Query psy17213
Match_columns 69
No_of_seqs 22 out of 24
Neff 2.0
Searched_HMMs 46136
Date Sat Aug 17 00:45:19 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17213.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17213hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd05715 Ig_P0-like Immunoglobu 63.7 23 0.00049 21.6 4.4 39 26-66 12-51 (116)
2 cd05886 Ig1_Nectin-1_like Firs 57.5 36 0.00078 21.2 4.6 36 28-66 1-36 (99)
3 smart00538 POP4 A domain found 48.9 17 0.00037 23.2 2.2 20 28-47 25-44 (92)
4 COG4460 Uncharacterized protei 43.7 23 0.0005 25.2 2.4 24 22-46 62-87 (130)
5 cd05879 Ig_P0 Immunoglobulin ( 42.7 62 0.0013 20.7 4.1 28 26-55 12-39 (116)
6 smart00350 MCM minichromosome 39.0 27 0.00058 27.3 2.3 26 12-37 106-131 (509)
7 PF09104 BRCA-2_OB3: BRCA2, ol 38.2 44 0.00095 23.6 3.1 24 40-63 68-91 (143)
8 cd03081 TRX_Fd_NuoE_FDH_gamma 36.4 27 0.00059 20.8 1.6 23 14-36 42-64 (80)
9 cd05753 Ig2_FcgammaR_like Seco 32.9 80 0.0017 18.3 3.2 30 25-60 12-41 (83)
10 cd05764 Ig_2 Subgroup of the i 31.3 68 0.0015 17.4 2.6 27 27-59 1-27 (74)
11 PF00047 ig: Immunoglobulin do 31.2 84 0.0018 16.3 4.9 30 27-61 1-30 (64)
12 PF07945 Toxin_16: Janus-atrac 30.1 23 0.00049 20.5 0.5 10 22-31 14-23 (36)
13 cd05846 Ig1_MRC-OX-2_like Firs 28.9 1.3E+02 0.0028 17.6 4.3 27 27-58 1-27 (97)
14 PF00677 Lum_binding: Lumazine 28.4 41 0.0009 20.6 1.5 15 19-33 69-83 (85)
15 PF08450 SGL: SMP-30/Gluconola 28.1 1E+02 0.0022 20.5 3.4 18 32-50 2-19 (246)
16 PF01257 2Fe-2S_thioredx: Thio 26.0 33 0.00072 22.7 0.8 22 14-35 106-127 (145)
17 cd03064 TRX_Fd_NuoE TRX-like [ 24.2 58 0.0013 18.9 1.5 21 15-35 43-63 (80)
18 PF04537 Herpes_UL55: Herpesvi 23.4 75 0.0016 23.2 2.3 24 11-39 113-136 (169)
19 cd05877 Ig_LP_like Immunoglobu 23.0 1.7E+02 0.0037 17.0 4.3 30 26-57 1-32 (106)
20 PF00947 Pico_P2A: Picornaviru 22.0 39 0.00084 23.6 0.6 9 21-29 84-92 (127)
21 cd03082 TRX_Fd_NuoE_W_FDH_beta 21.9 64 0.0014 19.2 1.4 22 14-35 34-55 (72)
22 PRK07539 NADH dehydrogenase su 21.6 79 0.0017 21.1 2.0 22 14-35 115-136 (154)
23 PF03376 Adeno_E3B: Adenovirus 21.4 39 0.00084 21.7 0.4 8 16-23 4-11 (67)
24 cd03083 TRX_Fd_NuoE_hoxF TRX-l 21.4 80 0.0017 18.7 1.8 22 14-35 42-63 (80)
25 TIGR02841 spore_YyaC putative 20.7 47 0.001 23.5 0.8 17 4-23 4-20 (140)
26 cd02980 TRX_Fd_family Thioredo 20.5 1E+02 0.0023 17.1 2.1 20 14-33 37-56 (77)
27 cd05880 Ig_EVA1 Immunoglobulin 20.1 2.3E+02 0.005 17.4 4.8 11 26-36 12-22 (115)
No 1
>cd05715 Ig_P0-like Immunoglobulin (Ig)-like domain of Protein zero (P0) and similar proteins. Ig_P0ex-like: domain similar to the immunoglobulin (Ig) domain of Protein zero (P0). P0 accounts for over 50% of the total protein in peripheral nervous system (PNS) myelin. P0 is a single-pass transmembrane glycoprotein with a highly basic intracellular domain and an extracellular Ig domain. The extracellular domain of P0 (P0-ED) is similar to the Ig variable domain, carrying one acceptor sequence for N-linked glycosylation. P0 plays a role in membrane adhesion in the spiral wraps of the myelin sheath. The intracellular domain is thought to mediate membrane apposition of the cytoplasmic faces and may, through electrostatic interactions, interact directly with lipid headgroups. It is thought that homophilic interactions of the P0 extracellular domain mediate membrane juxtaposition in the extracellular space of PNS myelin. This group also contains the Ig domain of Sodium channel subunit beta-2
Probab=63.74 E-value=23 Score=21.58 Aligned_cols=39 Identities=23% Similarity=0.404 Sum_probs=22.5
Q ss_pred CCcEeeeeeeEeeecCCeEEEEEeeEE-eeccCCceeeEEEE
Q psy17213 26 PGTSVTLEGIVWHETEGTSVTLEGIVW-HETEGKGISQSLFI 66 (69)
Q Consensus 26 pGTsV~LEGIVW~Etegg~l~vvnVtW-R~teg~~~~~~~~~ 66 (69)
.|.+|.|.|........... ..|.| +...+.+-.+.+|.
