Query psy10647
Match_columns 92
No_of_seqs 21 out of 23
Neff 1.8
Searched_HMMs 46136
Date Fri Aug 16 23:52:27 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10647.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10647hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00339 Arrestin_N: Arrestin 98.1 4.8E-06 1.1E-10 52.9 3.5 35 8-42 1-35 (149)
2 KOG3780|consensus 97.9 1.8E-05 4E-10 59.6 4.2 40 4-43 3-42 (427)
3 PF00339 Arrestin_N: Arrestin 97.0 0.0008 1.7E-08 42.7 3.2 34 56-89 1-34 (149)
4 KOG3780|consensus 96.6 0.0021 4.5E-08 48.6 3.1 38 52-89 3-40 (427)
5 PF01868 UPF0086: Domain of un 86.1 1.3 2.9E-05 29.1 3.6 52 25-76 30-81 (89)
6 PRK11556 multidrug efflux syst 75.8 3.5 7.5E-05 32.6 3.3 32 5-36 289-320 (415)
7 smart00538 POP4 A domain found 73.6 5.9 0.00013 26.4 3.6 52 25-76 29-80 (92)
8 cd08975 BaFpgNei_N_3 Uncharact 59.6 45 0.00097 22.5 5.7 22 50-71 89-111 (117)
9 PRK09783 copper/silver efflux 53.4 14 0.00031 29.2 2.9 28 5-32 295-322 (409)
10 cd08976 BaFpgNei_N_4 Uncharact 51.5 66 0.0014 21.0 6.2 21 48-68 86-106 (117)
11 KOG3052|consensus 49.5 6.9 0.00015 32.4 0.6 22 67-88 221-247 (311)
12 PRK15030 multidrug efflux syst 47.4 27 0.00059 27.1 3.5 30 6-35 274-303 (397)
13 PF12532 DUF3732: Protein of u 45.9 9.2 0.0002 28.1 0.7 13 10-22 104-116 (193)
14 PF12790 T6SS-SciN: Type VI se 45.1 70 0.0015 21.7 4.9 47 13-61 79-125 (142)
15 PF01835 A2M_N: MG2 domain; I 42.4 64 0.0014 19.8 4.0 27 8-36 2-28 (99)
16 PF03643 Vps26: Vacuolar prote 42.2 27 0.00059 27.3 2.8 20 16-35 32-51 (275)
17 PRK09859 multidrug efflux syst 42.1 42 0.00091 25.8 3.8 32 5-36 269-300 (385)
18 PRK09783 copper/silver efflux 38.8 49 0.0011 26.2 3.8 27 53-79 295-321 (409)
19 PRK09578 periplasmic multidrug 38.4 40 0.00086 25.9 3.1 31 6-36 273-303 (385)
20 PF02996 Prefoldin: Prefoldin 34.1 37 0.0008 21.6 2.1 31 56-86 39-70 (120)
21 PRK11556 multidrug efflux syst 33.5 43 0.00094 26.5 2.7 32 53-84 289-320 (415)
22 COG1588 POP4 RNase P/RNase MRP 32.1 60 0.0013 22.8 3.0 51 24-75 32-82 (95)
23 cd08972 PF_Nei_N N-terminal do 32.1 1.7E+02 0.0038 20.2 6.5 19 50-68 107-125 (137)
24 TIGR00999 8a0102 Membrane Fusi 32.0 63 0.0014 22.6 3.1 31 6-36 173-203 (265)
25 TIGR01730 RND_mfp RND family e 31.7 66 0.0014 22.8 3.2 32 5-36 220-251 (322)
26 cd01723 LSm4 The eukaryotic Sm 30.0 36 0.00077 21.4 1.4 18 74-91 11-28 (76)
27 cd08974 BaFpgNei_N_2 Uncharact 29.6 1.7E+02 0.0036 19.2 6.0 19 50-68 76-94 (98)
28 KOG3063|consensus 27.1 96 0.0021 25.8 3.8 23 17-39 40-62 (301)
29 PF01149 Fapy_DNA_glyco: Forma 26.2 1.9E+02 0.0041 18.7 5.7 48 7-69 59-107 (116)
30 PRK03879 ribonuclease P protei 25.7 1E+02 0.0022 20.9 3.1 35 25-60 31-65 (96)
31 PF01774 UreD: UreD urease acc 24.9 88 0.0019 22.6 2.9 55 28-86 28-90 (209)
32 cd06182 CYPOR_like NADPH cytoc 24.6 55 0.0012 24.2 1.8 22 4-25 16-38 (267)
33 cd08773 FpgNei_N N-terminal do 24.6 2E+02 0.0044 18.5 6.1 19 50-68 88-106 (117)
34 PRK11578 macrolide transporter 23.8 1E+02 0.0023 23.4 3.2 29 8-36 277-305 (370)
35 cd06208 CYPOR_like_FNR These f 23.5 58 0.0013 24.0 1.7 19 8-26 29-48 (286)
36 PF11611 DUF4352: Domain of un 22.5 98 0.0021 19.1 2.4 28 17-44 85-112 (123)
37 PF04019 DUF359: Protein of un 21.8 57 0.0012 22.9 1.4 23 14-38 86-108 (121)
38 PF12700 HlyD_2: HlyD family s 21.4 1.2E+02 0.0027 21.5 3.0 29 5-33 243-271 (328)
39 cd08966 EcFpg-like_N N-termina 21.2 2.4E+02 0.0053 18.2 6.2 24 49-72 88-113 (120)
40 PRK04163 exosome complex RNA-b 21.1 2.6E+02 0.0057 20.9 4.8 17 9-26 2-18 (235)
41 cd01721 Sm_D3 The eukaryotic S 21.0 57 0.0012 20.2 1.1 17 75-91 11-27 (70)
42 cd06221 sulfite_reductase_like 20.7 78 0.0017 22.8 1.9 25 4-28 10-37 (253)
43 PF13759 2OG-FeII_Oxy_5: Putat 20.0 2.4E+02 0.0052 17.7 4.0 56 20-75 18-85 (101)
No 1
>PF00339 Arrestin_N: Arrestin (or S-antigen), N-terminal domain; InterPro: IPR011021 G protein-coupled receptors are a large family of signalling molecules that respond to a wide variety of extracellular stimuli. The receptors relay the information encoded by the ligand through the activation of heterotrimeric G proteins and intracellular effector molecules. To ensure the appropriate regulation of the signalling cascade, it is vital to properly inactivate the receptor. This inactivation is achieved, in part, by the binding of a soluble protein, arrestin, which uncouples the receptor from the downstream G protein after the receptors are phosphorylated by G protein-coupled receptor kinases. In addition to the inactivation of G protein-coupled receptors, arrestins have also been implicated in the endocytosis of receptors and cross talk with other signalling pathways. Arrestin (retinal S-antigen) is a major protein of the retinal rod outer segments. It interacts with photo-activated phosphorylated rhodopsin, inhibiting or 'arresting' its ability to interact with transducin []. The protein binds calcium, and shows similarity in its C terminus to alpha-transducin and other purine nucleotide-binding proteins. In mammals, arrestin is associated with autoimmune uveitis. Arrestins comprise a family of closely-related proteins that includes beta-arrestin-1 and -2, which regulate the function of beta-adrenergic receptors by binding to their phosphorylated forms, impairing their capacity to activate G(S) proteins; Cone photoreceptors C-arrestin (arrestin-X) [], which could bind to phosphorylated red/green opsins; and Drosophila phosrestins I and II, which undergo light-induced phosphorylation, and probably play a role in photoreceptor transduction [, , ]. The crystal structure of bovine retinal arrestin comprises two domains of antiparallel beta-sheets connected through a hinge region and one short alpha-helix on the back of the amino-terminal fold []. The binding region for phosphorylated light-activated rhodopsin is located at the N-terminal domain, as indicated by the docking of the photoreceptor to the three-dimensional structure of arrestin. The N-terminal domain consists of an immunoglobulin-like beta-sandwich structure. This entry represents proteins with immunoglobulin-like domains that are similar to those found in arrestin.; PDB: 1SUJ_A 3UGX_A 1CF1_B 1AYR_A 3UGU_A 3P2D_B 1ZSH_A 2WTR_B 3GC3_A 1G4R_A ....
