Query 025751
Match_columns 248
No_of_seqs 309 out of 1330
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 09:08:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025751.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025751hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00018 AP2 DNA-binding domain 99.9 2E-21 4.4E-26 139.5 7.6 61 73-133 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 1.8E-20 3.8E-25 136.3 8.2 62 74-135 1-62 (64)
3 PHA00280 putative NHN endonucl 99.4 6E-13 1.3E-17 109.0 7.5 61 64-127 58-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.1 1.2E-10 2.6E-15 81.6 5.7 52 73-124 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 76.9 10 0.00022 25.5 5.5 38 85-122 1-42 (46)
6 cd00801 INT_P4 Bacteriophage P 63.7 15 0.00032 32.8 5.2 38 84-121 10-49 (357)
7 PF13356 DUF4102: Domain of un 57.1 29 0.00064 26.0 5.1 40 79-118 28-71 (89)
8 PHA02601 int integrase; Provis 56.1 18 0.0004 32.6 4.5 43 77-120 2-45 (333)
9 PRK09692 integrase; Provisiona 51.6 40 0.00087 31.8 6.2 36 78-113 33-74 (413)
10 PF05036 SPOR: Sporulation rel 41.9 31 0.00068 24.0 3.0 24 95-118 42-65 (76)
11 PF10729 CedA: Cell division a 32.9 81 0.0018 24.1 4.0 38 72-112 30-67 (80)
12 PF14112 DUF4284: Domain of un 32.0 30 0.00064 28.2 1.7 18 97-114 2-19 (122)
13 PF08846 DUF1816: Domain of un 28.0 1.2E+02 0.0025 22.8 4.1 38 85-122 9-46 (68)
14 PF00352 TBP: Transcription fa 26.4 1.9E+02 0.0042 21.6 5.2 45 74-121 37-82 (86)
15 PF07494 Reg_prop: Two compone 26.0 61 0.0013 18.9 1.9 11 95-105 14-24 (24)
16 PF08471 Ribonuc_red_2_N: Clas 25.6 76 0.0016 25.3 2.9 20 102-121 71-90 (93)
17 PF12404 DUF3663: Peptidase ; 24.2 36 0.00078 26.2 0.8 40 118-157 10-49 (77)
18 PLN00062 TATA-box-binding prot 23.3 3.3E+02 0.0071 23.8 6.7 57 73-132 34-91 (179)
19 cd04517 TLF TBP-like factors ( 23.0 3.4E+02 0.0074 23.4 6.8 46 74-122 35-81 (174)
20 cd04516 TBP_eukaryotes eukaryo 22.5 3.6E+02 0.0078 23.3 6.8 47 73-122 34-81 (174)
No 1
>cd00018 AP2 DNA-binding domain found in transcription regulators in plants such as APETALA2 and EREBP (ethylene responsive element binding protein). In EREBPs the domain specifically binds to the 11bp GCC box of the ethylene response element (ERE), a promotor element essential for ethylene responsiveness. EREBPs and the C-repeat binding factor CBF1, which is involved in stress response, contain a single copy of the AP2 domain. APETALA2-like proteins, which play a role in plant development contain two copies.