T Consensus 12 ~G~~vtL~C~~s~~~~~~~~--~~v~W~~~~~~~~~~~~v~~ 51 (116)
T cd05715 12 NGSDVRLKCTFSSSEPISDD--ISVTWSFQPEGSGDTESIFH 51 (116)
T ss_pred cCCCeEEEeEEeCCCCcCCc--eEEEEEEecCCCCCcEEEEE
Confidence 68889999977533221111 26889 45555554455544
No 2
>cd05886 Ig1_Nectin-1_like First immunoglobulin (Ig) domain of nectin-1 (also known as poliovirus receptor related protein 1, or as CD111) and similar proteins. Ig1_Nectin-1_like: domain similar to the first immunoglobulin (Ig) domain of nectin-1 (also known as poliovirus receptor related protein 1, or as CD111). Nectin-1 belongs to the nectin family comprised of four transmembrane glycoproteins (nectins-1 through -4). Nectins are synaptic cell adhesion molecules (CAMs) which facilitate adhesion and signaling at various intracellular junctions. Nectins form homophilic cis-dimers, followed by homophilic and heterophilic trans-dimers involved in cell-cell adhesion. In addition nectins heterophilically trans-interact with other CAMs such as nectin-like molecules (Necls), nectin-1 for example, has been shown to trans-interact with Necl-1. Nectins also interact with various other proteins, including the actin filament (F-actin)-binding protein, afadin. Mutation in the human nectin-1 gene is
Probab=57.47 E-value=36 Score=21.19 Aligned_cols=36 Identities=19% Similarity=0.329 Sum_probs=22.1
Q ss_pred cEeeeeeeEeeecCCeEEEEEeeEEeeccCCceeeEEEE
Q psy17213 28 TSVTLEGIVWHETEGTSVTLEGIVWHETEGKGISQSLFI 66 (69)
Q Consensus 28 TsV~LEGIVW~Etegg~l~vvnVtWR~teg~~~~~~~~~ 66 (69)
|.|.|.|.-+..-+..-+ ..|+|+.... |-.+++++
T Consensus 1 ~~v~L~C~f~~~~~~~~~--~~V~W~k~~~-~~~~~va~ 36 (99)
T cd05886 1 TDVVLHCSFINPLPPVKI--TQVTWQKLTN-GSKQNVAI 36 (99)
T ss_pred CcEEEEeEeecCCCCCCe--EEEEEEECCC-CCceEEEE
Confidence 467788877754444443 4899987653 33555544
No 3
>smart00538 POP4 A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins.
Probab=48.93 E-value=17 Score=23.19 Aligned_cols=20 Identities=40% Similarity=0.370 Sum_probs=16.3
Q ss_pred cEeeeeeeEeeecCCeEEEE
Q psy17213 28 TSVTLEGIVWHETEGTSVTL 47 (69)
Q Consensus 28 TsV~LEGIVW~Etegg~l~v 47 (69)
+.|-++|||..||..+.+++
T Consensus 25 s~vGi~GiVv~ET~nt~~I~ 44 (92)
T smart00538 25 SLVGIEGIVVDETRNTLKIE 44 (92)
T ss_pred CccCcEEEEEEeeeeEEEEE
Confidence 34568999999999998764
No 4
>COG4460 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.72 E-value=23 Score=25.21 Aligned_cols=24 Identities=33% Similarity=0.603 Sum_probs=19.2
Q ss_pred ccCCCCcEeeeeee--EeeecCCeEEE
Q psy17213 22 GPCEPGTSVTLEGI--VWHETEGTSVT 46 (69)
Q Consensus 22 GPCEpGTsV~LEGI--VW~Etegg~l~ 46 (69)
+.|-||=.+.+|+| +| ++++|.++
T Consensus 62 racrpGl~I~ie~i~l~a-~~~dga~l 87 (130)
T COG4460 62 RACRPGLAISIEDIRLGA-QTEDGAVL 87 (130)
T ss_pred cCCCCCeEEEEecccccc-cCCCceee
Confidence 46999999999987 67 67777654
No 5
>cd05879 Ig_P0 Immunoglobulin (Ig)-like domain of Protein zero (P0). Ig_P0ex: immunoglobulin (Ig) domain of Protein zero (P0). P0 accounts for over 50% of the total protein in peripheral nervous system (PNS) myelin. P0 is a single-pass transmembrane glycoprotein with a highly basic intracellular domain and an Ig domain. The extracellular domain of P0 (P0-ED) is similar to the Ig variable domain, carrying one acceptor sequence for N-linked glycosylation. P0 plays a role in membrane adhesion in the spiral wraps of the myelin sheath. The intracellular domain is thought to mediate membrane apposition of the cytoplasmic faces and may, through electrostatic interactions, interact directly with lipid headgroups. It is thought that homophilic interactions of the P0 extracellular domain mediate membrane juxtaposition in the extracellular space of PNS myelin.
