Query 031137
Match_columns 165
No_of_seqs 82 out of 84
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 09:45:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031137.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031137hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13259 DUF4050: Protein of u 100.0 4.6E-40 9.9E-45 251.8 6.8 113 49-165 1-122 (122)
2 PF07418 PCEMA1: Acidic phosph 48.2 7.7 0.00017 34.7 0.7 9 11-19 30-38 (282)
3 PF04818 CTD_bind: RNA polymer 35.0 31 0.00068 22.9 1.9 18 148-165 47-64 (64)
4 COG5208 HAP5 CCAAT-binding fac 33.7 22 0.00047 31.5 1.2 15 144-158 171-185 (286)
5 PLN00211 predicted protein; Pr 33.3 31 0.00068 24.5 1.7 13 147-159 29-41 (61)
6 PF09012 FeoC: FeoC like trans 27.9 50 0.0011 22.3 2.0 16 148-163 28-43 (69)
7 COG1709 Predicted transcriptio 27.6 47 0.001 29.3 2.2 25 130-154 94-127 (241)
8 PF09791 Oxidored-like: Oxidor 27.6 26 0.00055 23.6 0.5 8 8-15 19-26 (48)
9 KOG0126 Predicted RNA-binding 25.3 21 0.00046 30.8 -0.2 61 10-72 78-140 (219)
10 PRK07738 flagellar protein Fla 24.3 64 0.0014 25.3 2.2 22 143-164 91-112 (117)
11 TIGR03487 cas_csp2 CRISPR-asso 23.6 43 0.00094 31.3 1.3 13 143-155 180-192 (489)
12 cd03083 TRX_Fd_NuoE_hoxF TRX-l 23.1 37 0.00081 23.7 0.7 16 10-26 46-61 (80)
13 PRK00809 hypothetical protein; 21.7 57 0.0012 25.9 1.5 17 139-155 97-113 (144)
14 PRK10610 chemotaxis regulatory 21.5 95 0.0021 19.9 2.3 26 138-163 104-129 (129)
No 1
>PF13259 DUF4050: Protein of unknown function (DUF4050)
Probab=100.00 E-value=4.6e-40 Score=251.81 Aligned_cols=113 Identities=54% Similarity=0.946 Sum_probs=99.1
Q ss_pred cccccccccCcccccccccccCCCCCCCCCCCCCCCCCCCCCccchHHHHHHHHHHHhhhcCCCCCc-------cccccC
Q 031137 49 WTTSTCDMDNSAVQSQGSISSLGTNNLIPDTNGGSGSASAPSEFVNHGFLLWNQTRQRWIGNKKAEN-------RTHQVR 121 (165)
Q Consensus 49 WSsSt~eMdns~~qSq~sisSis~~n~~~d~~~~~~s~~~~~~FVNhGl~~W~q~R~qWvg~~~s~~-------~~~~~r 121 (165)
||||+++|||+++|+|+++++ .++..+.+..... ...++||||||++|+++|++|||++++.. +.+..+
T Consensus 1 ~s~s~~~~d~~~~~~~~~~s~---~~~~~~~~~~~~~-~~~~~~~N~Gl~lW~~rR~~W~~~~~~~~~~~~~l~~~~~~r 76 (122)
T PF13259_consen 1 WSSSPFRFDNSDAQSQRSISS---TNSSSDCSKRRKS-SEEEEFVNHGLILWEQRRQQWTGPKKSNKIIEPRLQQSNSIR 76 (122)
T ss_pred CCCCcccCcChhhhhhhcccc---ccchhhhhhhhcc-ccCccceeHHHHHHHHHHHHHcCCCCcccccccccccccccc
Confidence 999999999999999999954 4455555443333 34499999999999999999999988774 566788
Q ss_pred C--CeeecccchhhccCCCCCCCCCCChHHHHHHHHHHHhhcCCCC
Q 031137 122 E--PKLNWNATYESLLGSNKPFPQPIPLSEMVDFLVDIWEQEGMYD 165 (165)
Q Consensus 122 e--p~iswnatye~LLgsn~pF~qPIPL~EMVdfLVDiWE~EGLyd 165 (165)
+ |.++|++|||+||++++||++||||+|||+||||+|++||+||
T Consensus 77 ~~Ip~~~y~~iY~~Lv~~~~pf~~PI~L~dmv~~Lv~gW~~eg~w~ 122 (122)
T PF13259_consen 77 ESIPPISYPAIYEKLVGSNKPFKQPIPLSDMVDFLVDGWEEEGLWP 122 (122)
T ss_pred cccchhhHHHHHHHHhcCCCCCCCCcCHHHHHHHHHHHhhcCCccC
Confidence 8 9999999999999999999999999999999999999999997
No 2
>PF07418 PCEMA1: Acidic phosphoprotein precursor PCEMA1; InterPro: IPR010882 This family consists of several acidic phosphoprotein precursor PCEMA1 sequences which appear to be found exclusively in Plasmodium chabaudi. PCEMA1 is an antigen that is associated with the membrane of the infected erythrocyte throughout the entire intraerythrocytic cycle []. The exact function of this family is unclear.
