Query 041283
Match_columns 172
No_of_seqs 137 out of 347
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 05:38:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041283.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041283hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04398 DUF538: Protein of un 100.0 2.8E-43 6E-48 268.7 7.4 108 52-163 1-110 (110)
2 PF05963 Cytomega_US3: Cytomeg 54.8 26 0.00056 29.7 4.7 96 60-168 15-112 (187)
3 cd04089 eRF3_II eRF3_II: domai 52.4 57 0.0012 22.7 5.6 33 104-138 14-49 (82)
4 cd03695 CysN_NodQ_II CysN_NodQ 47.4 63 0.0014 22.7 5.2 31 106-138 17-50 (81)
5 cd02410 archeal_CPSF_KH The ar 46.6 24 0.00051 28.7 3.2 37 52-94 53-91 (145)
6 cd03694 GTPBP_II Domain II of 43.3 66 0.0014 22.7 4.8 33 104-138 15-54 (87)
7 cd03693 EF1_alpha_II EF1_alpha 42.9 90 0.0019 22.2 5.5 33 104-138 19-54 (91)
8 cd03698 eRF3_II_like eRF3_II_l 41.1 82 0.0018 21.9 5.0 34 103-138 14-50 (83)
9 PF08710 nsp9: nsp9 replicase; 37.0 87 0.0019 24.5 4.9 36 69-104 49-86 (111)
10 smart00540 LEM in nuclear memb 33.7 30 0.00066 22.6 1.6 17 51-67 9-25 (44)
11 cd03697 EFTU_II EFTU_II: Elong 32.0 1.6E+02 0.0035 20.6 5.3 33 104-138 15-52 (87)
12 PF10262 Rdx: Rdx family; Int 28.1 78 0.0017 22.0 3.1 20 71-90 32-52 (76)
13 PF05345 He_PIG: Putative Ig d 27.3 45 0.00099 21.7 1.7 23 60-90 10-32 (49)
14 KOG2455 Delta-1-pyrroline-5-ca 26.8 36 0.00078 32.8 1.5 15 53-67 242-256 (561)
15 cd07397 MPP_DevT Myxococcus xa 25.5 9.3 0.0002 32.9 -2.4 50 5-67 111-161 (238)
16 KOG2960 Protein involved in th 22.7 54 0.0012 29.3 1.7 42 22-63 100-143 (328)
17 PRK12442 translation initiatio 22.7 2.2E+02 0.0048 21.3 4.7 37 105-148 34-70 (87)
18 PF07311 Dodecin: Dodecin; In 22.0 1.7E+02 0.0037 20.7 3.8 31 128-158 35-65 (66)
19 TIGR00547 lolA periplasmic cha 21.5 2.4E+02 0.0053 23.3 5.3 48 124-171 146-201 (204)
20 PF06462 Hyd_WA: Propeller; I 21.1 73 0.0016 19.0 1.6 18 141-158 8-25 (32)
21 PF09822 ABC_transp_aux: ABC-t 20.5 35 0.00076 28.7 0.1 36 1-36 4-39 (271)
22 PF01820 Dala_Dala_lig_N: D-al 20.3 1.1E+02 0.0023 23.0 2.7 29 35-63 83-113 (117)
No 1
>PF04398 DUF538: Protein of unknown function, DUF538; InterPro: IPR007493 This family consists of several plant proteins of unknown function.; PDB: 1YDU_A.
