Query psy4340
Match_columns 218
No_of_seqs 146 out of 994
Neff 7.1
Searched_HMMs 46136
Date Fri Aug 16 23:05:48 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4340.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4340hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1944|consensus 100.0 2.7E-41 5.8E-46 285.9 15.1 166 12-178 48-216 (222)
2 PF04117 Mpv17_PMP22: Mpv17 / 99.9 4.1E-25 8.9E-30 154.3 5.1 68 108-175 1-68 (68)
3 COG3167 PilO Tfp pilus assembl 41.4 28 0.0006 29.1 2.9 52 134-191 15-66 (211)
4 PF05365 UCR_UQCRX_QCR9: Ubiqu 39.5 41 0.00088 22.3 3.0 22 1-23 1-23 (55)
5 COG3523 IcmF Type VI protein s 36.1 58 0.0013 34.5 4.9 40 132-171 25-65 (1188)
6 PF11998 DUF3493: Protein of u 33.5 1.7E+02 0.0037 20.6 5.7 51 47-97 14-64 (75)
7 TIGR02163 napH_ ferredoxin-typ 32.0 1.9E+02 0.0042 24.7 6.9 66 49-114 4-79 (255)
8 cd02577 PSTD1 PSTD1: Pseudouri 31.1 1E+02 0.0022 27.7 5.1 30 146-175 228-258 (319)
9 PF11700 ATG22: Vacuole efflux 24.4 60 0.0013 30.6 2.5 57 156-212 138-194 (477)
10 PF03988 DUF347: Repeat of Unk 22.1 2.3E+02 0.0051 18.3 4.5 20 16-35 5-24 (55)
11 PF06109 HlyE: Haemolysin E (H 21.7 1.4E+02 0.0029 25.3 3.8 43 90-132 178-223 (299)
12 PRK13456 DNA protection protei 21.1 1E+02 0.0023 25.5 3.0 53 160-212 28-81 (186)
13 PRK09609 hypothetical protein; 20.6 3.8E+02 0.0082 24.1 6.6 54 21-80 58-111 (312)
No 1
>KOG1944|consensus
Probab=100.00 E-value=2.7e-41 Score=285.92 Aligned_cols=166 Identities=36% Similarity=0.676 Sum_probs=157.8
Q ss_pred hchhHHHHHHHHHHH-HHHHHHHHhhhhhcccC-CCCccHHHHHHHHHHHh-hccchHHHHHHHhhhhcCCCchhHHHHH
Q psy4340 12 KYLFYTNTLGGGVLM-CLGDTIQQTIELYTKAD-KTGYDLKRVAHMGITGL-FMGPPQHFFYKYLDKYLPKRSGKSIALK 88 (218)
Q Consensus 12 ~~Pl~tk~~ts~~l~-~~gD~iaQ~~~~~~~~~-~~~~D~~Rt~rf~~~G~-~~gP~~h~wy~~Ld~~~p~~~~~~~~~K 88 (218)
.+|+++++++++.+. .+||+++|.++..++ . .+.+|+.|++||+++|+ +.||..|+||+.||+++|.++..++++|
T Consensus 48 ~~~~l~~~i~~~~~~~~~~d~~~q~~~~~~~-~~~~~~d~~rtlr~~~~G~~f~gp~~~~Wy~~L~~~~p~~~~~~~~~k 126 (222)
T KOG1944|consen 48 LYPLLTKAITTSLLLAAAGDVISQSLEGRSK-KLFQTLDLTRTLRMGIFGFLFVGPTLHYWYRLLSKLFPKKTLITVVKK 126 (222)
T ss_pred hhhHHHHHHHHHHHHHHhchhhhhhhhhhcc-cccccccHHHHHHHHhhhhheeccchhHHHHHHHHHccCccHHHHHHH
Confidence 688889999888888 999999999998643 2 57899999999999996 5999999999999999999999999999
Q ss_pred HHHHhhhhhhHHHHHHHHHHHHhcCCChHHHHHHHHhhhHHHHHhcCccchHHHHHhhhcccccchhHHHHHHHHHHHHH
Q psy4340 89 LCLDQAIISPVCIIIFLYGIGILEAKPKDEIKEEVRDKFLVIYTTDCLLWPPCQFINFTYISAQYRVIYVNLVSFVYDIL 168 (218)
Q Consensus 89 vl~Dq~v~~P~~~~~f~~~~~~leg~s~~~i~~~lk~~~~~~l~~~~~vWpp~q~inF~~VP~~~Rvl~~n~v~~~W~~y 168 (218)
