Query 029808
Match_columns 187
No_of_seqs 137 out of 511
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 03:59:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029808.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029808hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00501 BRIGHT BRIGHT, ARID 100.0 6.6E-29 1.4E-33 183.0 10.5 91 44-134 1-92 (93)
2 PF01388 ARID: ARID/BRIGHT DNA 99.9 1.7E-27 3.7E-32 174.3 8.5 89 42-130 3-92 (92)
3 KOG2744 DNA-binding proteins B 99.8 5.7E-20 1.2E-24 171.3 11.5 105 42-146 160-266 (512)
4 KOG2510 SWI-SNF chromatin-remo 99.5 5.3E-14 1.1E-18 129.5 9.0 92 44-142 292-384 (532)
5 smart00545 JmjN Small domain f 95.5 0.0051 1.1E-07 39.6 0.7 16 19-34 27-42 (42)
6 PF00249 Myb_DNA-binding: Myb- 89.1 0.94 2E-05 28.8 4.3 39 77-126 10-48 (48)
7 PF13921 Myb_DNA-bind_6: Myb-l 75.8 7 0.00015 25.6 4.5 36 78-126 8-43 (60)
8 cd00167 SANT 'SWI3, ADA2, N-Co 74.2 8.2 0.00018 22.7 4.2 36 78-125 9-44 (45)
9 PF09441 Abp2: ARS binding pro 72.0 14 0.00031 30.4 6.2 41 66-110 45-85 (175)
10 smart00717 SANT SANT SWI3, AD 66.9 15 0.00033 21.8 4.3 26 96-126 22-47 (49)
11 PF06145 Corona_NS1: Coronavir 63.8 2.8 6E-05 24.5 0.4 18 168-187 9-26 (29)
12 PLN03212 Transcription repress 58.1 16 0.00035 31.9 4.2 39 79-128 36-74 (249)
13 PF10545 MADF_DNA_bdg: Alcohol 57.4 11 0.00023 25.7 2.5 37 94-130 25-64 (85)
14 PRK02363 DNA-directed RNA poly 55.4 7.8 0.00017 30.5 1.7 66 47-122 3-71 (129)
15 PF13873 Myb_DNA-bind_5: Myb/S 52.5 15 0.00032 25.3 2.6 55 74-128 14-71 (78)
16 PF05066 HARE-HTH: HB1, ASXL, 50.5 31 0.00068 23.5 4.0 43 49-102 3-45 (72)
17 PF04967 HTH_10: HTH DNA bindi 50.5 25 0.00054 23.5 3.3 39 86-126 14-52 (53)
18 PF12776 Myb_DNA-bind_3: Myb/S 47.6 55 0.0012 23.0 5.1 60 77-136 11-72 (96)
19 PLN03091 hypothetical protein; 45.5 23 0.0005 33.5 3.4 39 78-127 24-62 (459)
20 COG3343 RpoE DNA-directed RNA 42.7 39 0.00084 28.1 3.9 68 45-122 12-82 (175)
21 PF02375 JmjN: jmjN domain; I 41.2 8 0.00017 23.6 -0.2 9 20-28 26-34 (34)
22 smart00595 MADF subfamily of S 40.5 30 0.00065 24.2 2.7 39 94-132 26-65 (89)
23 KOG0138 Glutaryl-CoA dehydroge 38.5 29 0.00062 31.8 2.8 41 23-63 36-76 (432)
24 PLN03091 hypothetical protein; 38.3 1.3E+02 0.0028 28.6 7.1 41 78-131 77-117 (459)
25 cd01468 trunk_domain trunk dom 37.1 54 0.0012 27.5 4.1 75 18-93 145-221 (239)
26 PF13725 tRNA_bind_2: Possible 34.3 23 0.0005 25.6 1.3 19 91-109 79-97 (101)
27 PF02337 Gag_p10: Retroviral G 34.1 76 0.0016 23.5 4.0 54 46-106 7-63 (90)
28 smart00576 BTP Bromodomain tra 34.0 72 0.0016 22.3 3.8 35 99-133 13-47 (77)
29 cd01670 Death Death Domain: a 31.8 42 0.00091 22.7 2.2 15 96-110 11-25 (79)
30 cd07268 Glo_EDI_BRP_like_4 Thi 31.4 13 0.00028 30.1 -0.5 51 39-89 4-54 (149)
31 cd08797 Death_NFkB1_p105 Death 31.2 68 0.0015 23.1 3.2 15 95-109 15-29 (76)
32 COG5227 SMT3 Ubiquitin-like pr 30.9 60 0.0013 24.5 3.0 66 12-77 3-77 (103)
33 PF08914 Myb_DNA-bind_2: Rap1 28.2 83 0.0018 21.7 3.2 51 78-132 12-63 (65)
34 PTZ00100 DnaJ chaperone protei 27.3 2.9E+02 0.0064 21.3 6.4 76 46-129 17-93 (116)
35 KOG2744 DNA-binding proteins B 26.5 4.8 0.0001 38.5 -4.4 91 44-134 308-400 (512)
36 smart00540 LEM in nuclear memb 26.0 1.3E+02 0.0028 19.4 3.5 31 98-130 11-41 (44)
37 cd08798 Death_NFkB2_p100 Death 25.7 93 0.002 22.4 3.1 15 95-109 15-29 (76)
38 cd08310 Death_NFkB-like Death 23.7 1.1E+02 0.0023 21.4 3.2 15 95-109 12-26 (72)
39 PRK02922 glycogen synthesis pr 23.7 40 0.00087 23.8 0.9 26 45-70 10-35 (67)
40 cd08777 Death_RIP1 Death Domai 23.4 45 0.00098 24.1 1.2 15 96-110 14-28 (86)
41 cd01479 Sec24-like Sec24-like: 23.4 1.2E+02 0.0027 25.6 4.1 77 17-94 141-219 (244)
42 PF04545 Sigma70_r4: Sigma-70, 23.2 97 0.0021 19.3 2.6 28 94-127 19-46 (50)
43 COG5182 CUS1 Splicing factor 3 22.8 2.3E+02 0.005 26.3 5.8 39 50-88 207-254 (429)
44 cd08306 Death_FADD Fas-associa 21.8 63 0.0014 23.2 1.7 15 96-110 14-28 (86)
45 cd08802 Death_UNC5B Death doma 21.7 1.1E+02 0.0024 22.3 3.0 14 95-108 20-33 (84)
46 cd08311 Death_p75NR Death doma 21.5 65 0.0014 22.9 1.7 16 95-110 15-30 (77)
47 cd08799 Death_UNC5C Death doma 21.4 1.2E+02 0.0026 22.1 3.1 15 95-109 20-34 (84)
48 PRK11700 hypothetical protein; 20.8 27 0.00059 29.3 -0.5 40 49-88 52-91 (187)
No 1
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=99.96 E-value=6.6e-29 Score=183.03 Aligned_cols=91 Identities=40% Similarity=0.652 Sum_probs=87.2
Q ss_pred hcHHHHHHHHHHHHHhcCCCC-CCCeeCCeecchhhHHHHHHhhCCccccccccChHHHHHHhCCCCCCCcHHHHHHHHH
Q 029808 44 QSSDLFWATLEAFHKSFGDKF-KVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYY 122 (187)
Q Consensus 44 ~~~~~Fl~~L~~F~~~rG~pl-~~P~I~gk~VDLy~Ly~~V~~~GG~~~V~~~k~W~eVa~~Lglp~~~t~a~~~Lk~~Y 122 (187)
++++.|+++|.+||+++|+++ ++|.|+|++||||+||.+|+++|||++|+++++|.+||++||+++++++++..||++|
T Consensus 1 ~~~~~F~~~L~~F~~~~g~~~~~~P~i~g~~vdL~~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y 80 (93)
T smart00501 1 RERVLFLDRLYKFMEERGSPLKKIPVIGGKPLDLYRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHY 80 (93)
T ss_pred CcHHHHHHHHHHHHHHcCCcCCcCCeECCEeCcHHHHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHH
Confidence 478999999999999999998 7999999999999999999999999999999999999999999988899999999999
Q ss_pred HHhHHHHHHHHH
Q 029808 123 LSLLYHFEQVYY 134 (187)
Q Consensus 123 ~kyLl~fE~~~~ 134 (187)
.+||++||+++.
T Consensus 81 ~k~L~~yE~~~~ 92 (93)
T smart00501 81 ERYLLPFERFLR 92 (93)
T ss_pred HHHhHHHHHHhh
Confidence 999999999863
No 2
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....
