Query 032352
Match_columns 142
No_of_seqs 104 out of 240
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 12:58:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032352.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032352hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1688 Golgi proteins involve 100.0 1.7E-59 3.7E-64 372.8 9.6 130 12-141 1-133 (188)
2 PF03248 Rer1: Rer1 family; I 100.0 2.4E-54 5.3E-59 343.2 11.0 115 28-142 2-125 (176)
3 COG5249 RER1 Golgi protein inv 100.0 7.3E-47 1.6E-51 296.1 8.2 116 27-142 10-129 (180)
4 PF12273 RCR: Chitin synthesis 48.6 7.8 0.00017 28.8 0.7 13 53-65 1-13 (130)
5 KOG3827 Inward rectifier K+ ch 35.4 25 0.00054 32.0 1.9 48 30-82 45-92 (400)
6 PRK11383 hypothetical protein; 30.5 33 0.00072 27.2 1.7 48 42-89 68-121 (145)
7 PF05360 YiaAB: yiaA/B two hel 29.3 34 0.00074 22.2 1.3 35 50-84 2-42 (53)
8 PF14373 Imm_superinfect: Supe 27.2 42 0.00091 21.3 1.4 14 79-92 16-29 (43)
9 PRK02655 psbI photosystem II r 23.7 1.5E+02 0.0032 18.6 3.4 19 76-94 6-25 (38)
10 PF10524 NfI_DNAbd_pre-N: Nucl 23.5 16 0.00035 23.5 -1.0 12 111-122 6-17 (44)
11 TIGR01299 synapt_SV2 synaptic 22.7 1.5E+02 0.0033 28.5 4.8 33 32-65 145-177 (742)
12 PF04418 DUF543: Domain of unk 21.2 66 0.0014 22.6 1.6 34 34-67 17-50 (75)
No 1
>KOG1688 consensus Golgi proteins involved in ER retention (RER) [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.7e-59 Score=372.83 Aligned_cols=130 Identities=55% Similarity=0.970 Sum_probs=124.6
Q ss_pred cccCCCCCCCCCchhHHHHHHHHHHHHHHHHhhccCccchhHHHHHHHHHHHHHHhhheeccEEEehhhHHHHHHHHHHh
Q 032352 12 AEDFSSSSSSTSPTAAISRWKYNVSRRYQHLLDKSVPHVLHRWVVCLAVVSIYAVRVYLVQGFYIITYGLGIYLLNLLMG 91 (142)
Q Consensus 12 ~~m~~~~~~~~~~~~~~~~~~~~~~~~yQ~~LDk~tp~~~~RW~~~~~L~~lf~lRv~~~~g~yiVtY~LgIylLnlfi~ 91 (142)
+++++.+++++++++|+.++.++++++||+||||+|||+..||+++++++++|++||+..|||||||||||||+||+||+
T Consensus 1 ~e~~~~~~~~~~~a~~v~~~~~~~~~~yQ~yLDr~tPh~~~RW~~tl~l~~iy~iRi~~~~G~YII~Y~LgIYlLNlfia 80 (188)
T KOG1688|consen 1 MEDDSSGEDSGGVASPVKRFFHELSQLYQHYLDRSTPHTAVRWVVTLVLLLIYCIRIYLVQGFYIITYALGIYLLNLFIA 80 (188)
T ss_pred CCccccCCCCCCcchHHHHHHHHHHHHHHHHHhccCCcchhhHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHH
Confidence 46777778888999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCCCCCC---CCCCCCCCCCCCCCCCcccCCcchhhHhHhHHHHhhhhcc
Q 032352 92 FLSPQIDPEY---SDGPTLPTRGSDEFRPFVRRLPEFKFCLTRTIRMMRNSLV 141 (142)
Q Consensus 92 FLtPk~Dp~l---~eg~~LP~~~~dEFrPFiRRLPEFkFW~~~trat~i~l~~ 141 (142)
|||||+||++ +||+.||++++||||||||||||||||+++|||+++|++.
