Query 000848
Match_columns 1255
No_of_seqs 29 out of 31
Neff 1.7
Searched_HMMs 46136
Date Tue Apr 2 00:28:10 2013
Command hhsearch -i /work/01045/syshi/lefta3m/000848.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/leftcdd/000848hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11635 Med16: Mediator compl 94.9 0.16 3.5E-06 60.2 11.1 159 471-677 214-392 (753)
2 PF12657 TFIIIC_delta: Transcr 94.0 0.16 3.5E-06 49.7 7.1 77 157-250 87-167 (173)
3 PF11635 Med16: Mediator compl 88.3 0.24 5.3E-06 58.8 1.9 57 1188-1252 693-752 (753)
4 smart00320 WD40 WD40 repeats. 63.2 15 0.00033 23.0 3.8 29 155-185 12-40 (40)
5 PF00400 WD40: WD domain, G-be 56.0 27 0.00057 25.5 4.5 31 153-185 9-39 (39)
6 PF08662 eIF2A: Eukaryotic tra 50.9 34 0.00073 34.4 5.7 79 101-186 11-90 (194)
7 TIGR02605 CxxC_CxxC_SSSS putat 48.6 14 0.0003 30.2 2.1 34 1206-1254 6-40 (52)
8 PF10263 SprT-like: SprT-like 43.6 13 0.00027 35.4 1.4 37 1202-1254 120-156 (157)
9 PF07295 DUF1451: Protein of u 35.8 22 0.00047 36.0 1.7 28 1206-1251 113-140 (146)
10 PF09723 Zn-ribbon_8: Zinc rib 34.7 32 0.0007 28.0 2.2 34 1206-1254 6-40 (42)
11 smart00834 CxxC_CXXC_SSSS Puta 34.0 33 0.00071 26.5 2.1 35 1206-1255 6-40 (41)
12 PF13453 zf-TFIIB: Transcripti 32.4 17 0.00037 29.1 0.3 12 1241-1252 19-30 (41)
13 cd00200 WD40 WD40 domain, foun 27.9 1.5E+02 0.0033 26.8 5.6 29 155-185 261-289 (289)
14 PRK00398 rpoP DNA-directed RNA 27.2 28 0.0006 28.4 0.7 30 1205-1252 3-32 (46)
15 cd00200 WD40 WD40 domain, foun 26.8 1.8E+02 0.0039 26.4 5.8 50 133-188 159-208 (289)
16 TIGR00373 conserved hypothetic 25.8 25 0.00053 35.3 0.2 34 1201-1251 105-138 (158)
17 PRK06266 transcription initiat 25.4 28 0.00061 35.7 0.5 34 1202-1252 114-147 (178)
18 PF13454 NAD_binding_9: FAD-NA 25.0 21 0.00046 34.3 -0.4 44 296-348 2-45 (156)
19 COG2072 TrkA Predicted flavopr 24.6 1.3E+02 0.0028 34.3 5.4 70 296-379 13-93 (443)
20 KOG2858 Uncharacterized conser 24.3 26 0.00055 40.4 0.0 15 1205-1219 29-43 (390)
21 cd00491 4Oxalocrotonate_Tautom 24.2 1E+02 0.0023 24.8 3.5 56 717-773 3-58 (58)
22 PF10272 Tmpp129: Putative tra 20.9 44 0.00096 38.1 1.0 34 1208-1250 316-349 (358)
No 1
>PF11635 Med16: Mediator complex subunit 16; InterPro: IPR021665 Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Med16 is one of the subunits of the Tail portion of the Mediator complex and is required for lipopolysaccharide gene-expression []. Several members including the human protein, Q9Y2X0 from SWISSPROT, have one or more WD40 domains on them, PF00400 from PFAM.
