Query 039261
Match_columns 182
No_of_seqs 134 out of 681
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 07:55:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039261.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039261hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3326 Uncharacterized conser 100.0 2.6E-28 5.6E-33 197.2 11.5 145 9-156 4-151 (154)
2 PF03937 Sdh5: Flavinator of s 99.9 6.7E-28 1.5E-32 173.5 7.3 73 67-144 2-74 (74)
3 COG2938 Uncharacterized conser 99.9 4.1E-26 8.8E-31 172.7 10.1 73 68-146 16-88 (94)
4 PRK10878 hypothetical protein; 99.8 4.6E-21 1E-25 138.7 8.6 62 79-145 1-62 (72)
5 PRK09458 pspB phage shock prot 65.1 5.7 0.00012 29.4 2.3 16 100-115 56-71 (75)
6 PF14261 DUF4351: Domain of un 58.0 14 0.00029 25.7 3.1 32 89-120 26-59 (59)
7 smart00389 HOX Homeodomain. DN 54.8 21 0.00046 22.7 3.5 42 81-124 11-52 (56)
8 PF13168 Poxvirus_B22R_C: Poxv 52.8 17 0.00038 31.3 3.5 42 114-162 49-92 (197)
9 PF05024 Gpi1: N-acetylglucosa 49.9 39 0.00084 28.3 5.1 60 81-143 10-73 (189)
10 TIGR02976 phageshock_pspB phag 43.0 30 0.00066 25.3 3.0 17 99-115 55-71 (75)
11 COG3095 MukE Uncharacterized p 42.6 89 0.0019 27.3 6.2 64 79-149 86-159 (238)
12 PF06667 PspB: Phage shock pro 40.9 34 0.00075 25.1 3.0 16 100-115 56-71 (75)
13 PF07130 YebG: YebG protein; 38.0 1E+02 0.0022 22.9 5.1 42 79-120 31-72 (75)
14 COG3141 DNA damage-inducible g 35.3 91 0.002 24.1 4.7 47 77-123 29-75 (97)
15 PRK03573 transcriptional regul 35.2 76 0.0016 24.2 4.4 31 81-111 102-132 (144)
16 PF03965 Penicillinase_R: Peni 34.2 1.3E+02 0.0029 22.4 5.5 51 56-111 65-115 (115)
17 cd00086 homeodomain Homeodomai 33.2 83 0.0018 19.9 3.7 39 85-124 14-52 (59)
18 PF00046 Homeobox: Homeobox do 32.2 88 0.0019 20.1 3.7 37 85-122 14-50 (57)
19 PRK10061 DNA damage-inducible 29.2 1.5E+02 0.0033 23.0 5.0 47 77-123 29-75 (96)
20 PF08621 RPAP1_N: RPAP1-like, 28.7 88 0.0019 21.1 3.3 34 92-125 10-44 (49)
21 PF14024 DUF4240: Protein of u 27.0 2.8E+02 0.006 21.5 6.3 52 86-144 24-83 (128)
22 PF13618 Gluconate_2-dh3: Gluc 26.9 2.5E+02 0.0054 21.0 5.9 80 75-167 49-128 (131)
23 cd00093 HTH_XRE Helix-turn-hel 26.5 1.4E+02 0.003 17.2 4.2 25 103-127 16-40 (58)
24 PHA01976 helix-turn-helix prot 25.5 1.7E+02 0.0036 19.3 4.3 30 95-127 14-43 (67)
25 PRK05256 condesin subunit E; P 24.8 3E+02 0.0065 24.5 6.7 66 77-149 86-161 (238)
26 PF11239 DUF3040: Protein of u 24.4 1.1E+02 0.0025 21.9 3.5 31 96-126 2-35 (82)
27 TIGR03830 CxxCG_CxxCG_HTH puta 24.4 2.9E+02 0.0064 20.3 7.5 29 96-127 78-106 (127)
28 PF00486 Trans_reg_C: Transcri 24.1 2.2E+02 0.0048 18.8 6.2 51 96-150 5-60 (77)
29 cd08767 Cdt1_c The C-terminal 23.8 1.5E+02 0.0032 23.2 4.3 50 70-122 52-101 (126)
30 PHA00542 putative Cro-like pro 23.2 2E+02 0.0044 20.5 4.6 42 96-145 31-73 (82)
31 KOG3888 Gamma-butyrobetaine,2- 22.6 90 0.0019 29.7 3.2 51 56-121 108-158 (407)
32 cd00383 trans_reg_C Effector d 21.6 2.8E+02 0.006 19.0 6.1 51 96-150 23-78 (95)
33 smart00530 HTH_XRE Helix-turn- 20.4 1.8E+02 0.004 16.5 4.2 24 104-127 15-38 (56)
No 1
>KOG3326 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.95 E-value=2.6e-28 Score=197.20 Aligned_cols=145 Identities=29% Similarity=0.406 Sum_probs=119.8
Q ss_pred hhhhhhcCCcccccccccccCCCcccccccccccccc-ccccccccCCCCCcHHHHHHHHHHHHHHhhccchhHHHHhHH
Q 039261 9 INVHRILRSSAVANRSSIASASPAASFETLLRPQYRW-VSNTTQSLDIDLSNDEKKKRLFNRLLYRSKQRGFLELDLVLG 87 (182)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-f~~~~~~~~~~~s~~E~krrl~kRL~wRc~rRGmlELDLLLg 87 (182)
+++||.++.+++...+++++++..+.+..+|+..--. +....+....+.++.|.|| +||+|||++|||+|+|||||
T Consensus 4 ~~~~~~~~~s~~~~~~~~~p~~a~t~~r~i~r~~~~~~~~~~~~~~~r~~e~~etkr---aRLlYqSrKRGiLEnDLLLs 80 (154)
T KOG3326|consen 4 INMHRSRSLSNLKGRSSTSPAAANTSYRIIFRYDDPDENLPSPEYPKRPNEPLETKR---ARLLYQSRKRGILENDLLLS 80 (154)
T ss_pred hhhHHHHHhhhhcccCCCCchhhccccceeeeCCCCcccccCCcccCCCCchhHHHH---HHHHHHHhhcchhHHHHHHH
Confidence 7889999999999888888766555444444331111 2223334556677778877 59999999999999999999
Q ss_pred HHHHHHhcCCCHHHHHHHHHHhcCC--CHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHHHhhhhcCCCCCC
Q 039261 88 KWVEEHIHSMDENGIKALVDVLNLE--NPDLWKWLTGQEQPPEAVKTNPVFSALHNKVMNNLNSYASPETR 156 (182)
Q Consensus 88 ~F~~~~l~~Lse~el~~Fe~LLd~e--D~DLy~Wl~G~~~pPe~~~~d~~~~~Li~~Ir~~~~~~~~~e~r 156 (182)
.|+++|+.+|+++|+.+|++||+.+ |||||+|+++++++|+.++++++|+.|.++++++...|..+.+.
