Query psy13311
Match_columns 873
No_of_seqs 89 out of 105
Neff 3.2
Searched_HMMs 46136
Date Fri Aug 16 16:17:20 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13311.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13311hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2243|consensus 100.0 3E-240 7E-245 1990.7 36.6 711 27-870 1802-2612(5019)
2 KOG2243|consensus 100.0 1E-113 2E-118 969.2 15.2 717 1-859 2204-3080(5019)
3 PF02026 RyR: RyR domain; Int 99.9 2E-26 4.3E-31 207.7 7.9 83 606-688 1-92 (94)
4 PF01365 RYDR_ITPR: RIH domain 99.6 4.4E-18 9.6E-23 168.2 -7.0 192 286-514 2-206 (207)
5 PF01365 RYDR_ITPR: RIH domain 98.5 2.7E-08 5.8E-13 99.1 -0.2 75 2-88 78-152 (207)
6 PF02026 RyR: RyR domain; Int 98.4 4.9E-08 1.1E-12 89.0 -1.2 69 419-543 1-72 (94)
7 KOG3533|consensus 97.9 3.6E-05 7.8E-10 93.7 8.6 321 321-863 1226-1573(2706)
8 TIGR02309 HpaB-1 4-hydroxyphen 83.0 1.6 3.5E-05 50.3 5.0 98 476-593 2-103 (477)
9 PF13637 Ank_4: Ankyrin repeat 66.6 5.1 0.00011 32.1 2.5 40 24-66 14-53 (54)
10 PF11794 HpaB_N: 4-hydroxyphen 54.8 2.7 5.8E-05 45.6 -1.3 96 477-592 1-102 (264)
11 TIGR02310 HpaB-2 4-hydroxyphen 40.0 24 0.00052 41.9 3.2 31 475-506 12-44 (519)
12 PRK13347 coproporphyrinogen II 28.9 37 0.00079 38.9 2.3 46 5-50 59-116 (453)
13 COG0240 GpsA Glycerol-3-phosph 25.6 73 0.0016 36.1 3.8 95 624-720 14-135 (329)
14 PF13857 Ank_5: Ankyrin repeat 24.8 32 0.00069 28.2 0.7 35 30-66 1-35 (56)
15 PF01479 S4: S4 domain; Inter 23.2 79 0.0017 25.0 2.6 29 450-498 5-37 (48)
16 KOG4825|consensus 21.1 2.3E+02 0.0051 34.0 6.7 83 581-689 127-212 (666)
17 PF09827 CRISPR_Cas2: CRISPR a 20.5 1.2E+02 0.0026 26.5 3.4 53 652-711 3-58 (78)
No 1
>KOG2243|consensus
Probab=100.00 E-value=3.4e-240 Score=1990.70 Aligned_cols=711 Identities=44% Similarity=0.729 Sum_probs=655.3
Q ss_pred HHHHHhcccccc--cCCCCCCCCccccccccccCchHHHHHHHHHHHhhccCchhHHHHHHHhCCCCCCCCccCCCc---
Q psy13311 27 LSFLLENSNILL--SRPSLRGSTPLDVAYSSVMENTELALALSRLLLVGMIRDEDVEKLLMMINPETWDPTFEKDGK--- 101 (873)
Q Consensus 27 ~~~Ll~~~~~~~--~~~s~~gstPlDVa~a~~~dn~pLlKL~d~LLv~Gv~~DeDl~kiL~LI~P~~f~~~~~~~g~--- 101 (873)
++.|-++-+-+. ++++.+|+|...+ .||+||++|||+||+|+|+|+++||.||+|++|+++..++.+
T Consensus 1802 i~mlteavk~~~~h~rdpvggs~ef~f--------vp~ikl~~tllimgif~~dd~k~il~lidpsvf~e~a~~~ee~dt 1873 (5019)
T KOG2243|consen 1802 IQMLTEAVKCGGAHARDPVGGSTEFLF--------VPLIKLFGTLLIMGIFDDDDLKHILLLIDPSVFGEAAAGEEEGDT 1873 (5019)
T ss_pred HHHHHHHHHhccccccCCCCCeeEEee--------ehHHHHHHHHHheeeccchhHHHHHHhcChhhhccccCCccccch
Confidence 455555544443 7799999999999 899999999999999999999999999999999998653221
Q ss_pred -------------------------cccccCceeeccccchhhhHHHHHHHhhhhhhhhhhhhhhhchhhhhhhhhhHHH
Q psy13311 102 -------------------------DEHRKGLLHMKMAEGAKLQMCYLLHHLCDIQLRHRVESIIAFSHDFVGDLQTDQL 156 (873)
Q Consensus 102 -------------------------~~~~~GLL~m~L~E~vKLqmC~lL~hLCD~qLrhRVEsivaFs~~fV~~lQ~dQ~ 156 (873)
...++|||||+|||+||||||.||+||||||+|||||+||+|+++||.+||.||+
T Consensus 1874 ~eke~vt~vdd~k~~~age~~~k~~krp~~gllq~klpe~vklqmc~ll~ylcdce~~hrieaivaf~d~~vaklq~nqk 1953 (5019)
T KOG2243|consen 1874 AEKEEVTQVDDAKAQEAGEEAAKEAKRPKEGLLQMKLPEPVKLQMCELLQYLCDCELQHRIEAIVAFGDDFVAKLQANQK 1953 (5019)
T ss_pred hhhhhhcchhhHhhhhhhhhhhhccCCchhhhhhccCCcchHHHHHHHHHHHhhhhHHhhhHhhhhhhHHHHHHhhcccc
Confidence 0123799999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcc-CCChHHhhhhhcccCCChHHhhhhhcc-c-ccccCCCchHHHHHHHHHHHHHHHhcccccccCch---hh
Q psy13311 157 RRYIEIKQS-DLPSAVAAKKTREFRCPPREQFQNLDR-K-TLKIARVVRDLRERMDHFHESLMKQVSLLALQEPE---RR 230 (873)
Q Consensus 157 ~RY~ei~~~-~Msaa~tAkkTrEFR~pp~eQ~~~l~~-~-~~e~cp~~edlr~~l~~FH~dL~~hcg~~~~~e~~---~~ 230 (873)
+||||+||+ |||||+|||||||||||||||++++.. + +.++|||||+||++|.+||+||+.|||++..+.++ ++
T Consensus 1954 fryne~mqalnmsaaltarktkefrsppqeqinmllnfk~~k~~cpcpeeirdel~dfhedll~hcgi~lded~~~d~~~ 2033 (5019)
T KOG2243|consen 1954 FRYNELMQALNMSAALTARKTKEFRSPPQEQINMLLNFKDDKEECPCPEEIRDELLDFHEDLLLHCGIELDEDEEEDEEE 2033 (5019)
T ss_pred ccHHHHHHHhhhHHHhhhhhhhhccCCcHHHHHHHhhcccCccCCCCcHHHHHHHHHHHHHHHHhcCCccCccccccccc
Confidence 999999998 999999999999999999999999743 3 45899999999999999999999999995432222 12
Q ss_pred h-----------hhhhccCCCC--CCc----------------------cc----------ccchhhhhhcccHHHHHHH
Q psy13311 231 V-----------KSIIYLGSDQ--FPC----------------------EL----------SDIGLLVRQYDSVGELIRA 265 (873)
Q Consensus 231 ~-----------~~i~~l~~~~--~p~----------------------~e----------~~fsLL~RQyd~igeL~~A 265 (873)
+ .+|+++.+.. .|. || .||.||||||||||||++|
