Query 008001
Match_columns 582
No_of_seqs 91 out of 102
Neff 3.0
Searched_HMMs 46136
Date Thu Mar 28 18:10:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008001.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008001hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2659 LisH motif-containing 100.0 8.8E-35 1.9E-39 284.0 12.3 146 330-475 59-210 (228)
2 PF10607 CLTH: CTLH/CRA C-term 99.8 3.1E-20 6.7E-25 163.9 10.3 134 335-471 1-143 (145)
3 smart00757 CRA CT11-RanBPM. pr 99.1 1.1E-10 2.5E-15 97.0 7.1 85 388-472 1-93 (99)
4 smart00668 CTLH C-terminal to 98.9 2.4E-09 5.2E-14 81.6 5.0 56 336-391 2-57 (58)
5 KOG0396 Uncharacterized conser 98.7 7.8E-08 1.7E-12 101.0 10.9 137 332-471 149-292 (389)
6 KOG2659 LisH motif-containing 98.4 3.9E-07 8.4E-12 90.8 6.4 87 7-106 138-224 (228)
7 KOG2817 Predicted E3 ubiquitin 96.7 0.003 6.5E-08 67.6 6.3 86 336-424 156-243 (394)
8 PRK06369 nac nascent polypepti 92.9 0.13 2.8E-06 47.4 4.1 38 112-149 73-110 (115)
9 TIGR00264 alpha-NAC-related pr 91.8 0.19 4.1E-06 46.5 3.8 37 113-149 76-112 (116)
10 COG1308 EGD2 Transcription fac 90.7 0.4 8.6E-06 44.8 4.8 48 101-148 70-117 (122)
11 PF10607 CLTH: CTLH/CRA C-term 90.2 1.4 3.1E-05 39.4 7.7 66 9-74 74-142 (145)
12 smart00757 CRA CT11-RanBPM. pr 85.4 4.6 0.0001 33.7 7.5 69 4-72 19-89 (99)
13 PF00627 UBA: UBA/TS-N domain; 84.3 1.4 3E-05 32.2 3.4 34 115-149 2-35 (37)
14 PF14555 UBA_4: UBA-like domai 79.3 5.1 0.00011 30.3 5.0 37 545-581 1-37 (43)
15 cd00194 UBA Ubiquitin Associat 72.7 10 0.00022 27.2 4.9 37 545-582 2-38 (38)
16 PF14559 TPR_19: Tetratricopep 69.9 9.6 0.00021 29.1 4.5 54 345-410 1-57 (68)
17 KOG1477 SPRY domain-containing 68.9 3.8 8.2E-05 45.4 2.9 122 341-462 304-440 (469)
18 PF02845 CUE: CUE domain; Int 68.6 11 0.00023 28.3 4.3 37 545-581 2-39 (42)
19 smart00668 CTLH C-terminal to 68.5 6.4 0.00014 29.9 3.3 40 378-417 5-44 (58)
20 PF00627 UBA: UBA/TS-N domain; 66.7 13 0.00029 27.0 4.5 35 544-579 2-36 (37)
21 cd00194 UBA Ubiquitin Associat 65.5 9.2 0.0002 27.5 3.4 30 118-148 4-33 (38)
22 smart00165 UBA Ubiquitin assoc 63.7 17 0.00037 26.0 4.5 36 545-581 2-37 (37)
23 KOG0293 WD40 repeat-containing 60.9 58 0.0013 36.7 9.8 128 338-469 52-186 (519)
24 smart00165 UBA Ubiquitin assoc 59.5 13 0.00029 26.6 3.3 31 117-148 3-33 (37)
25 smart00546 CUE Domain that may 58.0 20 0.00043 26.8 4.1 28 554-581 13-40 (43)
26 PRK06369 nac nascent polypepti 47.2 66 0.0014 30.1 6.5 61 513-579 51-111 (115)
27 COG1308 EGD2 Transcription fac 46.8 40 0.00086 31.9 5.1 39 541-579 81-119 (122)
28 KOG1333 Uncharacterized conser 37.1 18 0.00039 37.2 1.4 21 159-179 5-25 (241)
29 PRK10564 maltose regulon perip 34.3 35 0.00076 36.4 3.0 23 338-360 260-282 (303)
30 TIGR00264 alpha-NAC-related pr 31.5 94 0.002 29.3 5.0 37 542-578 76-112 (116)
31 TIGR01470 cysG_Nterm siroheme 31.1 56 0.0012 32.0 3.7 66 336-402 134-205 (205)
32 cd08800 Death_UNC5A Death doma 27.6 23 0.0005 31.5 0.3 30 108-137 52-82 (84)
33 PF08513 LisH: LisH; InterPro 23.9 45 0.00097 23.4 1.2 19 161-179 2-20 (27)
34 PF07729 FCD: FCD domain; Int 21.8 89 0.0019 25.5 2.7 66 336-401 30-123 (125)
35 PF13432 TPR_16: Tetratricopep 20.6 1.8E+02 0.0038 22.1 4.0 51 342-400 4-57 (65)
No 1
>KOG2659 consensus LisH motif-containing protein [Cytoskeleton]
Probab=100.00 E-value=8.8e-35 Score=283.97 Aligned_cols=146 Identities=22% Similarity=0.313 Sum_probs=133.2
Q ss_pred hhhhhhHHHHHHHHHHHhcCCHHHHHHHHhccCCCccccCcccchhhhHHHHHHHHhcCChhHHHHHHHhhcCcccccCc
Q 008001 330 REQQENYEIVLGMKELAGKGMAAEAVEEINAMDADFFVQNPMLLFQLKQVEFLKLVSCGDHSGALRVACAHLGPLAASHP 409 (582)
Q Consensus 330 ~~~dDsIE~R~~IReAIq~G~IqeAIelVNeLdPeILDtNP~L~FhLQQqqLIELIR~GdieeALeFAq~~LaPrae~nP 409 (582)
.-+.++++.|.+||++|..|+|++||+++|+|+|+|||+|++||||||||+||||||+|.+++||+|||++|+|.|++|+
T Consensus 59 ~~d~~~~~eR~~Ir~~I~~G~Ie~Aie~in~l~PeiLd~n~~l~F~Lq~q~lIEliR~~~~eeal~F~q~~LA~~a~e~~ 138 (228)
T KOG2659|consen 59 SIDLDSMDERLQIRRAIEEGQIEEAIEKVNQLNPEILDTNRELFFHLQQLHLIELIREGKTEEALEFAQTKLAPFAEENP 138 (228)
T ss_pred cCchhhHhHHHHHHHHHHhccHHHHHHHHHHhChHHHccchhHHHHHHHHHHHHHHHhhhHHHHHHHHHHHccccccccH
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchhhHHHHHHHhcCCCCc--cccC---CCChHHHHHHHHHHHHhhcCC-CCchHHHHHHHHHHhhhhhhhh
Q 008001 410 ALLKPLKETLLALLQPNED--VLVK---GFPLHTLATSLQVAIGRRLGI-EEPQLMKILRATLHTHNEWFKL 475 (582)
Q Consensus 410 ~fL~eLErTMALLAfP~e~--l~~~---~l~r~~VAseLNaAIL~~~g~-~EPKL~~LLKLlLWAQ~Ew~Kl 475 (582)
+++.+||+||++|+||.++ +... ...|+++|++||.|||++++. .+|+|++|+|++.|+|++--+-
T Consensus 139 ~~~~elE~~l~lLvf~~~~~sp~~~l~~~s~R~kvA~~vN~aiL~~~~~~~~~~l~~llk~~~~~~~~~~~~ 210 (228)
T KOG2659|consen 139 KKMEELERTLALLVFELSQESPSAELLSQSLRQKVASEVNSAILASQEHESEPKLPFLLKLISWAQEELDRE 210 (228)
T ss_pred HHHHHHHHHHHHHHcCCcccCcHHHHHHHHHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHhHh
Confidence 9999999999999997643 1111 126899999999999999987 4999999999999999875443
No 2
>PF10607 CLTH: CTLH/CRA C-terminal to LisH motif domain; InterPro: IPR019589 This entry represents the CRA (or CT11-RanBPM) domain, which is a protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi) and which is found in Ran-binding proteins such as Ran-binding protein 9 (RanBP9 or RanBPM) and RanBP10. RanBPM is a scaffolding protein important in regulating cellular function in both the immune system and the nervous system, and may act as an adapter protein to couple membrane receptors to intracellular signaling pathways. This domain is at the C terminus of the proteins and is the binding domain for the CRA motif, which is comprised of approximately 100 amino acids at the C-terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [].
