Query 041119
Match_columns 278
No_of_seqs 260 out of 1312
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 03:58:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041119.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041119hhsearch_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 99.8 9.2E-21 2E-25 138.3 7.5 61 59-119 1-61 (61)
2 PHA00280 putative NHN endonucl 99.8 2.6E-20 5.6E-25 155.2 7.5 88 23-113 31-119 (121)
3 smart00380 AP2 DNA-binding dom 99.8 6.2E-20 1.3E-24 135.6 8.3 62 60-121 1-62 (64)
4 PF00847 AP2: AP2 domain; Int 99.1 1.3E-10 2.7E-15 82.8 5.4 52 59-110 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 76.4 11 0.00023 26.0 5.6 38 71-108 1-42 (46)
6 PHA02601 int integrase; Provis 66.3 9.2 0.0002 35.1 4.5 44 63-107 2-46 (333)
7 PF13356 DUF4102: Domain of un 66.0 17 0.00037 27.9 5.3 43 65-107 28-74 (89)
8 cd00801 INT_P4 Bacteriophage P 63.1 17 0.00037 32.8 5.5 39 69-107 9-49 (357)
9 PRK09692 integrase; Provisiona 55.2 34 0.00074 32.8 6.4 37 64-100 33-75 (413)
10 PF13392 HNH_3: HNH endonuclea 53.4 1.9 4.1E-05 29.7 -1.8 27 23-49 20-46 (46)
11 PF05036 SPOR: Sporulation rel 44.4 23 0.0005 25.1 2.6 24 81-104 42-65 (76)
12 PF08846 DUF1816: Domain of un 43.7 53 0.0011 25.4 4.6 38 71-108 9-46 (68)
13 PF10729 CedA: Cell division a 42.4 40 0.00087 26.5 3.7 40 57-99 29-68 (80)
14 PLN00062 TATA-box-binding prot 34.4 1.8E+02 0.0038 26.0 7.1 58 58-118 33-91 (179)
15 PF15376 DUF4603: Domain of un 33.9 28 0.00062 38.4 2.3 16 63-78 253-268 (1286)
16 cd04516 TBP_eukaryotes eukaryo 32.5 2E+02 0.0043 25.5 7.1 58 58-118 33-91 (174)
17 PF08471 Ribonuc_red_2_N: Clas 31.0 52 0.0011 26.9 2.9 20 88-107 71-90 (93)
18 cd04517 TLF TBP-like factors ( 30.0 1.9E+02 0.0042 25.5 6.6 46 60-108 35-81 (174)
19 PF00352 TBP: Transcription fa 29.7 1.4E+02 0.003 22.9 5.0 46 59-107 36-82 (86)
20 PRK10113 cell division modulat 26.5 50 0.0011 25.9 2.0 38 59-99 31-68 (80)
21 KOG3422 Mitochondrial ribosoma 22.1 1.7E+02 0.0036 27.5 4.8 38 71-110 133-170 (221)
22 PF12404 DUF3663: Peptidase ; 21.4 40 0.00088 26.6 0.6 40 105-144 11-50 (77)
23 cd01433 Ribosomal_L16_L10e Rib 21.1 1.7E+02 0.0037 23.7 4.2 44 63-108 59-106 (112)
24 PF09954 DUF2188: Uncharacteri 20.4 2.6E+02 0.0056 20.1 4.7 39 64-106 3-41 (62)
25 cd00652 TBP_TLF TATA box bindi 20.3 4.5E+02 0.0097 23.1 7.0 48 58-108 33-81 (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=99.83 E-value=9.2e-21 Score=138.27 Aligned_cols=61 Identities=64% Similarity=1.111 Sum_probs=57.3
Q ss_pred CceeEEEeCCCCcEEEEEecCCCCeEeecCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 041119 59 PVYRGVRMRAWGKWVSEIREPRKKSRIWLGTFSTPEMAARAHDVAALSIKGASAILNFPKL 119 (278)
Q Consensus 59 S~YRGVr~r~~GKW~AeI~~~~~~kri~LGtFdT~EeAArAYD~AAikl~G~~A~lNFP~~ 119 (278)
|+||||+++++|||+|+|+++..++++|||+|+|+||||+|||+|+++++|.++.+|||+.
