Query 002224
Match_columns 951
No_of_seqs 26 out of 28
Neff 1.8
Searched_HMMs 46136
Date Thu Mar 28 19:19:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002224.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002224hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11635 Med16: Mediator compl 95.6 0.093 2E-06 60.7 11.6 159 167-373 214-392 (753)
2 PF11635 Med16: Mediator compl 90.0 0.15 3.2E-06 59.1 1.7 57 884-948 693-752 (753)
3 TIGR02605 CxxC_CxxC_SSSS putat 53.8 10 0.00022 30.1 2.1 34 902-950 6-40 (52)
4 PF10263 SprT-like: SprT-like 51.3 8.1 0.00018 35.6 1.4 37 898-950 120-156 (157)
5 COG1996 RPC10 DNA-directed RNA 48.6 8.6 0.00019 32.5 1.0 11 901-911 6-16 (49)
6 PF07295 DUF1451: Protein of u 39.9 17 0.00037 35.7 1.7 28 902-947 113-140 (146)
7 PF13453 zf-TFIIB: Transcripti 38.4 12 0.00026 29.1 0.3 12 937-948 19-30 (41)
8 PF09723 Zn-ribbon_8: Zinc rib 38.4 26 0.00056 27.7 2.2 34 902-950 6-40 (42)
9 smart00834 CxxC_CXXC_SSSS Puta 37.1 27 0.00059 26.1 2.1 35 902-951 6-40 (41)
10 PRK00398 rpoP DNA-directed RNA 32.1 22 0.00047 28.2 0.9 30 901-948 3-32 (46)
11 TIGR00373 conserved hypothetic 32.0 16 0.00035 35.6 0.1 34 897-947 105-138 (158)
12 PRK06266 transcription initiat 31.0 19 0.00041 36.0 0.4 34 898-948 114-147 (178)
13 KOG2858 Uncharacterized conser 29.9 17 0.00038 40.7 0.0 16 901-916 29-44 (390)
14 PF10272 Tmpp129: Putative tra 28.2 26 0.00056 38.9 0.9 34 904-946 316-349 (358)
15 cd00491 4Oxalocrotonate_Tautom 27.2 88 0.0019 24.5 3.5 56 413-469 3-58 (58)
16 smart00659 RPOLCX RNA polymera 22.6 41 0.00089 27.4 0.9 28 900-946 1-28 (44)
17 TIGR00354 polC DNA polymerase, 22.6 30 0.00065 43.0 0.1 125 765-913 509-637 (1095)
18 PRK00564 hypA hydrogenase nick 21.8 63 0.0014 30.3 2.1 15 937-951 87-102 (117)
19 TIGR00013 taut 4-oxalocrotonat 21.6 92 0.002 24.9 2.7 57 413-470 3-60 (63)
20 KOG0909 Peptide:N-glycanase [P 21.2 44 0.00095 38.7 1.1 38 903-945 163-202 (500)
21 KOG1105 Transcription elongati 21.0 48 0.001 36.2 1.3 41 900-948 254-294 (296)
22 cd03747 Ntn_PGA_like Penicilli 20.2 96 0.0021 32.7 3.2 27 584-611 25-58 (312)
23 COG4895 Uncharacterized conser 20.2 45 0.00098 29.6 0.7 40 650-689 23-63 (63)
24 cd03735 SOCS_SOCS1 SOCS (suppr 20.2 46 0.00099 27.5 0.7 10 725-734 5-14 (43)
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=95.61 E-value=0.093 Score=60.68 Aligned_cols=159 Identities=18% Similarity=0.181 Sum_probs=100.9
Q ss_pred eEEeeccCCCceeeeeccCCCCC--CCCCCCCceeEEEeeeecccCCCCccccccccCCCcccccccccccccccceeec
