Query 028969
Match_columns 201
No_of_seqs 116 out of 547
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 05:23:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028969.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028969hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2667 COPII vesicle protein 100.0 2E-50 4.3E-55 350.8 13.3 198 1-200 58-283 (379)
2 PF07970 COPIIcoated_ERV: Endo 100.0 1.6E-33 3.5E-38 232.7 12.7 124 77-200 9-147 (222)
3 PF13850 ERGIC_N: Endoplasmic 99.6 3.9E-15 8.4E-20 107.8 5.1 44 1-44 53-96 (96)
4 PF12421 DUF3672: Fibronectin 57.8 8.3 0.00018 29.4 2.2 24 112-135 30-53 (136)
5 KOG3111 D-ribulose-5-phosphate 36.7 18 0.00039 29.6 1.1 15 21-35 28-42 (224)
6 PF15631 Imm-NTF2-2: NTF2 fold 36.2 33 0.00072 22.9 2.2 26 113-138 30-55 (66)
7 PF10401 IRF-3: Interferon-reg 25.0 99 0.0022 24.3 3.6 18 160-178 144-161 (180)
8 TIGR02549 CRISPR_DxTHG CRISPR- 22.7 22 0.00047 19.4 -0.4 12 153-164 4-15 (26)
9 PF00834 Ribul_P_3_epim: Ribul 19.2 64 0.0014 26.1 1.4 13 23-35 25-37 (201)
10 PRK08883 ribulose-phosphate 3- 17.9 60 0.0013 26.7 0.9 12 22-33 24-35 (220)
No 1
>KOG2667 consensus COPII vesicle protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=2e-50 Score=350.80 Aligned_cols=198 Identities=36% Similarity=0.550 Sum_probs=142.2
Q ss_pred CeecCCCCCeeeEEEEEEeCccCCCeeeeeeeecCCCceeccCCceEEEEecCCCceeeee----------eecchhh-h
Q 028969 1 MSVDLKRGETLPIHINMTFPALPCDVLSVDAIDMSGKHEVDLDTNIWKLRLNSYGHIIGTE----------YLTDLVE-K 69 (201)
Q Consensus 1 ~~VD~~~~~kl~In~DItfp~~PC~~lslDv~D~~G~~~~dv~~~i~k~rld~~g~~i~~~----------~~~~~~~-~ 69 (201)
++||.+++++|+||||||||+|||++|+|||||.+|+.++++.++|+|.|+|. +++... ...+... .
T Consensus 58 ~~vd~s~~e~l~in~DItfp~lpC~~lsVDv~D~sg~~~l~i~~~i~k~rl~~--~~i~~~~~~~~~~~~k~~~p~~~~~ 135 (379)
T KOG2667|consen 58 LFVDDSRDEKLQINFDITFPALPCSILSVDVMDVSGEMVLDIDHLIYKLRLDP--EPIPLTIRRFDIFQHKQTIPTTDPI 135 (379)
T ss_pred EEEeCCCCceeeeeeeEEeccCccceEEEEeeccccccccchhhhhhhcccCc--cccccchhhhcccccccccCCCCcc
Confidence 57999999999999999999999999999999999999999999999999998 333310 0000001 1
Q ss_pred hhhcc----c----CCCCCCChhhHH--HhhhccCCC--CchHHHHHHH---HhhccCCCccEEEEEEEEEeeeeEEEEe
Q 028969 70 EHEEH----K----HDHNKDHKDDID--EKLHAFGFD--EDAENMIKKV---KHALESGEGCRVYGVLDVQRVAGNFHIS 134 (201)
Q Consensus 70 ~~~~~----~----~~~~~~~~~~~~--~~~~~~~~~--~~~~~~~~~~---~~~~~~~egCri~G~l~VnkV~G~fhi~ 134 (201)
.|+.+ . ...||..|+.+. ++..+|.+. ...+++.... ......+|||||+|++.||||||||||+
T Consensus 136 ~c~~~~~~~~~~~~~~~~~~~~~~v~~a~~~~g~~~~~~~~~~q~~~~~~~~~~~~~~geGCRi~G~l~VNKVaGnfHia 215 (379)
T KOG2667|consen 136 LCGLCYGAEDFNDGDIDCCNLCEDVREAYRKAGWDFADEDLIDQCKNEGFTNKAAEQKGEGCRIYGQLEVNKVAGNFHIA 215 (379)
T ss_pred chhhhhhhhccccccchhhhcchHHHHHhhhccccccCccchhhhcccccccccCCCCCCceEEEEEEEEeeecceEEEc
Confidence 22222 1 112334454443 233344433 2223222111 1223579999999999999999999999
Q ss_pred ecCccce--eeeehhCCCcceeeeEEeeEeeeCCCCCCCCCCCCCceEEecCCceeEEEEeEEEeeee
Q 028969 135 VHGLNIY--VAQMIFGGAKNVNVSHVIHDLSFGPKYPGIHNPLDGTVRMLHDTSGTFKYYIKVWPWFC 200 (201)
Q Consensus 135 ~~~~~~~--~~~~~~~~~~~~N~sH~I~~lsFG~~~~~~~~PLDg~~~~~~~~~~~~~Y~lkvVPT~~ 200 (201)
