Query 022437
Match_columns 297
No_of_seqs 113 out of 139
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 03:32:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022437.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022437hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11891 DUF3411: Domain of un 100.0 1.4E-38 3E-43 281.8 8.3 87 161-247 93-179 (180)
2 PF02979 NHase_alpha: Nitrile 82.5 0.77 1.7E-05 42.1 1.8 44 117-160 16-67 (188)
3 COG4907 Predicted membrane pro 81.4 0.98 2.1E-05 46.8 2.3 8 28-35 551-558 (595)
4 PF02957 TT_ORF2: TT viral ORF 75.5 8.8 0.00019 31.9 5.9 20 85-104 100-119 (122)
5 TIGR01323 nitrile_alph nitrile 60.1 7 0.00015 35.9 2.4 44 117-160 10-61 (185)
6 PLN03138 Protein TOC75; Provis 56.6 19 0.00042 39.5 5.4 6 164-169 178-183 (796)
7 TIGR03793 TOMM_pelo TOMM prope 46.9 6.5 0.00014 31.1 0.0 17 144-160 14-30 (77)
8 PLN02705 beta-amylase 38.6 62 0.0013 35.0 5.6 9 109-117 97-105 (681)
9 KOG4096 Uncharacterized conser 37.7 5.1 0.00011 32.0 -1.8 56 186-241 16-71 (75)
10 PHA02629 A-type inclusion body 34.9 20 0.00043 27.3 1.0 23 88-110 27-49 (61)
11 KOG3074 Transcriptional regula 34.9 24 0.00052 33.9 1.8 8 229-236 199-206 (263)
12 PF07631 PSD4: Protein of unkn 34.6 38 0.00082 28.9 2.8 33 109-159 17-51 (128)
13 PF08671 SinI: Anti-repressor 33.3 41 0.00088 22.5 2.2 22 114-136 9-30 (30)
14 TIGR03795 chp_BMA0021 conserve 30.7 29 0.00063 29.7 1.5 17 144-160 25-41 (114)
15 PF14407 Frankia_peptide: Ribo 30.2 19 0.00041 27.8 0.2 14 146-159 12-25 (61)
16 KOG3973 Uncharacterized conser 30.1 39 0.00085 34.4 2.5 12 25-36 294-305 (465)
17 PF10247 Romo1: Reactive mitoc 26.6 46 0.001 26.0 1.8 52 185-240 15-66 (67)
18 PHA00370 III attachment protei 26.2 1.2E+02 0.0026 29.7 4.9 26 88-113 143-168 (297)
19 KOG1456 Heterogeneous nuclear 25.6 28 0.0006 35.8 0.5 11 112-122 46-56 (494)
20 PHA00370 III attachment protei 25.1 64 0.0014 31.6 2.8 7 241-247 256-262 (297)
21 TIGR02877 spore_yhbH sporulati 24.6 85 0.0018 31.8 3.7 11 92-102 115-125 (371)
22 PF12095 DUF3571: Protein of u 24.4 75 0.0016 25.9 2.7 27 91-117 24-50 (83)
23 PF10415 FumaraseC_C: Fumarase 23.0 1.1E+02 0.0025 22.5 3.3 39 94-135 12-50 (55)
24 COG3028 Uncharacterized protei 21.9 1.1E+02 0.0023 28.4 3.5 28 140-167 113-145 (187)
25 cd00086 homeodomain Homeodomai 21.8 2.2E+02 0.0049 19.3 4.5 42 93-134 8-50 (59)
26 PF12244 DUF3606: Protein of u 21.2 1.5E+02 0.0032 22.0 3.6 36 98-133 21-56 (57)
27 PF08535 KorB: KorB domain; I 20.8 69 0.0015 25.1 1.8 22 106-127 25-46 (93)
No 1
>PF11891 DUF3411: Domain of unknown function (DUF3411); InterPro: IPR021825 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 168 to 186 amino acids in length. This domain has a conserved RYQ sequence motif.