Probab=99.85 E-value=2e-21 Score=139.53 Aligned_cols=61 Identities=64% Similarity=1.093 Sum_probs=57.8
Q ss_pred CceeeeEeCCCCcEEEEEecCCCCeeeecCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 025751 73 PTYRGVRMRQWGKWVSEIREPRKKSRIWLGTFATPEMAARAHDVAALAIKGHSAYLNFPEL 133 (248)
Q Consensus 73 s~yRGVr~r~~GkW~AeIr~p~~~kriwLGtf~T~EeAArAYD~AA~~l~G~~a~lNFp~~ 133 (248)
|+||||+++++|||+|+|+.+..++++|||+|+|+||||+|||.|+++++|.++.+|||++
T Consensus 1 s~~~GV~~~~~gkw~A~I~~~~~gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~ 61 (61)
T cd00018 1 SKYRGVRQRPWGKWVAEIRDPSGGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPDS 61 (61)
T ss_pred CCccCEEECCCCcEEEEEEeCCCCceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCCC
Confidence 5899999998899999999966699999999999999999999999999999999999985
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.83 E-value=1.8e-20 Score=136.29 Aligned_cols=62 Identities=61% Similarity=1.045 Sum_probs=59.0
Q ss_pred ceeeeEeCCCCcEEEEEecCCCCeeeecCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCCCC
Q 025751 74 TYRGVRMRQWGKWVSEIREPRKKSRIWLGTFATPEMAARAHDVAALAIKGHSAYLNFPELAH 135 (248)
Q Consensus 74 ~yRGVr~r~~GkW~AeIr~p~~~kriwLGtf~T~EeAArAYD~AA~~l~G~~a~lNFp~~~~ 135 (248)
+|+||+++++|||+|+|+.+.+++++|||+|+|+||||+|||.|+++++|..+.+|||.+.+
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y 62 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLY 62 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccC
Confidence 59999989899999999999999999999999999999999999999999999999998754
No 3
>PHA00280 putative NHN endonuclease
Probab=99.40 E-value=6e-13 Score=108.98 Aligned_cols=61 Identities=11% Similarity=0.136 Sum_probs=53.6
Q ss_pred cCCCCCCCCCceeeeEeC-CCCcEEEEEecCCCCeeeecCCCCCHHHHHHHHHHHHHHhcCCCCC
Q 025751 64 TRKVSDLKHPTYRGVRMR-QWGKWVSEIREPRKKSRIWLGTFATPEMAARAHDVAALAIKGHSAY 127 (248)
Q Consensus 64 ~~~~~~~~ss~yRGVr~r-~~GkW~AeIr~p~~~kriwLGtf~T~EeAArAYD~AA~~l~G~~a~ 127 (248)
+++.+++++|+|+||.++ ..|||+|+|+. +||+++||.|+++|+|+.||+ ++.+|+|.+|.
T Consensus 58 N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~--~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 58 NMKTPKSNTSGLKGLSWSKEREMWRGTVTA--EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred ccCCCCCCCCCCCeeEEecCCCeEEEEEEE--CCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 344456788999999977 66999999999 999999999999999999997 77889998875
No 4
>PF00847 AP2: AP2 domain; InterPro: IPR001471 Pathogenesis-related genes transcriptional activator binds to the GCC-box pathogenesis-related promoter element and activates the plant's defence genes. Ethylene, chemically the simplest plant hormone, participates in a number of stress responses and developmental processes: e.g., fruit ripening, inhibition of stem and root elongation, promotion of seed germination and flowering, senescence of leaves and flowers, and sex determination []. DNA sequence elements that confer ethylene responsiveness have been shown to contain two 11bp GCC boxes, which are necessary and sufficient for transcriptional control by ethylene. Ethylene responsive element binding proteins (EREBPs) have now been identified in a variety of plants. The proteins share a similar domain of around 59 amino acids, which interacts directly with the GCC box in the ERE.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3IGM_A 3GCC_A 1GCC_A 2GCC_A.
