Query 029015
Match_columns 200
No_of_seqs 234 out of 1330
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 06:07:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029015.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029015hhsearch_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 2.1E-21 4.7E-26 134.7 7.5 61 43-103 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 9.3E-21 2E-25 133.0 8.5 63 44-106 1-63 (64)
3 PHA00280 putative NHN endonucl 99.5 9.9E-14 2.2E-18 109.5 7.0 69 26-97 50-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.1 1.8E-10 4E-15 77.9 6.1 52 43-94 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 75.1 12 0.00026 24.1 5.3 37 55-91 1-41 (46)
6 cd00801 INT_P4 Bacteriophage P 64.3 15 0.00032 31.7 5.1 38 54-91 10-49 (357)
7 PF13356 DUF4102: Domain of un 64.0 25 0.00054 25.4 5.6 39 49-87 28-70 (89)
8 PHA02601 int integrase; Provis 57.8 17 0.00036 31.7 4.4 44 47-91 2-46 (333)
9 PF08846 DUF1816: Domain of un 57.2 22 0.00047 25.6 4.1 40 55-94 9-48 (68)
10 PF10729 CedA: Cell division a 51.3 25 0.00055 25.6 3.6 38 43-83 31-68 (80)
11 PRK09692 integrase; Provisiona 49.2 50 0.0011 30.0 6.2 39 48-86 33-77 (413)
12 PF05036 SPOR: Sporulation rel 41.4 14 0.00031 24.8 1.1 24 65-88 42-65 (76)
13 PRK10113 cell division modulat 35.5 30 0.00065 25.2 2.0 37 43-82 31-67 (80)
14 PF14112 DUF4284: Domain of un 34.5 28 0.0006 27.2 1.8 19 67-85 2-20 (122)
15 cd01433 Ribosomal_L16_L10e Rib 26.9 1.2E+02 0.0026 23.1 4.2 35 55-91 71-105 (112)
16 cd07998 WGR_DNA_ligase WGR dom 25.2 2.4E+02 0.0052 20.6 5.3 51 38-88 8-64 (77)
17 PF12404 DUF3663: Peptidase ; 24.6 34 0.00073 25.2 0.7 38 88-125 10-47 (77)
18 COG2185 Sbm Methylmalonyl-CoA 24.0 58 0.0013 26.6 2.0 17 67-83 42-58 (143)
19 PF07494 Reg_prop: Two compone 21.5 1.1E+02 0.0023 17.0 2.3 11 65-75 14-24 (24)
20 PF08471 Ribonuc_red_2_N: Clas 21.0 1.1E+02 0.0023 23.5 2.8 19 72-90 71-89 (93)
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=2.1e-21 Score=134.69 Aligned_cols=61 Identities=59% Similarity=0.925 Sum_probs=57.6
Q ss_pred CceeEEEECCCCeEEEEEeecCCCcEEeecCCCCHHHHHHHHHHHHHhhcCCCCCCCCCCC
Q 029015 43 PIFRGVRMRNNNKWVCELREPNKKSRIWLGTYPTPEMAARAHDVAALALRGKSTCLNFADS 103 (200)
Q Consensus 43 s~yrGVr~r~~GkW~AeIr~p~~~kri~LGtf~t~eeAArAyD~Aa~~l~G~~a~lNFp~s 103 (200)
|+|+||+++++|||+|+|+++..++++|||+|+|+|||++|||.|++.++|..+.+|||++
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 6799998888899999999966699999999999999999999999999999999999985
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.84 E-value=9.3e-21 Score=133.02 Aligned_cols=63 Identities=52% Similarity=0.895 Sum_probs=59.8
Q ss_pred ceeEEEECCCCeEEEEEeecCCCcEEeecCCCCHHHHHHHHHHHHHhhcCCCCCCCCCCCCCC
Q 029015 44 IFRGVRMRNNNKWVCELREPNKKSRIWLGTYPTPEMAARAHDVAALALRGKSTCLNFADSAWR 106 (200)
Q Consensus 44 ~yrGVr~r~~GkW~AeIr~p~~~kri~LGtf~t~eeAArAyD~Aa~~l~G~~a~lNFp~s~~~ 106 (200)
+|+||+++++|||+|+|++|.+++++|||+|+|+||||+|||.|++.++|..+.+|||.+.|.