Probab=100.00 E-value=1.4e-38 Score=281.79 Aligned_cols=87 Identities=53% Similarity=0.833 Sum_probs=85.4
Q ss_pred hhccCCCCchhhhHHHHhhcchhhhhhhhhHhhHHHHHHHHHHHHHHhcCcCCCCCCCCCCchhhhhHHHHHhhcchhhH
Q 022437 161 VAFTGTSYSLIQRIGAIVRNGAKLFAVGTSASLVGVGITNALINARKALDTSFAGEAEDVPIISTSVAYGVYMAVSSNLR 240 (297)
Q Consensus 161 ~a~pg~~fsl~qR~aa~v~KGa~l~~VGf~aGlvG~glSN~L~a~RK~~dpsf~~~~~~pPil~tA~~wg~fMGvSSNlR 240 (297)
+++||++||++||++||+|||++|++|||+||++|+++||+|+++||++||+||+++++||+++||++||+|||+|||+|
T Consensus 93 ~~~~g~~fsl~qR~~~~~~kg~~l~~VG~~ag~vg~~lsn~L~~~rk~~~~~~e~~~~~ppv~~ta~~~g~fmGvSsNlR 172 (180)
T PF11891_consen 93 KGYPGRSFSLAQRIGAFVYKGAKLAAVGFIAGLVGTGLSNALIAARKKVDPSFEPSVPVPPVLKTALGWGAFMGVSSNLR 172 (180)
T ss_pred cCCCCCcccHHHHHHHHHHcchHhhhhHHHHHHHHHHHHHHHHHHHHhcCccccCCCCCCCHHHHHHHHHHHHhhhHhHH
Confidence 56799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhh
Q 022437 241 YQVLAGV 247 (297)
Q Consensus 241 YQiL~Gl 247 (297)
||+|||+
T Consensus 173 YQil~Gi 179 (180)
T PF11891_consen 173 YQILNGI 179 (180)
T ss_pred HHHHcCC
Confidence 9999998
No 2
>PF02979 NHase_alpha: Nitrile hydratase, alpha chain; InterPro: IPR004232 Nitrile hydratases (4.2.1.84 from EC) are bacterial enzymes that catalyse the hydration of nitrile compounds to the corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and are normally active as a tetramer, alpha(2)beta(2). Nitrile hydratases contain either a non-haem iron or a non-corrinoid cobalt centre, both types sharing a highly conserved peptide sequence in the alpha subunit (CXLCSC) that provides all the residues involved in coordinating the metal ion. Each type of nitrile hydratase specifically incorporated its metal with the help of activator proteins encoded by flanking regions of the nitrile hydratase genes that are necessary for metal insertion. The Fe-containing enzyme is photo-regulated: in the dark the enzyme is inactivated due to the association of nitric oxide (NO) to the iron, while in the light the enzyme is active by photo-dissociation of NO. The NO is held in place by a claw setting formed through specific oxygen atoms in two modified cysteines and a serine residue in the active site [, ]. The cobalt-containing enzyme is unaffected by NO, but was shown to undergo a similar effect with carbon monoxide [, ]. Fe- and cobalt-containing enzymes also display different inhibition patterns with nitrophenols. Thiocyanate hydrolase (SCNase) is a cobalt-containing metalloenzyme with a cysteine-sulphinic acid ligand that hydrolyses thiocyanate to carbonyl sulphide and ammonia []. The two enzymes, nitrile hydratase and SCNase, are homologous over regions corresponding to almost the entire coding regions of the genes: the beta and alpha subunits of thiocyanate hydrolase were homologous to the amino- and carboxyl-terminal halves of the beta subunit of nitrile hydratase, and the gamma subunit of thiocyanate hydrolase was homologous to the alpha subunit of nitrile hydratase []. This entry represents the structural domain of the alpha subunit of both iron- and cobalt-containing nitrile hydratases; the alpha subunit is a duplication of two structural repeats, each consisting of 4 layers, alpha/beta/beta/alpha []. This structure is also found in the related protein, the gamma subunit of thiocyanate hydrolase (SCNase).; GO: 0003824 catalytic activity, 0046914 transition metal ion binding, 0006807 nitrogen compound metabolic process; PDB: 2DPP_A 3HHT_A 1V29_A 2ZZD_I 2DXC_F 2DXB_F 2DD5_C 2DD4_C 2ZPH_A 2CYZ_A ....