Probab=99.12 E-value=1.2e-10 Score=81.65 Aligned_cols=52 Identities=31% Similarity=0.505 Sum_probs=45.4
Q ss_pred CceeeeEeC-CCCcEEEEEecCCC---CeeeecCCCCCHHHHHHHHHHHHHHhcCC
Q 025751 73 PTYRGVRMR-QWGKWVSEIREPRK---KSRIWLGTFATPEMAARAHDVAALAIKGH 124 (248)
Q Consensus 73 s~yRGVr~r-~~GkW~AeIr~p~~---~kriwLGtf~T~EeAArAYD~AA~~l~G~ 124 (248)
|+|+||+++ ..++|+|+|+++.. +++++||.|+++++|++||+.+++.++|+
T Consensus 1 s~~~GV~~~~~~~~W~a~i~~~~~~g~~k~f~~g~fg~~~eA~~~a~~~r~~~~~e 56 (56)
T PF00847_consen 1 SGYKGVSWDKRRGRWRAQIRVWSENGKRKRFSVGKFGFEEEAKRAAIEARKELEGE 56 (56)
T ss_dssp SSSTTEEEETTTTEEEEEEEECCCTTEEEEEEECCCCCHHHHHHHHHHHHHHCTS-
T ss_pred CCcEEEEEcCCCCEEEEEEEEcccCcccEEEeCccCCCHHHHHHHHHHHHHHhcCC
Confidence 689999877 57999999999522 49999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=76.89 E-value=10 Score=25.47 Aligned_cols=38 Identities=16% Similarity=0.221 Sum_probs=29.4
Q ss_pred cEEEEEe--cC--CCCeeeecCCCCCHHHHHHHHHHHHHHhc
Q 025751 85 KWVSEIR--EP--RKKSRIWLGTFATPEMAARAHDVAALAIK 122 (248)
Q Consensus 85 kW~AeIr--~p--~~~kriwLGtf~T~EeAArAYD~AA~~l~ 122 (248)
+|...|. .+ ++.++++-+.|.|..||-.+.......+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 5788883 43 34478899999999999999888776653
No 6
>cd00801 INT_P4 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall reaction mechanism with the superfamily of DNA breaking-rejoining enzymes. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes.
Probab=63.68 E-value=15 Score=32.82 Aligned_cols=38 Identities=24% Similarity=0.352 Sum_probs=27.6
Q ss_pred CcEEEEEecCCCCeeeecCCCC--CHHHHHHHHHHHHHHh
Q 025751 84 GKWVSEIREPRKKSRIWLGTFA--TPEMAARAHDVAALAI 121 (248)
Q Consensus 84 GkW~AeIr~p~~~kriwLGtf~--T~EeAArAYD~AA~~l 121 (248)
+.|..+++..++.+++.||+|+ +.++|..........+
T Consensus 10 ~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 10 KSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred EEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 5699999997777789999995 6667766655543333
No 7
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=57.13 E-value=29 Score=26.04 Aligned_cols=40 Identities=23% Similarity=0.236 Sum_probs=25.8
Q ss_pred EeCCCC--cEEEEEecCCCCeeeecCCCCC--HHHHHHHHHHHH
Q 025751 79 RMRQWG--KWVSEIREPRKKSRIWLGTFAT--PEMAARAHDVAA 118 (248)
Q Consensus 79 r~r~~G--kW~AeIr~p~~~kriwLGtf~T--~EeAArAYD~AA 118 (248)
+..+.| .|.-+.+..++.+++.||.|+. ..+|........
T Consensus 28 ~v~~~G~kt~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~~ 71 (89)
T PF13356_consen 28 RVTPSGSKTFYFRYRINGKRRRITLGRYPELSLAEAREKARELR 71 (89)
T ss_dssp EE-TTS-EEEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHHH
T ss_pred EEEeCCCeEEEEEEEecceEEEeccCCCccCCHHHHHHHHHHHH
Confidence 333444 5999888866668899999975 555554444433
No 8
>PHA02601 int integrase; Provisional
Probab=56.09 E-value=18 Score=32.65 Aligned_cols=43 Identities=33% Similarity=0.378 Sum_probs=28.7
Q ss_pred eeEeCCCCcEEEEEecC-CCCeeeecCCCCCHHHHHHHHHHHHHH
Q 025751 77 GVRMRQWGKWVSEIREP-RKKSRIWLGTFATPEMAARAHDVAALA 120 (248)
Q Consensus 77 GVr~r~~GkW~AeIr~p-~~~kriwLGtf~T~EeAArAYD~AA~~ 120 (248)
+|++...|+|.++++.. ..|+++. .+|.|..||-+........
