Query psy11918
Match_columns 285
No_of_seqs 123 out of 177
Neff 3.4
Searched_HMMs 46136
Date Fri Aug 16 22:17:19 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11918.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11918hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2243|consensus 100.0 6.2E-72 1.4E-76 579.3 7.7 215 63-281 4604-4843(5019)
2 KOG3533|consensus 99.9 9E-26 2E-30 238.4 4.8 117 164-282 2327-2447(2706)
3 PF06459 RR_TM4-6: Ryanodine R 94.1 0.023 5.1E-07 53.7 1.4 53 27-81 7-59 (274)
4 PF06459 RR_TM4-6: Ryanodine R 93.3 0.028 6.1E-07 53.2 0.5 32 60-94 224-274 (274)
5 PF00520 Ion_trans: Ion transp 88.8 0.77 1.7E-05 36.9 4.6 58 226-283 66-123 (200)
6 KOG2301|consensus 63.3 11 0.00023 43.9 5.0 58 226-283 531-591 (1592)
7 KOG2301|consensus 62.0 5.8 0.00013 46.0 2.7 54 226-279 1256-1309(1592)
8 PLN03223 Polycystin cation cha 57.3 19 0.00041 41.8 5.5 52 231-282 1304-1355(1634)
9 KOG3208|consensus 39.8 45 0.00099 31.6 4.4 39 233-271 186-226 (231)
10 PF08016 PKD_channel: Polycyst 38.2 98 0.0021 30.1 6.6 77 205-282 284-360 (425)
11 PF14106 DUF4279: Domain of un 37.1 23 0.00051 27.9 1.8 20 153-172 2-21 (118)
12 KOG3155|consensus 34.6 21 0.00045 32.5 1.2 23 130-152 148-171 (173)
13 cd09216 GH64-LPHase-like glyco 32.5 25 0.00054 34.9 1.5 30 125-155 171-217 (353)
14 PF06056 Terminase_5: Putative 32.1 45 0.00097 24.7 2.5 28 145-172 2-29 (58)
15 PF09071 Alpha-amyl_C: Alpha-a 32.0 21 0.00045 28.0 0.7 13 127-139 38-50 (66)
16 KOG3713|consensus 30.3 81 0.0018 32.7 4.8 48 237-284 325-372 (477)
17 KOG2642|consensus 25.4 4E+02 0.0087 27.5 8.5 85 194-284 238-326 (446)
18 TIGR00994 3a0901s05TIC20 chlor 24.8 2.6E+02 0.0055 27.2 6.7 20 256-275 221-240 (267)
19 TIGR00257 IMPACT_YIGZ uncharac 24.3 11 0.00023 34.5 -2.4 15 14-28 95-109 (204)
20 TIGR01640 F_box_assoc_1 F-box 24.1 84 0.0018 27.3 3.2 34 50-86 26-59 (230)
21 PF09142 TruB_C: tRNA Pseudour 24.1 37 0.00081 24.9 0.9 43 38-85 2-52 (56)
22 PLN02777 photosystem I P subun 23.2 56 0.0012 29.6 2.0 27 38-64 16-42 (167)
23 PF04539 Sigma70_r3: Sigma-70 23.0 91 0.002 22.8 2.8 28 145-172 9-36 (78)
24 PRK11568 hypothetical protein; 22.9 11 0.00025 34.3 -2.5 15 14-28 95-109 (204)
25 KOG4608|consensus 21.1 56 0.0012 31.5 1.6 60 24-84 14-76 (270)
No 1
>KOG2243|consensus
Probab=100.00 E-value=6.2e-72 Score=579.28 Aligned_cols=215 Identities=42% Similarity=0.691 Sum_probs=201.8
Q ss_pred CCcceEEeeeecccCCCCeeeee-------------------eccCcceeeeecccccceeeeecccccccccCCCCCCC
Q psy11918 63 GGKPLEMFNLDVTKDDTGQYKMV-------------------PHESTPIKQTSTEEGVGGREMSQEGEGGEEHRAESEMP 123 (285)
Q Consensus 63 ~~~~~~~f~l~~~~e~~g~~~~~-------------------~~LkvPlviFkrE~KeiaR~Lefdg~~i~e~p~~dd~~ 123 (285)
...+...|-|+ |++|||.+. .|||||||||||| |||||||||||+||||||+|||||
T Consensus 4604 ~~~~~v~~vle---essgym~ptlr~laiihtiis~~ciigyyclkvplvifkre-keiarklefdglyiteqpseddik 4679 (5019)
T KOG2243|consen 4604 EEEAAVFFVLE---ESSGYMAPTLRALAIIHTIISFFCIIGYYCLKVPLVIFKRE-KEIARKLEFDGLYITEQPSEDDIK 4679 (5019)