Probab=100.00 E-value=2.8e-43 Score=268.68 Aligned_cols=108 Identities=34% Similarity=0.664 Sum_probs=81.5
Q ss_pred CHHHHHHhCCCCCCCCCCCceEEEEeCCCcEEEEEeCCceEEEEcCCeEEEEeeEEEEEEccCeeecccccEEEEE-EEE
Q 041283 52 ALPDLLRECNIPPGLFPRNITCYDFDESRSKLIVYLPSPCAVSFKDSSVVRYATRVKGTLSRGKLSGVEGMKIKVL-VWV 130 (172)
Q Consensus 52 t~~elL~e~gLP~GLLP~~V~~Y~l~~~tG~f~V~L~~~C~~~f~~~~~v~Y~t~VtG~l~~GkI~~L~GVk~K~L-lWv 130 (172)
||||||++||||+||||+++++|+||++||+|||+|+++|+|+|++ |.|+|+++|||+|++|+|++|+|||+|+| +|+
T Consensus 1 tayelL~~~glP~GLLP~~v~~y~l~~~tG~f~v~l~~~C~~~~~~-~~v~Y~~~ItG~i~~g~i~~L~GVk~k~l~~W~ 79 (110)
T PF04398_consen 1 TAYELLEEYGLPRGLLPLGVTEYGLNRDTGFFWVKLKSPCEFRFEG-YLVSYDSEITGYIEKGKIKNLTGVKVKELFLWV 79 (110)
T ss_dssp --HHHHHHHS-TT-TTTSSS-EEEE-TTT-SEEEE-SS-EEEESTT-SEEEE-SEEEEEE-SS-EEEEES-EEE-SSSEE
T ss_pred CHHHhHHHcCCCCCcCCCCceEEEEecCCcEEEEEecCCEEEEEEE-EEEEEcCeEEEEECCCcCccccCEEEEEEEEEe
Confidence 6899999999999999999999999999999999999999999987 89999999999999999999999999999 999
Q ss_pred EeeEEEEecCCCCeEEEEeee-cccccccccccC
Q 041283 131 KVTGVAVESYKSDKLWFTAGV-KVSRPKDAYEML 163 (172)
Q Consensus 131 ~VteI~vd~p~~~kI~F~~Gi-~ksfp~~aFe~~ 163 (172)
+|++|.+ ++++|+|++|. +++||+++|+.+
T Consensus 80 ~v~~i~~---~~~~i~F~~g~~s~sfp~~~F~~s 110 (110)
T PF04398_consen 80 PVTEISV---DGDKIYFKVGGISKSFPVSAFEES 110 (110)
T ss_dssp S---BEE----SSSEE-TTSSSS----TTTTSS-
T ss_pred eEEEEEE---cCCEEEEEEeeEeccCCHHHhccC
Confidence 9999999 89999999876 899999999864
No 2
>PF05963 Cytomega_US3: Cytomegalovirus US3 protein; InterPro: IPR009237 US3 of human cytomegalovirus is an endoplasmic reticulum resident transmembrane glycoprotein that binds to major histocompatibility complex class I molecules and prevents their departure. The endoplasmic reticulum retention signal of the US3 protein is contained in the luminal domain of the protein [].; PDB: 1IM3_L.
Probab=54.75 E-value=26 Score=29.68 Aligned_cols=96 Identities=16% Similarity=0.235 Sum_probs=36.6
Q ss_pred CCCCCCCC-C-CCceEEEEeCCCcEEEEEeCCceEEEEcCCeEEEEeeEEEEEEccCeeecccccEEEEEEEEEeeEEEE
Q 041283 60 CNIPPGLF-P-RNITCYDFDESRSKLIVYLPSPCAVSFKDSSVVRYATRVKGTLSRGKLSGVEGMKIKVLVWVKVTGVAV 137 (172)
Q Consensus 60 ~gLP~GLL-P-~~V~~Y~l~~~tG~f~V~L~~~C~~~f~~~~~v~Y~t~VtG~l~~GkI~~L~GVk~K~LlWv~VteI~v 137 (172)
.+||-|.= | ..+++ .+-..--.|+|. ...|. +++| ++...-+|+|.+.+--..+.-++.-|- +..+.+
T Consensus 15 l~~~~~~p~p~~~~~~-~~~a~~~~ftV~-~n~C~--ie~G-klf~~G~I~GN~t~~~fv~~~v~~~~~-----~enL~~ 84 (187)
T PF05963_consen 15 LGLTDGFPRPVPEITE-QLTARRAHFTVE-QNRCY--IEGG-KLFMTGRISGNFTKSHFVQVGVVGDSY-----RENLQV 84 (187)
T ss_dssp -------------------------EEEE-EEEEE--ESSS-EEEEEEEEEE--S-EEEEESSS-E---------EE---
T ss_pred cccccCCCCchHHHHh-hhccCCceEEEE-eeeEE--EECC-EEEEEEEEeeeeeeEEEEEEeeeeccc-----hhheEE
Confidence 56666653 5 56666 554322367774 45788 5655 689999999999876666666655443 233444
Q ss_pred ecCCCCeEEEEeeecccccccccccCcccee
Q 041283 138 ESYKSDKLWFTAGVKVSRPKDAYEMLRDAIR 168 (172)
Q Consensus 138 d~p~~~kI~F~~Gi~ksfp~~aFe~~~~c~~ 168 (172)