+++||++++|+.+.+||..++++||++.+++.++++++++|+++++|++||++|++||.|||+++|++++|+++++|++|
T Consensus 127 vl~dql~~~P~~~~~ff~~~~~legk~~~~~~~~~~~~~~p~l~~~~~~WP~~q~inF~~VP~~~rvl~~~~vsl~W~~~ 206 (222)
T KOG1944|consen 127 VLLDQLVFAPLFIVVFFLLMGLLEGKTNEEAKAKLKRKFWPTLKANWMVWPLVQFINFRLVPLQYRVLFVNIVSLVWNTY 206 (222)
T ss_pred HHHhhhhhchHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhhhheecchhheeeeEEccccceehhhhhHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhhccCcc
Q psy4340 169 LSYIKYNDDV 178 (218)
Q Consensus 169 LS~~~~~~~~ 178 (218)
||+++++..+
T Consensus 207 Ls~~~~~~~~ 216 (222)
T KOG1944|consen 207 LSYKNASLVE 216 (222)
T ss_pred HHHHhhcccc
Confidence 9999999843
No 2
>PF04117 Mpv17_PMP22: Mpv17 / PMP22 family ; InterPro: IPR007248 The 22 kDa peroxisomal membrane protein (PMP22) is a major component of peroxisomal membranes. PMP22 seems to be involved in pore-forming activity and may contribute to the unspecific permeability of the organelle membrane. PMP22 is synthesised on free cytosolic ribosomes and then directed to the peroxisome membrane by specific targeting information []. Mpv17 is a closely related peroxisomal protein involved in the development of early-onset glomerulosclerosis []. A member of this family found in Saccharomyces cerevisiae (Baker's yeast) is an integral membrane protein of the inner mitochondrial membrane and has been suggested to play a role in mitochondrial function during heat shock [].; GO: 0016021 integral to membrane
Probab=99.91 E-value=4.1e-25 Score=154.26 Aligned_cols=68 Identities=40% Similarity=0.848 Sum_probs=66.3
Q ss_pred HHHhcCCChHHHHHHHHhhhHHHHHhcCccchHHHHHhhhcccccchhHHHHHHHHHHHHHHhhhhcc
Q psy4340 108 IGILEAKPKDEIKEEVRDKFLVIYTTDCLLWPPCQFINFTYISAQYRVIYVNLVSFVYDILLSYIKYN 175 (218)
Q Consensus 108 ~~~leg~s~~~i~~~lk~~~~~~l~~~~~vWpp~q~inF~~VP~~~Rvl~~n~v~~~W~~yLS~~~~~ 175 (218)
|+++||+|+++++++++++|+++++++|++|||+|++||.|||++||++|+|+++++||+|||+++|+
T Consensus 1 Mg~l~g~s~~~~~~~l~~~~~~~~~~~~~~Wp~~~~vnF~~vP~~~Rv~~~~~v~~~W~~~LS~~~~r 68 (68)
T PF04117_consen 1 MGLLEGKSWEEIKEKLKRDYWPTLKASWKFWPPAQIVNFRYVPPHYRVLFVNVVSFFWNTYLSYIANR 68 (68)
T ss_pred CCcccCCCHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHhcccChhhhhhhhhhHHHHHHHHHHHHhcC
Confidence 57899999999999999999999999999999999999999999999999999999999999999885
No 3
>COG3167 PilO Tfp pilus assembly protein PilO [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=41.37 E-value=28 Score=29.13 Aligned_cols=52 Identities=15% Similarity=0.191 Sum_probs=34.4