T ss_pred hhhhheeeeee---cccCcccHHHHHHHHHHHHHHHHHHHhhHhhccceEEEehH-HHHHHhccccceEeecCCCccccc
Confidence 34566789999 999999874 3699999999999 999999999999999999999999
Q ss_pred CccceeeccCCCCCCcccchHHHHHHHHHhccccChHHHHHhhCCCCCcCCccccc------cccceeeeeeecceeEEE
Q psy11918 124 DPAVTLADLLGSFPVNYWDKFAKKKVRQKYSETYDFDSISNLLGMEKTSFSSQEEE------ESSGIISFILRIDWRYQV 197 (285)
Q Consensus 124 ~~wdrlvi~~~SFP~~YWDKfvK~KV~~Ky~~~y~~e~I~elLGmd~t~~~~~~~~------~~~~l~s~i~n~d~ky~i 197 (285)
||||||||||||||+|||||||||||++||||.||+|||+|||||||++++.+... ...++.+|++++|++|++
T Consensus 4680 gqwdrlvint~sfpnnywdkfvkrkv~~kygd~yg~driaellgldk~aldfs~~~ek~k~~~~ssl~a~l~sid~ky~~ 4759 (5019)
T KOG2243|consen 4680 GQWDRLVINTPSFPNNYWDKFVKRKVIDKYGDFYGADRIAELLGLDKAALDFSDAEEKKKAEAASSLSAVLNSIDMKYHI 4759 (5019)
T ss_pred cccceEEecCCCCCchHHHHHHHHHHHHhhhhhhhHHHHHHHhCCccccccCCchhhhccchhhhHHHHHHhhhhhhhee
Confidence 99999999999999999999999999999999999999999999999998765322 233489999999999999
Q ss_pred EeeeeeeecchhHHHHHHHHHHhhhchhhHHHHHHHHHHhcchhHHHHHHHhHhchhhHHHHHHHHHHHHHHhhhhheee
Q psy11918 198 WKAGVTITDNAFLYSLWYFTFSVMGNFNNFFFAAHLLDVAVGFKTLRTILQSVTHNGKQLVLTVMLLTIIVYIYYLCIPQ 277 (285)
Q Consensus 198 wkig~IltD~~flY~l~Yli~SiLGlfnpFFFAfHLlDIi~R~~TL~NVIkSVT~NgkqLiLT~~L~lIvvYiYSIIaF~ 277 (285)
||+|+++||++|+|..||+.+|+||++|+||||.||+||++.++||++|+.|||||||||+||+.|..+++|+|+++||.
T Consensus 4760 wklgvvftdnsflylawy~tmsvlghynnfffaahlldiamgfktlrtilssvthngkqlvltvgllavvvylytvvafn 4839 (5019)
T KOG2243|consen 4760 WKLGVVFTDNSFLYLAWYMTMSVLGHYNNFFFAAHLLDIAMGFKTLRTILSSVTHNGKQLVLTVGLLAVVVYLYTVVAFN 4839 (5019)
T ss_pred eeeeEEEecCchHHHHHHHHHHHHhccchHHHHHHHHHHHHhHHHHHHHHHHhccCCeEEEEeehhHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeec
Q psy11918 278 HCCD 281 (285)
Q Consensus 278 ~f~D 281 (285)
||+.
T Consensus 4840 ffrk 4843 (5019)
T KOG2243|consen 4840 FFRK 4843 (5019)
T ss_pred HHHH
Confidence 9863
No 2
>KOG3533|consensus
Probab=99.91 E-value=9e-26 Score=238.38 Aligned_cols=117 Identities=26% Similarity=0.426 Sum_probs=110.4
Q ss_pred HhhCCCCCc---CCccccccccceeeeeeecceeEEEEeeeeeeecchhHHHHHHHHHHhhhch-hhHHHHHHHHHHhcc
Q psy11918 164 NLLGMEKTS---FSSQEEEESSGIISFILRIDWRYQVWKAGVTITDNAFLYSLWYFTFSVMGNF-NNFFFAAHLLDVAVG 239 (285)
Q Consensus 164 elLGmd~t~---~~~~~~~~~~~l~s~i~n~d~ky~iwkig~IltD~~flY~l~Yli~SiLGlf-npFFFAfHLlDIi~R 239 (285)
..+|+.+|. ..++..||..+++||++|.|...+.+.. +++|.+++||++|+++|++|+| ||||||++|||+++|
T Consensus 2327 ~~iG~~~TL~ilGa~nl~nKiV~vvsfvgNkGt~~r~~~a--ii~d~~~lYh~~Yl~~c~lGL~vH~ffYsiLLFDliyr 2404 (2706)
T KOG3533|consen 2327 SSIGVTPTLYILGALNLVNKIVHVVSFVGNKGTFDRGYAA--ILADRNLLYHLVYLFICILGLFVHPFFYSILLFDLIYR 2404 (2706)
T ss_pred HHhCCcchHHHHHHHHHhhheeEEEEeecCCcccchhHHH--HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 568999997 3458899999999999999999988865 8899999999999999999998 999999999999999
Q ss_pred hhHHHHHHHhHhchhhHHHHHHHHHHHHHHhhhhheeeeeecc
Q psy11918 240 FKTLRTILQSVTHNGKQLVLTVMLLTIIVYIYYLCIPQHCCDQ 282 (285)
Q Consensus 240 ~~TL~NVIkSVT~NgkqLiLT~~L~lIvvYiYSIIaF~~f~DQ 282 (285)
.+||.|||+|||+||++++||++|++|++|+|||+||.||.|.