Probab=98.06 E-value=4.8e-06 Score=52.89 Aligned_cols=35 Identities=40% Similarity=0.719 Sum_probs=28.1
Q ss_pred EEEEeeCCceeEecCcccceeEEEEecCCcceeee
Q psy10647 8 FVILFDNTNLVYFPGQYLSGRVLIELKDDTPALGF 42 (92)
Q Consensus 8 f~IiFDn~~llYFPGQ~lSGRVLle~qe~t~~lgl 42 (92)
|.|.||++.-.|+||+.++|+|.|++.+++.+-++
T Consensus 1 ~~I~ld~~~~~y~~Ge~I~G~V~l~~~~~~~i~~i 35 (149)
T PF00339_consen 1 FEIELDNPKPVYFPGEVISGKVVLELSKPIKIKSI 35 (149)
T ss_dssp EEEEES-SEEEEESS--EEEEEEECTTT-TTTSEE
T ss_pred CEEEECCCCCEECCCCEEEEEEEEEECCccceeEE
Confidence 68999999999999999999999999998876554
No 2
>KOG3780|consensus
Probab=97.87 E-value=1.8e-05 Score=59.62 Aligned_cols=40 Identities=30% Similarity=0.620 Sum_probs=36.0
Q ss_pred cceEEEEEeeCCceeEecCcccceeEEEEecCCcceeeee
Q psy10647 4 KLIKFVILFDNTNLVYFPGQYLSGRVLIELKDDTPALGFH 43 (92)
Q Consensus 4 kl~kf~IiFDn~~llYFPGQ~lSGRVLle~qe~t~~lglh 43 (92)
+...|.|.||++..+|+|||.+||+|++++.+...+-++.
T Consensus 3 ~~~~~~i~~d~~~~iy~~G~~vsG~v~l~~~~~~~~~~i~ 42 (427)
T KOG3780|consen 3 TMSSFEIVLDNPEAIYFPGEPVSGSVVLSTKEPIKVRAIK 42 (427)
T ss_pred CcceEEEEeCCCccccCCCCeEEEEEEEEeCCccceeEEE
Confidence 4568999999999999999999999999999999887654
No 3
>PF00339 Arrestin_N: Arrestin (or S-antigen), N-terminal domain; InterPro: IPR011021 G protein-coupled receptors are a large family of signalling molecules that respond to a wide variety of extracellular stimuli. The receptors relay the information encoded by the ligand through the activation of heterotrimeric G proteins and intracellular effector molecules. To ensure the appropriate regulation of the signalling cascade, it is vital to properly inactivate the receptor. This inactivation is achieved, in part, by the binding of a soluble protein, arrestin, which uncouples the receptor from the downstream G protein after the receptors are phosphorylated by G protein-coupled receptor kinases. In addition to the inactivation of G protein-coupled receptors, arrestins have also been implicated in the endocytosis of receptors and cross talk with other signalling pathways. Arrestin (retinal S-antigen) is a major protein of the retinal rod outer segments. It interacts with photo-activated phosphorylated rhodopsin, inhibiting or 'arresting' its ability to interact with transducin []. The protein binds calcium, and shows similarity in its C terminus to alpha-transducin and other purine nucleotide-binding proteins. In mammals, arrestin is associated with autoimmune uveitis. Arrestins comprise a family of closely-related proteins that includes beta-arrestin-1 and -2, which regulate the function of beta-adrenergic receptors by binding to their phosphorylated forms, impairing their capacity to activate G(S) proteins; Cone photoreceptors C-arrestin (arrestin-X) [], which could bind to phosphorylated red/green opsins; and Drosophila phosrestins I and II, which undergo light-induced phosphorylation, and probably play a role in photoreceptor transduction [, , ]. The crystal structure of bovine retinal arrestin comprises two domains of antiparallel beta-sheets connected through a hinge region and one short alpha-helix on the back of the amino-terminal fold []. The binding region for phosphorylated light-activated rhodopsin is located at the N-terminal domain, as indicated by the docking of the photoreceptor to the three-dimensional structure of arrestin. The N-terminal domain consists of an immunoglobulin-like beta-sandwich structure. This entry represents proteins with immunoglobulin-like domains that are similar to those found in arrestin.; PDB: 1SUJ_A 3UGX_A 1CF1_B 1AYR_A 3UGU_A 3P2D_B 1ZSH_A 2WTR_B 3GC3_A 1G4R_A ....
Probab=97.01 E-value=0.0008 Score=42.70 Aligned_cols=34 Identities=41% Similarity=0.737 Sum_probs=26.6
Q ss_pred EEEEEeCCeeeEecCcccceeEEEEecCCccccc
Q psy10647 56 FVILFDNTNLVYFPGQYLSGRVLIELKDDTPALA 89 (92)
Q Consensus 56 f~ilfdnt~llyfpgq~lsgrvl~el~~~t~~lg 89 (92)
|-|.||+..-.|+||+.++|+|.+++.++..+-+
T Consensus 1 ~~I~ld~~~~~y~~Ge~I~G~V~l~~~~~~~i~~ 34 (149)
T PF00339_consen 1 FEIELDNPKPVYFPGEVISGKVVLELSKPIKIKS 34 (149)
T ss_dssp EEEEES-SEEEEESS--EEEEEEECTTT-TTTSE
T ss_pred CEEEECCCCCEECCCCEEEEEEEEEECCccceeE
Confidence 6799999999999999999999999988876644
No 4
>KOG3780|consensus
Probab=96.58 E-value=0.0021 Score=48.62 Aligned_cols=38 Identities=34% Similarity=0.656 Sum_probs=32.6
Q ss_pred hheeEEEEEeCCeeeEecCcccceeEEEEecCCccccc
Q psy10647 52 KLIKFVILFDNTNLVYFPGQYLSGRVLIELKDDTPALA 89 (92)
Q Consensus 52 kl~kf~ilfdnt~llyfpgq~lsgrvl~el~~~t~~lg 89 (92)
+...|-|+||+.+-+|+|||.+||+|++++.+...+-+
T Consensus 3 ~~~~~~i~~d~~~~iy~~G~~vsG~v~l~~~~~~~~~~ 40 (427)
T KOG3780|consen 3 TMSSFEIVLDNPEAIYFPGEPVSGSVVLSTKEPIKVRA 40 (427)
T ss_pred CcceEEEEeCCCccccCCCCeEEEEEEEEeCCccceeE
Confidence 34678999999999999999999999999887766543
No 5
>PF01868 UPF0086: Domain of unknown function UPF0086; InterPro: IPR002730 The p29 subunit (also known as Rpp29 or Pop4) of the related ribonucleoproteins ribonuclease (RNase) P and RNase MRP can be found in both eukaryotes and arachea []. The structure of the RNase P subunit, Rpp29, from Methanobacterium thermoautotrophicum has been determined. Mth Rpp29 is a member of the oligonucleotide/oligosaccharide binding fold family. It contains a structured beta-barrel core and unstructured N- and C-terminal extensions bearing several highly conserved amino acid residues that could be involved in RNA contacts in the protein-RNA complex []. Rpp29 (3.1.26.5 from EC) catalyses the endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor. It interacts with the Rpp25 and Pop5 subunits. RNase P is a ubiquitous ribonucleoprotein enzyme primarily responsible for cleaving the 5' leader sequence during maturation of tRNAs in all three domains of life. In eubacteria, this enzyme is made up of two subunits: a large RNA (approximately 120 kDa) responsible for mediating catalysis, and a small protein cofactor (approximately 15 kDa) that modulates substrate recognition and is required for efficient in vivo catalysis. In contrast, multiple proteins are associated with eukaryotic and archaeal RNase P, and these proteins exhibit no recognizable homology to the conserved bacterial protein subunit. In reconstitution experiments with recombinantly expressed and purified protein subunits Mth Rpp29, a homologue of the Rpp29 protein subunit from eukaryotic RNase P, is an essential protein component of the archaeal holoenzyme []. In Saccharomyces cerevisiae (Baker's yeast), RNase P consists of 9 protein subunits (Pop1, Pop3-8, Rpr2 and Rpp1), while in humans there are 10 subunits (Rpp14, 20, 21, 25, 29, 30, 38, 40, hPop1, 5). RNase MRP (mitochondrial RNA processing) is an rRNA processing enzyme that cleaves a specific site within precursor rRNA to generate the mature 5'-end of 5.8S rRNA []. RNase MRP also cleaves primers for mitochondrial DNA replication and CLB2 mRNA. In yeast, RNase MRP possesses one putatively catalytic RNA and at least 9 protein subunits and is highly related to RNase P (Pop1, Pop3-Pop8, Rpp1, Snm1 and Rmp1).; GO: 0003723 RNA binding, 0004540 ribonuclease activity, 0006364 rRNA processing, 0006379 mRNA cleavage, 0008033 tRNA processing, 0000172 ribonuclease MRP complex, 0030677 ribonuclease P complex; PDB: 1V76_B 2ZAE_C 1OQK_A 2KI7_A 1TSF_A 1TS9_A 1PC0_A.
