Query 034904
Match_columns 79
No_of_seqs 21 out of 23
Neff 2.1
Searched_HMMs 46136
Date Fri Mar 29 07:32:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034904.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034904hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10937 DUF2638: Protein of u 97.6 0.00022 4.7E-09 48.8 6.2 17 60-76 96-112 (112)
2 PF13442 Cytochrome_CBB3: Cyto 67.5 7.1 0.00015 22.3 2.6 19 54-72 46-64 (67)
3 KOG4849 mRNA cleavage factor I 59.1 36 0.00078 29.1 6.2 24 51-74 345-368 (498)
4 PF07637 PSD5: Protein of unkn 58.5 8.4 0.00018 23.2 1.8 14 59-72 15-28 (64)
5 COG0501 HtpX Zn-dependent prot 50.9 10 0.00023 26.7 1.6 11 62-72 151-161 (302)
6 PRK12469 RNA polymerase factor 50.3 10 0.00022 31.3 1.7 39 31-74 402-453 (481)
7 cd07321 Extradiol_Dioxygenase_ 48.9 13 0.00029 23.4 1.7 15 60-74 32-46 (77)
8 PF04604 L_biotic_typeA: Type- 48.6 12 0.00027 23.1 1.5 13 62-74 14-26 (51)
9 COG1508 RpoN DNA-directed RNA 46.0 13 0.00028 31.0 1.7 37 31-72 363-413 (444)
10 PF00034 Cytochrom_C: Cytochro 46.0 16 0.00035 20.0 1.6 11 62-72 74-84 (91)
11 PF01191 RNA_pol_Rpb5_C: RNA p 43.0 12 0.00027 24.1 0.9 20 54-73 6-25 (74)
12 cd07921 PCA_45_Doxase_A_like S 42.7 17 0.00036 25.2 1.5 15 60-74 42-56 (106)
13 PF11341 DUF3143: Protein of u 41.7 20 0.00044 22.9 1.7 14 62-75 50-63 (63)
14 cd07922 CarBa CarBa is the A s 41.0 18 0.00039 23.6 1.4 17 59-75 32-48 (81)
15 PRK09570 rpoH DNA-directed RNA 40.3 22 0.00048 23.3 1.8 20 54-73 9-28 (79)
16 PF12065 DUF3545: Protein of u 37.7 18 0.00039 23.0 1.0 13 57-72 22-34 (59)
17 PF08920 SF3b1: Splicing facto 37.7 12 0.00026 26.6 0.2 13 61-73 85-97 (144)
18 PF14584 DUF4446: Protein of u 35.5 24 0.00053 25.0 1.5 12 61-72 137-148 (151)
19 PF08708 PriCT_1: Primase C te 34.0 35 0.00077 20.0 1.8 13 60-72 50-62 (71)
20 cd02135 Arsenite_oxidase Nitro 33.9 35 0.00076 21.6 1.9 14 60-73 15-28 (160)
21 CHL00183 petJ cytochrome c553; 33.2 45 0.00099 20.9 2.3 21 52-72 77-97 (108)
22 COG0250 NusG Transcription ant 32.9 37 0.0008 24.5 2.1 21 49-72 88-108 (178)
23 PF09424 YqeY: Yqey-like prote 31.6 32 0.00068 23.9 1.5 16 56-73 86-101 (143)
24 PRK13697 cytochrome c6; Provis 30.8 59 0.0013 20.1 2.5 18 55-72 82-99 (111)
25 cd00179 SynN Syntaxin N-termin 29.8 41 0.00088 21.7 1.7 15 61-75 128-142 (151)
26 cd07923 Gallate_dioxygenase_C 29.6 40 0.00086 22.9 1.7 15 60-74 34-48 (94)
27 COG5227 SMT3 Ubiquitin-like pr 28.2 32 0.0007 24.2 1.1 22 56-77 74-102 (103)
28 PF11829 DUF3349: Protein of u 28.0 45 0.00097 22.6 1.7 10 63-72 36-45 (96)
29 KOG2737 Putative metallopeptid 27.9 41 0.00089 28.9 1.8 15 62-76 468-482 (492)
30 cd03370 NADH_oxidase NADPH_oxi 27.4 53 0.0011 21.4 1.9 14 60-73 16-29 (156)
31 PF05373 Pro_3_hydrox_C: L-pro 26.5 43 0.00092 23.1 1.4 19 57-75 19-37 (101)
32 smart00738 NGN In Spt5p, this 26.1 46 0.001 20.2 1.4 15 59-73 91-105 (106)
33 PF05952 ComX: Bacillus compet 25.6 49 0.0011 20.7 1.5 21 51-75 21-41 (57)
34 cd02136 Nitroreductase Nitrore 25.2 61 0.0013 21.1 1.9 12 61-72 17-28 (178)
35 PF05391 Lsm_interact: Lsm int 25.1 90 0.002 16.4 2.2 17 58-74 5-21 (21)
36 PF07746 LigA: Aromatic-ring-o 24.6 54 0.0012 21.5 1.6 15 60-74 27-41 (88)
37 PF04552 Sigma54_DBD: Sigma-54 24.6 52 0.0011 23.4 1.6 16 58-73 117-132 (160)
38 KOG0574 STE20-like serine/thre 24.4 48 0.001 28.3 1.6 18 56-73 119-136 (502)
39 cd01190 INT_SG5 INT_SG5, DNA b 23.9 69 0.0015 21.2 2.0 16 58-73 70-85 (260)
40 PF09860 DUF2087: Uncharacteri 23.8 61 0.0013 20.4 1.7 18 57-74 24-41 (71)
41 cd00799 INT_Cre Cre recombinas 23.6 67 0.0015 22.0 2.0 14 59-72 91-104 (287)
42 PF07128 DUF1380: Protein of u 22.9 57 0.0012 23.6 1.6 11 62-72 42-52 (139)
43 PF04695 Pex14_N: Peroxisomal 22.2 47 0.001 22.5 1.0 14 60-73 32-45 (136)
44 COG2378 Predicted transcriptio 21.8 56 0.0012 24.9 1.4 23 52-74 61-87 (311)
45 PF03147 FDX-ACB: Ferredoxin-f 21.3 67 0.0015 19.9 1.5 20 53-72 59-78 (94)
46 cd02062 Nitro_FMN_reductase Pr 21.1 88 0.0019 18.7 1.9 12 61-72 13-24 (122)
47 TIGR03553 F420_FbiB_CTERM F420 20.8 83 0.0018 21.0 1.9 14 61-74 15-28 (194)
48 PF04369 Lactococcin: Lactococ 20.8 53 0.0011 21.0 1.0 15 61-75 8-22 (60)
No 1
>PF10937 DUF2638: Protein of unknown function (DUF2638); InterPro: IPR020373 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a component of the mitochondrial small ribosomal subunit. Mature mitochondrial ribosomes consist of a small (37S) and a large (54S) subunit. The 37S subunit contains at least 33 different proteins and 1 molecule of RNA (15S). The 54S subunit contains at least 45 different proteins and 1 molecule of RNA (21S). This entry is represented by a mitochondrial ribosomal protein of the small subunit, which has similarity to human mitochondrial ribosomal protein MRP-S36 [, , ].