T Consensus 2405 EETL~NVIkSVTRNgrSIvlTa~LALILvYlFSIiGflffkdD 2447 (2706)
T KOG3533|consen 2405 EETLQNVIKSVTRNGRSIVLTALLALILVYLFSILGFLFFKDD 2447 (2706)
T ss_pred HHHHHHHHHHHhcCCceeHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 9999999999999999999999999999999999999999884
No 3
>PF06459 RR_TM4-6: Ryanodine Receptor TM 4-6; InterPro: IPR009460 The release of Ca2+ ions from intracellular stores is a key step in a wide variety of cellular functions. In striated muscle, the release of Ca2+ from the sarcoplasmic reticulum (SR) leads to muscle contraction. Ca2+ release occurs through large, high-conductance Ca2+ release channels, also known as ryanodine receptors (RyRs) because they bind the plant alkaloid ryanodine with high affinity and specificity []. This region covers TM regions 4-6 of the ryanodine receptor 1 family.; GO: 0005219 ryanodine-sensitive calcium-release channel activity, 0006874 cellular calcium ion homeostasis, 0016021 integral to membrane
Probab=94.06 E-value=0.023 Score=53.70 Aligned_cols=53 Identities=28% Similarity=0.377 Sum_probs=43.2
Q ss_pred HHhhcCCCCCCCCcchhhhhhhhcccCCCCCCCCCCCCcceEEeeeecccCCCCe
Q psy11918 27 MSLMRGPAIEEPTVEVKEVEKSHMRSYPALPPPPDEGGKPLEMFNLDVTKDDTGQ 81 (285)
Q Consensus 27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~l~~~~e~~g~ 81 (285)
...|||+..+++..+..+.+. -.|++|++ ...++....+++||+|++||.+++
T Consensus 7 q~~v~g~~~e~~~~~~~e~~~-~~~~~~~~-~~~~e~d~~~d~FGl~~kkEgg~~ 59 (274)
T PF06459_consen 7 QDGVHGDVPEEERAEAEEEEG-SERDLPAL-GEGEESDLMSDIFGLDIKKEGGQK 59 (274)
T ss_pred cccccCCCCCcccccccCCCC-cccccccC-CCccccchhhhhcCCccccccCCC
Confidence 357999999999876554433 37889988 778899999999999999998874
No 4
>PF06459 RR_TM4-6: Ryanodine Receptor TM 4-6; InterPro: IPR009460 The release of Ca2+ ions from intracellular stores is a key step in a wide variety of cellular functions. In striated muscle, the release of Ca2+ from the sarcoplasmic reticulum (SR) leads to muscle contraction. Ca2+ release occurs through large, high-conductance Ca2+ release channels, also known as ryanodine receptors (RyRs) because they bind the plant alkaloid ryanodine with high affinity and specificity []. This region covers TM regions 4-6 of the ryanodine receptor 1 family.; GO: 0005219 ryanodine-sensitive calcium-release channel activity, 0006874 cellular calcium ion homeostasis, 0016021 integral to membrane
Probab=93.32 E-value=0.028 Score=53.18 Aligned_cols=32 Identities=22% Similarity=0.337 Sum_probs=26.9
Q ss_pred CCCCCcceEEeeeecccCCCCeeeeee-------------------ccCcceee
Q psy11918 60 PDEGGKPLEMFNLDVTKDDTGQYKMVP-------------------HESTPIKQ 94 (285)
Q Consensus 60 ~~~~~~~~~~f~l~~~~e~~g~~~~~~-------------------~LkvPlvi 94 (285)
+++.....++|.|+ |++|||.++. ||||||||
T Consensus 224 ee~~e~~~~~~~Le---EstgYMep~Lr~lAvlHtiiSf~clIgYY~LKVPLVI 274 (274)
T PF06459_consen 224 EEEDEEGMEYFVLE---ESTGYMEPALRILAVLHTIISFACLIGYYCLKVPLVI 274 (274)
T ss_pred ccccccceEEEEEe---ccchhHHHHHHHHHHHHHHHHHHHHHHHHhccccccC
Confidence 35556778999999 9999999875 49999997
No 5
>PF00520 Ion_trans: Ion transport protein calcium channel signature potassium channel signature sodium channel signature; InterPro: IPR005821 This group of proteins is found in sodium, potassium, and calcium ion channels proteins. The proteins have 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some Na channels proteins the domain is repeated four times, whereas in others (e.g. K channels) the protein forms a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not included in the Pfam family due to it lacking the first four helices. ; GO: 0005216 ion channel activity, 0006811 ion transport, 0055085 transmembrane transport, 0016020 membrane; PDB: 3VMX_B 1QG9_A 1UJL_A 2LE7_A 2LCM_A 3A2A_A 3RW0_A 4EKW_A 3RVY_B 3RVZ_B ....
Probab=88.84 E-value=0.77 Score=36.94 Aligned_cols=58 Identities=19% Similarity=0.254 Sum_probs=52.2
Q ss_pred hHHHHHHHHHHhcchhHHHHHHHhHhchhhHHHHHHHHHHHHHHhhhhheeeeeeccC
Q psy11918 226 NFFFAAHLLDVAVGFKTLRTILQSVTHNGKQLVLTVMLLTIIVYIYYLCIPQHCCDQG 283 (285)
Q Consensus 226 pFFFAfHLlDIi~R~~TL~NVIkSVT~NgkqLiLT~~L~lIvvYiYSIIaF~~f~DQ~ 283 (285)
..+-.+.++.++.+++.++..++++.+..+++.-...+.+++++.|+++++..|.+..
