Query 028094
Match_columns 214
No_of_seqs 231 out of 1364
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 06:08:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028094.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028094hhsearch_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 4.5E-26 136.0 7.5 61 45-105 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 9.6E-21 2.1E-25 134.1 8.3 63 46-108 1-63 (64)
3 PHA00280 putative NHN endonucl 99.6 3.1E-16 6.8E-21 124.6 7.1 83 14-99 36-119 (121)
4 PF00847 AP2: AP2 domain; Int 99.1 1.9E-10 4.1E-15 78.5 6.0 52 45-96 1-56 (56)
5 PF14657 Integrase_AP2: AP2-li 73.7 14 0.00031 24.0 5.4 38 57-94 1-42 (46)
6 cd00801 INT_P4 Bacteriophage P 68.5 9.8 0.00021 33.2 4.9 39 55-93 9-49 (357)
7 PF13356 DUF4102: Domain of un 63.9 26 0.00057 25.5 5.8 33 57-89 36-70 (89)
8 PHA02601 int integrase; Provis 63.0 12 0.00026 33.0 4.4 42 49-91 2-44 (333)
9 PF10729 CedA: Cell division a 56.4 17 0.00037 26.6 3.5 38 44-84 30-67 (80)
10 PF08846 DUF1816: Domain of un 56.2 23 0.0005 25.6 4.1 39 56-94 8-46 (68)
11 PRK09692 integrase; Provisiona 45.3 56 0.0012 30.0 5.9 38 50-87 33-76 (413)
12 PF05036 SPOR: Sporulation rel 42.2 31 0.00068 23.3 3.0 24 67-90 42-65 (76)
13 PRK10113 cell division modulat 40.3 22 0.00048 26.0 1.9 37 45-84 31-67 (80)
14 PF14112 DUF4284: Domain of un 35.5 23 0.0005 27.9 1.6 19 69-87 2-20 (122)
15 PF07494 Reg_prop: Two compone 27.6 33 0.00072 19.3 0.9 11 67-77 14-24 (24)
16 KOG3422 Mitochondrial ribosoma 25.3 1.5E+02 0.0033 26.1 5.0 37 57-95 133-169 (221)
17 PF08471 Ribonuc_red_2_N: Clas 24.3 84 0.0018 24.2 2.8 20 73-92 70-89 (93)
18 COG2185 Sbm Methylmalonyl-CoA 23.0 62 0.0013 26.7 2.0 18 68-85 41-58 (143)
19 PF12404 DUF3663: Peptidase ; 22.3 41 0.00088 25.0 0.8 38 90-127 10-47 (77)
20 cd01433 Ribosomal_L16_L10e Rib 20.8 1.8E+02 0.004 22.3 4.2 34 58-93 72-105 (112)
21 PF09954 DUF2188: Uncharacteri 20.1 1.7E+02 0.0037 19.8 3.6 33 50-86 3-35 (62)
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=135.96 Aligned_cols=61 Identities=64% Similarity=0.994 Sum_probs=57.8
Q ss_pred CceeEEEECCCCceEEEEeecCCCceEEecCCCCHHHHHHHHHHHHHHhcCCccccCCCCC
Q 028094 45 PVYRGVRRRDSGKWVCEVREPNKKSRIWLGTFPTAEMAARAHDVAAIALRGRLACLNFADS 105 (214)
Q Consensus 45 s~yrGVr~r~~GkW~a~I~~~~~~kri~LGtf~t~eeAArAyD~aa~~~~G~~a~~NFp~s 105 (214)
|+||||+++++|||+|+|+++..++++|||+|+|+|||++|||.++++++|..+.+|||++
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 6899999888899999999976699999999999999999999999999999999999985
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.84 E-value=9.6e-21 Score=134.11 Aligned_cols=63 Identities=60% Similarity=0.970 Sum_probs=60.0
Q ss_pred ceeEEEECCCCceEEEEeecCCCceEEecCCCCHHHHHHHHHHHHHHhcCCccccCCCCCCCC
Q 028094 46 VYRGVRRRDSGKWVCEVREPNKKSRIWLGTFPTAEMAARAHDVAAIALRGRLACLNFADSSWR 108 (214)
Q Consensus 46 ~yrGVr~r~~GkW~a~I~~~~~~kri~LGtf~t~eeAArAyD~aa~~~~G~~a~~NFp~s~~~ 108 (214)
+|+||+++++|||+|+|++|.+++++|||+|+|+||||+|||.++++++|..+.+|||.+.|.