T Consensus 2034 d~s~~gkl~alv~ki~~~~k~e~ekp~e~d~k~~stlkelisetmi~waqe~~ied~elvr~mf~ll~rqyd~ig~l~~a 2113 (5019)
T KOG2243|consen 2034 DLSIRGKLCALVEKIKGLKKKEAEKPTEEDEKCPSTLKELISETMICWAQEDQIEDPELVRAMFNLLHRQYDGIGELLQA 2113 (5019)
T ss_pred ccchhhhHHHHHHHhcCCCcccccCCccccccCchHHHHHHHHHHHHhhhhhhccCHHHHHHHHHHHHHhhccHHHHHHh
Confidence 1 4566654322 121 22 2599999999999999999
Q ss_pred hhceEeeccCchhhHHHHHHhhhhhhcccccccChHHHHHHHHHHHHhhhccccccCchhHHHhhhhhhHHHHHHHhhhh
Q psy13311 266 LEKTYVINNKTKDDVSQMWVGLSQIRSLLPVQMSQEEEELMRERLWKLVNNHTFFQHPDLIRILRVHENVMAVMMNTLGR 345 (873)
Q Consensus 266 l~kTY~I~~~s~~D~~~ll~~L~qiRsLL~Vqmg~eEE~Lm~~~L~~lmnn~vF~QHPdLmR~L~~HetVM~vMvNvLg~ 345 (873)
|+||||||..||+||+|||++||||||||+|+||+|||.|||+|||+|||||||||||||||+||||||||+|||||||+
T Consensus 2114 l~ktyti~~~sv~dtinllaalgqirsllsvrmgkeee~lmi~glgdimnnkvfyqhpnlmr~lgmhetvmevmvnvlgg 2193 (5019)
T KOG2243|consen 2114 LPKTYTINGTSVEDTINLLAALGQIRSLLSVRMGKEEEKLMINGLGDIMNNKVFYQHPNLMRALGMHETVMEVMVNVLGG 2193 (5019)
T ss_pred ccceeEEcCccHHHHHHHHHHHHHHHHHHHHhccchhHHHHhhhhhhhhcCcccccCchHHHHhhhHHHHHHHHHHHhcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccccccCCCCCCCCCCCCCcccc---------ccCCCCCCccchHHHHHhhHHHhhhhcCCCCCCCCCCCCCcccccCCC
Q psy13311 346 RAQAQSDAPQTGTGQEGEPQSKH---------KENGEEPEKPGVFKKFYNFVNAVKELEEDPKVEPEPEKKTPEVLSRPS 416 (873)
Q Consensus 346 ~~~~~~~a~~~~~~~~~~~~~~~---------~~~SrqNQ~kamF~Hl~syL~av~~~L~~~~~~~~~~~ns~~~ls~ps 416 (873)
+++.+. ++|++.. ++.||||| ||||+|| ||| |+ ||++|+++|+
T Consensus 2194 ~e~~ei----------~fpkmva~ccrflcyfcrisrqnq-kamfdhl-syl------le----------nssvglaspa 2245 (5019)
T KOG2243|consen 2194 GEKKEI----------AFPKMVANCCRFLCYFCRISRQNQ-KAMFDHL-SYL------LE----------NSSVGLASPA 2245 (5019)
T ss_pred Ccccee----------ccHHHHHHHHHHHHHHhhcchhhH-HHHHHHH-HHH------Hh----------cCcccccCcc
Confidence 877653 4566653 45799999 8999999 999 99 9999999999
Q ss_pred CCCCCCcccccccccCcHHHHHHHhhhhhhHHHHHHhhccccchhhHHhhcCCCCCCCCccccccccchhhceeecCcch
Q psy13311 417 LRGSTPLDVAYSSVMENTELALALREHYLEKIAIYLSRCGLQSNSELVEKGYPDLGWDPVEGERYLDFLRFCVWVNGESV 496 (873)
Q Consensus 417 ~rg~~PldVa~ssv~dnnELalaL~E~~lekvv~yLa~cglqs~~~li~kGypdigW~PvegERyLdFLrf~VwvnGEsv 496 (873)
|||+||+|||++|||||||||++|+|+++||||.||||||+|||+|+++||||||||||+||||||||||||||||||||
T Consensus 2246 mrgstpldvaaasvmdnnelalal~epdlekvv~ylagcglqsc~ml~akgypdigwnpiegeryl~flrfavf~n~esv 2325 (5019)
T KOG2243|consen 2246 MRGSTPLDVAAASVMDNNELALALEEPDLEKVVRYLAGCGLQSCPMLLAKGYPDIGWNPIEGERYLDFLRFAVFCNGESV 2325 (5019)
T ss_pred ccCCCchhhHHhhhcccchhhhhccCcCHHHHHHHHhcCCcccchHHHhCCCCCCCCCcccchhhhhhhhhheeecCccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhHHHhhcCCccccccccCcc-ccHHHHHHHHhhhhhhHhhhcCCCCCCCCCccCCCCCCCCCCchhhHhhhhhH
Q psy13311 497 EENANLVIRLLIRRPECLGPALRGEG-EGLLQAIIEANKMSDRIAARRSIIPIDDGVTDFDHPLPESEDDEDYIDTGAAI 575 (873)
Q Consensus 497 eENanvv~RLLIrrPEClGpAlrgeG-~gLl~a~~eaiklSe~~~~~~~~~~~~~~~~~~~~~l~~~e~~~d~i~~G~ai 575 (873)
|||||||||||||||||||||||||| +|||+||++||||+|+|+ +|+|+|.+++.+..++.- +|+.+|+||||++|
T Consensus 2326 eena~vvvkllirrpecfgpalrgeggngllaame~aikiae~pa-~d~pspn~g~~k~~~ted--deeedd~ihmgnai 2402 (5019)
T KOG2243|consen 2326 EENANVVVKLLIRRPECFGPALRGEGGNGLLAAMEEAIKIAEDPA-LDGPSPNQGSKKELDTED--DEEEDDIIHMGNAI 2402 (5019)
T ss_pred cccchhhhhhhhcCccccCchhcCCCcccHHHHHHhhhhhccCcc-ccCCCCCCCcccccCccc--cchhhhHHHhhHHH
Confidence 99999999999999999999999999 999999999999999999 999999999877666532 45678999999999
Q ss_pred HHHHHHHHHhhhcCCCCchhhhhccCCCCCCCCCCCcccccccccHHHHHHHHHHHhhhhhHHHhhhhccCCCCCCCccc
Q psy13311 576 LNFYCTLVDLLGRCAPDSTVIAQDMGSGPGNYHPNPIDMTNLTLSREMQNMAERLAENSHDIWAKKKKEESGGSVHPQLV 655 (873)
Q Consensus 576 l~FYs~LiDLLgrCAPd~~~i~~~~~~~~~gy~P~P~D~s~v~L~~~~~~mve~lAeN~HnvWAkkr~~~~~~~~hP~LV 655 (873)
++|||+|||||||||||||+|+
T Consensus 2403 msfysalidllgrcapemhli~---------------------------------------------------------- 2424 (5019)
T KOG2243|consen 2403 MSFYSALIDLLGRCAPEMHLIH---------------------------------------------------------- 2424 (5019)
T ss_pred HHHHHHHHHHHhccCchhheec----------------------------------------------------------
Confidence 9999999999999999999998
Q ss_pred cccccchHHHhhhHHHHHHHHHHHHHccceeeeccccCcchhhHHHHHHhhcccccchhhhcccceeecCCCCCCCccCC
Q psy13311 656 PYDLLTDKEKKKDRERSQEFLKYLQYQGYKLRSIARRGKNESLRARAILRSLVPLEDLQGVLSLRFSIACPGPGEEKAKS 735 (873)
Q Consensus 656 PYd~Lt~~eK~~dRe~aqe~lk~Lq~~GY~v~~~~~~~~~e~lrara~~~rl~r~edL~~V~Sl~~~lp~~~~~~~~~~~ 735 (873)
.|+.|++|+|+|+|++++++||.||||.+|++|+.++++.+.+|