Probab=82.52 E-value=0.77 Score=42.10 Aligned_cols=44 Identities=36% Similarity=0.395 Sum_probs=31.7
Q ss_pred HHHcCCCCHHHHHHHHhcccc---hh--hHhhhh---ccchhhhhccchhhh
Q 022437 117 AIEAGRVPAAIVKRYLELEKS---PV--FRWLLN---FGGFRERLLADDLFL 160 (297)
Q Consensus 117 A~e~G~Vs~~~L~rfl~l~~~---p~--~~~l~r---f~gfR~RlLADP~FL 160 (297)
-+|.|.|+++.+.++.+...+ |- .+.+.| -|+||+|||+||.=.
T Consensus 16 l~ekg~~~~~~~~~~~~~~~~~~~P~~GarvVArAW~Dp~FK~rLLaD~~aA 67 (188)
T PF02979_consen 16 LIEKGLITPAEVDRIIETYESRVGPRNGARVVARAWTDPAFKARLLADPTAA 67 (188)
T ss_dssp HHHTTSS-HHHHHHHHHHHHHTSSHHHHHHHHHHHHH-HHHHHHHHHSHHHH
T ss_pred HHHcCCCCHHHHHHHHHHHHhccCccccceeehhhhCCHHHHHHHHHCHHHH
Confidence 368999999999998887654 43 123333 499999999999855
No 3
>COG4907 Predicted membrane protein [Function unknown]
Probab=81.43 E-value=0.98 Score=46.79 Aligned_cols=8 Identities=25% Similarity=0.434 Sum_probs=3.4
Q ss_pred eccccCCC
Q 022437 28 KNITRQIP 35 (297)
Q Consensus 28 ~~~~~~~~ 35 (297)
||-+|--.
T Consensus 551 ~nysr~~~ 558 (595)
T COG4907 551 NNYSRSFN 558 (595)
T ss_pred cchhhhhc
Confidence 44444433
No 4
>PF02957 TT_ORF2: TT viral ORF2; InterPro: IPR004118 This entry represents the Gyroviral VP2 protein and TT viral ORF2. Torque teno virus (TTV) is a nonenveloped and single-stranded DNA virus that was initially isolated from a Japanese patient with hepatitis of unknown aetiology, and which has since been found to infect both healthy and diseased individuals []. Numerous prevalence studies have raised questions about its role in unexplained hepatitis. ORF2 is a 150 residue protein of unknown function. Gyroviruses are small circular single stranded viruses, such as the Chicken anaemia virus. The VP2 protein contains a set of conserved cysteine and histidine residues suggesting a zinc binding domain. VP2 may act as a scaffold protein in virion assembly and may also play a role in intracellular signaling during viral replication.
Probab=75.54 E-value=8.8 Score=31.86 Aligned_cols=20 Identities=10% Similarity=-0.102 Sum_probs=13.0
Q ss_pred CCCCCCCCHHHHHHHHHHhc
Q 022437 85 DDDAGFHNCTEAIFALAKAG 104 (297)
Q Consensus 85 ~~~~~~~~r~ei~~Vl~e~g 104 (297)
.+.+++.+-++++++++++.
T Consensus 100 ~~~~ed~~~~dld~L~aa~~ 119 (122)
T PF02957_consen 100 EAAGEDYDEEDLDELFAAAA 119 (122)
T ss_pred cccccCCChHHHHHHhhhhh
Confidence 33455777777877777653
No 5
>TIGR01323 nitrile_alph nitrile hydratase, alpha subunit. This model describes both iron- and cobalt-containing nitrile hydratase alpha chains. It excludes the thiocyanate hydrolase gamma subunit of Thiobacillus thioparus, a sequence that appears to have evolved from within the family of nitrile hydratase alpha subunits but which differs by several indels and a more rapid accumulation of point mutations.