Probab=97.63 E-value=0.00022 Score=48.79 Aligned_cols=17 Identities=53% Similarity=0.687 Sum_probs=15.9
Q ss_pred cccCCHHHHHHHHhccc
Q 034904 60 RTPVSNREIEAIMMGFT 76 (79)
Q Consensus 60 RtpvS~~EIEAIllGG~ 76 (79)
|.|++|+|||+|+-||+
T Consensus 96 r~p~se~EiE~InsGGA 112 (112)
T PF10937_consen 96 RKPISEEEIEAINSGGA 112 (112)
T ss_pred cCCCCHHHHHHHHcCCC
Confidence 78999999999999995
No 2
>PF13442 Cytochrome_CBB3: Cytochrome C oxidase, cbb3-type, subunit III ; PDB: 1KB0_A 2DGE_D 2CE1_A 2CE0_A 2V07_A 1W2L_A 2ZOO_A 2ZBO_G 1DVV_A 2EXV_A ....
Probab=67.46 E-value=7.1 Score=22.25 Aligned_cols=19 Identities=32% Similarity=0.489 Sum_probs=14.7
Q ss_pred ccCCCCcccCCHHHHHHHH
Q 034904 54 ASLQPKRTPVSNREIEAIM 72 (79)
Q Consensus 54 ASlqPkRtpvS~~EIEAIl 72 (79)
-.+.+....||++||++|+
T Consensus 46 ~~Mp~~~~~ls~~e~~~l~ 64 (67)
T PF13442_consen 46 GGMPPFGGQLSDEEIEALA 64 (67)
T ss_dssp TTBSCTTTTSTHHHHHHHH
T ss_pred CCCCCCCCCCCHHHHHHHH
Confidence 3555666689999999986
No 3
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=59.06 E-value=36 Score=29.10 Aligned_cols=24 Identities=29% Similarity=0.373 Sum_probs=20.7
Q ss_pred CccccCCCCcccCCHHHHHHHHhc
Q 034904 51 GGKASLQPKRTPVSNREIEAIMMG 74 (79)
Q Consensus 51 gGkASlqPkRtpvS~~EIEAIllG 74 (79)
++.--+-|.++||||.|.|-||..
T Consensus 345 ~~~r~~~p~~~plSeAEFEdiM~R 368 (498)
T KOG4849|consen 345 LPPRHVNPQMFPLSEAEFEDIMTR 368 (498)
T ss_pred CCcccCCCCCccchHHHHHHHHhh
Confidence 566778899999999999999964
No 4
>PF07637 PSD5: Protein of unknown function (DUF1595); InterPro: IPR013043 A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also contain IPR011478 from INTERPRO, IPR013036 from INTERPRO, IPR013039 from INTERPRO and IPR013042 from INTERPRO.
Probab=58.54 E-value=8.4 Score=23.20 Aligned_cols=14 Identities=21% Similarity=0.610 Sum_probs=12.0
Q ss_pred CcccCCHHHHHHHH
Q 034904 59 KRTPVSNREIEAIM 72 (79)
Q Consensus 59 kRtpvS~~EIEAIl 72 (79)
-|.||+++|++.++
T Consensus 15 fRRp~~~~e~~~~~ 28 (64)
T PF07637_consen 15 FRRPLTDEEVDRYL 28 (64)
T ss_pred hCCCCCHHHHHHHH
Confidence 38899999999875
No 5
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=50.87 E-value=10 Score=26.67 Aligned_cols=11 Identities=27% Similarity=0.625 Sum_probs=10.1
Q ss_pred cCCHHHHHHHH
Q 034904 62 PVSNREIEAIM 72 (79)
Q Consensus 62 pvS~~EIEAIl 72 (79)
-+++|||||||
T Consensus 151 ~l~~dEl~aVl 161 (302)
T COG0501 151 LLNDDELEAVL 161 (302)
T ss_pred hCCHHHHHHHH
Confidence 68999999997
No 6
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=50.27 E-value=10 Score=31.35 Aligned_cols=39 Identities=18% Similarity=0.331 Sum_probs=26.7
Q ss_pred ccccccccCCCCCCCCccccCccccC-------------CCCcccCCHHHHHHHHhc
Q 034904 31 QNLSARSSSDVPAAPANTAVGGKASL-------------QPKRTPVSNREIEAIMMG 74 (79)
Q Consensus 31 ~~~~~~~ss~vp~~p~~tavgGkASl-------------qPkRtpvS~~EIEAIllG 74 (79)
-.+++||++.| .+..||-.|- -.+++|||+++|-.+|-.