Probab=99.82 E-value=3.1e-20 Score=163.85 Aligned_cols=134 Identities=25% Similarity=0.332 Sum_probs=120.4
Q ss_pred hHHHHHHHHHHHhcCCHHHHHHHHhccCCCccccCcccchhhhHHHHHHHHhcCChhHHHHHHHhhcCcccccCccchhh
Q 008001 335 NYEIVLGMKELAGKGMAAEAVEEINAMDADFFVQNPMLLFQLKQVEFLKLVSCGDHSGALRVACAHLGPLAASHPALLKP 414 (582)
Q Consensus 335 sIE~R~~IReAIq~G~IqeAIelVNeLdPeILDtNP~L~FhLQQqqLIELIR~GdieeALeFAq~~LaPrae~nP~fL~e 414 (582)
+++.|.+|+++|.+|++++||+.+|+..|++++.|+.|+|.|+.|+|||||++|++.+||+||+++|.|... .+.++
T Consensus 1 ~~~~r~~I~~~I~~g~i~~Ai~w~~~~~~~l~~~~~~L~f~L~~q~fiell~~~~~~~Ai~y~r~~l~~~~~---~~~~~ 77 (145)
T PF10607_consen 1 SFKERKKIRQAILNGDIDPAIEWLNENFPELLKRNSSLEFELRCQQFIELLREGDIMEAIEYARKHLSPFND---EFLEE 77 (145)
T ss_pred CHHHHHHHHHHHHcCCHHHHHHHHHHcCHHHHhcCCchhHHHHHHHHHHHHHHHhHHHHHHHHHHHhhhhHH---HHHHH
Confidence 478899999999999999999999999999999999999999999999999999999999999999976665 78999
Q ss_pred HHHHHHHhcCCCCcc-----cc---CCCChHHHHHHHHHHHHhhcCC-CCchHHHHHHHHHHhhhh
Q 008001 415 LKETLLALLQPNEDV-----LV---KGFPLHTLATSLQVAIGRRLGI-EEPQLMKILRATLHTHNE 471 (582)
Q Consensus 415 LErTMALLAfP~e~l-----~~---~~l~r~~VAseLNaAIL~~~g~-~EPKL~~LLKLlLWAQ~E 471 (582)
++++|+||+++.... .. ....+.+||..+|.+|+...|. .+|.|..+++...|+...
T Consensus 78 l~~~~~lL~~~~~~~~~~s~~~~l~~~~~~~~la~~~~~~~l~~~~~~~~s~L~~~~~~g~~~l~~ 143 (145)
T PF10607_consen 78 LKKLMSLLAYPDPEEPLPSPYKELLSPERREELAEEFNSAILKSYGLPKESPLEVILKAGLSALKT 143 (145)
T ss_pred HHHHHHHHHcCCcccccchHHHHHhChHHHHHHHHHHHHHHHHHhCcCCCCHHHHHHHHHHHHhhh
Confidence 999999999866432 11 1126789999999999999987 689999999999999864
No 3
>smart00757 CRA CT11-RanBPM. protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi)
Probab=99.13 E-value=1.1e-10 Score=97.00 Aligned_cols=85 Identities=31% Similarity=0.326 Sum_probs=72.3
Q ss_pred CChhHHHHHHHhhcCcccccCccchhhHHHHHHHhcCCCC-c--ccc---CCCChHHHHHHHHHHHHhhc-CC-CCchHH
Q 008001 388 GDHSGALRVACAHLGPLAASHPALLKPLKETLLALLQPNE-D--VLV---KGFPLHTLATSLQVAIGRRL-GI-EEPQLM 459 (582)
Q Consensus 388 GdieeALeFAq~~LaPrae~nP~fL~eLErTMALLAfP~e-~--l~~---~~l~r~~VAseLNaAIL~~~-g~-~EPKL~ 459 (582)
+++.+||.|||++|+|.+.+++.++++||++|+||||+.. . +.. ....+..||.++|.+|+... |. .+|.|.
T Consensus 1 ~~~~eAi~yar~~l~~~~~~~~~~~~el~~~m~llaf~~~~~~sp~~~ll~~~~~~~la~~~n~~~l~~~~~~~~~s~L~ 80 (99)
T smart00757 1 GKIEEALAYARELLAPFAKEHEKFLKELEKTMALLAYPDPTEPSPYKELLSPSQREKLAEELNSAILELLHGKSSESPLE 80 (99)
T ss_pred CcHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHHHhcCCCCCCccHHHHCCHHHHHHHHHHHHHHHHHHccCCCCCChHH
Confidence 4789999999999999999999999999999999999764 2 111 11167899999999999998 76 589999
Q ss_pred HHHHHHHHhhhhh
Q 008001 460 KILRATLHTHNEW 472 (582)
Q Consensus 460 ~LLKLlLWAQ~Ew 472 (582)
.++|..+|++..-
T Consensus 81 ~~~~~~~~~~~~l 93 (99)
T smart00757 81 ILLSAGLAALKTL 93 (99)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999998754
No 4
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=98.88 E-value=2.4e-09 Score=81.64 Aligned_cols=56 Identities=29% Similarity=0.429 Sum_probs=53.2
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHhccCCCccccCcccchhhhHHHHHHHHhcCChh
Q 008001 336 YEIVLGMKELAGKGMAAEAVEEINAMDADFFVQNPMLLFQLKQVEFLKLVSCGDHS 391 (582)
Q Consensus 336 IE~R~~IReAIq~G~IqeAIelVNeLdPeILDtNP~L~FhLQQqqLIELIR~Gdie 391 (582)
+..|..|+++|..|++++||+.++.++|.++..++.|+|.|++|+|||||+.|++.
