Query 011231
Match_columns 490
No_of_seqs 109 out of 120
Neff 3.4
Searched_HMMs 46136
Date Thu Mar 28 23:03:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011231.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011231hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01803 LIM_bind: LIM-domain 100.0 3.4E-43 7.3E-48 334.8 13.3 157 1-160 82-240 (240)
2 KOG2181 LIM domain binding pro 99.6 1.7E-15 3.6E-20 152.7 9.5 131 4-169 130-265 (415)
3 PF06249 EutQ: Ethanolamine ut 46.5 19 0.00042 34.2 3.1 56 5-61 75-143 (152)
4 PRK15457 ethanolamine utilizat 32.9 53 0.0012 33.4 3.9 41 2-42 152-192 (233)
5 COG4907 Predicted membrane pro 31.0 31 0.00067 38.5 2.1 19 409-427 571-589 (595)
6 PF13897 GOLD_2: Golgi-dynamic 27.3 51 0.0011 31.1 2.5 23 35-57 8-30 (136)
7 PF08076 TetM_leader: Tetracyc 26.1 23 0.00049 25.3 0.1 16 39-54 10-25 (28)
8 PF11197 DUF2835: Protein of u 23.7 93 0.002 26.1 3.2 19 32-50 49-67 (68)
9 PRK13254 cytochrome c-type bio 22.1 1.4E+02 0.003 28.2 4.4 33 28-64 100-132 (148)
10 PF03118 RNA_pol_A_CTD: Bacter 18.5 35 0.00077 27.7 -0.3 35 112-148 9-43 (66)
No 1
>PF01803 LIM_bind: LIM-domain binding protein; InterPro: IPR002691 The LIM-domain binding protein, binds to the LIM domain IPR001781 from INTERPRO of LIM homeodomain proteins which are transcriptional regulators of development. Nuclear LIM interactor (NLI) / LIM domain-binding protein 1 (LDB1) P70662 from SWISSPROT is located in the nuclei of neuronal cells during development, it is co-expressed with Isl1 in early motor neuron differentiation and has a suggested role in the Isl1 dependent development of motor neurons []. It is suggested that these proteins act synergistically to enhance transcriptional efficiency by acting as co-factors for LIM homeodomain and Otx class transcription factors both of which have essential roles in development []. The Drosophila melanogaster protein Chip O18353 from SWISSPROT is required for segmentation and activity of a remote wing margin enhancer []. Chip is a ubiquitous chromosomal factor required for normal expression of diverse genes at many stages of development []. It is suggested that Chip cooperates with different LIM domain proteins and other factors to structurally support remote enhancer-promoter interactions [].; GO: 0003712 transcription cofactor activity, 0005634 nucleus
Probab=100.00 E-value=3.4e-43 Score=334.82 Aligned_cols=157 Identities=38% Similarity=0.620 Sum_probs=146.9
Q ss_pred CCCccccCCCcEEEEecceeEEEEeec-eEEEEeeeEEEEECCCCceeEEEEeecceecccccchhhHHHhhhhHHHHHH
Q 011231 1 MPREYQNASGQIVLDYAKAIQESVFEQ-LRVVRDGQLRIVFSPDLKICSWEFCARRHEELIPRRLLIPQVSQLGAAAQKY 79 (490)
Q Consensus 1 ~PrE~~LpNG~~vVE~~KAs~~y~Fen-~qVV~~GtLRa~FdpdLKIEswEF~t~~HEEyIPR~~I~pqv~qL~~~aqe~ 79 (490)
.|||++|+||.++|||+||+++|||++ ++|+++|+||++||+++||||||||+++|+|||||++|+.++.+.+.++++|
T Consensus 82 ~~~e~~l~ng~i~ie~~~~~~~~~y~~gs~v~~~G~lr~~f~~~lKIe~~df~~~~~~e~I~r~~l~~~~~~~~~~~~~~ 161 (240)