T Consensus 402 feLK~FFs~~v-----~~~~g~~~Ss~~Ik~~Ik~lI~~Ed~~kPLSD~~I~~~L~~ 453 (481)
T PRK12469 402 FEFKHFFPRKL-----EAAGGGECSAAAVRALIKEMIAAEQAGDPLSDVALAEMLAG 453 (481)
T ss_pred EeHHHhhcccc-----CCCCCccccHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHh
Confidence 45788888876 3333443321 277899999999888743
No 7
>cd07321 Extradiol_Dioxygenase_3A_like Subunit A of Class III extradiol dioxygenases. Extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. There are two major groups of dioxygenases according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents subunit A of c
Probab=48.93 E-value=13 Score=23.37 Aligned_cols=15 Identities=13% Similarity=0.169 Sum_probs=12.4
Q ss_pred cccCCHHHHHHHHhc
Q 034904 60 RTPVSNREIEAIMMG 74 (79)
Q Consensus 60 RtpvS~~EIEAIllG 74 (79)
+-.||+||++||+-|
T Consensus 32 ~~~Lt~eE~~al~~r 46 (77)
T cd07321 32 EYGLTPEEKAALLAR 46 (77)
T ss_pred HcCCCHHHHHHHHcC
Confidence 347999999999865
No 8
>PF04604 L_biotic_typeA: Type-A lantibiotic; InterPro: IPR007682 Lantibiotics are antibiotic peptides distinguished by the presence of the rare thioether amino acids lanthionine and/or methyllanthionine. They are produced by Gram-positive bacteria as gene-encoded precursor peptides and undergo post-translational modification to generate the mature peptide. Based on their structural and functional features lantibiotics are currently divided into two major groups: the flexible amphiphilic type-A and the rather rigid and globular type-B. Type-A lantibiotics act primarily by pore formation in the bacterial membrane by a mechanism involving the interaction with specific docking molecules such as the membrane precursor lipid II [].; GO: 0019748 secondary metabolic process, 0005576 extracellular region
Probab=48.62 E-value=12 Score=23.14 Aligned_cols=13 Identities=38% Similarity=0.680 Sum_probs=11.5
Q ss_pred cCCHHHHHHHHhc
Q 034904 62 PVSNREIEAIMMG 74 (79)
Q Consensus 62 pvS~~EIEAIllG 74 (79)
.||++|++.|+=|
T Consensus 14 evs~eELd~ilGg 26 (51)
T PF04604_consen 14 EVSDEELDQILGG 26 (51)
T ss_pred hcCHHHHHHHhCC
Confidence 5899999999877
No 9
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=45.98 E-value=13 Score=30.96 Aligned_cols=37 Identities=30% Similarity=0.433 Sum_probs=27.3
Q ss_pred ccccccccCCCCCCCCccccCccccCC--------------CCcccCCHHHHHHHH
Q 034904 31 QNLSARSSSDVPAAPANTAVGGKASLQ--------------PKRTPVSNREIEAIM 72 (79)
Q Consensus 31 ~~~~~~~ss~vp~~p~~tavgGkASlq--------------PkRtpvS~~EIEAIl 72 (79)
-+++.||++.+ ++..||.++.. -++.||||.+|--+|
T Consensus 363 feLK~FFs~~i-----~s~~gg~~~S~~~Ik~~Ik~lI~~E~~~~pLSD~kIa~lL 413 (444)
T COG1508 363 FELKYFFSSSL-----ASSEGGEASSTEAIKALIKKLIEAEDKKKPLSDSKIAELL 413 (444)
T ss_pred eeHHHHHHHhc-----cCCCCCccccHHHHHHHHHHHHhhccCCCCCCHHHHHHHH
Confidence 45777888876 66678888776 344599999997665
No 10
>PF00034 Cytochrom_C: Cytochrome c; InterPro: IPR003088 Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes. Ambler [] recognised four classes of cytC. Class I includes the low-spin soluble cytC of mitochondria and bacteria, with the haem-attachment site towards the N terminus, and the sixth ligand provided by a methionine residue about 40 residues further on towards the C terminus. On the basis of sequence similarity, class I cytC were further subdivided into five classes, IA to IE. Class IB includes the eukaryotic mitochondrial cytC and prokaryotic 'short' cyt c2 exemplified by Rhodopila globiformis cyt c2; class IA includes 'long' cyt c2, such as Rhodospirillum rubrum cyt c2 and Aquaspirillum itersonii cyt c-550, which have several extra loops by comparison with class IB cytC.; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding; PDB: 1YNR_B 2AI5_A 1AYG_A 3O5C_C 1YEA_A 3CXH_W 1YTC_A 1YEB_A 2YBB_Y 2B4Z_A ....
Probab=45.96 E-value=16 Score=20.04 Aligned_cols=11 Identities=27% Similarity=0.407 Sum_probs=9.8
Q ss_pred cCCHHHHHHHH
Q 034904 62 PVSNREIEAIM 72 (79)
Q Consensus 62 pvS~~EIEAIl 72 (79)
.||++||++|+
T Consensus 74 ~ls~~e~~~l~ 84 (91)
T PF00034_consen 74 ILSDEEIADLA 84 (91)
T ss_dssp TSSHHHHHHHH
T ss_pred CCCHHHHHHHH
Confidence 59999999986
No 11
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=42.99 E-value=12 Score=24.07 Aligned_cols=20 Identities=25% Similarity=0.381 Sum_probs=15.6
Q ss_pred ccCCCCcccCCHHHHHHHHh
Q 034904 54 ASLQPKRTPVSNREIEAIMM 73 (79)
Q Consensus 54 ASlqPkRtpvS~~EIEAIll 73 (79)
-.|+||-.-||+||.+.+|-
T Consensus 6 H~lVPkH~ils~eE~~~lL~ 25 (74)
T PF01191_consen 6 HELVPKHEILSEEEKKELLK 25 (74)
T ss_dssp STTC-EEEEE-HHHHHHHHH
T ss_pred ceecCCeEEcCHHHHHHHHH
Confidence 36899999999999999874
No 12
>cd07921 PCA_45_Doxase_A_like Subunit A of the Class III Extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, and similar enzymes. This subfamily includes the A subunit of protocatechuate (PCA) 4,5-dioxygenase (LigAB) and two subfamilies of unknown function. The A subunit is the smaller, non-catalytic subunit of LigAB. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As members of the Class III extradiol dioxygenase family, the enzymes use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like class III enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit.
Probab=42.68 E-value=17 Score=25.20 Aligned_cols=15 Identities=7% Similarity=0.204 Sum_probs=12.7
Q ss_pred cccCCHHHHHHHHhc
Q 034904 60 RTPVSNREIEAIMMG 74 (79)
Q Consensus 60 RtpvS~~EIEAIllG 74 (79)
+-+||+||++||+-+
T Consensus 42 ~~gLTeEe~~AV~~r 56 (106)
T cd07921 42 KFGLTEEQKQAVLDR 56 (106)
T ss_pred HcCCCHHHHHHHHhC
Confidence 558999999999865
No 13
>PF11341 DUF3143: Protein of unknown function (DUF3143); InterPro: IPR021489 This family of proteins has no known function.