T Consensus 66 ~~l~~~R~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~a~~~~~lf~~~~ 123 (200)
T PF00520_consen 66 RLLRLLRLLRLLRRFRSLRRLLRALIRSFPDLFKFILLLFIVLLFFACIGYQLFGGSD 123 (200)
T ss_dssp HHHHHHHHHHHHHTTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS
T ss_pred Eeeccccccccccccccccccccccccccccccccccccccccccccchhheeccccc
Confidence 4666778999999999999999999999999999999999999999999998887653
No 6
>KOG2301|consensus
Probab=63.31 E-value=11 Score=43.94 Aligned_cols=58 Identities=22% Similarity=0.273 Sum_probs=49.0
Q ss_pred hHHHHHHHHH---HhcchhHHHHHHHhHhchhhHHHHHHHHHHHHHHhhhhheeeeeeccC
Q psy11918 226 NFFFAAHLLD---VAVGFKTLRTILQSVTHNGKQLVLTVMLLTIIVYIYYLCIPQHCCDQG 283 (285)
Q Consensus 226 pFFFAfHLlD---Ii~R~~TL~NVIkSVT~NgkqLiLT~~L~lIvvYiYSIIaF~~f~DQ~ 283 (285)
..+=+|+|+. ++...|+|+|.++++-.|+++|.--.++.++++++||++|-+.|.++-
T Consensus 531 svLr~frllRIfkl~k~wp~l~~lv~~i~ns~~~l~~L~l~l~i~i~Ifa~~gmqlFg~~~ 591 (1592)
T KOG2301|consen 531 SVLRSFRLLRIFKLIKSWPTLNDLVKSIFNSGKALGNLVLFLFIFIFIFAAIGMQLFGGVY 591 (1592)
T ss_pred HHHHHHHHHHHHHHHHhhHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHHHhhHHhhCccc
Confidence 4444455554 567899999999999999999999999999999999999999987654
No 7
>KOG2301|consensus
Probab=61.99 E-value=5.8 Score=45.96 Aligned_cols=54 Identities=24% Similarity=0.367 Sum_probs=48.9
Q ss_pred hHHHHHHHHHHhcchhHHHHHHHhHhchhhHHHHHHHHHHHHHHhhhhheeeee
Q psy11918 226 NFFFAAHLLDVAVGFKTLRTILQSVTHNGKQLVLTVMLLTIIVYIYYLCIPQHC 279 (285)
Q Consensus 226 pFFFAfHLlDIi~R~~TL~NVIkSVT~NgkqLiLT~~L~lIvvYiYSIIaF~~f 279 (285)
..|-...++-++-+.+++++.+-.+-.+..++.-.++|.+++.|+||++|-+.|
T Consensus 1256 rl~rV~R~l~Li~~~~~ir~LL~t~~~Sl~al~~i~lLl~ll~fiYAi~Gmq~F 1309 (1592)
T KOG2301|consen 1256 RLFRVGRFLRLIPQAKTIRTLLLTLMMSLPALFFIILLLFLLFFIYAIIGMQLF 1309 (1592)
T ss_pred HHHHHHHHHHhccccchhHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 455667888999999999999999999999999999999999999999987766
No 8
>PLN03223 Polycystin cation channel protein; Provisional
Probab=57.26 E-value=19 Score=41.76 Aligned_cols=52 Identities=12% Similarity=0.088 Sum_probs=46.1
Q ss_pred HHHHHHhcchhHHHHHHHhHhchhhHHHHHHHHHHHHHHhhhhheeeeeecc
Q psy11918 231 AHLLDVAVGFKTLRTILQSVTHNGKQLVLTVMLLTIIVYIYYLCIPQHCCDQ 282 (285)
Q Consensus 231 fHLlDIi~R~~TL~NVIkSVT~NgkqLiLT~~L~lIvvYiYSIIaF~~f~DQ 282 (285)
+=++-++.-+|.|+.+.+++.+-.+.|+-.++++++++|.|+++|+..|-.+
T Consensus 1304 LKfLRLLRFNPrL~vLt~TLrrAapDLa~F~IIF~IVF~AFAqLG~LLFGt~ 1355 (1634)
T PLN03223 1304 GRILKLMDFQPRLGVITRTLWLAGADLMHFFVIFGMVFVGYAFIGHVIFGNA 1355 (1634)
T ss_pred HHHHHHhccChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 4566667779999999999999999999999999999999999999888654
No 9
>KOG3208|consensus
Probab=39.80 E-value=45 Score=31.58 Aligned_cols=39 Identities=15% Similarity=0.374 Sum_probs=30.9
Q ss_pred HHHHhcchhHHHHHHHhHhchhh--HHHHHHHHHHHHHHhh
Q psy11918 233 LLDVAVGFKTLRTILQSVTHNGK--QLVLTVMLLTIIVYIY 271 (285)
Q Consensus 233 LlDIi~R~~TL~NVIkSVT~Ngk--qLiLT~~L~lIvvYiY 271 (285)
+-++..|+|..+++|+++..-++ +|+|.++.++++++++
T Consensus 186 ~~~~a~r~P~IN~Ll~kIk~kkrrdslILa~Vis~C~llll 226 (231)
T KOG3208|consen 186 VNNIANRFPAINQLLQKIKIKKRRDSLILAAVISVCTLLLL 226 (231)
T ss_pred HHHHHHhcchHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHH
Confidence 67899999999999999976555 6888777776665543
No 10
>PF08016 PKD_channel: Polycystin cation channel; InterPro: IPR013122 Polycystic kidney diseases (PKD) are disorders characterised by large numbers of cysts distributed throughout grossly-enlarged kidneys. Cyst development is associated with impairment of kidney function, and ultimately kidney failure and death []. Most cases of autosomal dominant PKD result from mutations in the PKD1 gene that cause premature protein termination. A second gene for autosomal dominant polycystic kidney disease has been identified by positional cloning []. The predicted 968-amino acid sequence of the PKD2 gene product (polycystin-2) contains 6 transmembrane domains, with intracellular N- and C-termini. Polycystin-2 shares some similarity with the family of voltage-activated calcium (and sodium) channels, and contains a potential calcium-binding domain. Polycystin-2 is strongly expressed in ovary, foetal and adult kidney, testis, and small intestine. Polycystin-1 requires