T Consensus 2 ~~~~~~~g~w~~~~~~~~~~g~r~~-~~f~tk~eA~~~~~~~~~~ 45 (333)
T PHA02601 2 AVRKLKDGKWLCEIYPNGRDGKRIR-KRFATKGEALAFENYTMAE 45 (333)
T ss_pred ceEEcCCCCEEEEEEECCCCCchhh-hhhcCHHHHHHHHHHHHHh
Confidence 46666778999999852 2355554 3699998887665554333
No 9
>PRK09692 integrase; Provisional
Probab=51.57 E-value=40 Score=31.80 Aligned_cols=36 Identities=17% Similarity=0.299 Sum_probs=22.8
Q ss_pred eEeCCCC--cEEEEEecCC--CCeeeecCCCC--CHHHHHHH
Q 025751 78 VRMRQWG--KWVSEIREPR--KKSRIWLGTFA--TPEMAARA 113 (248)
Q Consensus 78 Vr~r~~G--kW~AeIr~p~--~~kriwLGtf~--T~EeAArA 113 (248)
|+.++.| .|+.+.+.+. +.+++-||.|+ |..+|..+
T Consensus 33 l~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~ 74 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNY 74 (413)
T ss_pred EEEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHH
Confidence 4444444 4999887553 33457899999 56555443
No 10
>PF05036 SPOR: Sporulation related domain; InterPro: IPR007730 This 70 residue domain is composed of two 35 residue repeats that are found in bacterial proteins involved in sporulation and cell division, such as FtsN, CwlM and RlpA. This repeat might be involved in binding peptidoglycan. FtsN is an essential cell division protein with a simple bitopic topology: a short N-terminal cytoplasmic segment fused to a large carboxy periplasmic domain through a single transmembrane domain. The repeats lie at the periplasmic C terminus, which has an RNP-like fold []. FtsN localises to the septum ring complex. The CwlM protein is a cell wall hydrolase, where the C-terminal region, including the repeats, determines substrate specificity []. RlpA is a rare lipoprotein A protein that may be important for cell division. Its N-terminal cysteine may be attached to thioglyceride and N-fatty acyl residues [].; PDB: 1X60_A 1UTA_A.
Probab=41.87 E-value=31 Score=23.96 Aligned_cols=24 Identities=25% Similarity=0.248 Sum_probs=18.9
Q ss_pred CCeeeecCCCCCHHHHHHHHHHHH
Q 025751 95 KKSRIWLGTFATPEMAARAHDVAA 118 (248)
Q Consensus 95 ~~kriwLGtf~T~EeAArAYD~AA 118 (248)
..-+|.+|.|.+.++|..+-....
T Consensus 42 ~~yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 42 PWYRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp TCEEEEECCECTCCHHHHHHHHHH
T ss_pred ceEEEEECCCCCHHHHHHHHHHHh
Confidence 456888999999999988766544
No 11
>PF10729 CedA: Cell division activator CedA; InterPro: IPR019666 CedA is made up of four antiparallel beta-strands and an alpha-helix. It activates cell division by inhibiting chromosome over-replication. This is mediated by binding to dsDNA via the beta-sheet [, ]. ; GO: 0003677 DNA binding, 0051301 cell division; PDB: 2BN8_A 2D35_A.