Probab=60.09 E-value=7 Score=35.91 Aligned_cols=44 Identities=23% Similarity=0.257 Sum_probs=32.1
Q ss_pred HHHcCCCCHHHHHHHHhcccc---hh--hHhhhh---ccchhhhhccchhhh
Q 022437 117 AIEAGRVPAAIVKRYLELEKS---PV--FRWLLN---FGGFRERLLADDLFL 160 (297)
Q Consensus 117 A~e~G~Vs~~~L~rfl~l~~~---p~--~~~l~r---f~gfR~RlLADP~FL 160 (297)
-+|.|.|+++.+.+.++.... |. .+.+.| -|.||.|||+|..=-
T Consensus 10 l~eKGli~~~~id~~i~~~~~~~gP~nGA~vVArAW~Dp~fk~~Ll~d~~aa 61 (185)
T TIGR01323 10 LKSKGLIPEGAVDQLTSLYENEWGPENGAKVVAKAWVDPEFRALLLKDATAA 61 (185)
T ss_pred HHHcCCCCHHHHHHHHHHHHhccCCcchhhhhhHHhcCHHHHHHHHhChHHH
Confidence 368999999999888876544 43 223333 499999999998743
No 6
>PLN03138 Protein TOC75; Provisional
Probab=56.58 E-value=19 Score=39.45 Aligned_cols=6 Identities=33% Similarity=0.772 Sum_probs=2.7
Q ss_pred cCCCCc
Q 022437 164 TGTSYS 169 (297)
Q Consensus 164 pg~~fs 169 (297)
||..|+
T Consensus 178 pG~v~t 183 (796)
T PLN03138 178 PGGVYT 183 (796)
T ss_pred CCCccC
Confidence 444444
No 7
>TIGR03793 TOMM_pelo TOMM propeptide domain. This model represents a domain that is conserved among a large number of putative thiazole/oxazole-modified microcins (TOMM). Oddly, most of this seqence region appears homologous to nitrile hydratase subunits. This family is expanded especially in Pelotomaculum thermopropionicum SI.
Probab=46.92 E-value=6.5 Score=31.11 Aligned_cols=17 Identities=18% Similarity=0.180 Sum_probs=14.0
Q ss_pred hhccchhhhhccchhhh
Q 022437 144 LNFGGFRERLLADDLFL 160 (297)
Q Consensus 144 ~rf~gfR~RlLADP~FL 160 (297)
+.-+.||.|||+||.=.
T Consensus 14 w~Dp~Fr~~Ll~DPraa 30 (77)
T TIGR03793 14 WEDEAFKQALLTNPKEA 30 (77)
T ss_pred HcCHHHHHHHHHCHHHH
Confidence 34699999999999843
No 8
>PLN02705 beta-amylase
Probab=38.58 E-value=62 Score=35.02 Aligned_cols=9 Identities=0% Similarity=0.187 Sum_probs=3.5
Q ss_pred CchHHHHHH
Q 022437 109 DLPKDLAGA 117 (297)
Q Consensus 109 sLP~Dl~~A 117 (297)
.+-+.|-.+
T Consensus 97 ai~~ki~ag 105 (681)
T PLN02705 97 AITSRMLAG 105 (681)
T ss_pred HHHHHHHHH
Confidence 333334333
No 9
>KOG4096 consensus Uncharacterized conserved protein [Function unknown]
Probab=37.74 E-value=5.1 Score=31.97 Aligned_cols=56 Identities=11% Similarity=0.176 Sum_probs=30.4
Q ss_pred hhhhhHhhHHHHHHHHHHHHHHhcCcCCCCCCCCCCchhhhhHHHHHhhcchhhHH
Q 022437 186 AVGTSASLVGVGITNALINARKALDTSFAGEAEDVPIISTSVAYGVYMAVSSNLRY 241 (297)
Q Consensus 186 ~VGf~aGlvG~glSN~L~a~RK~~dpsf~~~~~~pPil~tA~~wg~fMGvSSNlRY 241 (297)
.+|+..|..-.++=-....+|-.+.+.---...-.-++.++.++|+||++-+-+||
T Consensus 16 ~mG~avG~a~G~lfGgf~~lR~g~~g~~~vr~iGkt~~~SagtFG~FM~igs~Ir~ 71 (75)
T KOG4096|consen 16 MMGGAVGGATGALFGGFAALRYGPRGRGLVRTIGKTMLQSAGTFGLFMGIGSGIRC 71 (75)
T ss_pred HHHhhhhhhhhhhccchhheeecCChhHHHHHHhHHHHhccchhhhhhhhhhheec
Confidence 34444443333333344455555433210001122366777899999999998887
No 10
>PHA02629 A-type inclusion body protein; Provisional
Probab=34.94 E-value=20 Score=27.27 Aligned_cols=23 Identities=4% Similarity=-0.054 Sum_probs=15.8
Q ss_pred CCCCCHHHHHHHHHHhccccCCc
Q 022437 88 AGFHNCTEAIFALAKAGRTLGDL 110 (297)
Q Consensus 88 ~~~~~r~ei~~Vl~e~gr~~~sL 110 (297)
.-+++|+.|.-.-+|.-|.|+.+
T Consensus 27 ~c~ferk~iavleaelr~~meti 49 (61)
T PHA02629 27 SCEFERKIIAVLEAELRKSMETI 49 (61)
T ss_pred hhHhhHHHHHHHHHHHHHHHHHH
Confidence 56788888776666666666553
No 11
>KOG3074 consensus Transcriptional regulator of the PUR family, single-stranded-DNA-binding [Transcription]
Probab=34.88 E-value=24 Score=33.94 Aligned_cols=8 Identities=38% Similarity=0.816 Sum_probs=3.8
Q ss_pred HHHHhhcc
Q 022437 229 YGVYMAVS 236 (297)
Q Consensus 229 wg~fMGvS 236 (297)
||.||=+|
T Consensus 199 ~G~f~riS 206 (263)
T KOG3074|consen 199 RGVFVRIS 206 (263)
T ss_pred ccceEEEE
Confidence 44555444
No 12
>PF07631 PSD4: Protein of unknown function (DUF1592); InterPro: IPR013042 A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also contain IPR011478 from INTERPRO, IPR013036 from INTERPRO, IPR013039 from INTERPRO and IPR013043 from INTERPRO.