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 5799999988899999999965599999999999999999999999999999999999973
No 2
>PHA00280 putative NHN endonuclease
Probab=99.82 E-value=2.6e-20 Score=155.19 Aligned_cols=88 Identities=11% Similarity=0.106 Sum_probs=82.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCchHhhccCCCCCCCCCCceeEEEeC-CCCcEEEEEecCCCCeEeecCCCCCHHHHHHHHH
Q 041119 23 LTNPPTGKPVTSDPDPTPTPDAAKKQKKRPRDDSKHPVYRGVRMR-AWGKWVSEIREPRKKSRIWLGTFSTPEMAARAHD 101 (278)
Q Consensus 23 l~~~~tG~p~dNr~~NlR~~t~~~n~rnr~~~s~~~S~YRGVr~r-~~GKW~AeI~~~~~~kri~LGtFdT~EeAArAYD 101 (278)
.++|.+|++.+|+++|||.+++.+|.+|+...++++++||||.++ ..|||+|+|+. +||+++||.|+++|+|+.||+
T Consensus 31 ~VdHidg~~~dnri~NLr~~T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~--~gK~~~lG~f~~~e~A~~a~~ 108 (121)
T PHA00280 31 YIDHIDGNPLNDALDNLRLALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTA--EGKQHNFRSRDLLEVVAWIYR 108 (121)
T ss_pred EEEcCCCCCCCCcHHHhhhcCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEEE--CCEEEEcCCCCCHHHHHHHHH
Confidence 589999999999999999999999999999888999999999975 57999999999 999999999999999999997
Q ss_pred HHHHHhcCCCCC
Q 041119 102 VAALSIKGASAI 113 (278)
Q Consensus 102 ~AAikl~G~~A~ 113 (278)
++.+++|++|.
T Consensus 109 -~~~~lhGeFa~ 119 (121)
T PHA00280 109 -TRRELHGQFAR 119 (121)
T ss_pred -HHHHHhhcccc
Confidence 77899999875
No 3
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.81 E-value=6.2e-20 Score=135.60 Aligned_cols=62 Identities=61% Similarity=1.025 Sum_probs=58.7
Q ss_pred ceeEEEeCCCCcEEEEEecCCCCeEeecCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCCCC
Q 041119 60 VYRGVRMRAWGKWVSEIREPRKKSRIWLGTFSTPEMAARAHDVAALSIKGASAILNFPKLAG 121 (278)
Q Consensus 60 ~YRGVr~r~~GKW~AeI~~~~~~kri~LGtFdT~EeAArAYD~AAikl~G~~A~lNFP~~~~ 121 (278)
+||||+++++|||+|+|+++.+++++|||+|+|+||||+|||.|+++++|..+.+|||...+
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 49999998889999999999899999999999999999999999999999999999998654
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=99.11 E-value=1.3e-10 Score=82.80 Aligned_cols=52 Identities=31% Similarity=0.476 Sum_probs=45.2
Q ss_pred CceeEEEeC-CCCcEEEEEecCCC---CeEeecCCCCCHHHHHHHHHHHHHHhcCC
Q 041119 59 PVYRGVRMR-AWGKWVSEIREPRK---KSRIWLGTFSTPEMAARAHDVAALSIKGA 110 (278)
Q Consensus 59 S~YRGVr~r-~~GKW~AeI~~~~~---~kri~LGtFdT~EeAArAYD~AAikl~G~ 110 (278)
|+|+||+++ ..++|+|+|++... +++++||.|++++||++||+.++++++|+
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 579999886 57999999998421 49999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=76.37 E-value=11 Score=26.02 Aligned_cols=38 Identities=16% Similarity=0.227 Sum_probs=29.0
Q ss_pred cEEEEEe--cC--CCCeEeecCCCCCHHHHHHHHHHHHHHhc
Q 041119 71 KWVSEIR--EP--RKKSRIWLGTFSTPEMAARAHDVAALSIK 108 (278)
Q Consensus 71 KW~AeI~--~~--~~~kri~LGtFdT~EeAArAYD~AAikl~ 108 (278)