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 499998888899999999999999999999999999999999999999999999999998874
No 3
>PHA00280 putative NHN endonuclease
Probab=99.65 E-value=3.1e-16 Score=124.62 Aligned_cols=83 Identities=17% Similarity=0.179 Sum_probs=75.5
Q ss_pred CCCCCccceeecccCCcccccCCCCCCCCCCCceeEEE-ECCCCceEEEEeecCCCceEEecCCCCHHHHHHHHHHHHHH
Q 028094 14 VGNFSDEDVVLLASSNPKKRAGRKKFRETRHPVYRGVR-RRDSGKWVCEVREPNKKSRIWLGTFPTAEMAARAHDVAAIA 92 (214)
Q Consensus 14 ~~~~~~~~~~~~~~~~~k~~~~r~~~~~~~~s~yrGVr-~r~~GkW~a~I~~~~~~kri~LGtf~t~eeAArAyD~aa~~ 92 (214)
.++..++++.+|+..++..+..|++.+.+++|+|+||. .+..|||+|+|++ ++|+++||.|+++|+|+.||+ ++.+
T Consensus 36 dg~~~dnri~NLr~~T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~--~gK~~~lG~f~~~e~A~~a~~-~~~~ 112 (121)
T PHA00280 36 DGNPLNDALDNLRLALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTA--EGKQHNFRSRDLLEVVAWIYR-TRRE 112 (121)
T ss_pred CCCCCCCcHHHhhhcCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEEE--CCEEEEcCCCCCHHHHHHHHH-HHHH
Confidence 36788899999999999999999998999999999995 5567999999998 999999999999999999997 7788
Q ss_pred hcCCccc
Q 028094 93 LRGRLAC 99 (214)
Q Consensus 93 ~~G~~a~ 99 (214)
|+|.+|+
T Consensus 113 lhGeFa~ 119 (121)
T PHA00280 113 LHGQFAR 119 (121)
T ss_pred Hhhcccc
Confidence 9998875
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=99.10 E-value=1.9e-10 Score=78.51 Aligned_cols=52 Identities=31% Similarity=0.502 Sum_probs=44.5
Q ss_pred CceeEEE-ECCCCceEEEEeecCC---CceEEecCCCCHHHHHHHHHHHHHHhcCC
Q 028094 45 PVYRGVR-RRDSGKWVCEVREPNK---KSRIWLGTFPTAEMAARAHDVAAIALRGR 96 (214)
Q Consensus 45 s~yrGVr-~r~~GkW~a~I~~~~~---~kri~LGtf~t~eeAArAyD~aa~~~~G~ 96 (214)
|+|+||+ .+..++|+|+|+++.. +++++||.|+++++|+++++.+.+.++|.
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 6899996 4556999999999532 49999999999999999999999999874
No 5
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=73.75 E-value=14 Score=23.95 Aligned_cols=38 Identities=21% Similarity=0.255 Sum_probs=28.9
Q ss_pred ceEEEEe--ec--CCCceEEecCCCCHHHHHHHHHHHHHHhc
Q 028094 57 KWVCEVR--EP--NKKSRIWLGTFPTAEMAARAHDVAAIALR 94 (214)
Q Consensus 57 kW~a~I~--~~--~~~kri~LGtf~t~eeAArAyD~aa~~~~ 94 (214)
+|...|. .| ++.++++-+-|.|..||..+.......+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 5777773 33 34578899999999999999887766553
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=68.49 E-value=9.8 Score=33.16 Aligned_cols=39 Identities=31% Similarity=0.473 Sum_probs=28.3
Q ss_pred CCceEEEEeecCCCceEEecCCC--CHHHHHHHHHHHHHHh
Q 028094 55 SGKWVCEVREPNKKSRIWLGTFP--TAEMAARAHDVAAIAL 93 (214)
Q Consensus 55 ~GkW~a~I~~~~~~kri~LGtf~--t~eeAArAyD~aa~~~ 93 (214)
.+.|..+++..++.+++.||+|+ +.++|..........+
T Consensus 9 ~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 9 SKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred CEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 35699999997777889999996 6677766655544443
No 7
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=63.90 E-value=26 Score=25.52 Aligned_cols=33 Identities=24% Similarity=0.314 Sum_probs=24.0
Q ss_pred ceEEEEeecCCCceEEecCCCC--HHHHHHHHHHH
Q 028094 57 KWVCEVREPNKKSRIWLGTFPT--AEMAARAHDVA 89 (214)
Q Consensus 57 kW~a~I~~~~~~kri~LGtf~t--~eeAArAyD~a 89 (214)
.|+-+.+..++.+++-||.|+. ..+|.......