..++++|..|-...-.+..++++|+=.+
T Consensus 85 ---~~~d~~~~~g~~~eWnvry~~V~pti~~ 112 (187)
T PF05963_consen 85 ---SEKDVTFSPGDYLEWNVRYYEVDPTIQT 112 (187)
T ss_dssp ----GGGEEEETTTEEEEEEEEEE--TT--E
T ss_pred ---ecceeEecCCcEEEEEecceecCCceeE
Confidence 4555555555444444455555554333
No 3
>cd04089 eRF3_II eRF3_II: domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-li
Probab=52.37 E-value=57 Score=22.71 Aligned_cols=33 Identities=30% Similarity=0.425 Sum_probs=26.8
Q ss_pred eeEEEEEEccCeeecccccEEEEE---EEEEeeEEEEe
Q 041283 104 ATRVKGTLSRGKLSGVEGMKIKVL---VWVKVTGVAVE 138 (172)
Q Consensus 104 ~t~VtG~l~~GkI~~L~GVk~K~L---lWv~VteI~vd 138 (172)
.+.++|+|+.|.|+ .|.++..+ ....|.+|.++
T Consensus 14 g~vv~G~v~~G~i~--~G~~v~i~P~~~~~~V~si~~~ 49 (82)
T cd04089 14 GTVVLGKVESGTIK--KGDKLLVMPNKTQVEVLSIYNE 49 (82)
T ss_pred CEEEEEEEeeeEEe--cCCEEEEeCCCcEEEEEEEEEC
Confidence 57899999999998 67777665 67888888874
No 4
>cd03695 CysN_NodQ_II CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which sho
Probab=47.43 E-value=63 Score=22.65 Aligned_cols=31 Identities=23% Similarity=0.334 Sum_probs=26.1
Q ss_pred EEEEEEccCeeecccccEEEEE---EEEEeeEEEEe
Q 041283 106 RVKGTLSRGKLSGVEGMKIKVL---VWVKVTGVAVE 138 (172)
Q Consensus 106 ~VtG~l~~GkI~~L~GVk~K~L---lWv~VteI~vd 138 (172)
.|+|+++.|.|+ .|-++..+ ....|.+|.++
T Consensus 17 ~v~Gkv~~G~v~--~Gd~v~~~P~~~~~~V~si~~~ 50 (81)
T cd03695 17 GYAGTIASGSIR--VGDEVVVLPSGKTSRVKSIETF 50 (81)
T ss_pred EEEEEEccceEE--CCCEEEEcCCCCeEEEEEEEEC
Confidence 399999999999 77888776 67789999884
No 5
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=46.61 E-value=24 Score=28.71 Aligned_cols=37 Identities=24% Similarity=0.368 Sum_probs=29.2
Q ss_pred CHHHHHHhCCCCCCCCC--CCceEEEEeCCCcEEEEEeCCceEEE
Q 041283 52 ALPDLLRECNIPPGLFP--RNITCYDFDESRSKLIVYLPSPCAVS 94 (172)
Q Consensus 52 t~~elL~e~gLP~GLLP--~~V~~Y~l~~~tG~f~V~L~~~C~~~ 94 (172)
.|.++..+ +.| .++++.-||++||.++++..++=-+.
T Consensus 53 ~A~~~I~~------ivP~ea~i~di~Fd~~tGEV~IeaeKPG~Vi 91 (145)
T cd02410 53 EAIKIILE------IVPEEAGITDIYFDDDTGEVIIEAEKPGLVI 91 (145)
T ss_pred HHHHHHHH------hCCCccCceeeEecCCCcEEEEEEcCCeEEE
Confidence 35566665 567 68999999999999999998885543
No 6
>cd03694 GTPBP_II Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
Probab=43.34 E-value=66 Score=22.74 Aligned_cols=33 Identities=27% Similarity=0.267 Sum_probs=26.0
Q ss_pred eeEEEEEEccCeeecccccEEEEE-E------EEEeeEEEEe
Q 041283 104 ATRVKGTLSRGKLSGVEGMKIKVL-V------WVKVTGVAVE 138 (172)
Q Consensus 104 ~t~VtG~l~~GkI~~L~GVk~K~L-l------Wv~VteI~vd 138 (172)
.+.|+|+++.|.|+ .|-+...+ . ...|.+|.++
T Consensus 15 GtVv~G~v~~G~v~--~g~~v~~~P~~~g~~~~~~V~sI~~~ 54 (87)
T cd03694 15 GTVVGGTVSKGVIR--LGDTLLLGPDQDGSFRPVTVKSIHRN 54 (87)
T ss_pred ceEEEEEEecCEEe--CCCEEEECCCCCCCEeEEEEEEEEEC
Confidence 57899999999999 67777665 4 6788888874
No 7
>cd03693 EF1_alpha_II EF1_alpha_II: this family represents the domain II of elongation factor 1-alpha (EF-1a) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression.