Probab=32.92 E-value=81 Score=24.06 Aligned_cols=38 Identities=26% Similarity=0.306 Sum_probs=24.4
Q ss_pred CCceeeeEeCCCCcEEEEEecCCCCeeeecCCCCCHHHHHH
Q 025751 72 HPTYRGVRMRQWGKWVSEIREPRKKSRIWLGTFATPEMAAR 112 (248)
Q Consensus 72 ss~yRGVr~r~~GkW~AeIr~p~~~kriwLGtf~T~EeAAr 112 (248)
--+||-|..-+ |||+|.+-. +..-..--.|..+|.|-|
T Consensus 30 ~dgfrdvw~lr-gkyvafvl~--ge~f~rsp~fs~pesaqr 67 (80)
T PF10729_consen 30 MDGFRDVWQLR-GKYVAFVLM--GEHFRRSPAFSVPESAQR 67 (80)
T ss_dssp TTTECCECCCC-CEEEEEEES--SS-EEE---BSSHHHHHH
T ss_pred cccccceeeec-cceEEEEEe--cchhccCCCcCCcHHHHH
Confidence 34688885545 999999988 444444467788877765
No 12
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=32.00 E-value=30 Score=28.17 Aligned_cols=18 Identities=22% Similarity=0.595 Sum_probs=14.0
Q ss_pred eeeecCCCCCHHHHHHHH
Q 025751 97 SRIWLGTFATPEMAARAH 114 (248)
Q Consensus 97 kriwLGtf~T~EeAArAY 114 (248)
..||||+|.+.++--.=.
T Consensus 2 VsiWiG~f~s~~el~~Y~ 19 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEYF 19 (122)
T ss_pred eEEEEecCCCHHHHHHHh
Confidence 469999999988766543
No 13
>PF08846 DUF1816: Domain of unknown function (DUF1816); InterPro: IPR014945 Q4C9H3 from SWISSPROT is associated with the IPR008213 from INTERPRO domain suggesting this protein could have a role in phycobilisomes.
Probab=27.95 E-value=1.2e+02 Score=22.83 Aligned_cols=38 Identities=21% Similarity=0.313 Sum_probs=27.9
Q ss_pred cEEEEEecCCCCeeeecCCCCCHHHHHHHHHHHHHHhc
Q 025751 85 KWVSEIREPRKKSRIWLGTFATPEMAARAHDVAALAIK 122 (248)
Q Consensus 85 kW~AeIr~p~~~kriwLGtf~T~EeAArAYD~AA~~l~ 122 (248)
.|=++|.--.-.-..|.|-|.|.+||..+.---..-+.
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~ 46 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLE 46 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHH
Confidence 46678877445567899999999999988655444443
No 14
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=26.36 E-value=1.9e+02 Score=21.62 Aligned_cols=45 Identities=18% Similarity=0.130 Sum_probs=33.6
Q ss_pred ceeeeEeC-CCCcEEEEEecCCCCeeeecCCCCCHHHHHHHHHHHHHHh
Q 025751 74 TYRGVRMR-QWGKWVSEIREPRKKSRIWLGTFATPEMAARAHDVAALAI 121 (248)
Q Consensus 74 ~yRGVr~r-~~GkW~AeIr~p~~~kriwLGtf~T~EeAArAYD~AA~~l 121 (248)
+|.||..| ..-+-.+.|.. .||-+..|. .++|++..|.+.....+
T Consensus 37 ~fpgl~~r~~~p~~t~~IF~--sGki~itGa-ks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 37 RFPGLIYRLRNPKATVLIFS--SGKIVITGA-KSEEEAKKAIEKILPIL 82 (86)
T ss_dssp TESSEEEEETTTTEEEEEET--TSEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred cCCeEEEeecCCcEEEEEEc--CCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 58898766 43466777777 888777775 78899999988876554
No 15
>PF07494 Reg_prop: Two component regulator propeller; InterPro: IPR011110 A large group of two component regulator proteins appear to have the same N-terminal structure of 14 tandem repeats. These repeats show homology to members of IPR002372 from INTERPRO and IPR001680 from INTERPRO indicating that they are likely to form a beta-propeller. This family has been built with artificially high cut-offs in order to avoid overlaps with other beta-propeller families. The fourteen repeats are likely to form two propellers; it is not clear if these structures are likely to recruit other proteins or interact with DNA.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
Probab=25.96 E-value=61 Score=18.86 Aligned_cols=11 Identities=27% Similarity=1.060 Sum_probs=8.6
Q ss_pred CCeeeecCCCC
Q 025751 95 KKSRIWLGTFA 105 (248)
Q Consensus 95 ~~kriwLGtf~ 105 (248)
+..+||+||+.