Probab=99.94 E-value=1.7e-27 Score=174.31 Aligned_cols=89 Identities=37% Similarity=0.693 Sum_probs=82.2
Q ss_pred hhhcHHHHHHHHHHHHHhcCCCC-CCCeeCCeecchhhHHHHHHhhCCccccccccChHHHHHHhCCCCCCCcHHHHHHH
Q 029808 42 IAQSSDLFWATLEAFHKSFGDKF-KVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRK 120 (187)
Q Consensus 42 ~~~~~~~Fl~~L~~F~~~rG~pl-~~P~I~gk~VDLy~Ly~~V~~~GG~~~V~~~k~W~eVa~~Lglp~~~t~a~~~Lk~ 120 (187)
.+++++.|++.|.+||+++|+++ ++|.|+|++||||+||.+|+++|||++|+++++|.+||++||+++..++.+..||+
T Consensus 3 ~~~~~~~F~~~L~~f~~~~g~~~~~~P~i~g~~vDL~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~ 82 (92)
T PF01388_consen 3 NTREREQFLEQLREFHESRGTPIDRPPVIGGKPVDLYKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQ 82 (92)
T ss_dssp SCHHHHHHHHHHHHHHHHTTSSSSS-SEETTSE-SHHHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHH
T ss_pred cchHHHHHHHHHHHHHHHcCCCCCCCCcCCCEeCcHHHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHH
Confidence 35789999999999999999997 79999999999999999999999999999999999999999999988888899999
Q ss_pred HHHHhHHHHH
Q 029808 121 YYLSLLYHFE 130 (187)
Q Consensus 121 ~Y~kyLl~fE 130 (187)
+|++||++||
T Consensus 83 ~Y~~~L~~fE 92 (92)
T PF01388_consen 83 HYEKYLLPFE 92 (92)
T ss_dssp HHHHHTHHHH
T ss_pred HHHHHhHhhC
Confidence 9999999998
No 3
>KOG2744 consensus DNA-binding proteins Bright/BRCAA1/RBP1 and related proteins containing BRIGHT domain [Transcription]
Probab=99.82 E-value=5.7e-20 Score=171.34 Aligned_cols=105 Identities=46% Similarity=0.769 Sum_probs=96.4
Q ss_pred hhhcHHHHHHHHHHHHHhcCCCCC-CCeeCCeecchhhHHHHHHhhCCccccccccChHHHHHHhCCCC-CCCcHHHHHH
Q 029808 42 IAQSSDLFWATLEAFHKSFGDKFK-VPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPT-TITSASFVLR 119 (187)
Q Consensus 42 ~~~~~~~Fl~~L~~F~~~rG~pl~-~P~I~gk~VDLy~Ly~~V~~~GG~~~V~~~k~W~eVa~~Lglp~-~~t~a~~~Lk 119 (187)
...+++.|+++|+.||+++|++++ +|+|+|+++|||+||.+|+++||+++|+.+++|++|...|.|+. ++|++++.||
T Consensus 160 ~~~~~eeF~~dl~~f~~~~~~~~~~iPii~~~~ldL~~Ly~lV~s~GG~~~V~~~k~Wrev~~~l~~pt~tiTsaaf~lr 239 (512)
T KOG2744|consen 160 VPKSSEEFMEDLRRFMKKRGTKVKSIPIIGGQPLDLHWLYALVTSRGGLDEVTNKKLWREVIDGLNFPTPTITSAAFTLR 239 (512)
T ss_pred ccccHHHHHHHHHHHHHHhCCcceeccccCCCcchHHHHHHHHhcCCchhHhhhhhhHHHHhccccCCCcccchHHHHHH
Confidence 455999999999999999999995 99999999999999999999999999999999999999999999 9999999999
Q ss_pred HHHHHhHHHHHHHHHhhccCCCCCCCC
Q 029808 120 KYYLSLLYHFEQVYYFRKEAPSSSMPD 146 (187)
Q Consensus 120 ~~Y~kyLl~fE~~~~~~~~~~~~~~~~ 146 (187)
+.|.|+|++||+.+.+....+.+.|..
T Consensus 240 ~~y~K~L~~ye~~~~~~~~~pln~p~~ 266 (512)
T KOG2744|consen 240 KQYLKLLFEYECEFEKNRHVPLNSPAE 266 (512)
T ss_pred HHHHHHHHHHHHHHHHhccCCCCCccc
Confidence 999999999999998775444444443
No 4
>KOG2510 consensus SWI-SNF chromatin-remodeling complex protein [Chromatin structure and dynamics]
Probab=99.50 E-value=5.3e-14 Score=129.52 Aligned_cols=92 Identities=30% Similarity=0.537 Sum_probs=86.1
Q ss_pred hcHHHHHHHHHHHHHhcCCCC-CCCeeCCeecchhhHHHHHHhhCCccccccccChHHHHHHhCCCCCCCcHHHHHHHHH
Q 029808 44 QSSDLFWATLEAFHKSFGDKF-KVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYY 122 (187)
Q Consensus 44 ~~~~~Fl~~L~~F~~~rG~pl-~~P~I~gk~VDLy~Ly~~V~~~GG~~~V~~~k~W~eVa~~Lglp~~~t~a~~~Lk~~Y 122 (187)
.+++.+++.|+.|++++.+++ .+|.++.|+||||+||..|..+||+.+|+++| +++|.-|| .++++.||++|
T Consensus 292 p~r~~wvDR~raF~ee~~Sp~t~~p~~gakPldl~rlYvsvke~gg~~~v~knk--rd~a~~lg-----ssaa~~l~k~y 364 (532)
T KOG2510|consen 292 PERKEWVDRLRAFTEERASPMTNLPAVGAKPLDLYRLYVSVKEIGGLTQVNKNK--RDLATNLG-----SSAASSLKKQY 364 (532)
T ss_pred cchhhHHHHHHHHHHhhcCcccccccccccchhHHHHHHHHHHhccceeeccch--hhhhhccc-----hHHHHHHHHHH
Confidence 579999999999999999998 58999999999999999999999999999998 99999888 56899999999
Q ss_pred HHhHHHHHHHHHhhccCCCC
Q 029808 123 LSLLYHFEQVYYFRKEAPSS 142 (187)
Q Consensus 123 ~kyLl~fE~~~~~~~~~~~~ 142 (187)
.+||+.||+...+++++++.
T Consensus 365 ~~~lf~fec~f~Rg~e~p~~ 384 (532)
T KOG2510|consen 365 IQYLFAFECKFERGEEPPPD 384 (532)
T ss_pred HHHHHhhceeeeccCCCCHH
Confidence 99999999999999988763
No 5
>smart00545 JmjN Small domain found in the jumonji family of transcription factors. To date, this domain always co-occurs with the JmjC domain (although the reverse is not true).