Q 002224 167 RVQRWESSVQPVVLHQIFGNPTS--SFGGQAPMQTVWVSKVDTSIPTSNFKIHQLAAAGPTCDVWKTTDSGLEKSKIVSF 244 (951)
Q Consensus 167 RvqrWESs~qpvvlhpifg~pts--~~gGqpp~qtvW~skvd~sIp~td~kn~q~~~~~~~~d~~~~s~~~~dk~k~~~f 244 (951)
-|.|||=.-++..|||+|..-.| +.++++|+.+.|+..-|+.++.. -+++
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 45578999999998877765432 2223
Q ss_pred CCCCCccchhhHhhheecccCCeEEEEEeeCceeEeeCCCCCcccee-----ee-------eccccccC------CccCc
Q 002224 245 DPFDLPSDIRSLARIVYSAHGGEIAIALLRGGVHIFSGPNFAPVDNY-----QI-------SVGSAIAA------PAFSS 306 (951)
Q Consensus 245 dpfdlP~dvr~lAriVySahgGEiavAflrGgVHIFSGpnf~pVdny-----qi-------nVgsaIa~------PaFSs 306 (951)
++..+ |+=++++|--|-||++.=-+|+++... .. .+|=..+. -|||+
T Consensus 266 ~~~~~---------------~~~v~~~~~DGsI~~~dr~t~~~~~~~~~~~~~~~~v~s~~~~Gf~fp~~~~~~~vafSP 330 (753)
T PF11635_consen 266 TSPEL---------------DIVVAFAFSDGSIEFRDRNTMKELNETRTNGEPPNTVTSLFQAGFHFPCIQPPLHVAFSP 330 (753)
T ss_pred Eeccc---------------CcEEEEEEcCCeEEEEecCcchhhcccccccCCccccccccccccccccCCCCceEEECc
Confidence 32222 347899999999999999999776554 11 13333432 26999
Q ss_pred cccccceeeecCCCCceeEEEEeecCCCccccccccchhhHHHHHHHHHhhhhhccccchhhhcccc
Q 002224 307 TSCCSASVWHDTNKDRTILKIIRVLPPAVPSSQVKANSSTWERAIAERFWWSLLVNVDWWDAVGCTQ 373 (951)
Q Consensus 307 TsCCsASVWHDt~kd~~iLkIirVlPPa~p~~q~ka~ss~weraiaerfwwSllvgvdWWDavgctq 373 (951)
|+|..+-. |...+.. |....+....-..|.-..+++ -.|++=-+=.-...+-|||+++-+++
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 99987765 2222211 555555554444443332221 12222223334567999999998776
No 2
>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=90.03 E-value=0.15 Score=59.07 Aligned_cols=57 Identities=30% Similarity=0.727 Sum_probs=39.1
Q ss_pred ccceeEEeeecCCCc---ceeehhhhcccccccccCCCCCCCCCCCccchheehhcccCCCCCCCceE
Q 002224 884 SRRDVVTAVWKTGLE---GVWYKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGGTWV 948 (951)
Q Consensus 884 SRRdVvTa~WKtgle---GvWyKciRC~RQTsAf~sp~a~~~p~qn~rE~wWisRW~~~CPMCGGtWv 948 (951)
..=|+++-++=.+-+ +.|-+|.||+.-|.+.-.. .+...-. |.-+|.-.| .|||-|+
T Consensus 693 ~~vD~~rk~~l~~~~~~~~~~RrC~RC~~vs~~~~~~------~s~~~~~-w~~~~~R~C-~CGG~W~ 752 (753)
T PF11635_consen 693 RYVDVLRKVHLGRSPTSTGKWRRCVRCGSVSEDEDPF------TSRATKR-WTMRWQRNC-ICGGMWV 752 (753)
T ss_pred cccceeeeeeeeecccCCCceEEeccCCCcccccCCC------Ccchhhh-hhhheeeee-ccCCeeC
Confidence 556788877765554 9999999999554433222 1111122 999999888 6999996
No 3