T Consensus 81 ~Fa~~~l~~m~e~~l~~YD~LiN~~~~dWDi~YWaTe~kp~Pe~~~s~~V~~~L~e~v~n~~r~~~lr~pd 151 (154)
T KOG3326|consen 81 NFAAKNLKKMSEEQLKEYDQLINEESNDWDIYYWATETKPPPEKVESSEVFKLLKEFVKNKERVHRLRMPD 151 (154)
T ss_pred HHHHHHHHhCCHHHHHHHHHHhcCCcCCchhhhhhccCCCCchhhhhHHHHHHHHHHHHhhhhcccccCcc
Confidence 9999999999999999999999998 99999999999999999999999999999999987777776644
No 2
>PF03937 Sdh5: Flavinator of succinate dehydrogenase; InterPro: IPR005631 This entry represents a group of uncharacterised small proteins found in both eukaryotes and prokaryotes, including NMA1147 from Neisseria meningitidis [] and YgfY from Escherichia coli []. YgfY may be involved in transcriptional regulation. The structure of these proteins consists of a complex bundle of five alpha-helices, which is composed of an up-down 3-helix bundle plus an orthogonal 2-helix bundle. ; PDB: 2LM4_A 1PUZ_A 2JR5_A 1X6I_A 1X6J_A.
Probab=99.95 E-value=6.7e-28 Score=173.51 Aligned_cols=73 Identities=44% Similarity=0.884 Sum_probs=64.8
Q ss_pred HHHHHHHhhccchhHHHHhHHHHHHHHhcCCCHHHHHHHHHHhcCCCHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHH
Q 039261 67 FNRLLYRSKQRGFLELDLVLGKWVEEHIHSMDENGIKALVDVLNLENPDLWKWLTGQEQPPEAVKTNPVFSALHNKVM 144 (182)
Q Consensus 67 ~kRL~wRc~rRGmlELDLLLg~F~~~~l~~Lse~el~~Fe~LLd~eD~DLy~Wl~G~~~pPe~~~~d~~~~~Li~~Ir 144 (182)
++||+|||+||||+|||+|||+|+++++++|+++|+++|+.||+++|+|||+|++|+++|| +...+.|+++|+
T Consensus 2 ~kRl~~r~~rRG~~ElDllL~~f~~~~~~~l~~~el~~fe~lL~~~D~dL~~wl~g~~~p~-----~~~~~~li~~ir 74 (74)
T PF03937_consen 2 RKRLRWRCKRRGMLELDLLLGRFADAHLDSLSEEELDAFERLLDLEDPDLYDWLMGREEPE-----DPELAALIEKIR 74 (74)
T ss_dssp HHHHHHHHSS-SSHHHHHHHHHHHHHHHHHS-HHHHHHHHHHHTS-HHHHHHHHCTSSEES-----CHHHHHHHHHHH
T ss_pred cHHHHHHhhcccHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHcCCCHHHHHHHhCCCCCC-----ChhHHHHHHHhC
Confidence 4689999999999999999999999999999999999999999999999999999996666 577888888875
No 3
>COG2938 Uncharacterized conserved protein [Function unknown]
Probab=99.93 E-value=4.1e-26 Score=172.66 Aligned_cols=73 Identities=32% Similarity=0.712 Sum_probs=67.3
Q ss_pred HHHHHHhhccchhHHHHhHHHHHHHHhcCCCHHHHHHHHHHhcCCCHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHHHh
Q 039261 68 NRLLYRSKQRGFLELDLVLGKWVEEHIHSMDENGIKALVDVLNLENPDLWKWLTGQEQPPEAVKTNPVFSALHNKVMNN 146 (182)
Q Consensus 68 kRL~wRc~rRGmlELDLLLg~F~~~~l~~Lse~el~~Fe~LLd~eD~DLy~Wl~G~~~pPe~~~~d~~~~~Li~~Ir~~ 146 (182)
+||+|||| |||+|||+|||+|+++|+++||++|+++|++||+++|+|||+|++|+.+|| +.....|+.+|++.