Probab=34.58 E-value=38 Score=28.86 Aligned_cols=33 Identities=30% Similarity=0.379 Sum_probs=23.3
Q ss_pred Cch-HHHHHHHHcCCC-CHHHHHHHHhcccchhhHhhhhccchhhhhccchhh
Q 022437 109 DLP-KDLAGAIEAGRV-PAAIVKRYLELEKSPVFRWLLNFGGFRERLLADDLF 159 (297)
Q Consensus 109 sLP-~Dl~~A~e~G~V-s~~~L~rfl~l~~~p~~~~l~rf~gfR~RlLADP~F 159 (297)
+.| +.|.+|++.|.+ +++++ ..-.+|||+||++
T Consensus 17 s~PD~~L~~aA~~g~L~~~~~l------------------~~q~~RML~dpr~ 51 (128)
T PF07631_consen 17 SPPDAELLDAAAAGELRTPEQL------------------RAQAERMLADPRA 51 (128)
T ss_pred CCCCHHHHHHHHhCCCCCHHHH------------------HHHHHHHHcCccH
Confidence 455 678888888887 44443 3346899999976
No 13
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=33.30 E-value=41 Score=22.50 Aligned_cols=22 Identities=23% Similarity=0.451 Sum_probs=15.5
Q ss_pred HHHHHHcCCCCHHHHHHHHhccc
Q 022437 114 LAGAIEAGRVPAAIVKRYLELEK 136 (297)
Q Consensus 114 l~~A~e~G~Vs~~~L~rfl~l~~ 136 (297)
|.+|.++ ++|.+.+.+||+.++
T Consensus 9 i~eA~~~-Gls~eeir~FL~~~k 30 (30)
T PF08671_consen 9 IKEAKES-GLSKEEIREFLEFNK 30 (30)
T ss_dssp HHHHHHT-T--HHHHHHHHHHHH
T ss_pred HHHHHHc-CCCHHHHHHHHHhCC
Confidence 5677666 589999999998753
No 14
>TIGR03795 chp_BMA0021 conserved hypothetical protein, BMA_0021 family. Members of this protein family are found sparsely, mostly in members of the genus Burkholderia. Members often occur as tandem homologous genes, such as BMA_0021 and BMA_0022 in Burkholderia mallei ATCC 23344. The genes regularly are encoded near the so-called docking protein of TOMM (thiazole/oxazole-modified microcins) biosynthetic clusters, suggesting a role in bacteriocin biosynthesis. The function is unknown.
Probab=30.75 E-value=29 Score=29.65 Aligned_cols=17 Identities=29% Similarity=0.366 Sum_probs=14.3
Q ss_pred hhccchhhhhccchhhh
Q 022437 144 LNFGGFRERLLADDLFL 160 (297)
Q Consensus 144 ~rf~gfR~RlLADP~FL 160 (297)
.+.+.||+|||+||.=.
T Consensus 25 W~DpaFr~eLl~DPk~~ 41 (114)
T TIGR03795 25 WHSPEFKDELLADPVDA 41 (114)
T ss_pred hCCHHHHHHHHHCHHHH
Confidence 35799999999999854
No 15
>PF14407 Frankia_peptide: Ribosomally synthesized peptide prototyped by Frankia Franean1_4349.
