCCCCccchh
Q 021095 214 NATKAI--AEGTPDSV--N-PSVVD--EE--EGLPSPPLDELAFFTGPSAGIELSQVFLMAWMILEILETVGNSSRTVKV 284 (317)
Q Consensus 214 ~~~~a~--se~sp~ss--~-~s~~~--ee--~~~P~~p~d~~af~~~~~T~d~vR~~~kc~emLy~AL~~~~~~~~t~~~ 284 (317)
...+.. ..+.|... + ++..+ +. ...++.+. .++-++.+++++.+| ++|++|||+||.++..++.+.++
T Consensus 83 ~~~k~~~~~~~~p~~~~~~~~s~~~~~~ks~~~~~~~~~-~~~~~~~~~~~d~~r--~k~~e~l~~al~~~~~~~~~~~~ 159 (296)
T KOG1105|consen 83 GREKSGDNKSHDPGEASSKSPSGAKQPEKSRGDSKRDKH-SGSKDPVPITNDPVR--DKCRELLYAALTTEDDSRVTGAD 159 (296)
T ss_pred ccccCccccCCCCCcCCcCCccCCCCccccccccccccc-cCcCCCCCCCCchHH--HHHHHHHHHHhcccccccccCCC
Confidence 111111 11112111 1 11111 00 01111110 112144677899999 99999999999999999999999
Q ss_pred hhhhHHHHHh
Q 021095 285 EENLQWRTKI 294 (317)
Q Consensus 285 e~~~~~~~~~ 294 (317)
.+.++.-++-
T Consensus 160 ~~~~a~~iE~ 169 (296)
T KOG1105|consen 160 PLELAVQIEE 169 (296)
T ss_pred HHHHHHHHHH
Confidence 7777766553
No 3
>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=9.7e-18 Score=130.65 Aligned_cols=74 Identities=51% Similarity=0.749 Sum_probs=68.9
Q ss_pred HHHHHHHHHHhcCCC-CChHHHHHHHHHHhcCcCcHHhhccCCcceeccccccCCCHHHHHHHHHHHHHHHHHHH
Q 021095 137 GEVLRIKEILHNSRD-ESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVD 210 (317)
Q Consensus 137 ~EV~rIkk~Lek~~~-~s~e~llelL~~L~~v~iT~dlL~~T~IGk~VnkLRKh~s~eV~~LAk~LIkkWK~~V~ 210 (317)
+||.+++++|+++.+ .+.+.++++|+.|+.+|||.++|++|+||+.||+||||.+++|+++|+.||++||++|+
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 57778999999999999999999999999999999999999999999999999999873
No 4
>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere).
Probab=99.66 E-value=7e-17 Score=125.89 Aligned_cols=70 Identities=43% Similarity=0.681 Sum_probs=61.7
Q ss_pred HHHHHHhcCCC--CChHHHHHHHHHHhcCcCcHHhhccCCcceeccccccCCCHHHHHHHHHHHHHHHHHHH
Q 021095 141 RIKEILHNSRD--ESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVD 210 (317)
Q Consensus 141 rIkk~Lek~~~--~s~e~llelL~~L~~v~iT~dlL~~T~IGk~VnkLRKh~s~eV~~LAk~LIkkWK~~V~ 210 (317)
++.++++++.. .+.+.++++|+.|+.++||.++|++|+||+.||+||||++++|+.+|+.||++||++|+
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 44556666432 44678999999999999999999999999999999999999999999999999999985
No 5
>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=99.46 E-value=3.2e-14 Score=103.24 Aligned_cols=52 Identities=54% Similarity=0.827 Sum_probs=47.3
Q ss_pred HHHHHHhcCcCcHHhhccCCcceeccccccC-CCHHHHHHHHHHHHHHHHHHH
Q 021095 159 ESLRRLQLMALTVDTLKATEIGKAVNGLRKH-GSKQIRHLARTLIEGWKDLVD 210 (317)
Q Consensus 159 elL~~L~~v~iT~dlL~~T~IGk~VnkLRKh-~s~eV~~LAk~LIkkWK~~V~ 210 (317)
