Query psy2199
Match_columns 179
No_of_seqs 172 out of 881
Neff 4.3
Searched_HMMs 46136
Date Fri Aug 16 18:44:47 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2199.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2199hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4272|consensus 100.0 2E-47 4.2E-52 309.8 7.7 161 4-179 1-161 (164)
2 PHA01886 TM2 domain-containing 99.8 6E-21 1.3E-25 139.8 2.9 52 116-167 2-53 (78)
3 PF05154 TM2: TM2 domain; Int 99.6 8.8E-17 1.9E-21 108.1 3.7 49 115-163 2-51 (51)
4 COG2314 XynA Predicted membran 98.4 1.4E-07 3E-12 70.3 1.7 37 115-151 7-43 (95)
5 KOG4272|consensus 79.5 1.9 4.1E-05 36.0 2.9 28 32-59 67-94 (164)
6 smart00208 TNFR Tumor necrosis 46.8 16 0.00035 22.1 1.8 38 5-45 1-39 (39)
7 PF11712 Vma12: Endoplasmic re 24.8 39 0.00084 26.6 1.1 50 117-167 84-133 (142)
8 PF14990 DUF4516: Domain of un 22.1 25 0.00053 23.8 -0.4 22 117-138 12-33 (47)
9 cd00185 TNFR Tumor necrosis fa 21.4 99 0.0021 22.6 2.7 28 17-47 52-79 (98)
10 TIGR03715 KxYKxGKxW KxYKxGKxW 21.2 58 0.0013 19.3 1.1 18 112-129 7-24 (29)
No 1
>KOG4272|consensus
Probab=100.00 E-value=2e-47 Score=309.79 Aligned_cols=161 Identities=43% Similarity=0.906 Sum_probs=151.8
Q ss_pred cCCCCCCcccCCCCceeccCCCCcccCCceEEEEEecCCcccCCCCeeeeecceeeeeecCCcccccccCCCCCcCCCCC
Q psy2199 4 THPLNMSCSELVYPWIRCSYNPKCTYGDLTKVSCTVVDGVSCIGEKTFDKEYVCQYCYQTEPWQHTCVKKASCSSVDSPP 83 (179)
Q Consensus 4 ~cp~~~~Cs~l~~~c~~c~~~~~C~yg~~~~~~C~~~~~v~C~g~~~~~~~~~CryC~q~~~~~~~c~~~~~C~~~~~~~ 83 (179)
.+|....+|.+.++| .|..|-.|.|++++.+.|..++ .|.++.+.+.+-+|++|+|....++.|++..
T Consensus 1 ~~~~l~~~s~~~~~~-~~~~~v~C~~l~~~~~~C~dp~--~~~~~~~~tQq~~~~~C~~~~~~~~~c~~at--------- 68 (164)
T KOG4272|consen 1 MCGVLLLLSRLSADC-PCTPNVKCRYLKPVQFLCKDPV--SCVGPDTKTQQPTCGFCWQLGGADYECEPAT--------- 68 (164)
T ss_pred CcCcceeEEEeecCC-CCCccEEeecCCceEEEcCCCc--ccCCccccccccccchhhhcCCceeEeecCC---------
Confidence 367888899999999 9999999999999999999775 6999887777778999999999999998764
Q ss_pred ceeeEEEEEcCCeeeeccceeecccccccCCCccHHHHHHHHHHhcCcceeeEEeCCchhhhHHHhhhcccchhhhhhhh
Q psy2199 84 VYYKTNCTVQNDVLCLGSRRFLKNVRCNWTGGYRWSTALILSITMGGFGADRFYLGHWQEGIGKVFSFGGLGVWTIIDVI 163 (179)
Q Consensus 84 ~~~~v~C~v~~~i~C~G~r~F~k~vpC~~~~~k~~~~a~lLs~flG~fG~hRFYLG~~~~Gi~~L~t~Gg~gIw~liD~i 163 (179)
.++|++.++++|+|+|+|.|++||+|++++++.+|+|||+|||+|||||||||+|++|++||+|+||+|||||||+|
T Consensus 69 ---~ikC~~~~~v~c~~~rtF~k~~pC~~~~Gy~~~ttlllSifLG~fG~DRFyLGy~~~glgKl~tlGGlgIw~lVDii 145 (164)
