Query 038285
Match_columns 178
No_of_seqs 233 out of 1195
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 09:27:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038285.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038285hhsearch_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 8.3E-21 1.8E-25 128.7 7.2 60 22-81 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 5.5E-20 1.2E-24 126.1 8.0 62 23-84 1-63 (64)
3 PHA00280 putative NHN endonucl 99.6 1.3E-14 2.8E-19 111.6 7.7 70 2-75 48-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.1 3.9E-10 8.6E-15 74.5 5.9 51 22-72 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 79.9 6.4 0.00014 24.7 4.9 38 33-70 1-42 (46)
6 cd00801 INT_P4 Bacteriophage P 57.3 26 0.00056 29.4 5.4 37 33-69 11-49 (357)
7 PF13356 DUF4102: Domain of un 54.2 72 0.0016 22.3 6.5 37 33-69 36-74 (89)
8 PF05036 SPOR: Sporulation rel 43.2 18 0.00039 23.7 1.8 25 42-66 41-65 (76)
9 PF14112 DUF4284: Domain of un 39.9 18 0.0004 27.5 1.6 17 45-61 2-18 (122)
10 PF10729 CedA: Cell division a 39.6 57 0.0012 23.1 3.8 39 20-60 29-67 (80)
11 PRK09692 integrase; Provisiona 36.0 1.2E+02 0.0027 26.8 6.5 32 33-64 42-77 (413)
12 PHA02601 int integrase; Provis 35.5 56 0.0012 27.7 4.1 43 26-69 2-46 (333)
13 PF08846 DUF1816: Domain of un 34.5 1.1E+02 0.0023 21.4 4.5 41 33-73 9-49 (68)
14 PF12404 DUF3663: Peptidase ; 34.2 26 0.00057 25.1 1.5 37 67-103 11-47 (77)
15 PF08460 SH3_5: Bacterial SH3 32.9 76 0.0017 21.5 3.6 28 20-49 35-63 (65)
16 PF00352 TBP: Transcription fa 31.7 68 0.0015 22.5 3.4 45 22-69 36-82 (86)
17 PF08471 Ribonuc_red_2_N: Clas 30.4 58 0.0013 24.1 2.8 21 49-69 70-90 (93)
18 PLN00062 TATA-box-binding prot 30.2 2.8E+02 0.006 22.6 7.1 57 20-79 32-90 (179)
19 cd04516 TBP_eukaryotes eukaryo 30.2 2.8E+02 0.006 22.4 7.1 57 20-79 32-90 (174)
20 PF09003 Phage_integ_N: Bacter 28.7 2.1E+02 0.0045 20.3 5.3 33 38-72 31-63 (75)
21 cd01433 Ribosomal_L16_L10e Rib 27.6 1.2E+02 0.0026 22.4 4.2 35 33-69 71-105 (112)
22 cd04518 TBP_archaea archaeal T 27.1 2.3E+02 0.0049 22.9 6.1 50 20-70 32-81 (174)
23 cd00652 TBP_TLF TATA box bindi 26.3 3E+02 0.0065 22.1 6.6 48 20-70 32-81 (174)
24 cd04517 TLF TBP-like factors ( 26.2 3.1E+02 0.0066 22.1 6.7 45 23-70 35-81 (174)
25 COG2185 Sbm Methylmalonyl-CoA 25.3 53 0.0012 26.1 2.0 30 33-62 30-59 (143)
26 PRK10113 cell division modulat 25.3 61 0.0013 22.9 2.1 37 22-60 31-67 (80)
27 TIGR01164 rplP_bact ribosomal 25.0 1.6E+02 0.0036 22.5 4.6 34 33-69 91-124 (126)
28 PRK09203 rplP 50S ribosomal pr 24.6 1.4E+02 0.0031 23.2 4.3 36 33-71 92-127 (138)
29 PF12286 DUF3622: Protein of u 23.3 1.8E+02 0.0039 20.5 4.1 39 23-63 8-50 (71)
30 PF07494 Reg_prop: Two compone 22.7 82 0.0018 16.9 1.9 11 43-53 14-24 (24)
31 COG5558 Transposase [DNA repli 22.0 73 0.0016 27.1 2.3 51 21-73 101-154 (261)
32 KOG3422 Mitochondrial ribosoma 20.4 2.5E+02 0.0054 23.9 5.1 37 33-71 133-169 (221)
