Query 042449
Match_columns 90
No_of_seqs 38 out of 40
Neff 1.5
Searched_HMMs 46136
Date Fri Mar 29 06:17:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042449.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042449hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00477 LEA_5: Small hydrophi 99.9 3.5E-27 7.6E-32 165.6 1.9 57 1-57 1-58 (109)
2 PF06858 NOG1: Nucleolar GTP-b 39.9 23 0.0005 22.5 1.7 17 22-38 23-39 (58)
3 COG1862 YajC Preprotein transl 32.0 32 0.0007 23.4 1.6 25 4-28 34-59 (97)
4 PF08923 MAPKK1_Int: Mitogen-a 28.9 65 0.0014 22.1 2.7 35 48-88 60-94 (119)
5 cd07703 Ig2_Nectin-2_like Seco 23.0 61 0.0013 20.9 1.6 18 63-84 74-91 (95)
6 KOG0880 Peptidyl-prolyl cis-tr 21.1 38 0.00083 26.7 0.4 21 12-32 96-117 (217)
7 COG4118 Phd Antitoxin of toxin 19.9 52 0.0011 21.6 0.8 17 5-21 12-28 (84)
8 PF00263 Secretin: Bacterial t 17.8 59 0.0013 21.3 0.7 19 12-30 105-123 (165)
9 cd01124 KaiC KaiC is a circadi 17.7 98 0.0021 19.9 1.7 25 19-43 2-27 (187)
10 PRK14556 pyrH uridylate kinase 17.5 77 0.0017 24.4 1.4 21 6-26 125-146 (249)
No 1
>PF00477 LEA_5: Small hydrophilic plant seed protein; InterPro: IPR000389 This entry contains a number of bacterial proteins annotated as stress-induced and members of the plant LEA (late embryogenesis abundant) proteins, which are small hydrophilic plant seed proteins that are structurally related. These proteins contains from 83 to 153 amino acid residues and may play a role [, ] in equipping the seed for survival, maintaining a minimal level of hydration in the dry organism and preventing the denaturation of cytoplasmic components. They may also play a role during imbibition by controlling water uptake.
Probab=99.93 E-value=3.5e-27 Score=165.60 Aligned_cols=57 Identities=56% Similarity=0.703 Sum_probs=54.6
Q ss_pred Ccc-hhchhhhhhcccCCCeeecCCCCCCchHHHHHHhhccCCCchhhhhhcccccce
Q 042449 1 MAS-QQGRQELDTRPRQGETVVPGGTGGKSLEAQEHLAEGFSGKNHVVAKRLVANDSI 57 (90)
Q Consensus 1 Mas-qq~R~ELD~rAr~GETVVpGGTGGkSLeAQe~LAEGRskGGqtRkeqlG~eg~i 57 (90)
||| |++|+|||++||+||||||||||||||+||++|||||+|||++|++++|.|+|-
T Consensus 1 ma~~q~~r~eld~~aregetvv~gGtggksl~aqe~laEggkKGGetr~e~~G~E~Yq 58 (109)
T PF00477_consen 1 MASGQESREELDARAREGETVVPGGTGGKSLEAQERLAEGGKKGGETRKEQHGKEFYQ 58 (109)
T ss_pred CcchhHHHHHHHHHHhcCCccccCCCCCCcchHHHHHHHHHhhcccchhhhcchhHHH
Confidence 899 668999999999999999999999999999999999999999999999999873
No 2
>PF06858 NOG1: Nucleolar GTP-binding protein 1 (NOG1); InterPro: IPR010674 This domain represents a conserved region of approximately 60 residues in length within nucleolar GTP-binding protein 1 (NOG1). The NOG1 family includes eukaryotic, bacterial and archaeal proteins. In Saccharomyces cerevisiae, the NOG1 gene has been shown to be essential for cell viability, suggesting that NOG1 may play an important role in nucleolar functions. In particular, NOG1 is believed to be functionally linked to ribosome biogenesis, which occurs in the nucleolus. In eukaryotes, NOG1 mutants were found to disrupt the biogenesis of the 60S ribosomal subunit []. The DRG and OBG proteins as well as the prokaryotic NOG-like proteins are homologous throughout their length to the amino half of eukaryotic NOG1, which contains the GTP binding motifs (IPR006073 from INTERPRO); the N-terminal GTP-binding motif is required for function.; GO: 0005525 GTP binding; PDB: 2E87_A.