Probab=42.88 E-value=90 Score=22.17 Aligned_cols=33 Identities=27% Similarity=0.331 Sum_probs=25.8
Q ss_pred eeEEEEEEccCeeecccccEEEEE---EEEEeeEEEEe
Q 041283 104 ATRVKGTLSRGKLSGVEGMKIKVL---VWVKVTGVAVE 138 (172)
Q Consensus 104 ~t~VtG~l~~GkI~~L~GVk~K~L---lWv~VteI~vd 138 (172)
.+.|+|+|+.|.|+ .|-++..+ ....|.+|.++
T Consensus 19 g~vv~G~v~~G~i~--~gd~v~i~P~~~~~~V~sI~~~ 54 (91)
T cd03693 19 GTVPVGRVETGVLK--PGMVVTFAPAGVTGEVKSVEMH 54 (91)
T ss_pred eEEEEEEEecceee--cCCEEEECCCCcEEEEEEEEEC
Confidence 46899999999998 56666655 67888888874
No 8
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=41.11 E-value=82 Score=21.89 Aligned_cols=34 Identities=26% Similarity=0.401 Sum_probs=26.9
Q ss_pred EeeEEEEEEccCeeecccccEEEEE---EEEEeeEEEEe
Q 041283 103 YATRVKGTLSRGKLSGVEGMKIKVL---VWVKVTGVAVE 138 (172)
Q Consensus 103 Y~t~VtG~l~~GkI~~L~GVk~K~L---lWv~VteI~vd 138 (172)
-.+.++|+|+.|.|+ .|-++..+ .-..|.+|.++
T Consensus 14 ~g~vv~G~v~~G~i~--~Gd~v~i~P~~~~~~V~si~~~ 50 (83)
T cd03698 14 GGTVVSGKVESGSIQ--KGDTLLVMPSKESVEVKSIYVD 50 (83)
T ss_pred CCcEEEEEEeeeEEe--CCCEEEEeCCCcEEEEEEEEEC
Confidence 356889999999998 57777665 67788888874
No 9
>PF08710 nsp9: nsp9 replicase; InterPro: IPR014822 Nsp9 is a single-stranded RNA-binding viral protein likely to be involved in RNA synthesis []. The structure comprises of a single beta barrel []. ; GO: 0003723 RNA binding, 0019079 viral genome replication, 0019034 viral replication complex; PDB: 2J97_A 2J98_A 3EE7_B 1QZ8_A 1UW7_A.
Probab=37.01 E-value=87 Score=24.50 Aligned_cols=36 Identities=19% Similarity=0.510 Sum_probs=23.2
Q ss_pred CCceEEEEeCCCcEEEEEeCCceEEEEcC--CeEEEEe
Q 041283 69 RNITCYDFDESRSKLIVYLPSPCAVSFKD--SSVVRYA 104 (172)
Q Consensus 69 ~~V~~Y~l~~~tG~f~V~L~~~C~~~f~~--~~~v~Y~ 104 (172)
.+..--.+..++|...+.|.-||.|..++ +-.+.|=
T Consensus 49 ~~Lk~vk~~~d~G~v~ieLePPckF~v~~~~g~~vkYL 86 (111)
T PF08710_consen 49 DNLKYVKWEKDDGKVVIELEPPCKFAVDVPKGPEVKYL 86 (111)
T ss_dssp S-EEEEEEE-TTSEEEEEB---EEEEEEETTSEEEEEE
T ss_pred CCceEEEEEccCCEEEEecCCCcEEEEEcCCCcEEEEE
Confidence 45555566667899999999999988864 6677764
No 10
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=33.73 E-value=30 Score=22.63 Aligned_cols=17 Identities=29% Similarity=0.612 Sum_probs=13.7
Q ss_pred CCHHHHHHhCCCCCCCC
Q 041283 51 KALPDLLRECNIPPGLF 67 (172)
Q Consensus 51 ~t~~elL~e~gLP~GLL 67 (172)
..+.+.|.+||+|.|=+
T Consensus 9 ~eL~~~L~~~G~~~gPI 25 (44)
T smart00540 9 AELRAELKQYGLPPGPI 25 (44)
T ss_pred HHHHHHHHHcCCCCCCc
Confidence 35778999999999844
No 11
>cd03697 EFTU_II EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the catalytic or G-domain. The G-domain is composed of about 200 amino acid residues, arranged into a predominantly parallel six-stranded beta-sheet core surrounded by seven a-helices. Non-catalytic domains II and III are beta-barrels of seven and six, respectively, antiparallel beta-strands that share an extended interface. Either non-catalytic domain is composed of about 100 amino acid residues. EF-Tu proteins exist in two principal conformations: in a compact one, EF-Tu*GTP, with tight interfaces between all three domains and a high affinity for aminoacyl-tRNA, and in an open one, EF-Tu*GDP, with essentially no G-domain-domain II interactions and a low affinity for aminoacyl-tRNA. EF-Tu has approximately a 100-fold higher