Probab=41.72 E-value=20 Score=22.86 Aligned_cols=14 Identities=21% Similarity=0.368 Sum_probs=12.6
Q ss_pred cCCHHHHHHHHhcc
Q 034904 62 PVSNREIEAIMMGF 75 (79)
Q Consensus 62 pvS~~EIEAIllGG 75 (79)
-||-++|||-+++|
T Consensus 50 sLSR~DvE~Ai~~G 63 (63)
T PF11341_consen 50 SLSREDVEAAIFSG 63 (63)
T ss_pred cCCHHHHHHHHhcC
Confidence 58999999999987
No 14
>cd07922 CarBa CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. 2-aminophenol 1,6-dioxygenase is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, the enzyme has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=40.95 E-value=18 Score=23.63 Aligned_cols=17 Identities=18% Similarity=0.139 Sum_probs=13.7
Q ss_pred CcccCCHHHHHHHHhcc
Q 034904 59 KRTPVSNREIEAIMMGF 75 (79)
Q Consensus 59 kRtpvS~~EIEAIllGG 75 (79)
++--||+||+.||+-|-
T Consensus 32 ~~~gLt~eE~~aL~~~D 48 (81)
T cd07922 32 EEYGLTPAERAALREGT 48 (81)
T ss_pred HHcCCCHHHHHHHHccC
Confidence 35579999999998773
No 15
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=40.28 E-value=22 Score=23.30 Aligned_cols=20 Identities=20% Similarity=0.363 Sum_probs=17.4
Q ss_pred ccCCCCcccCCHHHHHHHHh
Q 034904 54 ASLQPKRTPVSNREIEAIMM 73 (79)
Q Consensus 54 ASlqPkRtpvS~~EIEAIll 73 (79)
--|.||-..||+||.+.+|-
T Consensus 9 H~lVPkH~iLs~eE~~~lL~ 28 (79)
T PRK09570 9 HELVPEHEILSEEEAKKLLK 28 (79)
T ss_pred ccccCCeEECCHHHHHHHHH
Confidence 35899999999999999873
No 16
>PF12065 DUF3545: Protein of unknown function (DUF3545); InterPro: IPR021932 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 60 to 77 amino acids in length. This protein has two completely conserved residues (R and L) that may be functionally important.
Probab=37.73 E-value=18 Score=23.00 Aligned_cols=13 Identities=62% Similarity=0.629 Sum_probs=9.4
Q ss_pred CCCcccCCHHHHHHHH
Q 034904 57 QPKRTPVSNREIEAIM 72 (79)
Q Consensus 57 qPkRtpvS~~EIEAIl 72 (79)
.-||+ =+|||||-
T Consensus 22 ~~KRK---WREIEAik 34 (59)
T PF12065_consen 22 PKKRK---WREIEAIK 34 (59)
T ss_pred ccchh---HHHHHHHH
Confidence 45665 48999984
No 17
>PF08920 SF3b1: Splicing factor 3B subunit 1; InterPro: IPR015016 This group of proteins consists of several eukaryotic splicing factor 3B subunit 1 proteins, which associate with p14 through a C terminus beta-strand that interacts with beta-3 of the p14 RNA recognition motif (RRM) beta-sheet, which is in turn connected to an alpha-helix by a loop that makes extensive contacts with both the shorter C-terminal helix and RRM of p14. This subunit is required for 'A' splicing complex assembly (formed by the stable binding of U2 snRNP to the branchpoint sequence in pre-mRNA) and 'E' splicing complex assembly []. ; PDB: 2FHO_A 3LQV_P 2PEH_D 2F9J_P 2F9D_Q.
Probab=37.69 E-value=12 Score=26.64 Aligned_cols=13 Identities=23% Similarity=0.710 Sum_probs=9.0
Q ss_pred ccCCHHHHHHHHh
Q 034904 61 TPVSNREIEAIMM 73 (79)
Q Consensus 61 tpvS~~EIEAIll 73 (79)
-||||||+.+||=
T Consensus 85 rpLTDEELD~mLP 97 (144)
T PF08920_consen 85 RPLTDEELDAMLP 97 (144)
T ss_dssp S-S-HHHHHHTS-
T ss_pred CcCCHHHHHHhCC
Confidence 4999999999973
No 18
>PF14584 DUF4446: Protein of unknown function (DUF4446)
Probab=35.53 E-value=24 Score=24.96 Aligned_cols=12 Identities=42% Similarity=0.537 Sum_probs=10.4
Q ss_pred ccCCHHHHHHHH
Q 034904 61 TPVSNREIEAIM 72 (79)
Q Consensus 61 tpvS~~EIEAIl 72 (79)
-+||+||.|||-
T Consensus 137 ~~LS~EE~eal~ 148 (151)
T PF14584_consen 137 YPLSEEEKEALE 148 (151)
T ss_pred ccCCHHHHHHHH
Confidence 489999999984
No 19
>PF08708 PriCT_1: Primase C terminal 1 (PriCT-1); InterPro: IPR014820 This alpha helical domain is found at the C-terminal of primases.
Probab=34.02 E-value=35 Score=20.02 Aligned_cols=13 Identities=31% Similarity=0.616 Sum_probs=11.4
Q ss_pred cccCCHHHHHHHH
Q 034904 60 RTPVSNREIEAIM 72 (79)
Q Consensus 60 RtpvS~~EIEAIl 72 (79)
..||+++|+++|.
T Consensus 50 ~~PL~~~Ev~~i~ 62 (71)
T PF08708_consen 50 SPPLPESEVKAIA 62 (71)
T ss_pred CCCCCHHHHHHHH
Confidence 5799999999985
No 20
>cd02135 Arsenite_oxidase Nitroreductase-like family which includes NADH oxidase and arsenite oxidiase. NADH oxidase catalyses the oxidation of NAD(P)H and accepts a wide broad range of compounds as electron acceptors, such as nitrocompound. Arsenite oxidase in a beta-proteobacterial strain is able to oxidize arsenite to arsenate.
Probab=33.91 E-value=35 Score=21.63 Aligned_cols=14 Identities=14% Similarity=0.247 Sum_probs=11.8
Q ss_pred cccCCHHHHHHHHh
Q 034904 60 RTPVSNREIEAIMM 73 (79)
Q Consensus 60 RtpvS~~EIEAIll 73 (79)
.+||++|+|+.|+-
T Consensus 15 ~~~v~~e~l~~il~ 28 (160)
T cd02135 15 LPAPDREQLEQILE 28 (160)
T ss_pred CCCCCHHHHHHHHH
Confidence 35999999999874
No 21
>CHL00183 petJ cytochrome c553; Provisional
Probab=33.18 E-value=45 Score=20.86 Aligned_cols=21 Identities=24% Similarity=0.417 Sum_probs=14.8
Q ss_pred ccccCCCCcccCCHHHHHHHH
Q 034904 52 GKASLQPKRTPVSNREIEAIM 72 (79)
Q Consensus 52 GkASlqPkRtpvS~~EIEAIl 72 (79)
|+..+.+...-||++||++|+
T Consensus 77 G~~~MP~f~~~Ls~~ei~~i~ 97 (108)
T CHL00183 77 GKNAMPAFGGRLSDEDIEDVA 97 (108)
T ss_pred CccccccccCCCCHHHHHHHH
Confidence 333455555579999999986
No 22
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=32.89 E-value=37 Score=24.46 Aligned_cols=21 Identities=43% Similarity=0.639 Sum_probs=16.5
Q ss_pred ccCccccCCCCcccCCHHHHHHHH
Q 034904 49 AVGGKASLQPKRTPVSNREIEAIM 72 (79)
Q Consensus 49 avgGkASlqPkRtpvS~~EIEAIl 72 (79)
-||+.+ .+=+|++++||+.||
T Consensus 88 fVg~~~---~~P~pi~~~ei~~~l 108 (178)
T COG0250 88 FVGSGG---AKPVPLSEEEIEHIL 108 (178)
T ss_pred EeccCC---CCCcccCHHHHHHHH
Confidence 456655 777999999999865
No 23
>PF09424 YqeY: Yqey-like protein; InterPro: IPR019004 Putative protein of unknown function; the authentic protein is detected in highly purified mitochondria in high-throughput studies; YOR215C is not an essential gene. ; PDB: 1NG6_A.