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~ 63 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYD 63 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCC
Confidence 499998888899999999999999999999999999999999999999999999999998764
No 3
>PHA00280 putative NHN endonuclease
Probab=99.47 E-value=9.9e-14 Score=109.51 Aligned_cols=69 Identities=12% Similarity=0.140 Sum_probs=58.4
Q ss_pred CCccccCCCCCCCCCCCCceeEEE-ECCCCeEEEEEeecCCCcEEeecCCCCHHHHHHHHHHHHHhhcCCCCC
Q 029015 26 SSPKKRAGRRVFRETRHPIFRGVR-MRNNNKWVCELREPNKKSRIWLGTYPTPEMAARAHDVAALALRGKSTC 97 (200)
Q Consensus 26 ~~~k~~~~r~k~~~~~~s~yrGVr-~r~~GkW~AeIr~p~~~kri~LGtf~t~eeAArAyD~Aa~~l~G~~a~ 97 (200)
..+.....+++.+.+++|+|+||. ....|||+|+|+. ++|+++||.|+|+|+|+.||+ ++.+++|.+|+
T Consensus 50 ~T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~--~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 50 ALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTA--EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred cCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEEE--CCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 344455555666778999999995 5567999999999 999999999999999999997 77889999875
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=1.8e-10 Score=77.87 Aligned_cols=52 Identities=25% Similarity=0.428 Sum_probs=44.6
Q ss_pred CceeEEEE-CCCCeEEEEEeecCC---CcEEeecCCCCHHHHHHHHHHHHHhhcCC
Q 029015 43 PIFRGVRM-RNNNKWVCELREPNK---KSRIWLGTYPTPEMAARAHDVAALALRGK 94 (200)
Q Consensus 43 s~yrGVr~-r~~GkW~AeIr~p~~---~kri~LGtf~t~eeAArAyD~Aa~~l~G~ 94 (200)
|+|+||++ +..++|+|+|+++.. +++++||.|+++++|++|++.+++.++|+
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 67999965 457999999999532 49999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=75.13 E-value=12 Score=24.12 Aligned_cols=37 Identities=16% Similarity=0.226 Sum_probs=28.5
Q ss_pred eEEEEEe--ecC--CCcEEeecCCCCHHHHHHHHHHHHHhh
Q 029015 55 KWVCELR--EPN--KKSRIWLGTYPTPEMAARAHDVAALAL 91 (200)
Q Consensus 55 kW~AeIr--~p~--~~kri~LGtf~t~eeAArAyD~Aa~~l 91 (200)
+|...|. .|. +.++++-+.|.|..||-.+.......+
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~ 41 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAEL 41 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHH
Confidence 5778883 342 457789999999999999988766654
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=64.32 E-value=15 Score=31.67 Aligned_cols=38 Identities=32% Similarity=0.503 Sum_probs=27.8
Q ss_pred CeEEEEEeecCCCcEEeecCCC--CHHHHHHHHHHHHHhh
Q 029015 54 NKWVCELREPNKKSRIWLGTYP--TPEMAARAHDVAALAL 91 (200)
Q Consensus 54 GkW~AeIr~p~~~kri~LGtf~--t~eeAArAyD~Aa~~l 91 (200)
+.|..+++..++..++.||+|+ |.++|..........+
T Consensus 10 ~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 10 KSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred EEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 5699999997777788999996 6677776665544443
No 7
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=63.98 E-value=25 Score=25.41 Aligned_cols=39 Identities=26% Similarity=0.344 Sum_probs=25.7
Q ss_pred EECCCC--eEEEEEeecCCCcEEeecCCCC--HHHHHHHHHHH
Q 029015 49 RMRNNN--KWVCELREPNKKSRIWLGTYPT--PEMAARAHDVA 87 (200)
Q Consensus 49 r~r~~G--kW~AeIr~p~~~kri~LGtf~t--~eeAArAyD~A 87 (200)
+-.+.| .|+-+.+..++.+++-||.|++ ..+|.......
