Query psy205
Match_columns 108
No_of_seqs 122 out of 1201
Neff 4.0
Searched_HMMs 46136
Date Fri Aug 16 22:57:24 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy205.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/205hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3659|consensus 99.7 8.9E-19 1.9E-23 153.3 2.7 46 61-106 75-120 (629)
2 COG0733 Na+-dependent transpor 99.7 1.1E-18 2.4E-23 147.9 0.6 44 63-106 4-47 (439)
3 KOG3660|consensus 99.7 1.1E-18 2.3E-23 152.8 -2.5 48 60-107 30-77 (629)
4 PF00209 SNF: Sodium:neurotran 99.6 1.1E-17 2.5E-22 140.2 -4.3 44 64-107 1-44 (523)
5 PF14815 NUDIX_4: NUDIX domain 25.8 35 0.00076 22.7 0.9 13 84-96 22-34 (114)
6 KOG4245|consensus 24.0 29 0.00063 28.6 0.3 25 80-104 161-188 (297)
7 TIGR02230 ATPase_gene1 F0F1-AT 23.2 22 0.00047 25.2 -0.5 21 70-90 75-95 (100)
8 cd03431 DNA_Glycosylase_C DNA 20.9 42 0.00091 21.5 0.5 10 84-93 27-36 (118)
9 COG3911 Predicted ATPase [Gene 15.2 66 0.0014 25.3 0.5 21 1-21 6-34 (183)
10 PF05567 Neisseria_PilC: Neiss 12.6 89 0.0019 25.7 0.6 8 84-91 230-237 (335)
No 1
>KOG3659|consensus
Probab=99.73 E-value=8.9e-19 Score=153.32 Aligned_cols=46 Identities=54% Similarity=1.159 Sum_probs=44.0
Q ss_pred hhcCCCCCchHHHHHHHhhhhccCCceeecceeeeeeCCeeEEEee
Q psy205 61 VAERGSWGSRWEFLLSCVGLSVGIGNVWRFPYLAYQNGGGFLMRKQ 106 (108)
Q Consensus 61 ~~~R~~Wssk~~fiLa~iG~aVGLGNiWRFPyL~~~nGGgaFlIPY 106 (108)
.+.|+.|++|++|+||++|++|.|||+|||||||++||||+|++||
T Consensus 75 ~e~R~~W~~K~eflLa~vgfaV~lgnvWrFpYlC~~nGGgaFlvpY 120 (629)
T KOG3659|consen 75 LEQRPTWGSKTEFLLAVVGFAVDLGNVWRFPYLCYKNGGGAFLVPY 120 (629)
T ss_pred hccCCcchhHHHHHHHHHHHhhcccccceeeheeeeCCCEeEhHHH
Confidence 3349999999999999999999999999999999999999999999
No 2
>COG0733 Na+-dependent transporters of the SNF family [General function prediction only]
Probab=99.71 E-value=1.1e-18 Score=147.95 Aligned_cols=44 Identities=48% Similarity=1.048 Sum_probs=43.2
Q ss_pred cCCCCCchHHHHHHHhhhhccCCceeecceeeeeeCCeeEEEee
Q psy205 63 ERGSWGSRWEFLLSCVGLSVGIGNVWRFPYLAYQNGGGFLMRKQ 106 (108)
Q Consensus 63 ~R~~Wssk~~fiLa~iG~aVGLGNiWRFPyL~~~nGGgaFlIPY 106 (108)
+|++|+||++||||++|.||||||+|||||++++||||||+|||
T Consensus 4 ~re~w~SrlGFILAa~GsAVGLGNiWrFPy~~~~nGGgAFll~y 47 (439)
T COG0733 4 KREQWSSRLGFILAAAGSAVGLGNIWRFPYMAGENGGGAFLLPY 47 (439)
T ss_pred cccchhhHHHHHHHHHHHHhcccccccCCeEeeecCcchHHHHH
Confidence 68999999999999999999999999999999999999999998
No 3
>KOG3660|consensus
Probab=99.69 E-value=1.1e-18 Score=152.80 Aligned_cols=48 Identities=60% Similarity=1.228 Sum_probs=45.2
Q ss_pred hhhcCCCCCchHHHHHHHhhhhccCCceeecceeeeeeCCeeEEEeec
Q psy205 60 AVAERGSWGSRWEFLLSCVGLSVGIGNVWRFPYLAYQNGGGFLMRKQQ 107 (108)
Q Consensus 60 ~~~~R~~Wssk~~fiLa~iG~aVGLGNiWRFPyL~~~nGGgaFlIPY~ 107 (108)
.++.|++|+++.||+|+|+|++|||||||||||+|++||||||||||.