Probab=32.00 E-value=1.6e+02 Score=20.61 Aligned_cols=33 Identities=27% Similarity=0.509 Sum_probs=23.9
Q ss_pred eeEEEEEEccCeeecccccEEEEE-E----EEEeeEEEEe
Q 041283 104 ATRVKGTLSRGKLSGVEGMKIKVL-V----WVKVTGVAVE 138 (172)
Q Consensus 104 ~t~VtG~l~~GkI~~L~GVk~K~L-l----Wv~VteI~vd 138 (172)
.+.++|+|+.|.|+ .|-++..+ . ...|..|.++
T Consensus 15 G~vv~G~v~~G~v~--~gd~v~~~p~~~~~~~~V~si~~~ 52 (87)
T cd03697 15 GTVVTGRIERGTIK--VGDEVEIVGFGETLKTTVTGIEMF 52 (87)
T ss_pred EEEEEEEECCCCCc--cCCEEEEeCCCCCceEEEEEEEEC
Confidence 35799999999998 55555544 2 4678888774
No 12
>PF10262 Rdx: Rdx family; InterPro: IPR011893 This entry represents the Rdx family of selenoproteins, which includes mammalian selenoproteins SelW, SelV, SelT and SelH, bacterial SelW-like proteins and cysteine-containing proteins of unknown function in all three domains of life. Mammalian Rdx12 and its fish selenoprotein orthologues are also members of this family []. These proteins possess a thioredoxin-like fold and a conserved CXXC or CxxU (U is selenocysteine) motif near the N terminus, suggesting a redox function. Rdx proteins can use catalytic cysteine (or selenocysteine) to form transient mixed disulphides with substrate proteins. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins. Selenoprotein W (SelW) plays an important role in protection of neurons from oxidative stress during neuronal development [], []. Selenoprotein T (SelT) is conserved from plants to humans. SelT is localized to the endoplasmic reticulum through a hydrophobic domain. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding [, ]. The function of SelT is unknown, although it may have a role in PACAP signaling during PC12 cell differentiation [, ]. Selenoprotein H (SelH) protects neurons against UVB-induced damage by inhibiting apoptotic cell death pathways, by preventing mitochondrial depolarization, and by promoting cell survival pathways [].; GO: 0008430 selenium binding, 0045454 cell redox homeostasis; PDB: 2OJL_B 2FA8_A 2P0G_C 2NPB_A 3DEX_C 2OKA_A 2OBK_G.
Probab=28.06 E-value=78 Score=21.95 Aligned_cols=20 Identities=15% Similarity=0.149 Sum_probs=12.5
Q ss_pred ceEEEEeC-CCcEEEEEeCCc
Q 041283 71 ITCYDFDE-SRSKLIVYLPSP 90 (172)
Q Consensus 71 V~~Y~l~~-~tG~f~V~L~~~ 90 (172)
+.+.++.+ .+|.|+|++++.
T Consensus 32 ~~~v~~~~~~~G~FEV~v~g~ 52 (76)
T PF10262_consen 32 IAEVELSPGSTGAFEVTVNGE 52 (76)
T ss_dssp CSEEEEEEESTT-EEEEETTE
T ss_pred ceEEEEEeccCCEEEEEEccE
Confidence 33444433 589999999865
No 13
>PF05345 He_PIG: Putative Ig domain; InterPro: IPR008009 This alignment represents the conserved core region of a ~90 residue repeat found in several haemagglutinins and other cell surface proteins. Sequence similarities to Hyalin (IPR003410 from INTERPRO) and the PKD domain (IPR000601 from INTERPRO) suggest an Ig-like fold so this family may be similar in function to the (IPR003791 from INTERPRO) and (IPR003790 from INTERPRO) protein families.