Probab=94.94 E-value=0.16 Score=60.23 Aligned_cols=159 Identities=17% Similarity=0.167 Sum_probs=100.2
Q ss_pred eEEeeccCCCceeeeeccCCCCC--CCCCCCCceeEEEeeeecccCCCCccccccccCCCcccccccccccccccceecc
Q 000848 471 RVQRWESSVQPVVLHQIFGNPTS--SFGGQAPMQTVWVSKVDTSIPTSNFKIHQLAAAGPTCDVWKTTDSGLEKSKIVSF 548 (1255)
Q Consensus 471 RvqrWESs~qpvvlhpifgnpts--~~gGqpp~qtvW~skvd~sIp~tdfkn~q~~~~~~~~d~~k~s~~~~dksk~v~f 548 (1255)
-|.|||=.-++..|||+|..-.+ +.++++++.+.|+..-|+.++.. -+.+
T Consensus 214 iI~RweL~~~~~~lh~~F~ql~s~~~~~~~~~~~~~l~~~~~i~~~~~----------------------------V~si 265 (753)
T PF11635_consen 214 IIERWELREEQQPLHPAFQQLGSKKNSSSEPPPTYRLRRLDDITLNKR----------------------------VVSI 265 (753)
T ss_pred EEEEEEEEccCcccchhhhhcCCCCcCCCCCCCceeEEEecccccCCe----------------------------EEEE
Confidence 38999988888999999988763 45578999999998887765432 1112
Q ss_pred CCCCCccchhhhheeeeccCCceEEeeeeeCceeeeeCCCcCcccee-----ee-------eccccccc------CccCc
Q 000848 549 DPFDLPSDIRSLARIVYSAHGGEIAIALLRGGVHIFSGPNFAPVDNY-----QI-------SVGSAIAA------PAFSS 610 (1255)
Q Consensus 549 dpfdlP~d~rtLAriVySAhgGEiavAfl~GgVhiFSGpnf~pVdny-----qI-------nVgsaIa~------PaFSs 610 (1255)
+ +.--|+=++++|--|-||++.=-+|+++... .. .+|=..+. -|||+
T Consensus 266 ~---------------~~~~~~~v~~~~~DGsI~~~dr~t~~~~~~~~~~~~~~~~v~s~~~~Gf~fp~~~~~~~vafSP 330 (753)
T PF11635_consen 266 T---------------SPELDIVVAFAFSDGSIEFRDRNTMKELNETRTNGEPPNTVTSLFQAGFHFPCIQPPLHVAFSP 330 (753)
T ss_pred E---------------ecccCcEEEEEEcCCeEEEEecCcchhhcccccccCCccccccccccccccccCCCCceEEECc
Confidence 2 2223447899999999999999999776554 11 13434432 26999
Q ss_pred cccccceeeeccCCCceEEEEEeecCCCccccccccchhhHHHHHHHHHhhhhhcccccchhhcccc
Q 000848 611 TSCCSASVWHDTNKDRTILKIIRVLPPAVPSSQVKANSSTWERAIAERFWWSLLVNVDWWDAVGCTQ 677 (1255)
Q Consensus 611 TsCCsASVWHDt~kd~~iLkIirVLPPa~p~~q~ka~ss~weraiaerfwwSLlvgvdWWDaVgctQ 677 (1255)
|+|..+-. |...+.. |...++....-..|.-..+++ -.|++=-+=.-...+.|||+++-+++
T Consensus 331 t~c~~v~~--~~~~~~~--~~~~~~~~~~~~~~~~~~~a~-~~al~~~~a~~~~~~~DDl~~l~~~~ 392 (753)
T PF11635_consen 331 TMCSLVQI--DEDGKTK--KLLYMMRDSGSSPQDLYITAA-ALALRFSLACCSQTSSDDLLILIKTE 392 (753)
T ss_pred ccceEEEE--ecCCCce--eeEEeecCCCCCccccchhHH-HHHHHHHHHHHHhcCcchHHHhhhhh
Confidence 99987665 2222211 555555544443333332211 12222222333567999999998776
No 2
>PF12657 TFIIIC_delta: Transcription factor IIIC subunit delta N-term; InterPro: IPR024761 This entry represents a domain found towards the N terminus of the 90 kDa subunit of transcription factor IIIC (also known as subunit 9 in yeast []). The whole subunit is involved in RNA polymerase III-mediated transcription. It is possible that this N-terminal domain interacts with TFIIIC subunit 8 [].