T Consensus 30 ~~~~R~~w~~~~efllS~ig~~vGlgNvwRFP~~~y~nGGgaFLIpY~ 77 (629)
T KOG3660|consen 30 AEPDRGNWKSKIEFLLSCLGYAVGLGNVWRFPYLAYKNGGGAFLIPYL 77 (629)
T ss_pred cccccccchhHHHHHHHHHHHHhhhhHHHHHHHHHHhcCCchHHHHHH
Confidence 334799999999999999999999999999999999999999999994
No 4
>PF00209 SNF: Sodium:neurotransmitter symporter family; InterPro: IPR000175 Neurotransmitter transport systems are integral to the release, re-uptake and recycling of neurotransmitters at synapses. High affinity transport proteins found in the plasma membrane of presynaptic nerve terminals and glial cells are responsible for the removal from the extracellular space of released-transmitters, thereby terminating their actions []. Plasma membrane neurotransmitter transporters fall into two structurally and mechanistically distinct families. The majority of the transporters constitute an extensive family of homologous proteins that derive energy from the co-transport of Na+ and Cl-, in order to transport neurotransmitter molecules into the cell against their concentration gradient. The family has a common structure of 12 presumed transmembrane helices and includes carriers for gamma-aminobutyric acid (GABA), noradrenaline/adrenaline, dopamine, serotonin, proline, glycine, choline, betaine and taurine. They are structurally distinct from the second more-restricted family of plasma membrane transporters, which are responsible for excitatory amino acid transport. The latter couple glutamate and aspartate uptake to the cotransport of Na+ and the counter-transport of K+, with no apparent dependence on Cl- []. In addition, both of these transporter families are distinct from the vesicular neurotransmitter transporters [, ]. Sequence analysis of the Na+/Cl- neurotransmitter superfamily reveals that it can be divided into four subfamilies, these being transporters for monoamines, the amino acids proline and glycine, GABA, and a group of orphan transporters [].; GO: 0005328 neurotransmitter:sodium symporter activity, 0006836 neurotransmitter transport, 0016021 integral to membrane; PDB: 2QEI_A 3F3C_A 3USP_A 3USK_A 3TU0_A 3GWW_A 3TT3_A 3F4J_A 3USJ_B 3GJC_B ....
Probab=99.61 E-value=1.1e-17 Score=140.21 Aligned_cols=44 Identities=50% Similarity=1.207 Sum_probs=38.2
Q ss_pred CCCCCchHHHHHHHhhhhccCCceeecceeeeeeCCeeEEEeec
Q psy205 64 RGSWGSRWEFLLSCVGLSVGIGNVWRFPYLAYQNGGGFLMRKQQ 107 (108)
Q Consensus 64 R~~Wssk~~fiLa~iG~aVGLGNiWRFPyL~~~nGGgaFlIPY~ 107 (108)
|++|+||.+|+++|+|++||+||+|||||+|++||||+|+|||.
T Consensus 1 R~~w~~~~~~~l~~~g~~vglgn~wrfp~~~~~~gG~~Fli~y~ 44 (523)
T PF00209_consen 1 REKWSSKIGFILACIGYAVGLGNIWRFPYLCYENGGGAFLIPYL 44 (523)
T ss_dssp ----S-HHHHHHHHHHHHSSHHHHTHHHHHHHHTTTHHHHHHHH
T ss_pred CCcccccccccccccccccccccccccccccccccccccccccc
Confidence 78999999999999999999999999999999999999999994
No 5
>PF14815 NUDIX_4: NUDIX domain; PDB: 1VRL_A 1RRQ_A 3G0Q_A 3FSQ_A 1RRS_A 3FSP_A.
Probab=25.75 E-value=35 Score=22.69 Aligned_cols=13 Identities=23% Similarity=0.935 Sum_probs=7.0
Q ss_pred CCceeecceeeee
Q psy205 84 IGNVWRFPYLAYQ 96 (108)
Q Consensus 84 LGNiWRFPyL~~~ 96 (108)
++++|.||.+...
T Consensus 22 l~GLwefP~~e~~ 34 (114)
T PF14815_consen 22 LAGLWEFPLIESD 34 (114)
T ss_dssp TTT-EE--EEE-S
T ss_pred hhcCcccCEeCcc
Confidence 5789999988754
No 6
>KOG4245|consensus
Probab=23.96 E-value=29 Score=28.61 Aligned_cols=25 Identities=32% Similarity=0.716 Sum_probs=18.5
Q ss_pred hhccCCcee-ecce--eeeeeCCeeEEE
Q psy205 80 LSVGIGNVW-RFPY--LAYQNGGGFLMR 104 (108)
Q Consensus 80 ~aVGLGNiW-RFPy--L~~~nGGgaFlI 104 (108)
+++=+|||. .||. ||..+|||||-.