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=8.3e-21 Score=128.69 Aligned_cols=60 Identities=62% Similarity=1.130 Sum_probs=56.1
Q ss_pred CCeEEEEeeC-CeEEEEEeecCCCcEEEecCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCc
Q 038285 22 PVYKGVRRRN-GKWVCELREPNKKSRIWLGTFASPDKAARAYDAAALALRGNSASLNFPEA 81 (178)
Q Consensus 22 s~yrGVr~r~-~kW~A~I~~p~~~k~i~LGtf~t~eeAA~AyD~Aa~~l~g~~a~lNFp~s 81 (178)
|+|+||++++ +||+|+|+++..++++|||+|+|+|||++|||.|++.++|..+.+|||+|
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 6899998777 69999999966699999999999999999999999999999999999985
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.82 E-value=5.5e-20 Score=126.07 Aligned_cols=62 Identities=56% Similarity=1.052 Sum_probs=58.1
Q ss_pred CeEEEEeeC-CeEEEEEeecCCCcEEEecCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCcccc
Q 038285 23 VYKGVRRRN-GKWVCELREPNKKSRIWLGTFASPDKAARAYDAAALALRGNSASLNFPEAAGA 84 (178)
Q Consensus 23 ~yrGVr~r~-~kW~A~I~~p~~~k~i~LGtf~t~eeAA~AyD~Aa~~l~g~~a~lNFp~s~~~ 84 (178)
+|+||+++. |||+|+|++|.+++++|||+|+|+||||+|||.|++.++|..+.+|||.+.+.
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 599998766 69999999999999999999999999999999999999999999999998763
No 3
>PHA00280 putative NHN endonuclease
Probab=99.55 E-value=1.3e-14 Score=111.62 Aligned_cols=70 Identities=13% Similarity=0.145 Sum_probs=61.7
Q ss_pred CcchhhhhhccCCCCCCCCCCCeEEEEe--eCCeEEEEEeecCCCcEEEecCCCCHHHHHHHHHHHHHHhcCCCCC
Q 038285 2 KSSTAQKRKAGRKKFQETRHPVYKGVRR--RNGKWVCELREPNKKSRIWLGTFASPDKAARAYDAAALALRGNSAS 75 (178)
Q Consensus 2 r~~~~~k~~~gr~k~~~~~~s~yrGVr~--r~~kW~A~I~~p~~~k~i~LGtf~t~eeAA~AyD~Aa~~l~g~~a~ 75 (178)
|+++...+..|+++ +++++|+|+||+. +.+||+|+|++ +||+++||.|+|+|+|+.||+ ++.+|+|.+|.
T Consensus 48 r~~T~~eN~~N~~~-~~~N~SG~kGV~~~k~~~kw~A~I~~--~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 48 RLALPKENSWNMKT-PKSNTSGLKGLSWSKEREMWRGTVTA--EGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred hhcCHHHHhcccCC-CCCCCCCCCeeEEecCCCeEEEEEEE--CCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 67888889999765 5788999999975 44799999999 999999999999999999997 67789998875
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=99.06 E-value=3.9e-10 Score=74.47 Aligned_cols=51 Identities=31% Similarity=0.522 Sum_probs=44.1
Q ss_pred CCeEEEEeeC--CeEEEEEeecCC---CcEEEecCCCCHHHHHHHHHHHHHHhcCC
Q 038285 22 PVYKGVRRRN--GKWVCELREPNK---KSRIWLGTFASPDKAARAYDAAALALRGN 72 (178)
Q Consensus 22 s~yrGVr~r~--~kW~A~I~~p~~---~k~i~LGtf~t~eeAA~AyD~Aa~~l~g~ 72 (178)
|+|+||+... ++|+|+|+++.. +++++||.|.++++|++|++.+.+.++|.
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 6899998755 599999999521 49999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=79.85 E-value=6.4 Score=24.70 Aligned_cols=38 Identities=16% Similarity=0.279 Sum_probs=29.8
Q ss_pred eEEEEEe--ec--CCCcEEEecCCCCHHHHHHHHHHHHHHhc
Q 038285 33 KWVCELR--EP--NKKSRIWLGTFASPDKAARAYDAAALALR 70 (178)
Q Consensus 33 kW~A~I~--~p--~~~k~i~LGtf~t~eeAA~AyD~Aa~~l~ 70 (178)
+|...|. .| ++.++++-+-|.|..||-.+.......+.