Probab=95.53 E-value=0.0051 Score=39.56 Aligned_cols=16 Identities=6% Similarity=0.065 Sum_probs=14.5
Q ss_pred CCCCccccCCCCCCCC
Q 029808 19 SNSNNNNSKASSYYPP 34 (187)
Q Consensus 19 ~~sgi~~i~pp~~w~P 34 (187)
-.+|||||+||++|+|
T Consensus 27 ~~yGi~KIvPP~~w~p 42 (42)
T smart00545 27 EKYGICKVVPPKSWKP 42 (42)
T ss_pred hhCCEEEEECCCCCCc
Confidence 4689999999999987
No 6
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=89.11 E-value=0.94 Score=28.83 Aligned_cols=39 Identities=23% Similarity=0.310 Sum_probs=28.2
Q ss_pred hhHHHHHHhhCCccccccccChHHHHHHhCCCCCCCcHHHHHHHHHHHhH
Q 029808 77 HRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSLL 126 (187)
Q Consensus 77 y~Ly~~V~~~GG~~~V~~~k~W~eVa~~Lglp~~~t~a~~~Lk~~Y~kyL 126 (187)
-.|..+|...|.- .|..||..++... .+.+++..|.++|
T Consensus 10 ~~l~~~v~~~g~~-------~W~~Ia~~~~~~R----t~~qc~~~~~~~~ 48 (48)
T PF00249_consen 10 EKLLEAVKKYGKD-------NWKKIAKRMPGGR----TAKQCRSRYQNLL 48 (48)
T ss_dssp HHHHHHHHHSTTT-------HHHHHHHHHSSSS----THHHHHHHHHHHT
T ss_pred HHHHHHHHHhCCc-------HHHHHHHHcCCCC----CHHHHHHHHHhhC
Confidence 3566777776652 5999999999222 2448999999876
No 7
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=75.82 E-value=7 Score=25.56 Aligned_cols=36 Identities=19% Similarity=0.280 Sum_probs=23.8
Q ss_pred hHHHHHHhhCCccccccccChHHHHHHhCCCCCCCcHHHHHHHHHHHhH
Q 029808 78 RLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSLL 126 (187)
Q Consensus 78 ~Ly~~V~~~GG~~~V~~~k~W~eVa~~Lglp~~~t~a~~~Lk~~Y~kyL 126 (187)
.|...|...|. .|..||..|| .. ...+++..|.++|
T Consensus 8 ~L~~~~~~~g~--------~W~~Ia~~l~-~R----t~~~~~~r~~~~l 43 (60)
T PF13921_consen 8 LLLELVKKYGN--------DWKKIAEHLG-NR----TPKQCRNRWRNHL 43 (60)
T ss_dssp HHHHHHHHHTS---------HHHHHHHST-TS-----HHHHHHHHHHTT
T ss_pred HHHHHHHHHCc--------CHHHHHHHHC-cC----CHHHHHHHHHHHC
Confidence 45566666553 5999999996 12 1347888888866
No 8
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=74.24 E-value=8.2 Score=22.73 Aligned_cols=36 Identities=17% Similarity=0.248 Sum_probs=24.3
Q ss_pred hHHHHHHhhCCccccccccChHHHHHHhCCCCCCCcHHHHHHHHHHHh
Q 029808 78 RLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSL 125 (187)
Q Consensus 78 ~Ly~~V~~~GG~~~V~~~k~W~eVa~~Lglp~~~t~a~~~Lk~~Y~ky 125 (187)
.|...|...|- ..|..||..++-- .+..++..|.++
T Consensus 9 ~l~~~~~~~g~-------~~w~~Ia~~~~~r-----s~~~~~~~~~~~ 44 (45)
T cd00167 9 LLLEAVKKYGK-------NNWEKIAKELPGR-----TPKQCRERWRNL 44 (45)
T ss_pred HHHHHHHHHCc-------CCHHHHHhHcCCC-----CHHHHHHHHHHh
Confidence 45556666652 4799999999652 234788887765
No 9
>PF09441 Abp2: ARS binding protein 2; InterPro: IPR018562 This DNA-binding protein binds to the autonomously replicating sequence (ARS) binding element. It may play a role in regulating the cell cycle response to stress signals [].
Probab=72.03 E-value=14 Score=30.40 Aligned_cols=41 Identities=15% Similarity=0.327 Sum_probs=34.5
Q ss_pred CCeeCCeecchhhHHHHHHhhCCccccccccChHHHHHHhCCCCC
Q 029808 66 VPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTT 110 (187)
Q Consensus 66 ~P~I~gk~VDLy~Ly~~V~~~GG~~~V~~~k~W~eVa~~Lglp~~ 110 (187)
+|.-+||..+.|.||..|.++-.- +-|.|.++|-+||+.+.
T Consensus 45 pPkS~Gk~Fs~~~Lf~LI~k~~~k----eikTW~~La~~LGVepp 85 (175)
T PF09441_consen 45 PPKSDGKSFSTFTLFELIRKLESK----EIKTWAQLALELGVEPP 85 (175)
T ss_pred CCCcCCccchHHHHHHHHHHHhhh----hHhHHHHHHHHhCCCCC
Confidence 799999999999999999986542 23589999999999653
No 10
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=66.89 E-value=15 Score=21.82 Aligned_cols=26 Identities=15% Similarity=0.267 Sum_probs=18.5
Q ss_pred cChHHHHHHhCCCCCCCcHHHHHHHHHHHhH
Q 029808 96 RRWKEVVVVFNFPTTITSASFVLRKYYLSLL 126 (187)
Q Consensus 96 k~W~eVa~~Lglp~~~t~a~~~Lk~~Y~kyL 126 (187)
..|..||..|+-- .+..++..|..++
T Consensus 22 ~~w~~Ia~~~~~r-----t~~~~~~~~~~~~ 47 (49)
T smart00717 22 NNWEKIAKELPGR-----TAEQCRERWNNLL 47 (49)
T ss_pred CCHHHHHHHcCCC-----CHHHHHHHHHHHc
Confidence 4799999999721 2337888887764
No 11
>PF06145 Corona_NS1: Coronavirus nonstructural protein NS1; InterPro: IPR009314 One of the members of this family is a 4.9 kDa proteins, encoded by Bovine coronavirus NS1 [].
Probab=63.79 E-value=2.8 Score=24.48 Aligned_cols=18 Identities=44% Similarity=0.787 Sum_probs=14.7
Q ss_pred ccCCCCCCCCCccccccccC
Q 029808 168 QLGGQGMFHPRHFIHSSLII 187 (187)
Q Consensus 168 ~~~~~~~~~~~~~~~~~~~~ 187 (187)
-|-+|-|.|| |||.-|||
T Consensus 9 ll~pddilhp--~nhv~lii 26 (29)
T PF06145_consen 9 LLAPDDILHP--FNHVNLII 26 (29)
T ss_pred ecCcccccCc--ccceeEEE
Confidence 4668999999 58888886
No 12
>PLN03212 Transcription repressor MYB5; Provisional
Probab=58.09 E-value=16 Score=31.89 Aligned_cols=39 Identities=15% Similarity=0.234 Sum_probs=24.7
Q ss_pred HHHHHHhhCCccccccccChHHHHHHhCCCCCCCcHHHHHHHHHHHhHHH
Q 029808 79 LFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSLLYH 128 (187)
Q Consensus 79 Ly~~V~~~GG~~~V~~~k~W~eVa~~Lglp~~~t~a~~~Lk~~Y~kyLl~ 128 (187)
|...|.+.|. ..|..||..++...+ +.+.|.-|.+||.|
T Consensus 36 L~~lV~kyG~-------~nW~~IAk~~g~gRT----~KQCReRW~N~L~P 74 (249)
T PLN03212 36 LVSFIKKEGE-------GRWRSLPKRAGLLRC----GKSCRLRWMNYLRP 74 (249)
T ss_pred HHHHHHHhCc-------ccHHHHHHhhhcCCC----cchHHHHHHHhhch
Confidence 3445555553 359999998874432 23777778877744
No 13
>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.
Probab=57.39 E-value=11 Score=25.68 Aligned_cols=37 Identities=19% Similarity=0.255 Sum_probs=21.3
Q ss_pred cccChHHHHHHhCCCCC---CCcHHHHHHHHHHHhHHHHH
Q 029808 94 RDRRWKEVVVVFNFPTT---ITSASFVLRKYYLSLLYHFE 130 (187)
Q Consensus 94 ~~k~W~eVa~~Lglp~~---~t~a~~~Lk~~Y~kyLl~fE 130 (187)
+.+.|.+||..||...+ +...-..||..|.+.+...+
T Consensus 25 r~~aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~y~~~~~~~~ 64 (85)
T PF10545_consen 25 REEAWQEIARELGKEFSVDDCKKRWKNLRDRYRRELKKIK 64 (85)
T ss_pred HHHHHHHHHHHHccchhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45689999999984322 22223345555555554444
No 14
>PRK02363 DNA-directed RNA polymerase subunit delta; Reviewed
Probab=55.38 E-value=7.8 Score=30.50 Aligned_cols=66 Identities=14% Similarity=0.120 Sum_probs=48.3
Q ss_pred HHHHHHHHHHHHhcCCCCCCCeeCCeecchhhHHHHHHhhCCccccccccChHHHHHHhCCCCC---CCcHHHHHHHHH
Q 029808 47 DLFWATLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTT---ITSASFVLRKYY 122 (187)
Q Consensus 47 ~~Fl~~L~~F~~~rG~pl~~P~I~gk~VDLy~Ly~~V~~~GG~~~V~~~k~W~eVa~~Lglp~~---~t~a~~~Lk~~Y 122 (187)
..+++.-+.++++++.| +.++.|+..|++..|+..-....+=.+++..|.+... .++.-+.||.-|
T Consensus 3 ~S~idvAy~iL~~~~~~----------m~f~dL~~ev~~~~~~s~e~~~~~iaq~YtdLn~DGRFi~lG~n~WgLr~w~ 71 (129)
T PRK02363 3 LSLIEVAYEILKEKKEP----------MSFYDLVNEIQKYLGKSDEEIRERIAQFYTDLNLDGRFISLGDNKWGLRSWY 71 (129)
T ss_pred ccHHHHHHHHHHHcCCc----------ccHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhccCCeeEcCCCceeccccc
Confidence 35666677777777554 8999999999999998765555677788888888764 345566777644
No 15
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=52.51 E-value=15 Score=25.29 Aligned_cols=55 Identities=13% Similarity=0.176 Sum_probs=31.8
Q ss_pred cchhhHHHHHHhhC---CccccccccChHHHHHHhCCCCCCCcHHHHHHHHHHHhHHH
Q 029808 74 LDLHRLFVEVTSRG---GLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSLLYH 128 (187)
Q Consensus 74 VDLy~Ly~~V~~~G---G~~~V~~~k~W~eVa~~Lglp~~~t~a~~~Lk~~Y~kyLl~ 128 (187)
|+|+.-|..|..-- ......+...|.+|+..|.--....-.+.+||+.|.++...