T Consensus 16 ~RL~~rsr-RGmrElDlil~~Fae~~~~~lsd~el~~f~~LLe~~D~dL~~Wi~g~~~~~-----~~~~~~mv~~I~~~ 88 (94)
T COG2938 16 ARLRWRSR-RGMRELDLILGPFAEKEFDSLSDEELDEFERLLECEDNDLFNWIMGHGEPP-----DAELTPMVRKIQAR 88 (94)
T ss_pred HHHHHHHH-hccHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHcCCcHHHHHHHhCCCCCC-----cHHHHHHHHHHHHH
Confidence 37999996 999999999999999999999999999999999999999999999999999 56677777777753
No 4
>PRK10878 hypothetical protein; Provisional
Probab=99.85 E-value=4.6e-21 Score=138.74 Aligned_cols=62 Identities=19% Similarity=0.520 Sum_probs=60.8
Q ss_pred hhHHHHhHHHHHHHHhcCCCHHHHHHHHHHhcCCCHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHHH
Q 039261 79 FLELDLVLGKWVEEHIHSMDENGIKALVDVLNLENPDLWKWLTGQEQPPEAVKTNPVFSALHNKVMN 145 (182)
Q Consensus 79 mlELDLLLg~F~~~~l~~Lse~el~~Fe~LLd~eD~DLy~Wl~G~~~pPe~~~~d~~~~~Li~~Ir~ 145 (182)
|+|||+|||+|++++|.+||++|++.|++||+++|+|||+|+||+.+|| |+.++.|+++|++
T Consensus 1 m~ElDlll~~F~~~~~~~l~~~e~~~Fe~LL~~~D~dL~~W~~g~~~p~-----d~~l~~iV~~Ir~ 62 (72)
T PRK10878 1 MRELDISIMPFFEHEYDSLSDDEKRIFIRLLECDDPDLFNWLMNHGKPA-----DAELERMVRLIQT 62 (72)
T ss_pred CchHHHHHHHHHHHHHhhCCHHHHHHHHHHHcCCCHHHHHHHhCCCCCC-----CHHHHHHHHHHHH
Confidence 7999999999999999999999999999999999999999999999999 8999999999995
No 5
>PRK09458 pspB phage shock protein B; Provisional
Probab=65.06 E-value=5.7 Score=29.42 Aligned_cols=16 Identities=38% Similarity=0.673 Sum_probs=13.5
Q ss_pred HHHHHHHHHhcCCCHH
Q 039261 100 NGIKALVDVLNLENPD 115 (182)
Q Consensus 100 ~el~~Fe~LLd~eD~D 115 (182)
+-++.+|+|||.|+|+
T Consensus 56 ~RI~tLE~ILDae~P~ 71 (75)
T PRK09458 56 ERIQALEAILDAEHPN 71 (75)
T ss_pred HHHHHHHHHHcccCCC
Confidence 6788999999988874
No 6
>PF14261 DUF4351: Domain of unknown function (DUF4351)
Probab=57.98 E-value=14 Score=25.68 Aligned_cols=32 Identities=28% Similarity=0.591 Sum_probs=26.5
Q ss_pred HHHHHhcCCCHHHHHHHH-HHhcCCC-HHHHHHH
Q 039261 89 WVEEHIHSMDENGIKALV-DVLNLEN-PDLWKWL 120 (182)
Q Consensus 89 F~~~~l~~Lse~el~~Fe-~LLd~eD-~DLy~Wl 120 (182)
-+...+..+|.++++.+- .|||.++ .||.+||
T Consensus 26 ~~~~~I~~l~~eqLE~l~e~ildf~~l~dL~~wL 59 (59)
T PF14261_consen 26 EIQERIQQLSLEQLEALAEAILDFNSLEDLENWL 59 (59)
T ss_pred HHHHHHHcCCHHHHHHHHHHHhCCCCHHHHHhhC
Confidence 345789999999999986 9999988 6788885
No 7
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=54.79 E-value=21 Score=22.68 Aligned_cols=42 Identities=12% Similarity=0.240 Sum_probs=33.3
Q ss_pred HHHHhHHHHHHHHhcCCCHHHHHHHHHHhcCCCHHHHHHHhCCC
Q 039261 81 ELDLVLGKWVEEHIHSMDENGIKALVDVLNLENPDLWKWLTGQE 124 (182)
Q Consensus 81 ELDLLLg~F~~~~l~~Lse~el~~Fe~LLd~eD~DLy~Wl~G~~ 124 (182)
.+++|-.-|.... ..+.++++.+...+.+.-..+..|+..+.
T Consensus 11 ~~~~L~~~f~~~~--~P~~~~~~~la~~~~l~~~qV~~WF~nrR 52 (56)
T smart00389 11 QLEELEKEFQKNP--YPSREEREELAAKLGLSERQVKVWFQNRR 52 (56)
T ss_pred HHHHHHHHHHhCC--CCCHHHHHHHHHHHCcCHHHHHHhHHHHh
Confidence 4555555565555 45899999999999999999999998764
No 8
>PF13168 Poxvirus_B22R_C: Poxvirus B22R protein C-terminal
Probab=52.78 E-value=17 Score=31.33 Aligned_cols=42 Identities=29% Similarity=0.527 Sum_probs=28.5
Q ss_pred HHHHHHHhCCCCCCCCCCCCHHHHHHHHHHHHhhhhcCCCCCC--CCCCCC
Q 039261 114 PDLWKWLTGQEQPPEAVKTNPVFSALHNKVMNNLNSYASPETR--SEPGQP 162 (182)
Q Consensus 114 ~DLy~Wl~G~~~pPe~~~~d~~~~~Li~~Ir~~~~~~~~~e~r--~~p~~~ 162 (182)
.|||..|.|+.+|+ ||+++..-..-. .. +.....+| ++||..
T Consensus 49 ~~Iy~llsG~~~P~-----DPvi~kf~~Y~~-~v-s~~~aG~R~CmmP~sd 92 (197)
T PF13168_consen 49 KDIYYLLSGKEPPP-----DPVIEKFSTYAG-YV-STNEAGVRKCMMPGSD 92 (197)
T ss_pred hhhHhhhcCCCCCC-----CcHHHHHHHHHH-HH-hhhhhcCeEeeCCCCc
Confidence 57999999999888 798887654433 11 23333355 888864
No 9
>PF05024 Gpi1: N-acetylglucosaminyl transferase component (Gpi1); InterPro: IPR007720 Glycosylphosphatidylinositol (GPI) represents an important anchoring molecule for cell surface proteins. The first step in its synthesis is the transfer of N-acetylglucosamine (GlcNAc) from UDP-N-acetylglucosamine to phosphatidylinositol (PI). This chemically simple step is genetically complex because three or four genes are required in both Saccharomyces cerevisiae (GPI1, GPI2 and GPI3) and mammals (GPI1, PIG A, PIG H and PIG C), respectively [].; GO: 0017176 phosphatidylinositol N-acetylglucosaminyltransferase activity, 0006506 GPI anchor biosynthetic process, 0016021 integral to membrane
Probab=49.88 E-value=39 Score=28.26 Aligned_cols=60 Identities=22% Similarity=0.316 Sum_probs=42.9
Q ss_pred HHHHhHHHHHHHHhcCCCHHHHHHHHHHhc----CCCHHHHHHHhCCCCCCCCCCCCHHHHHHHHHH
Q 039261 81 ELDLVLGKWVEEHIHSMDENGIKALVDVLN----LENPDLWKWLTGQEQPPEAVKTNPVFSALHNKV 143 (182)
Q Consensus 81 ELDLLLg~F~~~~l~~Lse~el~~Fe~LLd----~eD~DLy~Wl~G~~~pPe~~~~d~~~~~Li~~I 143 (182)
=+|++||-.+-..+..-.+.-...+.++++ ..=..+..|++| -|.+++-|.++.......