Probab=42.70 E-value=62 Score=20.67 Aligned_cols=28 Identities=25% Similarity=0.404 Sum_probs=20.0
Q ss_pred CCcEeeeeeeEeeecCCeEEEEEeeEEeec
Q psy17213 26 PGTSVTLEGIVWHETEGTSVTLEGIVWHET 55 (69)
Q Consensus 26 pGTsV~LEGIVW~Etegg~l~vvnVtWR~t 55 (69)
.|++|.|.|..+...+.... .+|+|.-+
T Consensus 12 ~G~~v~L~C~f~~~~~~~~~--~~v~W~~~ 39 (116)
T cd05879 12 VGSDVTLSCSFWSSEWISDD--ISFTWHYQ 39 (116)
T ss_pred cCCcEEEEEEEecCCCCCCc--EEEEEEEc
Confidence 58999999999865544333 28999443
No 6
>smart00350 MCM minichromosome maintenance proteins.
Probab=38.97 E-value=27 Score=27.33 Aligned_cols=26 Identities=27% Similarity=0.493 Sum_probs=22.0
Q ss_pred eeeccCCCccccCCCCcEeeeeeeEe
Q psy17213 12 VGTITEPECLGPCEPGTSVTLEGIVW 37 (69)
Q Consensus 12 ~~t~TEp~clGPCEpGTsV~LEGIVW 37 (69)
+-.+=|.|..+.|.||..|.+-||+=
T Consensus 106 i~v~l~~dLvd~~~PGD~V~i~Gi~~ 131 (509)
T smart00350 106 VDVILDGDLVDKAKPGDRVEVTGIYR 131 (509)
T ss_pred EEEEEcccccCcccCCCEEEEEEEEE
Confidence 44455899999999999999999984
No 7
>PF09104 BRCA-2_OB3: BRCA2, oligonucleotide/oligosaccharide-binding, domain 3; InterPro: IPR015188 This domain assumes an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB3 has a pronounced groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for strong ssDNA binding []. ; PDB: 1IYJ_D 1MIU_A.
Probab=38.15 E-value=44 Score=23.57 Aligned_cols=24 Identities=17% Similarity=0.450 Sum_probs=15.9
Q ss_pred cCCeEEEEEeeEEeeccCCceeeE
Q psy17213 40 TEGTSVTLEGIVWHETEGKGISQS 63 (69)
Q Consensus 40 tegg~l~vvnVtWR~teg~~~~~~ 63 (69)
.++..+-..|+.||...-.+|.|.
T Consensus 68 k~~~liA~SNLqwR~~s~s~iP~~ 91 (143)
T PF09104_consen 68 KPGSLIAASNLQWRPESTSGIPTL 91 (143)
T ss_dssp -TT-EEEEEEEEE-S-TTSSS-EE
T ss_pred CcceEEEEeeeEeecccccCCCee
Confidence 578888889999998887888664
No 8
>cd03081 TRX_Fd_NuoE_FDH_gamma TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, NAD-dependent formate dehydrogenase (FDH) gamma subunit; composed of proteins similar to the gamma subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD+ to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH gamma subunit is closely related to NuoE, which is part of a multisubunit complex (Nuo) catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE. Similarly, the FDH gamma subunit is hypothesized to be involved in an electron transport chain involving other FDH subunits, upon the oxidat
Probab=36.44 E-value=27 Score=20.79 Aligned_cols=23 Identities=30% Similarity=0.613 Sum_probs=18.2
Q ss_pred eccCCCccccCCCCcEeeeeeeE
Q psy17213 14 TITEPECLGPCEPGTSVTLEGIV 36 (69)
Q Consensus 14 t~TEp~clGPCEpGTsV~LEGIV 36 (69)
++.+-.|||.|.-|=.+.+++++
T Consensus 42 ~l~~~~ClG~C~~gP~~~v~~~~ 64 (80)
T cd03081 42 TLEPVYCLGLCACSPAAMIDGEV 64 (80)
T ss_pred EEEEeeecCccCCCCEEEECCEE
Confidence 45577899999999888877763
No 9
>cd05753 Ig2_FcgammaR_like Second immunoglobulin (Ig)-like domain of Fcgamma-receptors (FcgammaRs) and similar proteins. Ig2_FcgammaR_like: domain similar to the second immunoglobulin (Ig)-like domain of Fcgamma-receptors (FcgammaRs). Interactions between IgG and FcgammaR are important to the initiation of cellular and humoral response. IgG binding to FcgammaR leads to a cascade of signals and ultimately to functions such as antibody-dependent-cellular-cytotoxicity (ADCC), endocytosis, phagocytosis, release of inflammatory mediators, etc. FcgammaR has two Ig-like domains. This group also contains FcepsilonRI, which binds IgE with high affinity.