Q ss_pred cCccchHHHHHhhhcccccchhHHHHHHHHHHHHHHhhhhccCcccCcccchhhhhhh
Q psy4340 134 DCLLWPPCQFINFTYISAQYRVIYVNLVSFVYDILLSYIKYNDDVFGLRGEEIVHHVE 191 (218)
Q Consensus 134 ~~~vWpp~q~inF~~VP~~~Rvl~~n~v~~~W~~yLS~~~~~~~~~~~~~~~~~~~~~ 191 (218)
|..=||.+-=+-|.. +...-+++++|..|+|-...+-.....++||++..-+
T Consensus 15 Ni~eWpl~~rlv~~l------L~~~~V~~lGy~f~~s~k~eel~~~~~eEe~LKs~~q 66 (211)
T COG3167 15 NIGEWPLAPRLVFCL------LAVAAVLGLGYAFYLSGKLEELEELEAEEEELKSTYQ 66 (211)
T ss_pred cccccchhHHHHHHH------HHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHH
Confidence 333488776666653 3556688999999999777665554555666666433
No 4
>PF05365 UCR_UQCRX_QCR9: Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like; InterPro: IPR008027 The UQCRX/QCR9 protein is the 9/10 subunit of complex III, and is a protein of about 7 kDa. Deletion of QCR9 results in the inability of Saccharomyces cerevisiae to grow on a fermentable carbon source []. The protein is part of the mitchondrial respiratory chain. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0006122 mitochondrial electron transport, ubiquinol to cytochrome c, 0005740 mitochondrial envelope; PDB: 3CX5_T 2IBZ_I 1KYO_I 3CXH_T 1EZV_I 1P84_I 1KB9_I 3H1L_W 3L71_W 3L73_W ....
Probab=39.52 E-value=41 Score=22.28 Aligned_cols=22 Identities=23% Similarity=0.487 Sum_probs=13.5
Q ss_pred ChHHHHHHhhhhch-hHHHHHHHH
Q psy4340 1 MTQILRTIFSQKYL-FYTNTLGGG 23 (218)
Q Consensus 1 m~~~Y~~~l~~~~P-l~tk~~ts~ 23 (218)
|+.+|+..++ |.. +++-++.++
T Consensus 1 ~~~~Y~~~fk-Rns~y~~~i~~ga 23 (55)
T PF05365_consen 1 MSTIYNTFFK-RNSTYVLTIFAGA 23 (55)
T ss_dssp -HHHHHHHTS-SHHHHHHHHHHHH
T ss_pred ChHHHHHHHh-cchHHHHHHHHHH
Confidence 8899999999 555 333333333
No 5
>COG3523 IcmF Type VI protein secretion system component VasK [Intracellular trafficking, secretion, and vesicular transport]
Probab=36.14 E-value=58 Score=34.46 Aligned_cols=40 Identities=13% Similarity=0.130 Sum_probs=32.6
Q ss_pred HhcCccchHHHHHhhhcc-cccchhHHHHHHHHHHHHHHhh
Q psy4340 132 TTDCLLWPPCQFINFTYI-SAQYRVIYVNLVSFVYDILLSY 171 (218)
Q Consensus 132 ~~~~~vWpp~q~inF~~V-P~~~Rvl~~n~v~~~W~~yLS~ 171 (218)
..-|.+||....--+.-. |..-|.+...++.++|-+|+.+
T Consensus 25 ~~vw~~gp~~~~g~~~p~~~~~~R~l~i~~~~~v~l~~~~~ 65 (1188)
T COG3523 25 VAVWFAGPLLEVGDVWPLESLAARLLAIGLIVLVWLLYSTI 65 (1188)
T ss_pred HHHHHhhhhhhhcccccCccHHHHHHHHHHHHHHHHHHHHH
Confidence 456777888887776644 7889999999999999999887
No 6
>PF11998 DUF3493: Protein of unknown function (DUF3493); InterPro: IPR021883 This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 79 to 331 amino acids in length.