Probab=94.05 E-value=0.16 Score=49.65 Aligned_cols=77 Identities=25% Similarity=0.372 Sum_probs=48.7
Q ss_pred ceEEEEecCCCCc----ceEEEEeccceEEEEecCCCCCCcccccccccchhhhccccceeeeecccCCCCccccccCCC
Q 000848 157 SVQFIEWSPTSCP----RALLIANFYGRVTIWTQPSHGPANLVRDASCWQREHEWRQDIAVVTKWLSGVSPYRWLSSKST 232 (1255)
Q Consensus 157 ~vq~ieWSp~~cp----RALLiAnf~GRvtIWtQPsqg~~nlv~da~~w~~eheWrqd~avvtkwlsg~spyrwlssk~s 232 (1255)
.|-.++|||.+|- =.|.+.+-.|||+||..+..- ..||. .+++|+|-|.. |--....+.
T Consensus 87 ~vv~~aWSP~Gl~~~~rClLavLTs~~~l~l~~~~~~~-------------~~~W~-~v~dvs~~l~~---~~~~~~~~~ 149 (173)
T PF12657_consen 87 QVVSAAWSPSGLGPNGRCLLAVLTSNGRLSLYGPPGNP-------------QGEWN-RVADVSEALYS---YFYNWEPSE 149 (173)
T ss_pred cEEEEEECCCCCCCCCceEEEEEcCCCeEEEEecCCCc-------------cccEe-eeeehhHHHHH---hhhccCCCc
Confidence 6889999998882 257788999999999887641 34666 45677776661 111112222
Q ss_pred CCCCcchhhHHhhhccCc
Q 000848 233 SPLNAKSIFEEKFLSQNS 250 (1255)
Q Consensus 233 ~~~n~kstFeEKflsqq~ 250 (1255)
........|.+.|..++.
T Consensus 150 ~~~~~~~~~~~~~~~~~i 167 (173)
T PF12657_consen 150 SSPLDFEEFQRRFRKQRI 167 (173)
T ss_pred ccccccchhhhhhhccce
Confidence 333334456677777664
No 3
>PF11635 Med16: Mediator complex subunit 16; InterPro: IPR021665 Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Med16 is one of the subunits of the Tail portion of the Mediator complex and is required for lipopolysaccharide gene-expression []. Several members including the human protein, Q9Y2X0 from SWISSPROT, have one or more WD40 domains on them, PF00400 from PFAM.
Probab=88.29 E-value=0.24 Score=58.78 Aligned_cols=57 Identities=30% Similarity=0.715 Sum_probs=38.9
Q ss_pred ccceeEEeeecCCCc---ceeehhhhcccccccccCCCCCCCCCCcchhhhhhhhcccCCCCCCCceE
Q 000848 1188 SRRDVVTAVWKTGLE---GVWYKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGGTWV 1252 (1255)
Q Consensus 1188 SRRDVvTa~WKtgle---GvWyKCiRC~RQTsAfasp~a~n~p~qn~re~wWisRW~~~CPMCGGtWv 1252 (1255)
..=|+++-++=.+-+ +.|-+|.||+.-|.+.-.. .+..- -=|.-+|.-.| .|||-|+
T Consensus 693 ~~vD~~rk~~l~~~~~~~~~~RrC~RC~~vs~~~~~~----~s~~~---~~w~~~~~R~C-~CGG~W~ 752 (753)
T PF11635_consen 693 RYVDVLRKVHLGRSPTSTGKWRRCVRCGSVSEDEDPF----TSRAT---KRWTMRWQRNC-ICGGMWV 752 (753)
T ss_pred cccceeeeeeeeecccCCCceEEeccCCCcccccCCC----Ccchh---hhhhhheeeee-ccCCeeC
Confidence 456777777765554 9999999999554443222 11111 12999999888 6999996
No 4
>smart00320 WD40 WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.
Probab=63.19 E-value=15 Score=23.01 Aligned_cols=29 Identities=24% Similarity=0.483 Sum_probs=24.8
Q ss_pred CCceEEEEecCCCCcceEEEEeccceEEEEe
Q 000848 155 RDSVQFIEWSPTSCPRALLIANFYGRVTIWT 185 (1255)
Q Consensus 155 ~d~vq~ieWSp~~cpRALLiAnf~GRvtIWt 185 (1255)
.+.|.++.|.+.. +-++.+..+|.|.+|.