T Consensus 14 v~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~ 71 (78)
T PF13873_consen 14 VELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSK 71 (78)
T ss_pred HHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHH
Confidence 34444454444331 11222345699999999963222233355999999887654
No 16
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=50.50 E-value=31 Score=23.50 Aligned_cols=43 Identities=14% Similarity=0.177 Sum_probs=26.2
Q ss_pred HHHHHHHHHHhcCCCCCCCeeCCeecchhhHHHHHHhhCCccccccccChHHHH
Q 029808 49 FWATLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVV 102 (187)
Q Consensus 49 Fl~~L~~F~~~rG~pl~~P~I~gk~VDLy~Ly~~V~~~GG~~~V~~~k~W~eVa 102 (187)
|++.-.+-+++.|. ++..-.|+..|+++|++.... +..|..|+
T Consensus 3 ~~eaa~~vL~~~~~----------pm~~~eI~~~i~~~~~~~~~~-k~p~~~i~ 45 (72)
T PF05066_consen 3 FKEAAYEVLEEAGR----------PMTFKEIWEEIQERGLYKKSG-KTPEATIA 45 (72)
T ss_dssp HHHHHHHHHHHH-S-----------EEHHHHHHHHHHHHTS---G-GGGGHHHH
T ss_pred HHHHHHHHHHhcCC----------CcCHHHHHHHHHHhCCCCccc-CCHHHHHH
Confidence 45555556666654 488899999999999998772 33555554
No 17
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=50.49 E-value=25 Score=23.46 Aligned_cols=39 Identities=21% Similarity=0.149 Sum_probs=31.7
Q ss_pred hCCccccccccChHHHHHHhCCCCCCCcHHHHHHHHHHHhH
Q 029808 86 RGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSLL 126 (187)
Q Consensus 86 ~GG~~~V~~~k~W~eVa~~Lglp~~~t~a~~~Lk~~Y~kyL 126 (187)
..||=.+-++-.=.+||++||+.+ ++++..||+.-.|.+
T Consensus 14 ~~GYfd~PR~~tl~elA~~lgis~--st~~~~LRrae~kli 52 (53)
T PF04967_consen 14 ELGYFDVPRRITLEELAEELGISK--STVSEHLRRAERKLI 52 (53)
T ss_pred HcCCCCCCCcCCHHHHHHHhCCCH--HHHHHHHHHHHHHHh
Confidence 457777888888999999999987 357789998887765
No 18
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=47.59 E-value=55 Score=22.98 Aligned_cols=60 Identities=17% Similarity=0.272 Sum_probs=38.3
Q ss_pred hhHHHHHHhhCCc--cccccccChHHHHHHhCCCCCCCcHHHHHHHHHHHhHHHHHHHHHhh
Q 029808 77 HRLFVEVTSRGGL--GKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSLLYHFEQVYYFR 136 (187)
Q Consensus 77 y~Ly~~V~~~GG~--~~V~~~k~W~eVa~~Lglp~~~t~a~~~Lk~~Y~kyLl~fE~~~~~~ 136 (187)
..|+......|.. ...=....|..|+.+|.-..+..-...+|+..|..+=..|..+....
T Consensus 11 l~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y~~~~~l~ 72 (96)
T PF12776_consen 11 LDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDYRIWKELR 72 (96)
T ss_pred HHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555655 12223347999999997644433234589999999888888865443
No 19
>PLN03091 hypothetical protein; Provisional
Probab=45.51 E-value=23 Score=33.46 Aligned_cols=39 Identities=18% Similarity=0.262 Sum_probs=25.7
Q ss_pred hHHHHHHhhCCccccccccChHHHHHHhCCCCCCCcHHHHHHHHHHHhHH
Q 029808 78 RLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSLLY 127 (187)
Q Consensus 78 ~Ly~~V~~~GG~~~V~~~k~W~eVa~~Lglp~~~t~a~~~Lk~~Y~kyLl 127 (187)
+|..+|.+.|- +.|..||..++...+ +.+.|.-|.+||.
T Consensus 24 ~L~~~V~kyG~-------~nWs~IAk~~g~gRT----~KQCRERW~NyLd 62 (459)
T PLN03091 24 KLLRHITKYGH-------GCWSSVPKQAGLQRC----GKSCRLRWINYLR 62 (459)
T ss_pred HHHHHHHHhCc-------CCHHHHhhhhccCcC----cchHhHHHHhccC
Confidence 56777777763 469999998875432 2256666766554
No 20
>COG3343 RpoE DNA-directed RNA polymerase, delta subunit [Transcription]
Probab=42.70 E-value=39 Score=28.10 Aligned_cols=68 Identities=15% Similarity=0.162 Sum_probs=51.6
Q ss_pred cHHHHHHHHHHHHHhcCCCCCCCeeCCeecchhhHHHHHHhhCCccccccccChHHHHHHhCCCCCC---CcHHHHHHHH
Q 029808 45 SSDLFWATLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTI---TSASFVLRKY 121 (187)
Q Consensus 45 ~~~~Fl~~L~~F~~~rG~pl~~P~I~gk~VDLy~Ly~~V~~~GG~~~V~~~k~W~eVa~~Lglp~~~---t~a~~~Lk~~ 121 (187)
....++..-+..++.+|. ++.+..|.+.|++++|+....-..+-...+..|...++. ...-+.||..
T Consensus 12 ~els~IevA~~ile~~~~----------~~~F~dii~EI~~~~~~s~~ei~~~i~~FYTdln~DgrFi~LGdn~WgLRsw 81 (175)
T COG3343 12 SELSLIEVAHAILEEKKK----------PFNFSDIINEIQKLLGVSKEEIRSRIGQFYTDLNIDGRFISLGDNKWGLRSW 81 (175)
T ss_pred HHHHHHHHHHHHHHHcCC----------CccHHHHHHHHHHHhCcCHHHHHHHHHHHHHHhccCCceeeccccccchhhc
Confidence 455666666666777765 478999999999999999988888888999999887652 3345567766
Q ss_pred H
Q 029808 122 Y 122 (187)
Q Consensus 122 Y 122 (187)
|
T Consensus 82 y 82 (175)
T COG3343 82 Y 82 (175)
T ss_pred c
Confidence 5
No 21
>PF02375 JmjN: jmjN domain; InterPro: IPR003349 Jumonji protein is required for neural tube formation in mice [].There is evidence of domain swapping within the jumonji family of transcription factors []. This domain is often associated with JmjC (see IPR003347 from INTERPRO).; PDB: 2XML_A 2W2I_C 3DXT_A 3DXU_A 2OX0_B 2OQ6_B 2WWJ_A 2Q8D_A 3PDQ_A 2YBK_A ....
Probab=41.24 E-value=8 Score=23.63 Aligned_cols=9 Identities=0% Similarity=-0.282 Sum_probs=6.5
Q ss_pred CCCccccCC
Q 029808 20 NSNNNNSKA 28 (187)
Q Consensus 20 ~sgi~~i~p 28 (187)
.+|||||+|
T Consensus 26 ~~Gi~KIvP 34 (34)
T PF02375_consen 26 KYGICKIVP 34 (34)
T ss_dssp GGSEEEE--
T ss_pred HCCEEEecC
Confidence 789999987
No 22
>smart00595 MADF subfamily of SANT domain.