Probab=32.91 E-value=80 Score=18.33 Aligned_cols=30 Identities=17% Similarity=0.287 Sum_probs=19.8
Q ss_pred CCCcEeeeeeeEeeecCCeEEEEEeeEEeeccCCce
Q psy17213 25 EPGTSVTLEGIVWHETEGTSVTLEGIVWHETEGKGI 60 (69)
Q Consensus 25 EpGTsV~LEGIVW~Etegg~l~vvnVtWR~teg~~~ 60 (69)
..|.+|.|.|-++...+. .++.|.+ .|+.+
T Consensus 12 ~~G~~vtL~C~~~~~~~~-----~~~~w~k-~g~~~ 41 (83)
T cd05753 12 FEGEPLVLRCHGWKNKPV-----YKVTYYR-DGKAK 41 (83)
T ss_pred cCCCCEEEEeeCCCCCcc-----eEEEEEE-CCeEc
Confidence 468999999998743322 2788885 45544
No 10
>cd05764 Ig_2 Subgroup of the immunoglobulin (Ig) superfamily. Ig_2: subgroup of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of the Ig superfamily are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond.
Probab=31.30 E-value=68 Score=17.38 Aligned_cols=27 Identities=26% Similarity=0.383 Sum_probs=14.8
Q ss_pred CcEeeeeeeEeeecCCeEEEEEeeEEeeccCCc
Q psy17213 27 GTSVTLEGIVWHETEGTSVTLEGIVWHETEGKG 59 (69)
Q Consensus 27 GTsV~LEGIVW~Etegg~l~vvnVtWR~teg~~ 59 (69)
|.++.|+|.+ .-.|.. .|+|....+.-
T Consensus 1 G~~~~l~C~~-~g~P~p-----~v~W~~~~~~~ 27 (74)
T cd05764 1 GQRATLRCKA-RGDPEP-----AIHWISPDGKL 27 (74)
T ss_pred CCeEEEEEEc-cCcCCC-----EEEEEeCCCEE
Confidence 5677787765 222322 56776544433
No 11
>PF00047 ig: Immunoglobulin domain The Prosite family only concerns antibodies and MHCs.; InterPro: IPR013151 Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions. The Pfam alignments do not include the first and last strand of the immunoglobulin-like domain.; PDB: 1B6U_A 3O4O_C 3VH8_H 1BIH_A 2C9A_A 2V5Y_A 1BQH_K 2ATP_A 3B9K_A 1NEZ_H ....
Probab=31.17 E-value=84 Score=16.29 Aligned_cols=30 Identities=23% Similarity=0.287 Sum_probs=19.5
Q ss_pred CcEeeeeeeEeeecCCeEEEEEeeEEeeccCCcee
Q psy17213 27 GTSVTLEGIVWHETEGTSVTLEGIVWHETEGKGIS 61 (69)
Q Consensus 27 GTsV~LEGIVW~Etegg~l~vvnVtWR~teg~~~~ 61 (69)
|.+|+|.|.+ ++.+.. .+++|......-+.
T Consensus 1 G~~v~L~C~~-~~~~~~----~~~~W~~~~~~~~~ 30 (64)
T PF00047_consen 1 GSSVTLTCSV-SSGPPP----TTVTWSKNGQSLPE 30 (64)
T ss_dssp TSEEEEEEEE-EESSST----SEEEEEETTTTTSE
T ss_pred CCeEEEEeec-CCCCCC----cEEEEEECCccccC
Confidence 7789999998 444433 37888766554443
No 12
>PF07945 Toxin_16: Janus-atracotoxin; InterPro: IPR012499 This family includes three peptides secreted by the spider Hadronyche versuta (Blue mountains funnel-web spider) (P82226 from SWISSPROT, P82227 from SWISSPROT, P82228 from SWISSPROT). These are insect-selective, excitatory neurotoxins that may function by antagonising muscle acetylcholine receptors, or acetylcholine receptor subtypes present in other invertebrate neurons []. Janus atracotoxin-Hv1c (J-ACTX-Hv1c, P82228 from SWISSPROT) is organised into a disulphide-rich globular core (residues 3-19) and a beta-hairpin (residues 20-34). There are 4 disulphide bridges, one of which is a vicinal disulphide bridge; this is known to be unimportant in the maintenance of structure but critical for insecticidal activity []. ; GO: 0009405 pathogenesis, 0005576 extracellular region; PDB: 1DL0_A.
Probab=30.08 E-value=23 Score=20.45 Aligned_cols=10 Identities=60% Similarity=1.099 Sum_probs=4.9
Q ss_pred ccCCCCcEee
Q psy17213 22 GPCEPGTSVT 31 (69)
Q Consensus 22 GPCEpGTsV~ 31 (69)
-||-||||-.