T Consensus 2 ~~~~~~i~~~i~~g~~~~a~~~~~~~~~~l~~~~~~l~f~L~~q~~lell~~~~~~ 57 (58)
T smart00668 2 FDERKRIRELILKGDWDEALEWLSSLKPPLLERNSKLEFELRKQKFLELVRQGKLE 57 (58)
T ss_pred hHHHHHHHHHHHcCCHHHHHHHHHHcCHHHhccCCCchhHHHHHHHHHHHHcCCcC
Confidence 46789999999999999999999999999999999999999999999999998764
No 5
>KOG0396 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.71 E-value=7.8e-08 Score=100.96 Aligned_cols=137 Identities=23% Similarity=0.274 Sum_probs=106.6
Q ss_pred hhhhHHHHHHHHHHHhcCCHHHHHHHHhccCCCccccCcccchhhhHHHHHHHHhcCChhHHHHHHHhhcCcccccCccc
Q 008001 332 QQENYEIVLGMKELAGKGMAAEAVEEINAMDADFFVQNPMLLFQLKQVEFLKLVSCGDHSGALRVACAHLGPLAASHPAL 411 (582)
Q Consensus 332 ~dDsIE~R~~IReAIq~G~IqeAIelVNeLdPeILDtNP~L~FhLQQqqLIELIR~GdieeALeFAq~~LaPrae~nP~f 411 (582)
|-|-++.-..|++++..|.++.|+.-.++=.-++=..+-.|=|++.+|+|||||+.+++.+|++||+.|++|.+.++
T Consensus 149 D~Dv~~~~~~I~~sll~~~l~~~Lswc~ehk~~LkK~~S~lEf~lRlQefIELi~~~~~~~Ai~~akk~f~~~~~~~--- 225 (389)
T KOG0396|consen 149 DSDVYKRAYGIRDSLLAGELEPALSWCKEHKVELKKEESSLEFQLRLQEFIELIKVDNYDKAIAFAKKHFAPWAKSH--- 225 (389)
T ss_pred hHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHHHHhccHHHHHHHHHHHHhhhhhhh---
Confidence 46778888999999999999999999999888888999999999999999999999999999999999999999966
Q ss_pred hhhHHHHHHHhcCCCCccccCC--C----ChHHHHHHHHHHHHhhcCC-CCchHHHHHHHHHHhhhh
Q 008001 412 LKPLKETLLALLQPNEDVLVKG--F----PLHTLATSLQVAIGRRLGI-EEPQLMKILRATLHTHNE 471 (582)
Q Consensus 412 L~eLErTMALLAfP~e~l~~~~--l----~r~~VAseLNaAIL~~~g~-~EPKL~~LLKLlLWAQ~E 471 (582)
.++|+.+|++||||...-.++- + +.+.+++---.--.+--|+ -.|.|-.++-+=|-+++-
T Consensus 226 ~~~Lk~a~g~laF~~~t~~sky~~l~~~~rw~~l~~lF~s~a~~l~~i~~~~~L~~~l~~GLsalKT 292 (389)
T KOG0396|consen 226 KSDLKLAMGLLAFPKYTSSSKYLNLLTADRWSVLADLFLSEALKLFGIPINPALTIYLQAGLSALKT 292 (389)
T ss_pred HHHHHHHHHhhcCccccCcccccCcccHHHHHHHHHHhhHHHHHHhCCCCCcHHHHHHHhhhhhccc
Confidence 5899999999999885533321 2 2222332111111222243 368888887776666644
No 6
>KOG2659 consensus LisH motif-containing protein [Cytoskeleton]
Probab=98.42 E-value=3.9e-07 Score=90.76 Aligned_cols=87 Identities=16% Similarity=0.117 Sum_probs=76.6
Q ss_pred HHHHHHHHHHHhhhhccCCCCCChhhHHHHHHHHHHHHHHHHHHHHHhhcccCchhHHHHHHHHHHhhhhhcccCCCCCc
Q 008001 7 KEAYEEFKHVLLTFIYDKDDPTSPVAIEWAERRRFEIAGLMSSVLRAHLHAYDPVFAMTLRYLISIHKEFCFHQGVPSPI 86 (582)
Q Consensus 7 peayeefk~vll~~iydkdd~~spva~ews~~rR~~lA~~~ss~lra~l~a~dP~~Sm~lRyLisiH~~~c~~~G~~spi 86 (582)
|++|+||+|+|..|+|| +.|.||+++.|+...|..+|+.|.+.|.++.+.+ ..++|++|| ++++.--
T Consensus 138 ~~~~~elE~~l~lLvf~-~~~~sp~~~l~~~s~R~kvA~~vN~aiL~~~~~~------~~~~l~~ll------k~~~~~~ 204 (228)
T KOG2659|consen 138 PKKMEELERTLALLVFE-LSQESPSAELLSQSLRQKVASEVNSAILASQEHE------SEPKLPFLL------KLISWAQ 204 (228)
T ss_pred HHHHHHHHHHHHHHHcC-CcccCcHHHHHHHHHHHHHHHHHHHHHHHHhccc------ccchHHHHH------HHHHHHH
Confidence 48999999999999999 9999999999999999999999999999999997 667778877 5565677
Q ss_pred cchhhhhcccCCCCCCCCcc
Q 008001 87 SDLTDRLLLEERDPPATPQE 106 (582)
Q Consensus 87 sdL~~rlL~~eRDPp~~p~e 106 (582)
++++.+...+.++-+.++-.
T Consensus 205 ~~~~~~~~~~~~~~~~~~~~ 224 (228)
T KOG2659|consen 205 EELDREKFSEPHFKDLTKIK 224 (228)
T ss_pred HHHhHhhccccccCCccccc
Confidence 78989999888887777644
No 7
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.68 E-value=0.003 Score=67.62 Aligned_cols=86 Identities=24% Similarity=0.346 Sum_probs=77.3
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHhccCCCccccCcccchhhhHHHHHHHHhcCChh--HHHHHHHhhcCcccccCccchh
Q 008001 336 YEIVLGMKELAGKGMAAEAVEEINAMDADFFVQNPMLLFQLKQVEFLKLVSCGDHS--GALRVACAHLGPLAASHPALLK 413 (582)
Q Consensus 336 IE~R~~IReAIq~G~IqeAIelVNeLdPeILDtNP~L~FhLQQqqLIELIR~Gdie--eALeFAq~~LaPrae~nP~fL~ 413 (582)
.-.-.+|-++++.||+.-|++-+-.=-=.+.+.|-.|=|-|..++|+.+|+.|..+ +||.+|++|.+|.+..+ ++
T Consensus 156 F~el~~Iv~~lke~Dl~~aLeWa~~~~~~L~~~~s~LE~~Lh~l~fl~l~~~g~~~~~eAl~Yar~~~~~F~~~~---~~ 232 (394)
T KOG2817|consen 156 FVELNQIVEALKERDLEPALEWAESNRQKLKEKSSSLEFKLHSLHFLSLIRGGKSDQREALRYARTHFAPFVADH---LR 232 (394)
T ss_pred HHHHHHHHHHHHhccchhHHHHHHHhhhhhccccccHHHHHHHHHHHHHHhcCCcCcHHHHHHHHHhcCccccch---HH
Confidence 34557899999999999999987766666778899999999999999999999999 99999999999999887 89
Q ss_pred hHHHHHHHhcC
Q 008001 414 PLKETLLALLQ 424 (582)
Q Consensus 414 eLErTMALLAf 424 (582)
|++..|.+|.+
T Consensus 233 eIQklm~sl~~ 243 (394)
T KOG2817|consen 233 EIQKLMGSLLY 243 (394)
T ss_pred HHHHHHHHHHH
Confidence 99999998775
No 8
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=92.90 E-value=0.13 Score=47.41 Aligned_cols=38 Identities=29% Similarity=0.351 Sum_probs=36.3
Q ss_pred CCCChhhHHHHHHHhccchhhHhHHHHhhhccHHHHHH
Q 008001 112 PPFDEVDIQALAHAVKITRQGAVDSLRFARGDLFQAFQ 149 (582)
Q Consensus 112 ppF~EvdiQaLahaveltRq~AvdsLr~akGDl~~Afq 149 (582)
..|++.||.-++.-...||..|+.+|+-++||+.+|..