+|..+|. .+ ++.++++-+-|.|..||..+...+...+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 5888883 33 34477899999999999999988776653
No 6
>PHA02601 int integrase; Provisional
Probab=66.27 E-value=9.2 Score=35.09 Aligned_cols=44 Identities=30% Similarity=0.363 Sum_probs=29.7
Q ss_pred EEEeCCCCcEEEEEecC-CCCeEeecCCCCCHHHHHHHHHHHHHHh
Q 041119 63 GVRMRAWGKWVSEIREP-RKKSRIWLGTFSTPEMAARAHDVAALSI 107 (278)
Q Consensus 63 GVr~r~~GKW~AeI~~~-~~~kri~LGtFdT~EeAArAYD~AAikl 107 (278)
+|+..+.|+|+++|... ..|+|+.. +|.|..||....+.....+
T Consensus 2 ~~~~~~~g~w~~~~~~~~~~g~r~~~-~f~tk~eA~~~~~~~~~~~ 46 (333)
T PHA02601 2 AVRKLKDGKWLCEIYPNGRDGKRIRK-RFATKGEALAFENYTMAEV 46 (333)
T ss_pred ceEEcCCCCEEEEEEECCCCCchhhh-hhcCHHHHHHHHHHHHHhc
Confidence 46666778999999852 23566553 6999998876665544333
No 7
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=66.04 E-value=17 Score=27.93 Aligned_cols=43 Identities=21% Similarity=0.223 Sum_probs=28.1
Q ss_pred EeCCCC--cEEEEEecCCCCeEeecCCCCC--HHHHHHHHHHHHHHh
Q 041119 65 RMRAWG--KWVSEIREPRKKSRIWLGTFST--PEMAARAHDVAALSI 107 (278)
Q Consensus 65 r~r~~G--KW~AeI~~~~~~kri~LGtFdT--~EeAArAYD~AAikl 107 (278)
+..+.| .|.-+.+..++.+++-||.|+. ..+|..........+
T Consensus 28 ~v~~~G~kt~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 28 RVTPSGSKTFYFRYRINGKRRRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp EE-TTS-EEEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred EEEeCCCeEEEEEEEecceEEEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 444554 4999988865667899999976 566655555444433
No 8
>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=63.14 E-value=17 Score=32.83 Aligned_cols=39 Identities=23% Similarity=0.308 Sum_probs=27.8
Q ss_pred CCcEEEEEecCCCCeEeecCCCC--CHHHHHHHHHHHHHHh
Q 041119 69 WGKWVSEIREPRKKSRIWLGTFS--TPEMAARAHDVAALSI 107 (278)
Q Consensus 69 ~GKW~AeI~~~~~~kri~LGtFd--T~EeAArAYD~AAikl 107 (278)
.+.|+.+++..++.+++.||+|+ +.++|....+.....+
T Consensus 9 ~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 9 SKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred CEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 35699999986666788999995 6677776655544433
No 9
>PRK09692 integrase; Provisional
Probab=55.17 E-value=34 Score=32.80 Aligned_cols=37 Identities=19% Similarity=0.310 Sum_probs=23.2
Q ss_pred EEeCCCC--cEEEEEecCCCC--eEeecCCCC--CHHHHHHHH
Q 041119 64 VRMRAWG--KWVSEIREPRKK--SRIWLGTFS--TPEMAARAH 100 (278)
Q Consensus 64 Vr~r~~G--KW~AeI~~~~~~--kri~LGtFd--T~EeAArAY 100 (278)
|+.++.| .|+.+.+.+.+| +++-||.|+ |..+|..+.
T Consensus 33 l~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a 75 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYR 75 (413)
T ss_pred EEEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHH
Confidence 4555555 499988754333 447899999 566654433
No 10
>PF13392 HNH_3: HNH endonuclease; PDB: 1U3E_M.