>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=53.79 E-value=10 Score=30.07 Aligned_cols=34 Identities=26% Similarity=0.693 Sum_probs=21.7
Q ss_pred ehhhhcccccccccCCCCCCCCCCCccchheehhcccCCCCCCCceE-Ee
Q 002224 902 YKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGGTWV-RV 950 (951)
Q Consensus 902 yKciRC~RQTsAf~sp~a~~~p~qn~rE~wWisRW~~~CPMCGGtWv-rv 950 (951)
|||..|+..-..+.+-+. . . ...||.||..-+ |+
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~------~--------~~~CP~Cg~~~~~r~ 40 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSD-D------P--------LATCPECGGEKLRRL 40 (52)
T ss_pred EEeCCCCCEeEEEEecCC-C------C--------CCCCCCCCCCceeEE
Confidence 899999986666543221 0 0 235999999544 65
No 4
>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=51.33 E-value=8.1 Score=35.65 Aligned_cols=37 Identities=30% Similarity=0.691 Sum_probs=23.8
Q ss_pred cceeehhhhcccccccccCCCCCCCCCCCccchheehhcccCCCCCCCceEEe
Q 002224 898 EGVWYKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGGTWVRV 950 (951)
Q Consensus 898 eGvWyKciRC~RQTsAf~sp~a~~~p~qn~rE~wWisRW~~~CPMCGGtWvrv 950 (951)
.-.+|+|-.|++--.... .. .+. .|-|+.|||..++|
T Consensus 120 ~~~~~~C~~C~~~~~r~~-----~~----~~~-------~~~C~~C~~~l~~~ 156 (157)
T PF10263_consen 120 KKYVYRCPSCGREYKRHR-----RS----KRK-------RYRCGRCGGPLVQV 156 (157)
T ss_pred cceEEEcCCCCCEeeeec-----cc----chh-------hEECCCCCCEEEEc
Confidence 457999999985421111 11 111 18999999999986
No 5
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=48.61 E-value=8.6 Score=32.52 Aligned_cols=11 Identities=55% Similarity=1.078 Sum_probs=9.6
Q ss_pred eehhhhccccc
Q 002224 901 WYKCIRCLRQT 911 (951)
Q Consensus 901 WyKciRC~RQT 911 (951)
=|||.||+++-
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 49999999875
No 6
>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=39.91 E-value=17 Score=35.74 Aligned_cols=28 Identities=32% Similarity=0.735 Sum_probs=20.5
Q ss_pred ehhhhcccccccccCCCCCCCCCCCccchheehhcccCCCCCCCce
Q 002224 902 YKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGGTW 947 (951)
Q Consensus 902 yKciRC~RQTsAf~sp~a~~~p~qn~rE~wWisRW~~~CPMCGGtW 947 (951)
|.|..|+.++. |..|+. .| -||-||++=
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 7
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=38.43 E-value=12 Score=29.12 Aligned_cols=12 Identities=50% Similarity=1.318 Sum_probs=10.3
Q ss_pred ccCCCCCCCceE
Q 002224 937 AFGCPMCGGTWV 948 (951)
Q Consensus 937 ~~~CPMCGGtWv 948 (951)
.+.||-|||.|.