Probab=31.61 E-value=32 Score=23.88 Aligned_cols=16 Identities=50% Similarity=0.657 Sum_probs=9.0
Q ss_pred CCCCcccCCHHHHHHHHh
Q 034904 56 LQPKRTPVSNREIEAIMM 73 (79)
Q Consensus 56 lqPkRtpvS~~EIEAIll 73 (79)
..|+ .+|++||++|+-
T Consensus 86 yLP~--~lseeEi~~~v~ 101 (143)
T PF09424_consen 86 YLPK--QLSEEEIEAIVE 101 (143)
T ss_dssp GS-------HHHHHHHHH
T ss_pred hCcC--CCCHHHHHHHHH
Confidence 4564 899999999973
No 24
>PRK13697 cytochrome c6; Provisional
Probab=30.77 E-value=59 Score=20.07 Aligned_cols=18 Identities=17% Similarity=0.311 Sum_probs=13.0
Q ss_pred cCCCCcccCCHHHHHHHH
Q 034904 55 SLQPKRTPVSNREIEAIM 72 (79)
Q Consensus 55 SlqPkRtpvS~~EIEAIl 72 (79)
.+.+....+|++||++|.
T Consensus 82 ~Mp~~~~~ls~~di~~l~ 99 (111)
T PRK13697 82 AMPAFKDRLSPDQIEDVA 99 (111)
T ss_pred CCCCCcCCCCHHHHHHHH
Confidence 344444569999999985
No 25
>cd00179 SynN Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may be identified by a specific member of the syntaxin family; syntaxins contain a moderately well conserved amino-terminal domain, called Habc, whose structure is an antiparallel three-helix bundle; a linker of about 30 amino acids connects this to the carboxy-terminal region, designated H3 (t_SNARE), of the syntaxin cytoplasmic domain; the highly conserved H3 region forms a single, long alpha-helix when it is part of the core SNARE complex and anchors the protein on the cytoplasmic surface of cellular membranes; H3 is not included in defining this domain
Probab=29.78 E-value=41 Score=21.69 Aligned_cols=15 Identities=13% Similarity=0.242 Sum_probs=12.8
Q ss_pred ccCCHHHHHHHHhcc
Q 034904 61 TPVSNREIEAIMMGF 75 (79)
Q Consensus 61 tpvS~~EIEAIllGG 75 (79)
..+|+|||+++|-.|
T Consensus 128 ~~~tdeei~~~~~~~ 142 (151)
T cd00179 128 GEATDEELEDMLESG 142 (151)
T ss_pred CCCChHHHHHHHHcC
Confidence 358999999999877
No 26
>cd07923 Gallate_dioxygenase_C The C-terminal domain of Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate. Gallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of gallate, an intermediate in the degradation of the aromatic compound, syringate. The reaction product of gallate dioxygenase is 4-oxalomesaconate. The amino acid sequence of the N-terminal and C-terminal regions of gallate dioxygenase exhibits homology with the sequence of the PCA 4,5-dioxygenase B (catalytic) and A subunits, respectively. This model represents the C-terminal domain, which is similar to the A subunit of PCA 4,5-dioxygenase (or LigAB). The enzyme is estimated to be a homodimer according to the Escherichia coli enzyme. Since enzymes in this subfamily have fused A and B subunits, the dimer interface may resemble the tetramer interface of classical LigAB enzymes. This enzyme belongs to the class III extradiol dioxygenase family, composed of enzymes whi
Probab=29.61 E-value=40 Score=22.86 Aligned_cols=15 Identities=13% Similarity=0.069 Sum_probs=11.8
Q ss_pred cccCCHHHHHHHHhc
Q 034904 60 RTPVSNREIEAIMMG 74 (79)
Q Consensus 60 RtpvS~~EIEAIllG 74 (79)
+-+||+||++||+-+
T Consensus 34 e~gLt~Ee~~av~~r 48 (94)
T cd07923 34 EAGLTEEERTLIRNR 48 (94)
T ss_pred HcCCCHHHHHHHHcc
Confidence 347999999998743
No 27
>COG5227 SMT3 Ubiquitin-like protein (sentrin) [Posttranslational modification, protein turnover, chaperones]
Probab=28.18 E-value=32 Score=24.15 Aligned_cols=22 Identities=36% Similarity=0.513 Sum_probs=17.0
Q ss_pred CCCCcccC-----CHHHHHHHH--hcccc
Q 034904 56 LQPKRTPV-----SNREIEAIM--MGFTE 77 (79)
Q Consensus 56 lqPkRtpv-----S~~EIEAIl--lGG~~ 77 (79)
+++..||= .++||||+. +|||.
T Consensus 74 I~~dqTP~dldmEdnd~iEav~eQvGG~t 102 (103)
T COG5227 74 IDLDQTPGDLDMEDNDEIEAVTEQVGGAT 102 (103)
T ss_pred cCCCCChhhcCCccchHHHHHHHHhcCcc
Confidence 57777874 589999984 89984
No 28
>PF11829 DUF3349: Protein of unknown function (DUF3349); InterPro: IPR021784 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 99 to 124 amino acids in length. ; PDB: 2KVC_A 3OL3_B 3OL4_A 2LKY_A.
Probab=28.02 E-value=45 Score=22.56 Aligned_cols=10 Identities=10% Similarity=0.478 Sum_probs=8.1
Q ss_pred CCHHHHHHHH
Q 034904 63 VSNREIEAIM 72 (79)
Q Consensus 63 vS~~EIEAIl 72 (79)
||++||.+|.