Probab=27.32 E-value=45 Score=21.70 Aligned_cols=23 Identities=26% Similarity=0.319 Sum_probs=17.3
Q ss_pred CCCCCCCCCCCceEEEEeCCCcEEEEEeCCc
Q 041283 60 CNIPPGLFPRNITCYDFDESRSKLIVYLPSP 90 (172)
Q Consensus 60 ~gLP~GLLP~~V~~Y~l~~~tG~f~V~L~~~ 90 (172)
.+||.||. ||+.||.+.=.-...
T Consensus 10 ~~LP~gLs--------~d~~tG~isGtp~~~ 32 (49)
T PF05345_consen 10 GGLPSGLS--------LDPSTGTISGTPTSS 32 (49)
T ss_pred CCCCCcEE--------EeCCCCEEEeecCCC
Confidence 46888875 899999998775444
No 14
>KOG2455 consensus Delta-1-pyrroline-5-carboxylate dehydrogenase [Amino acid transport and metabolism]
Probab=26.80 E-value=36 Score=32.80 Aligned_cols=15 Identities=40% Similarity=0.950 Sum_probs=13.9
Q ss_pred HHHHHHhCCCCCCCC
Q 041283 53 LPDLLRECNIPPGLF 67 (172)
Q Consensus 53 ~~elL~e~gLP~GLL 67 (172)
+|.+|+|-|||.|++
T Consensus 242 i~~il~EAGlP~Gvi 256 (561)
T KOG2455|consen 242 IYRILREAGLPPGVI 256 (561)
T ss_pred HHHHHHHcCCCccce
Confidence 689999999999987
No 15
>cd07397 MPP_DevT Myxococcus xanthus DevT and related proteins, metallophosphatase domain. DevT is a component in the C-signal response pathway in Myxococcus xanthus that stimulates the developmentally regulated expression of the FruA response regulator protein and is required for methylation of FrzCD during fruiting body formation. DevT mutants having an in-frame deletion in the devT gene, display delayed aggregation and a cell autonomous sporulation defect. DevT belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomy
Probab=25.49 E-value=9.3 Score=32.93 Aligned_cols=50 Identities=42% Similarity=0.565 Sum_probs=37.5
Q ss_pred cceeeeeh-hhHHhhhhccccccceeeeeccccceeeeeecccCCCCCCHHHHHHhCCCCCCCC
Q 041283 5 GTFWVSKK-AKEELSHITQDLSICVSLSNTLEEKAKLIFSMLKGKPLKALPDLLRECNIPPGLF 67 (172)
Q Consensus 5 ~~~~~~~~-a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lkg~~~~t~~elL~e~gLP~GLL 67 (172)
|+||+++. +++-+. +. |.++.+..++++++ ...+.-..+|-.+++|.|+.
T Consensus 111 g~~~~~~~~vr~~fg-----i~-------s~~eA~~~ive~~~-~~~~~~~~VliaH~~~~G~g 161 (238)
T cd07397 111 GGFWLSKKAVKAVYG-----VI-------SLEESAQRIIAAAK-KAPPDLPLILLAHNGPSGLG 161 (238)
T ss_pred CccccCHHHHHHHhC-----CC-------CHHHHHHHHHHHhh-hcCCCCCeEEEeCcCCcCCC
Confidence 78999983 333332 33 78899999999996 43444458999999999998
No 16
>KOG2960 consensus Protein involved in thiamine biosynthesis and DNA damage tolerance [General function prediction only]
Probab=22.74 E-value=54 Score=29.27 Aligned_cols=42 Identities=19% Similarity=0.169 Sum_probs=37.3
Q ss_pred cccccceeeeeccccceeeeeecccCCC--CCCHHHHHHhCCCC
Q 041283 22 QDLSICVSLSNTLEEKAKLIFSMLKGKP--LKALPDLLRECNIP 63 (172)
Q Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~~lkg~~--~~t~~elL~e~gLP 63 (172)
-|+.+|+-=||---+|-.||=-+|-..| .++++-.|+|.|.|
T Consensus 100 PdlkvaIIE~SVaPGGGaWLGGQLFSAMvvRKPAhLFL~Eigvp 143 (328)
T KOG2960|consen 100 PDLKVAIIESSVAPGGGAWLGGQLFSAMVVRKPAHLFLQEIGVP 143 (328)
T ss_pred CCceEEEEEeeecCCCcccccchhhhhhhhcChHHHHHHHhCCC
Confidence 6888898777777788899999999988 89999999999988
No 17
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=22.66 E-value=2.2e+02 Score=21.31 Aligned_cols=37 Identities=8% Similarity=0.217 Sum_probs=29.0
Q ss_pred eEEEEEEccCeeecccccEEEEEEEEEeeEEEEecCCCCeEEEE
Q 041283 105 TRVKGTLSRGKLSGVEGMKIKVLVWVKVTGVAVESYKSDKLWFT 148 (172)
Q Consensus 105 t~VtG~l~~GkI~~L~GVk~K~LlWv~VteI~vd~p~~~kI~F~ 148 (172)
..|+|.+...+|.=+.|=++++-+|- =+++-+.|.|.