T PF01803_consen 82 GPREQVLPNGSIFIECPRATFIYWYEDGSQVVHEGQLRAQFDPDLKIEWWDFCTRSHEEYIPRSALEQQASNLHPSVQIF 161 (240)
T ss_pred CCceEEcCCCeEEEEECCEEEEEEECCceEEEEEeEEEEEECccccEEEEEEEeecccccCcHHHHHHhhccchhhhHHh
Confidence 389999999999999999999999999 9999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhcCCCCCCchHhhhhhhhhHHHHHHHHhhccCCccCCCCCcccchhhhhHHHHHhchHHHHHHhh-ccCCChHHHH
Q 011231 80 QAATQNASSNLSAPELQNNCNMFVASARQLAKALEVPLVNDLGYTKRYVRCLQISEVVNSMKDLIDYSR-VTGTGPMESL 158 (490)
Q Consensus 80 qs~~qns~d~ksSpdmsKN~n~~l~aaRQLak~ldlP~VNe~GvpkrvmRcLEIAEVVnqMkDLm~FS~-~p~LGPiEAL 158 (490)
++.. ++.|+++|+.|+++.+..+.+++.+.|+...|+++|||+++||||||+|||++|+|||.|++ ++.++|+|||
T Consensus 162 ~~~~---~~~k~~~~~~~~~~~~~~~~~~~~~~Lp~~~v~~~Gi~~~~mr~Lqi~evms~M~~Lm~fs~~~~~~sP~eaL 238 (240)
T PF01803_consen 162 QKLS---PDQKQSPDMSKNSKARQQKSPQLPPSLPSSNVNEFGIPERVMRCLQIAEVMSQMKDLMSFSKQNNILSPLEAL 238 (240)
T ss_pred hhcc---cccccccchhhhhhhhhhcccccCCCcccCCCCcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHh
Confidence 9886 55889999999988877777888777665589999999999999999999999999999999 5559999999
Q ss_pred hh
Q 011231 159 AK 160 (490)
Q Consensus 159 kq 160 (490)
++
T Consensus 239 ~~ 240 (240)
T PF01803_consen 239 EQ 240 (240)
T ss_pred cC
Confidence 85
No 2
>KOG2181 consensus LIM domain binding protein LDB1/NLI/CLIM [Transcription]
Probab=99.61 E-value=1.7e-15 Score=152.71 Aligned_cols=131 Identities=18% Similarity=0.329 Sum_probs=111.5
Q ss_pred ccccCCCcEEEEecceeEEEEeec---eEEEEeeeEEEEEC--CCCceeEEEEeecceecccccchhhHHHhhhhHHHHH
Q 011231 4 EYQNASGQIVLDYAKAIQESVFEQ---LRVVRDGQLRIVFS--PDLKICSWEFCARRHEELIPRRLLIPQVSQLGAAAQK 78 (490)
Q Consensus 4 E~~LpNG~~vVE~~KAs~~y~Fen---~qVV~~GtLRa~Fd--pdLKIEswEF~t~~HEEyIPR~~I~pqv~qL~~~aqe 78 (490)
|+.|.||.+.+||..+++|+.|.. .+|.++|+|.++|. .-.||+.|+|+.++|.|+|||+.|+--+.
T Consensus 130 ket~hn~s~~~dcdq~~~iTqhgkp~ft~VctegrL~lEF~fDd~MRIK~Wh~~ik~~rElvprsil~~~a~-------- 201 (415)
T KOG2181|consen 130 KETLHNGSQAYDCDQVLQITQHGKPSFTEVCTEGRLYLEFAFDDVMRIKAWHLEIKRSRELVPRSILQNTAD-------- 201 (415)
T ss_pred hhhhcCCceeeeccceeEEeecCCccceeeeccceEEEEeehhhhhhhhheeeeeeccccccchhhhhccCC--------
Confidence 678999999999999999999999 99999999999974 55899999999999999999998873210
Q ss_pred HHHhhhcCCCCCCchHhhhhhhhhHHHHHHHHhhccCCccCCCCCcccchhhhhHHHHHhchHHHHHHhhccCCChHHHH
Q 011231 79 YQAATQNASSNLSAPELQNNCNMFVASARQLAKALEVPLVNDLGYTKRYVRCLQISEVVNSMKDLIDYSRVTGTGPMESL 158 (490)
Q Consensus 79 ~qs~~qns~d~ksSpdmsKN~n~~l~aaRQLak~ldlP~VNe~GvpkrvmRcLEIAEVVnqMkDLm~FS~~p~LGPiEAL 158 (490)
.|......++|| ++++||++.++.+|.++.|+..|++||.-.+...|+|+|+|
T Consensus 202 --------~dp~~ldq~~kN-------------------itR~G~~nsTlNylrlcvILePMQelMSrhKayalsPRdcl 254 (415)
T KOG2181|consen 202 --------YDPEALDQEQKN-------------------ITRMGFFNSTLNYLRLCVILEPMQELMSRHKAYALSPRDCL 254 (415)
T ss_pred --------CChhhhChhhcc-------------------ccccccchhhHHHHHHHHHHhHHHHHHHhccccCCCHHHHH
Confidence 111122334455 67999999999999999999999999999999999999999
Q ss_pred hhhhcccCCCC
Q 011231 159 AKFPRRTSGAS 169 (490)
Q Consensus 159 kqfv~q~~~~~ 169 (490)
|.-.=+.|...