Probab=86.12 E-value=1.3 Score=29.07 Aligned_cols=52 Identities=19% Similarity=0.167 Sum_probs=38.1
Q ss_pred cceeEEEEecCCcceeeeeecccchhhhheeEEEEEeCCeeeEecCccccee
Q psy10647 25 LSGRVLIELKDDTPALGFHRSKNNMTRKLIKFVILFDNTNLVYFPGQYLSGR 76 (92)
Q Consensus 25 lSGRVLle~qe~t~~lglh~~~~~m~rkl~kf~ilfdnt~llyfpgq~lsgr 76 (92)
++|.|+.||+.--.+..--..---.+++-.-|.+-+|+...+..-|.-|.+|
T Consensus 30 ~~GiVV~ETknt~~I~t~~~~~~~IpK~~~vF~~~~~~~~~~~i~G~~l~~r 81 (89)
T PF01868_consen 30 IEGIVVDETKNTFVIVTEDGKVKTIPKAGSVFEFELPGGSKVTIYGSRLVGR 81 (89)
T ss_dssp EEEEEEEEETTEEEEEETTEEEEEEESTTEEEEEEETTTEEEEEEGGGCSS-
T ss_pred CEEEEEEcccceEEEEecCCcEEEEecCCEEEEEEeCCCcEEEEEChhhccC
Confidence 8999999999876665322222246788888999999999777778777766
No 6
>PRK11556 multidrug efflux system subunit MdtA; Provisional
Probab=75.84 E-value=3.5 Score=32.55 Aligned_cols=32 Identities=28% Similarity=0.587 Sum_probs=26.7
Q ss_pred ceEEEEEeeCCceeEecCcccceeEEEEecCC
Q psy10647 5 LIKFVILFDNTNLVYFPGQYLSGRVLIELKDD 36 (92)
Q Consensus 5 l~kf~IiFDn~~llYFPGQ~lSGRVLle~qe~ 36 (92)
-.++.+.|||++--.+|||++..++.++..++
T Consensus 289 t~~v~a~~~n~~~~L~pG~~v~v~i~~~~~~~ 320 (415)
T PRK11556 289 TIKLKARFNNQDDALFPNQFVNARMLVDTLQN 320 (415)
T ss_pred EEEEEEEeCCCCCccCCCCEEEEEEEecCcCc
Confidence 35678999999888899999999988876655
No 7
>smart00538 POP4 A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins.
Probab=73.58 E-value=5.9 Score=26.41 Aligned_cols=52 Identities=17% Similarity=0.208 Sum_probs=35.6
Q ss_pred cceeEEEEecCCcceeeeeecccchhhhheeEEEEEeCCeeeEecCccccee
Q psy10647 25 LSGRVLIELKDDTPALGFHRSKNNMTRKLIKFVILFDNTNLVYFPGQYLSGR 76 (92)
Q Consensus 25 lSGRVLle~qe~t~~lglh~~~~~m~rkl~kf~ilfdnt~llyfpgq~lsgr 76 (92)
++|+|+-||+..-.+..--....-.|++-.-|.+-+++.......|.-+.+|
T Consensus 29 i~GiVv~ET~nt~~I~t~~~~~~~IpK~~~vF~f~l~~~~~~~i~G~~l~~r 80 (92)
T smart00538 29 IEGIVVDETRNTLKIETKEGRVKTVPKDGAVFEFELPGGEIVRIDGDRLVGR 80 (92)
T ss_pred cEEEEEEeeeeEEEEEeCCCcEEEEECCCeEEEEEECCCeEEEEECceeeeC
Confidence 7999999998765554321111235778888888888876666777766655
No 8
>cd08975 BaFpgNei_N_3 Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases. This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. One exception is mouse Nei-like glycosylase 3 (Neil3) which forms a Schiff base int
Probab=59.59 E-value=45 Score=22.50 Aligned_cols=22 Identities=27% Similarity=0.428 Sum_probs=15.0
Q ss_pred hhhheeEEEEEeCCe-eeEecCc
Q psy10647 50 TRKLIKFVILFDNTN-LVYFPGQ 71 (92)
Q Consensus 50 ~rkl~kf~ilfdnt~-llyfpgq 71 (92)
+.|-.++.+.|||.+ |.|-|-.