T Consensus 81 FLtPk~Dp~~~~~~dg~~Lpt~~~dEFrPFIRRLPEFKFW~s~~ka~~ia~~~ 133 (188)
T KOG1688|consen 81 FLTPKVDPELQDADDGPSLPTRKSDEFRPFIRRLPEFKFWYSSTKATLIALLC 133 (188)
T ss_pred HhCCCCCchhhcccCCCCCCCCCccccchHHHcCchhHHHHHHHHHHHHHHHH
Confidence 9999999997 7899999999999999999999999999999999999864
No 2
>PF03248 Rer1: Rer1 family; InterPro: IPR004932 RER1 family proteins are involved in involved in the retrieval of some endoplasmic reticulum membrane proteins from the early golgi compartment. The C terminus of yeast Rer1p interacts with a coatomer complex [].; GO: 0016021 integral to membrane
Probab=100.00 E-value=2.4e-54 Score=343.17 Aligned_cols=115 Identities=49% Similarity=0.941 Sum_probs=110.0
Q ss_pred HHHHHHHHHHHHHHHhhccCccchhHHHHHHHHHHHHHHhhheeccEEEehhhHHHHHHHHHHhhcCCCCCCCC------
Q 032352 28 ISRWKYNVSRRYQHLLDKSVPHVLHRWVVCLAVVSIYAVRVYLVQGFYIITYGLGIYLLNLLMGFLSPQIDPEY------ 101 (142)
Q Consensus 28 ~~~~~~~~~~~yQ~~LDk~tp~~~~RW~~~~~L~~lf~lRv~~~~g~yiVtY~LgIylLnlfi~FLtPk~Dp~l------ 101 (142)
++++.++++++||++|||||||++.||+++++|+++|++||+..|||||||||||||+||+||+|||||+||++
T Consensus 2 ~~~~~~~~~~~yQ~~LDk~tp~~~~RW~~~~~L~~lf~~Rv~~~~g~YiVtY~LgIylLnlfi~FltP~~Dp~l~~~~~~ 81 (176)
T PF03248_consen 2 VSRFFQKLKRTYQSYLDKSTPYTKYRWIAFLVLLFLFLLRVYYLQGWYIVTYALGIYLLNLFIAFLTPKFDPELEQDEED 81 (176)
T ss_pred HHHHHHHHHHHHHHHHHhcccCcHHHHHHHHHHHHHHHHHHHHhcceeeehHHHHHHHHHHHHHHhCCcCcccccccccc
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred -CCCCCCCC--CCCCCCCCcccCCcchhhHhHhHHHHhhhhccC
Q 032352 102 -SDGPTLPT--RGSDEFRPFVRRLPEFKFCLTRTIRMMRNSLVS 142 (142)
Q Consensus 102 -~eg~~LP~--~~~dEFrPFiRRLPEFkFW~~~trat~i~l~~s 142 (142)
|||+.||+ +++||||||+|||||||||++||||+++|++.+
T Consensus 82 ~~~g~~Lp~~~~~~~EFrPFiRRlPEFkFW~~~tka~~i~~~~t 125 (176)
T PF03248_consen 82 EEEGPELPTTNENDDEFRPFIRRLPEFKFWYSCTKATVISLFCT 125 (176)
T ss_pred ccccccCCCCcccccccCCccccchhhHHHHHHHHHHHHHHHHH
Confidence 35779999 899999999999999999999999999999753
No 3
>COG5249 RER1 Golgi protein involved in Golgi-to-ER retrieval [Intracellular trafficking and secretion]
Probab=100.00 E-value=7.3e-47 Score=296.13 Aligned_cols=116 Identities=34% Similarity=0.636 Sum_probs=106.3
Q ss_pred HHHHHHHHHHHHHHHHhhccCccchhHHHHHHHHHHHHHHhhheeccEEEehhhHHHHHHHHHHhhcCCCCCCCC---CC
Q 032352 27 AISRWKYNVSRRYQHLLDKSVPHVLHRWVVCLAVVSIYAVRVYLVQGFYIITYGLGIYLLNLLMGFLSPQIDPEY---SD 103 (142)
Q Consensus 27 ~~~~~~~~~~~~yQ~~LDk~tp~~~~RW~~~~~L~~lf~lRv~~~~g~yiVtY~LgIylLnlfi~FLtPk~Dp~l---~e 103 (142)
.+......+++.||+||||.+||+..||..+++|+++|+.||+..+|||+|||+|||||||+|++|||||+||+. +|