Probab=53.45 E-value=1.9 Score=29.68 Aligned_cols=27 Identities=7% Similarity=0.212 Sum_probs=18.6
Q ss_pred CCCCCCCCCCCCCCCCCCCCchHhhcc
Q 041119 23 LTNPPTGKPVTSDPDPTPTPDAAKKQK 49 (278)
Q Consensus 23 l~~~~tG~p~dNr~~NlR~~t~~~n~r 49 (278)
.++|..|++.+|+++||+..++.+|.|
T Consensus 20 ~v~H~~~~~~~n~~~NL~~~t~~en~r 46 (46)
T PF13392_consen 20 VVDHKDGNKTDNRPENLRWVTRSENSR 46 (46)
T ss_dssp EEEETTS-TT---GGGEEEE-HHHHH-
T ss_pred EEEeCCCCCCCCCHHHceECCHHHhCc
Confidence 577889999999999999999988764
No 11
>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=44.42 E-value=23 Score=25.13 Aligned_cols=24 Identities=29% Similarity=0.263 Sum_probs=18.7
Q ss_pred CCeEeecCCCCCHHHHHHHHHHHH
Q 041119 81 KKSRIWLGTFSTPEMAARAHDVAA 104 (278)
Q Consensus 81 ~~kri~LGtFdT~EeAArAYD~AA 104 (278)
..-++.+|.|++.++|..+-....
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 345788899999999988876554
No 12
>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=43.75 E-value=53 Score=25.37 Aligned_cols=38 Identities=21% Similarity=0.327 Sum_probs=29.1
Q ss_pred cEEEEEecCCCCeEeecCCCCCHHHHHHHHHHHHHHhc
Q 041119 71 KWVSEIREPRKKSRIWLGTFSTPEMAARAHDVAALSIK 108 (278)
Q Consensus 71 KW~AeI~~~~~~kri~LGtFdT~EeAArAYD~AAikl~ 108 (278)
.|-++|.-..-.-..|.|-|++.+||..+.-.-...+.
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~ 46 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLE 46 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHH
Confidence 58889987555577899999999999998655444443
No 13
>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=42.43 E-value=40 Score=26.51 Aligned_cols=40 Identities=30% Similarity=0.261 Sum_probs=26.6
Q ss_pred CCCceeEEEeCCCCcEEEEEecCCCCeEeecCCCCCHHHHHHH
Q 041119 57 KHPVYRGVRMRAWGKWVSEIREPRKKSRIWLGTFSTPEMAARA 99 (278)
Q Consensus 57 ~~S~YRGVr~r~~GKW~AeI~~~~~~kri~LGtFdT~EeAArA 99 (278)
+--+||-|+.-+ |||+|.+.. +..-.---.|.-+|.|-|-
T Consensus 29 k~dgfrdvw~lr-gkyvafvl~--ge~f~rsp~fs~pesaqrw 68 (80)
T PF10729_consen 29 KMDGFRDVWQLR-GKYVAFVLM--GEHFRRSPAFSVPESAQRW 68 (80)
T ss_dssp -TTTECCECCCC-CEEEEEEES--SS-EEE---BSSHHHHHHH
T ss_pred hcccccceeeec-cceEEEEEe--cchhccCCCcCCcHHHHHH
Confidence 345799997755 999999988 4444445678888888765
No 14
>PLN00062 TATA-box-binding protein; Provisional
Probab=34.42 E-value=1.8e+02 Score=26.03 Aligned_cols=58 Identities=17% Similarity=0.043 Sum_probs=39.6
Q ss_pred CCceeEEEeC-CCCcEEEEEecCCCCeEeecCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCC
Q 041119 58 HPVYRGVRMR-AWGKWVSEIREPRKKSRIWLGTFSTPEMAARAHDVAALSIKGASAILNFPK 118 (278)
Q Consensus 58 ~S~YRGVr~r-~~GKW~AeI~~~~~~kri~LGtFdT~EeAArAYD~AAikl~G~~A~lNFP~ 118 (278)
..+|-||.+| +.-|=.+-|.. .||-+--|. .++|+|..|.++.+..+....-..+|++
T Consensus 33 Pe~fpgli~Rl~~Pk~t~lIF~--SGKiviTGa-ks~e~a~~a~~~~~~~L~~lg~~~~~~~ 91 (179)
T PLN00062 33 PKRFAAVIMRIREPKTTALIFA--SGKMVCTGA-KSEHDSKLAARKYARIIQKLGFPAKFKD 91 (179)
T ss_pred CccCcEEEEEeCCCcEEEEEEC--CCeEEEEec-CCHHHHHHHHHHHHHHHHHcCCCcCCCc
Confidence 3469999776 34566777777 777666564 7889999999998877743332344443
No 15
>PF15376 DUF4603: Domain of unknown function (DUF4603)
Probab=33.94 E-value=28 Score=38.42 Aligned_cols=16 Identities=19% Similarity=0.181 Sum_probs=10.8
Q ss_pred EEEeCCCCcEEEEEec
Q 041119 63 GVRMRAWGKWVSEIRE 78 (278)
Q Consensus 63 GVr~r~~GKW~AeI~~ 78 (278)
-||+|.-||++-+-|.