T Consensus 2425 ------------------------------------~gkgeairirsilrslip~~dlvgiisi~~klpsi~kdg~v~ep 2468 (5019)
T KOG2243|consen 2425 ------------------------------------AGKGEAIRIRSILRSLIPLEDLVGIISIAFKLPSIAKDGNVSEP 2468 (5019)
T ss_pred ------------------------------------cCCCceEeHHHHHHhhcchhheeeeEEeeecCccccCCCCcCCc
Confidence 66899999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCchhHhhHhhhhhcccchhHHHHhhhhcccccchhhhhcccCCCChhhHHHHhhhhcccchHHHHHhhhhc
Q psy13311 736 DMPSGLIPGHKQSVVLFLERVYGIETQDLFFRILEEAFLPDLRTATMLDRSDGSESDMALAMNRYIGNSVLPLLISHAKF 815 (873)
Q Consensus 736 dm~~g~~P~HK~~~vlFLdrVyGi~~q~~~~~lle~~FLpDlraa~~ld~~~~~~~dmalalnrYi~~svlPll~~~a~~ 815 (873)
||.+||||+||++|||||||||||++|+|++||||+|||||||||++|||+.+|.||||||+|||||++||||||+||++
T Consensus 2469 dmaa~fcpdhka~mvlfldrvygi~~q~fllhllevgflpdlraaasldt~als~td~alalnryicsavlplltrcapl 2548 (5019)
T KOG2243|consen 2469 DMAAGFCPDHKAAMVLFLDRVYGIEDQDFLLHLLEVGFLPDLRAAASLDTAALSATDAALALNRYICSAVLPLLTRCAPL 2548 (5019)
T ss_pred ccccCCCCCcccceEEeeehhcCcchHHHHHHHHHhccchhhhhhcccchhhhhhhHHHHHHHHHHHHHHHHHHhhcchh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccchhhhHHHHHHHHHHhcccccccccCCCcccchhHhhH---------hhhchheeeccc
Q psy13311 816 YNDADNYANLLDATLHTVYRLSKNRMLTKGQPGLGDRRRVAGK---------DLANKVTYNISY 870 (873)
Q Consensus 816 ~~~~e~~~~l~d~~lhtvYrlsk~~~ltk~qr~~~~~~l~a~~---------~~~~~~~~~~~~ 870 (873)
|+++||+++|||++|||||||||++||||+|||+|++||+||- .|.+.+.+++..
T Consensus 2549 fagteh~~slids~l~tiyrlskg~sltkaqrdsie~cllaic~~lrpsmlq~llrrlvfdvp~ 2612 (5019)
T KOG2243|consen 2549 FAGTEHCASLIDSLLHTIYRLSKGCSLTKAQRDSIEECLLAICGHLRPSMLQHLLRRLVFDVPL 2612 (5019)
T ss_pred hccchHHHHHHHHHHHHHHHHhcCcchhhhhhhhHHHHHHHHHccCCHHHHHHHHHHHhcCcHh
Confidence 9999999999999999999999999999999999999999986 566666666543
No 2
>KOG2243|consensus
Probab=100.00 E-value=1.1e-113 Score=969.24 Aligned_cols=717 Identities=28% Similarity=0.377 Sum_probs=603.7
Q ss_pred ChhhhhhhhhhHhhcchhhHHHHHHHHHHHHhcccccccCCCCCCCCccccccccccCchHHHHHHHHHHHhhccCchhH
Q psy13311 1 MVVACCRFLCYFCRTSRQNQKAMFDHLSFLLENSNILLSRPSLRGSTPLDVAYSSVMENTELALALSRLLLVGMIRDEDV 80 (873)
Q Consensus 1 ~v~~cc~flc~f~~~s~qnq~a~~dh~~~Ll~~~~~~~~~~s~~gstPlDVa~a~~~dn~pLlKL~d~LLv~Gv~~DeDl 80 (873)
||+.||||||||||+|||||||||||++|||+||+|+++.|+|+||||||||+||+|||++|...+ ++.|+
T Consensus 2204 mva~ccrflcyfcrisrqnqkamfdhlsyllenssvglaspamrgstpldvaaasvmdnnelalal---------~epdl 2274 (5019)
T KOG2243|consen 2204 MVANCCRFLCYFCRISRQNQKAMFDHLSYLLENSSVGLASPAMRGSTPLDVAAASVMDNNELALAL---------EEPDL 2274 (5019)
T ss_pred HHHHHHHHHHHHhhcchhhHHHHHHHHHHHHhcCcccccCccccCCCchhhHHhhhcccchhhhhc---------cCcCH
Confidence 899999999999999999999999999999999999999999999999999999999999998877 67888
Q ss_pred HHH---------------------------------------------------------HHHhCCCCCCCCccCCCc--
Q psy13311 81 EKL---------------------------------------------------------LMMINPETWDPTFEKDGK-- 101 (873)
Q Consensus 81 ~ki---------------------------------------------------------L~LI~P~~f~~~~~~~g~-- 101 (873)
+|+ |++.+|+||||++++||-
T Consensus 2275 ekvv~ylagcglqsc~ml~akgypdigwnpiegeryl~flrfavf~n~esveena~vvvkllirrpecfgpalrgeggng 2354 (5019)
T KOG2243|consen 2275 EKVVRYLAGCGLQSCPMLLAKGYPDIGWNPIEGERYLDFLRFAVFCNGESVEENANVVVKLLIRRPECFGPALRGEGGNG 2354 (5019)
T ss_pred HHHHHHHhcCCcccchHHHhCCCCCCCCCcccchhhhhhhhhheeecCccccccchhhhhhhhcCccccCchhcCCCccc
Confidence 877 888999999999997761
Q ss_pred ----------------------------------cccccCceeeccc-------------------------cchhhhHH
Q psy13311 102 ----------------------------------DEHRKGLLHMKMA-------------------------EGAKLQMC 122 (873)
Q Consensus 102 ----------------------------------~~~~~GLL~m~L~-------------------------E~vKLqmC 122 (873)
++.++..+||+.+ +|..++++
T Consensus 2355 llaame~aikiae~pa~d~pspn~g~~k~~~teddeeedd~ihmgnaimsfysalidllgrcapemhli~~gkgeairir 2434 (5019)
T KOG2243|consen 2355 LLAAMEEAIKIAEDPALDGPSPNQGSKKELDTEDDEEEDDIIHMGNAIMSFYSALIDLLGRCAPEMHLIHAGKGEAIRIR 2434 (5019)
T ss_pred HHHHHHhhhhhccCccccCCCCCCCcccccCccccchhhhHHHhhHHHHHHHHHHHHHHhccCchhheeccCCCceEeHH
Confidence 2234568888877 88899999
Q ss_pred HHHHHhhhhhhhhhhhhhhhchhhhhhhhhhHHHHHHHHhhccCCChHHhhhhhcc----cCCChHHhhhhhcccccccC
Q psy13311 123 YLLHHLCDIQLRHRVESIIAFSHDFVGDLQTDQLRRYIEIKQSDLPSAVAAKKTRE----FRCPPREQFQNLDRKTLKIA 198 (873)
Q Consensus 123 ~lL~hLCD~qLrhRVEsivaFs~~fV~~lQ~dQ~~RY~ei~~~~Msaa~tAkkTrE----FR~pp~eQ~~~l~~~~~e~c 198 (873)
+||+.|.+.++..+|.||..-.|+..++.. +.++||+|+++++|+.. +.+++++..|++..+..|+.