T Consensus 73 ~~i~~edI~lv~~q~gvs~~~A~~AL~~~~gDl~~AI~ 110 (115)
T PRK06369 73 VEIPEEDIELVAEQTGVSEEEARKALEEANGDLAEAIL 110 (115)
T ss_pred CCCCHHHHHHHHHHHCcCHHHHHHHHHHcCCcHHHHHH
Confidence 57999999999999999999999999999999999975
No 9
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=91.79 E-value=0.19 Score=46.53 Aligned_cols=37 Identities=24% Similarity=0.355 Sum_probs=35.4
Q ss_pred CCChhhHHHHHHHhccchhhHhHHHHhhhccHHHHHH
Q 008001 113 PFDEVDIQALAHAVKITRQGAVDSLRFARGDLFQAFQ 149 (582)
Q Consensus 113 pF~EvdiQaLahaveltRq~AvdsLr~akGDl~~Afq 149 (582)
.|++.||.-++.-.+.||..|+.+|+-++||+..|.-
T Consensus 76 ~i~~eDI~lV~eq~gvs~e~A~~AL~~~~gDl~~AI~ 112 (116)
T TIGR00264 76 EITEDDIELVMKQCNVSKEEARRALEECGGDLAEAIM 112 (116)
T ss_pred CCCHHHHHHHHHHhCcCHHHHHHHHHHcCCCHHHHHH
Confidence 5999999999999999999999999999999999964
No 10
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=90.70 E-value=0.4 Score=44.82 Aligned_cols=48 Identities=27% Similarity=0.423 Sum_probs=39.6
Q ss_pred CCCCcccccCCCCCChhhHHHHHHHhccchhhHhHHHHhhhccHHHHH
Q 008001 101 PATPQESLYEAPPFDEVDIQALAHAVKITRQGAVDSLRFARGDLFQAF 148 (582)
Q Consensus 101 p~~p~e~~~e~ppF~EvdiQaLahaveltRq~AvdsLr~akGDl~~Af 148 (582)
|..|.|..-..=.|+|.||-=+++-+.-+|..|+.+|+-++|||.+|.
T Consensus 70 ~~~~ee~~~d~~~i~eeDIkLV~eQa~VsreeA~kAL~e~~GDlaeAI 117 (122)
T COG1308 70 VKKPEEKTVDESDISEEDIKLVMEQAGVSREEAIKALEEAGGDLAEAI 117 (122)
T ss_pred cccchhcccccCCCCHHHHHHHHHHhCCCHHHHHHHHHHcCCcHHHHH
Confidence 444444333333599999999999999999999999999999999996
No 11
>PF10607 CLTH: CTLH/CRA C-terminal to LisH motif domain; InterPro: IPR019589 This entry represents the CRA (or CT11-RanBPM) domain, which is a protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi) and which is found in Ran-binding proteins such as Ran-binding protein 9 (RanBP9 or RanBPM) and RanBP10. RanBPM is a scaffolding protein important in regulating cellular function in both the immune system and the nervous system, and may act as an adapter protein to couple membrane receptors to intracellular signaling pathways. This domain is at the C terminus of the proteins and is the binding domain for the CRA motif, which is comprised of approximately 100 amino acids at the C-terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [].
Probab=90.23 E-value=1.4 Score=39.36 Aligned_cols=66 Identities=21% Similarity=0.229 Sum_probs=57.1
Q ss_pred HHHHHHHHHhhhhccCCCC--CChhhHHHHHHHHHHHHHHHHHHHHHhhccc-CchhHHHHHHHHHHhh
Q 008001 9 AYEEFKHVLLTFIYDKDDP--TSPVAIEWAERRRFEIAGLMSSVLRAHLHAY-DPVFAMTLRYLISIHK 74 (582)
Q Consensus 9 ayeefk~vll~~iydkdd~--~spva~ews~~rR~~lA~~~ss~lra~l~a~-dP~~Sm~lRyLisiH~ 74 (582)
-.++++.++-+++|.+... .||++.-.+..||.++|..+.+.+-.+.+.- +|-|...++..++..+
T Consensus 74 ~~~~l~~~~~lL~~~~~~~~~~s~~~~l~~~~~~~~la~~~~~~~l~~~~~~~~s~L~~~~~~g~~~l~ 142 (145)
T PF10607_consen 74 FLEELKKLMSLLAYPDPEEPLPSPYKELLSPERREELAEEFNSAILKSYGLPKESPLEVILKAGLSALK 142 (145)
T ss_pred HHHHHHHHHHHHHcCCcccccchHHHHHhChHHHHHHHHHHHHHHHHHhCcCCCCHHHHHHHHHHHHhh
Confidence 5789999999999999887 8999999999999999999999888888765 4778888887777654
No 12
>smart00757 CRA CT11-RanBPM. protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi)
Probab=85.38 E-value=4.6 Score=33.72 Aligned_cols=69 Identities=13% Similarity=0.157 Sum_probs=53.0
Q ss_pred cccHHHHHHHHHHHhhhhccCCCCCChhhHHHHHHHHHHHHHHHHHHHHHhh-ccc-CchhHHHHHHHHHH
Q 008001 4 SMFKEAYEEFKHVLLTFIYDKDDPTSPVAIEWAERRRFEIAGLMSSVLRAHL-HAY-DPVFAMTLRYLISI 72 (582)
Q Consensus 4 ~aypeayeefk~vll~~iydkdd~~spva~ews~~rR~~lA~~~ss~lra~l-~a~-dP~~Sm~lRyLisi 72 (582)
+.+|.-..|+++++-.++|....+.||+..=++..||..+|..+-+.+=.+. +.. .|.|...++..+..
T Consensus 19 ~~~~~~~~el~~~m~llaf~~~~~~sp~~~ll~~~~~~~la~~~n~~~l~~~~~~~~~s~L~~~~~~~~~~ 89 (99)
T smart00757 19 KEHEKFLKELEKTMALLAYPDPTEPSPYKELLSPSQREKLAEELNSAILELLHGKSSESPLEILLSAGLAA 89 (99)
T ss_pred ccCHHHHHHHHHHHHHHhcCCCCCCccHHHHCCHHHHHHHHHHHHHHHHHHccCCCCCChHHHHHHHHHHH
Confidence 3445557899999999999877689999999999999999999986555555 332 36788888876653
No 13
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=84.29 E-value=1.4 Score=32.21 Aligned_cols=34 Identities=29% Similarity=0.445 Sum_probs=29.1
Q ss_pred ChhhHHHHHHHhccchhhHhHHHHhhhccHHHHHH
Q 008001 115 DEVDIQALAHAVKITRQGAVDSLRFARGDLFQAFQ 149 (582)
Q Consensus 115 ~EvdiQaLahaveltRq~AvdsLr~akGDl~~Afq 149 (582)
++..|+.|..- +.++..|..||+.++||+..|..