Probab=48.20 E-value=7.7 Score=34.69 Aligned_cols=9 Identities=33% Similarity=0.918 Sum_probs=7.8
Q ss_pred CcccCCCCC
Q 031137 11 GCLGCFIRP 19 (165)
Q Consensus 11 GC~Gc~~Kp 19 (165)
||||||.|-
T Consensus 30 gcF~f~rkK 38 (282)
T PF07418_consen 30 GCFGFCRKK 38 (282)
T ss_pred ceehhhccc
Confidence 999999854
No 3
>PF04818 CTD_bind: RNA polymerase II-binding domain.; InterPro: IPR006903 This entry represents a conserved region found in a number of uncharacterised eukaryotic proteins.; PDB: 2L0I_A 2KM4_A 3D9I_B 3D9N_B 3D9O_A 3D9P_B 3D9K_A 3D9M_A 3D9J_A 3D9L_A ....
Probab=35.00 E-value=31 Score=22.88 Aligned_cols=18 Identities=28% Similarity=0.761 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHhhcCCCC
Q 031137 148 SEMVDFLVDIWEQEGMYD 165 (165)
Q Consensus 148 ~EMVdfLVDiWE~EGLyd 165 (165)
-+=|.=|++||++-+.|+
T Consensus 47 ~~kv~rll~iW~~r~if~ 64 (64)
T PF04818_consen 47 RKKVQRLLNIWEERNIFS 64 (64)
T ss_dssp HHHHHHHHHHHHHCTSS-
T ss_pred HHHHHHHHHHhhCCCCCC
Confidence 344667899999999986
No 4
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=33.69 E-value=22 Score=31.53 Aligned_cols=15 Identities=53% Similarity=0.795 Sum_probs=12.2
Q ss_pred CCChHHHHHHHHHHH
Q 031137 144 PIPLSEMVDFLVDIW 158 (165)
Q Consensus 144 PIPL~EMVdfLVDiW 158 (165)
.|--+||.|||+||=
T Consensus 171 Av~kSeMfDFLidiv 185 (286)
T COG5208 171 AVKKSEMFDFLIDIV 185 (286)
T ss_pred HHHHHHHHhHHhhhc
Confidence 455689999999984
No 5
>PLN00211 predicted protein; Provisional
Probab=33.30 E-value=31 Score=24.48 Aligned_cols=13 Identities=46% Similarity=1.071 Sum_probs=12.1
Q ss_pred hHHHHHHHHHHHh
Q 031137 147 LSEMVDFLVDIWE 159 (165)
Q Consensus 147 L~EMVdfLVDiWE 159 (165)
|+-|.-||.|||-
T Consensus 29 lphMtsfLAeIwS 41 (61)
T PLN00211 29 LPHMTSFLAEIWS 41 (61)
T ss_pred cHHHHHHHHHHHH
Confidence 8899999999995
No 6
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=27.91 E-value=50 Score=22.32 Aligned_cols=16 Identities=19% Similarity=0.381 Sum_probs=14.0
Q ss_pred HHHHHHHHHHHhhcCC
Q 031137 148 SEMVDFLVDIWEQEGM 163 (165)
Q Consensus 148 ~EMVdfLVDiWE~EGL 163 (165)
+++|+.+.+.|++.|.