T Consensus 255 KttLFQkwQrM 265 (415)
T KOG2181|consen 255 KTTLFQKWQRM 265 (415)
T ss_pred HHHHHHHhhhh
Confidence 98777776543
No 3
>PF06249 EutQ: Ethanolamine utilisation protein EutQ; InterPro: IPR010424 The eut operon of Salmonella typhimurium encodes proteins involved in the cobalamin-dependent degradation of ethanolamine. The role of EutQ in this process is unclear [].; PDB: 2PYT_B 3LWC_A.
Probab=46.52 E-value=19 Score=34.18 Aligned_cols=56 Identities=13% Similarity=0.212 Sum_probs=38.5
Q ss_pred cccCCCcEEEEecceeEEEEeeceEEEEeeeEEEEECCCCce-------------eEEEEeecceecccc
Q 011231 5 YQNASGQIVLDYAKAIQESVFEQLRVVRDGQLRIVFSPDLKI-------------CSWEFCARRHEELIP 61 (490)
Q Consensus 5 ~~LpNG~~vVE~~KAs~~y~Fen~qVV~~GtLRa~FdpdLKI-------------EswEF~t~~HEEyIP 61 (490)
.++..|.+-+|...-.|.|.||...+|.+|+|++..+- -|+ -.+.|.+..|-+++.
T Consensus 75 ~~l~~Gf~~le~~~f~wtl~YDEi~~VlEG~L~i~~~G-~~~~A~~GDvi~iPkGs~I~fst~~~a~~~Y 143 (152)
T PF06249_consen 75 PRLSAGFMELEKTSFPWTLTYDEIKYVLEGTLEISIDG-QTVTAKPGDVIFIPKGSTITFSTPDYARFFY 143 (152)
T ss_dssp -SSEEEEEEEEEEEEEEE-SSEEEEEEEEEEEEEEETT-EEEEEETT-EEEE-TT-EEEEEEEEEEEEEE
T ss_pred CceeeEEEEEeCCCccEEeecceEEEEEEeEEEEEECC-EEEEEcCCcEEEECCCCEEEEecCCCEEEEE
Confidence 36778888888877677777777999999999998652 222 234566666665554
No 4
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=32.92 E-value=53 Score=33.39 Aligned_cols=41 Identities=15% Similarity=0.169 Sum_probs=34.0
Q ss_pred CCccccCCCcEEEEecceeEEEEeeceEEEEeeeEEEEECC
Q 011231 2 PREYQNASGQIVLDYAKAIQESVFEQLRVVRDGQLRIVFSP 42 (490)
Q Consensus 2 PrE~~LpNG~~vVE~~KAs~~y~Fen~qVV~~GtLRa~Fdp 42 (490)
+.+.++.-|.+.+|....-|.+-|+..-.|.+|.|+++.+-
T Consensus 152 ~d~s~m~aGf~~~~~~sf~wtl~~dEi~YVLEGe~~l~IdG 192 (233)
T PRK15457 152 DDGSSMAAGFMQWENAFFPWTLNYDEIDMVLEGELHVRHEG 192 (233)
T ss_pred CCCCceeeEEEEEecCccceeccceEEEEEEEeEEEEEECC
Confidence 34567788999999887777777888999999999999863
No 5
>COG4907 Predicted membrane protein [Function unknown]
Probab=31.01 E-value=31 Score=38.50 Aligned_cols=19 Identities=37% Similarity=0.589 Sum_probs=11.4
Q ss_pred CCCCcCCCCCCCCCCCCCc
Q 011231 409 NNPGIGTGGYGNMGGGLGQ 427 (490)
Q Consensus 409 ~~~~~~~~~~g~~g~g~g~ 427 (490)
..+|.||||+|.-|||+|-
T Consensus 571 ~~~~~~GGG~G~~gGg~GG 589 (595)
T COG4907 571 RRSSSSGGGGGFSGGGSGG 589 (595)
T ss_pred ccCCCCCCCCCcCCCCCCC
Confidence 3455666666666666654
No 6
>PF13897 GOLD_2: Golgi-dynamics membrane-trafficking
Probab=27.29 E-value=51 Score=31.14 Aligned_cols=23 Identities=26% Similarity=0.508 Sum_probs=20.7
Q ss_pred eEEEEECCCCceeEEEEeeccee
Q 011231 35 QLRIVFSPDLKICSWEFCARRHE 57 (490)
Q Consensus 35 tLRa~FdpdLKIEswEF~t~~HE 57 (490)
++|+-+-|+.|...|||+|.+|.
T Consensus 8 tvrVpt~~~G~~l~WeFaTd~yD 30 (136)
T PF13897_consen 8 TVRVPTHPEGKCLFWEFATDSYD 30 (136)
T ss_pred EEEcccCCCCCEEEEEEeeCCCC
Confidence 57888899999999999999984
No 7