T Consensus 19 id~C~~C~G~W~ 30 (41)
T PF13453_consen 19 IDVCPSCGGIWF 30 (41)
T ss_pred EEECCCCCeEEc
Confidence 366999999996
No 8
>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=38.35 E-value=26 Score=27.72 Aligned_cols=34 Identities=29% Similarity=0.668 Sum_probs=24.2
Q ss_pred ehhhhcccccccccCCCCCCCCCCCccchheehhcccCCCCCCC-ceEEe
Q 002224 902 YKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGG-TWVRV 950 (951)
Q Consensus 902 yKciRC~RQTsAf~sp~a~~~p~qn~rE~wWisRW~~~CPMCGG-tWvrv 950 (951)
|+|..|+.+-..+.+-+. .. ..-||-||+ .=.||
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 899999988887776433 11 136999999 55555
No 9
>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=37.08 E-value=27 Score=26.07 Aligned_cols=35 Identities=26% Similarity=0.645 Sum_probs=21.9
Q ss_pred ehhhhcccccccccCCCCCCCCCCCccchheehhcccCCCCCCCceEEeC
Q 002224 902 YKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGGTWVRVV 951 (951)
Q Consensus 902 yKciRC~RQTsAf~sp~a~~~p~qn~rE~wWisRW~~~CPMCGGtWvrvV 951 (951)
|+|..|+..-..+.+-.. .+ ...||.||+.=-||+
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 789999885554443211 00 235999999766654
No 10
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=32.07 E-value=22 Score=28.16 Aligned_cols=30 Identities=33% Similarity=0.700 Sum_probs=19.3
Q ss_pred eehhhhcccccccccCCCCCCCCCCCccchheehhcccCCCCCCCceE
Q 002224 901 WYKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGGTWV 948 (951)
Q Consensus 901 WyKciRC~RQTsAf~sp~a~~~p~qn~rE~wWisRW~~~CPMCGGtWv 948 (951)
=|+|.+|+.+...- +... ..-||.||+.-+
T Consensus 3 ~y~C~~CG~~~~~~------------~~~~------~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELD------------EYGT------GVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEEC------------CCCC------ceECCCCCCeEE
Confidence 38999999865431 1111 357999998654
No 11
>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=31.98 E-value=16 Score=35.60 Aligned_cols=34 Identities=21% Similarity=0.489 Sum_probs=24.1
Q ss_pred CcceeehhhhcccccccccCCCCCCCCCCCccchheehhcccCCCCCCCce
Q 002224 897 LEGVWYKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGGTW 947 (951)
Q Consensus 897 leGvWyKciRC~RQTsAf~sp~a~~~p~qn~rE~wWisRW~~~CPMCGGtW 947 (951)
-++.-|.|.+|.+.-+..- |.+ ..+-||.|||.=
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~e---A~~--------------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNE---AME--------------LNFTCPRCGAML 138 (158)
T ss_pred cCCCeEECCCCCcEeeHHH---HHH--------------cCCcCCCCCCEe
Confidence 3578999999996654332 221 378999999964
No 12
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=31.04 E-value=19 Score=35.96 Aligned_cols=34 Identities=21% Similarity=0.603 Sum_probs=25.0
Q ss_pred cceeehhhhcccccccccCCCCCCCCCCCccchheehhcccCCCCCCCceE
Q 002224 898 EGVWYKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGGTWV 948 (951)
Q Consensus 898 eGvWyKciRC~RQTsAf~sp~a~~~p~qn~rE~wWisRW~~~CPMCGGtWv 948 (951)
++.-|.|.+|.+.-+..-. . ...+-||.|||.=+
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 5789999999977665532 1 14789999999643
No 13
>KOG2858 consensus Uncharacterized conserved protein [General function prediction only]
Probab=29.94 E-value=17 Score=40.75 Aligned_cols=16 Identities=44% Similarity=0.910 Sum_probs=13.9