T KOG4272|consen 69 ---NIKCTVLDGVECHGNRTFPKEIPCNWTNGYSWTTTLLLSIFLGGFGADRFYLGYWALGLGKLFTLGGLGIWWLVDII 145 (164)
T ss_pred ---cceeEecCCceeecccccccccceeeecCeEehHHHHHHHHhhhccccEEEeCchHHhHhhhhccccchhHHHHHHH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhcccCCCCCCCCC
Q psy2199 164 LIAIRYLGPADGSLYL 179 (179)
Q Consensus 164 lI~~~~~~padGs~yi 179 (179)
||++|+++|||||.||
T Consensus 146 LI~lg~vgPaDGS~yi 161 (164)
T KOG4272|consen 146 LISLGYVGPADGSSYI 161 (164)
T ss_pred HHHhcccccCCCceEE
Confidence 9999999999999996
No 2
>PHA01886 TM2 domain-containing protein
Probab=99.81 E-value=6e-21 Score=139.78 Aligned_cols=52 Identities=35% Similarity=0.443 Sum_probs=50.8
Q ss_pred ccHHHHHHHHHHhcCcceeeEEeCCchhhhHHHhhhcccchhhhhhhhhhhh
Q psy2199 116 YRWSTALILSITMGGFGADRFYLGHWQEGIGKVFSFGGLGVWTIIDVILIAI 167 (179)
Q Consensus 116 k~~~~a~lLs~flG~fG~hRFYLG~~~~Gi~~L~t~Gg~gIw~liD~ilI~~ 167 (179)
||+.+|++||+|+|+||+||||||++++|++|++|+|+++|||+||+|+|+.
T Consensus 2 Ks~~~AylL~~flG~~G~HRFYlG~~~~Gi~~l~t~G~~gig~liD~flIp~ 53 (78)
T PHA01886 2 KSTAIAYVLWFFLGFFGIHRFYTGNIATGIIWLFTGGLFGIGWFIDLFLTAG 53 (78)
T ss_pred CcHHHHHHHHHHHhhcccchhhcCChhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 7899999999999999999999999999999999999999999999999985
No 3
>PF05154 TM2: TM2 domain; InterPro: IPR007829 This domain is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts.
Probab=99.65 E-value=8.8e-17 Score=108.07 Aligned_cols=49 Identities=43% Similarity=0.768 Sum_probs=47.2
Q ss_pred CccHHHHHHHHHHhcCcceeeEEeCCchhhhHHHhhh-cccchhhhhhhh
Q psy2199 115 GYRWSTALILSITMGGFGADRFYLGHWQEGIGKVFSF-GGLGVWTIIDVI 163 (179)
Q Consensus 115 ~k~~~~a~lLs~flG~fG~hRFYLG~~~~Gi~~L~t~-Gg~gIw~liD~i 163 (179)
+||+.+|++||+|+|++|+||||+|++..|++++++. |++++|++||+|
T Consensus 2 ~K~~~~a~lL~~~lG~~G~hrfYlg~~~~g~~~l~~~~g~~~i~~lid~i 51 (51)
T PF05154_consen 2 QKSKWIAYLLSFFLGWFGLHRFYLGKYGKGILYLLTFIGILGIWWLIDLI 51 (51)
T ss_pred CcCHHHHHHHHHHHhhccccceecCchHHHHHHHHHHHHHHHHHHHHHhC
Confidence 6899999999999999999999999999999999998 899999999986
No 4
>COG2314 XynA Predicted membrane protein [Function unknown]
Probab=98.37 E-value=1.4e-07 Score=70.26 Aligned_cols=37 Identities=30% Similarity=0.376 Sum_probs=32.3
Q ss_pred CccHHHHHHHHHHhcCcceeeEEeCCchhhhHHHhhh
Q psy2199 115 GYRWSTALILSITMGGFGADRFYLGHWQEGIGKVFSF 151 (179)
Q Consensus 115 ~k~~~~a~lLs~flG~fG~hRFYLG~~~~Gi~~L~t~ 151 (179)
.+++.++.++++++|++|+||||+|+.+.|+++++..