T Consensus 2435 silrslip~~dlvgiisi~~klpsi~kdg~---------v~epdmaa~fcpdhka~mvlfldrvygi~~q~fllhllevg 2505 (5019)
T KOG2243|consen 2435 SILRSLIPLEDLVGIISIAFKLPSIAKDGN---------VSEPDMAAGFCPDHKAAMVLFLDRVYGIEDQDFLLHLLEVG 2505 (5019)
T ss_pred HHHHhhcchhheeeeEEeeecCccccCCCC---------cCCcccccCCCCCcccceEEeeehhcCcchHHHHHHHHHhc
Confidence 999999999999999999999999999998 88899999999999998 79999999999988889999
Q ss_pred CCchHHHHHHHHHHHHHHHhcccccccCchhhhhhhhccCCCCCCcccccchhhhhhcccHHHHHHHhhceEeeccCchh
Q psy13311 199 RVVRDLRERMDHFHESLMKQVSLLALQEPERRVKSIIYLGSDQFPCELSDIGLLVRQYDSVGELIRALEKTYVINNKTKD 278 (873)
Q Consensus 199 p~~edlr~~l~~FH~dL~~hcg~~~~~e~~~~~~~i~~l~~~~~p~~e~~fsLL~RQyd~igeL~~Al~kTY~I~~~s~~ 278 (873)
+.||+|++...++..|+.+.++.++++ |+|+.+.|+ .+.|++|+.+..+.+.||+++.+|.|
T Consensus 2506 -flpdlraaasldt~als~td~alalnr---------yicsavlpl-ltrcaplfagteh~~slids~l~tiy------- 2567 (5019)
T KOG2243|consen 2506 -FLPDLRAAASLDTAALSATDAALALNR---------YICSAVLPL-LTRCAPLFAGTEHCASLIDSLLHTIY------- 2567 (5019)
T ss_pred -cchhhhhhcccchhhhhhhHHHHHHHH---------HHHHHHHHH-HhhcchhhccchHHHHHHHHHHHHHH-------
Confidence 999999999999999999999999998 999999999 99999999999999999999999999
Q ss_pred hHHHHHHhhhhhhcccccccChHHHHHHH-------HHHHHhhhccccccCchhHHHhhhhhhHHHHHHHhhhhcccccc
Q psy13311 279 DVSQMWVGLSQIRSLLPVQMSQEEEELMR-------ERLWKLVNNHTFFQHPDLIRILRVHENVMAVMMNTLGRRAQAQS 351 (873)
Q Consensus 279 D~~~ll~~L~qiRsLL~Vqmg~eEE~Lm~-------~~L~~lmnn~vF~QHPdLmR~L~~HetVM~vMvNvLg~~~~~~~ 351 (873)
+||+.|||++.|++..||||+. +||++|+++.|| |++.++++.++++++++|||++||+|||
T Consensus 2568 -------rlskg~sltkaqrdsie~cllaic~~lrpsmlq~llrrlvf----dvp~lne~~kmplklltnhye~cwkyyc 2636 (5019)
T KOG2243|consen 2568 -------RLSKGCSLTKAQRDSIEECLLAICGHLRPSMLQHLLRRLVF----DVPLLNEHAKMPLKLLTNHYEQCWKYYC 2636 (5019)
T ss_pred -------HHhcCcchhhhhhhhHHHHHHHHHccCCHHHHHHHHHHHhc----CcHhhhhhhcCcHHHHHhHHHHHHhhee
Confidence 9999999999999999999998 999999999999 9999999999999999999999999999
Q ss_pred CCCCCCCCCCCCCcccc----------ccCCCCCCccchHHHHHhhHHHhhhhcCCCCCCCCCCCCCcccccCCCCCCCC
Q psy13311 352 DAPQTGTGQEGEPQSKH----------KENGEEPEKPGVFKKFYNFVNAVKELEEDPKVEPEPEKKTPEVLSRPSLRGST 421 (873)
Q Consensus 352 ~a~~~~~~~~~~~~~~~----------~~~SrqNQ~kamF~Hl~syL~av~~~L~~~~~~~~~~~ns~~~ls~ps~rg~~ 421 (873)
.++|||++|.+++++.| ++.|++++++.+|+-++|||+||+++|+|||++.++..+.+...|..+.++|+
T Consensus 2637 lp~gwg~~g~a~eeelhls~klfwgifdals~kkyd~dlfklalpclsaiagalppdylds~~~a~lekq~s~dadgnf~ 2716 (5019)
T KOG2243|consen 2637 LPGGWGNFGAASEEELHLSEKLFWGIFDALSHKKYDPDLFKLALPCLSAIAGALPPDYLDSNITAMLEKQISMDADGNFD 2716 (5019)
T ss_pred ccCcccccccchHHHHhHHHHHHHHHHHHhhccccCHHHHHHhhHHHHHHhcCCCchhhhhhHHHHHHHhhcccCCCCCC
Confidence 99999999999998865 45699999999999999999999999999999999988899999999999999
Q ss_pred CcccccccccCcHHHHHHHh---hhhhhHHHHHHhhccccchhhHHhhcCCCCCCCCccccccccchhhceeecCcchhh
Q psy13311 422 PLDVAYSSVMENTELALALR---EHYLEKIAIYLSRCGLQSNSELVEKGYPDLGWDPVEGERYLDFLRFCVWVNGESVEE 498 (873)
Q Consensus 422 PldVa~ssv~dnnELalaL~---E~~lekvv~yLa~cglqs~~~li~kGypdigW~PvegERyLdFLrf~VwvnGEsveE 498 (873)
|.||+++++..|..|+.+++ ||.|+||+ ..++++| |+|||+.+|
T Consensus 2717 pkpi~t~n~sipekley~i~kyaehshdkwa-----------~dk~~~g----------------------w~yg~~~~d 2763 (5019)
T KOG2243|consen 2717 PKPIDTMNFSIPEKLEYFINKYAEHSHDKWA-----------CDKLANG----------------------WIYGEILDD 2763 (5019)
T ss_pred CCcccccccccHHHHHHHHHHHHhcccchhh-----------hhhhccC----------------------ceeeeeecc
Confidence 99999999999999999987 99999999 7899999 999999999
Q ss_pred hhhhhHHHhhcCCccccccccCccccHHHHHHHHhhhhhhHhhhcCCCCCCCCCccCCCCCCCCCCchhhHhhhhhHHHH
Q psy13311 499 NANLVIRLLIRRPECLGPALRGEGEGLLQAIIEANKMSDRIAARRSIIPIDDGVTDFDHPLPESEDDEDYIDTGAAILNF 578 (873)