T Consensus 10 ~nDi~lG~~l~~~L~~~~~~i~~~~~~~~~~~~~~~l~~~i~WL~~---~PaGlKLN~eL~~fLg~~ 73 (189)
T PF05024_consen 10 ANDILLGVLLGLLLSENRESIASFLHRLLEFYLVDSLKSLIEWLMG---NPAGLKLNTELASFLGSL 73 (189)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhc---CCCeeeeCHHHHHHHHHH
Confidence 379999988877776555555555555554 233678899986 788999999988776544
No 10
>TIGR02976 phageshock_pspB phage shock protein B. This model describes the PspB protein of the psp (phage shock protein) operon, as found in Escherichia coli and many related species. Expression of a phage protein called secretin protein IV, and a number of other stresses including ethanol, heat shock, and defects in protein secretion trigger sigma-54-dependent expression of the phage shock regulon. PspB is both a regulator and an effector protein of the phage shock response.
Probab=43.01 E-value=30 Score=25.34 Aligned_cols=17 Identities=35% Similarity=0.649 Sum_probs=14.0
Q ss_pred HHHHHHHHHHhcCCCHH
Q 039261 99 ENGIKALVDVLNLENPD 115 (182)
Q Consensus 99 e~el~~Fe~LLd~eD~D 115 (182)
++-++.+|+||+.++|+
T Consensus 55 ~eRI~tLE~ILd~e~P~ 71 (75)
T TIGR02976 55 EERIDTLERILDAEHPN 71 (75)
T ss_pred HHHHHHHHHHHcCCCcC
Confidence 36788999999998875
No 11
>COG3095 MukE Uncharacterized protein involved in chromosome partitioning [Cell division and chromosome partitioning]
Probab=42.57 E-value=89 Score=27.26 Aligned_cols=64 Identities=22% Similarity=0.318 Sum_probs=46.8
Q ss_pred hhHHHHhHHHHHHHHhcCCCHHH---------HHHHHHHhcC-CCHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHHHhhh
Q 039261 79 FLELDLVLGKWVEEHIHSMDENG---------IKALVDVLNL-ENPDLWKWLTGQEQPPEAVKTNPVFSALHNKVMNNLN 148 (182)
Q Consensus 79 mlELDLLLg~F~~~~l~~Lse~e---------l~~Fe~LLd~-eD~DLy~Wl~G~~~pPe~~~~d~~~~~Li~~Ir~~~~ 148 (182)
+.|+|.+.|+-+ +|--||++. ++-|++||.+ +...|.+.+..+..-. |-.-+.+.++|+..++
T Consensus 86 lseldmlvgkvl--cylylsperla~egifs~qelydell~lade~kllk~vn~rssgs-----dldkqkl~ekvr~sl~ 158 (238)
T COG3095 86 LSELDMMVGKIL--CYLYLSPERLANEGIFTQQELYDELLTLADEAKLLKLVNNRSTGS-----DLDRQKLQEKVRSSLN 158 (238)
T ss_pred HHHHHHHHhHhh--heeecCHHHHhhccccchHHHHHHHHhHhhHHHHHHHHhccCccc-----cccHHHHHHHHHHHHH
Confidence 679999999876 344455543 4568999998 4478999998887766 3446778888887655
Q ss_pred h
Q 039261 149 S 149 (182)
Q Consensus 149 ~ 149 (182)
.
T Consensus 159 r 159 (238)
T COG3095 159 R 159 (238)
T ss_pred H
Confidence 4
No 12
>PF06667 PspB: Phage shock protein B; InterPro: IPR009554 This family consists of several bacterial phage shock protein B (PspB) sequences. The phage shock protein (psp) operon is induced in response to heat, ethanol, osmotic shock and infection by filamentous bacteriophages []. Expression of the operon requires the alternative sigma factor sigma54 and the transcriptional activator PspF. In addition, PspA plays a negative regulatory role, and the integral-membrane proteins PspB and PspC play a positive one [].; GO: 0006355 regulation of transcription, DNA-dependent, 0009271 phage shock
Probab=40.87 E-value=34 Score=25.12 Aligned_cols=16 Identities=31% Similarity=0.630 Sum_probs=13.4
Q ss_pred HHHHHHHHHhcCCCHH
Q 039261 100 NGIKALVDVLNLENPD 115 (182)
Q Consensus 100 ~el~~Fe~LLd~eD~D 115 (182)
+-++.+|+|||.++|+
T Consensus 56 eRI~tLE~ILdae~P~ 71 (75)
T PF06667_consen 56 ERIETLERILDAEHPN 71 (75)
T ss_pred HHHHHHHHHHcCCCCC
Confidence 6788999999988874
No 13
>PF07130 YebG: YebG protein; InterPro: IPR009813 This family consists of several bacterial YebG proteins of around 75 residues in length. The exact function of this protein is unknown but it is thought to be involved in the SOS response. The induction of the yebG gene occurs as cell enter into the stationary growth phase and is dependent on is dependent on cyclic AMP and H-NS [].; PDB: 3ERM_E.