T Consensus 36 Ltd~ev~~Va 45 (96)
T PF11829_consen 36 LTDDEVAEVA 45 (96)
T ss_dssp S-HHHHHHHH
T ss_pred CCHHHHHHHH
Confidence 9999999886
No 29
>KOG2737 consensus Putative metallopeptidase [General function prediction only]
Probab=27.86 E-value=41 Score=28.87 Aligned_cols=15 Identities=47% Similarity=0.507 Sum_probs=12.5
Q ss_pred cCCHHHHHHHHhccc
Q 034904 62 PVSNREIEAIMMGFT 76 (79)
Q Consensus 62 pvS~~EIEAIllGG~ 76 (79)
|=+-|||||+|.||-
T Consensus 468 prtveeIEa~ma~g~ 482 (492)
T KOG2737|consen 468 PRTVEEIEACMAGGD 482 (492)
T ss_pred CCCHHHHHHHHhcCC
Confidence 456799999999985
No 30
>cd03370 NADH_oxidase NADPH_oxidase. Nitroreductase family containing NADH oxidase and other, uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=27.36 E-value=53 Score=21.43 Aligned_cols=14 Identities=7% Similarity=0.356 Sum_probs=11.8
Q ss_pred cccCCHHHHHHHHh
Q 034904 60 RTPVSNREIEAIMM 73 (79)
Q Consensus 60 RtpvS~~EIEAIll 73 (79)
.++|++|+|+.|+-
T Consensus 16 ~~~i~~e~l~~il~ 29 (156)
T cd03370 16 TDPIPEDLLRRLLE 29 (156)
T ss_pred CCCCCHHHHHHHHH
Confidence 45899999999875
No 31
>PF05373 Pro_3_hydrox_C: L-proline 3-hydroxylase, C-terminal; InterPro: IPR008035 Iron (II)/2-oxoglutarate (2-OG)-dependent oxygenases catalyse oxidative reactions in a range of metabolic processes. Proline 3-hydroxylase hydroxylates proline at position 3, the first of a 2-OG oxygenase catalysing oxidation of a free alpha-amino acid. The structure contains conserved motifs present in other 2-OG oxygenases including a jelly roll strand core and residues binding iron and 2-oxoglutarate, consistent with divergent evolution within the extended family. The structure differs significantly from many other 2-OG oxygenases in possessing a discrete C-terminal helical domain.; GO: 0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors, 0055114 oxidation-reduction process; PDB: 1E5S_A 1E5R_B.
Probab=26.50 E-value=43 Score=23.11 Aligned_cols=19 Identities=21% Similarity=0.256 Sum_probs=11.3
Q ss_pred CCCcccCCHHHHHHHHhcc
Q 034904 57 QPKRTPVSNREIEAIMMGF 75 (79)
Q Consensus 57 qPkRtpvS~~EIEAIllGG 75 (79)
...|.|++++|.|.|+-.|
T Consensus 19 i~~R~~~t~e~~e~Ll~ls 37 (101)
T PF05373_consen 19 IISRPPLTEEERERLLALS 37 (101)
T ss_dssp ----EE--HHHHHHHHGGG
T ss_pred ccCCCCCCHHHHHHHHHHH
Confidence 4679999999999998654
No 32
>smart00738 NGN In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. In Spt5p, this domain may confer affinity for Spt4p.Spt4p
Probab=26.06 E-value=46 Score=20.16 Aligned_cols=15 Identities=53% Similarity=0.762 Sum_probs=12.2
Q ss_pred CcccCCHHHHHHHHh
Q 034904 59 KRTPVSNREIEAIMM 73 (79)
Q Consensus 59 kRtpvS~~EIEAIll 73 (79)
+-.+|+++|||.++-
T Consensus 91 ~p~~v~~~e~~~l~~ 105 (106)
T smart00738 91 KPTPVPDDEIEKILK 105 (106)
T ss_pred eeeECCHHHHHHHhh
Confidence 346899999999874
No 33
>PF05952 ComX: Bacillus competence pheromone ComX; InterPro: IPR009233 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Natural genetic competence in Bacillus subtilis is controlled by quorum-sensing (QS). The ComP- ComA two-component system detects the signalling molecule ComX, and this signal is transduced by a conserved phosphotransfer mechanism. ComX is synthesised as an inactive precursor and is then cleaved and modified by ComQ before export to the extracellular environment [].
Probab=25.62 E-value=49 Score=20.70 Aligned_cols=21 Identities=43% Similarity=0.521 Sum_probs=16.7
Q ss_pred CccccCCCCcccCCHHHHHHHHhcc
Q 034904 51 GGKASLQPKRTPVSNREIEAIMMGF 75 (79)
Q Consensus 51 gGkASlqPkRtpvS~~EIEAIllGG 75 (79)
-|.|||. -|+++|.+||+-|-
T Consensus 21 ~g~asLI----Gv~~~e~~aIi~~F 41 (57)
T PF05952_consen 21 EGEASLI----GVDKDEQKAIIDAF 41 (57)
T ss_pred cCCeeEe----cCCHHHHHHHHHHH
Confidence 4778875 58999999999763
No 34
>cd02136 Nitroreductase Nitroreductase family. Members of this family utilize FMN as a cofactor and catalyze reduction of a variety of nitroaromatic compounds, including nitrofurans, nitrobenzens, nitrophenol, nitrobenzoate and quinones by using either NADH or NADPH as a source of reducing equivalents in an obligatory two-election transfer mechanism. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=25.17 E-value=61 Score=21.13 Aligned_cols=12 Identities=42% Similarity=0.733 Sum_probs=10.7
Q ss_pred ccCCHHHHHHHH
Q 034904 61 TPVSNREIEAIM 72 (79)
Q Consensus 61 tpvS~~EIEAIl 72 (79)
++|++++|+.|+
T Consensus 17 ~~v~~e~l~~il 28 (178)
T cd02136 17 DPVPRETIEEIL 28 (178)
T ss_pred CCCCHHHHHHHH
Confidence 489999999987
No 35
>PF05391 Lsm_interact: Lsm interaction motif; InterPro: IPR008669 This short motif is found at the C terminus of Prp24 proteins and probably interacts with the Lsm proteins to promote U4/U6 formation [].