Q Consensus 499 Nanvv~RLLIrrPEClGpAlrgeG~gLl~a~~eaiklSe~~~~~~~~~~~~~~~~~~~~~l~~~e~~~d~i~~G~ail~F 578 (873)
|.++||-+ ++++.+||++.++ +.||.+|+.+.+++-|+.+.--
T Consensus 2764 ~~k~~pl~-----------------------kp~k~lsekekei--------------yrwp~keslktmla~~~~~ert 2806 (5019)
T KOG2243|consen 2764 NSKTHPLI-----------------------KPFKLLSEKEKEI--------------YRWPAKESLKTMLARGMRTERT 2806 (5019)
T ss_pred ccccCccc-----------------------chhhhhhhhhHHH--------------HcCcHHHHHHHHHHhhceeeec
Confidence 99999955 7899999998866 5688889999999887765400
Q ss_pred H--HHHHHhhhcCCCCchhh---hhccCCCCCCCCCCCcccccccccHHHHHHHHHHHhhhhhHHHhhhhcc---CCCCC
Q psy13311 579 Y--CTLVDLLGRCAPDSTVI---AQDMGSGPGNYHPNPIDMTNLTLSREMQNMAERLAENSHDIWAKKKKEE---SGGSV 650 (873)
Q Consensus 579 Y--s~LiDLLgrCAPd~~~i---~~~~~~~~~gy~P~P~D~s~v~L~~~~~~mve~lAeN~HnvWAkkr~~~---~~~~~ 650 (873)
- .+||...- ......| .|.+.+..+||+|+|+|+|||+|++++++|||.+|||||||||||||.+ .|||+
T Consensus 2807 kegdalvq~~~--~~k~r~isq~~qvsvda~~~ysp~~idlsnv~lsrdl~~m~e~~aenyhniwakkkkleleskggg~ 2884 (5019)
T KOG2243|consen 2807 KEGDALVQMAE--NEKLRRISQANQVSVDAAHGYSPAAIDLSNVTLSRDLHAMAEMMAENYHNIWAKKKKLELESKGGGN 2884 (5019)
T ss_pred ccchHHHHHHH--HHHHHhhhhhcccccccccCCCCcccchhhceehHHHHHHHHHHHHHHHHHHhhhhhceeeccCCCC
Confidence 0 01111000 0000001 1222345789999999999999999999999999999999999999976 69999
Q ss_pred CCccccccccchHHHhhhHHHHHHHHHHHHHccceeeeccccCcch-----hhH---HHHHHhhcccccc-hhhhcccce
Q psy13311 651 HPQLVPYDLLTDKEKKKDRERSQEFLKYLQYQGYKLRSIARRGKNE-----SLR---ARAILRSLVPLED-LQGVLSLRF 721 (873)
Q Consensus 651 hP~LVPYd~Lt~~eK~~dRe~aqe~lk~Lq~~GY~v~~~~~~~~~e-----~lr---ara~~~rl~r~ed-L~~V~Sl~~ 721 (873)
||+||||||||+|||.+|||+|||++||||+|||.|.+ +.++. ++. +++++++++++.| .+..|...-
T Consensus 2885 hpllvpydtltakek~kdrekaqdi~kflqing~~vsr---g~kdleld~~siekrfay~flkkiikyvd~a~e~i~~~d 2961 (5019)
T KOG2243|consen 2885 HPLLVPYDTLTAKEKAKDREKAQDIFKFLQINGIAVSR---GFKDLELDAPSIEKRFAYKFLKKIIKYVDEAHEFIAEFD 2961 (5019)
T ss_pred CceeccccccchhhhhhhHHHHHHHHHHhhcccEEecc---cccccccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999965 55544 332 8999999999999 777777665
Q ss_pred eecCCCCCCCccCCCCCCCCCCCCchhHhhHhhhhhcccchhHHHHhhhhcccc-cchhhhhcccCCCChhhHHHHhhhh
Q psy13311 722 SIACPGPGEEKAKSDMPSGLIPGHKQSVVLFLERVYGIETQDLFFRILEEAFLP-DLRTATMLDRSDGSESDMALAMNRY 800 (873)
Q Consensus 722 ~lp~~~~~~~~~~~dm~~g~~P~HK~~~vlFLdrVyGi~~q~~~~~lle~~FLp-Dlraa~~ld~~~~~~~dmalalnrY 800 (873)
.|-+.++++.. ...|.+.+|...+..+.||.|--|-| -||- -+|.-.+=-.++-.+-+|.-.+
T Consensus 2962 ~i~s~gk~e~~-----------p~dqeikffakv~lplidqyf~~h~l--yflsa~~kpl~s~g~as~kekemv~~l--- 3025 (5019)
T KOG2243|consen 2962 AIGSRGKGEHF-----------PRDQEIKFFAKVLLPLIDQYFKNHCL--YFLSAALKPLCSGGHASHKEKEMVAGL--- 3025 (5019)
T ss_pred ccccCCCcCCC-----------chHHHHHHHHHHHHHHHHHHHhhcee--eeecccccccccCCcccchhHHHHHHH---
Confidence 56555555543 34788999999999999999865543 2321 1222222233444456665443
Q ss_pred cccchHHHHHhhhhccccccchhhhHHHHHHHHHHhcccccccccCCCcccchhHhhHh
Q psy13311 801 IGNSVLPLLISHAKFYNDADNYANLLDATLHTVYRLSKNRMLTKGQPGLGDRRRVAGKD 859 (873)
Q Consensus 801 i~~svlPll~~~a~~~~~~e~~~~l~d~~lhtvYrlsk~~~ltk~qr~~~~~~l~a~~~ 859 (873)
.+..--|..+.-++|... +.-+-+.||.+-+---.|..-|..-+.|..-|-|+-|
T Consensus 3026 -fckl~~lvrhrislfg~d---atsiv~clhil~qtld~rtvmksg~e~vka~lraf~d 3080 (5019)
T KOG2243|consen 3026 -FCKLAALVRHRISLFGND---ATSIVNCLHILAQTLDARTVMKSGLELVKAALRAFFD 3080 (5019)
T ss_pred -HHHHHHHHHHHHhhhcCc---hHHHHHHHHHHHhhhhHHHHHHhhHHHHHHHHHHHHH
Confidence 222233334445666542 3334455665555444555555555555555555543
No 3
>PF02026 RyR: RyR domain; InterPro: IPR003032 This domain is called RyR for Ryanodine receptor []. The domain is found in four copies in the ryanodine receptor. The function of this domain is unknown.; PDB: 4ETV_A 3RQR_A 4ETT_A 4ERT_A 4ESU_A 4ETU_A 4ERV_A 3NRT_E.