Probab=38.04 E-value=1e+02 Score=22.87 Aligned_cols=42 Identities=26% Similarity=0.312 Sum_probs=29.3
Q ss_pred hhHHHHhHHHHHHHHhcCCCHHHHHHHHHHhcCCCHHHHHHH
Q 039261 79 FLELDLVLGKWVEEHIHSMDENGIKALVDVLNLENPDLWKWL 120 (182)
Q Consensus 79 mlELDLLLg~F~~~~l~~Lse~el~~Fe~LLd~eD~DLy~Wl 120 (182)
|+|+==-|..|+.+....+++++.+++--+|..+--.+-.-|
T Consensus 31 mLd~Ad~L~~~L~~~~~~lde~~~E~l~l~LA~~kd~~~~~l 72 (75)
T PF07130_consen 31 MLDLADNLTDFLEQSVLGLDEAQAEELALYLAENKDELAKAL 72 (75)
T ss_dssp HHHHHHHHHHHHHHHSTT--HHHHHHHHHHHHTTHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCHHHHHHHH
Confidence 677767788888888888888888888877776544444433
No 14
>COG3141 DNA damage-inducible gene in SOS regulon, dependent on cyclic AMP and H-NS , pqiA [General function prediction only]
Probab=35.32 E-value=91 Score=24.13 Aligned_cols=47 Identities=21% Similarity=0.230 Sum_probs=37.3
Q ss_pred cchhHHHHhHHHHHHHHhcCCCHHHHHHHHHHhcCCCHHHHHHHhCC
Q 039261 77 RGFLELDLVLGKWVEEHIHSMDENGIKALVDVLNLENPDLWKWLTGQ 123 (182)
Q Consensus 77 RGmlELDLLLg~F~~~~l~~Lse~el~~Fe~LLd~eD~DLy~Wl~G~ 123 (182)
--|+++-=.|..|+.+-...|.+++..++--+|..+--+|-..|-++
T Consensus 29 DKMLd~Ad~L~e~L~ks~~~leeeq~E~Ls~flAenke~l~~~lk~~ 75 (97)
T COG3141 29 DKMLDTADLLDEWLTKSPVSLEEEQREALSLFLAENKDVLSTILKTG 75 (97)
T ss_pred HHHHHHHHHHHHHHhcCCccchHHHHHHHHHHHHHhHHHHHHHHhcC
Confidence 45888888899999999999999999999988887655555444444
No 15
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=35.21 E-value=76 Score=24.17 Aligned_cols=31 Identities=23% Similarity=0.423 Sum_probs=25.6
Q ss_pred HHHHhHHHHHHHHhcCCCHHHHHHHHHHhcC
Q 039261 81 ELDLVLGKWVEEHIHSMDENGIKALVDVLNL 111 (182)
Q Consensus 81 ELDLLLg~F~~~~l~~Lse~el~~Fe~LLd~ 111 (182)
++.-+...+.+..+..++++|++.|..+|.-
T Consensus 102 ~~~~~~~~~~~~~~~~l~~ee~~~l~~~l~~ 132 (144)
T PRK03573 102 EVEAVINKTRAEILHGISAEEIEQLITLIAK 132 (144)
T ss_pred HHHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4556677788888999999999999998863
No 16
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=34.19 E-value=1.3e+02 Score=22.38 Aligned_cols=51 Identities=16% Similarity=0.263 Sum_probs=31.0
Q ss_pred CCCcHHHHHHHHHHHHHHhhccchhHHHHhHHHHHHHHhcCCCHHHHHHHHHHhcC
Q 039261 56 DLSNDEKKKRLFNRLLYRSKQRGFLELDLVLGKWVEEHIHSMDENGIKALVDVLNL 111 (182)
Q Consensus 56 ~~s~~E~krrl~kRL~wRc~rRGmlELDLLLg~F~~~~l~~Lse~el~~Fe~LLd~ 111 (182)
-++.+|-.+...+.++=+- --| ...-++..|++.. .+|++|+++++++|+.
T Consensus 65 ~is~~e~~~~~~~~~l~~~-~~g--s~~~l~~~l~~~~--~ls~~el~~L~~li~e 115 (115)
T PF03965_consen 65 LISREEYLAQELRQFLDRL-FDG--SIPQLVAALVESE--ELSPEELEELRKLIDE 115 (115)
T ss_dssp SSSHHHHHHHHHHHHHHHH-STT--HHHHHHHHHHHCT---S-HHHHHHHHHHHH-
T ss_pred CCcHHHHHHHHHHHHHHHH-hCC--CHHHHHHHHHhcC--CCCHHHHHHHHHHHcC
Confidence 4555665555444443333 133 4566777777766 8999999999999873
No 17
>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=33.24 E-value=83 Score=19.88 Aligned_cols=39 Identities=18% Similarity=0.201 Sum_probs=30.2
Q ss_pred hHHHHHHHHhcCCCHHHHHHHHHHhcCCCHHHHHHHhCCC
Q 039261 85 VLGKWVEEHIHSMDENGIKALVDVLNLENPDLWKWLTGQE 124 (182)
Q Consensus 85 LLg~F~~~~l~~Lse~el~~Fe~LLd~eD~DLy~Wl~G~~ 124 (182)
+|..++.. -+..+.++++.+..-+.+.-..+-.||..+.
T Consensus 14 ~Le~~f~~-~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR 52 (59)
T cd00086 14 ELEKEFEK-NPYPSREEREELAKELGLTERQVKIWFQNRR 52 (59)
T ss_pred HHHHHHHh-CCCCCHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence 34444444 3477899999999999999999999997653
No 18
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=32.19 E-value=88 Score=20.07 Aligned_cols=37 Identities=19% Similarity=0.338 Sum_probs=29.1
Q ss_pred hHHHHHHHHhcCCCHHHHHHHHHHhcCCCHHHHHHHhC
Q 039261 85 VLGKWVEEHIHSMDENGIKALVDVLNLENPDLWKWLTG 122 (182)
Q Consensus 85 LLg~F~~~~l~~Lse~el~~Fe~LLd~eD~DLy~Wl~G 122 (182)
+|..+++. -+..+.++...+..-|.++...+..|+..
T Consensus 14 ~L~~~f~~-~~~p~~~~~~~la~~l~l~~~~V~~WF~n 50 (57)
T PF00046_consen 14 VLEEYFQE-NPYPSKEEREELAKELGLTERQVKNWFQN 50 (57)
T ss_dssp HHHHHHHH-SSSCHHHHHHHHHHHHTSSHHHHHHHHHH
T ss_pred HHHHHHHH-hccccccccccccccccccccccccCHHH
Confidence 34444444 55788899999999999999999999864
No 19
>PRK10061 DNA damage-inducible protein YebG; Provisional
Probab=29.21 E-value=1.5e+02 Score=22.99 Aligned_cols=47 Identities=19% Similarity=0.197 Sum_probs=36.3
Q ss_pred cchhHHHHhHHHHHHHHhcCCCHHHHHHHHHHhcCCCHHHHHHHhCC
Q 039261 77 RGFLELDLVLGKWVEEHIHSMDENGIKALVDVLNLENPDLWKWLTGQ 123 (182)
Q Consensus 77 RGmlELDLLLg~F~~~~l~~Lse~el~~Fe~LLd~eD~DLy~Wl~G~ 123 (182)
=-|+|+==-|..|+.+....|++++.+++--.|..+--.|...|-|.
T Consensus 29 DKMLD~Ad~L~~~L~~s~~~ldE~q~E~L~l~LA~nKd~l~~~lk~~ 75 (96)
T PRK10061 29 DKMLDTADLLDTWLTNSPVQMEDEQREALSLWLAEQKDVLSTILKTG 75 (96)
T ss_pred HHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 34777777889999999999999999999888887655555555444
No 20
>PF08621 RPAP1_N: RPAP1-like, N-terminal; InterPro: IPR013930 Inhibition of RNA polymerase II-associated protein 1 (RPAP1) synthesis in Saccharomyces cerevisiae (Baker's yeast) results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11 []. This entry represents the N-terminal region of RPAP-1 that is conserved from yeast to humans.