T Consensus 89 ~~kh~~l~l~~~dg~~L~f~~~~ 111 (117)
T cd08975 89 IPKKYQLLIEFDDDSFLVFTVAM 111 (117)
T ss_pred CCCeEEEEEEECCCCEEEEEEEE
Confidence 346677888888765 7776643
No 9
>PRK09783 copper/silver efflux system membrane fusion protein CusB; Provisional
Probab=53.44 E-value=14 Score=29.16 Aligned_cols=28 Identities=14% Similarity=0.133 Sum_probs=23.3
Q ss_pred ceEEEEEeeCCceeEecCcccceeEEEE
Q psy10647 5 LIKFVILFDNTNLVYFPGQYLSGRVLIE 32 (92)
Q Consensus 5 l~kf~IiFDn~~llYFPGQ~lSGRVLle 32 (92)
-.+.++.|||++....||++.+.++..+
T Consensus 295 t~~vrv~l~N~~~~L~pGm~v~v~i~~~ 322 (409)
T PRK09783 295 TLQLRLEVDNADEALKPGMNAWLQLNTA 322 (409)
T ss_pred EEEEEEEEeCCCCccCCCCEEEEEEecC
Confidence 3578899999999999999998887543
No 10
>cd08976 BaFpgNei_N_4 Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases. This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This N-terminal proline is conserved in this family. Escherichia coli Fpg prefers 8
Probab=51.46 E-value=66 Score=20.98 Aligned_cols=21 Identities=14% Similarity=0.273 Sum_probs=14.1
Q ss_pred chhhhheeEEEEEeCCeeeEe
Q psy10647 48 NMTRKLIKFVILFDNTNLVYF 68 (92)
Q Consensus 48 ~m~rkl~kf~ilfdnt~llyf 68 (92)
..+.|-.++.+.|||.+-|.|
T Consensus 86 ~~~~kh~~~~l~l~~g~~l~~ 106 (117)
T cd08976 86 EDPPKHARLLLHFEDGFRLAF 106 (117)
T ss_pred CCCCCEEEEEEEECCCCEEEE
Confidence 345677888888887664444
No 11
>KOG3052|consensus
Probab=49.49 E-value=6.9 Score=32.41 Aligned_cols=22 Identities=50% Similarity=0.972 Sum_probs=17.7
Q ss_pred EecCcccc-eeEE----EEecCCcccc
Q psy10647 67 YFPGQYLS-GRVL----IELKDDTPAL 88 (92)
Q Consensus 67 yfpgq~ls-grvl----~el~~~t~~l 88 (92)
||||+.++ +||| ||.+|.||+-
T Consensus 221 yFpGgaIaMa~~l~de~vEyeDgtPAT 247 (311)
T KOG3052|consen 221 YFPGGAIAMAKVLFDEVVEYEDGTPAT 247 (311)
T ss_pred CCCCcccccchhhcccceeecCCCchh
Confidence 89998776 5665 8999999973
No 12
>PRK15030 multidrug efflux system transporter AcrA; Provisional
Probab=47.36 E-value=27 Score=27.13 Aligned_cols=30 Identities=23% Similarity=0.482 Sum_probs=23.6
Q ss_pred eEEEEEeeCCceeEecCcccceeEEEEecC
Q psy10647 6 IKFVILFDNTNLVYFPGQYLSGRVLIELKD 35 (92)
Q Consensus 6 ~kf~IiFDn~~llYFPGQ~lSGRVLle~qe 35 (92)
....+.|||++....||++...++.....+
T Consensus 274 ~~V~~~~~n~~~~L~pGm~~~v~i~~~~~~ 303 (397)
T PRK15030 274 ITLRAIFPNPDHTLLPGMFVRARLEEGLNP 303 (397)
T ss_pred EEEEEEEeCCCCcccCCCEEEEEEeecCcC
Confidence 467788999998889999988777665433
No 13
>PF12532 DUF3732: Protein of unknown function (DUF3732); InterPro: IPR022205 This domain family is found in bacteria and eukaryotes, and is typically between 180 and 198 amino acids in length. There is a conserved DQP sequence motif.
Probab=45.87 E-value=9.2 Score=28.13 Aligned_cols=13 Identities=38% Similarity=0.968 Sum_probs=12.0
Q ss_pred EEeeCCceeEecC
Q psy10647 10 ILFDNTNLVYFPG 22 (92)
Q Consensus 10 IiFDn~~llYFPG 22 (92)
++||+|+=+|||=
T Consensus 104 L~lDQPSQvYfp~ 116 (193)
T PF12532_consen 104 LFLDQPSQVYFPS 116 (193)
T ss_pred eeecCCCcCcCCC
Confidence 5789999999998
No 14
>PF12790 T6SS-SciN: Type VI secretion lipoprotein; InterPro: IPR017734 This entry represents a family of lipoproteins associated with IAHP-related loci, thought to be type VI secretion system protein []. ; PDB: 3RX9_A.
Probab=45.14 E-value=70 Score=21.70 Aligned_cols=47 Identities=15% Similarity=0.175 Sum_probs=25.4
Q ss_pred eCCceeEecCcccceeEEEEecCCcceeeeeecccchhhhheeEEEEEe
Q psy10647 13 DNTNLVYFPGQYLSGRVLIELKDDTPALGFHRSKNNMTRKLIKFVILFD 61 (92)
Q Consensus 13 Dn~~llYFPGQ~lSGRVLle~qe~t~~lglh~~~~~m~rkl~kf~ilfd 61 (92)
+....+..|||..+ +-++..+++..+|+----.++...-.|.++=.+
T Consensus 79 ~~~e~~l~Pg~~~~--~~~~~~~~aryigvvA~fr~~~~~~wr~~~~~~ 125 (142)
T PF12790_consen 79 SVDEFVLQPGESRT--LTLDRDPDARYIGVVAGFRDPDGAQWRRVIPVP 125 (142)
T ss_dssp EEEEEEE-TT-EEE--EEEE--TT--EEEEEE--SS--TT-SEEEEEGG
T ss_pred cceEEEECCCCcEe--eeEccCCCCcEEEEEEEEeCCCCCceEEEEECC
Confidence 44567789999887 669999999999987666666655555544443
No 15
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) [] are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2B39_B 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 4ACQ_C 2P9R_B ....
Probab=42.35 E-value=64 Score=19.78 Aligned_cols=27 Identities=26% Similarity=0.450 Sum_probs=20.8
Q ss_pred EEEEeeCCceeEecCcccceeEEEEecCC
Q psy10647 8 FVILFDNTNLVYFPGQYLSGRVLIELKDD 36 (92)
Q Consensus 8 f~IiFDn~~llYFPGQ~lSGRVLle~qe~ 36 (92)
.-|.-|++ +|-|||-+.-|+++-..++
T Consensus 2 ~~i~TDr~--iYrPGetV~~~~~~~~~~~ 28 (99)
T PF01835_consen 2 IFIQTDRP--IYRPGETVHFRAIVRDLDN 28 (99)
T ss_dssp EEEEESSS--EE-TTSEEEEEEEEEEECT
T ss_pred EEEECCcc--CcCCCCEEEEEEEEecccc
Confidence 34566666 7999999999999888873
No 16
>PF03643 Vps26: Vacuolar protein sorting-associated protein 26 ; InterPro: IPR005377 The movement of lipid and protein components between intracellular organelles requires the regulated interactions of many molecules. Vacuolar protein sorting-associated protein (Vps)5 is a yeast protein that is a subunit of a large multimeric complex, termed the retromer complex, involved in retrograde transport of proteins from endosomes to the trans-Golgi network. Sorting nexin (SNX) 1 and SNX2 are its mammalian orthologs []. To carry out its biological functions, Vps5 forms the retromer complex with at least four other proteins: Vps17, Vps26, Vps29, and Vps35 []. This family of Vps26-proteins also contains Down syndrome critical region 3/A.; GO: 0007034 vacuolar transport, 0030904 retromer complex; PDB: 3LHA_A 3LH9_A 2R51_A 3LH8_B 2FAU_A.