Probab=40.53 E-value=30 Score=24.16 Aligned_cols=39 Identities=15% Similarity=0.266 Sum_probs=26.2
Q ss_pred cccChHHHHHHhCCCCC-CCcHHHHHHHHHHHhHHHHHHH
Q 029808 94 RDRRWKEVVVVFNFPTT-ITSASFVLRKYYLSLLYHFEQV 132 (187)
Q Consensus 94 ~~k~W~eVa~~Lglp~~-~t~a~~~Lk~~Y~kyLl~fE~~ 132 (187)
+...|.+||.+||.+.. +..-=..||..|.+.+......
T Consensus 26 r~~aW~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r~~~~ 65 (89)
T smart00595 26 KRKAWEEIAEELGLSVEECKKRWKNLRDRYRRELKRLQNG 65 (89)
T ss_pred HHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45599999999998432 2333446777777766665543
No 23
>KOG0138 consensus Glutaryl-CoA dehydrogenase [Amino acid transport and metabolism]
Probab=38.53 E-value=29 Score=31.83 Aligned_cols=41 Identities=7% Similarity=0.113 Sum_probs=35.2
Q ss_pred ccccCCCCCCCCCCCCchhhhhcHHHHHHHHHHHHHhcCCC
Q 029808 23 NNNSKASSYYPPPTAKYEDIAQSSDLFWATLEAFHKSFGDK 63 (187)
Q Consensus 23 i~~i~pp~~w~PPf~~~~d~~~~~~~Fl~~L~~F~~~rG~p 63 (187)
..+..-|+-|+.|+...+.++.|+..-.+..+.||+++=.|
T Consensus 36 ~~~s~~P~f~qD~~~l~dqLT~dE~air~~~Reycq~~l~P 76 (432)
T KOG0138|consen 36 LSKSSRPEFWQDPLVLEDQLTEDEIAIRDTFREYCQERLMP 76 (432)
T ss_pred cccccCCccccchhhhhhhcCHHHHHHHHHHHHHHHHHhhh
Confidence 45555666699999999999999999999999999998665
No 24
>PLN03091 hypothetical protein; Provisional
Probab=38.31 E-value=1.3e+02 Score=28.59 Aligned_cols=41 Identities=17% Similarity=0.260 Sum_probs=28.5
Q ss_pred hHHHHHHhhCCccccccccChHHHHHHhCCCCCCCcHHHHHHHHHHHhHHHHHH
Q 029808 78 RLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSLLYHFEQ 131 (187)
Q Consensus 78 ~Ly~~V~~~GG~~~V~~~k~W~eVa~~Lglp~~~t~a~~~Lk~~Y~kyLl~fE~ 131 (187)
+|...|..+| ++|..||..| +. .+ ..++|..|..+|..+-+
T Consensus 77 lLLeL~k~~G--------nKWskIAk~L--PG-RT--DnqIKNRWnslLKKklr 117 (459)
T PLN03091 77 LIIELHAVLG--------NRWSQIAAQL--PG-RT--DNEIKNLWNSCLKKKLR 117 (459)
T ss_pred HHHHHHHHhC--------cchHHHHHhc--CC-CC--HHHHHHHHHHHHHHHHH
Confidence 4455555566 4899999987 32 23 33899999998887644
No 25
>cd01468 trunk_domain trunk domain. COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is known as the trunk domain and has an alpha/beta vWA fold and forms the dimer interface. Some members of this family possess a partial MIDAS motif that is a characteristic feature of most vWA domain proteins.
Probab=37.13 E-value=54 Score=27.46 Aligned_cols=75 Identities=13% Similarity=0.083 Sum_probs=52.9
Q ss_pred CCCCCccccCCCCCCCCCCCCchh--hhhcHHHHHHHHHHHHHhcCCCCCCCeeCCeecchhhHHHHHHhhCCccccc
Q 029808 18 NSNSNNNNSKASSYYPPPTAKYED--IAQSSDLFWATLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVI 93 (187)
Q Consensus 18 ~~~sgi~~i~pp~~w~PPf~~~~d--~~~~~~~Fl~~L~~F~~~rG~pl~~P~I~gk~VDLy~Ly~~V~~~GG~~~V~ 93 (187)
+.+.|+.++..- .-...+..+.+ .......|+++|..-+.+.|..+.+-......+||..|-..+..-||.-..-
T Consensus 145 ~pt~GpG~l~~~-~~~~~~~~~~e~~~~~~a~~fY~~la~~~~~~~isvdlF~~~~~~~dl~~l~~l~~~TGG~v~~y 221 (239)
T cd01468 145 LPTVGPGKLKSR-EDKEPIRSHDEAQLLKPATKFYKSLAKECVKSGICVDLFAFSLDYVDVATLKQLAKSTGGQVYLY 221 (239)
T ss_pred CCCCCCCccccC-cccccCCCccchhcccccHHHHHHHHHHHHHcCeEEEEEeccccccCHHHhhhhhhcCCceEEEe
Confidence 556777666653 22222222222 3445678999999999999988777667778999999999999999965443
No 26
>PF13725 tRNA_bind_2: Possible tRNA binding domain; PDB: 2ZPA_B.
Probab=34.34 E-value=23 Score=25.59 Aligned_cols=19 Identities=26% Similarity=0.643 Sum_probs=12.8
Q ss_pred ccccccChHHHHHHhCCCC
Q 029808 91 KVIRDRRWKEVVVVFNFPT 109 (187)
Q Consensus 91 ~V~~~k~W~eVa~~Lglp~ 109 (187)
+|.+++.|.+||+++|++.
T Consensus 79 k~LQ~ksw~~~a~~l~l~g 97 (101)
T PF13725_consen 79 KGLQGKSWEEVAKELGLPG 97 (101)
T ss_dssp HHCS---HHHHHHHCT-SS
T ss_pred HHHCCCCHHHHHHHcCCCC
Confidence 4667889999999999985
No 27
>PF02337 Gag_p10: Retroviral GAG p10 protein; InterPro: IPR003322 Retroviral matrix proteins (or major core proteins) are components of envelope-associated capsids, which line the inner surface of virus envelopes and are associated with viral membranes []. Matrix proteins are produced as part of Gag precursor polyproteins. During viral maturation, the Gag polyprotein is cleaved into major structural proteins by the viral protease, yielding the matrix (MA), capsid (CA), nucleocapsid (NC), and some smaller peptides. Gag-derived proteins govern the entire assembly and release of the virus particles, with matrix proteins playing key roles in Gag stability, capsid assembly, transport and budding. Although matrix proteins from different retroviruses appear to perform similar functions and can have similar structural folds, their primary sequences can be very different. This entry represents matrix proteins from beta-retroviruses such as Mason-Pfizer monkey virus (MPMV) (Simian Mason-Pfizer virus) and Mouse mammary tumor virus (MMTV) [, ]. This entry also identifies matrix proteins from several eukaryotic endogenous retroviruses, which arise when one or more copies of the retroviral genome becomes integrated into the host genome [].; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 2F77_X 2F76_X.
Probab=34.06 E-value=76 Score=23.50 Aligned_cols=54 Identities=19% Similarity=0.124 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHHhcCCCCCCCeeCCeecchhhHHHHHHhhCCcccccc---ccChHHHHHHhC
Q 029808 46 SDLFWATLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIR---DRRWKEVVVVFN 106 (187)
Q Consensus 46 ~~~Fl~~L~~F~~~rG~pl~~P~I~gk~VDLy~Ly~~V~~~GG~~~V~~---~k~W~eVa~~Lg 106 (187)
++.|+..|+..++.||..++ .=||-++|..+.+..=.-.... -+.|..|.+.|.
T Consensus 7 ~~~fv~~Lk~lLk~rGi~v~-------~~~L~~f~~~i~~~~PWF~~eG~l~~~~W~kvG~~l~ 63 (90)
T PF02337_consen 7 KQPFVSILKHLLKERGIRVK-------KKDLINFLSFIDKVCPWFPEEGTLDLDNWKKVGEELK 63 (90)
T ss_dssp HHHHHHHHHHHHHCCT-----------HHHHHHHHHHHHHHTT-SS--SS-HHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHcCeeec-------HHHHHHHHHHHHHhCCCCCCCCCcCHHHHHHHHHHHH
Confidence 37999999999999999873 3467777777765432221111 247999988884
No 28
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=34.01 E-value=72 Score=22.28 Aligned_cols=35 Identities=14% Similarity=0.095 Sum_probs=29.5
Q ss_pred HHHHHHhCCCCCCCcHHHHHHHHHHHhHHHHHHHH
Q 029808 99 KEVVVVFNFPTTITSASFVLRKYYLSLLYHFEQVY 133 (187)
Q Consensus 99 ~eVa~~Lglp~~~t~a~~~Lk~~Y~kyLl~fE~~~ 133 (187)
.+|++..||.....++...|..++++||..+-+..