Probab=25.08 E-value=90 Score=16.44 Aligned_cols=17 Identities=18% Similarity=0.409 Sum_probs=13.4
Q ss_pred CCcccCCHHHHHHHHhc
Q 034904 58 PKRTPVSNREIEAIMMG 74 (79)
Q Consensus 58 PkRtpvS~~EIEAIllG 74 (79)
+..+|.||++....+|+
T Consensus 5 ~~~~p~SNddFrkmfl~ 21 (21)
T PF05391_consen 5 TTAKPKSNDDFRKMFLK 21 (21)
T ss_pred cccCccchHHHHHHHcC
Confidence 45679999999888774
No 36
>PF07746 LigA: Aromatic-ring-opening dioxygenase LigAB, LigA subunit; InterPro: IPR011986 Dioxygenases catalyse the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds. The substrates of ring-cleavage dioxygenases can be classified into two groups according to the mode of scission of the aromatic ring. Intradiol enzymes (IPR000627 from INTERPRO) use a non-haem Fe(III) to cleave the aromatic ring between two hydroxyl groups (ortho-cleavage), whereas extradiol enzymes use a non-haem Fe(II) to cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage) [, ]. These two subfamilies differ in sequence, structural fold, iron ligands, and the orientation of second sphere active site amino acid residues. Extradiol dioxygenases are usually homo-multimeric, bind one atom of ferrous ion per subunit and have a subunit size of about 33 kDa. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes (IPR000486 from INTERPRO) show sequence similarity, with the two-domain class II enzymes having evolved from a class I enzyme through gene duplication. Class III enzymes are different in sequence and structure, but they do share several common active-site characteristics with the class II enzymes, in particular the coordination sphere and the disposition of the putative catalytic base are very similar. Class III enzymes usually have two subunits, designated A (IPR004183 from INTERPRO) and B (IPR004183 from INTERPRO). LigAB is a protocatechuate 4,5-dioxygenase (1.13.11.8 from EC) that belongs to the extradiol class III enzyme family. The LigA subunit of this enzyme is multi-helical, containing a compact array of 6 short helices [].; PDB: 1BOU_A 1B4U_A.
Probab=24.64 E-value=54 Score=21.48 Aligned_cols=15 Identities=13% Similarity=0.195 Sum_probs=10.3
Q ss_pred cccCCHHHHHHHHhc
Q 034904 60 RTPVSNREIEAIMMG 74 (79)
Q Consensus 60 RtpvS~~EIEAIllG 74 (79)
+-.||+||.+||+-|
T Consensus 27 ~~~Lt~eer~av~~r 41 (88)
T PF07746_consen 27 EYGLTEEERQAVLDR 41 (88)
T ss_dssp CCT--HHHHHHHHCT
T ss_pred HcCCCHHHHHHHHcC
Confidence 457999999998754
No 37
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=24.58 E-value=52 Score=23.38 Aligned_cols=16 Identities=31% Similarity=0.675 Sum_probs=10.0
Q ss_pred CCcccCCHHHHHHHHh
Q 034904 58 PKRTPVSNREIEAIMM 73 (79)
Q Consensus 58 PkRtpvS~~EIEAIll 73 (79)
.+..|+||++|..+|-
T Consensus 117 d~~~PlSD~~i~~~L~ 132 (160)
T PF04552_consen 117 DKKKPLSDQEIAELLK 132 (160)
T ss_dssp -TTS---HHHHHHHHT
T ss_pred CCCCCCCHHHHHHHHH
Confidence 4578999999999884
No 38
>KOG0574 consensus STE20-like serine/threonine kinase MST [Signal transduction mechanisms]
Probab=24.36 E-value=48 Score=28.29 Aligned_cols=18 Identities=33% Similarity=0.750 Sum_probs=15.0
Q ss_pred CCCCcccCCHHHHHHHHh
Q 034904 56 LQPKRTPVSNREIEAIMM 73 (79)
Q Consensus 56 lqPkRtpvS~~EIEAIll 73 (79)
+.-.|+||||.||-+||-
T Consensus 119 ~R~R~K~L~E~EIs~iL~ 136 (502)
T KOG0574|consen 119 MRARRKPLSEQEISAVLR 136 (502)
T ss_pred HHHhcCCccHHHHHHHHH
Confidence 355789999999999984
No 39
>cd01190 INT_SG5 INT_SG5, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 5, N- and C-terminal domains. The CD contains mainly predicted bacterial integrase/recombinases.
Probab=23.94 E-value=69 Score=21.22 Aligned_cols=16 Identities=25% Similarity=0.472 Sum_probs=13.2
Q ss_pred CCcccCCHHHHHHHHh
Q 034904 58 PKRTPVSNREIEAIMM 73 (79)
Q Consensus 58 PkRtpvS~~EIEAIll 73 (79)
++++.++++|+++|+-
T Consensus 70 ~~~~~lt~~e~~~l~~ 85 (260)
T cd01190 70 PLVTYLTREEVQALLA 85 (260)
T ss_pred CCCCCCCHHHHHHHHh
Confidence 5667899999999873
No 40
>PF09860 DUF2087: Uncharacterized protein conserved in bacteria (DUF2087); InterPro: IPR018656 This domain, found in various hypothetical prokaryotic proteins and transcriptional activators, has no known function.
Probab=23.76 E-value=61 Score=20.37 Aligned_cols=18 Identities=17% Similarity=0.211 Sum_probs=14.4
Q ss_pred CCCcccCCHHHHHHHHhc
Q 034904 57 QPKRTPVSNREIEAIMMG 74 (79)
Q Consensus 57 qPkRtpvS~~EIEAIllG 74 (79)
.+.....||.||.+||..
T Consensus 24 f~~g~~y~E~EVN~~L~~ 41 (71)
T PF09860_consen 24 FEPGREYSEKEVNEILKR 41 (71)
T ss_pred CCCCCccCHHHHHHHHHH
Confidence 456678999999999864
No 41
>cd00799 INT_Cre Cre recombinase, C-terminal catalytic domain. Cre-like recombinases belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The bacteriophage P1 Cre recombinase maintains the circular phage replicon in a monomeric state by catalyzing a site-specific recombination between two loxP sites. The catalytic core domain of Cre recombinase is linked to a more divergent helical N-terminal domain, which interacts primarily with the DNA major groove proximal to the crossover region.
Probab=23.65 E-value=67 Score=21.95 Aligned_cols=14 Identities=0% Similarity=0.223 Sum_probs=12.1
Q ss_pred CcccCCHHHHHHHH
Q 034904 59 KRTPVSNREIEAIM 72 (79)
Q Consensus 59 kRtpvS~~EIEAIl 72 (79)
++.++|++||++|+
T Consensus 91 ~~~~lt~eei~~l~ 104 (287)
T cd00799 91 QALAILPEDLDKLR 104 (287)
T ss_pred CCCCCCHHHHHHHH
Confidence 45699999999997
No 42
>PF07128 DUF1380: Protein of unknown function (DUF1380); InterPro: IPR009811 This family consists of several hypothetical bacterial proteins of around 140 residues in length. Members of this family seem to be specific to Enterobacteria. The function of this family is unknown.