Probab=42.19 E-value=27 Score=27.28 Aligned_cols=20 Identities=40% Similarity=0.635 Sum_probs=16.7
Q ss_pred ceeEecCcccceeEEEEecC
Q psy10647 16 NLVYFPGQYLSGRVLIELKD 35 (92)
Q Consensus 16 ~llYFPGQ~lSGRVLle~qe 35 (92)
+-+|.+|..++|.|.+..++
T Consensus 32 ~~iY~~gE~V~G~V~I~~~~ 51 (275)
T PF03643_consen 32 NPIYSDGETVSGKVVITSKP 51 (275)
T ss_dssp EEEEETC--EEEEEEEEESS
T ss_pred eceEcCCCEEEEEEEEEECC
Confidence 36999999999999999999
No 17
>PRK09859 multidrug efflux system protein MdtE; Provisional
Probab=42.05 E-value=42 Score=25.82 Aligned_cols=32 Identities=22% Similarity=0.355 Sum_probs=24.5
Q ss_pred ceEEEEEeeCCceeEecCcccceeEEEEecCC
Q psy10647 5 LIKFVILFDNTNLVYFPGQYLSGRVLIELKDD 36 (92)
Q Consensus 5 l~kf~IiFDn~~llYFPGQ~lSGRVLle~qe~ 36 (92)
.....+.+||++-...||++.+.++-....++
T Consensus 269 t~~v~~~~~n~~~~l~pGm~v~v~i~~~~~~~ 300 (385)
T PRK09859 269 SVTLRAIFPNPNGDLLPGMYVTALVDEGSRQN 300 (385)
T ss_pred eEEEEEEEECCCCeECCCCEEEEEEeccccCC
Confidence 34677889999989999999887776654443
No 18
>PRK09783 copper/silver efflux system membrane fusion protein CusB; Provisional
Probab=38.82 E-value=49 Score=26.20 Aligned_cols=27 Identities=15% Similarity=0.138 Sum_probs=22.0
Q ss_pred heeEEEEEeCCeeeEecCcccceeEEE
Q psy10647 53 LIKFVILFDNTNLVYFPGQYLSGRVLI 79 (92)
Q Consensus 53 l~kf~ilfdnt~llyfpgq~lsgrvl~ 79 (92)
-.+.-+.+||.+....||+|...++-.
T Consensus 295 t~~vrv~l~N~~~~L~pGm~v~v~i~~ 321 (409)
T PRK09783 295 TLQLRLEVDNADEALKPGMNAWLQLNT 321 (409)
T ss_pred EEEEEEEEeCCCCccCCCCEEEEEEec
Confidence 356788899999889999998877644
No 19
>PRK09578 periplasmic multidrug efflux lipoprotein precursor; Reviewed
Probab=38.44 E-value=40 Score=25.87 Aligned_cols=31 Identities=19% Similarity=0.322 Sum_probs=23.6
Q ss_pred eEEEEEeeCCceeEecCcccceeEEEEecCC
Q psy10647 6 IKFVILFDNTNLVYFPGQYLSGRVLIELKDD 36 (92)
Q Consensus 6 ~kf~IiFDn~~llYFPGQ~lSGRVLle~qe~ 36 (92)
....+.|||++--..||++.+.++..+.+++
T Consensus 273 ~~V~~~~~n~~~~L~pGm~~~v~i~~~~~~~ 303 (385)
T PRK09578 273 VAMRALFPNPERELLPGAYVRIALDRAVNPR 303 (385)
T ss_pred EEEEEEEeCCCCcCCCCCEEEEEEEccCcCc
Confidence 4567889999888899999887776654444
No 20
>PF02996 Prefoldin: Prefoldin subunit; InterPro: IPR004127 This entry comprises of several prefoldin subunits. Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal alpha subunit, eukaryotic prefoldin subunits 3 and 5 and the UXT (ubiquitously expressed transcript) family. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 1FXK_C 2ZDI_C.
Probab=34.12 E-value=37 Score=21.65 Aligned_cols=31 Identities=26% Similarity=0.325 Sum_probs=24.5
Q ss_pred EEEEEeCCeeeEecCcc-cceeEEEEecCCcc
Q psy10647 56 FVILFDNTNLVYFPGQY-LSGRVLIELKDDTP 86 (92)
Q Consensus 56 f~ilfdnt~llyfpgq~-lsgrvl~el~~~t~ 86 (92)
.-++++-++-+|.||.+ -+.+|+|.+-.+..
T Consensus 39 ~~~lvplg~~~~v~g~i~~~~~vlV~lG~~~~ 70 (120)
T PF02996_consen 39 HEILVPLGSGVFVPGKIPDTDKVLVSLGAGYY 70 (120)
T ss_dssp -EEEEEECTTEEEEEE-SSTTEEEEEEETTEE
T ss_pred ceeeecCCCCeEEEEEeCCCCEEEEEeeCCeE
Confidence 46788889999999988 78899999877643
No 21
>PRK11556 multidrug efflux system subunit MdtA; Provisional
Probab=33.55 E-value=43 Score=26.48 Aligned_cols=32 Identities=28% Similarity=0.587 Sum_probs=25.2
Q ss_pred heeEEEEEeCCeeeEecCcccceeEEEEecCC
Q psy10647 53 LIKFVILFDNTNLVYFPGQYLSGRVLIELKDD 84 (92)
Q Consensus 53 l~kf~ilfdnt~llyfpgq~lsgrvl~el~~~ 84 (92)
-.++.+-|||..-..+||+|...++.++...+
T Consensus 289 t~~v~a~~~n~~~~L~pG~~v~v~i~~~~~~~ 320 (415)
T PRK11556 289 TIKLKARFNNQDDALFPNQFVNARMLVDTLQN 320 (415)
T ss_pred EEEEEEEeCCCCCccCCCCEEEEEEEecCcCc
Confidence 46778889998777899999988887765444
No 22
>COG1588 POP4 RNase P/RNase MRP subunit p29 [Translation, ribosomal structure and biogenesis]
Probab=32.15 E-value=60 Score=22.82 Aligned_cols=51 Identities=20% Similarity=0.115 Sum_probs=29.2
Q ss_pred ccceeEEEEecCCcceeeeeecccchhhhheeEEEEEeCCeeeEecCcccce
Q psy10647 24 YLSGRVLIELKDDTPALGFHRSKNNMTRKLIKFVILFDNTNLVYFPGQYLSG 75 (92)
Q Consensus 24 ~lSGRVLle~qe~t~~lglh~~~~~m~rkl~kf~ilfdnt~llyfpgq~lsg 75 (92)
=++|||+-||+.---...-- ..--.|+....|-+=.......=.+|..|-|
T Consensus 32 GI~G~VVdETkNtLvi~t~~-~~~~VpK~~~vfef~~~~G~~vkVdG~lL~~ 82 (95)
T COG1588 32 GIEGRVVDETKNTLVIDTGS-REKVVPKDGAVFEFEGPDGEKVKVDGRLLLG 82 (95)
T ss_pred ceeEEEEeeeccEEEEECCC-ceEEEecCcEEEEEEcCCCcEEEEcchhhhc
Confidence 48999999998654444333 3334566666666544444443344444433
No 23
>cd08972 PF_Nei_N N-terminal domain of the plant and fungal Nei and related proteins. This family contains the N-terminal domain of plant and Fungi Nei and related proteins. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. The plant and fungal FpgNei glycosylases prefer the
Probab=32.10 E-value=1.7e+02 Score=20.21 Aligned_cols=19 Identities=21% Similarity=0.499 Sum_probs=14.1
Q ss_pred hhhheeEEEEEeCCeeeEe
Q psy10647 50 TRKLIKFVILFDNTNLVYF 68 (92)
Q Consensus 50 ~rkl~kf~ilfdnt~llyf 68 (92)
+.|-.++.+.|||..-|.|
T Consensus 107 ~~kh~~~~l~l~~g~~L~f 125 (137)
T cd08972 107 PPRFYKFVLTLEDGTELAF 125 (137)
T ss_pred CCceEEEEEEeCCCCEEEE
Confidence 4678888999988765555
No 24
>TIGR00999 8a0102 Membrane Fusion Protein cluster 2 (function with RND porters).