T Consensus 2 ~~~~v~~L~~m-Gf~~~~~~~AL~~~~~nve~A~~ 35 (37)
T PF00627_consen 2 DEEKVQQLMEM-GFSREQAREALRACNGNVERAVD 35 (37)
T ss_dssp HHHHHHHHHHH-TS-HHHHHHHHHHTTTSHHHHHH
T ss_pred CHHHHHHHHHc-CCCHHHHHHHHHHcCCCHHHHHH
Confidence 46778888887 99999999999999999999853
No 14
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=79.31 E-value=5.1 Score=30.29 Aligned_cols=37 Identities=22% Similarity=0.295 Sum_probs=30.9
Q ss_pred hhhHHHHHHHhcCChhHHHHHHHHhcCCHHHHHHHHh
Q 008001 545 ENAILKVMEFLALPRADAIHLLAQYNGNAETVIQQIF 581 (582)
Q Consensus 545 e~ail~vmeflalpr~dai~ll~qy~g~~e~viqq~~ 581 (582)
|..|-..|++.-.++..|+++|...|+|.|.-|.-.|
T Consensus 1 ~e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~ 37 (43)
T PF14555_consen 1 DEKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYF 37 (43)
T ss_dssp HHHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHH
T ss_pred CHHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3567888999999999999999999999999988766
No 15
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=72.72 E-value=10 Score=27.23 Aligned_cols=37 Identities=22% Similarity=0.416 Sum_probs=30.4
Q ss_pred hhhHHHHHHHhcCChhHHHHHHHHhcCCHHHHHHHHhC
Q 008001 545 ENAILKVMEFLALPRADAIHLLAQYNGNAETVIQQIFA 582 (582)
Q Consensus 545 e~ail~vmeflalpr~dai~ll~qy~g~~e~viqq~~~ 582 (582)
+..|-.+|+ +-.++..++.-|...+||.+..+.-||.
T Consensus 2 ~~~v~~L~~-mGf~~~~~~~AL~~~~~d~~~A~~~L~~ 38 (38)
T cd00194 2 EEKLEQLLE-MGFSREEARKALRATNNNVERAVEWLLE 38 (38)
T ss_pred HHHHHHHHH-cCCCHHHHHHHHHHhCCCHHHHHHHHhC
Confidence 445666666 4578999999999999999999988873
No 16
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=69.94 E-value=9.6 Score=29.12 Aligned_cols=54 Identities=28% Similarity=0.318 Sum_probs=37.0
Q ss_pred HHhcCCHHHHHHHHhcc---CCCccccCcccchhhhHHHHHHHHhcCChhHHHHHHHhhcCcccccCcc
Q 008001 345 LAGKGMAAEAVEEINAM---DADFFVQNPMLLFQLKQVEFLKLVSCGDHSGALRVACAHLGPLAASHPA 410 (582)
Q Consensus 345 AIq~G~IqeAIelVNeL---dPeILDtNP~L~FhLQQqqLIELIR~GdieeALeFAq~~LaPrae~nP~ 410 (582)
++..|+.++|++.++++ +|+ |+...|.|=++ +++.|+.++| .+.|.-....+|+
T Consensus 1 ll~~~~~~~A~~~~~~~l~~~p~----~~~~~~~la~~----~~~~g~~~~A----~~~l~~~~~~~~~ 57 (68)
T PF14559_consen 1 LLKQGDYDEAIELLEKALQRNPD----NPEARLLLAQC----YLKQGQYDEA----EELLERLLKQDPD 57 (68)
T ss_dssp HHHTTHHHHHHHHHHHHHHHTTT----SHHHHHHHHHH----HHHTT-HHHH----HHHHHCCHGGGTT
T ss_pred ChhccCHHHHHHHHHHHHHHCCC----CHHHHHHHHHH----HHHcCCHHHH----HHHHHHHHHHCcC
Confidence 57899999999997764 555 66666654433 6789999997 5555555555554
No 17
>KOG1477 consensus SPRY domain-containing proteins [General function prediction only]
Probab=68.87 E-value=3.8 Score=45.38 Aligned_cols=122 Identities=16% Similarity=0.071 Sum_probs=92.9
Q ss_pred HHHHHHhcCCHHHHHHHHhccCCCccc-------cCcccchhhhHHHHHHHHhcCChhHHHHHHHhhcCcccc--cCccc
Q 008001 341 GMKELAGKGMAAEAVEEINAMDADFFV-------QNPMLLFQLKQVEFLKLVSCGDHSGALRVACAHLGPLAA--SHPAL 411 (582)
Q Consensus 341 ~IReAIq~G~IqeAIelVNeLdPeILD-------tNP~L~FhLQQqqLIELIR~GdieeALeFAq~~LaPrae--~nP~f 411 (582)
..+.-+..|.+--++...+++-|+..- ..|...+.+.-...|++.|.|.+..++..=..+|++.-. -+-.+
T Consensus 304 ~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~g~v~~e~~~~k~~l~~~~g~~~~~~~ 383 (469)
T KOG1477|consen 304 DYHQRKGRGQFTRNGAYNAALIPTYRKVGQVFEVDYPQRGAKDPCGLHVNLGRAGFVFIEANAKKWELAKDYGIKKNSAA 383 (469)
T ss_pred hhhhhcCcceeechhhhcccccccccccceeecccccchhhccchhhhhhHHHHHHHHHHHHHHHHhhhhhhCcCccccc
Confidence 333336666666777777777776655 557888888888899999999999999988999998877 67788
Q ss_pred hhhHHHHHHHhcC--CCCccc---cCCCChHHHHHHHHHHHHhhcCC-CCchHHHHH
Q 008001 412 LKPLKETLLALLQ--PNEDVL---VKGFPLHTLATSLQVAIGRRLGI-EEPQLMKIL 462 (582)
Q Consensus 412 L~eLErTMALLAf--P~e~l~---~~~l~r~~VAseLNaAIL~~~g~-~EPKL~~LL 462 (582)
-+.++-.++||++ |.+++. ...-.+.-+++.+|.|||...+. ++|+|..++
T Consensus 384 ~~~~~~s~~Llays~p~~s~~g~~~~~~~~e~v~~~~n~~il~t~~~~~~~~l~~~l 440 (469)
T KOG1477|consen 384 VGMLSDSSSLLAYSDPEESPVGYLLDPIQREPVAEALNSAILETDNNSKDPDLERVL 440 (469)
T ss_pred cccccchHHHHHhcCcccCccccccCcccchhHHhhhcccccccCCCCccchhhhhh
Confidence 8999999999995 333332 22336778999999999999976 688854444
No 18
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=68.62 E-value=11 Score=28.32 Aligned_cols=37 Identities=24% Similarity=0.414 Sum_probs=29.3
Q ss_pred hhhHHHHHHHh-cCChhHHHHHHHHhcCCHHHHHHHHh
Q 008001 545 ENAILKVMEFL-ALPRADAIHLLAQYNGNAETVIQQIF 581 (582)
Q Consensus 545 e~ail~vmefl-alpr~dai~ll~qy~g~~e~viqq~~ 581 (582)
++.|-.++|-. -+++..-.+.|.+++||+|.+|..|+
T Consensus 2 ~~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL 39 (42)