T Consensus 28 ~v~~~G~kt~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~ 70 (89)
T PF13356_consen 28 RVTPSGSKTFYFRYRINGKRRRITLGRYPELSLAEAREKAREL 70 (89)
T ss_dssp EE-TTS-EEEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHH
T ss_pred EEEeCCCeEEEEEEEecceEEEeccCCCccCCHHHHHHHHHHH
Confidence 444443 4998888866678899999986 55555444433
No 8
>PHA02601 int integrase; Provisional
Probab=57.77 E-value=17 Score=31.68 Aligned_cols=44 Identities=23% Similarity=0.393 Sum_probs=29.6
Q ss_pred EEEECCCCeEEEEEeec-CCCcEEeecCCCCHHHHHHHHHHHHHhh
Q 029015 47 GVRMRNNNKWVCELREP-NKKSRIWLGTYPTPEMAARAHDVAALAL 91 (200)
Q Consensus 47 GVr~r~~GkW~AeIr~p-~~~kri~LGtf~t~eeAArAyD~Aa~~l 91 (200)
+|++.+.|+|.++|+.. ..|+++.. +|.|..||....+.....+
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 46666778999999863 23566553 6999988876655544333
No 9
>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=57.18 E-value=22 Score=25.61 Aligned_cols=40 Identities=20% Similarity=0.322 Sum_probs=30.7
Q ss_pred eEEEEEeecCCCcEEeecCCCCHHHHHHHHHHHHHhhcCC
Q 029015 55 KWVCELREPNKKSRIWLGTYPTPEMAARAHDVAALALRGK 94 (200)
Q Consensus 55 kW~AeIr~p~~~kri~LGtf~t~eeAArAyD~Aa~~l~G~ 94 (200)
.|-++|.--.-.-..|.|-|.|.+||..+.-.-...+..+
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~~E 48 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLESE 48 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHHhh
Confidence 4778988855567889999999999999876655555443
No 10
>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=51.31 E-value=25 Score=25.64 Aligned_cols=38 Identities=24% Similarity=0.169 Sum_probs=24.6
Q ss_pred CceeEEEECCCCeEEEEEeecCCCcEEeecCCCCHHHHHHH
Q 029015 43 PIFRGVRMRNNNKWVCELREPNKKSRIWLGTYPTPEMAARA 83 (200)
Q Consensus 43 s~yrGVr~r~~GkW~AeIr~p~~~kri~LGtf~t~eeAArA 83 (200)
-+||-|+.-+ |||+|.+.. ...-..--.|..+|.|-|=
T Consensus 31 dgfrdvw~lr-gkyvafvl~--ge~f~rsp~fs~pesaqrw 68 (80)
T PF10729_consen 31 DGFRDVWQLR-GKYVAFVLM--GEHFRRSPAFSVPESAQRW 68 (80)
T ss_dssp TTECCECCCC-CEEEEEEES--SS-EEE---BSSHHHHHHH
T ss_pred ccccceeeec-cceEEEEEe--cchhccCCCcCCcHHHHHH
Confidence 4699997654 899999887 4433344568888777653
No 11
>PRK09692 integrase; Provisional
Probab=49.23 E-value=50 Score=29.97 Aligned_cols=39 Identities=18% Similarity=0.353 Sum_probs=24.6
Q ss_pred EEECCCC--eEEEEEeecC--CCcEEeecCCC--CHHHHHHHHHH
Q 029015 48 VRMRNNN--KWVCELREPN--KKSRIWLGTYP--TPEMAARAHDV 86 (200)
Q Consensus 48 Vr~r~~G--kW~AeIr~p~--~~kri~LGtf~--t~eeAArAyD~ 86 (200)
|+-++.| .|+.+.+.|. +.+++-||.|+ |..+|..+...