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 44 34578999999999999999988777664
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=57.32 E-value=26 Score=29.42 Aligned_cols=37 Identities=30% Similarity=0.456 Sum_probs=27.7
Q ss_pred eEEEEEeecCCCcEEEecCCC--CHHHHHHHHHHHHHHh
Q 038285 33 KWVCELREPNKKSRIWLGTFA--SPDKAARAYDAAALAL 69 (178)
Q Consensus 33 kW~A~I~~p~~~k~i~LGtf~--t~eeAA~AyD~Aa~~l 69 (178)
.|+.+++..++..++.||+|+ |.++|..........+
T Consensus 11 ~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 11 SWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred EEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 799999996666778899996 6777777666655444
No 7
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=54.18 E-value=72 Score=22.32 Aligned_cols=37 Identities=19% Similarity=0.237 Sum_probs=25.7
Q ss_pred eEEEEEeecCCCcEEEecCCCC--HHHHHHHHHHHHHHh
Q 038285 33 KWVCELREPNKKSRIWLGTFAS--PDKAARAYDAAALAL 69 (178)
Q Consensus 33 kW~A~I~~p~~~k~i~LGtf~t--~eeAA~AyD~Aa~~l 69 (178)
.|+-+.+..++.+++-||.|++ ..+|..........+
T Consensus 36 t~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 36 TFYFRYRINGKRRRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp EEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred EEEEEEEecceEEEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 7998888855667899999986 555555555444444
No 8
>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=43.25 E-value=18 Score=23.66 Aligned_cols=25 Identities=24% Similarity=0.326 Sum_probs=20.1
Q ss_pred CCCcEEEecCCCCHHHHHHHHHHHH
Q 038285 42 NKKSRIWLGTFASPDKAARAYDAAA 66 (178)
Q Consensus 42 ~~~k~i~LGtf~t~eeAA~AyD~Aa 66 (178)
...-++.+|.|+|.++|..+-....
T Consensus 41 ~~~yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 41 GPWYRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp TTCEEEEECCECTCCHHHHHHHHHH
T ss_pred CceEEEEECCCCCHHHHHHHHHHHh
Confidence 3456899999999999988877655
No 9
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=39.94 E-value=18 Score=27.49 Aligned_cols=17 Identities=35% Similarity=0.747 Sum_probs=13.1
Q ss_pred cEEEecCCCCHHHHHHH
Q 038285 45 SRIWLGTFASPDKAARA 61 (178)
Q Consensus 45 k~i~LGtf~t~eeAA~A 61 (178)
-.||||+|.|.++--.=
T Consensus 2 VsiWiG~f~s~~el~~Y 18 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEY 18 (122)
T ss_pred eEEEEecCCCHHHHHHH
Confidence 36899999998875543
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=39.63 E-value=57 Score=23.09 Aligned_cols=39 Identities=21% Similarity=0.277 Sum_probs=26.3
Q ss_pred CCCCeEEEEeeCCeEEEEEeecCCCcEEEecCCCCHHHHHH
Q 038285 20 RHPVYKGVRRRNGKWVCELREPNKKSRIWLGTFASPDKAAR 60 (178)
Q Consensus 20 ~~s~yrGVr~r~~kW~A~I~~p~~~k~i~LGtf~t~eeAA~ 60 (178)
+--+||-|-.-.|||+|.+.. +.....--.|..+|.|-|
T Consensus 29 k~dgfrdvw~lrgkyvafvl~--ge~f~rsp~fs~pesaqr 67 (80)
T PF10729_consen 29 KMDGFRDVWQLRGKYVAFVLM--GEHFRRSPAFSVPESAQR 67 (80)
T ss_dssp -TTTECCECCCCCEEEEEEES--SS-EEE---BSSHHHHHH
T ss_pred hcccccceeeeccceEEEEEe--cchhccCCCcCCcHHHHH
Confidence 345789998778999999988 544444557888887765
No 11
>PRK09692 integrase; Provisional
Probab=35.96 E-value=1.2e+02 Score=26.75 Aligned_cols=32 Identities=13% Similarity=0.271 Sum_probs=21.4
Q ss_pred eEEEEEeecC--CCcEEEecCCC--CHHHHHHHHHH
Q 038285 33 KWVCELREPN--KKSRIWLGTFA--SPDKAARAYDA 64 (178)
Q Consensus 33 kW~A~I~~p~--~~k~i~LGtf~--t~eeAA~AyD~ 64 (178)
.|+.+-+.|. +.+++-||.|+ |..+|..+...