T Consensus 10 n~~~k~n~~k~LyqhylDr~~P~~~~RW~i~ggL~~lf~iRI~~~~gwY~icY~LgiyLLn~flaFLTPKfdms~eq~e~ 89 (180)
T COG5249 10 NLITKMNDLKTLYQHYLDRLAPRPDVRWGITGGLFLLFCIRIWSTGGWYLICYCLGIYLLNAFLAFLTPKFDMSFEQIED 89 (180)
T ss_pred HHHHHHHHHHHHHHHHHhhcCCCCcchhhHHHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHhCCCCcccHhhhcc
Confidence 355667889999999999999999999999999999999999999999999999999999999999999999988 33
Q ss_pred -CCCCCCCCCCCCCCcccCCcchhhHhHhHHHHhhhhccC
Q 032352 104 -GPTLPTRGSDEFRPFVRRLPEFKFCLTRTIRMMRNSLVS 142 (142)
Q Consensus 104 -g~~LP~~~~dEFrPFiRRLPEFkFW~~~trat~i~l~~s 142 (142)
+....+++|+|||||||||||||||+++||||++||+.|
T Consensus 90 d~eieeg~kd~EFrPFIRrLPEFkFWy~s~rat~~aLi~s 129 (180)
T COG5249 90 DDEIEEGEKDNEFRPFIRRLPEFKFWYFSTRATGMALIGS 129 (180)
T ss_pred ccccccccccchhhHHHHcCchhHHHHHHHHHHHHHHHHH
Confidence 334445689999999999999999999999999999865
No 4
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=48.63 E-value=7.8 Score=28.81 Aligned_cols=13 Identities=23% Similarity=0.611 Sum_probs=9.5
Q ss_pred HHHHHHHHHHHHH
Q 032352 53 RWVVCLAVVSIYA 65 (142)
Q Consensus 53 RW~~~~~L~~lf~ 65 (142)
||+++++++++++
T Consensus 1 RW~l~~iii~~i~ 13 (130)
T PF12273_consen 1 RWVLFAIIIVAIL 13 (130)
T ss_pred CeeeHHHHHHHHH
Confidence 7888887776554
No 5
>KOG3827 consensus Inward rectifier K+ channel [Inorganic ion transport and metabolism]
Probab=35.37 E-value=25 Score=31.96 Aligned_cols=48 Identities=17% Similarity=0.400 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHhhccCccchhHHHHHHHHHHHHHHhhheeccEEEehhhHH
Q 032352 30 RWKYNVSRRYQHLLDKSVPHVLHRWVVCLAVVSIYAVRVYLVQGFYIITYGLG 82 (142)
Q Consensus 30 ~~~~~~~~~yQ~~LDk~tp~~~~RW~~~~~L~~lf~lRv~~~~g~yiVtY~Lg 82 (142)
+..+=++..+-.++| .+.||..+++.+...+.=.++.--||+|+|+.|
T Consensus 45 ~~~rYl~DifTTlVD-----~kWR~~lliF~~sf~~SWl~Fg~iwwlIA~~hG 92 (400)
T KOG3827|consen 45 KRLRYLQDIFTTLVD-----LKWRWMLLIFSLSFVLSWLFFGVIWWLIAYAHG 92 (400)
T ss_pred HHHHHHHHHHHHHhh-----hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 344555666677777 688888877777655544555445777777654
No 6
>PRK11383 hypothetical protein; Provisional
Probab=30.50 E-value=33 Score=27.17 Aligned_cols=48 Identities=15% Similarity=0.240 Sum_probs=37.5
Q ss_pred HhhccCccchhHHHHHHHHHHHHHHhhhee------ccEEEehhhHHHHHHHHH
Q 032352 42 LLDKSVPHVLHRWVVCLAVVSIYAVRVYLV------QGFYIITYGLGIYLLNLL 89 (142)
Q Consensus 42 ~LDk~tp~~~~RW~~~~~L~~lf~lRv~~~------~g~yiVtY~LgIylLnlf 89 (142)
=+|-+-.|...-|.++++.+.+++.=++.. .|||..+|.|++|=--..