T Consensus 13 aqil~~~Gf~~~~~sale~ltdi~~~yl~~l~~~~ 47 (77)
T smart00576 13 AQILESAGFDSFQESALETLTDILQSYIQELGRTA 47 (77)
T ss_pred HHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHH
Confidence 46788889998778889999999999999886643
No 29
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (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. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=31.79 E-value=42 Score=22.71 Aligned_cols=15 Identities=13% Similarity=0.510 Sum_probs=13.1
Q ss_pred cChHHHHHHhCCCCC
Q 029808 96 RRWKEVVVVFNFPTT 110 (187)
Q Consensus 96 k~W~eVa~~Lglp~~ 110 (187)
+.|.++|+.||++..
T Consensus 11 ~~W~~la~~Lgl~~~ 25 (79)
T cd01670 11 KDWKKLARKLGLSDG 25 (79)
T ss_pred hHHHHHHHHhCCCHH
Confidence 589999999998863
No 30
>cd07268 Glo_EDI_BRP_like_4 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.
Probab=31.44 E-value=13 Score=30.09 Aligned_cols=51 Identities=10% Similarity=0.036 Sum_probs=41.5
Q ss_pred chhhhhcHHHHHHHHHHHHHhcCCCCCCCeeCCeecchhhHHHHHHhhCCc
Q 029808 39 YEDIAQSSDLFWATLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGL 89 (187)
Q Consensus 39 ~~d~~~~~~~Fl~~L~~F~~~rG~pl~~P~I~gk~VDLy~Ly~~V~~~GG~ 89 (187)
+.++........+++++-+.+.|.-+..-.|+||+|-||+|..-+.-.|..
T Consensus 4 HialR~n~~~~A~~w~~~l~~~G~llSen~INGRPI~l~~L~qPl~~~~~~ 54 (149)
T cd07268 4 HIALRVNENQTAERWKEGLLQCGELLSENEINGRPIALIKLEKPLQFAGWS 54 (149)
T ss_pred eEEEeeCCHHHHHHHHHHHHHhchhhhccccCCeeEEEEEcCCCceeCCcE
Confidence 344555667778889999999999888899999999999999988765543
No 31
>cd08797 Death_NFkB1_p105 Death domain of the Nuclear Factor-KappaB1 precursor protein p105. Death Domain (DD) of the Nuclear Factor-KappaB1 (NF-kB1) precursor protein p105. The NF-kB family of transcription factors play a central role in cardiovascular growth, stress response, and inflammation by controlling the expression of a network of different genes. There are five NF-kB proteins, all containing an N-terminal REL Homology Domain (RHD). NF-kB1 (or p50) is produced from the processing of the precursor protein p105, which contains ANK repeats and a C-terminal DD in addition to the RHD. It is regulated by the classical (or canonical) NF-kB pathway. In the cytosol, p50 forms an inactive complex with RelA (or p65) and the Inhibitor of NF-kB (IkB). Activation is triggered by the phosphorylation and degradation of IkB, resulting in the active DNA-binding p50-RelA dimer to migrate to the nucleus. The classical pathway regulates the majority of genes activated by NF-kB including those encod
Probab=31.23 E-value=68 Score=23.10 Aligned_cols=15 Identities=13% Similarity=0.532 Sum_probs=12.5
Q ss_pred ccChHHHHHHhCCCC
Q 029808 95 DRRWKEVVVVFNFPT 109 (187)
Q Consensus 95 ~k~W~eVa~~Lglp~ 109 (187)
++.|..+|++||+..
T Consensus 15 ~g~Wr~LA~kL~l~~ 29 (76)
T cd08797 15 DKNWETLAQKLGLGI 29 (76)
T ss_pred CCCHHHHHHHHCchh
Confidence 345999999999875
No 32
>COG5227 SMT3 Ubiquitin-like protein (sentrin) [Posttranslational modification, protein turnover, chaperones]
Probab=30.91 E-value=60 Score=24.48 Aligned_cols=66 Identities=21% Similarity=0.238 Sum_probs=46.0
Q ss_pred cCCCCCCCCCCccccCCCCCCCCCCCCc-hh------hhhcHHHHHHHHHHHHHhcCCCCC-C-CeeCCeecchh
Q 029808 12 SATSNSNSNSNNNNSKASSYYPPPTAKY-ED------IAQSSDLFWATLEAFHKSFGDKFK-V-PTVGGKALDLH 77 (187)
Q Consensus 12 ~~~~~~~~~sgi~~i~pp~~w~PPf~~~-~d------~~~~~~~Fl~~L~~F~~~rG~pl~-~-P~I~gk~VDLy 77 (187)
+.+|+++..+.++-.+-|..-.-+..+- +| -+...-.|-+-+..|.+++|..+. . -.++|+.|||=
T Consensus 3 ~S~~~~e~kt~~~p~vkp~t~hinLkvv~qd~telfFkiKktT~f~klm~af~~rqGK~m~slRfL~dG~rI~~d 77 (103)
T COG5227 3 SSDSGSEFKTNENPLVKPITKHINLKVVDQDGTELFFKIKKTTTFKKLMDAFSRRQGKNMSSLRFLFDGKRIDLD 77 (103)
T ss_pred ccccchhhccccCccccccccccceEEecCCCCEEEEEEeccchHHHHHHHHHHHhCcCcceeEEEEcceecCCC
Confidence 4457777777777766666555554442 22 245667899999999999999874 3 45689999874
No 33
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=28.24 E-value=83 Score=21.72 Aligned_cols=51 Identities=25% Similarity=0.266 Sum_probs=27.9
Q ss_pred hHHHHHHhhCCc-cccccccChHHHHHHhCCCCCCCcHHHHHHHHHHHhHHHHHHH
Q 029808 78 RLFVEVTSRGGL-GKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLSLLYHFEQV 132 (187)
Q Consensus 78 ~Ly~~V~~~GG~-~~V~~~k~W~eVa~~Lglp~~~t~a~~~Lk~~Y~kyLl~fE~~ 132 (187)
.|+.-|.+.... ..++-++.|.++++.- +. .-.-+.+|..|.|.|.+.+..
T Consensus 12 ~l~~~v~~~~~~~~~~~Gn~iwk~le~~~--~t--~HtwQSwR~Ry~K~L~~~~~~ 63 (65)
T PF08914_consen 12 ALLDYVKENERQGGSVSGNKIWKELEEKH--PT--RHTWQSWRDRYLKHLRGRPRK 63 (65)
T ss_dssp HHHHHHHHT--STTTTTSSHHHHHHHHS---SS--S--SHHHHHHHHHHT------
T ss_pred HHHHHHHHhccCCCCCchHHHHHHHHHHc--CC--CCCHHHHHHHHHHHHhccccC
Confidence 455666433221 3577788999998874 21 123458999999999876654
No 34
>PTZ00100 DnaJ chaperone protein; Provisional
Probab=27.30 E-value=2.9e+02 Score=21.30 Aligned_cols=76 Identities=14% Similarity=0.081 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHHHhcCCCCCCCeeCC-eecchhhHHHHHHhhCCccccccccChHHHHHHhCCCCCCCcHHHHHHHHHHH
Q 029808 46 SDLFWATLEAFHKSFGDKFKVPTVGG-KALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNFPTTITSASFVLRKYYLS 124 (187)
Q Consensus 46 ~~~Fl~~L~~F~~~rG~pl~~P~I~g-k~VDLy~Ly~~V~~~GG~~~V~~~k~W~eVa~~Lglp~~~t~a~~~Lk~~Y~k 124 (187)
-..|+..+.++....+...-.|.-+- +.+.-+.|+. ..+|++..-.. .+-++.||++++.+ ...+|+.|.+
T Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~---~~~~f~~~Ms~---~eAy~ILGv~~~As--~~eIkkaYRr 88 (116)
T PTZ00100 17 VRYGYRYLKNQKIFGSNNMSFPLSGFNPSLGSLFLKN---DLKGFENPMSK---SEAYKILNISPTAS--KERIREAHKQ 88 (116)
T ss_pred HHHHHHHHHHHhhccCccccCCchhhhHHHHHHHhcc---ccccccCCCCH---HHHHHHcCCCCCCC--HHHHHHHHHH
Confidence 34566666666665554433332111 1122222222 67888875443 57789999998754 3589999998
Q ss_pred hHHHH
Q 029808 125 LLYHF 129 (187)
Q Consensus 125 yLl~f 129 (187)
....|
T Consensus 89 La~~~ 93 (116)
T PTZ00100 89 LMLRN 93 (116)
T ss_pred HHHHh
Confidence 87766
No 35
>KOG2744 consensus DNA-binding proteins Bright/BRCAA1/RBP1 and related proteins containing BRIGHT domain [Transcription]
Probab=26.51 E-value=4.8 Score=38.47 Aligned_cols=91 Identities=22% Similarity=0.265 Sum_probs=74.9
Q ss_pred hcHHHHHHHHHHHHHhcCCCCC-CCeeCCeecchhhHHHHHHhhCCccccccccChHHHHHHhCC-CCCCCcHHHHHHHH
Q 029808 44 QSSDLFWATLEAFHKSFGDKFK-VPTVGGKALDLHRLFVEVTSRGGLGKVIRDRRWKEVVVVFNF-PTTITSASFVLRKY 121 (187)
Q Consensus 44 ~~~~~Fl~~L~~F~~~rG~pl~-~P~I~gk~VDLy~Ly~~V~~~GG~~~V~~~k~W~eVa~~Lgl-p~~~t~a~~~Lk~~ 121 (187)
.....|+..|-.|++..+..++ .+........+++....+...||...+.....|..++..+++ +..+..+....+-.