++|+.|+.+|||.++|++|+||++||.|||| .+++|+++|+.||++||.+|+
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 888999999999999999874
No 6
>KOG2821 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin A [Transcription]
Probab=97.25 E-value=0.00015 Score=73.24 Aligned_cols=70 Identities=31% Similarity=0.450 Sum_probs=63.3
Q ss_pred HHHHHHHHHHhcCCCCChHHHHHHHHHHhcCcCcHHhhccCCcceeccccccCCCHHHHHHHHHHHHHHHHHHH
Q 021095 137 GEVLRIKEILHNSRDESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIEGWKDLVD 210 (317)
Q Consensus 137 ~EV~rIkk~Lek~~~~s~e~llelL~~L~~v~iT~dlL~~T~IGk~VnkLRKh~s~eV~~LAk~LIkkWK~~V~ 210 (317)
.-|.++...|++. .+...++..|..|..+|++++.|.+|.+|+.|+.||||. .|..++..|+..||+.|-
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 GAVRKLQARLENR--IDPKRLLKRIQKLSNLPHLFKHLLETGKGKTLNSLRKIS--HVGKLAFDLVALWKDLVL 78 (433)
T ss_pred HHHHHHHHHHHhC--ccHHHHHHHHHHhccchHHHHHHHHhhhhHHHHHHHHhh--cccccccchHHHHHHhcc
Confidence 5677888888875 356789999999999999999999999999999999997 799999999999999984
No 7
>KOG1793 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.42 E-value=0.017 Score=58.06 Aligned_cols=52 Identities=27% Similarity=0.376 Sum_probs=45.8
Q ss_pred HHHHHHHhcCcCcH-HhhccCCcceeccccccCCCH--HHHHHHHHHHHHHHHHH
Q 021095 158 FESLRRLQLMALTV-DTLKATEIGKAVNGLRKHGSK--QIRHLARTLIEGWKDLV 209 (317)
Q Consensus 158 lelL~~L~~v~iT~-dlL~~T~IGk~VnkLRKh~s~--eV~~LAk~LIkkWK~~V 209 (317)
..+|.-|..+||-. +.|+..+||++|-=|-||+.+ +++.+|..||.+|-.-+
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 45677788888877 999999999999999999765 99999999999998754
No 8
>COG5139 Uncharacterized conserved protein [Function unknown]
Probab=93.91 E-value=0.069 Score=52.30 Aligned_cols=51 Identities=22% Similarity=0.433 Sum_probs=43.2
Q ss_pred HHHHHHhcCcCcHHhhccCCcceeccccc--cCCCHHHHHHHHHHHHHHHHHH
Q 021095 159 ESLRRLQLMALTVDTLKATEIGKAVNGLR--KHGSKQIRHLARTLIEGWKDLV 209 (317)
Q Consensus 159 elL~~L~~v~iT~dlL~~T~IGk~VnkLR--Kh~s~eV~~LAk~LIkkWK~~V 209 (317)
.+|..|..|||-.++|++.+||+.|-=.- |...++|+.+|+.||..|-.-|
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 46677888999999999999999997664 4456699999999999998754
No 9
>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=93.56 E-value=0.2 Score=42.04 Aligned_cols=59 Identities=24% Similarity=0.272 Sum_probs=47.1
Q ss_pred CChHHHHHHHHHHhcCcCcHHhhcc-CCcceeccccccCC-CHHHHHHHHHHHHHHHHHHH
Q 021095 152 ESDSVLFESLRRLQLMALTVDTLKA-TEIGKAVNGLRKHG-SKQIRHLARTLIEGWKDLVD 210 (317)
Q Consensus 152 ~s~e~llelL~~L~~v~iT~dlL~~-T~IGk~VnkLRKh~-s~eV~~LAk~LIkkWK~~V~ 210 (317)
.+...++++|..|..+++|..+|+. +.+--++.+||+.. |..|++.|..|+.+-|.++.