T Consensus 42 ~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~~ 77 (413)
T PRK09692 42 IWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRAE 77 (413)
T ss_pred EEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHHH
Confidence 7998877553 33447899999 66666554433
No 12
>PHA02601 int integrase; Provisional
Probab=35.50 E-value=56 Score=27.70 Aligned_cols=43 Identities=28% Similarity=0.506 Sum_probs=28.0
Q ss_pred EEEee-CCeEEEEEeec-CCCcEEEecCCCCHHHHHHHHHHHHHHh
Q 038285 26 GVRRR-NGKWVCELREP-NKKSRIWLGTFASPDKAARAYDAAALAL 69 (178)
Q Consensus 26 GVr~r-~~kW~A~I~~p-~~~k~i~LGtf~t~eeAA~AyD~Aa~~l 69 (178)
+|++. +|+|.++|+.. ..|+++. .+|.|..+|-...+.....+
T Consensus 2 ~~~~~~~g~w~~~~~~~~~~g~r~~-~~f~tk~eA~~~~~~~~~~~ 46 (333)
T PHA02601 2 AVRKLKDGKWLCEIYPNGRDGKRIR-KRFATKGEALAFENYTMAEV 46 (333)
T ss_pred ceEEcCCCCEEEEEEECCCCCchhh-hhhcCHHHHHHHHHHHHHhc
Confidence 45554 46999999862 2366664 36999998876665544444
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=34.48 E-value=1.1e+02 Score=21.42 Aligned_cols=41 Identities=22% Similarity=0.404 Sum_probs=30.0
Q ss_pred eEEEEEeecCCCcEEEecCCCCHHHHHHHHHHHHHHhcCCC
Q 038285 33 KWVCELREPNKKSRIWLGTFASPDKAARAYDAAALALRGNS 73 (178)
Q Consensus 33 kW~A~I~~p~~~k~i~LGtf~t~eeAA~AyD~Aa~~l~g~~ 73 (178)
.|=++|.--.-.-..|.|-|.|.+||..+.-.-..-|....
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~~Eg 49 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLESEG 49 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHHhhC
Confidence 56678777434467899999999999998776666555443
No 14
>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=34.24 E-value=26 Score=25.07 Aligned_cols=37 Identities=35% Similarity=0.440 Sum_probs=28.2
Q ss_pred HHhcCCCCCCCCCCcccccccCCCCChHHHHHHHHHH
Q 038285 67 LALRGNSASLNFPEAAGALRRAKSDDVRDIQCAAMEA 103 (178)
Q Consensus 67 ~~l~g~~a~lNFp~s~~~lp~p~s~~~~~i~~aa~~a 103 (178)
-..+|.+|.+.|-+.--.+..-.......||+||.+-
T Consensus 11 ~a~WG~~AllSf~~~ga~IHl~~~~~l~~IQrAaRkL 47 (77)
T PF12404_consen 11 AAHWGEKALLSFNEQGATIHLSEGDDLRAIQRAARKL 47 (77)
T ss_pred hhHhCcCcEEEEcCCCEEEEECCCcchHHHHHHHHHH
Confidence 3468888888888876666666667788888888765
No 15
>PF08460 SH3_5: Bacterial SH3 domain; InterPro: IPR013667 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. The SH3 domain has been found in a number of different bacterial proteins including glycyl-glycine endopeptidase, bacteriocin and some hypothetical proteins.; GO: 0016787 hydrolase activity; PDB: 1R77_B.