T Consensus 36 t~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~ 70 (89)
T PF13356_consen 36 TFYFRYRINGKRRRITLGRYPELSLAEAREKAREL 70 (89)
T ss_dssp EEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHH
T ss_pred EEEEEEEecceEEEeccCCCccCCHHHHHHHHHHH
Confidence 4998888866778999999986 55555444433
No 8
>PHA02601 int integrase; Provisional
Probab=63.03 E-value=12 Score=33.02 Aligned_cols=42 Identities=29% Similarity=0.493 Sum_probs=28.8
Q ss_pred EEEECCCCceEEEEeec-CCCceEEecCCCCHHHHHHHHHHHHH
Q 028094 49 GVRRRDSGKWVCEVREP-NKKSRIWLGTFPTAEMAARAHDVAAI 91 (214)
Q Consensus 49 GVr~r~~GkW~a~I~~~-~~~kri~LGtf~t~eeAArAyD~aa~ 91 (214)
+|++.++|+|.++++.. ..|+++. .+|.|..||.........
T Consensus 2 ~~~~~~~g~w~~~~~~~~~~g~r~~-~~f~tk~eA~~~~~~~~~ 44 (333)
T PHA02601 2 AVRKLKDGKWLCEIYPNGRDGKRIR-KRFATKGEALAFENYTMA 44 (333)
T ss_pred ceEEcCCCCEEEEEEECCCCCchhh-hhhcCHHHHHHHHHHHHH
Confidence 46677779999999863 2356554 369999988766554433
No 9
>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=56.39 E-value=17 Score=26.62 Aligned_cols=38 Identities=26% Similarity=0.220 Sum_probs=24.9
Q ss_pred CCceeEEEECCCCceEEEEeecCCCceEEecCCCCHHHHHH
Q 028094 44 HPVYRGVRRRDSGKWVCEVREPNKKSRIWLGTFPTAEMAAR 84 (214)
Q Consensus 44 ~s~yrGVr~r~~GkW~a~I~~~~~~kri~LGtf~t~eeAAr 84 (214)
--+||-|+.-+ |||+|.+.. +..-.---.|..+|.|-|
T Consensus 30 ~dgfrdvw~lr-gkyvafvl~--ge~f~rsp~fs~pesaqr 67 (80)
T PF10729_consen 30 MDGFRDVWQLR-GKYVAFVLM--GEHFRRSPAFSVPESAQR 67 (80)
T ss_dssp TTTECCECCCC-CEEEEEEES--SS-EEE---BSSHHHHHH
T ss_pred cccccceeeec-cceEEEEEe--cchhccCCCcCCcHHHHH
Confidence 45799997654 999999986 433334456888887765
No 10
>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=56.17 E-value=23 Score=25.64 Aligned_cols=39 Identities=23% Similarity=0.302 Sum_probs=28.7
Q ss_pred CceEEEEeecCCCceEEecCCCCHHHHHHHHHHHHHHhc
Q 028094 56 GKWVCEVREPNKKSRIWLGTFPTAEMAARAHDVAAIALR 94 (214)
Q Consensus 56 GkW~a~I~~~~~~kri~LGtf~t~eeAArAyD~aa~~~~ 94 (214)
-.|-++|.--.-.-..|.|-|.|.+||..+.---...+.
T Consensus 8 laWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~ 46 (68)
T PF08846_consen 8 LAWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLE 46 (68)
T ss_pred CcEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHH
Confidence 358889987444567789999999999988655444443
No 11
>PRK09692 integrase; Provisional
Probab=45.34 E-value=56 Score=30.04 Aligned_cols=38 Identities=21% Similarity=0.375 Sum_probs=23.8
Q ss_pred EEECCCC--ceEEEEeecC--CCceEEecCCC--CHHHHHHHHH
Q 028094 50 VRRRDSG--KWVCEVREPN--KKSRIWLGTFP--TAEMAARAHD 87 (214)
Q Consensus 50 Vr~r~~G--kW~a~I~~~~--~~kri~LGtf~--t~eeAArAyD 87 (214)
|+-+..| .|+.+.+.+. +.+++-||.|+ |..+|.....
