Query 046401
Match_columns 127
No_of_seqs 41 out of 43
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 11:44:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046401.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046401hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05617 Prolamin_like: Prolam 99.4 4.2E-13 9.2E-18 87.7 3.1 53 52-104 1-70 (70)
2 PLN00213 predicted protein; Pr 99.4 2.1E-12 4.5E-17 97.3 7.0 105 1-114 1-117 (118)
3 PF07172 GRP: Glycine rich pro 95.5 0.01 2.2E-07 42.7 2.2 28 1-29 1-28 (95)
4 KOG0673 Thymidylate synthase [ 63.7 5.1 0.00011 34.6 2.1 33 66-98 66-111 (293)
5 PF03058 Sar8_2: Sar8.2 family 53.3 10 0.00022 28.1 1.9 29 1-32 1-32 (93)
6 PF02479 Herpes_IE68: Herpesvi 43.8 14 0.00031 28.6 1.5 32 67-101 64-98 (132)
7 PF01465 GRIP: GRIP domain; I 28.3 33 0.00071 21.5 1.0 18 82-99 28-45 (46)
8 PHA02602 56 dCTP pyrophosphata 26.7 39 0.00085 27.5 1.5 30 60-102 128-157 (172)
9 PF15284 PAGK: Phage-encoded v 23.2 74 0.0016 22.0 2.1 16 3-18 4-19 (61)
10 PF07499 RuvA_C: RuvA, C-termi 21.6 42 0.00092 20.6 0.6 12 86-97 10-21 (47)
11 PF09402 MSC: Man1-Src1p-C-ter 21.1 32 0.00069 28.0 0.0 24 90-113 11-34 (334)
12 PF15080 DUF4547: Domain of un 20.2 56 0.0012 27.0 1.2 26 79-105 39-64 (196)
No 1
>PF05617 Prolamin_like: Prolamin-like; InterPro: IPR008502 This entry consists of several proteins of unknown function found exclusively in Arabidopsis thaliana.
Probab=99.36 E-value=4.2e-13 Score=87.67 Aligned_cols=53 Identities=25% Similarity=0.547 Sum_probs=48.9
Q ss_pred hHHhhhhhcchhHHHHHHHHhcCc-CC------------CCCchhhHhhhcCCCcchhh----hhhhccc
Q 046401 52 ECWNTLMELKSCSNEIVIFFLNSQ-AD------------TRNCWPAMLTSLGFTAEEGN----ILRGYCD 104 (127)
Q Consensus 52 ~CW~sL~elksCt~EIvlFFLnGe-t~------------~~~CWP~Ml~slGFT~eE~d----iLrGyCd 104 (127)
+||+++.++++|.+||+.+|+||+ .. +++|||+|+..+++++++.. .|++||+
T Consensus 1 kc~~~~~~~~~C~~eI~~~~~~g~~~~i~~~CC~~i~~~g~~C~~~l~~~~~~~p~~~~~~r~~l~~~C~ 70 (70)
T PF05617_consen 1 KCLSSCAKSPGCGDEIFNSFFNGNKKNIGPECCKAINKMGKDCHPALFKMFPFTPFFKPLLRDLLWNHCS 70 (70)
T ss_pred ChHHHcCCccchHHHHHHHHHcCCCCCCChHHHHHHHHHhHhHHHHHHHHccCCCCccchhHHHHHhhcC
Confidence 599999999999999999999988 33 99999999999999999888 9999996
No 2
>PLN00213 predicted protein; Provisional
Probab=99.35 E-value=2.1e-12 Score=97.27 Aligned_cols=105 Identities=22% Similarity=0.438 Sum_probs=74.4
Q ss_pred CcchhHHHHHHHHHHHHHhhhhhcccccccCCCCCCCCchhhhhccCCchhhHHhhhhhcchhHHHHHHHHhcCcCC---
Q 046401 1 MTLKHVFFILAFTCLIIANIANATSRNDRLNNNMKPCNDLVTRLEVSEGLTECWNTLMELKSCSNEIVIFFLNSQAD--- 77 (127)
Q Consensus 1 Ma~~~~fl~~~l~ll~~a~~~~~~~~r~l~~~~m~~~~~L~~RL~~~~~~~~CW~sL~elksCt~EIvlFFLnGet~--- 77 (127)
|..|+++.+++++.+++.-|+. ...+.-+.+.+-+. .++.+-.+...||++|+.++.|..||...-.+||.+