T Consensus 33 l~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~ 77 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAE 77 (413)
T ss_pred EEEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHH
Confidence 4444544 3998887553 34447899999 66666554433
No 12
>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=41.42 E-value=14 Score=24.77 Aligned_cols=24 Identities=21% Similarity=0.212 Sum_probs=19.2
Q ss_pred CCcEEeecCCCCHHHHHHHHHHHH
Q 029015 65 KKSRIWLGTYPTPEMAARAHDVAA 88 (200)
Q Consensus 65 ~~kri~LGtf~t~eeAArAyD~Aa 88 (200)
..-+|.+|.|+|.++|..+.....
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 456889999999999988876544
No 13
>PRK10113 cell division modulator; Provisional
Probab=35.50 E-value=30 Score=25.20 Aligned_cols=37 Identities=30% Similarity=0.346 Sum_probs=23.8
Q ss_pred CceeEEEECCCCeEEEEEeecCCCcEEeecCCCCHHHHHH
Q 029015 43 PIFRGVRMRNNNKWVCELREPNKKSRIWLGTYPTPEMAAR 82 (200)
Q Consensus 43 s~yrGVr~r~~GkW~AeIr~p~~~kri~LGtf~t~eeAAr 82 (200)
-+||-|+.-+ |||+|.+.. .-.--.--.|..+|.|-|
T Consensus 31 d~frDVW~Lr-GKYVAFvl~--ge~FrRSPaFs~PEsAQR 67 (80)
T PRK10113 31 DSFRDVWMLR-GKYVAFVLM--GESFLRSPAFSVPESAQR 67 (80)
T ss_pred cchhhhheec-cceEEEEEe--chhhccCCccCCcHHHHH
Confidence 3588997654 899998877 222222246777776655
No 14
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=34.46 E-value=28 Score=27.22 Aligned_cols=19 Identities=16% Similarity=0.574 Sum_probs=14.5
Q ss_pred cEEeecCCCCHHHHHHHHH
Q 029015 67 SRIWLGTYPTPEMAARAHD 85 (200)
Q Consensus 67 kri~LGtf~t~eeAArAyD 85 (200)
..||||+|.|.++--.=.+
T Consensus 2 VsiWiG~f~s~~el~~Y~e 20 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEYFE 20 (122)
T ss_pred eEEEEecCCCHHHHHHHhC
Confidence 4689999999887665543
No 15
>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=26.92 E-value=1.2e+02 Score=23.08 Aligned_cols=35 Identities=26% Similarity=0.308 Sum_probs=26.9
Q ss_pred eEEEEEeecCCCcEEeecCCCCHHHHHHHHHHHHHhh
Q 029015 55 KWVCELREPNKKSRIWLGTYPTPEMAARAHDVAALAL 91 (200)
Q Consensus 55 kW~AeIr~p~~~kri~LGtf~t~eeAArAyD~Aa~~l 91 (200)
.|+|.|.. ...-+-++.....+.|..|...|+.++
T Consensus 71 ~~~a~v~~--G~iifEi~~~~~~~~~~~alk~a~~Kl 105 (112)
T cd01433 71 GWVARVKP--GQILFEVRGVPEEEVAKEALRRAAKKL 105 (112)
T ss_pred EEEEEECC--CCEEEEEeCcCcHHHHHHHHHHhhccC
Confidence 49999988 666666777666888888888877665
No 16
>cd07998 WGR_DNA_ligase WGR domain of bacterial DNA ligases. The WGR domain is found in a small family of predicted bacterial DNA ligases. It has been called WGR after the most conserved central motif of the domain. The domain typically occurs in together with an ATP-dependent DNA ligase domain, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain.