T Consensus 33 l~v~~~G~k~~~~rY~~~~~gk~~~~~lG~yp~~sl~~AR~~a~ 76 (413)
T PRK09692 33 LLIKSSGSKIWQFRYYRPLTKTRAKKSFGPYPSVTLADARNYRA 76 (413)
T ss_pred EEEECCCcEEEEEEEecCCCCceeeeeCCCCCCCCHHHHHHHHH
Confidence 3444444 3998887553 34457899999 6666655433
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=42.24 E-value=31 Score=23.27 Aligned_cols=24 Identities=25% Similarity=0.242 Sum_probs=18.4
Q ss_pred CCceEEecCCCCHHHHHHHHHHHH
Q 028094 67 KKSRIWLGTFPTAEMAARAHDVAA 90 (214)
Q Consensus 67 ~~kri~LGtf~t~eeAArAyD~aa 90 (214)
..-+|.+|.|++.++|..+-....
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 456888999999999887766543
No 13
>PRK10113 cell division modulator; Provisional
Probab=40.32 E-value=22 Score=25.96 Aligned_cols=37 Identities=30% Similarity=0.298 Sum_probs=23.9
Q ss_pred CceeEEEECCCCceEEEEeecCCCceEEecCCCCHHHHHH
Q 028094 45 PVYRGVRRRDSGKWVCEVREPNKKSRIWLGTFPTAEMAAR 84 (214)
Q Consensus 45 s~yrGVr~r~~GkW~a~I~~~~~~kri~LGtf~t~eeAAr 84 (214)
-+||-|+.-+ |||+|.+.. ...-----.|..+|.|-|
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 4688897654 899999886 222222345777776655
No 14
>PF14112 DUF4284: Domain of unknown function (DUF4284)
Probab=35.47 E-value=23 Score=27.89 Aligned_cols=19 Identities=21% Similarity=0.616 Sum_probs=14.2
Q ss_pred ceEEecCCCCHHHHHHHHH
Q 028094 69 SRIWLGTFPTAEMAARAHD 87 (214)
Q Consensus 69 kri~LGtf~t~eeAArAyD 87 (214)
-.||||+|.+.++-..=.+
T Consensus 2 VsiWiG~f~s~~el~~Y~e 20 (122)
T PF14112_consen 2 VSIWIGNFKSEDELEEYFE 20 (122)
T ss_pred eEEEEecCCCHHHHHHHhC
Confidence 3699999999887655433
No 15
>PF07494 Reg_prop: Two component regulator propeller; InterPro: IPR011110 A large group of two component regulator proteins appear to have the same N-terminal structure of 14 tandem repeats. These repeats show homology to members of IPR002372 from INTERPRO and IPR001680 from INTERPRO indicating that they are likely to form a beta-propeller. This family has been built with artificially high cut-offs in order to avoid overlaps with other beta-propeller families. The fourteen repeats are likely to form two propellers; it is not clear if these structures are likely to recruit other proteins or interact with DNA.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
Probab=27.57 E-value=33 Score=19.26 Aligned_cols=11 Identities=27% Similarity=1.042 Sum_probs=8.6
Q ss_pred CCceEEecCCC
Q 028094 67 KKSRIWLGTFP 77 (214)
Q Consensus 67 ~~kri~LGtf~ 77 (214)
+..+||+||+.