T Consensus 1 m~iknV~~ll~v~cIvvsVna~-lpqf~~~fp~~~p~----~~~pg~pd~~kCwSSl~~vpGCv~EI~~si~~gkf~~Ig 75 (118)
T PLN00213 1 MSIKNVFLLLAVLCIIVSVNAQ-LPQFPAQLPFLFPF----QLIPGLPDITKCFSSVMDIPGCIAEISQSIFTGKFGNLG 75 (118)
T ss_pred CchHHHHHHHHHHHHHheeccC-CCCCCCCCCCCCCc----cCCCCCccHHHHHHHHcCCcchHHHHHHHHHhchhcccc
Confidence 8899999888888775532211 01111111110011 334455577889999999999999999999999996
Q ss_pred ---------CCCchhhHhhhcCCCcchhhhhhhcccCCCCCCCCcc
Q 046401 78 ---------TRNCWPAMLTSLGFTAEEGNILRGYCDASSAPSPSGI 114 (127)
Q Consensus 78 ---------~~~CWP~Ml~slGFT~eE~diLrGyCd~~~~~s~~~~ 114 (127)
+++|||+| ....|. ...||+.|...+.+++|++
T Consensus 76 ~aCCKAf~~~dnCwP~~-P~~P~f---Pp~LK~~Cs~i~~~~~~~~ 117 (118)
T PLN00213 76 PACCKAFLDADNCIPKI-PFIPFF---PPMLKEQCSRVAGATPPIP 117 (118)
T ss_pred hHHHHHHHhhhccccCC-cCCCcc---chHHHHHHhcccCCCCCCC
Confidence 66999996 755555 7889999999987777654
No 3
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=95.47 E-value=0.01 Score=42.70 Aligned_cols=28 Identities=18% Similarity=0.294 Sum_probs=16.8
Q ss_pred CcchhHHHHHHHHHHHHHhhhhhcccccc
Q 046401 1 MTLKHVFFILAFTCLIIANIANATSRNDR 29 (127)
Q Consensus 1 Ma~~~~fl~~~l~ll~~a~~~~~~~~r~l 29 (127)
||||. ||+++|.|.++..+++.+++|++
T Consensus 1 MaSK~-~llL~l~LA~lLlisSevaa~~~ 28 (95)
T PF07172_consen 1 MASKA-FLLLGLLLAALLLISSEVAAREL 28 (95)
T ss_pred CchhH-HHHHHHHHHHHHHHHhhhhhHHh
Confidence 99776 44444443333334468888888
No 4
>KOG0673 consensus Thymidylate synthase [Nucleotide transport and metabolism]
Probab=63.69 E-value=5.1 Score=34.57 Aligned_cols=33 Identities=36% Similarity=0.809 Sum_probs=25.9
Q ss_pred HHHHHHhcCcCC-------CCCchh-----hHhhhcCCC-cchhhh
Q 046401 66 EIVIFFLNSQAD-------TRNCWP-----AMLTSLGFT-AEEGNI 98 (127)
Q Consensus 66 EIvlFFLnGet~-------~~~CWP-----~Ml~slGFT-~eE~di 98 (127)
|=+++||.|.|. +-+=|- +.|.++||| -||||+
T Consensus 66 EElLwfi~G~t~ak~l~~kgv~IWd~ngsrefLds~G~~~re~GDl 111 (293)
T KOG0673|consen 66 EELLWFISGSTDAKVLEEKGVHIWDGNGSREFLDSVGFTAREEGDL 111 (293)
T ss_pred HHHHHHHhCCCccchhhhcCceeecCCchHHHHHhcCCCccccCCc
Confidence 557899999998 445576 899999999 456664
No 5
>PF03058 Sar8_2: Sar8.2 family; InterPro: IPR004297 Members of this family are found in Solanaceae spp. plants, a taxonomic group (family) that includes pepper and tobacco plant species. Synthesis of these proteins is induced by Tobacco mosaic virus and salicylic acid []; indeed they are thought to be involved in the development of systemic acquired resistance (SAR) after an initial hypersensitive response to microbial infection [, ]. SAR is characterised by long-lasting resistance to infection by a wide range of pathogens, extending to plant tissues distant from the initial infection site [].