Probab=30.24 E-value=19 Score=27.83 Aligned_cols=14 Identities=43% Similarity=0.425 Sum_probs=12.1
Q ss_pred ccchhhhhccchhh
Q 022437 146 FGGFRERLLADDLF 159 (297)
Q Consensus 146 f~gfR~RlLADP~F 159 (297)
-++||.||+|||.-
T Consensus 12 D~~FRqqllad~~~ 25 (61)
T PF14407_consen 12 DEAFRQQLLADPEE 25 (61)
T ss_pred CHHHHHHHhcCHHH
Confidence 48899999999986
No 16
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=30.10 E-value=39 Score=34.41 Aligned_cols=12 Identities=17% Similarity=-0.031 Sum_probs=6.5
Q ss_pred ceeeccccCCCC
Q 022437 25 FVIKNITRQIPN 36 (297)
Q Consensus 25 ~~~~~~~~~~~~ 36 (297)
.|-+.|-|.|..
T Consensus 294 i~k~~igrvPDR 305 (465)
T KOG3973|consen 294 IHKLSIGRVPDR 305 (465)
T ss_pred hcccccccCCCC
Confidence 344456666653
No 17
>PF10247 Romo1: Reactive mitochondrial oxygen species modulator 1; InterPro: IPR018450 The majority of endogenous reactive oxygen species (ROS) in cells are produced by the mitochondrial respiratory chain. An increase or imbalance in ROS alters the intracellular redox homeostasis, triggers DNA damage, and may contribute to cancer development and progression. This entry contains the mitochondrial protein, reactive oxygen species modulator 1 (Romo1), that is responsible for increasing the level of ROS in cells. In various cancer cell lines with elevated levels of ROS there is also an increased abundance of Romo1 []. Increased Romo1 expression can have a number of other affects including: inducing premature senescence of cultured human fibroblasts [, ] and increased resistance to 5-fluorouracil [].
Probab=26.64 E-value=46 Score=26.01 Aligned_cols=52 Identities=15% Similarity=0.126 Sum_probs=30.4
Q ss_pred hhhhhhHhhHHHHHHHHHHHHHHhcCcCCCCCCCCCCchhhhhHHHHHhhcchhhH
Q 022437 185 FAVGTSASLVGVGITNALINARKALDTSFAGEAEDVPIISTSVAYGVYMAVSSNLR 240 (297)
Q Consensus 185 ~~VGf~aGlvG~glSN~L~a~RK~~dpsf~~~~~~pPil~tA~~wg~fMGvSSNlR 240 (297)
++||.+.|++-.. ....|....+..--.....-++.++.++|.||++=+=+|
T Consensus 15 ~~VG~~~G~l~G~----~~~~r~g~~~~~~~~~lg~~~l~sg~tFG~Fm~iGs~IR 66 (67)
T PF10247_consen 15 GAVGGAFGALFGT----FSAFRYGARGRGLMRTLGKYMLGSGATFGFFMSIGSVIR 66 (67)
T ss_pred hHHHhhhhhhhhh----HHHhccCCCCcchHhHHhHHHhcchhHHHHHHhhhcccc
Confidence 4455555555444 345555554432111233456778899999999877655
No 18
>PHA00370 III attachment protein
Probab=26.17 E-value=1.2e+02 Score=29.73 Aligned_cols=26 Identities=19% Similarity=-0.072 Sum_probs=11.3
Q ss_pred CCCCCHHHHHHHHHHhccccCCchHH
Q 022437 88 AGFHNCTEAIFALAKAGRTLGDLPKD 113 (297)
Q Consensus 88 ~~~~~r~ei~~Vl~e~gr~~~sLP~D 113 (297)
.+++|-..+.-..+.+-..-.+.-++
T Consensus 143 s~d~d~~kma~a~kdaltE~~d~~~~ 168 (297)
T PHA00370 143 AGDFDYPKMANANKDALTEDNDQNAL 168 (297)
T ss_pred ccccccHHHhhhhhhhhccccccchh
Confidence 34555555544444433333333333
No 19
>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]
Probab=25.59 E-value=28 Score=35.77 Aligned_cols=11 Identities=27% Similarity=0.199 Sum_probs=6.9