T Consensus 7 ~~~k~~~~~~~~~~g~~G~hkfYlg~~~~gi~~~~~~ 43 (95)
T COG2314 7 KKNKLIAGLLAALFGIFGLHKFYLGQGGKGILTLLLN 43 (95)
T ss_pred hhhHHHHHHHHHHhcccchHHHHcCCchhhhHHHHHH
Confidence 4677788899999999999999999999999977754
No 5
>KOG4272|consensus
Probab=79.55 E-value=1.9 Score=36.00 Aligned_cols=28 Identities=50% Similarity=1.050 Sum_probs=24.8
Q ss_pred ceEEEEEecCCcccCCCCeeeeecceee
Q psy2199 32 LTKVSCTVVDGVSCIGEKTFDKEYVCQY 59 (179)
Q Consensus 32 ~~~~~C~~~~~v~C~g~~~~~~~~~Cry 59 (179)
..+++|++++++.|.++|+|.|.-.|++
T Consensus 67 at~ikC~~~~~v~c~~~rtF~k~~pC~~ 94 (164)
T KOG4272|consen 67 ATNIKCTVLDGVECHGNRTFPKEIPCNW 94 (164)
T ss_pred CCcceeEecCCceeecccccccccceee
Confidence 3478999999999999999999988876
No 6
>smart00208 TNFR Tumor necrosis factor receptor / nerve growth factor receptor repeats. Repeats in growth factor receptors that are involved in growth factor binding. TNF/TNFR
Probab=46.83 E-value=16 Score=22.12 Aligned_cols=38 Identities=26% Similarity=0.546 Sum_probs=26.2
Q ss_pred CCCCCCcccCC-CCceeccCCCCcccCCceEEEEEecCCccc
Q psy2199 5 HPLNMSCSELV-YPWIRCSYNPKCTYGDLTKVSCTVVDGVSC 45 (179)
Q Consensus 5 cp~~~~Cs~l~-~~c~~c~~~~~C~yg~~~~~~C~~~~~v~C 45 (179)
||.+.-.+.-. ..|+.|. .|.=|..+...|+......|
T Consensus 1 C~~g~y~~~~~~~~C~~C~---~C~~g~~~~~~Ct~~~dt~C 39 (39)
T smart00208 1 CKEGTYCSDGNHSSCLRCR---RCPPGLVVKQPCTATSDTVC 39 (39)
T ss_pred CCCCeecCCCCCccCccCC---CCCCCCEEecCCCCcCcccC
Confidence 55555555544 5677776 67779999999988766555
No 7
>PF11712 Vma12: Endoplasmic reticulum-based factor for assembly of V-ATPase; InterPro: IPR021013 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. The yeast vacuolar proton-translocating ATPase (V-ATPase) is the best characterised member of the V-ATPase family. A total of thirteen genes are required for encoding the subunits of the enzyme complex itself and an additional three for providing factors necessary for the assembly of the whole. Vma12 is one of these latter, all three of which are localised to the endoplasmic reticulum [].
Probab=24.84 E-value=39 Score=26.58 Aligned_cols=50 Identities=14% Similarity=0.169 Sum_probs=27.2
Q ss_pred cHHHHHHHHHHhcCcceeeEEeCCchhhhHHHhhhcccchhhhhhhhhhhh
Q psy2199 117 RWSTALILSITMGGFGADRFYLGHWQEGIGKVFSFGGLGVWTIIDVILIAI 167 (179)
Q Consensus 117 ~~~~a~lLs~flG~fG~hRFYLG~~~~Gi~~L~t~Gg~gIw~liD~ilI~~ 167 (179)
+..++.+..+++|++++...+ +.+-.+.=-++.+.+..+-.++|+++...