T Consensus 14 cpccpgtsc~ 23 (36)
T PF07945_consen 14 CPCCPGTSCQ 23 (36)
T ss_dssp ----TTEEEE
T ss_pred cCCCCCcccc
Confidence 4899999863
No 13
>cd05846 Ig1_MRC-OX-2_like First immunoglobulin (Ig) domain of rat MRC OX-2 antigen (also known as CD200) and similar proteins. Ig1_ MRC-OX-2_like: domain similar to the first immunoglobulin (Ig) domain of rat MRC OX-2 antigen (also known as CD200). MRC OX-2 is a membrane glycoprotein expressed in a variety of lymphoid and non-lymphoid cells in rats. It has a similar broad distribution pattern in humans. MRC OX-2 may regulate myeloid cell activity. The protein has an extracellular portion containing two Ig-like domains, a transmembrane portion, and a cytoplasmic portion.
Probab=28.92 E-value=1.3e+02 Score=17.64 Aligned_cols=27 Identities=22% Similarity=0.408 Sum_probs=17.5
Q ss_pred CcEeeeeeeEeeecCCeEEEEEeeEEeeccCC
Q psy17213 27 GTSVTLEGIVWHETEGTSVTLEGIVWHETEGK 58 (69)
Q Consensus 27 GTsV~LEGIVW~Etegg~l~vvnVtWR~teg~ 58 (69)
|++|.|.|....+. . +..|.|.+..++
T Consensus 1 G~~vtL~C~~~~~~--~---~~~v~W~k~~~~ 27 (97)
T cd05846 1 GGNVTLSCNLTLPE--E---VLQVTWQKIQGS 27 (97)
T ss_pred CCcEEEEEEeCCCC--e---eEEEEEEEcCCC
Confidence 67899999755332 1 237899876544
No 14
>PF00677 Lum_binding: Lumazine binding domain; InterPro: IPR001783 The following proteins have been shown [, ] to be structurally and evolutionary related: Riboflavin synthase alpha chain (2.5.1.9 from EC) (RS-alpha) (gene ribC in Escherichia coli, ribB in Bacillus subtilis and Photobacterium leiognathi, RIB5 in yeast. This enzyme synthesises riboflavin from two moles of 6,7- dimethyl-8-(1'-D-ribityl)lumazine (Lum), a pteridine-derivative. Photobacterium phosphoreum lumazine protein (LumP) (gene luxL). LumP is a protein that modulates the colour of the bioluminescence emission of bacterial luciferase. In the presence of LumP, light emission is shifted to higher energy values (shorter wavelength). LumP binds non-covalently to 6,7-dimethyl-8-(1'-D-ribityl)lumazine. Vibrio fischeri yellow fluorescent protein (YFP) (gene luxY). Like LumP, YFP modulates light emission but towards a longer wavelength. YFP binds non-covalently to FMN. These proteins seem to have evolved from the duplication of a domain of about 100 residues. In its C-terminal section, this domain contains a conserved motif [KR]-V-N-[LI]-E which has been proposed to be the binding site for lumazine (Lum) and some of its derivatives. RS-alpha which binds two molecules of Lum has two perfect copies of this motif, while LumP which binds one molecule of Lum, has a Glu instead of Lys/Arg in the first position of the second copy of the motif. Similarly, YFP, which binds to one molecule of FMN, also seems to have a potentially dysfunctional binding site by substitution of Gly for Glu in the last position of the first copy of the motif.; GO: 0004746 riboflavin synthase activity, 0009231 riboflavin biosynthetic process; PDB: 3DDY_A 1KZL_A 3A3G_B 3A35_B 3A3B_B 1I8D_C 1PKV_B 1HZE_B 1I18_B.
Probab=28.42 E-value=41 Score=20.55 Aligned_cols=15 Identities=40% Similarity=0.554 Sum_probs=10.7
Q ss_pred CccccCCCCcEeeee
Q psy17213 19 ECLGPCEPGTSVTLE 33 (69)
Q Consensus 19 ~clGPCEpGTsV~LE 33 (69)
--++--.+|+.||||
T Consensus 69 T~l~~~~~G~~VNlE 83 (85)
T PF00677_consen 69 TTLGNLKVGDRVNLE 83 (85)
T ss_dssp SSGGG--TTSEEEEE
T ss_pred chhccCCCCCEEEEe
Confidence 456888999999998
No 15
>PF08450 SGL: SMP-30/Gluconolaconase/LRE-like region; InterPro: IPR013658 This family describes a region that is found in proteins expressed by a variety of eukaryotic and prokaryotic species. These proteins include various enzymes, such as senescence marker protein 30 (SMP-30, Q15493 from SWISSPROT), gluconolactonase (Q01578 from SWISSPROT) and luciferin-regenerating enzyme (LRE, Q86DU5 from SWISSPROT). SMP-30 is known to hydrolyse diisopropyl phosphorofluoridate in the liver, and has been noted as having sequence similarity, in the region described in this family, with PON1 (P52430 from SWISSPROT) and LRE. ; PDB: 2GHS_A 2DG0_L 2DG1_D 2DSO_D 3E5Z_A 2IAT_A 2IAV_A 2GVV_A 3HLI_A 2GVU_A ....