Probab=33.50 E-value=1.7e+02 Score=20.60 Aligned_cols=51 Identities=10% Similarity=0.030 Sum_probs=33.1
Q ss_pred ccHHHHHHHHHHHhhccchHHHHHHHhhhhcCCCchhHHHHHHHHHhhhhh
Q psy4340 47 YDLKRVAHMGITGLFMGPPQHFFYKYLDKYLPKRSGKSIALKLCLDQAIIS 97 (218)
Q Consensus 47 ~D~~Rt~rf~~~G~~~gP~~h~wy~~Ld~~~p~~~~~~~~~Kvl~Dq~v~~ 97 (218)
-.+-|.+|.++|+.+.+--.---+-.+-+...+++...++.-+++|-...+
T Consensus 14 ~aPfR~lR~f~y~a~~aSa~iG~~i~~~rl~a~~~l~~~l~nlaI~igava 64 (75)
T PF11998_consen 14 QAPFRGLRRFFYGAFGASAGIGLFIFLFRLIAGPDLNEALPNLAIQIGAVA 64 (75)
T ss_pred HCchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCccHHHHhhhHhHHHHHHH
Confidence 446799999999876322222334455566667777777777777765443
No 7
>TIGR02163 napH_ ferredoxin-type protein, NapH/MauN family. Most members of this family are the NapH protein, found next to NapG,in operons that encode the periplasmic nitrate reductase. Some species with this reductase lack NapC but accomplish electron transfer to NapAB in some other manner, likely to involve NapH, NapG, and/or some other protein. A few members of this protein are designated MauN and are found in methylamine utilization operons in species that appear to lack a periplasmic nitrate reductase.
Probab=31.97 E-value=1.9e+02 Score=24.71 Aligned_cols=66 Identities=18% Similarity=0.277 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHhh-ccchHHHHH--HHhh--h---hcCCCchhHHHHHHHHHhhhhhhHHHHHHH--HHHHHhcCC
Q psy4340 49 LKRVAHMGITGLF-MGPPQHFFY--KYLD--K---YLPKRSGKSIALKLCLDQAIISPVCIIIFL--YGIGILEAK 114 (218)
Q Consensus 49 ~~Rt~rf~~~G~~-~gP~~h~wy--~~Ld--~---~~p~~~~~~~~~Kvl~Dq~v~~P~~~~~f~--~~~~~leg~ 114 (218)
+||...+++..++ .||..+.|. +.|. + -+|......++.-++....+..++++...+ ...+++-|+
T Consensus 4 ~r~~~~~~~~~lf~~~~~~~~~~~~G~l~~s~~~~~~~l~dP~~~lq~~~a~~~~~~~~~~~~~iv~~~~~l~~GR 79 (255)
T TIGR02163 4 LRRLVQLSILGLFLLGPYAGVWILKGNLSSSRLLGTIPLSDPLITLQILLAGHSPPTNALIGALIIVAFYALFGGR 79 (255)
T ss_pred HHHHHHHHHHHHHHcchhhcceEEEecchHHHhcCCccCcCHHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHhcc
Confidence 5788888888876 789887775 3332 2 245566677777777777766666655544 334566665
No 8
>cd02577 PSTD1 PSTD1: Pseudouridine synthase, a subgroup of the TruD family. This group consists of several hypothetical archeal pseudouridine synthases assigned to the TruD family of psuedouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). The TruD family is comprised of proteins related to Escherichia coli TruD.