Probab=28.68 E-value=88 Score=21.12 Aligned_cols=34 Identities=21% Similarity=0.360 Sum_probs=28.1
Q ss_pred HHhcCCCHHHHHHHH-HHhcCCCHHHHHHHhCCCC
Q 039261 92 EHIHSMDENGIKALV-DVLNLENPDLWKWLTGQEQ 125 (182)
Q Consensus 92 ~~l~~Lse~el~~Fe-~LLd~eD~DLy~Wl~G~~~ 125 (182)
+.+..||++|+.+=. .|++-=||.|.++|..+..
T Consensus 10 ~rL~~MS~eEI~~er~eL~~~LdP~li~~L~~R~~ 44 (49)
T PF08621_consen 10 ARLASMSPEEIEEEREELLESLDPKLIEFLKKRAN 44 (49)
T ss_pred HHHHhCCHHHHHHHHHHHHHhCCHHHHHHHHHhhh
Confidence 467899999987655 8999999999999987654
No 21
>PF14024 DUF4240: Protein of unknown function (DUF4240)
Probab=27.02 E-value=2.8e+02 Score=21.53 Aligned_cols=52 Identities=17% Similarity=0.235 Sum_probs=36.4
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHhcC-----CCHHHH---HHHhCCCCCCCCCCCCHHHHHHHHHHH
Q 039261 86 LGKWVEEHIHSMDENGIKALVDVLNL-----ENPDLW---KWLTGQEQPPEAVKTNPVFSALHNKVM 144 (182)
Q Consensus 86 Lg~F~~~~l~~Lse~el~~Fe~LLd~-----eD~DLy---~Wl~G~~~pPe~~~~d~~~~~Li~~Ir 144 (182)
.-..+.+.+..|+.+++.+|+.+++. ..++|| ..+.|. .. +..|...+..|.
T Consensus 24 ~~~~L~~~L~~l~~~ei~~F~~~~~~~~~~~~~~~lw~Aa~ii~gg--~S-----dD~F~yFR~wLI 83 (128)
T PF14024_consen 24 VAEPLVELLAKLPPEEIVAFDKILDQLLDEAYTWDLWAAAYIINGG--CS-----DDGFLYFRCWLI 83 (128)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccHHHHHHHHHHcCC--Cc-----hhhHHHHHHHHH
Confidence 34455778999999999999977664 788998 555553 33 355666555554
No 22
>PF13618 Gluconate_2-dh3: Gluconate 2-dehydrogenase subunit 3
Probab=26.86 E-value=2.5e+02 Score=21.02 Aligned_cols=80 Identities=21% Similarity=0.276 Sum_probs=49.5
Q ss_pred hccchhHHHHhHHHHHHHHhcCCCHHHHHHHHHHhcCCCHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHHHhhhhcCCCC
Q 039261 75 KQRGFLELDLVLGKWVEEHIHSMDENGIKALVDVLNLENPDLWKWLTGQEQPPEAVKTNPVFSALHNKVMNNLNSYASPE 154 (182)
Q Consensus 75 ~rRGmlELDLLLg~F~~~~l~~Lse~el~~Fe~LLd~eD~DLy~Wl~G~~~pPe~~~~d~~~~~Li~~Ir~~~~~~~~~e 154 (182)
.+.|+..+|=....-..+.+..|+.+|.+++-.-++..+. ..+.++.......|..|+..+...+-. +|.
T Consensus 49 ~~~gl~~ld~~a~~~~g~~F~~l~~~~~~~lL~~~~~~~~--------~~~~~~~~~~~~ff~~lr~~~~~gyyt--~p~ 118 (131)
T PF13618_consen 49 FRAGLAALDAYAQKRYGKSFAELSPAQREALLDALEKSEA--------AGPDWDGIPGARFFQQLRNLTLQGYYT--SPE 118 (131)
T ss_pred HHHHHHHHHHHHHHHhCCChhhCCHHHHHHHHHHHHhccc--------cccccccCcHHHHHHHHHHHHHHHHhc--CCc
Confidence 3569999998887777888999999999888766665544 111222222235666666666654333 333
Q ss_pred CCCCCCCCCcccc
Q 039261 155 TRSEPGQPWVRGW 167 (182)
Q Consensus 155 ~r~~p~~~w~rgw 167 (182)
-.|..=+.||
T Consensus 119 ---ygG~~~~~~y 128 (131)
T PF13618_consen 119 ---YGGNKNVLGY 128 (131)
T ss_pred ---cccCCCCCcc
Confidence 2234445666
No 23
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=26.48 E-value=1.4e+02 Score=17.17 Aligned_cols=25 Identities=16% Similarity=0.384 Sum_probs=19.8
Q ss_pred HHHHHHhcCCCHHHHHHHhCCCCCC
Q 039261 103 KALVDVLNLENPDLWKWLTGQEQPP 127 (182)
Q Consensus 103 ~~Fe~LLd~eD~DLy~Wl~G~~~pP 127 (182)
..+...+.....-+.+|+.|...++
T Consensus 16 ~~~a~~~~~~~~~v~~~~~g~~~~~ 40 (58)
T cd00093 16 EELAEKLGVSRSTISRIENGKRNPS 40 (58)
T ss_pred HHHHHHHCCCHHHHHHHHcCCCCCC
Confidence 3556778888899999999987555
No 24
>PHA01976 helix-turn-helix protein
Probab=25.55 E-value=1.7e+02 Score=19.25 Aligned_cols=30 Identities=7% Similarity=0.179 Sum_probs=22.9
Q ss_pred cCCCHHHHHHHHHHhcCCCHHHHHHHhCCCCCC
Q 039261 95 HSMDENGIKALVDVLNLENPDLWKWLTGQEQPP 127 (182)
Q Consensus 95 ~~Lse~el~~Fe~LLd~eD~DLy~Wl~G~~~pP 127 (182)
..|+.+ +|.+.+...-..+.+|..|...|+
T Consensus 14 ~glt~~---~lA~~~gvs~~~v~~~e~g~~~p~ 43 (67)
T PHA01976 14 RAWSAP---ELSRRAGVRHSLIYDFEADKRLPN 43 (67)
T ss_pred cCCCHH---HHHHHhCCCHHHHHHHHcCCCCCC
Confidence 355544 456678888899999999998776
No 25
>PRK05256 condesin subunit E; Provisional
Probab=24.76 E-value=3e+02 Score=24.55 Aligned_cols=66 Identities=21% Similarity=0.294 Sum_probs=44.7
Q ss_pred cchhHHHHhHHHHHHHHhcCCCHHHH---------HHHHHHhcC-CCHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHHHh
Q 039261 77 RGFLELDLVLGKWVEEHIHSMDENGI---------KALVDVLNL-ENPDLWKWLTGQEQPPEAVKTNPVFSALHNKVMNN 146 (182)
Q Consensus 77 RGmlELDLLLg~F~~~~l~~Lse~el---------~~Fe~LLd~-eD~DLy~Wl~G~~~pPe~~~~d~~~~~Li~~Ir~~ 146 (182)
+=+-|+|.+.|.-+--- -||.+.+ +-|++|+.+ ++.-|.+.+..++.-. +-..+.|.++|++.