Probab=32.89 E-value=76 Score=21.52 Aligned_cols=28 Identities=18% Similarity=0.439 Sum_probs=19.4
Q ss_pred CCCCeEEEEeeCC-eEEEEEeecCCCcEEEe
Q 038285 20 RHPVYKGVRRRNG-KWVCELREPNKKSRIWL 49 (178)
Q Consensus 20 ~~s~yrGVr~r~~-kW~A~I~~p~~~k~i~L 49 (178)
.+=.|-+|....| .|...++. +|.|.||
T Consensus 35 ~~V~YD~~~~~dGy~Wisy~~~--sG~r~Yv 63 (65)
T PF08460_consen 35 QSVNYDQVIKADGYVWISYISY--SGQRRYV 63 (65)
T ss_dssp -EEEEEEEEEETTEEEEEEE-T--T--EEEE
T ss_pred CEEEEEEEEEeCCEEEEEEECC--CCeEEEE
Confidence 3446778877888 99999988 8888876
No 16
>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=31.70 E-value=68 Score=22.50 Aligned_cols=45 Identities=18% Similarity=0.147 Sum_probs=32.6
Q ss_pred CCeEEEEeeC--CeEEEEEeecCCCcEEEecCCCCHHHHHHHHHHHHHHh
Q 038285 22 PVYKGVRRRN--GKWVCELREPNKKSRIWLGTFASPDKAARAYDAAALAL 69 (178)
Q Consensus 22 s~yrGVr~r~--~kW~A~I~~p~~~k~i~LGtf~t~eeAA~AyD~Aa~~l 69 (178)
..|.||..|. .+-..-|.. .||-+..|. .++|++..|.+.....|
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 3678875544 365556666 999988886 78899999988876654
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=30.41 E-value=58 Score=24.12 Aligned_cols=21 Identities=33% Similarity=0.455 Sum_probs=17.7
Q ss_pred ecCCCCHHHHHHHHHHHHHHh
Q 038285 49 LGTFASPDKAARAYDAAALAL 69 (178)
Q Consensus 49 LGtf~t~eeAA~AyD~Aa~~l 69 (178)
-|.|+|+|+|..=||.-...|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 389999999999999876554
No 18
>PLN00062 TATA-box-binding protein; Provisional
Probab=30.22 E-value=2.8e+02 Score=22.58 Aligned_cols=57 Identities=14% Similarity=0.037 Sum_probs=39.2
Q ss_pred CCCCeEEEEeeC--CeEEEEEeecCCCcEEEecCCCCHHHHHHHHHHHHHHhcCCCCCCCCC
Q 038285 20 RHPVYKGVRRRN--GKWVCELREPNKKSRIWLGTFASPDKAARAYDAAALALRGNSASLNFP 79 (178)
Q Consensus 20 ~~s~yrGVr~r~--~kW~A~I~~p~~~k~i~LGtf~t~eeAA~AyD~Aa~~l~g~~a~lNFp 79 (178)
+..+|-||..|. -+=.+-|.. .||-+-.|. .+.|+|..|.+..+..+..-....+|+
T Consensus 32 ePe~fpgli~Rl~~Pk~t~lIF~--SGKiviTGa-ks~e~a~~a~~~~~~~L~~lg~~~~~~ 90 (179)
T PLN00062 32 NPKRFAAVIMRIREPKTTALIFA--SGKMVCTGA-KSEHDSKLAARKYARIIQKLGFPAKFK 90 (179)
T ss_pred CCccCcEEEEEeCCCcEEEEEEC--CCeEEEEec-CCHHHHHHHHHHHHHHHHHcCCCcCCC
Confidence 345789986555 376666666 898887765 788999999988877774333344444
No 19
>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=30.21 E-value=2.8e+02 Score=22.42 Aligned_cols=57 Identities=16% Similarity=0.067 Sum_probs=39.2
Q ss_pred CCCCeEEEEeeC--CeEEEEEeecCCCcEEEecCCCCHHHHHHHHHHHHHHhcCCCCCCCCC
Q 038285 20 RHPVYKGVRRRN--GKWVCELREPNKKSRIWLGTFASPDKAARAYDAAALALRGNSASLNFP 79 (178)
Q Consensus 20 ~~s~yrGVr~r~--~kW~A~I~~p~~~k~i~LGtf~t~eeAA~AyD~Aa~~l~g~~a~lNFp 79 (178)
+..+|.||..|. -+=.+-|.. .||-+-.|. .+.|+|..|.+..+..|..-.-..+|+
T Consensus 32 ePe~fpgli~Rl~~Pk~t~lIF~--SGKiviTGa-ks~e~a~~a~~~i~~~L~~~g~~~~~~ 90 (174)
T cd04516 32 NPKRFAAVIMRIREPKTTALIFS--SGKMVCTGA-KSEDDSKLAARKYARIIQKLGFPAKFT 90 (174)
T ss_pred CCccCcEEEEEeCCCcEEEEEEC--CCeEEEEec-CCHHHHHHHHHHHHHHHHHcCCCCCCC
Confidence 345788985555 376667777 999888876 578889999988877774333233554
No 20
>PF09003 Phage_integ_N: Bacteriophage lambda integrase, N-terminal domain ; InterPro: IPR015094 The amino terminal domain of bacteriophage lambda integrase folds into a three-stranded, antiparallel beta-sheet that packs against a C-terminal alpha-helix, adopting a fold that is structurally related to the three-stranded beta-sheet family of DNA-binding domains (which includes the GCC-box DNA-binding domain and the N-terminal domain of Tn916 integrase). This domain is responsible for high-affinity binding to each of the five DNA arm-type sites and is also a context-sensitive modulator of DNA cleavage []. ; GO: 0003677 DNA binding, 0008907 integrase activity, 0015074 DNA integration; PDB: 1Z1G_B 1Z1B_A 2WCC_3 1KJK_A.