T Consensus 12 ~~~i~~~~~~~~~--~~~~~~~~d~~~~~~~ 40 (40)
T smart00320 12 TGPVTSVAFSPDG--KYLASASDDGTIKLWD 40 (40)
T ss_pred CCceeEEEECCCC--CEEEEecCCCeEEEcC
Confidence 4579999999987 7788889999999984
No 5
>PF00400 WD40: WD domain, G-beta repeat; InterPro: IPR019781 WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide. WD40 repeats usually assume a 7-8 bladed beta-propeller fold, but proteins have been found with 4 to 16 repeated units, which also form a circularised beta-propeller structure. WD-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control and apoptosis. Repeated WD40 motifs act as a site for protein-protein interaction, and proteins containing WD40 repeats are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins. The specificity of the proteins is determined by the sequences outside the repeats themselves. Examples of such complexes are G proteins (beta subunit is a beta-propeller), TAFII transcription factor, and E3 ubiquitin ligase [, ]. In Arabidopsis spp., several WD40-containing proteins act as key regulators of plant-specific developmental events.; PDB: 2ZKQ_a 3CFV_B 3CFS_B 1PEV_A 1NR0_A 1VYH_T 3RFH_A 3O2Z_T 3FRX_C 3U5G_g ....
Probab=56.03 E-value=27 Score=25.53 Aligned_cols=31 Identities=26% Similarity=0.519 Sum_probs=27.4
Q ss_pred CCCCceEEEEecCCCCcceEEEEeccceEEEEe
Q 000848 153 CPRDSVQFIEWSPTSCPRALLIANFYGRVTIWT 185 (1255)
Q Consensus 153 sp~d~vq~ieWSp~~cpRALLiAnf~GRvtIWt 185 (1255)
.-.+.|..|.|+|. .+-|+.+-.+|.|.||.
T Consensus 9 ~h~~~i~~i~~~~~--~~~~~s~~~D~~i~vwd 39 (39)
T PF00400_consen 9 GHSSSINSIAWSPD--GNFLASGSSDGTIRVWD 39 (39)
T ss_dssp SSSSSEEEEEEETT--SSEEEEEETTSEEEEEE
T ss_pred CCCCcEEEEEEecc--cccceeeCCCCEEEEEC
Confidence 45678999999999 78899999999999994
No 6
>PF08662 eIF2A: Eukaryotic translation initiation factor eIF2A; InterPro: IPR013979 This entry contains beta propellor domains found in eukaryotic translation initiation factors and TolB domain-containing proteins.
Probab=50.91 E-value=34 Score=34.37 Aligned_cols=79 Identities=15% Similarity=0.279 Sum_probs=51.9
Q ss_pred hhhhccccceeeccccccccCCCCCCCCceeeEEEe-cCCCCcceeEEEeecCCCCCceEEEEecCCCCcceEEEEeccc
Q 000848 101 VAWCGKLNAIACASETCARIPSSNANTPFWIPIHIV-IPERPTECAVFNVIADCPRDSVQFIEWSPTSCPRALLIANFYG 179 (1255)
Q Consensus 101 vawc~klN~iaca~etCarip~S~~np~fwiPihIv-iPerPtE~avfnv~adsp~d~vq~ieWSp~~cpRALLiAnf~G 179 (1255)
+.|..+-+.+++.+.| |..++....--=.=|+++ +.+.| +..+++..++| |..++|||.+=.-|++..+..+
T Consensus 11 ~~W~~~G~~l~~~~~~--~~~~~~ks~~~~~~l~~~~~~~~~--~~~i~l~~~~~---I~~~~WsP~g~~favi~g~~~~ 83 (194)
T PF08662_consen 11 LHWQPSGDYLLVKVQT--RVDKSGKSYYGEFELFYLNEKNIP--VESIELKKEGP---IHDVAWSPNGNEFAVIYGSMPA 83 (194)
T ss_pred EEecccCCEEEEEEEE--eeccCcceEEeeEEEEEEecCCCc--cceeeccCCCc---eEEEEECcCCCEEEEEEccCCc
Confidence 4688899999998874 333343311111234444 44444 45556655544 9999999999777777667778
Q ss_pred eEEEEec
Q 000848 180 RVTIWTQ 186 (1255)
Q Consensus 180 RvtIWtQ 186 (1255)
+|+||.-
T Consensus 84 ~v~lyd~ 90 (194)
T PF08662_consen 84 KVTLYDV 90 (194)
T ss_pred ccEEEcC
Confidence 9999975
No 7
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=48.61 E-value=14 Score=30.23 Aligned_cols=34 Identities=29% Similarity=0.776 Sum_probs=22.2
Q ss_pred ehhhhcccccccccCCCCCCCCCCcchhhhhhhhcccCCCCCCCceE-Ee
Q 000848 1206 YKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGGTWV-RV 1254 (1255)
Q Consensus 1206 yKCiRC~RQTsAfasp~a~n~p~qn~re~wWisRW~~~CPMCGGtWv-rv 1254 (1255)