Probab=53.26 E-value=10 Score=28.08 Aligned_cols=29 Identities=21% Similarity=0.361 Sum_probs=18.5
Q ss_pred Ccchh-HHHHHHH--HHHHHHhhhhhcccccccCC
Q 046401 1 MTLKH-VFFILAF--TCLIIANIANATSRNDRLNN 32 (127)
Q Consensus 1 Ma~~~-~fl~~~l--~ll~~a~~~~~~~~r~l~~~ 32 (127)
|++|+ .||.+.| .|++|+ +-+.+|+.+.+
T Consensus 1 M~~Ktnlfl~lSLailLmIIS---Sqv~AREms~A 32 (93)
T PF03058_consen 1 MVSKTNLFLCLSLAILLMIIS---SQVDAREMSKA 32 (93)
T ss_pred CcchhhhHHHHHHHHHHHHHh---hHHHHHHHhcc
Confidence 88988 4666666 444443 56777877633
No 6
>PF02479 Herpes_IE68: Herpesvirus immediate early protein; InterPro: IPR003403 This regulatory protein is expressed from an immediate early gene in the cell cycle of Herpesviridae. The protein is known by various names including IE-68, US1, ICP22 and IR4.
Probab=43.78 E-value=14 Score=28.58 Aligned_cols=32 Identities=28% Similarity=0.641 Sum_probs=25.7
Q ss_pred HHHHHhcCcCC---CCCchhhHhhhcCCCcchhhhhhh
Q 046401 67 IVIFFLNSQAD---TRNCWPAMLTSLGFTAEEGNILRG 101 (127)
Q Consensus 67 IvlFFLnGet~---~~~CWP~Ml~slGFT~eE~diLrG 101 (127)
++-|+|-|-+. +..||..||. .+++++--||-
T Consensus 64 l~D~YlmGy~~~Rl~~~~We~lLQ---lsp~qs~~LR~ 98 (132)
T PF02479_consen 64 LLDFYLMGYTRQRLTPACWERLLQ---LSPEQSRRLRR 98 (132)
T ss_pred HHHHHHHhhccCCCCHHHHHHHHh---hCcccchHHHH
Confidence 56789999888 9999999999 67777666653
No 7
>PF01465 GRIP: GRIP domain; InterPro: IPR000237 The GRIP (golgin-97, RanBP2alpha,Imh1p and p230/golgin-245) domain [, , ] is found in many large coiled-coil proteins. It has been shown to be sufficient for targeting to the Golgi []. The GRIP domain contains a completely conserved tyrosine residue.; GO: 0005515 protein binding, 0000042 protein targeting to Golgi; PDB: 1R4A_H 1UPT_B.
Probab=28.25 E-value=33 Score=21.51 Aligned_cols=18 Identities=33% Similarity=0.517 Sum_probs=13.2
Q ss_pred hhhHhhhcCCCcchhhhh
Q 046401 82 WPAMLTSLGFTAEEGNIL 99 (127)
Q Consensus 82 WP~Ml~slGFT~eE~diL 99 (127)
=|.+-+.|.||++|...+
T Consensus 28 lpvi~tlL~fs~~e~~~i 45 (46)
T PF01465_consen 28 LPVIATLLKFSPEEKQKI 45 (46)
T ss_dssp HHHHHHHTT--HHHHHHH
T ss_pred HHHHHHHHCCCHHHHHhh
Confidence 489999999999997654
No 8
>PHA02602 56 dCTP pyrophosphatase; Provisional
Probab=26.72 E-value=39 Score=27.46 Aligned_cols=30 Identities=37% Similarity=0.507 Sum_probs=22.3
Q ss_pred cchhHHHHHHHHhcCcCCCCCchhhHhhhcCCCcchhhhhhhc
Q 046401 60 LKSCSNEIVIFFLNSQADTRNCWPAMLTSLGFTAEEGNILRGY 102 (127)
Q Consensus 60 lksCt~EIvlFFLnGet~~~~CWP~Ml~slGFT~eE~diLrGy 102 (127)
++-=.-+|++|+++ |+-.||||.+| |.+.|
T Consensus 128 ~k~ElID~~HF~l~-----------~~~~LG~t~ee--I~~aY 157 (172)
T PHA02602 128 IKFELIDQLHFVLN-----------KFIALGMDAEE--IFKLY 157 (172)
T ss_pred HHHHHHHHHHHHHH-----------HHHHcCCCHHH--HHHHH