Probab=28.69 E-value=2.1e+02 Score=20.28 Aligned_cols=33 Identities=24% Similarity=0.201 Sum_probs=22.1
Q ss_pred EeecCCCcEEEecCCCCHHHHHHHHHHHHHHhcCC
Q 038285 38 LREPNKKSRIWLGTFASPDKAARAYDAAALALRGN 72 (178)
Q Consensus 38 I~~p~~~k~i~LGtf~t~eeAA~AyD~Aa~~l~g~ 72 (178)
-+.|..|+.+.||+ +.++|..+=-.|-+.+...
T Consensus 31 Yr~P~tGk~~~LG~--d~~~Ai~~A~eaN~~i~~~ 63 (75)
T PF09003_consen 31 YRNPITGKEHGLGT--DRAEAIAQAIEANLRIAEQ 63 (75)
T ss_dssp EE-TTTS-EEEEES---HHHHHHHHHHHHHHHTSS
T ss_pred EecCCCCceeeCCC--CHHHHHHHHHHHHHHHHHh
Confidence 35788999999999 7777776666666666443
No 21
>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=27.58 E-value=1.2e+02 Score=22.44 Aligned_cols=35 Identities=20% Similarity=0.245 Sum_probs=26.7
Q ss_pred eEEEEEeecCCCcEEEecCCCCHHHHHHHHHHHHHHh
Q 038285 33 KWVCELREPNKKSRIWLGTFASPDKAARAYDAAALAL 69 (178)
Q Consensus 33 kW~A~I~~p~~~k~i~LGtf~t~eeAA~AyD~Aa~~l 69 (178)
.|+|.|.. +..-+-++.....+.|..|...|+.+|
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 79999998 666666666665888888888777655
No 22
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, 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=27.11 E-value=2.3e+02 Score=22.92 Aligned_cols=50 Identities=14% Similarity=0.041 Sum_probs=35.5
Q ss_pred CCCCeEEEEeeCCeEEEEEeecCCCcEEEecCCCCHHHHHHHHHHHHHHhc
Q 038285 20 RHPVYKGVRRRNGKWVCELREPNKKSRIWLGTFASPDKAARAYDAAALALR 70 (178)
Q Consensus 20 ~~s~yrGVr~r~~kW~A~I~~p~~~k~i~LGtf~t~eeAA~AyD~Aa~~l~ 70 (178)
+..+|.|+..|-..-.+.+.+...||-+-.|. .+.++|..|-++.+..|.
T Consensus 32 ~P~~fpgli~Rl~~Pk~t~lIF~SGKiv~tGa-ks~~~a~~a~~~~~~~L~ 81 (174)
T cd04518 32 NPDQFPGLVYRLEDPKIAALIFRSGKMVCTGA-KSVEDLHRAVKEIIKKLK 81 (174)
T ss_pred CCCcCcEEEEEccCCcEEEEEECCCeEEEEcc-CCHHHHHHHHHHHHHHHH
Confidence 44678998766643334444444999887775 788999999988887775
No 23
>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=26.30 E-value=3e+02 Score=22.07 Aligned_cols=48 Identities=21% Similarity=0.113 Sum_probs=34.5
Q ss_pred CCCCeEEEEeeCC--eEEEEEeecCCCcEEEecCCCCHHHHHHHHHHHHHHhc
Q 038285 20 RHPVYKGVRRRNG--KWVCELREPNKKSRIWLGTFASPDKAARAYDAAALALR 70 (178)
Q Consensus 20 ~~s~yrGVr~r~~--kW~A~I~~p~~~k~i~LGtf~t~eeAA~AyD~Aa~~l~ 70 (178)
+..+|.||..|.. +=.+-|.. .||-+-.|. .+.|+|..|.++.+..|.
T Consensus 32 ePe~fpgli~R~~~P~~t~lIf~--sGKivitGa-ks~~~~~~a~~~~~~~L~ 81 (174)
T cd00652 32 NPKRFPGVIMRLREPKTTALIFS--SGKMVITGA-KSEEDAKLAARKYARILQ 81 (174)
T ss_pred CCCccceEEEEcCCCcEEEEEEC--CCEEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 3457899866664 54555555 999887776 578888888888777764
No 24
>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=26.19 E-value=3.1e+02 Score=22.10 Aligned_cols=45 Identities=22% Similarity=0.144 Sum_probs=34.7
Q ss_pred CeEEEEeeC--CeEEEEEeecCCCcEEEecCCCCHHHHHHHHHHHHHHhc
Q 038285 23 VYKGVRRRN--GKWVCELREPNKKSRIWLGTFASPDKAARAYDAAALALR 70 (178)
Q Consensus 23 ~yrGVr~r~--~kW~A~I~~p~~~k~i~LGtf~t~eeAA~AyD~Aa~~l~ 70 (178)
+|.||..|. -+=.+-|.. .||-+-.| ..+.|+|.+|.+..+..+.