|||..|+..-..+.+-+. .. ...||.||+.-+ |+
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~--------------~~~CP~Cg~~~~~r~ 40 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSD-DP--------------LATCPECGGEKLRRL 40 (52)
T ss_pred EEeCCCCCEeEEEEecCC-CC--------------CCCCCCCCCCceeEE
Confidence 899999987666643222 11 236999999544 65
No 8
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=43.63 E-value=13 Score=35.43 Aligned_cols=37 Identities=30% Similarity=0.687 Sum_probs=23.8
Q ss_pred cceeehhhhcccccccccCCCCCCCCCCcchhhhhhhhcccCCCCCCCceEEe
Q 000848 1202 EGVWYKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGGTWVRV 1254 (1255)
Q Consensus 1202 eGvWyKCiRC~RQTsAfasp~a~n~p~qn~re~wWisRW~~~CPMCGGtWvrv 1254 (1255)
.-.+|+|-.|++--....- . .+. .|-|+.|||..++|
T Consensus 120 ~~~~~~C~~C~~~~~r~~~-----~----~~~-------~~~C~~C~~~l~~~ 156 (157)
T PF10263_consen 120 KKYVYRCPSCGREYKRHRR-----S----KRK-------RYRCGRCGGPLVQV 156 (157)
T ss_pred cceEEEcCCCCCEeeeecc-----c----chh-------hEECCCCCCEEEEc
Confidence 4578999999854211111 0 000 18999999999986
No 9
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=35.75 E-value=22 Score=36.00 Aligned_cols=28 Identities=32% Similarity=0.735 Sum_probs=20.7
Q ss_pred ehhhhcccccccccCCCCCCCCCCcchhhhhhhhcccCCCCCCCce
Q 000848 1206 YKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGGTW 1251 (1255)
Q Consensus 1206 yKCiRC~RQTsAfasp~a~n~p~qn~re~wWisRW~~~CPMCGGtW 1251 (1255)
|.|..|+.++. |..|+. .| -||-||++=
T Consensus 113 l~C~~Cg~~~~-~~~~~~--l~---------------~Cp~C~~~~ 140 (146)
T PF07295_consen 113 LVCENCGHEVE-LTHPER--LP---------------PCPKCGHTE 140 (146)
T ss_pred EecccCCCEEE-ecCCCc--CC---------------CCCCCCCCe
Confidence 78999999885 455542 22 399999974
No 10
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=34.73 E-value=32 Score=28.03 Aligned_cols=34 Identities=29% Similarity=0.668 Sum_probs=24.8
Q ss_pred ehhhhcccccccccCCCCCCCCCCcchhhhhhhhcccCCCCCCC-ceEEe
Q 000848 1206 YKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGG-TWVRV 1254 (1255)
Q Consensus 1206 yKCiRC~RQTsAfasp~a~n~p~qn~re~wWisRW~~~CPMCGG-tWvrv 1254 (1255)
|+|..|+.+-..+.+-+. .. ..-||-||+ .=.||
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~--------------~~~CP~Cg~~~~~r~ 40 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISE-DD--------------PVPCPECGSTEVRRV 40 (42)
T ss_pred EEeCCCCCEEEEEEEcCC-CC--------------CCcCCCCCCCceEEe
Confidence 899999988888876444 22 246999999 55555
No 11
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=34.02 E-value=33 Score=26.47 Aligned_cols=35 Identities=29% Similarity=0.724 Sum_probs=22.4
Q ss_pred ehhhhcccccccccCCCCCCCCCCcchhhhhhhhcccCCCCCCCceEEeC
Q 000848 1206 YKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGGTWVRVV 1255 (1255)
Q Consensus 1206 yKCiRC~RQTsAfasp~a~n~p~qn~re~wWisRW~~~CPMCGGtWvrvV 1255 (1255)
|+|..|+..-..+.+-.. .. ...||.||+.=-||+
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~--------------~~~CP~Cg~~~~r~~ 40 (41)
T smart00834 6 YRCEDCGHTFEVLQKISD-DP--------------LATCPECGGDVRRLI 40 (41)
T ss_pred EEcCCCCCEEEEEEecCC-CC--------------CCCCCCCCCcceecc
Confidence 789999886555544221 11 236999999766654
No 12
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=32.40 E-value=17 Score=29.15 Aligned_cols=12 Identities=50% Similarity=1.318 Sum_probs=10.4
Q ss_pred ccCCCCCCCceE
Q 000848 1241 AFGCPMCGGTWV 1252 (1255)
Q Consensus 1241 ~~~CPMCGGtWv 1252 (1255)
.+.||-|||.|.