Q ss_pred eehhhhcccccccccC
Q 002224 901 WYKCIRCLRQTAAFAS 916 (951)
Q Consensus 901 WyKciRC~RQTsAf~s 916 (951)
=|||.||+-||+.|--
T Consensus 29 KYkCPRCl~rtCsLeC 44 (390)
T KOG2858|consen 29 KYKCPRCLARTCSLEC 44 (390)
T ss_pred cccCcchhhhheeccc
Confidence 3999999999998853
No 14
>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=28.19 E-value=26 Score=38.95 Aligned_cols=34 Identities=32% Similarity=0.857 Sum_probs=25.6
Q ss_pred hhhcccccccccCCCCCCCCCCCccchheehhcccCCCCCCCc
Q 002224 904 CIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGGT 946 (951)
Q Consensus 904 ciRC~RQTsAf~sp~a~~~p~qn~rE~wWisRW~~~CPMCGGt 946 (951)
|+.||-+ -|||- | +|.+||.|.-+|= -||||--+
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 8888865 46652 2 6789999998874 59999765
No 15
>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=27.18 E-value=88 Score=24.50 Aligned_cols=56 Identities=18% Similarity=0.413 Sum_probs=41.2
Q ss_pred eeeeeccccchhHHHHHHHHhHHHHHHHHhhccccccccCCCccCCCcccccccccc
Q 002224 413 IKCRLLEGTNAQEVRAMVLDMQARLLLDMLGKGIESALINPSALVPDPWQASGETLS 469 (951)
Q Consensus 413 Ikcrlleg~naqeVRa~vlDmQarlllDmLgkgiesaLinpsalvpepWqas~etls 469 (951)
|.+.+.+|.+.++-|++ ..-=.+.|.+.+|+--|...|+=...-++-|-..|.+||
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 57889999985555555 455567888999998888877766677777777766654
No 16
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=22.60 E-value=41 Score=27.42 Aligned_cols=28 Identities=29% Similarity=0.527 Sum_probs=19.1
Q ss_pred eeehhhhcccccccccCCCCCCCCCCCccchheehhcccCCCCCCCc
Q 002224 900 VWYKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGGT 946 (951)
Q Consensus 900 vWyKciRC~RQTsAf~sp~a~~~p~qn~rE~wWisRW~~~CPMCGGt 946 (951)
+.|+|.+|++....- ++=.--||.||.+
T Consensus 1 ~~Y~C~~Cg~~~~~~-------------------~~~~irC~~CG~r 28 (44)
T smart00659 1 MIYICGECGRENEIK-------------------SKDVVRCRECGYR 28 (44)
T ss_pred CEEECCCCCCEeecC-------------------CCCceECCCCCce
Confidence 469999999864421 1223569999975
No 17
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=22.56 E-value=30 Score=42.99 Aligned_cols=125 Identities=20% Similarity=0.184 Sum_probs=71.0
Q ss_pred hhhhhcccCcccccCCCCCCccccchhhhhhccCCChHHHHhhcccCCCCCCCCCCCCCCCCCccccccCCCCCCCCCCC
Q 002224 765 PEVVEASLGPHMQNMPRPRGADAAGLLLRELELHPPAEEWHRRNMFGGPWSDPEDVGPVDDTPKLSNWVDSVDVNSSGNH 844 (951)
Q Consensus 765 PEVVEAsLgphMQNmPRpRgADaaGLLlRELELhPPaEewhRrnmFggp~sdp~d~~~~~d~pk~~~~s~~ld~ss~e~~ 844 (951)
-|+.|.=+=||.+.==+..- +..--|++.|.|- |++.+.+ + ..+++.++++...++... +..
T Consensus 509 K~~LE~L~v~H~v~~~~i~i-~~~~~l~~~Lg~~---~~l~~~~---------~---~~~~~~~~vn~~s~~~ir--~ra 570 (1095)
T TIGR00354 509 KRILEALGLEHKVRESFVVI-ETWRAFIRCLGLD---EKLSKVL---------E---VSKDVLEIVNGISPIKVR--PKA 570 (1095)
T ss_pred HHHHHHhCCceEecCCeEEe-cchHHHHHHhCCc---hhhhhcc---------c---ccccHHHHHHhhCCcEee--ccC
Confidence 46888888999995322222 2224678888875 4666511 1 223555565544444432 345
Q ss_pred ccccccCCcccccccccccccccccccccccccchhcccccceeEEeeecCC----Ccceeehhhhccccccc
Q 002224 845 DVYYDSHGLWPRKRRMSERDAAFGLNTSVGLGAYLGIMGSRRDVVTAVWKTG----LEGVWYKCIRCLRQTAA 913 (951)
Q Consensus 845 d~~~g~~~lwPrKrRmsErDAAfglnTsvgLGaylgimGSRRdVvTa~WKtg----leGvWyKciRC~RQTsA 913 (951)
-++-|+.==.|-|-. ||+.-=-.++=.=+|-+ =|++|||..|. +.| .|=-=.||..|+.-|-.