Probab=39.86 E-value=23 Score=22.51 Aligned_cols=17 Identities=35% Similarity=0.411 Sum_probs=13.6
Q ss_pred cCCCCCCchHHHHHHhh
Q 042449 22 PGGTGGKSLEAQEHLAE 38 (90)
Q Consensus 22 pGGTGGkSLeAQe~LAE 38 (90)
|.|+-|-|+|.|.+|-+
T Consensus 23 ~Se~CGysie~Q~~L~~ 39 (58)
T PF06858_consen 23 PSEQCGYSIEEQLSLFK 39 (58)
T ss_dssp TT-TTSS-HHHHHHHHH
T ss_pred CCCCCCCCHHHHHHHHH
Confidence 89999999999999864
No 3
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=32.03 E-value=32 Score=23.41 Aligned_cols=25 Identities=32% Similarity=0.399 Sum_probs=18.9
Q ss_pred hhchhhhhhcccCCCeeecCC-CCCC
Q 042449 4 QQGRQELDTRPRQGETVVPGG-TGGK 28 (90)
Q Consensus 4 qq~R~ELD~rAr~GETVVpGG-TGGk 28 (90)
+++++++-.-.+.|+.||-.| -=|+
T Consensus 34 ~K~~~~ml~sL~kGD~VvT~gGi~G~ 59 (97)
T COG1862 34 MKEHQELLNSLKKGDEVVTIGGIVGT 59 (97)
T ss_pred HHHHHHHHHhccCCCEEEEcCCeEEE
Confidence 557888989999999998654 4444
No 4
>PF08923 MAPKK1_Int: Mitogen-activated protein kinase kinase 1 interacting; InterPro: IPR015019 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This entry represents Mitogen-activated protein kinase kinase 1 interacting protein, which is a small subcellular adaptor protein required for MAPK signalling and ERK1/2 activation. The overall topology of this domain has a central five-stranded beta-sheet sandwiched between a two alpha-helix and a one alpha-helix layer []. ; PDB: 1VEU_A 1VET_A 1SKO_A 2ZL1_A 3CPT_A.
Probab=28.92 E-value=65 Score=22.14 Aligned_cols=35 Identities=26% Similarity=0.264 Sum_probs=23.6
Q ss_pred hhhcccccceeeeeecceecccceeeeecCCCeeEEEeccC
Q 042449 48 AKRLVANDSISTSVHSTCRVSHARLVHMNRGPQLLTIFFGS 88 (90)
Q Consensus 48 keqlG~eg~istsvhstcrvsharlvhmnrgpqlltiffgs 88 (90)
|=.+|.+-+| +|..+.--+||+|..|-.+|++-.+
T Consensus 60 KL~lG~nk~i------i~~Y~~~qvv~~~~~pl~it~ias~ 94 (119)
T PF08923_consen 60 KLGLGKNKSI------IAYYDSYQVVQFNKLPLYITFIASS 94 (119)
T ss_dssp TSSS-SEEEE------EEEESSEEEEEEEETTEEEEEEEET
T ss_pred ccCCCCceEE------EEEeCCEEEEEEeCCCeEEEEEecC
Confidence 3345555554 4666777889999999888876443
No 5
>cd07703 Ig2_Nectin-2_like Second immunoglobulin (Ig) domain of nectin-2 (also known as poliovirus receptor related protein 2 or CD112) and similar proteins. Ig2_Nectin-2_like: domain similar to the second immunoglobulin (Ig) domain of nectin-2 (also known as poliovirus receptor related protein 2 or CD112). Nectin-2 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. Nectin-2 and nectin-3 localize at Sertoli-spermatid junctions where they form heterophilic trans-interactions between the cells that are essential for the formation and maintenance of the junctions and for spermatid development.
Probab=22.99 E-value=61 Score=20.93 Aligned_cols=18 Identities=50% Similarity=0.949 Sum_probs=12.7
Q ss_pred cceecccceeeeecCCCeeEEE
Q 042449 63 STCRVSHARLVHMNRGPQLLTI 84 (90)
Q Consensus 63 stcrvsharlvhmnrgpqllti 84 (90)
-+|+++|.-| +.|++|.+
T Consensus 74 ltC~v~h~al----~~~~~~~~ 91 (95)
T cd07703 74 VTCKVEHETL----QEPQLLPV 91 (95)
T ss_pred EEEEEeCccc----CCCeEEEE
Confidence 3799999866 35666654
No 6
>KOG0880 consensus Peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=21.05 E-value=38 Score=26.74 Aligned_cols=21 Identities=43% Similarity=0.563 Sum_probs=16.4
Q ss_pred hcccCCCeeecC-CCCCCchHH
Q 042449 12 TRPRQGETVVPG-GTGGKSLEA 32 (90)
Q Consensus 12 ~rAr~GETVVpG-GTGGkSLeA 32 (90)
.-+=||--+.+| ||||+|+-.