Probab=32.01 E-value=63 Score=22.59 Aligned_cols=31 Identities=29% Similarity=0.467 Sum_probs=22.8
Q ss_pred eEEEEEeeCCceeEecCcccceeEEEEecCC
Q psy10647 6 IKFVILFDNTNLVYFPGQYLSGRVLIELKDD 36 (92)
Q Consensus 6 ~kf~IiFDn~~llYFPGQ~lSGRVLle~qe~ 36 (92)
..+.+.|++++--..||+.++.++.....++
T Consensus 173 ~~v~~~~~~~~~~l~~G~~v~v~i~~~~~~~ 203 (265)
T TIGR00999 173 AKVRVLIKNENLTLKPGLFVQVRVETKIGEP 203 (265)
T ss_pred EEEEEEEeCCCCccCCCCEEEEEEecCCCCc
Confidence 4567788888767789999887776655444
No 25
>TIGR01730 RND_mfp RND family efflux transporter, MFP subunit. This model represents the MFP (membrane fusion protein) component of the RND family of transporters. RND refers to Resistance, Nodulation, and cell Division. It is, in part, a subfamily of pfam00529 (Pfam release 7.5) but hits substantial numbers of proteins missed by that model. The related HlyD secretion protein, for which pfam00529 is named, is outside the scope of this model. Attributed functions imply outward transport. These functions include nodulation, acriflavin resistance, heavy metal efflux, and multidrug resistance proteins. Most members of this family are found in Gram-negative bacteria. The proposed function of MFP proteins is to bring the inner and outer membranes together and enable transport to the outside of the outer membrane. Note, however, that a few members of this family are found in Gram-positive bacteria, where there is no outer membrane.
Probab=31.70 E-value=66 Score=22.82 Aligned_cols=32 Identities=13% Similarity=0.306 Sum_probs=25.0
Q ss_pred ceEEEEEeeCCceeEecCcccceeEEEEecCC
Q psy10647 5 LIKFVILFDNTNLVYFPGQYLSGRVLIELKDD 36 (92)
Q Consensus 5 l~kf~IiFDn~~llYFPGQ~lSGRVLle~qe~ 36 (92)
..++.+.||+++.-+.||++++-++...-.++
T Consensus 220 ~~~v~~~~~~~~~~l~~G~~v~v~i~~~~~~~ 251 (322)
T TIGR01730 220 TVRVRATFPNPDGRLLPGMFGRVTISLKVRSS 251 (322)
T ss_pred eEEEEEEEcCCCCcCCCCCEEEEEEecCccCC
Confidence 46778889998888899999887777765544
No 26
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=29.99 E-value=36 Score=21.37 Aligned_cols=18 Identities=28% Similarity=0.331 Sum_probs=15.0
Q ss_pred ceeEEEEecCCccccccc
Q psy10647 74 SGRVLIELKDDTPALALL 91 (92)
Q Consensus 74 sgrvl~el~~~t~~lgl~ 91 (92)
.=+|.||+++++.+-|.|
T Consensus 11 g~~V~VeLkng~~~~G~L 28 (76)
T cd01723 11 NHPMLVELKNGETYNGHL 28 (76)
T ss_pred CCEEEEEECCCCEEEEEE
Confidence 348999999999988865
No 27
>cd08974 BaFpgNei_N_2 Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases. This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This N-terminal proline is conserved in this family. Escherichia coli Fpg prefers 8
Probab=29.59 E-value=1.7e+02 Score=19.16 Aligned_cols=19 Identities=21% Similarity=0.420 Sum_probs=14.1
Q ss_pred hhhheeEEEEEeCCeeeEe
Q psy10647 50 TRKLIKFVILFDNTNLVYF 68 (92)
Q Consensus 50 ~rkl~kf~ilfdnt~llyf 68 (92)
+.|-..+.+.|||.++++|
T Consensus 76 ~~~~~~~~l~~~~g~~~~~ 94 (98)
T cd08974 76 KDAPPRLSLGFDNGELNFY 94 (98)
T ss_pred CCCcEEEEEEeCCCcEEEE
Confidence 4567777888888877766
No 28
>KOG3063|consensus
Probab=27.08 E-value=96 Score=25.79 Aligned_cols=23 Identities=30% Similarity=0.618 Sum_probs=20.3
Q ss_pred eeEecCcccceeEEEEecCCcce
Q psy10647 17 LVYFPGQYLSGRVLIELKDDTPA 39 (92)
Q Consensus 17 llYFPGQ~lSGRVLle~qe~t~~ 39 (92)
.+|.-|.-+||+|-++++++-++
T Consensus 40 ~lf~dgEtv~G~V~l~lk~gkkl 62 (301)
T KOG3063|consen 40 PLFYDGETVSGKVNLRLKDGKKL 62 (301)
T ss_pred eeEecCCeeeeEEEEEEcCCccc
Confidence 58999999999999999986554
No 29
>PF01149 Fapy_DNA_glyco: Formamidopyrimidine-DNA glycosylase N-terminal domain; InterPro: IPR012319 This entry represents the catalytic domain of DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway []. These enzymes are primarily from bacteria, and have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC). Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines [, ]. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above (3.2.2 from EC, 4.2.99.18 from EC), but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine []. These protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger []. The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a beta-hairpin loop formed by the zinc finger [].; GO: 0003684 damaged DNA binding, 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0008270 zinc ion binding, 0016799 hydrolase activity, hydrolyzing N-glycosyl compounds, 0006284 base-excision repair; PDB: 1K82_C 3GQ3_A 3JR5_A 3SAT_A 3GPX_A 2F5Q_A 3SBJ_A 3U6S_A 3SAU_A 3SAR_A ....
Probab=26.16 E-value=1.9e+02 Score=18.67 Aligned_cols=48 Identities=15% Similarity=0.313 Sum_probs=30.3
Q ss_pred EEEEEeeCCceeE-ecCcccceeEEEEecCCcceeeeeecccchhhhheeEEEEEeCCeeeEec
Q psy10647 7 KFVILFDNTNLVY-FPGQYLSGRVLIELKDDTPALGFHRSKNNMTRKLIKFVILFDNTNLVYFP 69 (92)
Q Consensus 7 kf~IiFDn~~llY-FPGQ~lSGRVLle~qe~t~~lglh~~~~~m~rkl~kf~ilfdnt~llyfp 69 (92)
.+.+.||++..+. =.| +||++.+ ....-+.|-.++.+-||+..-|.|=
T Consensus 59 ~L~~~l~~~~~l~~Hlg--MtG~~~~-------------~~~~~~~~~~~~~l~~~~g~~L~f~ 107 (116)
T PF01149_consen 59 YLFFHLDGGLVLVVHLG--MTGRLRL-------------DPPDWPPKHTRLRLRFEDGSRLRFV 107 (116)
T ss_dssp EEEEEETTTEEEEEE-T--TTEEEEE-------------STTCG-STTEEEEEEETSSEEEEEE
T ss_pred EEEEEeCCCCEEEEeeC--CcEEEEe-------------cCCCCCCCeEEEEEEECCCCEEEEE
Confidence 4566776644333 344 6787777 3334567888999999888766663
No 30
>PRK03879 ribonuclease P protein component 1; Validated
Probab=25.65 E-value=1e+02 Score=20.85 Aligned_cols=35 Identities=14% Similarity=0.119 Sum_probs=23.7
Q ss_pred cceeEEEEecCCcceeeeeecccchhhhheeEEEEE
Q psy10647 25 LSGRVLIELKDDTPALGFHRSKNNMTRKLIKFVILF 60 (92)
Q Consensus 25 lSGRVLle~qe~t~~lglh~~~~~m~rkl~kf~ilf 60 (92)
++|+|+-||+.--.+..=.+ ..-.|++-.-|.+-+
T Consensus 31 i~GiVv~ETknt~~I~~~~~-~~~VPK~~~iF~f~~ 65 (96)
T PRK03879 31 IKGRVVDETRNTLVIETDGK-EWMVPKDGATFEFEL 65 (96)
T ss_pred ceEEEEEeceeEEEEEcCCc-EEEEeCCCeEEEEEE
Confidence 79999999997666651101 112567778888877
No 31
>PF01774 UreD: UreD urease accessory protein; InterPro: IPR002669 UreD is a urease accessory protein. Urease IPR005848 from INTERPRO hydrolyses urea into ammonia and carbamic acid []. UreD is involved in activation of the urease enzyme via the UreD-UreF-UreG-urease complex [] and is required for urease nickel metallocentre assembly []. See also UreF IPR002639 from INTERPRO, UreG IPR004400 from INTERPRO.; GO: 0016151 nickel ion binding, 0006807 nitrogen compound metabolic process; PDB: 3SF5_D.