Q ss_pred HHHHHHHHcCC
Q 022437 112 KDLAGAIEAGR 122 (297)
Q Consensus 112 ~Dl~~A~e~G~ 122 (297)
+|+.+|++.++
T Consensus 46 adl~eal~~fG 56 (494)
T KOG1456|consen 46 ADLVEALSNFG 56 (494)
T ss_pred hHHHHHHhcCC
Confidence 56777766554
No 20
>PHA00370 III attachment protein
Probab=25.12 E-value=64 Score=31.55 Aligned_cols=7 Identities=29% Similarity=0.866 Sum_probs=4.7
Q ss_pred HHHHhhh
Q 022437 241 YQVLAGV 247 (297)
Q Consensus 241 YQiL~Gl 247 (297)
||+..+-
T Consensus 256 Ye~~I~C 262 (297)
T PHA00370 256 YEFIIGC 262 (297)
T ss_pred hhhhhcc
Confidence 6777665
No 21
>TIGR02877 spore_yhbH sporulation protein YhbH. This protein family, typified by YhbH in Bacillus subtilis, is found in nearly every endospore-forming bacterium and in no other genome (but note that the trusted cutoff score is set high to exclude a single high-scoring sequence from Nitrosococcus oceani ATCC 19707, which is classified in the Gammaproteobacteria). The gene in Bacillus subtilis was shown to be in the regulon of the sporulation sigma factor, sigma-E, and its mutation was shown to create a sporulation defect.
Probab=24.64 E-value=85 Score=31.77 Aligned_cols=11 Identities=18% Similarity=0.005 Sum_probs=6.5
Q ss_pred CHHHHHHHHHH
Q 022437 92 NCTEAIFALAK 102 (297)
Q Consensus 92 ~r~ei~~Vl~e 102 (297)
.++|+..+|=|
T Consensus 115 s~eE~~~~lfE 125 (371)
T TIGR02877 115 TLEELFELLFE 125 (371)
T ss_pred cHHHHHHHHHh
Confidence 46666666544
No 22
>PF12095 DUF3571: Protein of unknown function (DUF3571); InterPro: IPR021954 This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 85 to 97 amino acids in length. ; PDB: 2KRX_A.
Probab=24.44 E-value=75 Score=25.87 Aligned_cols=27 Identities=30% Similarity=0.212 Sum_probs=21.7
Q ss_pred CCHHHHHHHHHHhccccCCchHHHHHH
Q 022437 91 HNCTEAIFALAKAGRTLGDLPKDLAGA 117 (297)
Q Consensus 91 ~~r~ei~~Vl~e~gr~~~sLP~Dl~~A 117 (297)
-..+|..+-|++|-.+.++||.|+++-
T Consensus 24 lt~~Ell~~Lk~~L~~~~~LP~dL~~~ 50 (83)
T PF12095_consen 24 LTPEELLEKLKEWLQNQDDLPPDLAKF 50 (83)
T ss_dssp E-HHHHHHHHHHHHHHTTTS-HHHHH-
T ss_pred CCHHHHHHHHHHHHHcCCCCCHHHHhC
Confidence 356899999999999999999999853
No 23
>PF10415 FumaraseC_C: Fumarase C C-terminus; InterPro: IPR018951 Fumarase C catalyses the stereo-specific interconversion of fumarate to L-malate as part of the Krebs cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The core of the molecule consists of a bundle of 20 alpha-helices from the five-helix bundle of domain 2. The projections from the core of the tetramer are generated from domains 1 and 3 of each subunit []. This entry does not appear to be part of either the active site or the activation site but is helical in structure forming a little bundle. ; GO: 0016829 lyase activity, 0006099 tricarboxylic acid cycle; PDB: 3RRP_A 3OCE_D 3OCF_D 3E04_B 3GTD_A 3R6V_F 3R6Q_F 1J3U_B 1FUR_A 1YFE_A ....