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 899986655 376677777 88887666 4789999999988877774
No 25
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=25.28 E-value=53 Score=26.08 Aligned_cols=30 Identities=30% Similarity=0.345 Sum_probs=20.9
Q ss_pred eEEEEEeecCCCcEEEecCCCCHHHHHHHH
Q 038285 33 KWVCELREPNKKSRIWLGTFASPDKAARAY 62 (178)
Q Consensus 33 kW~A~I~~p~~~k~i~LGtf~t~eeAA~Ay 62 (178)
|..+++..-..=.-|++|.|.|+||++++=
T Consensus 30 kvia~~l~d~GfeVi~~g~~~tp~e~v~aA 59 (143)
T COG2185 30 KVIARALADAGFEVINLGLFQTPEEAVRAA 59 (143)
T ss_pred HHHHHHHHhCCceEEecCCcCCHHHHHHHH
Confidence 444444332334679999999999998865
No 26
>PRK10113 cell division modulator; Provisional
Probab=25.26 E-value=61 Score=22.89 Aligned_cols=37 Identities=24% Similarity=0.339 Sum_probs=25.9
Q ss_pred CCeEEEEeeCCeEEEEEeecCCCcEEEecCCCCHHHHHH
Q 038285 22 PVYKGVRRRNGKWVCELREPNKKSRIWLGTFASPDKAAR 60 (178)
Q Consensus 22 s~yrGVr~r~~kW~A~I~~p~~~k~i~LGtf~t~eeAA~ 60 (178)
-+||-|-.-.|||+|.+.. +-....--.|..+|.|-|
T Consensus 31 d~frDVW~LrGKYVAFvl~--ge~FrRSPaFs~PEsAQR 67 (80)
T PRK10113 31 DSFRDVWMLRGKYVAFVLM--GESFLRSPAFSVPESAQR 67 (80)
T ss_pred cchhhhheeccceEEEEEe--chhhccCCccCCcHHHHH
Confidence 4688887777999999887 333333346778877765
No 27
>TIGR01164 rplP_bact ribosomal protein L16, bacterial/organelle. This model describes bacterial and organellar ribosomal protein L16. The homologous protein of the eukaryotic cytosol is designated L10
Probab=24.95 E-value=1.6e+02 Score=22.52 Aligned_cols=34 Identities=24% Similarity=0.302 Sum_probs=27.3
Q ss_pred eEEEEEeecCCCcEEEecCCCCHHHHHHHHHHHHHHh
Q 038285 33 KWVCELREPNKKSRIWLGTFASPDKAARAYDAAALAL 69 (178)
Q Consensus 33 kW~A~I~~p~~~k~i~LGtf~t~eeAA~AyD~Aa~~l 69 (178)
.|+|.|.. +..-+-++. .+++.|..|...|+.+|
T Consensus 91 ~~varV~~--G~ilfEi~~-~~~~~a~~al~~a~~KL 124 (126)
T TIGR01164 91 YWVAVVKP--GKILFEIAG-VPEEVAREAFRLAASKL 124 (126)
T ss_pred EEEEEECC--CCEEEEEeC-CCHHHHHHHHHHHHhcC
Confidence 69999998 656666666 89999999998887765
No 28
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=24.55 E-value=1.4e+02 Score=23.21 Aligned_cols=36 Identities=22% Similarity=0.205 Sum_probs=28.4
Q ss_pred eEEEEEeecCCCcEEEecCCCCHHHHHHHHHHHHHHhcC
Q 038285 33 KWVCELREPNKKSRIWLGTFASPDKAARAYDAAALALRG 71 (178)
Q Consensus 33 kW~A~I~~p~~~k~i~LGtf~t~eeAA~AyD~Aa~~l~g 71 (178)
.|+|.|.. +..-+-++. .+++.|..|...|+.+|-+
T Consensus 92 ~~varVk~--G~iifEi~~-~~~~~a~~al~~a~~KLP~ 127 (138)
T PRK09203 92 YWVAVVKP--GRILFEIAG-VSEELAREALRLAAAKLPI 127 (138)
T ss_pred EEEEEECC--CCEEEEEeC-CCHHHHHHHHHHHhccCCC
Confidence 69999998 666666666 8899999999988876643
No 29
>PF12286 DUF3622: Protein of unknown function (DUF3622); InterPro: IPR022069 This family of proteins is found in bacteria. Proteins in this family are typically between 72 and 107 amino acids in length. There is a conserved VSK sequence motif.