T Consensus 34 a~isGKmR~~rIrIl~GD~V~VE~sp-------YDltkGRIiyR 70 (87)
T PRK12442 34 AYASGRMRKHRIRILAGDRVTLELSP-------YDLTKGRINFR 70 (87)
T ss_pred EEeccceeeeeEEecCCCEEEEEECc-------ccCCceeEEEE
Confidence 67999999999999999999886662 13466778775
No 18
>PF07311 Dodecin: Dodecin; InterPro: IPR009923 This entry represents proteins with a Dodecin-like topology. Dodecin flavoprotein is a small dodecameric flavin-binding protein from Halobacterium salinarium (Halobacterium halobium) that contains two flavins stacked in a single binding pocket between two tryptophan residues to form an aromatic tetrade []. Dodecin binds riboflavin, although it appears to have a broad specificity for flavins. Lumichrome, a molecule associated with flavin metabolism, appears to be a ligand of dodecin, which could act as a waste-trapping device. ; PDB: 2VYX_L 2DEG_F 2V18_K 2V19_D 2UX9_B 2CZ8_E 2V21_F 2CC8_A 2CCB_A 2VX9_A ....
Probab=22.02 E-value=1.7e+02 Score=20.66 Aligned_cols=31 Identities=16% Similarity=0.152 Sum_probs=21.8
Q ss_pred EEEEeeEEEEecCCCCeEEEEeeeccccccc
Q 041283 128 VWVKVTGVAVESYKSDKLWFTAGVKVSRPKD 158 (172)
Q Consensus 128 lWv~VteI~vd~p~~~kI~F~~Gi~ksfp~~ 158 (172)
-|+-|.+++..-.++.-.+|++.+.-+|.++
T Consensus 35 ~~~eV~e~~~~v~dg~i~~y~v~lkv~F~le 65 (66)
T PF07311_consen 35 RWFEVKEQRGHVEDGKITEYQVNLKVSFRLE 65 (66)
T ss_dssp EEEEEEEEEEEEETTCEEEEEEEEEEEEECS
T ss_pred EEEEEEEEEEEEeCCcEEEEEEEEEEEEEEC
Confidence 4677777777655666778998887766543
No 19
>TIGR00547 lolA periplasmic chaperone LolA. This protein, LolA, is known so far only in the gamma and beta subdivisions of the Proteobacteria. The E. coli major outer lipoprotein (Lpp) of E. coli is released from the inner membrane as a complex with this chaperone in an energy-requiring process, and is then delivered to LolB for insertion into the outer membrane. LolA is involved in the delivery of lipoproteins generally, rather than just Lpp, and is an essential protein in E. coli, unlike Lpp itself.
Probab=21.47 E-value=2.4e+02 Score=23.34 Aligned_cols=48 Identities=8% Similarity=0.241 Sum_probs=35.1
Q ss_pred EEEE-EEEE----eeEEEEecCCCCeEEEEe-ee-ccccccccccc-Cccceeecc
Q 041283 124 IKVL-VWVK----VTGVAVESYKSDKLWFTA-GV-KVSRPKDAYEM-LRDAIRVEQ 171 (172)
Q Consensus 124 ~K~L-lWv~----VteI~vd~p~~~kI~F~~-Gi-~ksfp~~aFe~-~~~c~~v~~ 171 (172)
.+.+ +|+. +.+|.+.+..|....+.. .+ ....+.+.|+- +|+++.|++
T Consensus 146 f~~~~l~fd~~~~l~~~~v~D~~Gq~t~i~f~~~~n~~l~~~~F~F~pP~GvdV~~ 201 (204)
T TIGR00547 146 IKQFDINVDADGIIHNFSATEKDDQRNLYQLKNIQNGALDAAKFQFKPEKGVEVDD 201 (204)
T ss_pred eEEEEEEECCCCCEEEEEEEecCCCEEEEEEcCCcCCCCChhhEEEcCCCCCeecc
Confidence 3456 8884 899999988888655542 24 57888889976 788888853
No 20
>PF06462 Hyd_WA: Propeller; InterPro: IPR006624 Tectonins I and II are two dominant proteins in the nuclei and nuclear matrix from plasmodia of Physarum polycephalum (Slime mold) which encode 217 and 353 amino acids, respectively. Tectonin I is homologous to the C-terminal two-thirds of tectonin II. Both proteins contain six tandem repeats that are each 33-37 amino acids in length and define a new consensus sequence. Homologous repeats are found in L-6, a bacterial lipopolysaccharide-binding lectin from horseshoe crab hemocytes. The repetitive sequences of the tectonins and L-6 are reminiscent of the WD repeats of the beta-subunit of G proteins, suggesting that they form beta-propeller domains. The tectonins may be lectins that function as part of a transmembrane signalling complex during phagocytosis [].