T Consensus 571 ptrIG~RmGRPEKa~--~RkMkPp~h~LFPiG~a---GG~~R~i~~A~-~~g~~i~vev~~RKCPkCG~yTlk 637 (1095)
T TIGR00354 571 LSYIGARMGRPEKAK--ERKMSPPPHILFPIGMA---GGNTRDIKNAI-NYTKEIEVEIAIRKCPQCGKESFW 637 (1095)
T ss_pred CceeecccCCCcccc--cccCCCCCccccccccc---CcchhhHHHHh-ccCCeeEEEEEEEECCCCCccccc
Confidence 566666655665522 33322222221122222 37999999998 555 45557899999988754
No 18
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.82 E-value=63 Score=30.35 Aligned_cols=15 Identities=27% Similarity=0.713 Sum_probs=11.3
Q ss_pred ccC-CCCCCCceEEeC
Q 002224 937 AFG-CPMCGGTWVRVV 951 (951)
Q Consensus 937 ~~~-CPMCGGtWvrvV 951 (951)
.+. ||.||+.=++++
T Consensus 87 ~~~~CP~Cgs~~~~i~ 102 (117)
T PRK00564 87 DYGVCEKCHSKNVIIT 102 (117)
T ss_pred cCCcCcCCCCCceEEe
Confidence 344 999999877764
No 19
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=21.61 E-value=92 Score=24.95 Aligned_cols=57 Identities=19% Similarity=0.397 Sum_probs=45.7
Q ss_pred eeeeec-cccchhHHHHHHHHhHHHHHHHHhhccccccccCCCccCCCccccccccccC
Q 002224 413 IKCRLL-EGTNAQEVRAMVLDMQARLLLDMLGKGIESALINPSALVPDPWQASGETLSG 470 (951)
Q Consensus 413 Ikcrll-eg~naqeVRa~vlDmQarlllDmLgkgiesaLinpsalvpepWqas~etls~ 470 (951)
|...++ +|.++++-+++.-.+. +.|.+.||+.-|+..|.=...-++-|-..|.+++.
T Consensus 3 i~i~i~~~grt~eqK~~l~~~it-~~l~~~lg~~~~~v~V~i~e~~~~~w~~gG~~~~~ 60 (63)
T TIGR00013 3 VNIYILKEGRTDEQKRQLIEGVT-EAMAETLGANLESIVVIIDEMPKNNYGIGGELVSD 60 (63)
T ss_pred EEEEECCCCCCHHHHHHHHHHHH-HHHHHHhCCCcccEEEEEEEcCHHHeeECCEEhhH
Confidence 467788 8988888888877765 56789999999988888777778888888877764
No 20
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=21.19 E-value=44 Score=38.68 Aligned_cols=38 Identities=29% Similarity=0.602 Sum_probs=28.3
Q ss_pred hhhhcccccccccCCCCCCCCCCCccchheehhc--ccCCCCCCC
Q 002224 903 KCIRCLRQTAAFASPGATNPPNQNDREAWWISRW--AFGCPMCGG 945 (951)
Q Consensus 903 KciRC~RQTsAf~sp~a~~~p~qn~rE~wWisRW--~~~CPMCGG 945 (951)
-|..|+-+|| ++--..+| ||.|.||--+= .|-|-|||-
T Consensus 163 pC~~CG~et~---~~l~~~~p--~eeE~~~Ga~rVEiy~C~~C~~ 202 (500)
T KOG0909|consen 163 PCNKCGGETS---SGLGNQPP--NEEEKKFGAGRVEIYKCNRCGT 202 (500)
T ss_pred Cccccccccc---ccccCCCC--chhHhhcCCceEEEEEecCCCC
Confidence 4999999998 44444444 89999885443 588999985
No 21
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=20.97 E-value=48 Score=36.25 Aligned_cols=41 Identities=20% Similarity=0.594 Sum_probs=26.9
Q ss_pred eeehhhhcccccccccCCCCCCCCCCCccchheehhcccCCCCCCCceE
Q 002224 900 VWYKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGGTWV 948 (951)
Q Consensus 900 vWyKciRC~RQTsAf~sp~a~~~p~qn~rE~wWisRW~~~CPMCGGtWv 948 (951)
.|+||-+|.+-.+.+..+-.-..- |- |.- --.|--||++|-
T Consensus 254 d~fkcgkckk~~cty~q~Qtrs~D-----eP-mtT--fv~C~ecgnrWk 294 (296)
T KOG1105|consen 254 DLFKCGKCKKKNCTYTQLQTRSAD-----EP-MTT--FVTCNECGNRWK 294 (296)
T ss_pred cceeeccccccceeEEeeccCCCC-----CC-cce--eeeecccCCccc
Confidence 399999999999998654322211 11 111 236999999993
No 22
>cd03747 Ntn_PGA_like Penicillin G acylase (PGA) belongs to a family of beta-lactam acylases that includes cephalosporin acylase (CA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and 7-aminocephalosporanic acid (7-ACA), which can be used to synthesize semi-synthetic penicillins and cephalosporins, respectively. While both PGA and CA have a conserved Ntn (N-terminal nucleophile) hydrolase fold and the structural similarity at their active sites is very high, their sequence similarity is low.