the presence of this protein for stable expression and is believed to interact with it via its C terminus. All mutations between exons 1 and 11 result in a truncated polycystin-2 that lacks a calcium-binding EF-hand domain and the cytoplasmic domains required for the interaction of polycystin-2 with polycystin-1 []. PKD2, although clinically milder than PKD1, has a deleterious impact on life expectancy. This entry contains proteins belonging to the polycystin family including Mucolipin and Polycystin-1 and -2 (PKD1 and PKD2). The domain contains the cation channel region of PKD1 and PKD2 proteins. PKD1 and PKD2 may function through a common signalling pathway that is necessary for normal tubulogenesis. The PKD2 gene product has six transmembrane spans with intracellular amino- and carboxyl-termini []. Mucolipin is a cationic channel which probably plays a role in the endocytic pathway and in the control of membrane trafficking of proteins and lipids. It could play a major role in the calcium ion transport regulating lysosomal exocytosis [, , ].
Probab=38.25 E-value=98 Score=30.08 Aligned_cols=77 Identities=13% Similarity=0.015 Sum_probs=55.0
Q ss_pred ecchhHHHHHHHHHHhhhchhhHHHHHHHHHHhcchhHHHHHHHhHhchhhHHHHHHHHHHHHHHhhhhheeeeeecc
Q psy11918 205 TDNAFLYSLWYFTFSVMGNFNNFFFAAHLLDVAVGFKTLRTILQSVTHNGKQLVLTVMLLTIIVYIYYLCIPQHCCDQ 282 (285)
Q Consensus 205 tD~~flY~l~Yli~SiLGlfnpFFFAfHLlDIi~R~~TL~NVIkSVT~NgkqLiLT~~L~lIvvYiYSIIaF~~f~DQ 282 (285)
.|++.+-.+-...-.++|+ .-|+-.+-++-.+.-++.+..+.+++.+-.++|+..+++.++++..|+..++..|.++
T Consensus 284 v~f~~~a~~~~~~~~l~a~-~vfl~~lrll~~l~f~~~~~~~~~tl~~a~~~l~~f~~~~~i~~~~fa~~g~l~fG~~ 360 (425)
T PF08016_consen 284 VDFQELAQWDQLYRYLLAF-LVFLLWLRLLKLLRFNRRLSLLSRTLRRAAKDLLGFFVIFLIIFLAFAQAGYLLFGSY 360 (425)
T ss_pred CCHHHHHHHHHHHHHHHHH-HHHHHHHHHhhheeecchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCC
Confidence 3444433333333333333 2333445666667778999999999999999999999999999999999999888654
No 11
>PF14106 DUF4279: Domain of unknown function (DUF4279)
Probab=37.09 E-value=23 Score=27.90 Aligned_cols=20 Identities=45% Similarity=0.840 Sum_probs=18.7
Q ss_pred hccccChHHHHHhhCCCCCc
Q psy11918 153 YSETYDFDSISNLLGMEKTS 172 (285)
Q Consensus 153 y~~~y~~e~I~elLGmd~t~ 172 (285)
||+..+.|.|+++||+.|+.
T Consensus 2 ~g~~~~p~eiT~~Lgi~Pt~ 21 (118)
T PF14106_consen 2 YGDDFDPDEITRLLGIEPTE 21 (118)
T ss_pred CCCCCCHHHHHHHHCCCceE
Confidence 78999999999999999985
No 12
>KOG3155|consensus
Probab=34.57 E-value=21 Score=32.46 Aligned_cols=23 Identities=26% Similarity=0.384 Sum_probs=19.0
Q ss_pred eccCCC-CCCcccchHHHHHHHHH
Q psy11918 130 ADLLGS-FPVNYWDKFAKKKVRQK 152 (285)
Q Consensus 130 vi~~~S-FP~~YWDKfvK~KV~~K 152 (285)
|-.++. -|+.+|--|+|||-|+|
T Consensus 148 v~~~~~d~PsKwW~cF~kRrFMnk 171 (173)
T KOG3155|consen 148 VYDTPKDKPSKWWLCFAKRRFMNK 171 (173)
T ss_pred hcCCCCCCcchhHHHHHHHHhhhc
Confidence 444444 89999999999999998
No 13
>cd09216 GH64-LPHase-like glycoside hydrolase family 64: laminaripentaose-producing, beta-1,3-glucanase (LPHase)-like. This subfamily is represented by the laminaripentaose-producing, beta-1,3-glucanase (LPHase) of Streptomyces matensis and related bacterial and ascomycete proteins. LPHase is a member of glycoside hydrolase family 64 (GH64), it is an inverting enzyme involved in the cleavage of long-chain polysaccharide beta-1,3-glucans, into specific pentasaccharide oligomers. LPHase is a two-domain crescent fold structure: one domain is composed of 10 beta-strands, eight coming from the N-terminus of the protein and two from the C-terminal region, and the protein has a second inserted domain; this cd includes both domains. This protein has an electronegative, substrate-binding cleft, and conserved Glu and Asp residues involved in the cleavage of the beta-1,3-glucan, laminarin, a plant and fungal cell wall component. Among bacteria, many beta-1,3-glucanases are implicated in fungal cel
Probab=32.51 E-value=25 Score=34.91 Aligned_cols=30 Identities=27% Similarity=0.459 Sum_probs=24.4
Q ss_pred ccceeecc----------CCC-------CCCcccchHHHHHHHHHhcc
Q psy11918 125 PAVTLADL----------LGS-------FPVNYWDKFAKKKVRQKYSE 155 (285)
Q Consensus 125 ~wdrlvi~----------~~S-------FP~~YWDKfvK~KV~~Ky~~ 155 (285)
.|++||+. +|+ ||.+|||-+|-+ |-+||..