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 5677999999999999999998874 55888899999875 56999999999999999985
No 10
>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=90.37 E-value=0.35 Score=38.54 Aligned_cols=42 Identities=17% Similarity=0.252 Sum_probs=33.7
Q ss_pred CCChhhHHHHhhhcCCchHHHHHHHHHHHhcCCchHHHHhhhhhHHHHhhh
Q 021095 5 SGSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTC 55 (317)
Q Consensus 5 ~~~ld~Wr~~f~~ag~di~~~Id~AI~VAA~D~p~elr~RRD~I~ErL~~~ 55 (317)
-.++++|+.|||..|-. |+.|..|-.++ +..||.+-++|-.=
T Consensus 8 ~VP~~~wk~F~R~LGLs-----dn~Ie~~E~~~----~~~rda~y~ML~~W 49 (77)
T cd08815 8 AVPARRWKEFVRTLGLR-----EAEIEAVELEI----GRFRDQQYEMLKRW 49 (77)
T ss_pred cCChHHHHHHHHHcCCc-----HhHHHHHHhcc----cchHHHHHHHHHHH
Confidence 46889999999997753 77899888777 56679999988753
No 11
>PLN02976 amine oxidase
Probab=82.54 E-value=2.1 Score=50.15 Aligned_cols=59 Identities=25% Similarity=0.400 Sum_probs=47.8
Q ss_pred HHHHHHHHhcCcCcHHhhccCCcceecc-ccccCCCHHHHHHHHHHHHHHHHHHHHhhhh
Q 021095 157 LFESLRRLQLMALTVDTLKATEIGKAVN-GLRKHGSKQIRHLARTLIEGWKDLVDEWVNA 215 (317)
Q Consensus 157 llelL~~L~~v~iT~dlL~~T~IGk~Vn-kLRKh~s~eV~~LAk~LIkkWK~~V~~~~~~ 215 (317)
+..+|+-|-.++..+-.|+..+||++|. ++--|.+.+|+.+|+.|+..|-+++..++.+
T Consensus 1303 ~~~~~~ll~~~~~d~~a~r~sg~~~~~k~~~~~h~~~~~r~~a~~~~~~w~~~~~~~~~~ 1362 (1713)
T PLN02976 1303 LRHCVRLLVLVSTDLLAVRLSGIGKTVKEKVCVHTSRDIRAIASQLVSVWLEVFRREKAS 1362 (1713)
T ss_pred HHHHHHHHhhcchhHHHHHhccchHHHHhhhhhcccHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 3445555555777788889999999984 6688999999999999999999999766543
No 12
>smart00510 TFS2M Domain in the central regions of transcription elongation factor S-II (and elsewhere).
Probab=74.11 E-value=4.7 Score=33.26 Aligned_cols=22 Identities=9% Similarity=0.102 Sum_probs=18.9
Q ss_pred cchhhHHHHHHHHHHHHHhcCCCC
Q 021095 256 IELSQVFLMAWMILEILETVGNSS 279 (317)
Q Consensus 256 d~vR~~~kc~emLy~AL~~~~~~~ 279 (317)
|++| ++|++|||+||+.+..+.