||+.... .+........++||||+|||||||+.+|++.|||||+..++.+...+|+||+|||||.|
T Consensus 216 ~g~~~~~~~~h~hd~~~~~~~n~SH~InhLSFG~~~p~~~nPLdG~~~~~~~~~~~~~Yf~KvVPT~y 283 (379)
T KOG2667|consen 216 PGKSSQHSNAHVHDLSLLDNLNFSHRINHLSFGEYIPGIVNPLDGTNFIANEHLTTFQYFLKVVPTVY 283 (379)
T ss_pred cCCCccccccccchhhhcccCCceEEEeeeccCCCCcccccCCCCccccccCCccceeeEEEEcceEE
Confidence 9864321 11111111157999999999999999999999999999999999999999999999987
No 2
>PF07970 COPIIcoated_ERV: Endoplasmic reticulum vesicle transporter ; InterPro: IPR012936 This domain occurs in many hypothetical proteins, and also two partially characterised proteins. One of these proteins, PTX1 Q96RQ1 from SWISSPROT, is a homeodomain-containing transcription factor involved in regulating all pituitary hormone genes []. This protein is down regulated in prostate carcinoma []. The other protein, ERGIC-32 Q969X5 from SWISSPROT, is involved in protein transport from the ER to the Golgi [].
Probab=100.00 E-value=1.6e-33 Score=232.66 Aligned_cols=124 Identities=33% Similarity=0.606 Sum_probs=94.5
Q ss_pred CCCCCChhhHHH--hhhccCCCC--chHHHHHHH----HhhccCCCccEEEEEEEEEeeeeEEEEeecCccce----eee
Q 028969 77 DHNKDHKDDIDE--KLHAFGFDE--DAENMIKKV----KHALESGEGCRVYGVLDVQRVAGNFHISVHGLNIY----VAQ 144 (201)
Q Consensus 77 ~~~~~~~~~~~~--~~~~~~~~~--~~~~~~~~~----~~~~~~~egCri~G~l~VnkV~G~fhi~~~~~~~~----~~~ 144 (201)
..||..|+++.+ +.++|.+.. .++||..++ +.....+|||||+|++.||||+|||||+||+.... .+.
T Consensus 9 ~~CCnTC~~V~~ay~~~~w~~~~~~~~eQC~~~~~~~~~~~~~~~egCri~G~l~VnkV~Gnfhi~~g~~~~~~~~h~hd 88 (222)
T PF07970_consen 9 GKCCNTCEDVREAYRKKGWAFPDLENIEQCRREYVKKIKEQVNEGEGCRIYGSLEVNKVPGNFHIAPGRSFQQDGGHIHD 88 (222)
T ss_pred CCcCcCHHHHHHHHHHhCCCCCCccccccccchhhhhhhhhccCCCCCEEEEEEEEEEEEEEEEEEecchhccCCcceee
Confidence 457778888743 455666543 467766553 33445679999999999999999999999974321 121
Q ss_pred ehhCCCc-ceeeeEEeeEeeeCCCCCCCCCCCCCceEE--ecCCceeEEEEeEEEeeee
Q 028969 145 MIFGGAK-NVNVSHVIHDLSFGPKYPGIHNPLDGTVRM--LHDTSGTFKYYIKVWPWFC 200 (201)
Q Consensus 145 ~~~~~~~-~~N~sH~I~~lsFG~~~~~~~~PLDg~~~~--~~~~~~~~~Y~lkvVPT~~ 200 (201)
....... .+||||+|||||||+++|+..|||||+.++ ++....+|+||||||||+|
T Consensus 89 ~~~~~~~~~~N~SH~I~~lsFG~~~~~~~~PLdg~~~~~~~~~~~~~~~YflkvVPT~y 147 (222)
T PF07970_consen 89 LSPFDDEPKFNFSHTINHLSFGEEIPGIVNPLDGTQKIVQTDNGNYMYQYFLKVVPTTY 147 (222)
T ss_pred hhhhccccCCCCCeEEEEEEeccccccccccccCccccccCCCCceeEEEEEEEeeeee
Confidence 1111222 799999999999999999999999999983 5777899999999999998
No 3
>PF13850 ERGIC_N: Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC)
Probab=99.56 E-value=3.9e-15 Score=107.81 Aligned_cols=44 Identities=48% Similarity=0.881 Sum_probs=41.9
Q ss_pred CeecCCCCCeeeEEEEEEeCccCCCeeeeeeeecCCCceeccCC
Q 028969 1 MSVDLKRGETLPIHINMTFPALPCDVLSVDAIDMSGKHEVDLDT 44 (201)
Q Consensus 1 ~~VD~~~~~kl~In~DItfp~~PC~~lslDv~D~~G~~~~dv~~ 44 (201)
|.||.+++++|+||||||||+|||++|++|++|++|++++|++|
T Consensus 53 ~~VD~~~~~~l~in~ditf~~~pC~~l~vDv~D~~G~~~~dv~h 96 (96)
T PF13850_consen 53 LVVDTSRDEKLQINFDITFPHMPCDFLSVDVQDASGDHQLDVTH 96 (96)