Probab=25.22 E-value=2.4e+02 Score=20.65 Aligned_cols=51 Identities=20% Similarity=0.197 Sum_probs=34.3
Q ss_pred CCCCCCceeEEEEC--CCCeEEEEEeecCCCcEEeec----CCCCHHHHHHHHHHHH
Q 029015 38 RETRHPIFRGVRMR--NNNKWVCELREPNKKSRIWLG----TYPTPEMAARAHDVAA 88 (200)
Q Consensus 38 ~~~~~s~yrGVr~r--~~GkW~AeIr~p~~~kri~LG----tf~t~eeAArAyD~Aa 88 (200)
+..++.+|-=|-.. ..+.|...|+.-+.|...-.| +|.++++|.+++++-.
T Consensus 8 ~dg~S~Kfyev~~~~~~d~g~~v~~~yGR~Gt~gq~~tkt~~~~~~~~A~k~~~Klv 64 (77)
T cd07998 8 QEGNSDKVYEVDLFEVSDDGYVVNFRYGRRGSALREGTKTVAPVTLEAAEKIFDKLV 64 (77)
T ss_pred ecCCCceEEEEEEEeccCCceEEEEEEccccCCcccccccCCCCCHHHHHHHHHHHH
Confidence 45566667666332 346688888886656544443 4579999999999843
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=24.60 E-value=34 Score=25.25 Aligned_cols=38 Identities=21% Similarity=0.323 Sum_probs=28.2
Q ss_pred HHhhcCCCCCCCCCCCCCCCCCCCCCChHHHHHHHHHH
Q 029015 88 ALALRGKSTCLNFADSAWRLPVPASADADDVRKAAAEA 125 (200)
Q Consensus 88 a~~l~G~~a~lNFp~s~~~lp~p~~~~~~~i~~aa~~a 125 (200)
+-..+|++|.+-|.+.-..+..-.......||+||++-
T Consensus 10 A~a~WG~~AllSf~~~ga~IHl~~~~~l~~IQrAaRkL 47 (77)
T PF12404_consen 10 AAAHWGEKALLSFNEQGATIHLSEGDDLRAIQRAARKL 47 (77)
T ss_pred ChhHhCcCcEEEEcCCCEEEEECCCcchHHHHHHHHHH
Confidence 34568999999998876666655556677899988874
No 18
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=24.00 E-value=58 Score=26.63 Aligned_cols=17 Identities=53% Similarity=0.669 Sum_probs=15.5
Q ss_pred cEEeecCCCCHHHHHHH
Q 029015 67 SRIWLGTYPTPEMAARA 83 (200)
Q Consensus 67 kri~LGtf~t~eeAArA 83 (200)
.-|++|.|.|+||++++
T Consensus 42 eVi~~g~~~tp~e~v~a 58 (143)
T COG2185 42 EVINLGLFQTPEEAVRA 58 (143)
T ss_pred eEEecCCcCCHHHHHHH
Confidence 56899999999999987
No 19
>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=21.51 E-value=1.1e+02 Score=17.00 Aligned_cols=11 Identities=36% Similarity=1.123 Sum_probs=8.2
Q ss_pred CCcEEeecCCC
Q 029015 65 KKSRIWLGTYP 75 (200)
Q Consensus 65 ~~kri~LGtf~ 75 (200)
+..+||+||+.
T Consensus 14 ~~G~lWigT~~ 24 (24)
T PF07494_consen 14 SDGNLWIGTYN 24 (24)
T ss_dssp TTSCEEEEETS
T ss_pred CCcCEEEEeCC
Confidence 55689999873
No 20
>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=20.99 E-value=1.1e+02 Score=23.47 Aligned_cols=19 Identities=26% Similarity=0.204 Sum_probs=16.2
Q ss_pred cCCCCHHHHHHHHHHHHHh
Q 029015 72 GTYPTPEMAARAHDVAALA 90 (200)
Q Consensus 72 Gtf~t~eeAArAyD~Aa~~ 90 (200)
|.|+|+|+|..-||.-...
T Consensus 71 GYF~t~eDA~~FydEl~~m 89 (93)
T PF08471_consen 71 GYFATEEDAEAFYDELTYM 89 (93)
T ss_pred CCcCCHHHHHHHHHHHHHH
Confidence 8999999999999985543
Done!