T Consensus 1 d~~R--~~~~~~L~~al~~~~~~~ 22 (102)
T smart00510 1 DKVR--DKCQEMLYKALQKISDPE 22 (102)
T ss_pred ChHH--HHHHHHHHHHHHhcCCCC
Confidence 5789 999999999999886543
No 13
>PF07500 TFIIS_M: Transcription factor S-II (TFIIS), central domain; InterPro: IPR003618 Transcription factor S-II (TFIIS) is a eukaryotic protein which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites. TFIIS shows DNA-binding activity only in the presence of RNA polymerase II []. It is widely distributed being found in mammals, Drosophila, yeast and in the archaebacteria Sulfolobus acidocaldarius []. S-II proteins have a relatively conserved C-terminal region but variable N-terminal region, and some members of this family are expressed in a tissue-specific manner [, ]. TFIIS is a modular factor that comprises an N-terminal domain I, a central domain II, and a C-terminal domain III []. The weakly conserved domain I forms a four-helix bundle and is not required for TFIIS activity. Domain II forms a three-helix bundle, and domain III adopts a zinc-ribbon fold with a thin protruding beta-hairpin. Domain II and the linker between domains II and III are required for Pol II binding, whereas domain III is essential for stimulation of RNA cleavage. TFIIS extends from the polymerase surface via a pore to the internal active site, spanning a distance of 100 Angstroms. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. This domain is found in the central region of transcription elongation factor S-II and in several hypothetical proteins.; GO: 0006351 transcription, DNA-dependent; PDB: 3PO3_S 1ENW_A 3GTM_S 1Y1V_S 3NDQ_A 2DME_A.
Probab=62.10 E-value=13 Score=30.72 Aligned_cols=23 Identities=4% Similarity=0.020 Sum_probs=20.2
Q ss_pred CCcchhhHHHHHHHHHHHHHhcCCC
Q 021095 254 AGIELSQVFLMAWMILEILETVGNS 278 (317)
Q Consensus 254 T~d~vR~~~kc~emLy~AL~~~~~~ 278 (317)
|++++| ++|+++|+++|......
T Consensus 1 ~~~~~R--~k~~~~L~~~l~~~~~~ 23 (115)
T PF07500_consen 1 TNDKVR--DKARKLLYKALQKRSDE 23 (115)
T ss_dssp -TCHHH--HHHHHHHHHHHHHCCCC
T ss_pred CCcHHH--HHHHHHHHHHHHhcCcc
Confidence 689999 99999999999999655
No 14
>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=47.77 E-value=30 Score=26.99 Aligned_cols=41 Identities=34% Similarity=0.520 Sum_probs=32.2
Q ss_pred CChhhHHHHhhhcCCchHHHHHHHHHHHhcCCchHHHHhhhhhHHHHhhh
Q 021095 6 GSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTC 55 (317)
Q Consensus 6 ~~ld~Wr~~f~~ag~di~~~Id~AI~VAA~D~p~elr~RRD~I~ErL~~~ 55 (317)
.+.++|+.|+|..|-. ++-|...-.|+|+ + ++.+.|+|..=
T Consensus 9 v~~~~Wk~laR~LGls-----~~~I~~ie~~~~~-~---~eq~~~mL~~W 49 (79)
T cd08784 9 VPFDQHKRFFRKLGLS-----DNEIKVAELDNPQ-H---RDRVYELLRIW 49 (79)
T ss_pred CCHHHHHHHHHHcCCC-----HHHHHHHHHcCCc-h---HHHHHHHHHHH
Confidence 4789999999998754 6778888899996 3 57777777753
No 15
>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=41.34 E-value=37 Score=27.95 Aligned_cols=41 Identities=15% Similarity=0.286 Sum_probs=32.3
Q ss_pred ChhhHHHHhhhcCCchHHHHHHHHHHHhcCCchHHHHhhhhhHHHHhhh
Q 021095 7 SLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTC 55 (317)
Q Consensus 7 ~ld~Wr~~f~~ag~di~~~Id~AI~VAA~D~p~elr~RRD~I~ErL~~~ 55 (317)
+..+|+.|+|..|-. ++-|.-.-.|||.. .++...|+|..=
T Consensus 19 ~~~~wK~faR~lgls-----e~~Id~I~~~~~~d---~~Eq~~qmL~~W 59 (97)
T cd08316 19 TLKDVKKFVRKSGLS-----EPKIDEIKLDNPQD---TAEQKVQLLRAW 59 (97)
T ss_pred CHHHHHHHHHHcCCC-----HHHHHHHHHcCCCC---hHHHHHHHHHHH
Confidence 567899999998743 66777788899944 488899999863
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=38.81 E-value=45 Score=26.55 Aligned_cols=40 Identities=20% Similarity=0.289 Sum_probs=29.6
Q ss_pred CChhhHHHHhhhcCCchHHHHHHHHHHHhcCCchHHHHhhhhhHHHHhh
Q 021095 6 GSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFT 54 (317)
Q Consensus 6 ~~ld~Wr~~f~~ag~di~~~Id~AI~VAA~D~p~elr~RRD~I~ErL~~ 54 (317)
.++.+|+.|+|..|-. |+-|..+-.||| .+ |+...|+|..