T Consensus 171 ~w~~Lv~~~~~g~~lRvlsP~~~~~~g~~~~~Y~d~YId~-vW~kY~~ 217 (353)
T cd09216 171 AWAGLVQRRPDGTVLRVIAPGHGLDAGAFPATYLDGYIDE-VWNKYRT 217 (353)
T ss_pred ccHhheEecCCCCceeEECCCcccccCccchhhHHHHHHH-HHHhhcC
Confidence 58988872 344 999999999975 9999976
No 14
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=32.10 E-value=45 Score=24.72 Aligned_cols=28 Identities=21% Similarity=0.502 Sum_probs=25.2
Q ss_pred HHHHHHHHhccccChHHHHHhhCCCCCc
Q psy11918 145 AKKKVRQKYSETYDFDSISNLLGMEKTS 172 (285)
Q Consensus 145 vK~KV~~Ky~~~y~~e~I~elLGmd~t~ 172 (285)
+|++.+.-|-.-|.-..||+.||+....
T Consensus 2 ~k~~A~~LY~~G~~~~eIA~~Lg~~~~T 29 (58)
T PF06056_consen 2 VKEQARSLYLQGWSIKEIAEELGVPRST 29 (58)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCCChHH
Confidence 7899999999999999999999998643
No 15
>PF09071 Alpha-amyl_C: Alpha-amylase, C terminal; InterPro: IPR015156 This C-terminal domain is found in the prokaryotic protein glycosyltrehalose trehalohydrolase; it assumes a gamma-crystallin-type fold with a five-stranded anti-parallel beta-sheet that packs against the C-terminal side of a beta-alpha barrel. The domain is common to family 13 glycosidases and typically contains a five to ten strand beta-sheet, however its precise fold varies []. ; PDB: 1EHA_A 3VGD_A 3VGB_A 3VGF_A 3VGE_A 3VGH_A 1EH9_A 3VGG_A.
Probab=31.99 E-value=21 Score=27.98 Aligned_cols=13 Identities=38% Similarity=0.261 Sum_probs=9.1
Q ss_pred ceeeccCCCCCCc
Q psy11918 127 VTLADLLGSFPVN 139 (285)
Q Consensus 127 drlvi~~~SFP~~ 139 (285)
-.|++|++|||..
T Consensus 38 G~Lllss~sFP~~ 50 (66)
T PF09071_consen 38 GTLLLSSSSFPKK 50 (66)
T ss_dssp EEEEEESS-S-SE
T ss_pred eeEEEecCCCChh
Confidence 3699999999974
No 16
>KOG3713|consensus
Probab=30.35 E-value=81 Score=32.74 Aligned_cols=48 Identities=19% Similarity=0.167 Sum_probs=42.0
Q ss_pred hcchhHHHHHHHhHhchhhHHHHHHHHHHHHHHhhhhheeeeeeccCC
Q psy11918 237 AVGFKTLRTILQSVTHNGKQLVLTVMLLTIIVYIYYLCIPQHCCDQGH 284 (285)
Q Consensus 237 i~R~~TL~NVIkSVT~NgkqLiLT~~L~lIvvYiYSIIaF~~f~DQ~~ 284 (285)
+-.+..||+......+..+++.|-++..++.|-+||.+.|..-.|+.+
T Consensus 325 aRhS~GLr~lg~Tlr~S~~ElglLllfL~~GI~iFStlvY~~Ek~~~~ 372 (477)
T KOG3713|consen 325 ARHSTGLRTLGLTLRRSYRELGLLLLFLAVGIVIFSTLVYFAEKDEPD 372 (477)
T ss_pred HhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC
Confidence 345677888888999999999999999999999999999998888764
No 17
>KOG2642|consensus
Probab=25.43 E-value=4e+02 Score=27.48 Aligned_cols=85 Identities=18% Similarity=0.235 Sum_probs=51.9
Q ss_pred eEEEEeeeeeeecchhH---HHHHHHHHHhhhchhhHHHHHHHHHHhcchhHHHHHHHhHhchhh-HHHHHHHHHHHHHH
Q psy11918 194 RYQVWKAGVTITDNAFL---YSLWYFTFSVMGNFNNFFFAAHLLDVAVGFKTLRTILQSVTHNGK-QLVLTVMLLTIIVY 269 (285)
Q Consensus 194 ky~iwkig~IltD~~fl---Y~l~Yli~SiLGlfnpFFFAfHLlDIi~R~~TL~NVIkSVT~Ngk-qLiLT~~L~lIvvY 269 (285)
.|.+|+-+.++-|.+.- .|+..+.-.+ -|..+|-+-......-.+|.++.|.+-+. +++.+.+-..++++
T Consensus 238 ~fl~wn~sIvLGDkssHqa~lH~~QifY~f------~F~~~fS~p~l~s~s~ik~llslv~k~k~~~~~v~~~~v~li~~ 311 (446)
T KOG2642|consen 238 AFLVWNGSIVLGDKSSHQACLHFPQIFYFF------SFTLFFSFPHLLSPSKIKTLLSLVWKRKILFLVVTLVSVFLIWK 311 (446)
T ss_pred eeeEecCeEEEcccccccccccHHHHHHHH------HHHHHHhhHhhcChhHHHHHHHHHHHcchHHHHHHHHHHHHHHH
Confidence 67888888888877432 1222111110 01122333355566677889999998887 77777776777888
Q ss_pred hhhhheeeeeeccCC
Q psy11918 270 IYYLCIPQHCCDQGH 284 (285)
Q Consensus 270 iYSIIaF~~f~DQ~~ 284 (285)