T Consensus 161 cs~img~i~~~fpklklcfahggga~p~ 188 (297)
T KOG4245|consen 161 CSMIMGGIFEKFPKLKLCFAHGGGAFPF 188 (297)
T ss_pred HHHHHhhHHHhCchheeeeecCCcccce
Confidence 345567777 5996 699999999843
No 7
>TIGR02230 ATPase_gene1 F0F1-ATPase subunit, putative. This model represents a protein found encoded in F1F0-ATPase operons in several genomes, including Methanosarcina barkeri (archaeal) and Chlorobium tepidum (bacterial). It is a small protein (about 100 amino acids) with long hydrophic stretches and is presumed to be a subunit of the enzyme.
Probab=23.18 E-value=22 Score=25.21 Aligned_cols=21 Identities=29% Similarity=0.817 Sum_probs=17.8
Q ss_pred hHHHHHHHhhhhccCCceeec
Q psy205 70 RWEFLLSCVGLSVGIGNVWRF 90 (108)
Q Consensus 70 k~~fiLa~iG~aVGLGNiWRF 90 (108)
-+..++..+|.++|.-|+|.+
T Consensus 75 ~~tl~~lllGv~~G~~n~w~w 95 (100)
T TIGR02230 75 SWTLTMLIVGVVIGCLNAWHW 95 (100)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 467788889999999999975
No 8
>cd03431 DNA_Glycosylase_C DNA glycosylase (MutY in bacteria and hMYH in humans) is responsible for repairing misread A*oxoG residues to C*G by removing the inappropriately paired adenine base from the DNA backbone. It belongs to the Nudix hydrolase superfamily and is important for the repair of various genotoxic lesions. Enzymes belonging to this superfamily requires a divalent cation, such as Mg2+ or Mn2+ for their activity. They are also recognized by a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V). However, DNA glycosylase does not seem to contain this signature motif. DNA glycosylase consists of 2 domains: the N-terminal domain contains the catalytic properties of the enzyme and the C-terminal domain affects substrate (oxoG) binding and enzymatic turnover. The C-terminal domain is highly similar to MutT, based on secondary structure and topology, despite low sequence identity. MutT sanitizes the nucleotide precursor pool by hydrolyzing oxo-dGTP to
Probab=20.91 E-value=42 Score=21.51 Aligned_cols=10 Identities=30% Similarity=1.152 Sum_probs=8.0
Q ss_pred CCceeeccee
Q psy205 84 IGNVWRFPYL 93 (108)
Q Consensus 84 LGNiWRFPyL 93 (108)
++++|.||-+
T Consensus 27 ~~glwefP~~ 36 (118)
T cd03431 27 LAGLWEFPSV 36 (118)
T ss_pred CCcceeCCCc
Confidence 5789999964
No 9
>COG3911 Predicted ATPase [General function prediction only]
Probab=15.23 E-value=66 Score=25.33 Aligned_cols=21 Identities=33% Similarity=0.585 Sum_probs=16.2
Q ss_pred CCc--ccccCCCCCCc------ccccCCc
Q psy205 1 MNR--FFSSSGVPRGG------SLRERTY 21 (108)
Q Consensus 1 ~~~--~~~~~~~~~~~------~~r~~~y 21 (108)
||| +|-.||-||++ .|+..+|
T Consensus 6 ~nR~~~fIltGgpGaGKTtLL~aLa~~Gf 34 (183)
T COG3911 6 FNRHKRFILTGGPGAGKTTLLAALARAGF 34 (183)
T ss_pred cccceEEEEeCCCCCcHHHHHHHHHHcCc
Confidence 688 99999999987 3555555
No 10
>PF05567 Neisseria_PilC: Neisseria PilC beta-propeller domain; InterPro: IPR008707 This domain is found in several PilC protein sequences from Neisseria gonorrhoeae and Neisseria meningitidis. PilC is a phase-variable protein associated with pilus-mediated adherence of pathogenic Neisseria to target cells [].; PDB: 3HX6_A.
Probab=12.56 E-value=89 Score=25.68 Aligned_cols=8 Identities=63% Similarity=1.369 Sum_probs=5.9
Q ss_pred CCceeecc
Q psy205 84 IGNVWRFP 91 (108)
Q Consensus 84 LGNiWRFP 91 (108)
.||||||=
T Consensus 230 ~GnlwR~d 237 (335)
T PF05567_consen 230 GGNLWRFD 237 (335)
T ss_dssp TSEEEEEE
T ss_pred CCcEEEEE
Confidence 38888874
Done!