T Consensus 253 q~rhk~egk~rprsws 268 (1286)
T PF15376_consen 253 QIRHKSEGKIRPRSWS 268 (1286)
T ss_pred ccccCcCCCCCCcccC
Confidence 4677777887766554
No 16
>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=32.50 E-value=2e+02 Score=25.53 Aligned_cols=58 Identities=17% Similarity=0.061 Sum_probs=39.7
Q ss_pred CCceeEEEeC-CCCcEEEEEecCCCCeEeecCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCC
Q 041119 58 HPVYRGVRMR-AWGKWVSEIREPRKKSRIWLGTFSTPEMAARAHDVAALSIKGASAILNFPK 118 (278)
Q Consensus 58 ~S~YRGVr~r-~~GKW~AeI~~~~~~kri~LGtFdT~EeAArAYD~AAikl~G~~A~lNFP~ 118 (278)
..+|-||.+| ..-|-.+-|.. .||-+--|. .++|+|..|.++.+..+..-.-..+|++
T Consensus 33 Pe~fpgli~Rl~~Pk~t~lIF~--SGKiviTGa-ks~e~a~~a~~~i~~~L~~~g~~~~~~~ 91 (174)
T cd04516 33 PKRFAAVIMRIREPKTTALIFS--SGKMVCTGA-KSEDDSKLAARKYARIIQKLGFPAKFTD 91 (174)
T ss_pred CccCcEEEEEeCCCcEEEEEEC--CCeEEEEec-CCHHHHHHHHHHHHHHHHHcCCCCCCCc
Confidence 3468999776 34566777777 888777776 5788999999988877743222234544
No 17
>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=30.95 E-value=52 Score=26.94 Aligned_cols=20 Identities=30% Similarity=0.273 Sum_probs=17.5
Q ss_pred CCCCCHHHHHHHHHHHHHHh
Q 041119 88 GTFSTPEMAARAHDVAALSI 107 (278)
Q Consensus 88 GtFdT~EeAArAYD~AAikl 107 (278)
|+|+|+|+|..-||..+..|
T Consensus 71 GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 71 GYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCcCCHHHHHHHHHHHHHHH
Confidence 99999999999999876554
No 18
>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=29.98 E-value=1.9e+02 Score=25.51 Aligned_cols=46 Identities=22% Similarity=0.151 Sum_probs=35.2
Q ss_pred ceeEEEeC-CCCcEEEEEecCCCCeEeecCCCCCHHHHHHHHHHHHHHhc
Q 041119 60 VYRGVRMR-AWGKWVSEIREPRKKSRIWLGTFSTPEMAARAHDVAALSIK 108 (278)
Q Consensus 60 ~YRGVr~r-~~GKW~AeI~~~~~~kri~LGtFdT~EeAArAYD~AAikl~ 108 (278)
+|.||.+| ..-|-.+-|.. .||-+-.| ..+.|+|++|.++.+..+.
