Query 046420
Match_columns 69
No_of_seqs 12 out of 14
Neff 1.8
Searched_HMMs 46136
Date Fri Mar 29 11:55:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046420.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046420hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03690 UPF0160: Uncharacteri 30.4 23 0.00049 27.2 0.7 23 17-42 62-84 (318)
2 PF08845 SymE_toxin: Toxin Sym 28.8 19 0.00041 21.4 0.0 13 33-45 28-40 (57)
3 cd07283 PX_SNX30 The phosphoin 26.9 33 0.00072 22.1 0.9 27 20-59 40-66 (116)
4 KOG4227 WD40 repeat protein [G 22.6 28 0.00062 29.6 -0.0 34 27-60 60-99 (609)
5 KOG3404 G10 protein/predicted 21.0 26 0.00056 25.3 -0.5 8 15-22 50-57 (145)
6 PRK13605 endoribonuclease SymE 19.6 38 0.00082 23.3 0.1 13 33-45 42-54 (113)
7 PF13682 CZB: Chemoreceptor zi 18.1 34 0.00074 18.4 -0.3 15 33-47 31-45 (70)
8 PF03943 TAP_C: TAP C-terminal 17.4 89 0.0019 17.8 1.3 23 36-58 26-48 (51)
9 cd07284 PX_SNX7 The phosphoino 16.6 60 0.0013 21.0 0.5 27 20-59 40-66 (116)
10 cd07294 PX_SNX12 The phosphoin 16.2 77 0.0017 21.1 1.0 26 20-59 43-68 (132)
No 1
>PF03690 UPF0160: Uncharacterised protein family (UPF0160); InterPro: IPR003226 The function of this domain is not known, but it is found in several uncharacterised proteins and a probable metal dependent protein hydrolase.
Probab=30.39 E-value=23 Score=27.17 Aligned_cols=23 Identities=48% Similarity=0.563 Sum_probs=16.2
Q ss_pred eehhhhccccccccCCCCCcchhhhh
Q 046420 17 VHHQRQWSSEKFLESSSNGRWLQSAW 42 (69)
Q Consensus 17 vHHQRQ~Sdnnfld~ssnGRWlQSag 42 (69)
=||||-|.+ .| ...++-=|-|+|
T Consensus 62 DHHQ~~f~~-tf--~~~~~~~lSSAG 84 (318)
T PF03690_consen 62 DHHQRGFNE-TF--SRENGIKLSSAG 84 (318)
T ss_pred ccccccCcc-cc--ccCCCceeeccc
Confidence 599999987 55 445555667777
No 2
>PF08845 SymE_toxin: Toxin SymE, type I toxin-antitoxin system; InterPro: IPR014944 This entry represents a SOS-induced gene whose product shows homology to the antitoxin MazE (SymE), the coding region contains a cis-encoded antisense RNA. The small antisense RNA and the gene have the all the hallmarks of a toxin-antitoxin module. The synthesis of the SymE is tightly repressed at multiple levels; at the transcriptional level by the LexA repressor, at the level of mRNA stability and translation by the SymR RNA and at the level of protein stability by the Lon protease. SymE co-purifies with ribosomes and overproduction of the protein leads to cell growth inhibition, decreased protein synthesis and increased RNA degradation. These properties are shared with several RNA endonuclease toxins of toxin-antitoxin modules. It seems probable that the SymE protein represents an evolutionary derivative of a toxin containing the AbrB fold, whose representatives are typically antitoxins. The SymE promoted cleavage of RNA cleavage may be important for the recycling of RNAs damaged under SOS-inducing conditions []. ; GO: 0003723 RNA binding, 0016788 hydrolase activity, acting on ester bonds, 0016070 RNA metabolic process, 0005737 cytoplasm