.||..-=..-.|..|
T Consensus 312 f~T~~HpyLLADNRH 326 (446)
T KOG2642|consen 312 FYTYAHPYLLADNRH 326 (446)
T ss_pred hhhccCceEeecCce
Confidence 888765555555544
No 18
>TIGR00994 3a0901s05TIC20 chloroplast protein import component, Tic20 family. Two families of proteins are involved in the chloroplast envelope import appartus.They are the three proteins of the outer membrane (TOC) and four proteins in the inner membrane (TIC). This family is specific for the Tic20 protein.
Probab=24.76 E-value=2.6e+02 Score=27.24 Aligned_cols=20 Identities=10% Similarity=0.102 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHHHhhhhhe
Q psy11918 256 QLVLTVMLLTIIVYIYYLCI 275 (285)
Q Consensus 256 qLiLT~~L~lIvvYiYSIIa 275 (285)
.+.+...+++.+.++||++-
T Consensus 221 ~~~~~ifl~vl~~~ifsviq 240 (267)
T TIGR00994 221 KFGMYYWTAIGFTYLFTLLE 240 (267)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 36677788888888888764
No 19
>TIGR00257 IMPACT_YIGZ uncharacterized protein, YigZ family. This uncharacterized protein family includes YigZ, which has been crystallized, from E. coli. YigZ is homologous to the protein product of the mouse IMPACT gene. Crystallography shows a two-domain stucture, and the C-terminal domain is suggested to bind nucleic acids. The function is unknown. Note that the ortholog from E. coli was shown fused to the pepQ gene in GenBank entry X54687. This caused occasional misidentification of this protein as pepQ; this family is found in a number of species that lack pepQ.
Probab=24.30 E-value=11 Score=34.47 Aligned_cols=15 Identities=40% Similarity=0.753 Sum_probs=13.2
Q ss_pred EeehhhHHHHHHHHH
Q psy11918 14 LTVTVQRYFARILMS 28 (285)
Q Consensus 14 ~~~~~~~~~~~~~~~ 28 (285)
..|+|+|||-||+||
T Consensus 95 v~vVVtRYFGGikLG 109 (204)
T TIGR00257 95 IGAVVVRYFGGILLG 109 (204)
T ss_pred EEEEEEEecCCcccC
Confidence 468899999999996
No 20
>TIGR01640 F_box_assoc_1 F-box protein interaction domain. This model describes a large family of plant domains, with several hundred members in Arabidopsis thaliana. Most examples are found C-terminal to an F-box (pfam00646), a 60 amino acid motif involved in ubiquitination of target proteins to mark them for degradation. Two-hybid experiments support the idea that most members are interchangeable F-box subunits of SCF E3 complexes. Some members have two copies of this domain.
Probab=24.14 E-value=84 Score=27.31 Aligned_cols=34 Identities=18% Similarity=0.157 Sum_probs=20.9
Q ss_pred cccCCCCCCCCCCCCcceEEeeeecccCCCCeeeeee
Q psy11918 50 MRSYPALPPPPDEGGKPLEMFNLDVTKDDTGQYKMVP 86 (285)
Q Consensus 50 ~~~~~~~~~~~~~~~~~~~~f~l~~~~e~~g~~~~~~ 86 (285)
-|.+|+.|.+...+......||.| ..++.||++-
T Consensus 26 ~~~LP~~~~~~~~~~~~~~~~G~d---~~~~~YKVv~ 59 (230)
T TIGR01640 26 SRWLPTPKSRRSNKESDTYFLGYD---PIEKQYKVLC 59 (230)
T ss_pred EEecCCCCCcccccccceEEEeec---ccCCcEEEEE
Confidence 366765333222222225689998 6899999975
No 21
>PF09142 TruB_C: tRNA Pseudouridine synthase II, C terminal; InterPro: IPR015225 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA []. The C-terminal domain adopts a secondary structure consisting of a four-stranded beta sheet and one alpha helix, similar to that found in PUA domains. It is predominantly involved in RNA-binding, being mostly found in tRNA pseudouridine synthase B (TruB) []. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 1SGV_B.