Probab=99.93 E-value=2e-26 Score=207.70 Aligned_cols=83 Identities=45% Similarity=0.804 Sum_probs=67.5
Q ss_pred CCCCCCcccccccccHHHHHHHHHHHhhhhhHHHhhhhc---------cCCCCCCCccccccccchHHHhhhHHHHHHHH
Q psy13311 606 NYHPNPIDMTNLTLSREMQNMAERLAENSHDIWAKKKKE---------ESGGSVHPQLVPYDLLTDKEKKKDRERSQEFL 676 (873)
Q Consensus 606 gy~P~P~D~s~v~L~~~~~~mve~lAeN~HnvWAkkr~~---------~~~~~~hP~LVPYd~Lt~~eK~~dRe~aqe~l 676 (873)
||+|+|+|+|+|+|+++++.|+|+||||.||+||++|+. +.++++||+||||+.|+++||++||+.+++++
T Consensus 1 ~y~P~Pvdts~v~L~~~l~~~~E~lAen~H~~Wa~~r~~~GW~yG~~~d~~~k~hP~Lvpy~~L~e~eK~~dr~~~~e~l 80 (94)
T PF02026_consen 1 GYKPKPVDTSQVTLPPELEELIEKLAENEHDRWAKERIEQGWTYGEVRDDSRKTHPCLVPYDELSEEEKEKDRDMVRETL 80 (94)
T ss_dssp C-----B-GTT----HHHHHHHHHHHHHHHHHHHHHHHHTT-BE-SSHBTTTTBETT-S-GGGS-HHHHHHHHHHHHHHH
T ss_pred CCcCCCcCcCCeecCHHHHHHHHHHHHHHHHHHHHHHHhccceeccccccCCCCCCCCcChhhCCHHHHHHhHHHHHHHH
Confidence 899999999999999999999999999999999999996 36899999999999999999999999999999
Q ss_pred HHHHHccceeee
Q psy13311 677 KYLQYQGYKLRS 688 (873)
Q Consensus 677 k~Lq~~GY~v~~ 688 (873)
|+|+.+||.|++
T Consensus 81 k~l~~~Gy~i~~ 92 (94)
T PF02026_consen 81 KTLLALGYHIER 92 (94)
T ss_dssp HHHHHTTEEEEE
T ss_pred HHHHHcCcEEee
Confidence 999999999976
No 4
>PF01365 RYDR_ITPR: RIH domain; InterPro: IPR000699 Ryanodine and Inositol 1,4,5-trisphosphate (IP3) receptors are intracellular Ca2+-release channels. They become activated upon binding of their respective ligands, Ca2+ and IP3, opening an intrgral Ca2+ channel. Ryanodine receptor activation is a key component of muscular contraction, their activation allowing release of Ca2+ from the sarcoplasmic reticulum. Mutations in the ryanodine receptor lead to malignant hyperthermia susceptibility the and central core disease of muscle.; GO: 0005262 calcium channel activity, 0070588 calcium ion transmembrane transport, 0016020 membrane; PDB: 1N4K_A 2XOA_A 3UJ0_B 3UJ4_A 3T8S_A.
Probab=99.62 E-value=4.4e-18 Score=168.21 Aligned_cols=192 Identities=24% Similarity=0.290 Sum_probs=80.9
Q ss_pred hhhhhhcccccccChHHHHHHHHHHHHhhhccccccCchhHHHhhhhhhHHHHHHHhhhhccccccCCCCCCCCCCCCCc
Q psy13311 286 GLSQIRSLLPVQMSQEEEELMRERLWKLVNNHTFFQHPDLIRILRVHENVMAVMMNTLGRRAQAQSDAPQTGTGQEGEPQ 365 (873)
Q Consensus 286 ~L~qiRsLL~Vqmg~eEE~Lm~~~L~~lmnn~vF~QHPdLmR~L~~HetVM~vMvNvLg~~~~~~~~a~~~~~~~~~~~~ 365 (873)
-+++||+|+.+.|+++||.. .++++.++.++.+|+++||-+|+|+.||++|.+.++.. .... + ..+.....
T Consensus 2 v~~~l~~Li~f~~~~~~~~~---~~~~~~~~~~~~~rQ~llrnl~i~~~v~~~L~~~~~~~-~~~~----~-~~~~~~~~ 72 (207)
T PF01365_consen 2 VLKILRDLIKFCMGSEEEDQ---HLLKQRNGQPNRERQKLLRNLGIHELVLDLLKNPFDQF-QGDF----K-DLGDQKDS 72 (207)
T ss_dssp HHHHHHHHHHHHTTTS--SS----SHHCCCCHHHHHHHHHHHHTTHHHHHHHHHHHHCTS---------------STGGH
T ss_pred HHHHHHHHHhHhCCCCcccc---hHHHHhcCCcchhhHHHHHHHHHHHHHHHHhhhhhhcc-cchh----h-hhcchhcc
Confidence 47899999999999999988 88999999999999999999999999999999999753 1110 0 00000000
Q ss_pred c-cc------------ccCCCCCCccchHHHHHhhHHHhhhhcCCCCCCCCCCCCCcccccCCCCCCCCCcccccccccC
Q psy13311 366 S-KH------------KENGEEPEKPGVFKKFYNFVNAVKELEEDPKVEPEPEKKTPEVLSRPSLRGSTPLDVAYSSVME 432 (873)
Q Consensus 366 ~-~~------------~~~SrqNQ~kamF~Hl~syL~av~~~L~~~~~~~~~~~ns~~~ls~ps~rg~~PldVa~ssv~d 432 (873)
. .. ...+|+|| ..||+|+ +|+ +. .....+...|..+.+|.++.+.|
T Consensus 73 ~~~~l~~~~~~lL~~f~~~n~~NQ-~~l~~~~-~~l------~~-------------~~~~~~~~~~~~~~d~l~~i~~d 131 (207)
T PF01365_consen 73 SFKELFRLCYRLLRQFCRGNRENQ-KYLFKHL-DFL------IS-------------IFMQLQIGYGLGALDVLTEIFRD 131 (207)
T ss_dssp CHHHHHHHHHHHHHHHHTT-HHHH-HHHHHHH-H------------------------HHCCCH-TTHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHHhCHHHH-HHHHHHH-hHH------HH-------------HHHHhhccCCchHHHHHHHHHHC
Confidence 0 00 22499999 8999999 877 32 33345566778899999999999
Q ss_pred cHHHHHHHhhhhhhHHHHHHhhccccchhhHHhhcCCCCCCCCccccccccchhhceeecCcchhhhhhhhHHHhhcCCc
Q psy13311 433 NTELALALREHYLEKIAIYLSRCGLQSNSELVEKGYPDLGWDPVEGERYLDFLRFCVWVNGESVEENANLVIRLLIRRPE 512 (873)
Q Consensus 433 nnELalaL~E~~lekvv~yLa~cglqs~~~li~kGypdigW~PvegERyLdFLrf~VwvnGEsveENanvv~RLLIrrPE 512 (873)
|.+|...+.|...++++.+|++||.|+....+-+.++..+|.|+.+.+ +++...+|..|+ +++.++..+++||
T Consensus 132 N~~L~~~i~e~~I~~~i~ll~~~gr~~~~L~~L~~lc~~~g~pI~~nQ--~lI~~~ll~~~~-----~dll~~~~~~~~~ 204 (207)
T PF01365_consen 132 NPELCESISEEHIEKFIELLRKHGRQPRYLDFLSSLCVCNGNPIPENQ--NLICQELLLEGE-----ADLLVFTNDRKPE 204 (207)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cHHHHHHhhHHHHHHHHHHHHHcCCChHHHHHHhhhcccCCcCCHHHH--HHHHHHHcCCCC-----ccEEEEeeccccc
Confidence 999999999999999999999999999999999999999999999999 999999999987 9999999999999
Q ss_pred cc
Q psy13311 513 CL 514 (873)
Q Consensus 513 Cl 514 (873)
|+
T Consensus 205 ~~ 206 (207)
T PF01365_consen 205 CS 206 (207)
T ss_dssp --
T ss_pred cc
Confidence 96
No 5
>PF01365 RYDR_ITPR: RIH domain; InterPro: IPR000699 Ryanodine and Inositol 1,4,5-trisphosphate (IP3) receptors are intracellular Ca2+-release channels. They become activated upon binding of their respective ligands, Ca2+ and IP3, opening an intrgral Ca2+ channel. Ryanodine receptor activation is a key component of muscular contraction, their activation allowing release of Ca2+ from the sarcoplasmic reticulum. Mutations in the ryanodine receptor lead to malignant hyperthermia susceptibility the and central core disease of muscle.; GO: 0005262 calcium channel activity, 0070588 calcium ion transmembrane transport, 0016020 membrane; PDB: 1N4K_A 2XOA_A 3UJ0_B 3UJ4_A 3T8S_A.