Probab=21.15 E-value=73 Score=19.04 Aligned_cols=18 Identities=22% Similarity=0.621 Sum_probs=15.0
Q ss_pred CCCeEEEEeeeccccccc
Q 041283 141 KSDKLWFTAGVKVSRPKD 158 (172)
Q Consensus 141 ~~~kI~F~~Gi~ksfp~~ 158 (172)
..++|+|..|++.+.|.-
T Consensus 8 ~~G~v~~R~Gis~~~P~G 25 (32)
T PF06462_consen 8 SDGSVYFRTGISPSNPEG 25 (32)
T ss_pred CCCCEEEECcCCCCCCCC
Confidence 568899999999888853
No 21
>PF09822 ABC_transp_aux: ABC-type uncharacterized transport system; InterPro: IPR019196 This domain is found in various eukaryotic and prokaryotic intra-flagellar transport proteins involved in gliding motility, as well as in several hypothetical proteins.
Probab=20.46 E-value=35 Score=28.67 Aligned_cols=36 Identities=25% Similarity=0.343 Sum_probs=30.2
Q ss_pred CccccceeeeehhhHHhhhhccccccceeeeecccc
Q 041283 1 LTKVGTFWVSKKAKEELSHITQDLSICVSLSNTLEE 36 (172)
Q Consensus 1 ~~k~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~ 36 (172)
||+=+.|=+|.-.++-++++.+|++|-+-+|..+..
T Consensus 4 lT~~k~ysLS~~T~~~L~~L~~pV~i~~~~s~~l~~ 39 (271)
T PF09822_consen 4 LTANKRYSLSDQTKKVLKSLDEPVTITVYFSRELPP 39 (271)
T ss_pred cCCCCCccCCHHHHHHHHhCCCCEEEEEEECCCcch
Confidence 466678899999999999999999998888875443
No 22
>PF01820 Dala_Dala_lig_N: D-ala D-ala ligase N-terminus; InterPro: IPR011127 This entry represents the N-terminal region of the D-alanine--D-alanine ligase enzyme (6.3.2.4 from EC) which is thought to be involved in substrate binding []. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF) [].; GO: 0008716 D-alanine-D-alanine ligase activity, 0009252 peptidoglycan biosynthetic process, 0005618 cell wall; PDB: 4EG0_B 3E5N_A 3RFC_A 3R5F_A 1IOV_A 1IOW_A 2DLN_A 3Q1K_D 3I12_C 3N8D_B ....
Probab=20.33 E-value=1.1e+02 Score=23.02 Aligned_cols=29 Identities=24% Similarity=0.439 Sum_probs=23.4
Q ss_pred ccceeeeeecccCCC--CCCHHHHHHhCCCC
Q 041283 35 EEKAKLIFSMLKGKP--LKALPDLLRECNIP 63 (172)
Q Consensus 35 ~~~~~~~~~~lkg~~--~~t~~elL~e~gLP 63 (172)
-...-.+|+-|+|.. +=++.-+|+-+|+|
T Consensus 83 ~~~~DvvFp~lHG~~GEDG~iQglle~~~iP 113 (117)
T PF01820_consen 83 KLEVDVVFPVLHGPNGEDGTIQGLLELLGIP 113 (117)
T ss_dssp CTTCSEEEEECCSTTTSSSHHHHHHHHTT-E
T ss_pred cccCCEEEEeccCCCCcccHHHHHHHHcCCC
Confidence 345668999999998 66799999999988
Done!