T Consensus 28 ~~~ve~mL~~l~~kG~ 43 (69)
T PF09012_consen 28 PEAVEAMLEQLIRKGY 43 (69)
T ss_dssp HHHHHHHHHHHHCCTS
T ss_pred HHHHHHHHHHHHHCCc
Confidence 5789999999999884
No 7
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=27.59 E-value=47 Score=29.27 Aligned_cols=25 Identities=36% Similarity=0.701 Sum_probs=19.8
Q ss_pred chhhccCCCCC---------CCCCCChHHHHHHH
Q 031137 130 TYESLLGSNKP---------FPQPIPLSEMVDFL 154 (165)
Q Consensus 130 tye~LLgsn~p---------F~qPIPL~EMVdfL 154 (165)
.|+.+|+++.+ |+.||+|.|.++..
T Consensus 94 ~l~~~l~~~~~~~aildirEf~~pv~l~~~~~ai 127 (241)
T COG1709 94 ALARVLGSEFPSKAILDIREFDIPVTLEELVEAI 127 (241)
T ss_pred HHHHHhccCCchhheEehhhcCCCcCHHHHHHHh
Confidence 37777777655 99999999998753
No 8
>PF09791 Oxidored-like: Oxidoreductase-like protein, N-terminal; InterPro: IPR019180 This entry represents the N-terminal domain of various oxidoreductase-like proteins whose exact function is, as yet, unknown.
Probab=27.58 E-value=26 Score=23.55 Aligned_cols=8 Identities=50% Similarity=1.124 Sum_probs=4.4
Q ss_pred cCCCcccC
Q 031137 8 QSSGCLGC 15 (165)
Q Consensus 8 ~~gGC~Gc 15 (165)
||+||..|
T Consensus 19 CgSGC~~C 26 (48)
T PF09791_consen 19 CGSGCAPC 26 (48)
T ss_pred cccCCccc
Confidence 45566554
No 9
>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=25.33 E-value=21 Score=30.81 Aligned_cols=61 Identities=16% Similarity=0.213 Sum_probs=44.6
Q ss_pred CCcccCCC-CCCcccccCCCccccCCCCcccCCCCCCCCccccc-cccccCcccccccccccCCC
Q 031137 10 SGCLGCFI-RPPVNTSASNLSKELGVPGRSAGKRSISEDFWTTS-TCDMDNSAVQSQGSISSLGT 72 (165)
Q Consensus 10 gGC~Gc~~-Kp~~i~~vde~sKgl~~qg~~v~k~s~sedfWSsS-t~eMdns~~qSq~sisSis~ 72 (165)
|=||=||. .-..|.+||.- .|+.|-||++|-+..+ .||--. ..+||....+-|....+-..
T Consensus 78 GFaFLcYEDQRSTILAVDN~-NGiki~gRtirVDHv~-~Yk~pk~~E~~d~~t~~L~~~g~~~~~ 140 (219)
T KOG0126|consen 78 GFAFLCYEDQRSTILAVDNL-NGIKILGRTIRVDHVS-NYKKPKESEEMDAVTKELQEEGCSPKN 140 (219)
T ss_pred ceEEEEecCccceEEEEecc-CCceecceeEEeeecc-cccCCchhhhhhHHHHHHhhccCCCCc
Confidence 45999997 22348899975 6899999998777654 466664 78999988877776665543
No 10
>PRK07738 flagellar protein FlaG; Provisional
Probab=24.33 E-value=64 Score=25.26 Aligned_cols=22 Identities=23% Similarity=0.490 Sum_probs=20.0
Q ss_pred CCCChHHHHHHHHHHHhhcCCC
Q 031137 143 QPIPLSEMVDFLVDIWEQEGMY 164 (165)
Q Consensus 143 qPIPL~EMVdfLVDiWE~EGLy 164 (165)
+=||=.||+|++..+||--||.