Probab=98.47 E-value=2.7e-08 Score=99.09 Aligned_cols=75 Identities=35% Similarity=0.585 Sum_probs=44.0
Q ss_pred hhhhhhhhhhHhhcchhhHHHHHHHHHHHHhcccccccCCCCCCCCccccccccccCchHHHHHHHHHHHhhccCchhHH
Q psy13311 2 VVACCRFLCYFCRTSRQNQKAMFDHLSFLLENSNILLSRPSLRGSTPLDVAYSSVMENTELALALSRLLLVGMIRDEDVE 81 (873)
Q Consensus 2 v~~cc~flc~f~~~s~qnq~a~~dh~~~Ll~~~~~~~~~~s~~gstPlDVa~a~~~dn~pLlKL~d~LLv~Gv~~DeDl~ 81 (873)
+..||+|||+||+.+++||+.|++|++|+ ..+++.++...|..+.|+..+.++||.+|+.-+ .++.++
T Consensus 78 ~~~~~~lL~~f~~~n~~NQ~~l~~~~~~l---~~~~~~~~~~~~~~~~d~l~~i~~dN~~L~~~i---------~e~~I~ 145 (207)
T PF01365_consen 78 FRLCYRLLRQFCRGNRENQKYLFKHLDFL---ISIFMQLQIGYGLGALDVLTEIFRDNPELCESI---------SEEHIE 145 (207)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHH--------HHCCCH-TTHHHHHHHHHHHTT-----------------------
T ss_pred HHHHHHHHHHHHHhCHHHHHHHHHHHhHH---HHHHHHhhccCCchHHHHHHHHHHCcHHHHHHh---------hHHHHH
Confidence 56899999999999999999999999998 566667788888999999999999999999888 466678
Q ss_pred HHHHHhC
Q psy13311 82 KLLMMIN 88 (873)
Q Consensus 82 kiL~LI~ 88 (873)
++..+|.
T Consensus 146 ~~i~ll~ 152 (207)
T PF01365_consen 146 KFIELLR 152 (207)
T ss_dssp -------
T ss_pred HHHHHHH
Confidence 8777763
No 6
>PF02026 RyR: RyR domain; InterPro: IPR003032 This domain is called RyR for Ryanodine receptor []. The domain is found in four copies in the ryanodine receptor. The function of this domain is unknown.; PDB: 4ETV_A 3RQR_A 4ETT_A 4ERT_A 4ESU_A 4ETU_A 4ERV_A 3NRT_E.
Probab=98.36 E-value=4.9e-08 Score=89.01 Aligned_cols=69 Identities=26% Similarity=0.366 Sum_probs=48.0
Q ss_pred CCCCcccccccccCcHHHHHH---HhhhhhhHHHHHHhhccccchhhHHhhcCCCCCCCCccccccccchhhceeecCcc
Q psy13311 419 GSTPLDVAYSSVMENTELALA---LREHYLEKIAIYLSRCGLQSNSELVEKGYPDLGWDPVEGERYLDFLRFCVWVNGES 495 (873)
Q Consensus 419 g~~PldVa~ssv~dnnELala---L~E~~lekvv~yLa~cglqs~~~li~kGypdigW~PvegERyLdFLrf~VwvnGEs 495 (873)
|++|.||+++.|..+.+|... |+|+.|+.|+ .++++.| |+||+.
T Consensus 1 ~y~P~Pvdts~v~L~~~l~~~~E~lAen~H~~Wa-----------~~r~~~G----------------------W~yG~~ 47 (94)
T PF02026_consen 1 GYKPKPVDTSQVTLPPELEELIEKLAENEHDRWA-----------KERIEQG----------------------WTYGEV 47 (94)
T ss_dssp C-----B-GTT----HHHHHHHHHHHHHHHHHHH-----------HHHHHTT-----------------------BE-SS
T ss_pred CCcCCCcCcCCeecCHHHHHHHHHHHHHHHHHHH-----------HHHHhcc----------------------ceeccc
Confidence 789999999999999888764 7799999999 8999999 999999
Q ss_pred hhhhhhhhHHHhhcCCccccccccCccccHHHHHHHHhhhhhhHhhhc
Q psy13311 496 VEENANLVIRLLIRRPECLGPALRGEGEGLLQAIIEANKMSDRIAARR 543 (873)
Q Consensus 496 veENanvv~RLLIrrPEClGpAlrgeG~gLl~a~~eaiklSe~~~~~~ 543 (873)
.++..+.|+.| ++|..||+..++++
T Consensus 48 ~d~~~k~hP~L-----------------------vpy~~L~e~eK~~d 72 (94)
T PF02026_consen 48 RDDSRKTHPCL-----------------------VPYDELSEEEKEKD 72 (94)
T ss_dssp HBTTTTBETT------------------------S-GGGS-HHHHHHH
T ss_pred cccCCCCCCCC-----------------------cChhhCCHHHHHHh
Confidence 99999999977 77889998877553
No 7
>KOG3533|consensus
Probab=97.86 E-value=3.6e-05 Score=93.75 Aligned_cols=321 Identities=21% Similarity=0.290 Sum_probs=212.2
Q ss_pred cCchhHHHhhhhhhHHHHHHHhhhhccccccCCCCCCCCCCCCCccc------c------ccCCCCCCccchHHHHHhhH
Q psy13311 321 QHPDLIRILRVHENVMAVMMNTLGRRAQAQSDAPQTGTGQEGEPQSK------H------KENGEEPEKPGVFKKFYNFV 388 (873)
Q Consensus 321 QHPdLmR~L~~HetVM~vMvNvLg~~~~~~~~a~~~~~~~~~~~~~~------~------~~~SrqNQ~kamF~Hl~syL 388 (873)
||.-|.|-.|+|+.|++++-+-+.+. ...++. | +...+||| .-+.+|+ ++.
T Consensus 1226 ~~QrLLkNmg~h~VvLdllqiPydkk---------------~D~~M~elm~laHeFLqnFC~gN~qNQ-~lLhkhi-~lf 1288 (2706)
T KOG3533|consen 1226 MNQRLLKNMGVHEVVLELLQIPYDKK---------------HDHKMMELMTLAHEFLQNFCKGNKQNQ-SLLHKHI-SLF 1288 (2706)
T ss_pred HHHHHHHhcchHHHHHHHHhCccccc---------------chHHHHHHHHHHHHHHHHHhcCCchhH-HHHHHHH-Hhh
Confidence 34457777899999999988888541 011222 1 23489999 8999999 777
Q ss_pred HHhhhhcCCCCCCCCCCCCCcccccCCCCCCCCCcccccccccCcHHHHHHHhhhhhhHHHHHHhhccccchhhHHhhcC
Q psy13311 389 NAVKELEEDPKVEPEPEKKTPEVLSRPSLRGSTPLDVAYSSVMENTELALALREHYLEKIAIYLSRCGLQSNSELVEKGY 468 (873)
Q Consensus 389 ~av~~~L~~~~~~~~~~~ns~~~ls~ps~rg~~PldVa~ssv~dnnELalaL~E~~lekvv~yLa~cglqs~~~li~kGy 468 (873)
|+|-+.+ .+ ---+..++|-+|+--+.|.-+.-+| -+|+-.