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 79999776 34577778887 77765555 5899999999998877663
No 19
>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=29.67 E-value=1.4e+02 Score=22.93 Aligned_cols=46 Identities=17% Similarity=0.092 Sum_probs=33.9
Q ss_pred CceeEEEeC-CCCcEEEEEecCCCCeEeecCCCCCHHHHHHHHHHHHHHh
Q 041119 59 PVYRGVRMR-AWGKWVSEIREPRKKSRIWLGTFSTPEMAARAHDVAALSI 107 (278)
Q Consensus 59 S~YRGVr~r-~~GKW~AeI~~~~~~kri~LGtFdT~EeAArAYD~AAikl 107 (278)
.+|.||.+| ..-+-...|.. .||-+..|. .++|+|..|.++....+
T Consensus 36 e~fpgl~~r~~~p~~t~~IF~--sGki~itGa-ks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 36 ERFPGLIYRLRNPKATVLIFS--SGKIVITGA-KSEEEAKKAIEKILPIL 82 (86)
T ss_dssp TTESSEEEEETTTTEEEEEET--TSEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred ccCCeEEEeecCCcEEEEEEc--CCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 358898766 33466667776 888777775 78999999998876655
No 20
>PRK10113 cell division modulator; Provisional
Probab=26.51 E-value=50 Score=25.92 Aligned_cols=38 Identities=34% Similarity=0.391 Sum_probs=26.3
Q ss_pred CceeEEEeCCCCcEEEEEecCCCCeEeecCCCCCHHHHHHH
Q 041119 59 PVYRGVRMRAWGKWVSEIREPRKKSRIWLGTFSTPEMAARA 99 (278)
Q Consensus 59 S~YRGVr~r~~GKW~AeI~~~~~~kri~LGtFdT~EeAArA 99 (278)
-+||-|+.-+ |||+|.+.. +..-.---.|..+|.|-|-
T Consensus 31 d~frDVW~Lr-GKYVAFvl~--ge~FrRSPaFs~PEsAQRW 68 (80)
T PRK10113 31 DSFRDVWMLR-GKYVAFVLM--GESFLRSPAFSVPESAQRW 68 (80)
T ss_pred cchhhhheec-cceEEEEEe--chhhccCCccCCcHHHHHH
Confidence 4688887765 999999887 3222233568888877764
No 21
>KOG3422 consensus Mitochondrial ribosomal protein L16 [Translation, ribosomal structure and biogenesis]
Probab=22.14 E-value=1.7e+02 Score=27.48 Aligned_cols=38 Identities=21% Similarity=0.191 Sum_probs=31.5
Q ss_pred cEEEEEecCCCCeEeecCCCCCHHHHHHHHHHHHHHhcCC
Q 041119 71 KWVSEIREPRKKSRIWLGTFSTPEMAARAHDVAALSIKGA 110 (278)
Q Consensus 71 KW~AeI~~~~~~kri~LGtFdT~EeAArAYD~AAikl~G~ 110 (278)
.|+|.|.. ++--+=+|---++++|..|.+.||.++-+.
T Consensus 133 ~wva~V~~--GrIl~EmgG~~~~~~Ar~al~~aa~klp~~ 170 (221)
T KOG3422|consen 133 HWVARVKA--GRILFEMGGDVEEEEARQALLQAAHKLPFK 170 (221)
T ss_pred eeEEEecC--CcEEEEeCCcccHHHHHHHHHHHHhcCCcc
Confidence 59999998 666666777789999999999999987653
No 22
>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=21.43 E-value=40 Score=26.64 Aligned_cols=40 Identities=23% Similarity=0.278 Sum_probs=24.0
Q ss_pred HHhcCCCCCCCCCCCCCCCCCCCCCChhHHHHHHHHHhhc
Q 041119 105 LSIKGASAILNFPKLAGSLPRPASKSPRDVQAAAAKAASM 144 (278)
Q Consensus 105 ikl~G~~A~lNFP~~~~~lp~p~s~s~~diqaaAa~aA~~ 144 (278)
-..+|++|.+-|-+.--.+..-.....+.||+||+|--.+
T Consensus 11 ~a~WG~~AllSf~~~ga~IHl~~~~~l~~IQrAaRkLd~q 50 (77)
T PF12404_consen 11 AAHWGEKALLSFNEQGATIHLSEGDDLRAIQRAARKLDGQ 50 (77)
T ss_pred hhHhCcCcEEEEcCCCEEEEECCCcchHHHHHHHHHHhhC
Confidence 3467777777776543333333444567778777776544
No 23
>cd01433 Ribosomal_L16_L10e Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with the 30S subunit, binding of aminoacyl-tRNA and interaction with antibiotics. L16 is required for the function of elongation factor P (EF-P), a protein involved in peptide bond synthesis through the stimulation of peptidyl transferase activity by the ribosome. Mutations in L16 and the adjoining bases of 23S rRNA confer antibiotic resistance in bacteria, suggesting a role for L16 in the formation of the antibiotic binding site. The GTPase RbgA (YlqF) is essential for the assembly of the large subunit, and it is believed to regulate the incorporation of L16. L10e is the archaeal and eukaryotic cytosolic homolog of bacterial L16. L16 and L10e exhibit structural differences at the N-terminus.