Probab=23.04 E-value=1.1e+02 Score=22.47 Aligned_cols=39 Identities=15% Similarity=0.088 Sum_probs=28.1
Q ss_pred HHHHHHHHHhccccCCchHHHHHHHHcCCCCHHHHHHHHhcc
Q 022437 94 TEAIFALAKAGRTLGDLPKDLAGAIEAGRVPAAIVKRYLELE 135 (297)
Q Consensus 94 ~ei~~Vl~e~gr~~~sLP~Dl~~A~e~G~Vs~~~L~rfl~l~ 135 (297)
+.+.++-+++.++..++..- +++.|.++.+++.+.|+.+
T Consensus 12 e~aa~iAk~A~~~g~svre~---v~~~g~lt~ee~d~ll~p~ 50 (55)
T PF10415_consen 12 EKAAEIAKEALAEGRSVREV---VLEEGLLTEEELDELLDPE 50 (55)
T ss_dssp HHHHHHHHHHHHHT--HHHH---HHHTTSS-HHHHHHHTSHH
T ss_pred HHHHHHHHHHHHcCCCHHHH---HHHcCCCCHHHHHHHcCHH
Confidence 45667788888888887643 4588999999999999865
No 24
>COG3028 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.95 E-value=1.1e+02 Score=28.42 Aligned_cols=28 Identities=25% Similarity=0.478 Sum_probs=21.1
Q ss_pred hHhhhhccchhhhhccc-----hhhhhhccCCC
Q 022437 140 FRWLLNFGGFRERLLAD-----DLFLVAFTGTS 167 (297)
Q Consensus 140 ~~~l~rf~gfR~RlLAD-----P~FL~a~pg~~ 167 (297)
...|++---+|+||+|| +.||-.+|-.+
T Consensus 113 ~a~lHklE~~RdrLia~GD~Alt~~l~~~P~aD 145 (187)
T COG3028 113 VALLHKLEQLRDRLIAEGDGALTEFLNQYPDAD 145 (187)
T ss_pred HHHHHHHHHHHHHHHhcCchHHHHHHHHCCccc
Confidence 34566678899999999 66777777544
No 25
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=21.78 E-value=2.2e+02 Score=19.34 Aligned_cols=42 Identities=12% Similarity=-0.012 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhccccCCch-HHHHHHHHcCCCCHHHHHHHHhc
Q 022437 93 CTEAIFALAKAGRTLGDLP-KDLAGAIEAGRVPAAIVKRYLEL 134 (297)
Q Consensus 93 r~ei~~Vl~e~gr~~~sLP-~Dl~~A~e~G~Vs~~~L~rfl~l 134 (297)
-++...+|.+|+..-.... .++.+-++.-.++..++..||.-
T Consensus 8 ~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~n 50 (59)
T cd00086 8 TPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQN 50 (59)
T ss_pred CHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence 3566788999998855433 56777777777999999998863
No 26
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=21.21 E-value=1.5e+02 Score=21.96 Aligned_cols=36 Identities=22% Similarity=0.297 Sum_probs=30.1
Q ss_pred HHHHHhccccCCchHHHHHHHHcCCCCHHHHHHHHh
Q 022437 98 FALAKAGRTLGDLPKDLAGAIEAGRVPAAIVKRYLE 133 (297)
Q Consensus 98 ~Vl~e~gr~~~sLP~Dl~~A~e~G~Vs~~~L~rfl~ 133 (297)
.-++-|.+++.-=++.|++|++.-+-+.+.+.+||.
T Consensus 21 ~ev~ywa~~~gvt~~~L~~AV~~vG~~~~~V~~~L~ 56 (57)
T PF12244_consen 21 YEVRYWAKRFGVTEEQLREAVRAVGNSRAAVRAYLG 56 (57)
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHHCcCHHHHHHHHc
Confidence 345677777777789999999999999999999874
No 27
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=20.77 E-value=69 Score=25.10 Aligned_cols=22 Identities=27% Similarity=0.557 Sum_probs=14.2
Q ss_pred ccCCchHHHHHHHHcCCCCHHH
Q 022437 106 TLGDLPKDLAGAIEAGRVPAAI 127 (297)
Q Consensus 106 ~~~sLP~Dl~~A~e~G~Vs~~~ 127 (297)
++.+||.+++++++.|.|+...
T Consensus 25 ~Ll~lP~~i~~~v~~g~~~~~~ 46 (93)
T PF08535_consen 25 ALLDLPEEIKELVRSGRISDIR 46 (93)
T ss_dssp GGGS--HHHHHHHHTTS---HH
T ss_pred HHHcCCHHHHHHHHcCCCchHH
Confidence 3668999999999999997543
Done!