T PF02845_consen 2 EEMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALL 39 (42)
T ss_dssp HHHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 45666777744 58888889999999999999998875
No 19
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=68.51 E-value=6.4 Score=29.91 Aligned_cols=40 Identities=23% Similarity=0.234 Sum_probs=33.1
Q ss_pred HHHHHHHHhcCChhHHHHHHHhhcCcccccCccchhhHHH
Q 008001 378 QVEFLKLVSCGDHSGALRVACAHLGPLAASHPALLKPLKE 417 (582)
Q Consensus 378 QqqLIELIR~GdieeALeFAq~~LaPrae~nP~fL~eLEr 417 (582)
..++.+.|..||+++|++.++++-.+.-..++.+.-.|-+
T Consensus 5 ~~~i~~~i~~g~~~~a~~~~~~~~~~l~~~~~~l~f~L~~ 44 (58)
T smart00668 5 RKRIRELILKGDWDEALEWLSSLKPPLLERNSKLEFELRK 44 (58)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHcCHHHhccCCCchhHHHH
Confidence 4578899999999999999999888887788776666544
No 20
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=66.75 E-value=13 Score=27.04 Aligned_cols=35 Identities=31% Similarity=0.502 Sum_probs=30.2
Q ss_pred ChhhHHHHHHHhcCChhHHHHHHHHhcCCHHHHHHH
Q 008001 544 DENAILKVMEFLALPRADAIHLLAQYNGNAETVIQQ 579 (582)
Q Consensus 544 ~e~ail~vmeflalpr~dai~ll~qy~g~~e~viqq 579 (582)
|+..|-++||- -.++.+|++-|...+||.|..+.-
T Consensus 2 ~~~~v~~L~~m-Gf~~~~~~~AL~~~~~nve~A~~~ 36 (37)
T PF00627_consen 2 DEEKVQQLMEM-GFSREQAREALRACNGNVERAVDW 36 (37)
T ss_dssp HHHHHHHHHHH-TS-HHHHHHHHHHTTTSHHHHHHH
T ss_pred CHHHHHHHHHc-CCCHHHHHHHHHHcCCCHHHHHHh
Confidence 57788888887 899999999999999999998764
No 21
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=65.53 E-value=9.2 Score=27.45 Aligned_cols=30 Identities=20% Similarity=0.339 Sum_probs=25.2
Q ss_pred hHHHHHHHhccchhhHhHHHHhhhccHHHHH
Q 008001 118 DIQALAHAVKITRQGAVDSLRFARGDLFQAF 148 (582)
Q Consensus 118 diQaLahaveltRq~AvdsLr~akGDl~~Af 148 (582)
.||.|.. .+.+++.++.+|+.++||+..|-
T Consensus 4 ~v~~L~~-mGf~~~~~~~AL~~~~~d~~~A~ 33 (38)
T cd00194 4 KLEQLLE-MGFSREEARKALRATNNNVERAV 33 (38)
T ss_pred HHHHHHH-cCCCHHHHHHHHHHhCCCHHHHH
Confidence 4566554 68999999999999999999884
No 22
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=63.75 E-value=17 Score=25.96 Aligned_cols=36 Identities=28% Similarity=0.493 Sum_probs=28.9
Q ss_pred hhhHHHHHHHhcCChhHHHHHHHHhcCCHHHHHHHHh
Q 008001 545 ENAILKVMEFLALPRADAIHLLAQYNGNAETVIQQIF 581 (582)
Q Consensus 545 e~ail~vmeflalpr~dai~ll~qy~g~~e~viqq~~ 581 (582)
+..|-.+++. -.|+.+|+.-|...+||.+..+.-||
T Consensus 2 ~~~v~~L~~m-Gf~~~~a~~aL~~~~~d~~~A~~~L~ 37 (37)
T smart00165 2 EEKIDQLLEM-GFSREEALKALRAANGNVERAAEYLL 37 (37)
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHhCCCHHHHHHHHC
Confidence 4455555554 58999999999999999999987765
No 23
>KOG0293 consensus WD40 repeat-containing protein [Function unknown]
Probab=60.93 E-value=58 Score=36.70 Aligned_cols=128 Identities=16% Similarity=0.123 Sum_probs=92.0
Q ss_pred HHHHHHHHHhcCCHHHHHHHHhccCCCccccCcccchhhhHHHHHHHHhcCChhHHHHHHHhhcCcccccCccchhhHHH
Q 008001 338 IVLGMKELAGKGMAAEAVEEINAMDADFFVQNPMLLFQLKQVEFLKLVSCGDHSGALRVACAHLGPLAASHPALLKPLKE 417 (582)
Q Consensus 338 ~R~~IReAIq~G~IqeAIelVNeLdPeILDtNP~L~FhLQQqqLIELIR~GdieeALeFAq~~LaPrae~nP~fL~eLEr 417 (582)
.-....++|..|+...++...-.+--+..++-.+-.|-++.|.|+|+.+.|++..||..-+....+.-.. ++.++|
T Consensus 52 t~klf~q~vlqg~w~q~v~~~~~i~~~de~~~~ea~fLv~kQ~fLEf~k~~~is~al~~l~~~~~~lr~~----~kk~~e 127 (519)
T KOG0293|consen 52 TTKLFDQQVLQGQWDQQVMSLVRISFEDERNRKEAMFLVNKQIFLEFLKTGSISHALPVLRNPVLYLRKN----KKKFHE 127 (519)
T ss_pred hHHHHHHHHHcccHHHHHHHHhhccCcchhhhHHHHHHHHHHHHHHHHhhccHhhhhHhhhcchhhhhhh----HHHHHH
Confidence 3445667899999999988887776666888889999999999999999999999998888776665432 345566
Q ss_pred HHHHhcCCCCcc-------ccCCCChHHHHHHHHHHHHhhcCCCCchHHHHHHHHHHhh
Q 008001 418 TLLALLQPNEDV-------LVKGFPLHTLATSLQVAIGRRLGIEEPQLMKILRATLHTH 469 (582)
Q Consensus 418 TMALLAfP~e~l-------~~~~l~r~~VAseLNaAIL~~~g~~EPKL~~LLKLlLWAQ 469 (582)
-..-|+.+++.- .+-...|.+|-.+|..-|-...=..+-+|--|++--+.-|
T Consensus 128 l~~sll~sn~~~~ne~~~~~~~~n~R~~ll~elskyi~p~illP~rRLehLl~qAv~~Q 186 (519)
T KOG0293|consen 128 LASSLLVSNDQFSNEENTTAQLNNERDKLLDELSKYIPPNILLPKRRLEHLLEQAVKYQ 186 (519)
T ss_pred HHHHHhccccccccccchhhhhchhHHHHHHHHHhhCCHhhcCChHHHHHHHHHHHHHH
Confidence 666666555321 1112367778777766554444446778888888765444
No 24
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=59.47 E-value=13 Score=26.57 Aligned_cols=31 Identities=29% Similarity=0.409 Sum_probs=25.0
Q ss_pred hhHHHHHHHhccchhhHhHHHHhhhccHHHHH
Q 008001 117 VDIQALAHAVKITRQGAVDSLRFARGDLFQAF 148 (582)
Q Consensus 117 vdiQaLahaveltRq~AvdsLr~akGDl~~Af 148 (582)
..|+.|. +.+.+++.|+.+|+.++||+..|.