Probab=28.78 E-value=19 Score=21.42 Aligned_cols=13 Identities=31% Similarity=0.675 Sum_probs=10.8
Q ss_pred CCCcchhhhhhhh
Q 046420 33 SNGRWLQSAWLQH 45 (69)
Q Consensus 33 snGRWlQSaglqh 45 (69)
=.|+||..+||.=
T Consensus 28 L~G~WL~~aGF~~ 40 (57)
T PF08845_consen 28 LKGKWLEEAGFTI 40 (57)
T ss_pred EchhhhHHhCCCC
Confidence 4699999999854
No 3
>cd07283 PX_SNX30 The phosphoinositide binding Phox Homology domain of Sorting Nexin 30. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX30 harbors a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature, C-terminal to the PX domain, similar to the sorting nexins SNX1-2, SNX4-8, and SNX32
Probab=26.91 E-value=33 Score=22.14 Aligned_cols=27 Identities=41% Similarity=0.859 Sum_probs=17.1
Q ss_pred hhhccccccccCCCCCcchhhhhhhhhhhccCCCCCCCee
Q 046420 20 QRQWSSEKFLESSSNGRWLQSAWLQHLQQSSATGTIPPLQ 59 (69)
Q Consensus 20 QRQ~Sdnnfld~ssnGRWlQSaglqhlq~s~~~G~~~~~~ 59 (69)
+|.||| |. ||+. +|+.....--||||-
T Consensus 40 ~RRYsD--F~-------~L~~----~L~~~~p~~~iPpLP 66 (116)
T cd07283 40 RRRYQD--FD-------WLRN----KLEESQPTHLIPPLP 66 (116)
T ss_pred eCCccH--HH-------HHHH----HHHHhCCCcccCCCC
Confidence 688888 55 7774 455554333578864
No 4
>KOG4227 consensus WD40 repeat protein [General function prediction only]
Probab=22.61 E-value=28 Score=29.62 Aligned_cols=34 Identities=26% Similarity=0.298 Sum_probs=22.2
Q ss_pred ccccCCCCCcchhhhh------hhhhhhccCCCCCCCeee
Q 046420 27 KFLESSSNGRWLQSAW------LQHLQQSSATGTIPPLQV 60 (69)
Q Consensus 27 nfld~ssnGRWlQSag------lqhlq~s~~~G~~~~~~~ 60 (69)
|.+.++-|||||-|+| +-|..+.--.-.-.|+||
T Consensus 60 NAlqFS~N~~~L~SGGDD~~~~~W~~de~~~~k~~KPI~~ 99 (609)
T KOG4227|consen 60 NALQFSHNDRFLASGGDDMHGRVWNVDELMVRKTPKPIGV 99 (609)
T ss_pred ceeeeccCCeEEeecCCcceeeeechHHHHhhcCCCCcee
Confidence 6788999999999998 334433333334345554
No 5
>KOG3404 consensus G10 protein/predicted nuclear transcription regulator [Transcription]
Probab=21.05 E-value=26 Score=25.32 Aligned_cols=8 Identities=63% Similarity=1.007 Sum_probs=6.6
Q ss_pred ceeehhhh
Q 046420 15 VQVHHQRQ 22 (69)
Q Consensus 15 ~~vHHQRQ 22 (69)
.|+||||.
T Consensus 50 fqlhHQrs 57 (145)
T KOG3404|consen 50 FQLHHQRS 57 (145)
T ss_pred HHHhhhhh
Confidence 58999985
No 6
>PRK13605 endoribonuclease SymE; Provisional
Probab=19.55 E-value=38 Score=23.33 Aligned_cols=13 Identities=31% Similarity=0.710 Sum_probs=10.7
Q ss_pred CCCcchhhhhhhh
Q 046420 33 SNGRWLQSAWLQH 45 (69)
Q Consensus 33 snGRWlQSaglqh 45 (69)
=.|+||..+||.=
T Consensus 42 LkG~WLeeAGF~t 54 (113)
T PRK13605 42 LKGQWLEAAGFAT 54 (113)
T ss_pred ECchhHHhhCCCC
Confidence 3599999999864
No 7
>PF13682 CZB: Chemoreceptor zinc-binding domain
Probab=18.14 E-value=34 Score=18.43 Aligned_cols=15 Identities=20% Similarity=0.445 Sum_probs=10.7
Q ss_pred CCCcchhhhhhhhhh
Q 046420 33 SNGRWLQSAWLQHLQ 47 (69)
Q Consensus 33 snGRWlQSaglqhlq 47 (69)
.=|+|+.+.|-..+.