Probab=21.07 E-value=1.7e+02 Score=23.74 Aligned_cols=44 Identities=23% Similarity=0.280 Sum_probs=31.4
Q ss_pred EEEeCC-CC---cEEEEEecCCCCeEeecCCCCCHHHHHHHHHHHHHHhc
Q 041119 63 GVRMRA-WG---KWVSEIREPRKKSRIWLGTFSTPEMAARAHDVAALSIK 108 (278)
Q Consensus 63 GVr~r~-~G---KW~AeI~~~~~~kri~LGtFdT~EeAArAYD~AAikl~ 108 (278)
++|+.+ .| .|+|+|.. +..-+-++.....+.|..|...|+.++-
T Consensus 59 ~~rMGkGKG~~~~~~a~v~~--G~iifEi~~~~~~~~~~~alk~a~~Klp 106 (112)
T cd01433 59 ETRMGKGKGKPEGWVARVKP--GQILFEVRGVPEEEVAKEALRRAAKKLP 106 (112)
T ss_pred ccccCCCCCCccEEEEEECC--CCEEEEEeCcCcHHHHHHHHHHhhccCC
Confidence 456553 33 49999997 6655666666558999999888887763
No 24
>PF09954 DUF2188: Uncharacterized protein conserved in bacteria (DUF2188); InterPro: IPR018691 This family has no known function.
Probab=20.43 E-value=2.6e+02 Score=20.09 Aligned_cols=39 Identities=28% Similarity=0.225 Sum_probs=25.0
Q ss_pred EEeCCCCcEEEEEecCCCCeEeecCCCCCHHHHHHHHHHHHHH
Q 041119 64 VRMRAWGKWVSEIREPRKKSRIWLGTFSTPEMAARAHDVAALS 106 (278)
Q Consensus 64 Vr~r~~GKW~AeI~~~~~~kri~LGtFdT~EeAArAYD~AAik 106 (278)
|..+..|.|..+... ..+. ..+|+|.++|-.+=...|..
T Consensus 3 V~p~~~~~W~v~~eg--~~ra--~~~~~Tk~eAi~~Ar~~a~~ 41 (62)
T PF09954_consen 3 VVPREDGGWAVKKEG--AKRA--SKTFDTKAEAIEAARELAKN 41 (62)
T ss_pred EEecCCCCceEEeCC--Cccc--ccccCcHHHHHHHHHHHHHh
Confidence 333455789887664 3222 68999999987765444443
No 25
>cd00652 TBP_TLF 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. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=20.28 E-value=4.5e+02 Score=23.11 Aligned_cols=48 Identities=23% Similarity=0.108 Sum_probs=34.6
Q ss_pred CCceeEEEeCC-CCcEEEEEecCCCCeEeecCCCCCHHHHHHHHHHHHHHhc
Q 041119 58 HPVYRGVRMRA-WGKWVSEIREPRKKSRIWLGTFSTPEMAARAHDVAALSIK 108 (278)
Q Consensus 58 ~S~YRGVr~r~-~GKW~AeI~~~~~~kri~LGtFdT~EeAArAYD~AAikl~ 108 (278)
..+|.||.+|- .-|-.+-|.. .||-+-.|. .+.|+|.+|.++.+..++
T Consensus 33 Pe~fpgli~R~~~P~~t~lIf~--sGKivitGa-ks~~~~~~a~~~~~~~L~ 81 (174)
T cd00652 33 PKRFPGVIMRLREPKTTALIFS--SGKMVITGA-KSEEDAKLAARKYARILQ 81 (174)
T ss_pred CCccceEEEEcCCCcEEEEEEC--CCEEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 34699997763 3455666666 888776675 578889999888877663
Done!