Probab=20.24 E-value=96 Score=32.70 Aligned_cols=27 Identities=41% Similarity=0.877 Sum_probs=23.8
Q ss_pred CCCCCCccceeeeecC-------CCCCCcceeeec
Q 002224 584 PISGPSSFMPISINTG-------TFPGTPAVRLIG 611 (951)
Q Consensus 584 pisGpssfmpiSInTg-------TFPGTPAVRLIg 611 (951)
+.++|+.+..+.+..+ ||||.|.| +||
T Consensus 25 ~~~~P~~wy~~~l~~~~~~v~G~s~pG~P~i-~iG 58 (312)
T cd03747 25 PLSGPSIWYEAHLSGPGLDVTGATLPGLPGI-VIG 58 (312)
T ss_pred CcCCCceEEEEEEecCCcceEeeccCCCceE-EEe
Confidence 6899999999998876 89999996 677
No 23
>COG4895 Uncharacterized conserved protein [Function unknown]
Probab=20.22 E-value=45 Score=29.60 Aligned_cols=40 Identities=33% Similarity=0.403 Sum_probs=27.5
Q ss_pred CCCCCCCCCceecccCCCC-CCccceeecccccccccceee
Q 002224 650 QKPQVSAPGKVEEINSVPG-KPTSAMVKLDEGQVARAGQTV 689 (951)
Q Consensus 650 qk~q~~~~gkvee~~~v~~-k~~~~~~k~edgq~~R~~q~v 689 (951)
||.-+...|-|+.+-+-|. .|----||.+|||++|.-+++
T Consensus 23 QkTGKlTrGvVk~iLT~S~~HPHGIKVrL~dGqvGRvq~iv 63 (63)
T COG4895 23 QKTGKLTRGVVKAILTRSPSHPHGIKVRLTDGQVGRVQAIV 63 (63)
T ss_pred ccCCcchhHHHHHHHhCCCCCCCceEEEeecCcccceeecC
Confidence 5555566666777654433 566667999999999966543
No 24
>cd03735 SOCS_SOCS1 SOCS (suppressors of cytokine signaling) box of SOCS1-like proteins. Together with CIS1, the CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. SOCS1, like CIS1 and SOCS3, is involved in the down-regulation of the JAK/STAT pathway. SOCS1 has a dual function as a direct potent JAK kinase inhibitor and as a component of an E3 ubiquitin-ligase complex recruiting substrates to the protein degradation machinery.
Probab=20.19 E-value=46 Score=27.48 Aligned_cols=10 Identities=40% Similarity=0.889 Sum_probs=8.4
Q ss_pred HHHHHhhhcc
Q 002224 725 ILMDLCRRTA 734 (951)
Q Consensus 725 iLmDLCrRTa 734 (951)
-|++|||||-
T Consensus 5 sLQhLCR~tI 14 (43)
T cd03735 5 PLQELCRKSI 14 (43)
T ss_pred CHHHHHHHHH
Confidence 4899999984
Done!