T Consensus 31 ~fG~Wl~~~~~~~~~ 45 (70)
T PF13682_consen 31 RFGKWLYGEGRERFG 45 (70)
T ss_pred CCCceecccChhhhh
Confidence 348999988855543
No 8
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1). Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.
Probab=17.42 E-value=89 Score=17.80 Aligned_cols=23 Identities=35% Similarity=0.603 Sum_probs=16.4
Q ss_pred cchhhhhhhhhhhccCCCCCCCe
Q 046420 36 RWLQSAWLQHLQQSSATGTIPPL 58 (69)
Q Consensus 36 RWlQSaglqhlq~s~~~G~~~~~ 58 (69)
-|=-...++-+....+.|.|||-
T Consensus 26 ~Wd~~~A~~~F~~l~~~~~IP~e 48 (51)
T PF03943_consen 26 NWDYERALQNFEELKAQGKIPPE 48 (51)
T ss_dssp TT-CCHHHHHHHHCCCTT-S-CC
T ss_pred CCCHHHHHHHHHHHHHcCCCChH
Confidence 46666778889999999999985
No 9
>cd07284 PX_SNX7 The phosphoinositide binding Phox Homology domain of Sorting Nexin 7. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX7 harbors a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature, C-terminal to the PX domain, similar to the sorting nexins SNX1-2, SNX4-6, SNX8, SNX30,
Probab=16.65 E-value=60 Score=21.00 Aligned_cols=27 Identities=41% Similarity=0.904 Sum_probs=17.0
Q ss_pred hhhccccccccCCCCCcchhhhhhhhhhhccCCCCCCCee
Q 046420 20 QRQWSSEKFLESSSNGRWLQSAWLQHLQQSSATGTIPPLQ 59 (69)
Q Consensus 20 QRQ~Sdnnfld~ssnGRWlQSaglqhlq~s~~~G~~~~~~ 59 (69)
.|-||| |. ||+. +|+..-...-||||-
T Consensus 40 ~RRysD--F~-------~L~~----~L~~~~p~~~iPplP 66 (116)
T cd07284 40 RRRYQD--FL-------WLKG----RLEEAHPTLIIPPLP 66 (116)
T ss_pred eCCchH--HH-------HHHH----HHHHHCCCceeCCCC
Confidence 688888 55 7875 465554434477764
No 10
>cd07294 PX_SNX12 The phosphoinositide binding Phox Homology domain of Sorting Nexin 12. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. The specific function of SNX12 has yet to be elucidated.
Probab=16.18 E-value=77 Score=21.12 Aligned_cols=26 Identities=35% Similarity=0.848 Sum_probs=15.9
Q ss_pred hhhccccccccCCCCCcchhhhhhhhhhhccCCCCCCCee
Q 046420 20 QRQWSSEKFLESSSNGRWLQSAWLQHLQQSSATGTIPPLQ 59 (69)
Q Consensus 20 QRQ~Sdnnfld~ssnGRWlQSaglqhlq~s~~~G~~~~~~ 59 (69)
.|-||| |. ||+. +|+.. ....||||-
T Consensus 43 ~RRYsD--F~-------~L~~----~L~~~-~g~~iPpLP 68 (132)
T cd07294 43 RRRYSD--FE-------WLKN----ELERD-SKIVVPPLP 68 (132)
T ss_pred eCCccH--HH-------HHHH----HHHHc-CCCccCCCC
Confidence 688888 55 8874 45433 233577753
Done!