T Consensus 91 RQIPpEe~L~l~~~m~e~~GlL 112 (117)
T PRK07738 91 REIPPKKLLDMYAAMMEFVGLL 112 (117)
T ss_pred eeCCCHHHHHHHHHHHHHhcce
Confidence 4599999999999999999985
No 11
>TIGR03487 cas_csp2 CRISPR-associated protein, Csp2 family. Members of this protein family are cas, or CRISPR-associated, proteins. The two sequences in the alignment seed are found within cas gene clusters that are adjacent to CRISPR DNA repeats in two members of the order Bacteroidales, Porphyromonas gingivalis W83 and Bacteroides forsythus ATCC 43037. This cas protein family is unique to the Pging (Porphyromonas gingivalis) subtype.
Probab=23.56 E-value=43 Score=31.34 Aligned_cols=13 Identities=54% Similarity=1.032 Sum_probs=11.1
Q ss_pred CCCChHHHHHHHH
Q 031137 143 QPIPLSEMVDFLV 155 (165)
Q Consensus 143 qPIPL~EMVdfLV 155 (165)
.-||+.|||||+.
T Consensus 180 pdipi~emvdfi~ 192 (489)
T TIGR03487 180 PDIPINEMVDFIA 192 (489)
T ss_pred cCCcHHHHHHHHH
Confidence 4699999999974
No 12
>cd03083 TRX_Fd_NuoE_hoxF TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, hoxF; composed of proteins similar to the NAD-reducing hydrogenase (hoxS) alpha subunit of Alcaligenes eutrophus H16. HoxS is a cytoplasmic hydrogenase catalyzing the oxidation of molecular hydrogen accompanied by the reduction of NAD. It is composed of four structural subunits encoded by the genes hoxF, hoxU, hoxY and hoxH. The hoxF protein (or alpha subunit) is a fusion protein containing an N-terminal NuoE-like domain and a C-terminal NuoF domain. NuoE and NuoF are components of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster in NuoE and the [4Fe-4S] cluster in NuoF. In addition, NuoF is also the NADH- and FMN-binding subunit. HoxF may be involved
Probab=23.13 E-value=37 Score=23.75 Aligned_cols=16 Identities=19% Similarity=0.353 Sum_probs=11.7
Q ss_pred CCcccCCCCCCcccccC
Q 031137 10 SGCLGCFIRPPVNTSAS 26 (165)
Q Consensus 10 gGC~Gc~~Kp~~i~~vd 26 (165)
-||+|.|.+.|. ..||
T Consensus 46 ~gClG~C~~~P~-v~V~ 61 (80)
T cd03083 46 TSCTGLCDQGPA-LLIN 61 (80)
T ss_pred eceecCcCCCCe-EEEC
Confidence 389999998874 4454
No 13
>PRK00809 hypothetical protein; Provisional
Probab=21.67 E-value=57 Score=25.88 Aligned_cols=17 Identities=29% Similarity=0.501 Sum_probs=14.2
Q ss_pred CCCCCCCChHHHHHHHH
Q 031137 139 KPFPQPIPLSEMVDFLV 155 (165)
Q Consensus 139 ~pF~qPIPL~EMVdfLV 155 (165)
+-|..||||.+|++-|.
T Consensus 97 ~~~~~~v~l~~L~~~L~ 113 (144)
T PRK00809 97 KIFEEPIDFKPLIPKLK 113 (144)
T ss_pred eecCCcccHHHHHhhhh
Confidence 55889999999988773
No 14
>PRK10610 chemotaxis regulatory protein CheY; Provisional
Probab=21.46 E-value=95 Score=19.92 Aligned_cols=26 Identities=23% Similarity=0.365 Sum_probs=22.1
Q ss_pred CCCCCCCCChHHHHHHHHHHHhhcCC
Q 031137 138 NKPFPQPIPLSEMVDFLVDIWEQEGM 163 (165)
Q Consensus 138 n~pF~qPIPL~EMVdfLVDiWE~EGL 163 (165)
..-+.+|+...++.+.|..+|+..|+
T Consensus 104 ~~~i~~p~~~~~l~~~l~~~~~~~~~ 129 (129)
T PRK10610 104 SGYVVKPFTAATLEEKLNKIFEKLGM 129 (129)
T ss_pred CeEEECCCCHHHHHHHHHHHHHHccC
Confidence 34567899999999999999998875
Done!