T Consensus 84 Nilvsv~~~~~~~~~~~~~~~-~~~~~~~Rvllgl~~al~vlvAEv~l~~~ 133 (142)
T PF11712_consen 84 NILVSVFAVFFAGWYWAGYSF-GGWSFPYRVLLGLFGALLVLVAEVVLYIR 133 (142)
T ss_pred HHHHHHHHHHHHHHHHHHHhh-cccchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555555667776666544 23333333333333344667788888775
No 8
>PF14990 DUF4516: Domain of unknown function (DUF4516)
Probab=22.11 E-value=25 Score=23.84 Aligned_cols=22 Identities=23% Similarity=0.238 Sum_probs=18.6
Q ss_pred cHHHHHHHHHHhcCcceeeEEe
Q psy2199 117 RWSTALILSITMGGFGADRFYL 138 (179)
Q Consensus 117 ~~~~a~lLs~flG~fG~hRFYL 138 (179)
...++.++|++.|.--+||+|-
T Consensus 12 ~~~~~s~~sM~aGA~vVH~~yk 33 (47)
T PF14990_consen 12 KSLVASLLSMLAGASVVHNIYK 33 (47)
T ss_pred HHHHHHHHHHHhhhHHHHHHhC
Confidence 4567788899999999999984
No 9
>cd00185 TNFR Tumor necrosis factor receptor (TNFR) domain; superfamily of TNF-like receptor domains. When bound to TNF-like cytokines, TNFRs trigger multiple signal transduction pathways, they are involved in inflammation response, apoptosis, autoimmunity and organogenesis. TNFRs domains are elongated with generally three tandem repeats of cysteine-rich domains (CRDs). They fit in the grooves between protomers within the ligand trimer. Some TNFRs, such as NGFR and HveA, bind ligands with no structural similarity to TNF and do not bind ligand trimers.
Probab=21.36 E-value=99 Score=22.60 Aligned_cols=28 Identities=25% Similarity=0.566 Sum_probs=21.8
Q ss_pred CceeccCCCCcccCCceEEEEEecCCcccCC
Q psy2199 17 PWIRCSYNPKCTYGDLTKVSCTVVDGVSCIG 47 (179)
Q Consensus 17 ~c~~c~~~~~C~yg~~~~~~C~~~~~v~C~g 47 (179)
.|..| ..|..|+.+...|+......|.=
T Consensus 52 ~C~~c---~~C~~g~~~~~~ct~t~dt~C~C 79 (98)
T cd00185 52 KCLSC---RTCDSGLVEKAPCTATRNTVCGC 79 (98)
T ss_pred cCCcC---ccCCCCCEEEccCCCCCCCeEeC
Confidence 56665 45888999999998888888863
No 10
>TIGR03715 KxYKxGKxW KxYKxGKxW signal peptide. This model describes a novel form of signal peptide that occurs as an N-terminal domain with a recognizable motif, reminiscent of the YSIRK and PEP-CTERM forms of signal peptide. This domain tends to occur on long, low-complexity (usually Serine-rich and heavily glycosylated) proteins of the Firmicutes, and (as with YSIRK) the majority of these proteins have the LPXTG cell wall-anchoring motif at the C-terminus.
Probab=21.24 E-value=58 Score=19.26 Aligned_cols=18 Identities=22% Similarity=0.625 Sum_probs=13.4
Q ss_pred cCCCccHHHHHHHHHHhc
Q psy2199 112 WTGGYRWSTALILSITMG 129 (179)
Q Consensus 112 ~~~~k~~~~a~lLs~flG 129 (179)
|.++|+|.+|.+..+.++
T Consensus 7 yKsGK~Wv~a~~~~~~l~ 24 (29)
T TIGR03715 7 YKSGKQWVFAAITTLALA 24 (29)
T ss_pred EecccHHHHHHHHHHHHH
Confidence 568899999887765443
Done!