T Consensus 308 ~~~g~f~~~~~~~~~~~s~~ln~~~~~~~~~~~~~k~~~~~~~~~~~~~~p~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 387 (512)
T KOG2744|consen 308 EILGNFLQGLLVFMKDGSEPLNGVLYLGPPDLNLFKVFRLECHQGGDSNIPSALQWKQVAKDLGLLPNLNSAASSNTKLA 387 (512)
T ss_pred hhhccccccCceeccCcchhccCccccccCcccccccccceeeccCcCcCCchhheeccccccccccccccccccccccc
Confidence 4578899999999999998884 677788899999999999999999999999999999999984 44344455577888
Q ss_pred HHHhHHHHHHHHH
Q 029808 122 YLSLLYHFEQVYY 134 (187)
Q Consensus 122 Y~kyLl~fE~~~~ 134 (187)
|.++|..+|....
T Consensus 388 ~k~~l~~~~~~~~ 400 (512)
T KOG2744|consen 388 YKKSLSENEEYCS 400 (512)
T ss_pred cchhhccccccch
Confidence 8888887777643
No 36
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=26.02 E-value=1.3e+02 Score=19.39 Aligned_cols=31 Identities=16% Similarity=0.232 Sum_probs=22.4
Q ss_pred hHHHHHHhCCCCCCCcHHHHHHHHHHHhHHHHH
Q 029808 98 WKEVVVVFNFPTTITSASFVLRKYYLSLLYHFE 130 (187)
Q Consensus 98 W~eVa~~Lglp~~~t~a~~~Lk~~Y~kyLl~fE 130 (187)
-.+-..++|++.+... ...|++|+|-|..+.
T Consensus 11 L~~~L~~~G~~~gPIt--~sTR~vy~kkL~~~~ 41 (44)
T smart00540 11 LRAELKQYGLPPGPIT--DTTRKLYEKKLRKLR 41 (44)
T ss_pred HHHHHHHcCCCCCCcC--cchHHHHHHHHHHHH
Confidence 3455678899876322 278999999998764
No 37
>cd08798 Death_NFkB2_p100 Death domain of the Nuclear Factor-KappaB2 precursor protein p100. Death Domain (DD) of the Nuclear Factor-KappaB2 (NF-kB2) precursor protein p100. The NF-kB family of transcription factors play a central role in cardiovascular growth, stress response, and inflammation by controlling the expression of a network of different genes. There are five NF-kB proteins, all containing an N-terminal REL Homology Domain (RHD). NF-kB2 (or p52) is produced from the processing of the precursor protein p100, which contains ANK repeats and a C-terminal DD in addition to the RHD. It is regulated by the non-canonical NF-kB pathway. The p100 precursor is cytosolic and interacts with RelB. Upon phosphorylation by IKKalpha, p100 is processed to its 52kDa active, DNA binding form and the p52/RelB complex is translocated into the nucleus. The non-canonical pathway plays a role in adaptive immunity and lymphorganogenesis. In general, DDs are protein-protein interaction domains found i
Probab=25.69 E-value=93 Score=22.42 Aligned_cols=15 Identities=20% Similarity=0.488 Sum_probs=13.1
Q ss_pred ccChHHHHHHhCCCC
Q 029808 95 DRRWKEVVVVFNFPT 109 (187)
Q Consensus 95 ~k~W~eVa~~Lglp~ 109 (187)
.+.|..+|++||+..
T Consensus 15 g~dW~~LA~kL~l~~ 29 (76)
T cd08798 15 DVPWMELAERLGLQS 29 (76)
T ss_pred CCCHHHHHHHHCcch
Confidence 568999999999874
No 38
>cd08310 Death_NFkB-like Death domain of Nuclear Factor-KappaB precursor proteins. Death Domain (DD) of Nuclear Factor-KappaB (NF-kB) precursor proteins. The NF-kB family of transcription factors play a central role in cardiovascular growth, stress response, and inflammation by controlling the expression of a network of different genes. There are five NF-kB proteins, all containing an N-terminal REL Homology Domain (RHD). Two of these, NF-kB1 and NF-kB2 are produced from the processing of the precursor proteins p105 and p100, respectively. In addition to RHD, p105 and p100 contain ANK repeats and a C-terminal DD. NF-kBs are regulated by the Inhibitor of NF-kB (IkB) Kinase (IKK) complex through classical and non-canonical pathways, which differ in the IKK subunits involved and downstream targets. IKKs facilitate the release of NF-kB dimers from an inactive state, allowing them to migrate to the nucleus where they regulate gene transcription. The precursor proteins p105 and p100 function
Probab=23.74 E-value=1.1e+02 Score=21.40 Aligned_cols=15 Identities=13% Similarity=0.547 Sum_probs=13.0
Q ss_pred ccChHHHHHHhCCCC
Q 029808 95 DRRWKEVVVVFNFPT 109 (187)
Q Consensus 95 ~k~W~eVa~~Lglp~ 109 (187)
.+.|..+|++||+..
T Consensus 12 ~~dWr~LA~~L~~~~ 26 (72)
T cd08310 12 GCDWRELAQLLDLGH 26 (72)
T ss_pred CCCHHHHHHHcCcHH
Confidence 568999999999874
No 39
>PRK02922 glycogen synthesis protein GlgS; Provisional
Probab=23.71 E-value=40 Score=23.77 Aligned_cols=26 Identities=19% Similarity=0.048 Sum_probs=20.6
Q ss_pred cHHHHHHHHHHHHHhcCCCCCCCeeC
Q 029808 45 SSDLFWATLEAFHKSFGDKFKVPTVG 70 (187)
Q Consensus 45 ~~~~Fl~~L~~F~~~rG~pl~~P~I~ 70 (187)
..-.|+.+-..||+.+|.++.+..|.
T Consensus 10 ~~~DFlAsS~A~Me~Qgr~Idvd~V~ 35 (67)
T PRK02922 10 NNFDFLARSFARMHAEGRPVDIQAVT 35 (67)
T ss_pred cchhHHHHHHHHHHHcCCCccHHHHH
Confidence 35679999999999999987655443
No 40
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=23.43 E-value=45 Score=24.10 Aligned_cols=15 Identities=20% Similarity=0.678 Sum_probs=13.2
Q ss_pred cChHHHHHHhCCCCC
Q 029808 96 RRWKEVVVVFNFPTT 110 (187)
Q Consensus 96 k~W~eVa~~Lglp~~ 110 (187)
+.|.++|++|||...