T Consensus 86 svLSeldMlvGkvLc~L--yLsperLa~~gift~qeL~deL~~ladE~kllklvn~R~~Gs-----DlD~~Kl~ekvr~s 158 (238)
T PRK05256 86 SVLSELDMLVGKILCYL--YLSPERLAHEGIFTQQELYDELLTLADEAKLLKLVNNRSTGS-----DLDKQKLQEKVRTS 158 (238)
T ss_pred HHhhHHHHHHHHHHHHH--hcCHHHHhcCCceeHHHHHHHHHHhhcHHHHHHHhcCCCCcc-----hhhHHHHHHHHHHH
Confidence 44889999999876432 3444433 457888887 5567777777555543 34477888888876
Q ss_pred hhh
Q 039261 147 LNS 149 (182)
Q Consensus 147 ~~~ 149 (182)
+..
T Consensus 159 Lrr 161 (238)
T PRK05256 159 LNR 161 (238)
T ss_pred HHH
Confidence 654
No 26
>PF11239 DUF3040: Protein of unknown function (DUF3040); InterPro: IPR021401 Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed.
Probab=24.43 E-value=1.1e+02 Score=21.88 Aligned_cols=31 Identities=16% Similarity=0.243 Sum_probs=22.7
Q ss_pred CCCHHHHHHH---HHHhcCCCHHHHHHHhCCCCC
Q 039261 96 SMDENGIKAL---VDVLNLENPDLWKWLTGQEQP 126 (182)
Q Consensus 96 ~Lse~el~~F---e~LLd~eD~DLy~Wl~G~~~p 126 (182)
.||++|+..+ |+=|..+||++-.=+.+....
T Consensus 2 ~LSe~E~r~L~eiEr~L~~~DP~fa~~l~~~~~~ 35 (82)
T PF11239_consen 2 PLSEHEQRRLEEIERQLRADDPRFAARLRSGRPR 35 (82)
T ss_pred CCCHHHHHHHHHHHHHHHhcCcHHHHHhccCCCC
Confidence 3778875555 555788999999999984443
No 27
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=24.38 E-value=2.9e+02 Score=20.29 Aligned_cols=29 Identities=10% Similarity=0.269 Sum_probs=24.3
Q ss_pred CCCHHHHHHHHHHhcCCCHHHHHHHhCCCCCC
Q 039261 96 SMDENGIKALVDVLNLENPDLWKWLTGQEQPP 127 (182)
Q Consensus 96 ~Lse~el~~Fe~LLd~eD~DLy~Wl~G~~~pP 127 (182)
.|+.. +|..+|...-..+..|..|...|+
T Consensus 78 gltq~---~lA~~lg~~~~tis~~e~g~~~p~ 106 (127)
T TIGR03830 78 GLSQR---EAAELLGGGVNAFSRYERGEVRPS 106 (127)
T ss_pred CCCHH---HHHHHhCCCHHHHHHHHCCCCCCC
Confidence 67655 466889999999999999998776
No 28
>PF00486 Trans_reg_C: Transcriptional regulatory protein, C terminal; InterPro: IPR001867 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain that is almost always found associated with the response regulator receiver domain (see IPR001789 from INTERPRO). It may play a role in DNA binding [].; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2K4J_A 2JPB_A 1ODD_A 1OPC_A 1KGS_A 2PMU_E 2JZY_A 1GXP_B 1QQI_A 2Z33_A ....
Probab=24.05 E-value=2.2e+02 Score=18.80 Aligned_cols=51 Identities=14% Similarity=0.174 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHHHhcCCC-----HHHHHHHhCCCCCCCCCCCCHHHHHHHHHHHHhhhhc
Q 039261 96 SMDENGIKALVDVLNLEN-----PDLWKWLTGQEQPPEAVKTNPVFSALHNKVMNNLNSY 150 (182)
Q Consensus 96 ~Lse~el~~Fe~LLd~eD-----~DLy~Wl~G~~~pPe~~~~d~~~~~Li~~Ir~~~~~~ 150 (182)
.|+..|..-|+.|+...+ .+|.+-+-+...... +..+...+..+|+.+...