Probab=31.13 E-value=1e+02 Score=27.65 Aligned_cols=30 Identities=20% Similarity=0.371 Sum_probs=25.4
Q ss_pred hhcccccchhHHHHHH-HHHHHHHHhhhhcc
Q psy4340 146 FTYISAQYRVIYVNLV-SFVYDILLSYIKYN 175 (218)
Q Consensus 146 F~~VP~~~Rvl~~n~v-~~~W~~yLS~~~~~ 175 (218)
|.-+|...|.+|++.. |++||-.+|..-..
T Consensus 228 l~~iP~~lr~myvhAYQSylfN~~lS~Ri~~ 258 (319)
T cd02577 228 FLALPKNLRRMFVHAYQSYLFNEILSERIEE 258 (319)
T ss_pred HHhcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4469999999999866 99999999987753
No 9
>PF11700 ATG22: Vacuole effluxer Atg22 like; InterPro: IPR024671 Autophagy is a major survival mechanism in which eukaryotes recycle cellular nutrients during stress conditions. Atg22, Avt3 and Avt4 are partially redundant vacuolar effluxers, which mediate the efflux of leucine and other amino acids resulting from autophagy []. This family also includes other transporter proteins.
Probab=24.41 E-value=60 Score=30.59 Aligned_cols=57 Identities=12% Similarity=0.073 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHHhhhhccCcccCcccchhhhhhhhhhHHHHHHHHHhhhhhcCCC
Q psy4340 156 IYVNLVSFVYDILLSYIKYNDDVFGLRGEEIVHHVEKDKIEESLANAVDKRLESNGN 212 (218)
Q Consensus 156 l~~n~v~~~W~~yLS~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 212 (218)
+..++..+++|.||..+..++....-..|+..+..+.++..+........|+|+.|-
T Consensus 138 v~~~~~~vfyna~LP~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vS~~G~ 194 (477)
T PF11700_consen 138 VGYEASNVFYNAYLPDLARPEPRVRAAREPSANGNISDSEYEAVDSLTRGRVSGLGW 194 (477)
T ss_pred HHHHHHHHHHHHHhHhhcCCChhhhhhhhhhccCCCChhhhhhHHHhhhchhHHHHH
Confidence 455788899999999998877543222333333333333333333444477777663
No 10
>PF03988 DUF347: Repeat of Unknown Function (DUF347) ; InterPro: IPR007136 This repeat is found as four tandem repeats in a family of bacterial membrane proteins. Each repeat contains two transmembrane regions and a conserved tryptophan.
Probab=22.07 E-value=2.3e+02 Score=18.33 Aligned_cols=20 Identities=20% Similarity=0.202 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q psy4340 16 YTNTLGGGVLMCLGDTIQQT 35 (218)
Q Consensus 16 ~tk~~ts~~l~~~gD~iaQ~ 35 (218)
.++.++..+-...||.++|.
T Consensus 5 ~a~ilt~~lGt~~~D~l~~~ 24 (55)
T PF03988_consen 5 IAKILTTTLGTTAGDFLSKT 24 (55)
T ss_pred HHHHHHHHhHHHHHHHHHhc
Confidence 46788888889999999995
No 11
>PF06109 HlyE: Haemolysin E (HlyE); InterPro: IPR010356 This family consists of several enterobacterial haemolysin (HlyE) proteins. Haemolysin E (HlyE) is a novel pore-forming toxin of Escherichia coli, Salmonella typhi, and Shigella flexneri. HlyE is unrelated to the well characterised pore-forming E. coli haemolysins of the RTX family, haemolysin A (HlyA), and the enterohaemolysin encoded by the plasmid borne ehxA gene of E. coli 0157. However, it is evident that expression of HlyE in the absence of the RTX toxins is sufficient to give a haemolytic phenotype in E. coli. HlyE is a protein of 34 kDa that is expressed during anaerobic growth of E. coli. Anaerobic expression is controlled by the transcription factor, FNR, such that, upon ingestion and entry into the anaerobic mammalian intestine, HlyE is produced and may then contribute to the colonisation of the host [].; PDB: 2WCD_P 1QOY_A.