T Consensus 68 gi~vt~~f~~~cw~a~l~~i~LL~iGLwNA~l~lsEKGfY~~af~lsLFgai~v 121 (145)
T PRK11383 68 GIPTTSIYYMTCLTVFIISVALLMVGLWNATLLLSEKGFYGLAFFLSLFGAVAV 121 (145)
T ss_pred CCChhHHHHHHHHHHHHHHHHHHHHHHhcCCcchhhhhHHHHHHHHHHHHHHHH
Confidence 455566789999999999999988887765 699999988887754433
No 7
>PF05360 YiaAB: yiaA/B two helix domain; InterPro: IPR008024 This domain consists of two transmembrane helices and a conserved linking section.
Probab=29.34 E-value=34 Score=22.17 Aligned_cols=35 Identities=11% Similarity=0.388 Sum_probs=25.9
Q ss_pred chhHHHHHHHHHHHHHHhhhee------ccEEEehhhHHHH
Q 032352 50 VLHRWVVCLAVVSIYAVRVYLV------QGFYIITYGLGIY 84 (142)
Q Consensus 50 ~~~RW~~~~~L~~lf~lRv~~~------~g~yiVtY~LgIy 84 (142)
...-|+++++-+.++..=++.. .|||.+++.++++
T Consensus 2 ~~~~~~~f~i~~~~~~iGl~~~~~~l~~KGy~~~~~l~~l~ 42 (53)
T PF05360_consen 2 VGQSWISFGISIVLMLIGLWNAPLDLSEKGYYAMGLLFLLF 42 (53)
T ss_pred hhHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHH
Confidence 4567999998888887777765 6777777765554
No 8
>PF14373 Imm_superinfect: Superinfection immunity protein
Probab=27.21 E-value=42 Score=21.30 Aligned_cols=14 Identities=50% Similarity=0.933 Sum_probs=11.6
Q ss_pred hhHHHHHHHHHHhh
Q 032352 79 YGLGIYLLNLLMGF 92 (142)
Q Consensus 79 Y~LgIylLnlfi~F 92 (142)
...+|+++|+|+|+
T Consensus 16 ~~~~I~~~Nl~lGW 29 (43)
T PF14373_consen 16 NKWAIFLLNLLLGW 29 (43)
T ss_pred cchhhHhHHHHHHh
Confidence 45789999999886
No 9
>PRK02655 psbI photosystem II reaction center I protein I; Provisional
Probab=23.73 E-value=1.5e+02 Score=18.59 Aligned_cols=19 Identities=37% Similarity=0.731 Sum_probs=13.4
Q ss_pred EehhhHHHHHHHHHH-hhcC
Q 032352 76 IITYGLGIYLLNLLM-GFLS 94 (142)
Q Consensus 76 iVtY~LgIylLnlfi-~FLt 94 (142)
++.|+.-|+...+|+ |||+
T Consensus 6 i~Vy~vV~ffvsLFiFGfls 25 (38)
T PRK02655 6 ISVYIVVFFFVGLFVFGFLS 25 (38)
T ss_pred eeehhhHHHHHHHHHcccCC
Confidence 456877788887775 6763
No 10
>PF10524 NfI_DNAbd_pre-N: Nuclear factor I protein pre-N-terminus; InterPro: IPR019548 Nuclear factor I (NF-I) or CCAAT box-binding transcription factor (CTF) [, ] (also known as TGGCA-binding proteins) are a family of vertebrate nuclear proteins which recognise and bind, as dimers, the palindromic DNA sequence 5'-TGGCANNNTGCCA-3'. CTF/NF-I binding sites are present in viral and cellular promoters and in the origin of DNA replication of Human adenovirus 2 (HAdV-2). The CTF/NF-I proteins were first identified as nuclear factor I, a collection of proteins that activate the replication of several Adenovirus serotypes (together with NF-II and NF-III) []. The family of proteins was also identified as the CTF transcription factors, before the NFI and CTF families were found to be identical []. The CTF/NF-I proteins are individually capable of activating transcription and DNA replication. In a given species, there are a large number of different CTF/NF-I proteins, generated both by alternative splicing and by the occurrence of four different genes. CTF/NF-1 proteins contain 400 to 600 amino acids. The N-terminal 200 amino-acid sequence, almost perfectly conserved in all species and genes sequenced, mediates site-specific DNA recognition, protein dimerisation and Adenovirus DNA replication. The C-terminal 100 amino acids contain the transcriptional activation domain. This activation domain is the target of gene expression regulatory pathways elicited by growth factors and it interacts with basal transcription factors and with histone H3 []. This entry represents the N terminus, of which 200 residues contain the DNA-binding and dimerisation domain, but also has an 8-47 residue highly conserved region 5' of this, whose function is not known. Deletion of the N-terminal 200 amino acids removes the DNA-binding activity, dimerisation-ability and the stimulation of adenovirus DNA replication [].