T Consensus 14 ~~G~lWigT~~ 24 (24)
T PF07494_consen 14 SDGNLWIGTYN 24 (24)
T ss_dssp TTSCEEEEETS
T ss_pred CCcCEEEEeCC
Confidence 56789999873
No 16
>KOG3422 consensus Mitochondrial ribosomal protein L16 [Translation, ribosomal structure and biogenesis]
Probab=25.29 E-value=1.5e+02 Score=26.09 Aligned_cols=37 Identities=27% Similarity=0.195 Sum_probs=29.0
Q ss_pred ceEEEEeecCCCceEEecCCCCHHHHHHHHHHHHHHhcC
Q 028094 57 KWVCEVREPNKKSRIWLGTFPTAEMAARAHDVAAIALRG 95 (214)
Q Consensus 57 kW~a~I~~~~~~kri~LGtf~t~eeAArAyD~aa~~~~G 95 (214)
.|++.|.. .+--+=+|---++++|..|.+.|+.++-+
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 49999986 44455588888999999999998877643
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=24.33 E-value=84 Score=24.15 Aligned_cols=20 Identities=30% Similarity=0.149 Sum_probs=16.7
Q ss_pred ecCCCCHHHHHHHHHHHHHH
Q 028094 73 LGTFPTAEMAARAHDVAAIA 92 (214)
Q Consensus 73 LGtf~t~eeAArAyD~aa~~ 92 (214)
-|.|+|+|+|..-||.-...
T Consensus 70 ~GYF~t~eDA~~FydEl~~m 89 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYM 89 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHH
Confidence 49999999999999975543
No 18
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=23.01 E-value=62 Score=26.66 Aligned_cols=18 Identities=50% Similarity=0.471 Sum_probs=16.0
Q ss_pred CceEEecCCCCHHHHHHH
Q 028094 68 KSRIWLGTFPTAEMAARA 85 (214)
Q Consensus 68 ~kri~LGtf~t~eeAArA 85 (214)
=.-|++|.|.|+||++++
T Consensus 41 feVi~~g~~~tp~e~v~a 58 (143)
T COG2185 41 FEVINLGLFQTPEEAVRA 58 (143)
T ss_pred ceEEecCCcCCHHHHHHH
Confidence 367999999999999887
No 19
>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=22.31 E-value=41 Score=24.97 Aligned_cols=38 Identities=32% Similarity=0.372 Sum_probs=27.2
Q ss_pred HHHhcCCccccCCCCCCCCCCCCCCCCchHHHHHHHHH
Q 028094 90 AIALRGRLACLNFADSSWRLPLPASTDPKDIQKAAAEA 127 (214)
Q Consensus 90 a~~~~G~~a~~NFp~s~~~~~~p~~~~~~~i~~aaa~A 127 (214)
+-..+|++|.+-|...-..+.+-.......||+||..-
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 34568888888888776666555556678888888654
No 20
>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=20.84 E-value=1.8e+02 Score=22.26 Aligned_cols=34 Identities=29% Similarity=0.360 Sum_probs=24.1
Q ss_pred eEEEEeecCCCceEEecCCCCHHHHHHHHHHHHHHh
Q 028094 58 WVCEVREPNKKSRIWLGTFPTAEMAARAHDVAAIAL 93 (214)
Q Consensus 58 W~a~I~~~~~~kri~LGtf~t~eeAArAyD~aa~~~ 93 (214)
|+|.|.. ...-+-++.....+.|..|...|+.++
T Consensus 72 ~~a~v~~--G~iifEi~~~~~~~~~~~alk~a~~Kl 105 (112)
T cd01433 72 WVARVKP--GQILFEVRGVPEEEVAKEALRRAAKKL 105 (112)
T ss_pred EEEEECC--CCEEEEEeCcCcHHHHHHHHHHhhccC
Confidence 9999995 444444666655888888887776654
No 21
>PF09954 DUF2188: Uncharacterized protein conserved in bacteria (DUF2188); InterPro: IPR018691 This family has no known function.
Probab=20.15 E-value=1.7e+02 Score=19.79 Aligned_cols=33 Identities=30% Similarity=0.391 Sum_probs=21.7
Q ss_pred EEECCCCceEEEEeecCCCceEEecCCCCHHHHHHHH
Q 028094 50 VRRRDSGKWVCEVREPNKKSRIWLGTFPTAEMAARAH 86 (214)
Q Consensus 50 Vr~r~~GkW~a~I~~~~~~kri~LGtf~t~eeAArAy 86 (214)
|..+..|.|..+... ..+. ..+|+|.++|-.+=
T Consensus 3 V~p~~~~~W~v~~eg--~~ra--~~~~~Tk~eAi~~A 35 (62)
T PF09954_consen 3 VVPREDGGWAVKKEG--AKRA--SKTFDTKAEAIEAA 35 (62)
T ss_pred EEecCCCCceEEeCC--Cccc--ccccCcHHHHHHHH
Confidence 333455789877764 2222 68999999886653
Done!