T Consensus 96 nfmIQGGd~t~g~gtGg~SIyG 117 (217)
T KOG0880|consen 96 NFMIQGGDFTKGDGTGGKSIYG 117 (217)
T ss_pred CceeecCccccCCCCCCeEeec
Confidence 345578889999 999999854
No 7
>COG4118 Phd Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]
Probab=19.92 E-value=52 Score=21.59 Aligned_cols=17 Identities=41% Similarity=0.472 Sum_probs=13.9
Q ss_pred hchhhhhhcccCCCeee
Q 042449 5 QGRQELDTRPRQGETVV 21 (90)
Q Consensus 5 q~R~ELD~rAr~GETVV 21 (90)
++=++|=+|++.||.|+
T Consensus 12 ~~~S~lL~rV~aGEev~ 28 (84)
T COG4118 12 THLSELLRRVRAGEEVI 28 (84)
T ss_pred HHHHHHHHHHhCCCEEE
Confidence 44578889999999886
No 8
>PF00263 Secretin: Bacterial type II and III secretion system protein; InterPro: IPR004846 This family includes: protein D that is involved in the general (type II) secretion pathway (GSP) within Gram-negative bacteria, a signal sequence-dependent process responsible for protein export [, , ,, , , ] and protein G from the type III secretion system. A number of proteins are involved in the GSP; one of these is known as protein D (GSPD protein), the most probable location of which is the outer membrane []. This suggests that protein D constitutes the apparatus of the accessory mechanism, and is thus involved in transporting exoproteins from the periplasm, across the outer membrane, to the extracellular environment. The type III secretion system is of great interest, as it is used to transport virulence factors from the pathogen directly into the host cell and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis. However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part of the flagellum itself [], type III subunits in the outer membrane translocate secreted proteins through a channel-like structure. Protein G aids in the structural assembly of the invasion complex []. ; GO: 0009306 protein secretion
Probab=17.79 E-value=59 Score=21.32 Aligned_cols=19 Identities=47% Similarity=0.518 Sum_probs=14.3
Q ss_pred hcccCCCeeecCCCCCCch
Q 042449 12 TRPRQGETVVPGGTGGKSL 30 (90)
Q Consensus 12 ~rAr~GETVVpGGTGGkSL 30 (90)
-+++.|||||-||.--+..
T Consensus 105 v~v~~GetvvigGl~~~~~ 123 (165)
T PF00263_consen 105 VRVRDGETVVIGGLIQDQN 123 (165)
T ss_pred EEECCCCEEEeeeeecccc
Confidence 3578899999999765443
No 9
>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs. A related protein is found in archaea.
Probab=17.74 E-value=98 Score=19.88 Aligned_cols=25 Identities=36% Similarity=0.591 Sum_probs=18.8
Q ss_pred eeecCCCC-CCchHHHHHHhhccCCC
Q 042449 19 TVVPGGTG-GKSLEAQEHLAEGFSGK 43 (90)
Q Consensus 19 TVVpGGTG-GkSLeAQe~LAEGRskG 43 (90)
++|-|.+| ||+.=++.-+.++=..|
T Consensus 2 ~li~G~~G~GKT~l~~~~~~~~~~~g 27 (187)
T cd01124 2 TLLSGGPGTGKTTFALQFLYAGLARG 27 (187)
T ss_pred EEEEcCCCCCHHHHHHHHHHHHHHCC
Confidence 56778877 89998888777775444
No 10
>PRK14556 pyrH uridylate kinase; Provisional
Probab=17.52 E-value=77 Score=24.38 Aligned_cols=21 Identities=29% Similarity=0.672 Sum_probs=17.7
Q ss_pred chhhhhhcccCCCeee-cCCCC
Q 042449 6 GRQELDTRPRQGETVV-PGGTG 26 (90)
Q Consensus 6 ~R~ELD~rAr~GETVV-pGGTG 26 (90)
.+++..+...+|..|| .||||
T Consensus 125 ~~~~~~~~l~~g~vvi~~gg~G 146 (249)
T PRK14556 125 SAHEFNQELAKGRVLIFAGGTG 146 (249)
T ss_pred CHHHHHHHHhCCCEEEEECCCC
Confidence 5777888888999999 99986
Done!