T Consensus 3 ~~v~~L~-~mGf~~~~a~~aL~~~~~d~~~A~ 33 (37)
T smart00165 3 EKIDQLL-EMGFSREEALKALRAANGNVERAA 33 (37)
T ss_pred HHHHHHH-HcCCCHHHHHHHHHHhCCCHHHHH
Confidence 3455544 458999999999999999999884
No 25
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=57.99 E-value=20 Score=26.84 Aligned_cols=28 Identities=29% Similarity=0.411 Sum_probs=25.5
Q ss_pred HhcCChhHHHHHHHHhcCCHHHHHHHHh
Q 008001 554 FLALPRADAIHLLAQYNGNAETVIQQIF 581 (582)
Q Consensus 554 flalpr~dai~ll~qy~g~~e~viqq~~ 581 (582)
|=.+++......|..++||+|.+|..+.
T Consensus 13 FP~l~~~~I~~~L~~~~g~ve~~i~~LL 40 (43)
T smart00546 13 FPNLDEEVIKAVLEANNGNVEATINNLL 40 (43)
T ss_pred CCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 6679999999999999999999998875
No 26
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=47.16 E-value=66 Score=30.10 Aligned_cols=61 Identities=21% Similarity=0.241 Sum_probs=44.1
Q ss_pred CCCcceeeccCccccCCCCCCCcccCCccccChhhHHHHHHHhcCChhHHHHHHHHhcCCHHHHHHH
Q 008001 513 QGSSQITISSNARVSEDGSSPNQVSSADFVCDENAILKVMEFLALPRADAIHLLAQYNGNAETVIQQ 579 (582)
Q Consensus 513 ~~ssq~t~s~~~~~~~~g~sp~q~~~~~~~~~e~ail~vmeflalpr~dai~ll~qy~g~~e~viqq 579 (582)
.|+.+-.+.|..+..+-.+.. +.-+++.+|-.|||=.-.+|.+|+.-|..-|||.-+-|-.
T Consensus 51 ~g~~tY~I~Ge~~~e~~~~~~------~~~i~~edI~lv~~q~gvs~~~A~~AL~~~~gDl~~AI~~ 111 (115)
T PRK06369 51 QGQKTYQIVGEPEEVEKEAEK------EVEIPEEDIELVAEQTGVSEEEARKALEEANGDLAEAILK 111 (115)
T ss_pred CCCcEEEEEeccEEeeccccc------cCCCCHHHHHHHHHHHCcCHHHHHHHHHHcCCcHHHHHHH
Confidence 444444555555553322111 4568999999999999999999999999999997665543
No 27
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=46.83 E-value=40 Score=31.94 Aligned_cols=39 Identities=28% Similarity=0.319 Sum_probs=34.7
Q ss_pred cccChhhHHHHHHHhcCChhHHHHHHHHhcCCHHHHHHH
Q 008001 541 FVCDENAILKVMEFLALPRADAIHLLAQYNGNAETVIQQ 579 (582)
Q Consensus 541 ~~~~e~ail~vmeflalpr~dai~ll~qy~g~~e~viqq 579 (582)
.-++|.+|-+|||=.-.+|.+||.-|.--|||.-+-|=.
T Consensus 81 ~~i~eeDIkLV~eQa~VsreeA~kAL~e~~GDlaeAIm~ 119 (122)
T COG1308 81 SDISEEDIKLVMEQAGVSREEAIKALEEAGGDLAEAIMK 119 (122)
T ss_pred CCCCHHHHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHHH
Confidence 358999999999999999999999999999998766543
No 28
>KOG1333 consensus Uncharacterized conserved protein [Function unknown]
Probab=37.07 E-value=18 Score=37.18 Aligned_cols=21 Identities=48% Similarity=0.755 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHhhhccccCC
Q 008001 159 VSMLDELVREYCVYRGIVDSG 179 (582)
Q Consensus 159 ~~lldeLv~eYc~yRGiv~~~ 179 (582)
|.-+|+||+||-++||.+.+=
T Consensus 5 v~~tDelvReYL~frgf~~tL 25 (241)
T KOG1333|consen 5 VERTDELVREYLLFRGFTHTL 25 (241)
T ss_pred HHHHHHHHHHHHHHhhHHHHH
Confidence 566899999999999998653
No 29
>PRK10564 maltose regulon periplasmic protein; Provisional
Probab=34.29 E-value=35 Score=36.43 Aligned_cols=23 Identities=17% Similarity=0.267 Sum_probs=21.1
Q ss_pred HHHHHHHHHhcCCHHHHHHHHhc
Q 008001 338 IVLGMKELAGKGMAAEAVEEINA 360 (582)
Q Consensus 338 ~R~~IReAIq~G~IqeAIelVNe 360 (582)
....|++||..|||++|+.++|+
T Consensus 260 y~~aI~~AVk~gDi~KAL~LldE 282 (303)
T PRK10564 260 FNQAIKQAVKKGDVDKALKLLDE 282 (303)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHH
Confidence 56899999999999999999886
No 30
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=31.50 E-value=94 Score=29.27 Aligned_cols=37 Identities=22% Similarity=0.266 Sum_probs=33.7
Q ss_pred ccChhhHHHHHHHhcCChhHHHHHHHHhcCCHHHHHH
Q 008001 542 VCDENAILKVMEFLALPRADAIHLLAQYNGNAETVIQ 578 (582)
Q Consensus 542 ~~~e~ail~vmeflalpr~dai~ll~qy~g~~e~viq 578 (582)
-+++.+|-.|||=.-.+|++|++.|..-|||.-+-|-
T Consensus 76 ~i~~eDI~lV~eq~gvs~e~A~~AL~~~~gDl~~AI~ 112 (116)
T TIGR00264 76 EITEDDIELVMKQCNVSKEEARRALEECGGDLAEAIM 112 (116)
T ss_pred CCCHHHHHHHHHHhCcCHHHHHHHHHHcCCCHHHHHH
Confidence 5899999999999999999999999999999766553
No 31
>TIGR01470 cysG_Nterm siroheme synthase, N-terminal domain. This model represents a subfamily of CysG N-terminal region-related sequences. All sequences in the seed alignment for this model are N-terminal regions of known or predicted siroheme synthases. The C-terminal region of each is uroporphyrin-III C-methyltransferase (EC 2.1.1.107), which catalyzes the first step committed to the biosynthesis of either siroheme or cobalamin (vitamin B12) rather than protoheme (heme). The region represented by this model completes the process of oxidation and iron insertion to yield siroheme. Siroheme is a cofactor for nitrite and sulfite reductases, so siroheme synthase is CysG of cysteine biosynthesis in some organisms.