Probab=24.88 E-value=88 Score=22.61 Aligned_cols=55 Identities=20% Similarity=0.379 Sum_probs=22.7
Q ss_pred eEEEEecCCcceeeeeecccch-hhhheeEEEEEeCCeeeEecCcc-------cceeEEEEecCCcc
Q psy10647 28 RVLIELKDDTPALGFHRSKNNM-TRKLIKFVILFDNTNLVYFPGQY-------LSGRVLIELKDDTP 86 (92)
Q Consensus 28 RVLle~qe~t~~lglh~~~~~m-~rkl~kf~ilfdnt~llyfpgq~-------lsgrvl~el~~~t~ 86 (92)
+++|.+|..|++ |++.++= ++.-.. +-+=+|..|-|+|.+. ..-+.-+++.++.-
T Consensus 28 ~~~ltTqaatkv---y~~~~~~~a~q~~~-~~v~~ga~Le~lP~p~I~f~~A~~~q~~~v~l~~~A~ 90 (209)
T PF01774_consen 28 RLLLTTQAATKV---YRMRGGRPARQRIR-ITVEEGAYLEYLPDPTIPFAGARFRQRTRVDLAPGAS 90 (209)
T ss_dssp EEEEE----EEE------TTS--EEEEEE-EEE-TT-EEEE----EEE-TT-EEEEEEEEEE-TT-E
T ss_pred EEEEechhhhhh---cCCCCCCcEEEEEE-EEECCCCEEEEcCCCCEeeCCCEEEEEEEEEECCCCE
Confidence 677778877775 6776554 443333 3345677777777654 34556666655543
No 32
>cd06182 CYPOR_like NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. CYPOR has a C-terminal ferredoxin reducatase (FNR)- like FAD and NAD binding module, an FMN-binding domain, and an additional conecting domain (inserted within the FAD binding region) that orients the FNR and FMN binding domains. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria and participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-t
Probab=24.62 E-value=55 Score=24.18 Aligned_cols=22 Identities=23% Similarity=0.315 Sum_probs=14.1
Q ss_pred cceEEEEEeeC-CceeEecCccc
Q psy10647 4 KLIKFVILFDN-TNLVYFPGQYL 25 (92)
Q Consensus 4 kl~kf~IiFDn-~~llYFPGQ~l 25 (92)
...-|.+..++ ...-|-|||++
T Consensus 16 ~v~~l~l~~~~~~~~~~~pGQ~v 38 (267)
T cd06182 16 STRHLEFDLSGNSVLKYQPGDHL 38 (267)
T ss_pred ceEEEEEecCCCCcCccCCCCEE
Confidence 34445555554 45669999997
No 33
>cd08773 FpgNei_N N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. These enzymes initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycolsylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. The FpgNei DNA glycosylases represent one of the two structural superfamilies of DNA glycosylases that recognize oxidized bases (the other is the HTH-GPD superfamily exemplified by Escherichia coli Nth). Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. One e
Probab=24.59 E-value=2e+02 Score=18.48 Aligned_cols=19 Identities=21% Similarity=0.284 Sum_probs=12.0
Q ss_pred hhhheeEEEEEeCCeeeEe
Q psy10647 50 TRKLIKFVILFDNTNLVYF 68 (92)
Q Consensus 50 ~rkl~kf~ilfdnt~llyf 68 (92)
+.|-.+..+.|||..-|.|
T Consensus 88 ~~~~~~~~~~~~~~~~l~f 106 (117)
T cd08773 88 PPKHDRLVLRLANGSQLRF 106 (117)
T ss_pred CCCeEEEEEEECCCCEEEE
Confidence 3466677777777654444
No 34
>PRK11578 macrolide transporter subunit MacA; Provisional
Probab=23.85 E-value=1e+02 Score=23.41 Aligned_cols=29 Identities=7% Similarity=-0.140 Sum_probs=21.7
Q ss_pred EEEEeeCCceeEecCcccceeEEEEecCC
Q psy10647 8 FVILFDNTNLVYFPGQYLSGRVLIELKDD 36 (92)
Q Consensus 8 f~IiFDn~~llYFPGQ~lSGRVLle~qe~ 36 (92)
..+..+|++....||++...++.++..++
T Consensus 277 v~~~~~~~~~~l~~Gm~v~v~i~~~~~~~ 305 (370)
T PRK11578 277 ARFEVPNPNGLLRLDMTAQVHIQLTDVKN 305 (370)
T ss_pred EEEEecCCcCcCCCCCEEEEEEEEcccCC
Confidence 34456888888899999888887765554
No 35
>cd06208 CYPOR_like_FNR These ferredoxin reductases are related to the NADPH cytochrome p450 reductases (CYPOR), but lack the FAD-binding region connecting sub-domain. Ferredoxin-NADP+ reductase (FNR) is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins, such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap between the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2, which then
Probab=23.46 E-value=58 Score=24.01 Aligned_cols=19 Identities=32% Similarity=0.557 Sum_probs=12.6
Q ss_pred EEEEeeCC-ceeEecCcccc
Q psy10647 8 FVILFDNT-NLVYFPGQYLS 26 (92)
Q Consensus 8 f~IiFDn~-~llYFPGQ~lS 26 (92)
+.+.|+-+ .+=|.|||+++
T Consensus 29 ~~~~l~~~~~~~~~pGQ~v~ 48 (286)
T cd06208 29 CHIVIDHGGKLPYLEGQSIG 48 (286)
T ss_pred EEEEEeCCCcccccCCceEE
Confidence 45556554 44589999964
No 36
>PF11611 DUF4352: Domain of unknown function (DUF4352); InterPro: IPR021652 This entry is represented by Bacteriophage A118, Gp32. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a group of putative lipoproteins of unknown function.; PDB: 3CFU_A.
Probab=22.53 E-value=98 Score=19.14 Aligned_cols=28 Identities=18% Similarity=0.401 Sum_probs=18.4
Q ss_pred eeEecCcccceeEEEEecCCcceeeeee
Q psy10647 17 LVYFPGQYLSGRVLIELKDDTPALGFHR 44 (92)
Q Consensus 17 llYFPGQ~lSGRVLle~qe~t~~lglh~ 44 (92)
--.=||+-.+|.++.|..++.+-.-|.-
T Consensus 85 ~~i~pG~~~~g~l~F~vp~~~~~~~l~~ 112 (123)
T PF11611_consen 85 ETIKPGESVTGKLVFEVPKDDKPYTLEY 112 (123)
T ss_dssp EEE-TT-EEEEEEEEEESTT-GG-EEEE
T ss_pred cEECCCCEEEEEEEEEECCCCccEEEEE
Confidence 3456999999999999999887544443
No 37
>PF04019 DUF359: Protein of unknown function (DUF359); InterPro: IPR007164 This is family of archaebacterial proteins, which are about 170 amino acids in length. They have no known function. The most conserved portion of the protein contains the sequence GEEDL that may be important for its function.