T Consensus 14 ~~Wk~lar~LG~s~~ 28 (86)
T cd08777 14 KKWKRCARKLGFTES 28 (86)
T ss_pred HHHHHHHHHcCCCHH
Confidence 479999999999864
No 41
>cd01479 Sec24-like Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes of vesicular carriers within the endocytic and the biosynthetic pathways are COP- and clathrin-coated vesicles. Formation of COPII vesicles requires the ordered assembly of the coat built from several cytosolic components GTPase Sar1, complexes of Sec23-Sec24 and Sec13-Sec31. The process is initiated by the conversion of GDP to GTP by the GTPase Sar1 which then recruits the heterodimeric complex of Sec23 and Sec24. This heterodimeric complex generates the pre-budding complex. The final step leading to membrane deformation and budding of COPII-coated vesicles is carried by the heterodimeric complex Sec13-Sec31. The members of this CD belong to the Sec23-like family. Sec 24 is very similar to Sec23. The Sec23 and Sec24
Probab=23.43 E-value=1.2e+02 Score=25.61 Aligned_cols=77 Identities=12% Similarity=-0.020 Sum_probs=52.1
Q ss_pred CCCCCCccccCCCCCCCCCCCCchh--hhhcHHHHHHHHHHHHHhcCCCCCCCeeCCeecchhhHHHHHHhhCCcccccc
Q 029808 17 SNSNSNNNNSKASSYYPPPTAKYED--IAQSSDLFWATLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGGLGKVIR 94 (187)
Q Consensus 17 ~~~~sgi~~i~pp~~w~PPf~~~~d--~~~~~~~Fl~~L~~F~~~rG~pl~~P~I~gk~VDLy~Ly~~V~~~GG~~~V~~ 94 (187)
.+++.|+.+++.-+.-+. ...+.+ .......|+++|..-+.+.|..+.+-......+||..|-..+..-||.-....
T Consensus 141 ~~pt~GpG~l~~~~~~~~-~~~~~e~~~~~p~~~fY~~la~~~~~~~isvDlF~~~~~~~dla~l~~l~~~TGG~v~~y~ 219 (244)
T cd01479 141 SLPTLGAGKLKSREDPKL-LSTDKEKQLLQPQTDFYKKLALECVKSQISVDLFLFSNQYVDVATLGCLSRLTGGQVYYYP 219 (244)
T ss_pred CCCCcCCcccccCccccc-cCchhhhhhcCcchHHHHHHHHHHHHcCeEEEEEEccCcccChhhhhhhhhhcCceEEEEC
Confidence 344567766665432111 011111 22334689999999999999888776777788999999999999999655543
No 42
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=23.25 E-value=97 Score=19.29 Aligned_cols=28 Identities=11% Similarity=0.163 Sum_probs=19.4
Q ss_pred cccChHHHHHHhCCCCCCCcHHHHHHHHHHHhHH
Q 029808 94 RDRRWKEVVVVFNFPTTITSASFVLRKYYLSLLY 127 (187)
Q Consensus 94 ~~k~W~eVa~~Lglp~~~t~a~~~Lk~~Y~kyLl 127 (187)
.+..+.+||+.||++.. .++++..+-|.
T Consensus 19 ~~~t~~eIa~~lg~s~~------~V~~~~~~al~ 46 (50)
T PF04545_consen 19 EGLTLEEIAERLGISRS------TVRRILKRALK 46 (50)
T ss_dssp ST-SHHHHHHHHTSCHH------HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCcHH------HHHHHHHHHHH
Confidence 34579999999999863 56666555543
No 43
>COG5182 CUS1 Splicing factor 3b, subunit 2 [RNA processing and modification]
Probab=22.80 E-value=2.3e+02 Score=26.26 Aligned_cols=39 Identities=21% Similarity=0.359 Sum_probs=29.8
Q ss_pred HHHHHHHHHhc--CCCCC-------CCeeCCeecchhhHHHHHHhhCC
Q 029808 50 WATLEAFHKSF--GDKFK-------VPTVGGKALDLHRLFVEVTSRGG 88 (187)
Q Consensus 50 l~~L~~F~~~r--G~pl~-------~P~I~gk~VDLy~Ly~~V~~~GG 88 (187)
+.+++..|.++ |.+|+ .|.+++-.||.-+||.+-.+.|-
T Consensus 207 I~qmR~~~~e~ea~msLre~~RervqPkmG~ldvDy~kLhdaFF~~g~ 254 (429)
T COG5182 207 IPQMRRMMREREAGMSLRERIRERVQPKMGGLDVDYRKLHDAFFSLGP 254 (429)
T ss_pred hHHHHHhhhhccccCcHHHHHHHhhCccccccchhHHHHHHHHHhcCC
Confidence 44566666555 45552 69999999999999999999884
No 44
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. 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),
Probab=21.81 E-value=63 Score=23.18 Aligned_cols=15 Identities=20% Similarity=0.621 Sum_probs=13.1
Q ss_pred cChHHHHHHhCCCCC
Q 029808 96 RRWKEVVVVFNFPTT 110 (187)
Q Consensus 96 k~W~eVa~~Lglp~~ 110 (187)
..|.++|+.||++.+
T Consensus 14 ~~Wk~laR~LGlse~ 28 (86)
T cd08306 14 RDWRKLARKLGLSET 28 (86)
T ss_pred hhHHHHHHHcCCCHH
Confidence 479999999999864
No 45
>cd08802 Death_UNC5B Death domain found in Uncoordinated-5B. Death Domain (DD) found in Uncoordinated-5B (UNC5B). UNC5B is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5B signaling is involved in the netrin-1-induced proliferation and migration of renal proximal tubular cells. It is also required for vascular patterning during embryonic development, and its activation inhibits sprouting angiogenesis. 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 activatio
Probab=21.66 E-value=1.1e+02 Score=22.30 Aligned_cols=14 Identities=7% Similarity=0.399 Sum_probs=12.4
Q ss_pred ccChHHHHHHhCCC
Q 029808 95 DRRWKEVVVVFNFP 108 (187)
Q Consensus 95 ~k~W~eVa~~Lglp 108 (187)
.+.|..+|++||+.
T Consensus 20 g~DW~~LAekL~ld 33 (84)
T cd08802 20 GNDWRLLAQKLSMD 33 (84)
T ss_pred CCcHHHHHHHcCch
Confidence 45799999999998
No 46
>cd08311 Death_p75NR Death domain of p75 Neurotophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. 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 adaptor
Probab=21.50 E-value=65 Score=22.91 Aligned_cols=16 Identities=13% Similarity=0.526 Sum_probs=13.7
Q ss_pred ccChHHHHHHhCCCCC
Q 029808 95 DRRWKEVVVVFNFPTT 110 (187)
Q Consensus 95 ~k~W~eVa~~Lglp~~ 110 (187)
.+.|..+|++|||+..
T Consensus 15 G~dW~~LA~~LG~~~~ 30 (77)
T cd08311 15 GRDWRSLAGELGYEDE 30 (77)
T ss_pred ccCHHHHHHHcCCCHH
Confidence 4579999999999863
No 47
>cd08799 Death_UNC5C Death domain found in Uncoordinated-5C. Death Domain (DD) found in Uncoordinated-5C (UNC5C). UNC5C is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5C plays a critical role in the development of spinal accesory motor neurons. Methylation of the UNC5C gene is associated with early stages of colorectal carcinogenesis. 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.
Probab=21.37 E-value=1.2e+02 Score=22.10 Aligned_cols=15 Identities=13% Similarity=0.448 Sum_probs=12.8
Q ss_pred ccChHHHHHHhCCCC
Q 029808 95 DRRWKEVVVVFNFPT 109 (187)
Q Consensus 95 ~k~W~eVa~~Lglp~ 109 (187)
.+.|..+|++||+..
T Consensus 20 g~DWr~LAekLgl~~ 34 (84)
T cd08799 20 GNDWRMLAHKLNLDR 34 (84)
T ss_pred CCCHHHHHHHcCCHH
Confidence 457999999999984
No 48
>PRK11700 hypothetical protein; Provisional
Probab=20.83 E-value=27 Score=29.28 Aligned_cols=40 Identities=10% Similarity=0.005 Sum_probs=26.7
Q ss_pred HHHHHHHHHHhcCCCCCCCeeCCeecchhhHHHHHHhhCC
Q 029808 49 FWATLEAFHKSFGDKFKVPTVGGKALDLHRLFVEVTSRGG 88 (187)
Q Consensus 49 Fl~~L~~F~~~rG~pl~~P~I~gk~VDLy~Ly~~V~~~GG 88 (187)
-.++++.-+.+.|+-+..-.|+||+|-||+|..-+.-.|.
T Consensus 52 tAe~w~~~l~~~G~llSen~INGRPI~l~~L~qPl~~~~w 91 (187)
T PRK11700 52 TAERWRQGFLQCGELLSENIINGRPICLFELDQPLQVGHW 91 (187)
T ss_pred HHHHHHHHHHHhchhhhccccCCeeEEEEEcCCCceeCCc
Confidence 3344444444444444455799999999999998875554
Done!