T ss_pred EEEcCCCCceEEEEEEEEECCCccCeeeeEeEccCCCeeccccC
Confidence 57999999999999999999999999999999999999999875
No 4
>PF12421 DUF3672: Fibronectin type III protein ; InterPro: IPR021034 This entry represents a region of bacterial and viral proteins that are typically between 126 and 146 amino acids in length. The signature is found at the C terminus in association with PF09327 from PFAM and PF00041 from PFAM. There are two completely conserved G residues that may be functionally important. Many of the proteins in this entry are annotated as fibronectin type III however there is little accompanying literature to confirm this. It is also found in Host specificity protein J from Enterobacteria phage lambda (Bacteriophage lambda).
Probab=57.80 E-value=8.3 Score=29.42 Aligned_cols=24 Identities=17% Similarity=0.405 Sum_probs=21.3
Q ss_pred CCCccEEEEEEEEEeeeeEEEEee
Q 028969 112 SGEGCRVYGVLDVQRVAGNFHISV 135 (201)
Q Consensus 112 ~~egCri~G~l~VnkV~G~fhi~~ 135 (201)
..|.|.+.|+|+.+|+-|.+--+.
T Consensus 30 ~~~~~~~~Gtv~A~~i~GDiv~~~ 53 (136)
T PF12421_consen 30 IAESCTFKGTVYANKIIGDIVKAY 53 (136)
T ss_pred EcccceEEeEEEehhEecceeEEE
Confidence 378999999999999999987754
No 5
>KOG3111 consensus D-ribulose-5-phosphate 3-epimerase [Carbohydrate transport and metabolism]
Probab=36.68 E-value=18 Score=29.60 Aligned_cols=15 Identities=27% Similarity=0.299 Sum_probs=12.2
Q ss_pred ccCCCeeeeeeeecC
Q 028969 21 ALPCDVLSVDAIDMS 35 (201)
Q Consensus 21 ~~PC~~lslDv~D~~ 35 (201)
+.-|++||+||||-.
T Consensus 28 ~~GadwlHlDVMDg~ 42 (224)
T KOG3111|consen 28 DAGADWLHLDVMDGH 42 (224)
T ss_pred HcCCCeEEEeeeccc
Confidence 346899999999954
No 6
>PF15631 Imm-NTF2-2: NTF2 fold immunity protein
Probab=36.15 E-value=33 Score=22.93 Aligned_cols=26 Identities=27% Similarity=0.368 Sum_probs=21.0
Q ss_pred CCccEEEEEEEEEeeeeEEEEeecCc
Q 028969 113 GEGCRVYGVLDVQRVAGNFHISVHGL 138 (201)
Q Consensus 113 ~egCri~G~l~VnkV~G~fhi~~~~~ 138 (201)
+..=-|.|++...-..|+|||.-.+.
T Consensus 30 ~~~WiV~Gtl~~~~~GGv~~I~I~K~ 55 (66)
T PF15631_consen 30 GDSWIVEGTLPPGMLGGVFYIEIRKK 55 (66)
T ss_pred CCeEEEEeecCCCccCCeEEEEEEcc
Confidence 44478999998888999999997643
No 7
>PF10401 IRF-3: Interferon-regulatory factor 3; InterPro: IPR019471 This is the interferon-regulatory factor 3 chain of the hetero-dimeric structure which also contains the shorter chain CREB-binding protein. These two subunits make up the DRAF1 (double-stranded RNA-activated factor 1). Viral dsRNA produced during viral transcription or replication leads to the activation of DRAF1. The DNA-binding specificity of DRAF1 correlates with transcriptional induction of ISG (interferon-alpha, beta-stimulated gene). IRF-3 pre-exists in the cytoplasm of uninfected cells and translocates to the nucleus following viral infection. Translocation of IRF-3 is accompanied by an increase in serine and threonine phosphorylation, and association with the CREB coactivator occurs only after infection. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1J2F_A 1QWT_A 3A77_B 1ZOQ_A 3DSH_A.