Probab=21.84 E-value=57 Score=22.87 Aligned_cols=23 Identities=26% Similarity=0.533 Sum_probs=17.7
Q ss_pred CCceeEecCcccceeEEEEecCCcc
Q psy10647 14 NTNLVYFPGQYLSGRVLIELKDDTP 38 (92)
Q Consensus 14 n~~llYFPGQ~lSGRVLle~qe~t~ 38 (92)
++..+| ||+=.|-|+++..++++
T Consensus 86 gs~V~Y--GQP~eGvV~v~v~~~~k 108 (121)
T PF04019_consen 86 GSVVLY--GQPGEGVVLVKVTEEAK 108 (121)
T ss_pred CCEEEE--CCCCCeEEEEEeCHHHH
Confidence 344455 99999999999987654
No 38
>PF12700 HlyD_2: HlyD family secretion protein; PDB: 3LNN_B 4DK0_A 4DK1_C 3FPP_B 2K32_A 2K33_A 3OW7_B 3OOC_A 3T53_B 4DNT_C ....
Probab=21.44 E-value=1.2e+02 Score=21.51 Aligned_cols=29 Identities=21% Similarity=0.337 Sum_probs=20.5
Q ss_pred ceEEEEEeeCCceeEecCcccceeEEEEe
Q psy10647 5 LIKFVILFDNTNLVYFPGQYLSGRVLIEL 33 (92)
Q Consensus 5 l~kf~IiFDn~~llYFPGQ~lSGRVLle~ 33 (92)
...+.+.+||++--+.||+++...+.+..
T Consensus 243 ~~~v~~~~~~~~~~l~~g~~v~v~i~~~~ 271 (328)
T PF12700_consen 243 TFKVRVSLDNPNGNLRPGMFVEVSIILGS 271 (328)
T ss_dssp EEEEEEEEE-SSS-S-TT-EEEEEEESEE
T ss_pred eeEEEEEeccccchhhhcccccceecccc
Confidence 34788999999999999999998877665
No 39
>cd08966 EcFpg-like_N N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases. This family contains the N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. Es
Probab=21.17 E-value=2.4e+02 Score=18.18 Aligned_cols=24 Identities=17% Similarity=0.319 Sum_probs=15.6
Q ss_pred hhhhheeEEEEEeCCe-eeEe-cCcc
Q psy10647 49 MTRKLIKFVILFDNTN-LVYF-PGQY 72 (92)
Q Consensus 49 m~rkl~kf~ilfdnt~-llyf-pgq~ 72 (92)
.+.|-.++.+.|||.. |.|- |..|
T Consensus 88 ~~~~~~~l~l~~~~g~~l~f~D~R~f 113 (120)
T cd08966 88 PPEKHDHVIFELDDGRELRFNDPRRF 113 (120)
T ss_pred CCCCcEEEEEEeCCCCEEEEEcCCCC
Confidence 3456788888888854 5554 5544
No 40
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=21.12 E-value=2.6e+02 Score=20.86 Aligned_cols=17 Identities=24% Similarity=0.626 Sum_probs=12.5
Q ss_pred EEEeeCCceeEecCcccc
Q psy10647 9 VILFDNTNLVYFPGQYLS 26 (92)
Q Consensus 9 ~IiFDn~~llYFPGQ~lS 26 (92)
+|.+++.++ .+||+.++
T Consensus 2 ~~~~~~~~~-V~PGd~l~ 18 (235)
T PRK04163 2 KIFVEDRKI-VVPGDLLA 18 (235)
T ss_pred eeeeeCCcE-ECCCCCcC
Confidence 466777654 79999983
No 41
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=21.00 E-value=57 Score=20.19 Aligned_cols=17 Identities=29% Similarity=0.167 Sum_probs=14.0
Q ss_pred eeEEEEecCCccccccc
Q psy10647 75 GRVLIELKDDTPALALL 91 (92)
Q Consensus 75 grvl~el~~~t~~lgl~ 91 (92)
=+|.|||++++-+-|-|
T Consensus 11 ~~V~VeLk~g~~~~G~L 27 (70)
T cd01721 11 HIVTVELKTGEVYRGKL 27 (70)
T ss_pred CEEEEEECCCcEEEEEE
Confidence 47899999998887765
No 42
>cd06221 sulfite_reductase_like Anaerobic sulfite reductase contains an FAD and NADPH binding module with structural similarity to ferredoxin reductase and sequence similarity to dihydroorotate dehydrogenases. Clostridium pasteurianum inducible dissimilatory type sulfite reductase is linked to ferredoxin and reduces NH2OH and SeO3 at a lesser rate than it's normal substate SO3(2-). Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to orotate coupled with the reduction of NAD+.
Probab=20.65 E-value=78 Score=22.83 Aligned_cols=25 Identities=16% Similarity=0.460 Sum_probs=18.1
Q ss_pred cceEEEEEeeCC---ceeEecCccccee
Q psy10647 4 KLIKFVILFDNT---NLVYFPGQYLSGR 28 (92)
Q Consensus 4 kl~kf~IiFDn~---~llYFPGQ~lSGR 28 (92)
....|.+.++.+ ..-|-|||++.=+
T Consensus 10 ~v~~~~l~~~~~~~~~~~~~pGQ~i~l~ 37 (253)
T cd06221 10 DIKTFTLRLEDDDEELFTFKPGQFVMLS 37 (253)
T ss_pred CceEEEEEeCCCccccCCcCCCCEEEEE
Confidence 345677788776 3779999997643
No 43
>PF13759 2OG-FeII_Oxy_5: Putative 2OG-Fe(II) oxygenase; PDB: 3BVC_B 2RG4_A.
Probab=20.01 E-value=2.4e+02 Score=17.65 Aligned_cols=56 Identities=21% Similarity=0.467 Sum_probs=31.3
Q ss_pred ecCcccceeEEEEecCCcceeeeeecccc--hhhh----------heeEEEEEeCCeeeEecCcccce
Q psy10647 20 FPGQYLSGRVLIELKDDTPALGFHRSKNN--MTRK----------LIKFVILFDNTNLVYFPGQYLSG 75 (92)
Q Consensus 20 FPGQ~lSGRVLle~qe~t~~lglh~~~~~--m~rk----------l~kf~ilfdnt~llyfpgq~lsg 75 (92)
=||-.+||-.-+.+.++...+-++....+ |... -..+.+--....|+.||+...-+
T Consensus 18 H~~s~~SgVyYv~~p~~~~~l~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~G~lvlFPs~l~H~ 85 (101)
T PF13759_consen 18 HPNSWLSGVYYVQVPEGSGPLRFHDPRGSFSFGAPFDNYDQNDLNSPYYIVEPEEGDLVLFPSWLWHG 85 (101)
T ss_dssp -TT-SEEEEEECE--TTS-SEEEE-TTCCCGTTS----TTTTCCC-SEEEE---TTEEEEEETTSEEE
T ss_pred CCCcCEEEEEEEECCCCCCceeeeCCCccceecccccccccCcccCceEEeCCCCCEEEEeCCCCEEe
Confidence 37788999999999998877777765332 2211 12445555678899999876543
Done!