Probab=28.09 E-value=1e+02 Score=20.49 Aligned_cols=18 Identities=33% Similarity=0.466 Sum_probs=12.6
Q ss_pred eeeeEeeecCCeEEEEEee
Q psy17213 32 LEGIVWHETEGTSVTLEGI 50 (69)
Q Consensus 32 LEGIVW~Etegg~l~vvnV 50 (69)
.||++|++..+..+. +++
T Consensus 2 ~Egp~~d~~~g~l~~-~D~ 19 (246)
T PF08450_consen 2 GEGPVWDPRDGRLYW-VDI 19 (246)
T ss_dssp EEEEEEETTTTEEEE-EET
T ss_pred CcceEEECCCCEEEE-EEc
Confidence 499999777776654 444
No 16
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=26.01 E-value=33 Score=22.66 Aligned_cols=22 Identities=36% Similarity=0.838 Sum_probs=17.6
Q ss_pred eccCCCccccCCCCcEeeeeee
Q psy17213 14 TITEPECLGPCEPGTSVTLEGI 35 (69)
Q Consensus 14 t~TEp~clGPCEpGTsV~LEGI 35 (69)
++.+-.|+|.|.-|=.|.+.|.
T Consensus 106 ~l~~~~ClG~C~~aP~v~V~~~ 127 (145)
T PF01257_consen 106 TLEETGCLGACDQAPVVMVDGE 127 (145)
T ss_dssp EEEEESSSSSGGGSSEEEECCC
T ss_pred EEEECCCccccCCCCEEEECCE
Confidence 3456689999999988888775
No 17
>cd03064 TRX_Fd_NuoE TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes. It is a multisubunit complex with at least 14 core subunits. It catalyzes the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane, providing the proton motive force required for energy-consuming processes. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE core subunit, also called the 24 kD subunit of Complex 1. This subfamily also include formate dehydrogenases, NiFe hydrogenases and NAD-reducing hydrogenases, that contain a NuoE domain. A subset of these proteins contain both NuoE and NuoF in a single chain. NuoF, also called the 51 kD subunit of Complex 1, contains one [4Fe-4S] clu
Probab=24.15 E-value=58 Score=18.89 Aligned_cols=21 Identities=29% Similarity=0.683 Sum_probs=16.3
Q ss_pred ccCCCccccCCCCcEeeeeee
Q psy17213 15 ITEPECLGPCEPGTSVTLEGI 35 (69)
Q Consensus 15 ~TEp~clGPCEpGTsV~LEGI 35 (69)
+.+-.|+|.|..|=.|.+.|+
T Consensus 43 v~~t~ClG~C~~gP~v~v~g~ 63 (80)
T cd03064 43 LEEVECLGACDLAPVMMINDD 63 (80)
T ss_pred EEEecCcCcCCCCCEEEECCE
Confidence 456789999998888777653
No 18
>PF04537 Herpes_UL55: Herpesvirus UL55 protein; InterPro: IPR007622 In infected cells, UL55 is associated with the nuclear matrix, and found adjacent to compartments containing the capsid protein ICP35. UL55 was not detected in assembled virions. It is thought that UL55 may play a role in virion assembly or maturation [].; GO: 0019067 viral assembly, maturation, egress, and release
Probab=23.39 E-value=75 Score=23.18 Aligned_cols=24 Identities=29% Similarity=0.436 Sum_probs=16.2
Q ss_pred ceeeccCCCccccCCCCcEeeeeeeEeee
Q psy17213 11 SVGTITEPECLGPCEPGTSVTLEGIVWHE 39 (69)
Q Consensus 11 s~~t~TEp~clGPCEpGTsV~LEGIVW~E 39 (69)
|.||+..-.--| -.++++||+.|+
T Consensus 113 SaaTi~d~~~~~-----~~~~I~Gl~yHC 136 (169)
T PF04537_consen 113 SAATIKDSPDDG-----YEYTINGLCYHC 136 (169)
T ss_pred ccceeeccCCCC-----CceEEEEEEEEe
Confidence 456666533323 389999999997
No 19
>cd05877 Ig_LP_like Immunoglobulin (Ig)-like domain of human cartilage link protein (LP). Ig_LP_like: immunoglobulin (Ig)-like domain similar to that that found in human cartilage link protein (LP). In cartilage, chondroitin-keratan sulfate proteoglycan (CSPG), aggrecan, forms cartilage link protein stabilized aggregates with hyaluronan (HA). These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.
Probab=23.03 E-value=1.7e+02 Score=17.04 Aligned_cols=30 Identities=23% Similarity=0.269 Sum_probs=16.3
Q ss_pred CCcEeeeeeeEeeec--CCeEEEEEeeEEeeccC
Q psy17213 26 PGTSVTLEGIVWHET--EGTSVTLEGIVWHETEG 57 (69)
Q Consensus 26 pGTsV~LEGIVW~Et--egg~l~vvnVtWR~teg 57 (69)
.|..|.|.|-.=... .+.. ...|.|.+...