Probab=24.97 E-value=99 Score=24.30 Aligned_cols=18 Identities=28% Similarity=0.606 Sum_probs=13.4
Q ss_pred eEeeeCCCCCCCCCCCCCc
Q 028969 160 HDLSFGPKYPGIHNPLDGT 178 (201)
Q Consensus 160 ~~lsFG~~~~~~~~PLDg~ 178 (201)
=+|.||+..|. ..|+...
T Consensus 144 i~LcfGe~~~~-~~~~~~k 161 (180)
T PF10401_consen 144 IYLCFGEEWPD-GRPWEKK 161 (180)
T ss_dssp EEEEESSSSTT-SSCCCCS
T ss_pred EEEEEcccCCC-CCCccCc
Confidence 57999999987 4565553
No 8
>TIGR02549 CRISPR_DxTHG CRISPR-associated DxTHG motif protein. This model describes a short region highly conserved between two otherwise substantially different CRISPR-associated (cas) proteins, TIGR02221 and TIGR01987. This region includes the motif [VIL]-D-x-[ST]-H-[GS].
Probab=22.73 E-value=22 Score=19.35 Aligned_cols=12 Identities=17% Similarity=0.404 Sum_probs=9.7
Q ss_pred eeeeEEeeEeee
Q 028969 153 VNVSHVIHDLSF 164 (201)
Q Consensus 153 ~N~sH~I~~lsF 164 (201)
+|+||-+++++|
T Consensus 4 lDiTHGfr~~P~ 15 (26)
T TIGR02549 4 LDVTHGFNFMPL 15 (26)
T ss_pred EEecCcccchHH
Confidence 688898888876
No 9
>PF00834 Ribul_P_3_epim: Ribulose-phosphate 3 epimerase family; InterPro: IPR000056 Ribulose-phosphate 3-epimerase (5.1.3.1 from EC) (also known as pentose-5-phosphate 3-epimerase or PPE) is the enzyme that converts D-ribulose 5-phosphate into D-xylulose 5-phosphate in Calvin's reductive pentose phosphate cycle. In Ralstonia eutropha (Alcaligenes eutrophus) two copies of the gene coding for PPE are known [], one is chromosomally encoded P40117 from SWISSPROT, the other one is on a plasmid Q04539 from SWISSPROT. PPE has been found in a wide range of bacteria, archaebacteria, fungi and plants. All the proteins have from 209 to 241 amino acid residues. The enzyme has a TIM barrel structure.; GO: 0004750 ribulose-phosphate 3-epimerase activity, 0005975 carbohydrate metabolic process; PDB: 3CTL_A 3CT7_D 3CU2_A 1RPX_A 3OVR_A 3OVP_A 3OVQ_B 3QC3_B 3INP_A 1TQJ_D ....
Probab=19.18 E-value=64 Score=26.15 Aligned_cols=13 Identities=31% Similarity=0.394 Sum_probs=9.9
Q ss_pred CCCeeeeeeeecC
Q 028969 23 PCDVLSVDAIDMS 35 (201)
Q Consensus 23 PC~~lslDv~D~~ 35 (201)
-++++|+||||-.
T Consensus 25 g~d~lHiDiMDg~ 37 (201)
T PF00834_consen 25 GADWLHIDIMDGH 37 (201)
T ss_dssp T-SEEEEEEEBSS
T ss_pred CCCEEEEeecccc
Confidence 4789999999933
No 10
>PRK08883 ribulose-phosphate 3-epimerase; Provisional
Probab=17.91 E-value=60 Score=26.69 Aligned_cols=12 Identities=33% Similarity=0.542 Sum_probs=10.7
Q ss_pred cCCCeeeeeeee
Q 028969 22 LPCDVLSVDAID 33 (201)
Q Consensus 22 ~PC~~lslDv~D 33 (201)
..++++|+||||
T Consensus 24 ~g~~~lH~DvmD 35 (220)
T PRK08883 24 AGADVVHFDVMD 35 (220)
T ss_pred cCCCEEEEeccc
Confidence 468999999999
Done!