T Consensus 14 ~~G~lWigT~~ 24 (24)
T PF07494_consen 14 SDGNLWIGTYN 24 (24)
T ss_dssp TTSCEEEEETS
T ss_pred CCcCEEEEeCC
Confidence 56689999873
No 16
>PF08471 Ribonuc_red_2_N: Class II vitamin B12-dependent ribonucleotide reductase; InterPro: IPR013678 This domain is found to the N terminus of the ribonucleotide reductase barrel domain (IPR000788 from INTERPRO). It occurs in bacterial class II ribonucleotide reductase proteins which depend upon coenzyme B12 (deoxyadenosylcobalamine) []. ; GO: 0004748 ribonucleoside-diphosphate reductase activity, 0050897 cobalt ion binding, 0055114 oxidation-reduction process
Probab=25.60 E-value=76 Score=25.27 Aligned_cols=20 Identities=35% Similarity=0.306 Sum_probs=17.4
Q ss_pred CCCCCHHHHHHHHHHHHHHh
Q 025751 102 GTFATPEMAARAHDVAALAI 121 (248)
Q Consensus 102 Gtf~T~EeAArAYD~AA~~l 121 (248)
|+|+|+|+|..-||.-...|
T Consensus 71 GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 71 GYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCcCCHHHHHHHHHHHHHHH
Confidence 99999999999999866554
No 17
>PF12404 DUF3663: Peptidase ; InterPro: IPR008330 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This family represents the peptidase B group of leucyl aminopeptidases, which are restricted to the gammaproteobacteria. They contain a C-terminal aminopeptidase catalytic domain and an N-terminal domain of unknown function. They are zinc-dependent exopeptidases (3.4.11.1 from EC) and belong to MEROPS peptidase family M17 (leucyl aminopeptidase family, clan MF). They selectively release N-terminal amino acid residues from polypeptides and proteins and are involved in the processing, catabolism and degradation of intracellular proteins [, , ]. Leucyl aminopeptidase forms a homohexamer containing two trimers stacked on top of one another []. Each monomer binds two zinc ions. The zinc-binding and catalytic sites are located within the C-terminal catalytic domain []. The same catalytic aminopeptidase domain is found in the other M17 peptidases IPR011356 from INTERPRO. These two groups of aminopeptidases differ by their N-terminal domains. The N-terminal domain in members of IPR011356 from INTERPRO has been implicated in DNA binding [, ] and it is not associated with members of this family which have a different N-terminal domain and therefore are not expected to bind DNA or be involved in transcriptional regulation. In addition, there are related proteins with the same catalytic domain and unique N-terminal sequences unrelated to any of the two N-terminal domains discussed above. For additional information please see [, , , ]. ; GO: 0004177 aminopeptidase activity, 0008235 metalloexopeptidase activity, 0030145 manganese ion binding, 0005737 cytoplasm
Probab=24.18 E-value=36 Score=26.17 Aligned_cols=40 Identities=30% Similarity=0.272 Sum_probs=27.3
Q ss_pred HHHhcCCCCCCCCCCCCCCCCCCCCCChHHHHHHHHHHHH
Q 025751 118 ALAIKGHSAYLNFPELAHELPRPATSSPKDIQAAAAKAAA 157 (248)
Q Consensus 118 A~~l~G~~a~lNFp~~~~~~p~p~~~~~~diq~aa~~aa~ 157 (248)
|-..||.+|.+-|-+.-..+..-.......||+||.+--.