Probab=21.71 E-value=1.4e+02 Score=25.30 Aligned_cols=43 Identities=21% Similarity=0.376 Sum_probs=29.6
Q ss_pred HHHhhhhhhHH-HHHHHHHHHHhcCCChHHHHHHHHh--hhHHHHH
Q psy4340 90 CLDQAIISPVC-IIIFLYGIGILEAKPKDEIKEEVRD--KFLVIYT 132 (218)
Q Consensus 90 l~Dq~v~~P~~-~~~f~~~~~~leg~s~~~i~~~lk~--~~~~~l~ 132 (218)
+.--++..|+. +..|-...++.||+-..+.+++++. +|+.++.
T Consensus 178 aaagvv~~pfgliisysiaagvvegklip~lk~klksv~~ff~~l~ 223 (299)
T PF06109_consen 178 AAAGVVGRPFGLIISYSIAAGVVEGKLIPELKNKLKSVQNFFESLS 223 (299)
T ss_dssp HGGGGSS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHH
T ss_pred ccccccccCceEEEeehhhhhhhcccccHHHHHHHHHHHHHHHHHH
Confidence 34456788995 5666677899999987888888765 5555443
No 12
>PRK13456 DNA protection protein DPS; Provisional
Probab=21.12 E-value=1e+02 Score=25.54 Aligned_cols=53 Identities=19% Similarity=0.294 Sum_probs=37.0
Q ss_pred HHHHHHHHHHhhhhccCcccCcccchhhhhhhhhhHHHH-HHHHHhhhhhcCCC
Q psy4340 160 LVSFVYDILLSYIKYNDDVFGLRGEEIVHHVEKDKIEES-LANAVDKRLESNGN 212 (218)
Q Consensus 160 ~v~~~W~~yLS~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~ 212 (218)
..+-=|.||+-|..+...+.++.++++++..|....|+. =|+.+-.|+.-=||
T Consensus 28 AlA~E~~a~~~Y~~~a~~~~G~~~e~V~e~le~a~~EEl~HA~~lAeRI~qLGG 81 (186)
T PRK13456 28 NAAAEFTTYYYYTILRAHLIGLEGEGLKEIAEDARLEDRNHFEALVPRIYELGG 81 (186)
T ss_pred HHHHHHHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 344558888999999988888888888877766664443 44555567665554
No 13
>PRK09609 hypothetical protein; Provisional
Probab=20.63 E-value=3.8e+02 Score=24.12 Aligned_cols=54 Identities=22% Similarity=0.215 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHHHHhhhhhcccCCCCccHHHHHHHHHHHhhccchHHHHHHHhhhhcCCC
Q psy4340 21 GGGVLMCLGDTIQQTIELYTKADKTGYDLKRVAHMGITGLFMGPPQHFFYKYLDKYLPKR 80 (218)
Q Consensus 21 ts~~l~~~gD~iaQ~~~~~~~~~~~~~D~~Rt~rf~~~G~~~gP~~h~wy~~Ld~~~p~~ 80 (218)
.+++..+++|++.=.+. +..+.+.=++.-++.|++.|-+.++.|+.+.++|.++
T Consensus 58 ~G~ivG~lsDLLs~li~------pG~ffPgFTLsa~l~GlI~Glf~~~~fk~~~~~f~~~ 111 (312)
T PRK09609 58 VGFFTGLLSDLISFLFV------PGVYHPYYTLAAMVYGFIPGIVGWFFFKFGKKFFGKE 111 (312)
T ss_pred HHHHHHHHHHHHHHHhc------CCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHH
Confidence 46777888999986553 1477888888888889999999999999999988664
Done!