T Consensus 19 id~C~~C~G~W~ 30 (41)
T PF13453_consen 19 IDVCPSCGGIWF 30 (41)
T ss_pred EEECCCCCeEEc
Confidence 467999999996
No 13
>cd00200 WD40 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and botto
Probab=27.90 E-value=1.5e+02 Score=26.82 Aligned_cols=29 Identities=31% Similarity=0.654 Sum_probs=24.5
Q ss_pred CCceEEEEecCCCCcceEEEEeccceEEEEe
Q 000848 155 RDSVQFIEWSPTSCPRALLIANFYGRVTIWT 185 (1255)
Q Consensus 155 ~d~vq~ieWSp~~cpRALLiAnf~GRvtIWt 185 (1255)
.+.|..+.|+|. .+.|+.+..+|.|.||.
T Consensus 261 ~~~i~~~~~~~~--~~~l~~~~~d~~i~iw~ 289 (289)
T cd00200 261 TNSVTSLAWSPD--GKRLASGSADGTIRIWD 289 (289)
T ss_pred CCcEEEEEECCC--CCEEEEecCCCeEEecC
Confidence 456999999987 46888999999999994
No 14
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=27.20 E-value=28 Score=28.42 Aligned_cols=30 Identities=33% Similarity=0.657 Sum_probs=19.4
Q ss_pred eehhhhcccccccccCCCCCCCCCCcchhhhhhhhcccCCCCCCCceE
Q 000848 1205 WYKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGGTWV 1252 (1255)
Q Consensus 1205 WyKCiRC~RQTsAfasp~a~n~p~qn~re~wWisRW~~~CPMCGGtWv 1252 (1255)
=|+|.+|+.+...- .. .. ..-||.||++-+
T Consensus 3 ~y~C~~CG~~~~~~---~~---------~~------~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELD---EY---------GT------GVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEEC---CC---------CC------ceECCCCCCeEE
Confidence 38999999865431 11 11 357999998654
No 15
>cd00200 WD40 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and botto
Probab=26.78 E-value=1.8e+02 Score=26.38 Aligned_cols=50 Identities=18% Similarity=0.295 Sum_probs=33.6
Q ss_pred EEEecCCCCcceeEEEeecCCCCCceEEEEecCCCCcceEEEEeccceEEEEecCC
Q 000848 133 IHIVIPERPTECAVFNVIADCPRDSVQFIEWSPTSCPRALLIANFYGRVTIWTQPS 188 (1255)
Q Consensus 133 ihIviPerPtE~avfnv~adsp~d~vq~ieWSp~~cpRALLiAnf~GRvtIWtQPs 188 (1255)
|+|+..+.......|. ...+.|..+.|+|.. +-|+++..+|.|.||.-.+
T Consensus 159 i~i~d~~~~~~~~~~~----~~~~~i~~~~~~~~~--~~l~~~~~~~~i~i~d~~~ 208 (289)
T cd00200 159 IKLWDLRTGKCVATLT----GHTGEVNSVAFSPDG--EKLLSSSSDGTIKLWDLST 208 (289)
T ss_pred EEEEEccccccceeEe----cCccccceEEECCCc--CEEEEecCCCcEEEEECCC
Confidence 3444444344444443 334579999999987 5677777799999997654
No 16
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=25.82 E-value=25 Score=35.32 Aligned_cols=34 Identities=18% Similarity=0.471 Sum_probs=23.9
Q ss_pred CcceeehhhhcccccccccCCCCCCCCCCcchhhhhhhhcccCCCCCCCce
Q 000848 1201 LEGVWYKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGGTW 1251 (1255)