T Consensus 10 A~a~WG~~AllSf~~~ga~IHl~~~~~l~~IQrAaRkLd~ 49 (77)
T PF12404_consen 10 AAAHWGEKALLSFNEQGATIHLSEGDDLRAIQRAARKLDG 49 (77)
T ss_pred ChhHhCcCcEEEEcCCCEEEEECCCcchHHHHHHHHHHhh
Confidence 3347888888888877655555444456788888876543
No 18
>PLN00062 TATA-box-binding protein; Provisional
Probab=23.28 E-value=3.3e+02 Score=23.75 Aligned_cols=57 Identities=18% Similarity=0.064 Sum_probs=38.6
Q ss_pred CceeeeEeC-CCCcEEEEEecCCCCeeeecCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCC
Q 025751 73 PTYRGVRMR-QWGKWVSEIREPRKKSRIWLGTFATPEMAARAHDVAALAIKGHSAYLNFPE 132 (248)
Q Consensus 73 s~yRGVr~r-~~GkW~AeIr~p~~~kriwLGtf~T~EeAArAYD~AA~~l~G~~a~lNFp~ 132 (248)
.+|-||..| +.-|-.+-|.. .||-+--| ..++|+|..|.++.+..+..-.-..+|++
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~--SGKiviTG-aks~e~a~~a~~~~~~~L~~lg~~~~~~~ 91 (179)
T PLN00062 34 KRFAAVIMRIREPKTTALIFA--SGKMVCTG-AKSEHDSKLAARKYARIIQKLGFPAKFKD 91 (179)
T ss_pred ccCcEEEEEeCCCcEEEEEEC--CCeEEEEe-cCCHHHHHHHHHHHHHHHHHcCCCcCCCc
Confidence 368899777 44567777777 77766555 47889999999988777743222344443
No 19
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=22.97 E-value=3.4e+02 Score=23.38 Aligned_cols=46 Identities=22% Similarity=0.180 Sum_probs=35.1
Q ss_pred ceeeeEeC-CCCcEEEEEecCCCCeeeecCCCCCHHHHHHHHHHHHHHhc
Q 025751 74 TYRGVRMR-QWGKWVSEIREPRKKSRIWLGTFATPEMAARAHDVAALAIK 122 (248)
Q Consensus 74 ~yRGVr~r-~~GkW~AeIr~p~~~kriwLGtf~T~EeAArAYD~AA~~l~ 122 (248)
+|.||..| +.-|-.+-|.. .||-+=-| ..+.|+|.+|.++.+..+.
T Consensus 35 ~fpgli~R~~~Pk~t~lIF~--sGKiviTG-aks~~~~~~a~~~~~~~l~ 81 (174)
T cd04517 35 RYPKVTMRLREPRATASVWS--SGKITITG-ATSEEEAKQAARRAARLLQ 81 (174)
T ss_pred CCCEEEEEecCCcEEEEEEC--CCeEEEEc-cCCHHHHHHHHHHHHHHHH
Confidence 79999777 44577788887 77755444 5899999999998877763
No 20
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=22.48 E-value=3.6e+02 Score=23.32 Aligned_cols=47 Identities=19% Similarity=0.111 Sum_probs=35.4
Q ss_pred CceeeeEeC-CCCcEEEEEecCCCCeeeecCCCCCHHHHHHHHHHHHHHhc
Q 025751 73 PTYRGVRMR-QWGKWVSEIREPRKKSRIWLGTFATPEMAARAHDVAALAIK 122 (248)
Q Consensus 73 s~yRGVr~r-~~GkW~AeIr~p~~~kriwLGtf~T~EeAArAYD~AA~~l~ 122 (248)
.+|-||..| ..-+-.+-|.. .||-+--|. .++|+|..|.++.+..+.
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~--SGKiviTGa-ks~e~a~~a~~~i~~~L~ 81 (174)
T cd04516 34 KRFAAVIMRIREPKTTALIFS--SGKMVCTGA-KSEDDSKLAARKYARIIQ 81 (174)
T ss_pred ccCcEEEEEeCCCcEEEEEEC--CCeEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 468899776 44577788887 888776676 578889989888777764
Done!