Probab=23.51 E-value=16 Score=23.48 Aligned_cols=12 Identities=50% Similarity=1.016 Sum_probs=9.6
Q ss_pred CCCCCCCcccCC
Q 032352 111 GSDEFRPFVRRL 122 (142)
Q Consensus 111 ~~dEFrPFiRRL 122 (142)
..|||+|||..|
T Consensus 6 ~~de~hpFiEal 17 (44)
T PF10524_consen 6 QQDEFHPFIEAL 17 (44)
T ss_pred hHHHhhhHHHHH
Confidence 468999999754
No 11
>TIGR01299 synapt_SV2 synaptic vesicle protein SV2. This model describes a tightly conserved subfamily of the larger family of sugar (and other) transporters described by pfam model pfam00083. Members of this subfamily include closely related forms SV2A and SV2B of synaptic vesicle protein from vertebrates and a more distantly related homolog (below trusted cutoff) from Drosophila melanogaster. Members are predicted to have two sets of six transmembrane helices.
Probab=22.73 E-value=1.5e+02 Score=28.49 Aligned_cols=33 Identities=9% Similarity=0.337 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHhhccCccchhHHHHHHHHHHHHH
Q 032352 32 KYNVSRRYQHLLDKSVPHVLHRWVVCLAVVSIYA 65 (142)
Q Consensus 32 ~~~~~~~yQ~~LDk~tp~~~~RW~~~~~L~~lf~ 65 (142)
...+.+.|...+|+ .++...+|...+++.+.++
T Consensus 145 ~~~~~~~~d~~l~~-~~~~~~~~~l~~i~~l~~~ 177 (742)
T TIGR01299 145 EEELAQQYELIIQE-CGHGRFQWALFFVLGLALM 177 (742)
T ss_pred hhHHHHHHHHHHHH-cCCCHHHHHHHHHHHHHHH
Confidence 34577888889999 8888888877666555443
No 12
>PF04418 DUF543: Domain of unknown function (DUF543); InterPro: IPR007512 This family of short eukaryotic proteins has no known function. Most of the members of this family are only 80 amino acid residues long. However the Arabidopsis homologue is over 300 residues long. These proteins contain a conserved N-terminal cysteine and a conserved motif GXGXGXG in the carboxy terminal half that may be functionally important.
Probab=21.19 E-value=66 Score=22.55 Aligned_cols=34 Identities=6% Similarity=0.185 Sum_probs=27.3
Q ss_pred HHHHHHHHHhhccCccchhHHHHHHHHHHHHHHh
Q 032352 34 NVSRRYQHLLDKSVPHVLHRWVVCLAVVSIYAVR 67 (142)
Q Consensus 34 ~~~~~yQ~~LDk~tp~~~~RW~~~~~L~~lf~lR 67 (142)
.+.+++.+|||...-++..-=++-++..++|+-|
T Consensus 17 ~~~~kwD~cl~~~l~k~~~G~~~G~~~s~l~frr 50 (75)
T PF04418_consen 17 ELGEKWDRCLSDTLVKTGLGFGIGVVFSLLFFRR 50 (75)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHcc
Confidence 8889999999999888887777766666766655
Done!