Q Consensus 1201 leGvWyKCiRC~RQTsAfasp~a~n~p~qn~re~wWisRW~~~CPMCGGtW 1251 (1255)
-++.-|.|.+|.+.-+..-. . ...+-||.|||.=
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA---~--------------~~~F~Cp~Cg~~L 138 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEA---M--------------ELNFTCPRCGAML 138 (158)
T ss_pred cCCCeEECCCCCcEeeHHHH---H--------------HcCCcCCCCCCEe
Confidence 35789999999966443322 1 1478999999964
No 17
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=25.37 E-value=28 Score=35.74 Aligned_cols=34 Identities=21% Similarity=0.603 Sum_probs=24.9
Q ss_pred cceeehhhhcccccccccCCCCCCCCCCcchhhhhhhhcccCCCCCCCceE
Q 000848 1202 EGVWYKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGGTWV 1252 (1255)
Q Consensus 1202 eGvWyKCiRC~RQTsAfasp~a~n~p~qn~re~wWisRW~~~CPMCGGtWv 1252 (1255)
++.-|.|.+|.+.-+..-. . ...+-||.|||.=+
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA---~--------------~~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEA---M--------------EYGFRCPQCGEMLE 147 (178)
T ss_pred CCCEEECCCCCcEEeHHHH---h--------------hcCCcCCCCCCCCe
Confidence 5789999999977655432 1 14789999999643
No 18
>PF13454 NAD_binding_9: FAD-NAD(P)-binding
Probab=25.00 E-value=21 Score=34.28 Aligned_cols=44 Identities=23% Similarity=0.479 Sum_probs=34.3
Q ss_pred cccCCcccccccceEEecCCceEEeeecccCCceEEEEEecCCCCCCcccccc
Q 000848 296 LLGAGPSGIMAADVIITDSGAMHVAGVPIVNPSTVVVWEVTPGPGNGFQAAPK 348 (1255)
Q Consensus 296 lLg~GpSGIma~DAIItdsGamhVAGVpi~NPSTVVVWEV~pg~gng~q~tpk 348 (1255)
++|+||+|+.+...++... .-..|..|.|+|- ...|-|.-.-++
T Consensus 2 IIG~G~~G~~~l~~L~~~~--------~~~~~~~I~vfd~-~~~G~G~~~~~~ 45 (156)
T PF13454_consen 2 IIGGGPSGLAVLERLLRQA--------DPKPPLEITVFDP-SPFGAGGAYRPD 45 (156)
T ss_pred EECcCHHHHHHHHHHHHhc--------CCCCCCEEEEEcC-CCccccccCCCC
Confidence 5799999999999988765 5567888999998 556767655544
No 19
>COG2072 TrkA Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]
Probab=24.57 E-value=1.3e+02 Score=34.29 Aligned_cols=70 Identities=33% Similarity=0.512 Sum_probs=40.4
Q ss_pred cccCCcccccccceEEecCCceEEeeecccCCceEEEEEecCCCCCCcc---------ccccccccCCCCCCC--CCCCc
Q 000848 296 LLGAGPSGIMAADVIITDSGAMHVAGVPIVNPSTVVVWEVTPGPGNGFQ---------AAPKTTTSNGVPPSL--SPPKW 364 (1255)
Q Consensus 296 lLg~GpSGIma~DAIItdsGamhVAGVpi~NPSTVVVWEV~pg~gng~q---------~tpktS~~~~vpp~l--~~p~W 364 (1255)
++|+|+|||.+|=+... +|++- ++|.|-....|-.-- .+||--. ++|..- ....|
T Consensus 13 IIGaG~sGlaaa~~L~~-------~g~~~-----~~i~Ek~~~~Gg~W~~~ry~~l~~~~p~~~~--~~~~~p~~~~~~~ 78 (443)