T Consensus 5 ~Lt~~e~~lL~~L~~~~~~~vs~~~l~~~~w~~~~~~~----~~~l~~~I~rLR~kL~~~ 60 (77)
T PF00486_consen 5 KLTPKEFRLLELLLRNPGRVVSREELIEALWGDEEDVS----DNSLDVHISRLRKKLEDA 60 (77)
T ss_dssp ESSHHHHHHHHHHHHTTTSEEEHHHHHHHHTSSSSTTC----THHHHHHHHHHHHHHHSS
T ss_pred ecCHHHHHHHHHHHhCCCCCCCHHHhCChhhhcccccc----hhhHHHHHHHHHHHHhhc
Confidence 578889999999998765 689999998888221 578899999999888775
No 29
>cd08767 Cdt1_c The C-terminal fold of replication licensing factor Cdt1 is essential for Cdt1 activity and directly interacts with MCM2-7 helicase. Cdt1 is a replication licensing factor in eukaryotes that recruits the Minichromosome Maintenance Complex (MCM2-7) to the Origin Recognition Complex (ORC). The Cdt1 protein is divided into three regions based on sequence comparison and biochemical analyses: the N-terminal region (Cdt1_n) binds DNA in a sequence-, strand-, and conformation-independent manner; the middle winged helix fold (Cdt1_m) binds geminin to inhibit both binding of the MCM complex to origins of replication and DNA; and the C-terminal region (Cdt1_c) is essential for Cdt1 activity and directly interacts with the MCM2-7 helicase. Precise duplication of chromosomal DNA is required for genomic stability during replication. Assembly of replication factors to start DNA replication in eukaryotes must occur only once per cell cycle. To form a pre-replicative complex on replicat
Probab=23.79 E-value=1.5e+02 Score=23.19 Aligned_cols=50 Identities=14% Similarity=0.292 Sum_probs=42.7
Q ss_pred HHHHhhccchhHHHHhHHHHHHHHhcCCCHHHHHHHHHHhcCCCHHHHHHHhC
Q 039261 70 LLYRSKQRGFLELDLVLGKWVEEHIHSMDENGIKALVDVLNLENPDLWKWLTG 122 (182)
Q Consensus 70 L~wRc~rRGmlELDLLLg~F~~~~l~~Lse~el~~Fe~LLd~eD~DLy~Wl~G 122 (182)
.+|.+.+|+...++.++.+-.+-|-.-++.+|+.+-.+||..-=| +|+.-
T Consensus 52 ~if~s~~k~~l~~e~l~~kl~~S~~~~~s~~E~E~~l~LL~el~P---~Wis~ 101 (126)
T cd08767 52 NIFVSEKKTVLPLEELVYKLQASYPSILSRGEVEEHLRLLAELAP---DWISE 101 (126)
T ss_pred HHHHhcccccccHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHhCh---HHhee
Confidence 478999999999999999999999999999999999999984222 46543
No 30
>PHA00542 putative Cro-like protein
Probab=23.16 E-value=2e+02 Score=20.52 Aligned_cols=42 Identities=19% Similarity=0.451 Sum_probs=31.4
Q ss_pred CCCHHHHHHHHHHhcCCCHHHHHHHhCCC-CCCCCCCCCHHHHHHHHHHHH
Q 039261 96 SMDENGIKALVDVLNLENPDLWKWLTGQE-QPPEAVKTNPVFSALHNKVMN 145 (182)
Q Consensus 96 ~Lse~el~~Fe~LLd~eD~DLy~Wl~G~~-~pPe~~~~d~~~~~Li~~Ir~ 145 (182)
.++..| +.+.+...-+.++.|..|.. .|+ ...+..|.+.+++
T Consensus 31 glTq~e---lA~~lgIs~~tIsr~e~g~~~~p~-----~~~l~ki~~~~~~ 73 (82)
T PHA00542 31 GWSQEQ---IADATDVSQPTICRIYSGRHKDPR-----YSVVEKLRHLVLN 73 (82)
T ss_pred CCCHHH---HHHHHCcCHHHHHHHHcCCCCCCC-----HHHHHHHHHHHHH
Confidence 556554 55788899999999999995 454 3677777777763
No 31
>KOG3888 consensus Gamma-butyrobetaine,2-oxoglutarate dioxygenase [Lipid transport and metabolism]
Probab=22.64 E-value=90 Score=29.68 Aligned_cols=51 Identities=18% Similarity=0.311 Sum_probs=39.7
Q ss_pred CCCcHHHHHHHHHHHHHHhhccchhHHHHhHHHHHHHHhcCCCHHHHHHHHHHhcCCCHHHHHHHh
Q 039261 56 DLSNDEKKKRLFNRLLYRSKQRGFLELDLVLGKWVEEHIHSMDENGIKALVDVLNLENPDLWKWLT 121 (182)
Q Consensus 56 ~~s~~E~krrl~kRL~wRc~rRGmlELDLLLg~F~~~~l~~Lse~el~~Fe~LLd~eD~DLy~Wl~ 121 (182)
+-|....++.++.=-+++|+.=|=.|+..+...|. |+++|+. |..||+||.
T Consensus 108 ~fs~~~~~~~~r~~yrp~~qlWgk~e~ed~~k~f~--------------yee~l~~-Ds~l~qwLq 158 (407)
T KOG3888|consen 108 CFSSQVRQRYLREVYRPPPQLWGKAEFEDIVKDFS--------------YEEVLDQ-DSVLFQWLQ 158 (407)
T ss_pred CcchHHHHHHHHHhcCCchhhcchhhhhhHHHhcc--------------HHHHhCc-HHHHHHHHH
Confidence 46666777776677778888888888888877775 6778887 889999985
No 32
>cd00383 trans_reg_C Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase.
Probab=21.58 E-value=2.8e+02 Score=19.00 Aligned_cols=51 Identities=8% Similarity=0.091 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHhcCCC-----HHHHHHHhCCCCCCCCCCCCHHHHHHHHHHHHhhhhc
Q 039261 96 SMDENGIKALVDVLNLEN-----PDLWKWLTGQEQPPEAVKTNPVFSALHNKVMNNLNSY 150 (182)
Q Consensus 96 ~Lse~el~~Fe~LLd~eD-----~DLy~Wl~G~~~pPe~~~~d~~~~~Li~~Ir~~~~~~ 150 (182)
.|+..|..-|..|+...+ .+|++.+-+..+.+. +..+...+..||+.+..+
T Consensus 23 ~Lt~~e~~lL~~L~~~~~~~vs~~~l~~~lw~~~~~~~----~~~l~~~I~rLRkkl~~~ 78 (95)
T cd00383 23 ELTPKEFELLELLARNPGRVLSREQLLEAVWGDDYDVD----DRTVDVHISRLRKKLEDD 78 (95)
T ss_pred EeCHHHHHHHHHHHhCCCCcCCHHHHHHHhcCCCCCCC----cccHHHHHHHHHHHhccC
Confidence 577888888888887644 678888877665221 356888888999888654
No 33
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=20.43 E-value=1.8e+02 Score=16.45 Aligned_cols=24 Identities=21% Similarity=0.411 Sum_probs=19.1
Q ss_pred HHHHHhcCCCHHHHHHHhCCCCCC
Q 039261 104 ALVDVLNLENPDLWKWLTGQEQPP 127 (182)
Q Consensus 104 ~Fe~LLd~eD~DLy~Wl~G~~~pP 127 (182)
.+.+.+......+..|..|...++
T Consensus 15 ~la~~~~i~~~~i~~~~~~~~~~~ 38 (56)
T smart00530 15 ELAEKLGVSRSTLSRIENGKRKPS 38 (56)
T ss_pred HHHHHhCCCHHHHHHHHCCCCCCC
Confidence 455667888899999999987665
Done!