Probab=31.11 E-value=56 Score=32.05 Aligned_cols=66 Identities=12% Similarity=0.022 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHhccCCCccc------cCcccchhhhHHHHHHHHhcCChhHHHHHHHhhcC
Q 008001 336 YEIVLGMKELAGKGMAAEAVEEINAMDADFFV------QNPMLLFQLKQVEFLKLVSCGDHSGALRVACAHLG 402 (582)
Q Consensus 336 IE~R~~IReAIq~G~IqeAIelVNeLdPeILD------tNP~L~FhLQQqqLIELIR~GdieeALeFAq~~La 402 (582)
-..|.+|.+.+-. .+.+-++.+.++-..+.. ....++..+..-.+.+++++|+.++|.+.+.+.|+
T Consensus 134 ~~lr~~ie~~l~~-~~~~~~~~~~~~R~~~k~~~~~~~~r~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~ 205 (205)
T TIGR01470 134 RLLRERIETLLPP-SLGDLATLAATWRDAVKKRLPNGAARRRFWEKFFDGAFAERVLAGREEQAERVLATRLA 205 (205)
T ss_pred HHHHHHHHHhcch-hHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHhccHHHHHHHcCCHHHHHHHHHHhhC
Confidence 3455556665543 234444555554444433 33366666667789999999999999999988764
No 32
>cd08800 Death_UNC5A Death domain found in Uncoordinated-5A. Death Domain (DD) found in Uncoordinated-5A (UNC5A). UNC5A is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a critical role in neuronal development and differentiation, as well as axon-guidance. It also plays a role in regulating apoptosis in non-neuronal cells as a downstream target of p53. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathway
Probab=27.58 E-value=23 Score=31.49 Aligned_cols=30 Identities=37% Similarity=0.469 Sum_probs=27.1
Q ss_pred ccCCCCCChhhHHHHHHHh-ccchhhHhHHH
Q 008001 108 LYEAPPFDEVDIQALAHAV-KITRQGAVDSL 137 (582)
Q Consensus 108 ~~e~ppF~EvdiQaLahav-eltRq~AvdsL 137 (582)
.+|+.-|++-+|..|+.++ |+-|++|++.|
T Consensus 52 ~WEa~~~~~g~l~~L~~~l~emGR~da~~~~ 82 (84)
T cd08800 52 LWEAQHFPNGNLNQLAAVVAEIGKQDAMLFL 82 (84)
T ss_pred HHHhccCCCCcHHHHHHHHHHhCchHHHHHh
Confidence 6999999999999999997 68999999865
No 33
>PF08513 LisH: LisH; InterPro: IPR013720 The LisH motif is found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerization motif, and that other structural elements are likely to play an important role in dimerisation [, , ]. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex []. ; PDB: 2XTE_L 2XTC_B 2XTD_A 1UUJ_B.
Probab=23.86 E-value=45 Score=23.41 Aligned_cols=19 Identities=26% Similarity=0.529 Sum_probs=15.5
Q ss_pred HHHHHHHHHHhhhccccCC
Q 008001 161 MLDELVREYCVYRGIVDSG 179 (582)
Q Consensus 161 lldeLv~eYc~yRGiv~~~ 179 (582)
.|+.||++|.+-+|..++.
T Consensus 2 ~Ln~lI~~YL~~~Gy~~tA 20 (27)
T PF08513_consen 2 ELNQLIYDYLVENGYKETA 20 (27)
T ss_dssp HHHHHHHHHHHHCT-HHHH
T ss_pred HHHHHHHHHHHHCCcHHHH
Confidence 6899999999999987653
No 34
>PF07729 FCD: FCD domain; InterPro: IPR011711 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector binding or oligomerisation domain at the C terminus. The winged-helix DNA-binding domain is well conserved in structure for the whole of the GntR family (IPR000524 from INTERPRO), and is similar in structure to other transcriptional regulator families. The C-terminal effector-binding and oligomerisation domains are more variable and are consequently used to define the subfamilies. Based on the sequence and structure of the C-terminal domains, the GtnR family can be divided into four major groups, as represented by FadR (IPR008920 from INTERPRO), HutC, MocR and YtrA, as well as some minor groups such as those represented by AraR and PlmA []. This entry represents the C-terminal ligand binding domain of many members of the GntR family. This domain probably binds to a range of effector molecules that regulate the transcription of genes through the action of the N-terminal DNA-binding domain. This domain is found in P45427 from SWISSPROT and P31460 from SWISSPROT that are regulators of sugar biosynthesis operons.; PDB: 3SXK_A 3SXY_A 3SXM_B 3SXZ_A 3FMS_A 2DI3_B 2HS5_A 3IHU_B 3C7J_A.
Probab=21.80 E-value=89 Score=25.52 Aligned_cols=66 Identities=21% Similarity=0.244 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHhccCCCccc--cCcccchhh--------------------------hHHHHHHHHhc
Q 008001 336 YEIVLGMKELAGKGMAAEAVEEINAMDADFFV--QNPMLLFQL--------------------------KQVEFLKLVSC 387 (582)
Q Consensus 336 IE~R~~IReAIq~G~IqeAIelVNeLdPeILD--tNP~L~FhL--------------------------QQqqLIELIR~ 387 (582)
-+...++++++..|++.+.++.-.+++=.|+. .||.|.--+ .-.++++.|+.
T Consensus 30 ~~~~~~~~~~~~~~d~~~~~~~~~~fh~~l~~~~~N~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~h~~i~~ai~~ 109 (125)
T PF07729_consen 30 EELLEQMEEAIEDEDIEEFIEADIEFHRALAEASGNPYLIQILERLRDRLQRFRYLSIRSKEDLERSLEEHREIIDAIRA 109 (125)
T ss_dssp HHHHHHHHHHHHCTHHHHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHHHc
Confidence 34455677788888888777765555444332 333332111 14578999999
Q ss_pred CChhHHHHHHHhhc
Q 008001 388 GDHSGALRVACAHL 401 (582)
Q Consensus 388 GdieeALeFAq~~L 401 (582)
||.+.|-+..+.|+
T Consensus 110 ~d~~~a~~~~~~h~ 123 (125)
T PF07729_consen 110 GDPEAAREALRQHI 123 (125)
T ss_dssp T-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHh
Confidence 99999999988886
No 35
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=20.63 E-value=1.8e+02 Score=22.14 Aligned_cols=51 Identities=24% Similarity=0.298 Sum_probs=34.5
Q ss_pred HHHHHhcCCHHHHHHHHhc---cCCCccccCcccchhhhHHHHHHHHhcCChhHHHHHHHhh
Q 008001 342 MKELAGKGMAAEAVEEINA---MDADFFVQNPMLLFQLKQVEFLKLVSCGDHSGALRVACAH 400 (582)
Q Consensus 342 IReAIq~G~IqeAIelVNe---LdPeILDtNP~L~FhLQQqqLIELIR~GdieeALeFAq~~ 400 (582)
-+.++..|+.++|++.++. .+|+ |+..+|.|=.+.+ +.|+.++|++.-+.-
T Consensus 4 a~~~~~~g~~~~A~~~~~~~l~~~P~----~~~a~~~lg~~~~----~~g~~~~A~~~~~~a 57 (65)
T PF13432_consen 4 ARALYQQGDYDEAIAAFEQALKQDPD----NPEAWYLLGRILY----QQGRYDEALAYYERA 57 (65)
T ss_dssp HHHHHHCTHHHHHHHHHHHHHCCSTT----HHHHHHHHHHHHH----HTT-HHHHHHHHHHH
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHCCC----CHHHHHHHHHHHH----HcCCHHHHHHHHHHH
Confidence 3567899999999988664 4554 5555555544433 689999998766543
Done!