T Consensus 1 ~G~~vtL~C~~~~~~~~~~~~--~~~v~W~k~~~ 32 (106)
T cd05877 1 RGGNVTLPCRYHYEPELSAPR--KIRVKWTKLES 32 (106)
T ss_pred CCCcEEEEeEeECCCcCCCCc--cceEEEEEecC
Confidence 477788888543221 1121 13678877653
No 20
>PF00947 Pico_P2A: Picornavirus core protein 2A; InterPro: IPR000081 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This domain defines cysteine peptidases belong to MEROPS peptidase family C3 (picornain, clan PA(C)), subfamilies 3CA and 3CB. The protein fold of this peptidase domain for members of this family resembles that of the serine peptidase, chymotrypsin [], the type example for clan PA. Picornaviral proteins are expressed as a single polyprotein which is cleaved by the viral 3C cysteine protease []. The poliovirus polyprotein is selectively cleaved between the Gln-|-Gly bond. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly. ; GO: 0008233 peptidase activity, 0006508 proteolysis, 0016032 viral reproduction; PDB: 2HRV_B 1Z8R_A.
Probab=22.04 E-value=39 Score=23.59 Aligned_cols=9 Identities=56% Similarity=1.103 Sum_probs=5.8
Q ss_pred cccCCCCcE
Q psy17213 21 LGPCEPGTS 29 (69)
Q Consensus 21 lGPCEpGTs 29 (69)
.||||||.-
T Consensus 84 ~Gp~~PGdC 92 (127)
T PF00947_consen 84 EGPAEPGDC 92 (127)
T ss_dssp E-SSSTT-T
T ss_pred cccCCCCCC
Confidence 599999973
No 21
>cd03082 TRX_Fd_NuoE_W_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E family, Tungsten-containing formate dehydrogenase (W-FDH) beta subunit; composed of proteins similar to the W-FDH beta subunit of Methylobacterium extorquens. W-FDH is a heterodimeric NAD-dependent enzyme catalyzing the conversion of formate to carbon dioxide. The beta subunit is a fusion protein containing an N-terminal NuoE domain and a C-terminal NuoF domain. NuoE and NuoF are components of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster in NuoE and the [4Fe-4S] cluster in NuoF. In addition, NuoF is also the NADH- and FMN-binding subunit. Similarly, the beta subunit of W-FDH is most likely involved in the electron transport chain during the NAD-dependen
Probab=21.88 E-value=64 Score=19.20 Aligned_cols=22 Identities=18% Similarity=0.522 Sum_probs=16.9
Q ss_pred eccCCCccccCCCCcEeeeeee
Q psy17213 14 TITEPECLGPCEPGTSVTLEGI 35 (69)
Q Consensus 14 t~TEp~clGPCEpGTsV~LEGI 35 (69)
++..-.|+|.|..|=.+.+.+-
T Consensus 34 ~l~~~~ClG~C~~gP~v~V~~~ 55 (72)
T cd03082 34 RVVRAPCVGRCERAPAALVGQR 55 (72)
T ss_pred EEEecCcCCccCCCCeEEECCE
Confidence 4557789999999887776654
No 22
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=21.58 E-value=79 Score=21.11 Aligned_cols=22 Identities=36% Similarity=0.720 Sum_probs=17.6
Q ss_pred eccCCCccccCCCCcEeeeeee
Q psy17213 14 TITEPECLGPCEPGTSVTLEGI 35 (69)
Q Consensus 14 t~TEp~clGPCEpGTsV~LEGI 35 (69)
++.+-.|+|.|.-|=.|.+.+.