>PF08076 TetM_leader: Tetracycline resistance determinant leader peptide; InterPro: IPR012992 The antibiotic tetracycline has a broad spectrum of activity, acting to inhibit bacterial protein synthesis by binding to the 30S ribosomal subunit, which prevents the association of the aminoacyl-tRNA to the ribosomal acceptor A site. Tetracycline binding is reversible, therefore diluting out the antibiotic can reverse its effects. Tetracycline resistance genes are often located on mobile elements, such as plasmids, transposons and/or conjugative transposons, which can sometimes be transferred between bacterial species. In certain cases, tetracycline can enhance the transfer of these elements, thereby promoting resistance amongst a bacterial colony. There are three types of tetracycline resistance: tetracycline efflux, ribosomal protection, and tetracycline modification [, ]: Tetracycline efflux proteins belong to the major facilitator superfamily. Efflux proteins are membrane-associated proteins that recognise and export tetracycline from the cell. They are found in both Gram-positive and Gram-negative bacteria []. There are at least 22 different tetracycline efflux proteins, grouped according to sequence similarity: Group 1 are Tet(A), Tet(B), Tet(C), Tet(D), Tet(E), Tet(G), Tet(H), Tet(J), Tet(Z) and Tet(30); Group 2 are Tet(K) and Tet(L); Group 3 are Otr(B) and Tcr(3); Group 4 is TetA(P); Group 5 is Tet(V). In addition, there are the efflux proteins Tet(31), Tet(33), Tet(V), Tet(Y), Tet(34), and Tet(35). Ribosomal protection proteins are cytoplasmic proteins that display homology with the elongation factors EF-Tu and EF-G. Protection proteins bind the ribosome, causing an alteration in ribosomal conformation that prevents tetracycline from binding. There are at least ten ribosomal protection proteins: Tet(M), Tet(O), Tet(S), Tet(W), Tet(32), Tet(36), Tet(Q), Tet(T), Otr(A), and TetB(P). Both Tet(M) and Tet(O) have ribosome-dependent GTPase activity, the hydrolysis of GTP providing the energy for the ribosomal conformational changes. Tetracycline modification proteins include the enzymes Tet(37) and Tet(X), both of which inactivate tetracycline. In addition, there are the tetracycline resistance proteins Tet(U) and Otr(C). The expression of several of these tet genes is controlled by a family of tetracycline transcriptional regulators known as TetR. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity []. The TetR proteins identified in over 115 genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. This entry represents the tetracycline resistance leader peptide, which can be found in Tet(M) ribosomal protection proteins. A short open reading frame corresponding to a 28 amino acid peptide, which contains a number of inverted repeat sequences was found immediately upstream of tet(M). Transcriptional analyses has found that expression of tet(M) resulted from an extension of a small transcript representing the upstream leader region into the resistance determinant. Therefore, this leader sequence is responsible for transcriptional attenuation and thus regulation of the transcription of tet(M) [].