Probab=22.89 E-value=57 Score=23.59 Aligned_cols=11 Identities=18% Similarity=0.480 Sum_probs=10.0
Q ss_pred cCCHHHHHHHH
Q 034904 62 PVSNREIEAIM 72 (79)
Q Consensus 62 pvS~~EIEAIl 72 (79)
-||++||++||
T Consensus 42 ~lTd~E~~aVL 52 (139)
T PF07128_consen 42 NLTDDEARAVL 52 (139)
T ss_pred CCCHHHHHHHH
Confidence 58999999998
No 43
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=22.23 E-value=47 Score=22.53 Aligned_cols=14 Identities=14% Similarity=0.280 Sum_probs=9.0
Q ss_pred cccCCHHHHHHHHh
Q 034904 60 RTPVSNREIEAIMM 73 (79)
Q Consensus 60 RtpvS~~EIEAIll 73 (79)
.+-||++||+..|-
T Consensus 32 sKGLt~~EI~~al~ 45 (136)
T PF04695_consen 32 SKGLTEEEIDEALG 45 (136)
T ss_dssp HCT--HHHHHHHHH
T ss_pred cCCCCHHHHHHHHH
Confidence 34799999998763
No 44
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=21.80 E-value=56 Score=24.87 Aligned_cols=23 Identities=26% Similarity=0.439 Sum_probs=16.7
Q ss_pred ccccCCCCcc----cCCHHHHHHHHhc
Q 034904 52 GKASLQPKRT----PVSNREIEAIMMG 74 (79)
Q Consensus 52 GkASlqPkRt----pvS~~EIEAIllG 74 (79)
|---++|... -+|++|++||++|
T Consensus 61 ~gy~~~~~~~L~pl~ft~~E~~Al~~~ 87 (311)
T COG2378 61 GGYRLRPGFKLPPLMFTEEEAEALLLA 87 (311)
T ss_pred ccEEEccCCCCCcccCCHHHHHHHHHH
Confidence 4445555543 4899999999987
No 45
>PF03147 FDX-ACB: Ferredoxin-fold anticodon binding domain; InterPro: IPR005121 Aminoacyl-tRNA synthetases (aaRSs) play a crucial role in the translation of the genetic code by means of covalent attachment of amino acids to their cognate tRNAs. Phenylalanine-tRNA synthetase (PheRS) is known to be among the most complex enzymes of the aaRS family. Bacterial and mitochondrial PheRSs share a ferredoxin-fold anticodon binding (FDX-ACB) domain, which represents a canonical double split alpha+beta motif having no insertions. The FDX-ACB domain displays a typical RNA recognition fold (RRM) (see PDOC00030 from PROSITEDOC) formed by the four-stranded antiparallel beta sheet, with two helices packed against it [, , , , ].; GO: 0000049 tRNA binding, 0000287 magnesium ion binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation, 0008033 tRNA processing; PDB: 1JJC_B 1EIY_B 1PYS_B 3HFZ_B 3TEH_B 3PCO_D 2RHS_D 2RHQ_B 2AKW_B 1B70_B ....
Probab=21.26 E-value=67 Score=19.94 Aligned_cols=20 Identities=15% Similarity=0.356 Sum_probs=11.7
Q ss_pred cccCCCCcccCCHHHHHHHH
Q 034904 53 KASLQPKRTPVSNREIEAIM 72 (79)
Q Consensus 53 kASlqPkRtpvS~~EIEAIl 72 (79)
...+|..-..|+++||++++
T Consensus 59 rl~~~~~~~TLt~~ev~~~~ 78 (94)
T PF03147_consen 59 RLTYQSPDRTLTDEEVNEIH 78 (94)
T ss_dssp EEEE--SSS---HHHHHHHH
T ss_pred EEEEECCCCCCCHHHHHHHH
Confidence 34568877889999999986
No 46
>cd02062 Nitro_FMN_reductase Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are described as NAD(P)H:FMN oxidoreductases, oxygen-insensitive nitroreductase, flavin reductase P, dihydropteridine reductase, NADH oxidase or NADH dehydrogenase.
Probab=21.09 E-value=88 Score=18.72 Aligned_cols=12 Identities=33% Similarity=0.653 Sum_probs=10.6
Q ss_pred ccCCHHHHHHHH
Q 034904 61 TPVSNREIEAIM 72 (79)
Q Consensus 61 tpvS~~EIEAIl 72 (79)
+||++++|+.|+
T Consensus 13 ~~i~~~~l~~l~ 24 (122)
T cd02062 13 EPVPEEVLEKIL 24 (122)
T ss_pred CCCCHHHHHHHH
Confidence 499999999987
No 47
>TIGR03553 F420_FbiB_CTERM F420 biosynthesis protein FbiB, C-terminal domain. Coenzyme F420 differs between the Archaea and the Actinobacteria, where the numbers of glutamate residues attached are 2 (Archaea) or 5-6 (Mycobacterium). The enzyme in the Archaea is homologous to the N-terminal domain of FbiB from Mycobacterium bovis, and is responsible for glutamate ligation. Therefore it seems likely that the C-terminal domain of FbiB, modeled by this alignment, is involved in additional glutamate ligation.
Probab=20.83 E-value=83 Score=21.03 Aligned_cols=14 Identities=21% Similarity=0.401 Sum_probs=11.8
Q ss_pred ccCCHHHHHHHHhc
Q 034904 61 TPVSNREIEAIMMG 74 (79)
Q Consensus 61 tpvS~~EIEAIllG 74 (79)
+||++|+|+.|+--
T Consensus 15 ~~V~~e~l~~il~a 28 (194)
T TIGR03553 15 DPVDPDAVRAAVAA 28 (194)
T ss_pred CCCCHHHHHHHHHH
Confidence 48999999999853
No 48
>PF04369 Lactococcin: Lactococcin-like family; InterPro: IPR007464 Bacteriocins are produced by bacteria to inhibit the growth of similar or closely related bacterial strains. The class II bacteriocins are small heat-stable proteins for which disulphide bonds are the only modification to the peptide. Lactococcin A and B are class-IId bacteriocins (one-peptide non-pediocin-like bacteriocin) [, ].; GO: 0042742 defense response to bacterium, 0005576 extracellular region
Probab=20.80 E-value=53 Score=21.00 Aligned_cols=15 Identities=27% Similarity=0.233 Sum_probs=12.1
Q ss_pred ccCCHHHHHHHHhcc
Q 034904 61 TPVSNREIEAIMMGF 75 (79)
Q Consensus 61 tpvS~~EIEAIllGG 75 (79)
+-||+||++-|--||
T Consensus 8 ~~~sdeeL~~i~GG~ 22 (60)
T PF04369_consen 8 NILSDEELSKINGGG 22 (60)
T ss_pred eecCHHHHhhccCCc
Confidence 468999999987664
Done!