T Consensus 115 ~l~~~~ClG~C~~gPvv~V~~~ 136 (154)
T PRK07539 115 TLLEVECLGACDNAPVVMINDD 136 (154)
T ss_pred EEEEccccCccCCCCEEEECCE
Confidence 3456789999999988888764
No 23
>PF03376 Adeno_E3B: Adenovirus E3B protein; InterPro: IPR005041 Adenoviruses are medium-sized, non-enveloped viruses containing double-stranded DNA. They can cause a variety of diseases including pneumonia, cystitis, conjunctivitis and diarrhoea, all of which can be fatal to patients who are immunocompromised []. These viruses have many mechanisms to evade the host immune response, including several proteins which are expressed as part of the early transcription unit 3 (E3) []. One of the regions of E3, known as the E3B region, encodes three proteins known as 10.4K, 14.5K and 14.7K. Two of these proteins, 10.4K and 14.5K, form the RID complex (receptor internalisation and degradation) which protects the infected cell from host-induced lysis by clearing the the TNF and Fas receptors from the cell surface []. Other receptors, such as the epidermal growth factor receptor, are also known to be cleared by RID []. This entry represents the E3B region 10.4K protein, also known as the RID alpha subunit.; GO: 0016020 membrane
Probab=21.37 E-value=39 Score=21.73 Aligned_cols=8 Identities=63% Similarity=1.418 Sum_probs=6.6
Q ss_pred cCCCcccc
Q psy17213 16 TEPECLGP 23 (69)
Q Consensus 16 TEp~clGP 23 (69)
-||||++|
T Consensus 4 l~pdCl~p 11 (67)
T PF03376_consen 4 LEPDCLPP 11 (67)
T ss_pred CCCcccch
Confidence 48999987
No 24
>cd03083 TRX_Fd_NuoE_hoxF TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, hoxF; composed of proteins similar to the NAD-reducing hydrogenase (hoxS) alpha subunit of Alcaligenes eutrophus H16. HoxS is a cytoplasmic hydrogenase catalyzing the oxidation of molecular hydrogen accompanied by the reduction of NAD. It is composed of four structural subunits encoded by the genes hoxF, hoxU, hoxY and hoxH. The hoxF protein (or alpha subunit) is a fusion protein containing an N-terminal NuoE-like domain and a C-terminal NuoF domain. NuoE and NuoF are components of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster in NuoE and the [4Fe-4S] cluster in NuoF. In addition, NuoF is also the NADH- and FMN-binding subunit. HoxF may be involved
Probab=21.37 E-value=80 Score=18.75 Aligned_cols=22 Identities=18% Similarity=0.522 Sum_probs=17.0
Q ss_pred eccCCCccccCCCCcEeeeeee
Q psy17213 14 TITEPECLGPCEPGTSVTLEGI 35 (69)
Q Consensus 14 t~TEp~clGPCEpGTsV~LEGI 35 (69)
++.+-.|+|.|.-|=.+.+.++
T Consensus 42 ~l~~~gClG~C~~~P~v~V~~~ 63 (80)
T cd03083 42 GLFFTSCTGLCDQGPALLINNR 63 (80)
T ss_pred EEEEeceecCcCCCCeEEECCE
Confidence 3456689999999988888654
No 25
>TIGR02841 spore_YyaC putative sporulation protein YyaC. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, also called YyaC, is a member of that panel and is otherwise uncharacterized. The second round of PSI-BLAST shows many similarities to the germination protease GPR, which is found in exactly the same set of organisms and has a known role in the sporulation/germination process.
Probab=20.66 E-value=47 Score=23.53 Aligned_cols=17 Identities=47% Similarity=0.857 Sum_probs=10.4
Q ss_pred eeeeeecceeeccCCCcccc
Q psy17213 4 ADVCIGTSVGTITEPECLGP 23 (69)
Q Consensus 4 ~~~~v~ts~~t~TEp~clGP 23 (69)
.=+|+||--.| -|||||
T Consensus 4 v~lCIGTDRst---GDsLGP 20 (140)
T TIGR02841 4 VLLCIGTDRST---GDALGP 20 (140)
T ss_pred EEEEECCCCCc---ccccch
Confidence 44788884322 367777
No 26
>cd02980 TRX_Fd_family Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:ubiquinone oxidoreductase (NuoE). TRX-like Fds are soluble low-potential electron carriers containing a single [2Fe-2S] cluster. The exact role of TRX-like Fd is still unclear. It has been suggested that it may be involved in nitrogen fixation. Its homologous domains in large redox enzymes (such as Nuo and hydrogenases) function as electron carriers.
Probab=20.48 E-value=1e+02 Score=17.10 Aligned_cols=20 Identities=30% Similarity=0.604 Sum_probs=16.0
Q ss_pred eccCCCccccCCCCcEeeee
Q psy17213 14 TITEPECLGPCEPGTSVTLE 33 (69)
Q Consensus 14 t~TEp~clGPCEpGTsV~LE 33 (69)
.+.+-.|+|.|.-|=.|.+.
T Consensus 37 ~v~~~~Clg~C~~~P~v~i~ 56 (77)
T cd02980 37 TVERVGCLGACGLAPVVVVY 56 (77)
T ss_pred EEEEcCCcCcccCCCEEEEe
Confidence 34577899999998887776
No 27
>cd05880 Ig_EVA1 Immunoglobulin (Ig)-like domain of epithelial V-like antigen 1 (EVA). Ig_EVA: immunoglobulin (Ig) domain of epithelial V-like antigen 1 (EVA). EVA is also known as myelin protein zero-like 2. EVA is an adhesion molecule, which may play a role in structural organization of the thymus and early lymphocyte development.
Probab=20.06 E-value=2.3e+02 Score=17.44 Aligned_cols=11 Identities=36% Similarity=0.444 Sum_probs=8.1
Q ss_pred CCcEeeeeeeE
Q psy17213 26 PGTSVTLEGIV 36 (69)
Q Consensus 26 pGTsV~LEGIV 36 (69)
.|.+|.|.|..
T Consensus 12 ~G~~v~L~C~~ 22 (115)
T cd05880 12 NGTDVRLKCTF 22 (115)
T ss_pred cCCCEEEEEEE
Confidence 57788888764
Done!