Probab=23.26 E-value=1.8e+02 Score=20.54 Aligned_cols=39 Identities=21% Similarity=0.439 Sum_probs=22.5
Q ss_pred CeEEEEeeCCeEEEEEeecCCCcEEEe----cCCCCHHHHHHHHH
Q 038285 23 VYKGVRRRNGKWVCELREPNKKSRIWL----GTFASPDKAARAYD 63 (178)
Q Consensus 23 ~yrGVr~r~~kW~A~I~~p~~~k~i~L----Gtf~t~eeAA~AyD 63 (178)
-|| |.+..+.|.|+|.--...++.-+ -.|.|+++|. ++-
T Consensus 8 ~~r-v~q~~~~W~aEItR~vTsrkTvVSK~~~GF~SEaeAq-~W~ 50 (71)
T PF12286_consen 8 DFR-VTQKRNGWTAEITRRVTSRKTVVSKRQDGFASEAEAQ-AWG 50 (71)
T ss_pred cEE-EEecCCceeeeeeeeecCceeEEEecccCcccHHHHH-HHH
Confidence 444 45556789999986432222212 3588888754 443
No 30
>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=22.69 E-value=82 Score=16.91 Aligned_cols=11 Identities=27% Similarity=1.060 Sum_probs=8.4
Q ss_pred CCcEEEecCCC
Q 038285 43 KKSRIWLGTFA 53 (178)
Q Consensus 43 ~~k~i~LGtf~ 53 (178)
+.-+||+||+.
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 31
>COG5558 Transposase [DNA replication, recombination, and repair]
Probab=21.99 E-value=73 Score=27.06 Aligned_cols=51 Identities=16% Similarity=0.290 Sum_probs=35.1
Q ss_pred CCCeEEEEeeCC---eEEEEEeecCCCcEEEecCCCCHHHHHHHHHHHHHHhcCCC
Q 038285 21 HPVYKGVRRRNG---KWVCELREPNKKSRIWLGTFASPDKAARAYDAAALALRGNS 73 (178)
Q Consensus 21 ~s~yrGVr~r~~---kW~A~I~~p~~~k~i~LGtf~t~eeAA~AyD~Aa~~l~g~~ 73 (178)
+-.||-|+++.| +|+-.|..-..+-+|..|+|.--| .-||.+|...+..-.
T Consensus 101 t~h~rs~~~k~g~~~ry~f~iidl~t~myvg~~~~~rse--~da~eka~~ml~~mg 154 (261)
T COG5558 101 TKHYRSNPKRKGKDFRYVFRIIDIDTGMYVGFGYSDRSE--KDAFEKALGMLKSMG 154 (261)
T ss_pred ehhhhcChhhcCccceEEEEEEEeccceEEEeeccccch--hHHHHHHHHHHHHhC
Confidence 345777877776 788899885556666666666554 457888888775443
No 32
>KOG3422 consensus Mitochondrial ribosomal protein L16 [Translation, ribosomal structure and biogenesis]
Probab=20.38 E-value=2.5e+02 Score=23.92 Aligned_cols=37 Identities=22% Similarity=0.248 Sum_probs=31.4
Q ss_pred eEEEEEeecCCCcEEEecCCCCHHHHHHHHHHHHHHhcC
Q 038285 33 KWVCELREPNKKSRIWLGTFASPDKAARAYDAAALALRG 71 (178)
Q Consensus 33 kW~A~I~~p~~~k~i~LGtf~t~eeAA~AyD~Aa~~l~g 71 (178)
.|++.|.. ++--+=+|---++++|..|.+.|+.++-+
T Consensus 133 ~wva~V~~--GrIl~EmgG~~~~~~Ar~al~~aa~klp~ 169 (221)
T KOG3422|consen 133 HWVARVKA--GRILFEMGGDVEEEEARQALLQAAHKLPF 169 (221)
T ss_pred eeEEEecC--CcEEEEeCCcccHHHHHHHHHHHHhcCCc
Confidence 79999988 77777788888999999999999987643
Done!