T COG2072 13 IIGAGQSGLAAAYALKQ-------AGVPD-----FVIFEKRDDVGGTWRYNRYPGLRLDSPKWLL--GFPFLPFRWDEAF 78 (443)
T ss_pred EECCCHHHHHHHHHHHH-------cCCCc-----EEEEEccCCcCCcchhccCCceEECCchhee--ccCCCccCCcccC
Confidence 68999999999854322 23321 556666554443311 1222222 333222 35789
Q ss_pred CCcchhhhhhhHHHH
Q 000848 365 AGFAPLAAYLFSWQE 379 (1255)
Q Consensus 365 ~GFapLaAYLfswq~ 379 (1255)
++|+++-.|+-.+.+
T Consensus 79 ~~~~~~~~y~~~~~~ 93 (443)
T COG2072 79 APFAEIKDYIKDYLE 93 (443)
T ss_pred CCcccHHHHHHHHHH
Confidence 999988888777664
No 20
>KOG2858 consensus Uncharacterized conserved protein [General function prediction only]
Probab=24.30 E-value=26 Score=40.43 Aligned_cols=15 Identities=47% Similarity=0.968 Sum_probs=13.5
Q ss_pred eehhhhccccccccc
Q 000848 1205 WYKCIRCLRQTAAFA 1219 (1255)
Q Consensus 1205 WyKCiRC~RQTsAfa 1219 (1255)
=|||.||+-||+.|-
T Consensus 29 KYkCPRCl~rtCsLe 43 (390)
T KOG2858|consen 29 KYKCPRCLARTCSLE 43 (390)
T ss_pred cccCcchhhhheecc
Confidence 499999999999885
No 21
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=24.19 E-value=1e+02 Score=24.84 Aligned_cols=56 Identities=18% Similarity=0.413 Sum_probs=41.4
Q ss_pred eeeeeccccchhHHHHHHHHhHHHHHHHHhhccccccccCCCccCCCcccccccccc
Q 000848 717 IKCRLLEGTNAQEVRAMVLDMQARLLLDMLGKGIESALINPSALVPDPWQASGETLS 773 (1255)
Q Consensus 717 Ikcrlleg~naqeVRamvlDmQarlllDmLgkgiesaLinpsalv~epWqas~etls 773 (1255)
|.+.+++|.+.++-|++ ..-=.+.|.+.+|+--|...|+=...-++-|-..|.+||
T Consensus 3 i~i~~~~grt~eqk~~l-~~~i~~~l~~~~g~~~~~v~V~i~e~~~~~~~~gg~~~~ 58 (58)
T cd00491 3 VQIYILEGRTDEQKREL-IERVTEAVSEILGAPEATIVVIIDEMPKENWGIGGESAS 58 (58)
T ss_pred EEEEEcCCCCHHHHHHH-HHHHHHHHHHHhCcCcccEEEEEEEeCchhceECCEECc
Confidence 57889999985555554 455567888999998888877766677777777776654
No 22
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=20.92 E-value=44 Score=38.13 Aligned_cols=34 Identities=32% Similarity=0.857 Sum_probs=26.1
Q ss_pred hhhcccccccccCCCCCCCCCCcchhhhhhhhcccCCCCCCCc
Q 000848 1208 CIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGGT 1250 (1255)
Q Consensus 1208 CiRC~RQTsAfasp~a~n~p~qn~re~wWisRW~~~CPMCGGt 1250 (1255)
|+.||-+ -|||- | +|.+||.|.-+|= -||||--+
T Consensus 316 C~~Cm~k--wFasr----Q-d~~~~~~Wl~~~~--~CPtCRa~ 349 (358)
T PF10272_consen 316 CLECMGK--WFASR----Q-DQQHPETWLSGKC--PCPTCRAK 349 (358)
T ss_pred HHHHHHH--Hhhhc----C-CCCChhhhhcCCC--CCCCCccc
Confidence 8899865 46553 2 7788999999984 59999765
Done!