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 4788999999998853 566667777888 43 5667777764
No 17
>PF14726 RTTN_N: Rotatin, an armadillo repeat protein, centriole functioning
Probab=36.81 E-value=36 Score=28.15 Aligned_cols=67 Identities=15% Similarity=0.154 Sum_probs=50.0
Q ss_pred HHHHHHHHHHhcCC---CCChHHHHHHHHHHhcCcCcHHhhccCCcceeccccccCCCHHHHHHHHHHHH
Q 021095 137 GEVLRIKEILHNSR---DESDSVLFESLRRLQLMALTVDTLKATEIGKAVNGLRKHGSKQIRHLARTLIE 203 (317)
Q Consensus 137 ~EV~rIkk~Lek~~---~~s~e~llelL~~L~~v~iT~dlL~~T~IGk~VnkLRKh~s~eV~~LAk~LIk 203 (317)
++..-++..|+-.. -.-.+.++++|.+|-+-|....+|+.-+.-...++||++.++..+...-.|+.
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 45556666666442 13456899999999999999999998887777999999887776666555543
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=29.47 E-value=63 Score=26.31 Aligned_cols=41 Identities=20% Similarity=0.344 Sum_probs=32.4
Q ss_pred CChhhHHHHhhhcCCchHHHHHHHHHHHhcCCchHHHHhhhhhHHHHhhh
Q 021095 6 GSLDNWRNYFRSANGDIFDIIDHAVMVAALDCPKEFKLRRDRIAEKLFTC 55 (317)
Q Consensus 6 ~~ld~Wr~~f~~ag~di~~~Id~AI~VAA~D~p~elr~RRD~I~ErL~~~ 55 (317)
.+.++|+.|.|..|-. ++-|..+-.|+|+ . ++.+.|+|..=
T Consensus 17 V~~~~Wk~laR~LGLs-----e~~I~~i~~~~~~---~-~eq~~qmL~~W 57 (96)
T cd08315 17 VPFDSWNRLMRQLGLS-----ENEIDVAKANERV---T-REQLYQMLLTW 57 (96)
T ss_pred CCHHHHHHHHHHcCCC-----HHHHHHHHHHCCC---C-HHHHHHHHHHH
Confidence 4678999999987743 7788888899995 3 77888888753
No 19
>PRK15330 cell invasion protein SipD; Provisional
Probab=22.87 E-value=57 Score=32.73 Aligned_cols=55 Identities=24% Similarity=0.265 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHhcCCCCccchhhhhhHHHHHhhcccchhhhhhhccCceeeeeeC
Q 021095 263 LMAWMILEILETVGNSSRTVKVEENLQWRTKISQSGNSKLLMSRMCLPRITIVYR 317 (317)
Q Consensus 263 kc~emLy~AL~~~~~~~~t~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 317 (317)
-.+.-|...|..-...-..+.-|.|-..|-.-+--+.+-+..+-|++||+||-|+
T Consensus 78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~iS~a 132 (343)
T PRK15330 78 LARQQLTSSLNALAKSGVSLSAEQNENLRSAFSAPTSALFSASPMAQPRTTISDA 132 (343)
T ss_pred HHHHHHHHHHHHHHhccccccHhhhhhhhccCCCcHHHHhccCcccCCCCcccHH
Confidence 3444454444433444456666666677777777777788889999999999884
Done!