Confidence 33335678999999 99999999775 44544
No 9
>PF15284 PAGK: Phage-encoded virulence factor
Probab=23.20 E-value=74 Score=22.00 Aligned_cols=16 Identities=25% Similarity=0.461 Sum_probs=12.1
Q ss_pred chhHHHHHHHHHHHHH
Q 046401 3 LKHVFFILAFTCLIIA 18 (127)
Q Consensus 3 ~~~~fl~~~l~ll~~a 18 (127)
+|++||.+.++|..++
T Consensus 4 ~ksifL~l~~~LsA~~ 19 (61)
T PF15284_consen 4 FKSIFLALVFILSAAG 19 (61)
T ss_pred HHHHHHHHHHHHHHhh
Confidence 4778888888887653
No 10
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=21.56 E-value=42 Score=20.63 Aligned_cols=12 Identities=42% Similarity=0.756 Sum_probs=9.1
Q ss_pred hhhcCCCcchhh
Q 046401 86 LTSLGFTAEEGN 97 (127)
Q Consensus 86 l~slGFT~eE~d 97 (127)
|.+|||+..|.+
T Consensus 10 L~~LGy~~~e~~ 21 (47)
T PF07499_consen 10 LISLGYSKAEAQ 21 (47)
T ss_dssp HHHTTS-HHHHH
T ss_pred HHHcCCCHHHHH
Confidence 678999998875
No 11
>PF09402 MSC: Man1-Src1p-C-terminal domain; InterPro: IPR018996 This entry represents the Inner nuclear membrane proteins MAN1 (also known as LEM domain-containing protein 3) and LEM domain-containing protein 2 (or LEM protein 2). Emerin and MAN1 are LEM domain-containing integral membrane proteins of the vertebrate nuclear envelope []. MAN1 is an integral protein of the inner nuclear membrane which binds to chromatin associated proteins and plays a role in nuclear organisation. The C-terminal nulceoplasmic region forms a DNA binding winged helix and binds to Smad []. LEM protein 2 is an essential protein involved in chromosome segregation and cell division, probably via its interaction with lmn-1, the main component of nuclear lamina. Has some overlapping function with emr-1.; GO: 0005639 integral to nuclear inner membrane; PDB: 2CH0_A.
Probab=21.14 E-value=32 Score=27.97 Aligned_cols=24 Identities=29% Similarity=0.497 Sum_probs=0.0
Q ss_pred CCCcchhhhhhhcccCCCCCCCCc
Q 046401 90 GFTAEEGNILRGYCDASSAPSPSG 113 (127)
Q Consensus 90 GFT~eE~diLrGyCd~~~~~s~~~ 113 (127)
|+-..|--+..||||.+.++.+-+
T Consensus 11 ~~wyr~~~~~vgyC~~~~~~~~~~ 34 (334)
T PF09402_consen 11 GLWYREQKIAVGYCGTESPSPSFA 34 (334)
T ss_dssp ------------------------
T ss_pred cccccccccccccccccccccccc
Confidence 445567778899999997776443
No 12
>PF15080 DUF4547: Domain of unknown function (DUF4547)
Probab=20.24 E-value=56 Score=26.98 Aligned_cols=26 Identities=42% Similarity=0.612 Sum_probs=18.9
Q ss_pred CCchhhHhhhcCCCcchhhhhhhcccC
Q 046401 79 RNCWPAMLTSLGFTAEEGNILRGYCDA 105 (127)
Q Consensus 79 ~~CWP~Ml~slGFT~eE~diLrGyCd~ 105 (127)
..=|-+.++ ++||+.|-|||-.|--.
T Consensus 39 dE~Wtavl~-l~FtsmElnilYSYvie 64 (196)
T PF15080_consen 39 DEMWTAVLA-LKFTSMELNILYSYVIE 64 (196)
T ss_pred HHHHHHHHH-hcCChHHHHHHHHHHHH
Confidence 334666554 78999999999888543
Done!