Probab=24.06 E-value=37 Score=24.91 Aligned_cols=43 Identities=28% Similarity=0.414 Sum_probs=16.6
Q ss_pred CCcchhhhhhh---hcccCCCCCCCCCCCCcceEEeeee-----cccCCCCeeeee
Q psy11918 38 PTVEVKEVEKS---HMRSYPALPPPPDEGGKPLEMFNLD-----VTKDDTGQYKMV 85 (285)
Q Consensus 38 ~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~f~l~-----~~~e~~g~~~~~ 85 (285)
|..+.+|+|.. |+|.+|+- ..++++-+|.=| +-.+..|++|++
T Consensus 2 P~~~ls~~ea~~l~~Gr~l~~~-----~~~g~~aa~~pdG~lvAL~~~~g~~~rp~ 52 (56)
T PF09142_consen 2 PVRELSAEEARDLRHGRRLPAA-----GPPGPVAAFAPDGRLVALLEERGGRARPV 52 (56)
T ss_dssp EEEE--HHHHHHHHTT---B----------S-EEEE-TTS-EEEEEEEETTEEEEE
T ss_pred CceECCHHHHHHHhCCCccCCC-----CCCceEEEECCCCcEEEEEEccCCcEeEE
Confidence 45566666665 89988875 334455555332 113455555543
No 22
>PLN02777 photosystem I P subunit (PSI-P)
Probab=23.19 E-value=56 Score=29.63 Aligned_cols=27 Identities=26% Similarity=0.485 Sum_probs=16.7
Q ss_pred CCcchhhhhhhhcccCCCCCCCCCCCC
Q psy11918 38 PTVEVKEVEKSHMRSYPALPPPPDEGG 64 (285)
Q Consensus 38 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 (285)
+.+++...-..+.-+||+|||||-..+
T Consensus 16 ~~~~~~~a~~~~~~~lp~lppp~~~~~ 42 (167)
T PLN02777 16 KAPRSSAAASPQCVSLPTLPPPPVQSH 42 (167)
T ss_pred CCCCcCcccCCccccCCCCCCCCcccC
Confidence 333333334457778999999776433
No 23
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=23.03 E-value=91 Score=22.85 Aligned_cols=28 Identities=18% Similarity=0.311 Sum_probs=21.2
Q ss_pred HHHHHHHHhccccChHHHHHhhCCCCCc
Q psy11918 145 AKKKVRQKYSETYDFDSISNLLGMEKTS 172 (285)
Q Consensus 145 vK~KV~~Ky~~~y~~e~I~elLGmd~t~ 172 (285)
++++..++.|..=..+.||+.|||+...
T Consensus 9 a~~~L~~~lgr~Pt~eEiA~~lgis~~~ 36 (78)
T PF04539_consen 9 ARRELEQELGREPTDEEIAEELGISVEE 36 (78)
T ss_dssp HHHHHHHHHSS--BHHHHHHHHTS-HHH
T ss_pred HHHHHHHHhCCCCCHHHHHHHHcccHHH
Confidence 5677888888888999999999998764
No 24
>PRK11568 hypothetical protein; Provisional
Probab=22.95 E-value=11 Score=34.32 Aligned_cols=15 Identities=40% Similarity=0.791 Sum_probs=13.2
Q ss_pred EeehhhHHHHHHHHH
Q psy11918 14 LTVTVQRYFARILMS 28 (285)
Q Consensus 14 ~~~~~~~~~~~~~~~ 28 (285)
..|+|+|||-||+||
T Consensus 95 v~vVVtRYFGGikLG 109 (204)
T PRK11568 95 ITAVVVRYYGGILLG 109 (204)
T ss_pred EEEEEEEEcCCcccc
Confidence 468899999999996
No 25
>KOG4608|consensus
Probab=21.07 E-value=56 Score=31.53 Aligned_cols=60 Identities=32% Similarity=0.403 Sum_probs=38.3
Q ss_pred HHHHHhhcCCCCCCCCcchhhhhhh--hcccCCCCCCCCCCCCcce-EEeeeecccCCCCeeee
Q psy11918 24 RILMSLMRGPAIEEPTVEVKEVEKS--HMRSYPALPPPPDEGGKPL-EMFNLDVTKDDTGQYKM 84 (285)
Q Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~-~~f~l~~~~e~~g~~~~ 84 (285)
+-++.+-|=|++|+-++ ++++-+. -...+-|.++||++|.+.+ +.|+-||++|-+--+++
T Consensus 14 ~~~~~~~~~~~te~~ta-d~~v~~e~~~~k~~eave~ppeTgwerlk~lfg~dis~e~a~v~~v 76 (270)
T KOG4608|consen 14 RALCLFPRVFATEAVTA-DSEVLEERQKRKPYEAVEYPPETGWERLKELFGKDISKELANVCKV 76 (270)
T ss_pred HHHhcCCCCCCcccccC-chHHHHhhcccccccccCCCCccchHHHHHHhCCCcchhhHHHHHH
Confidence 34455555555554444 4443333 3455668889999999887 68999988887654443
Done!