Probab=26.15 E-value=23 Score=25.27 Aligned_cols=16 Identities=38% Similarity=0.960 Sum_probs=12.9
Q ss_pred EECCCCceeEEEEeec
Q 011231 39 VFSPDLKICSWEFCAR 54 (490)
Q Consensus 39 ~FdpdLKIEswEF~t~ 54 (490)
+|-.|.-|.+||||+.
T Consensus 10 ~fP~D~S~y~WDF~~~ 25 (28)
T PF08076_consen 10 HFPSDKSIYHWDFCSL 25 (28)
T ss_pred cCCCccceeehhhhhh
Confidence 4556899999999974
No 8
>PF11197 DUF2835: Protein of unknown function (DUF2835); InterPro: IPR021363 This is a bacterial family of uncharacterised proteins. One member of this family (A4VM42 from SWISSPROT) is annotated as the A subunit of Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV).
Probab=23.69 E-value=93 Score=26.07 Aligned_cols=19 Identities=32% Similarity=0.517 Sum_probs=16.9
Q ss_pred EeeeEEEEECCCCceeEEE
Q 011231 32 RDGQLRIVFSPDLKICSWE 50 (490)
Q Consensus 32 ~~GtLRa~FdpdLKIEswE 50 (490)
..|..|++||.+.|+.++|
T Consensus 49 v~G~F~l~~d~~~kf~sle 67 (68)
T PF11197_consen 49 VHGRFRLEFDDNNKFVSLE 67 (68)
T ss_pred ceEEEEEEECCCCCEEEeE
Confidence 3699999999999999886
No 9
>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=22.06 E-value=1.4e+02 Score=28.21 Aligned_cols=33 Identities=24% Similarity=0.371 Sum_probs=25.2
Q ss_pred eEEEEeeeEEEEECCCCceeEEEEeecceecccccch
Q 011231 28 LRVVRDGQLRIVFSPDLKICSWEFCARRHEELIPRRL 64 (490)
Q Consensus 28 ~qVV~~GtLRa~FdpdLKIEswEF~t~~HEEyIPR~~ 64 (490)
..||.+|+| +.+.++..=+.-+++.|+|-|+..
T Consensus 100 ~~VVv~G~~----~~~g~F~A~~vLaKc~skY~p~ev 132 (148)
T PRK13254 100 QGVVAEGRL----QDGGVFVADEVLAKHDENYMPKEV 132 (148)
T ss_pred CEEEEEEEE----CCCCeEEEEEEEecCCCCCCCHHH
Confidence 445555543 456789999999999999999764
No 10
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=18.54 E-value=35 Score=27.72 Aligned_cols=35 Identities=34% Similarity=0.717 Sum_probs=25.8
Q ss_pred hccCCccCCCCCcccchhhhhHHHHHhchHHHHHHhh
Q 011231 112 ALEVPLVNDLGYTKRYVRCLQISEVVNSMKDLIDYSR 148 (490)
Q Consensus 112 ~ldlP~VNe~GvpkrvmRcLEIAEVVnqMkDLm~FS~ 148 (490)
.++.| |.++|++.|.++||.=+ -+....||+.|+.
T Consensus 9 ~~~~~-I~~L~LS~Ra~n~L~~~-~I~tv~dL~~~s~ 43 (66)
T PF03118_consen 9 LLDTP-IEDLGLSVRAYNCLKRA-GIHTVGDLVKYSE 43 (66)
T ss_dssp HHCSB-GGGSTSBHHHHHHHHCT-T--BHHHHHCS-H
T ss_pred HhcCc-HHHhCCCHHHHHHHHHh-CCcCHHHHHhCCH
Confidence 35566 99999999999999866 4567777877765
Done!