T Consensus 1289 ------l~pG~LE--------a~-------------Tm~~IF~nN~~Lcsev~e~vvqHfV------------h~ie~h- 1328 (2706)
T KOG3533|consen 1289 ------LDPGMLE--------AG-------------TMVAIFRNNRELCSEVPEEVVQHFV------------HLIETH- 1328 (2706)
T ss_pred ------cCcchhh--------HH-------------HHHHHHHhhHHHHhhCcHHHHHHHH------------HHHHHc-
Confidence 6632222 00 0224567887777666654433333 234432
Q ss_pred CCCCCCCccccccccchhhceeecCcchhhhhhhhHHHhhcCCccccccccCcc--ccHHHHHHHHhhhhhhHhhhcCCC
Q psy13311 469 PDLGWDPVEGERYLDFLRFCVWVNGESVEENANLVIRLLIRRPECLGPALRGEG--EGLLQAIIEANKMSDRIAARRSII 546 (873)
Q Consensus 469 pdigW~PvegERyLdFLrf~VwvnGEsveENanvv~RLLIrrPEClGpAlrgeG--~gLl~a~~eaiklSe~~~~~~~~~ 546 (873)
|.+| .||+||.--|-++|.-+.---..|.-=||.--|=.---+---+ +-|+++|+.. ..+ ..
T Consensus 1329 ---gR~v----~yl~fLqt~Vkae~k~ikkcQdmVm~El~nagddVlvfYnD~aSf~~l~~MM~~e-----rdr----~~ 1392 (2706)
T KOG3533|consen 1329 ---GRNV----IYLEFLQTLVKAEGKEIKKCQDMVMNELCNAGDDVLVFYNDNASFEELEAMMKDE-----RDR----KG 1392 (2706)
T ss_pred ---CcCH----HHHHHHHHHHHhcchHHHHHHHHHHHHHhcCCCcEEEEecCcccHHHHHHHHHHH-----Hhc----cc
Confidence 3443 4999999999999998887777777777766554333333323 5566666654 121 10
Q ss_pred CCCCCCccCCCCCCCCCCchhhHhhhhhHHHHHHHHHHhhhcCCCCchhhhhccCCCCCCCCCCCcccccccccHHHHHH
Q psy13311 547 PIDDGVTDFDHPLPESEDDEDYIDTGAAILNFYCTLVDLLGRCAPDSTVIAQDMGSGPGNYHPNPIDMTNLTLSREMQNM 626 (873)
Q Consensus 547 ~~~~~~~~~~~~l~~~e~~~d~i~~G~ail~FYs~LiDLLgrCAPd~~~i~~~~~~~~~gy~P~P~D~s~v~L~~~~~~m 626 (873)
.. .|. .-+-|+-.||+||+-|+.-.
T Consensus 1393 ~~-----------------s~~-----spL~YHI~LV~LLA~Ct~GK--------------------------------- 1417 (2706)
T KOG3533|consen 1393 RS-----------------SSR-----SPLKYHIELVRLLAMCTEGK--------------------------------- 1417 (2706)
T ss_pred cc-----------------ccC-----CchhhHHHHHHHHHHHhcCC---------------------------------
Confidence 00 011 12233445999999999542
Q ss_pred HHHHHhhhhhHHHhhhhccCCCCCCCccccccccchHHHhhhHHHHHHHHHHHHHccceeeeccccCcchhhHHHHHHhh
Q psy13311 627 AERLAENSHDIWAKKKKEESGGSVHPQLVPYDLLTDKEKKKDRERSQEFLKYLQYQGYKLRSIARRGKNESLRARAILRS 706 (873)
Q Consensus 627 ve~lAeN~HnvWAkkr~~~~~~~~hP~LVPYd~Lt~~eK~~dRe~aqe~lk~Lq~~GY~v~~~~~~~~~e~lrara~~~r 706 (873)
|||.--.| -+
T Consensus 1418 -------------------------------------------------------NvyTEiKC---------------ns 1427 (2706)
T KOG3533|consen 1418 -------------------------------------------------------NVYTEIKC---------------NS 1427 (2706)
T ss_pred -------------------------------------------------------ccceeeee---------------cc
Confidence 34443222 27
Q ss_pred cccccchhhhcccceeecCCCCCCCccCCCCCCCCCCCCchhHhhHhhhhhc--------ccchhHHHHhhhhcccccch
Q psy13311 707 LVPLEDLQGVLSLRFSIACPGPGEEKAKSDMPSGLIPGHKQSVVLFLERVYG--------IETQDLFFRILEEAFLPDLR 778 (873)
Q Consensus 707 l~r~edL~~V~Sl~~~lp~~~~~~~~~~~dm~~g~~P~HK~~~vlFLdrVyG--------i~~q~~~~~lle~~FLpDlr 778 (873)
+++++|+..|.-++-.| |.-|.+.|-||---|= |=..+-+.+|.|. ||-|++
T Consensus 1428 llplddIVrVVth~dCi-------------------pEVK~aYvnflnHCYiDTevEMKeiYtsnh~w~lfen-flvDi~ 1487 (2706)
T KOG3533|consen 1428 LLPLDDIVRVVTHKDCI-------------------PEVKTAYVNFLNHCYIDTEVEMKEIYTSNHVWHLFEN-FLVDIR 1487 (2706)
T ss_pred cCChhHheeeechhhhh-------------------HHHHHHHHHHHHHhhcccHHHHHHHHhhhhHHHHHHH-HHHHHH
Confidence 89999999999988777 5669999999998883 2234567899999 999998
Q ss_pred hhhhcccCCCChhhHHHHhhhhcccchHHHHHhh-hhccccc----cchhhhHHHHHHHHHHhcccccccccCCCcccch
Q psy13311 779 TATMLDRSDGSESDMALAMNRYIGNSVLPLLISH-AKFYNDA----DNYANLLDATLHTVYRLSKNRMLTKGQPGLGDRR 853 (873)
Q Consensus 779 aa~~ld~~~~~~~dmalalnrYi~~svlPll~~~-a~~~~~~----e~~~~l~d~~lhtvYrlsk~~~ltk~qr~~~~~~ 853 (873)
....=- +....| --+-.|+|+.|+-.+++. +.-|.++ .+|...+-.+|+.+.|+-+|+-+..+||..|+.|
T Consensus 1488 r~~~~~--~~~~ad--~tLekyv~~~V~~~l~~FF~sPfSd~st~~qthq~~fvqlLq~~~rl~~c~wl~~~~r~sVe~C 1563 (2706)
T KOG3533|consen 1488 RLCVEK--LTGAAD--ATLEKYVCHTVTEVLIKFFESPFSDASTDVQTHQKTFVQLLQELTRLEKCKWLGSSSRYSVEEC 1563 (2706)
T ss_pred HHhccc--ccccch--hHHHHHHHHHHHHHHHHHhcCccccccchhhhccHHHHHHHHHHHHHhcCCCCCccchhhHHHH
Confidence 765432 111122 235789999999999863 3334433 3455677788999999999999999999999999
Q ss_pred hHhhHhhhch
Q psy13311 854 RVAGKDLANK 863 (873)
Q Consensus 854 l~a~~~~~~~ 863 (873)
+--+.+.|..
T Consensus 1564 IrtLt~~Ak~ 1573 (2706)
T KOG3533|consen 1564 IRTLTKVAKE 1573 (2706)
T ss_pred HHHHHHHHHh
Confidence 9888877753
No 8
>TIGR02309 HpaB-1 4-hydroxyphenylacetate 3-monooxygenase, oxygenase component. This gene for this monooxygenase is found within apparent operons for the degradation of 4-hydroxyphenylacetic acid in Deinococcus, Thermus and Oceanobacillus. Phylogenetic trees support inclusion of the Bacillus halodurans sequence above trusted although the complete 4-hydroxyphenylacetic acid degradation pathway may not exist in that organism. Generally, this enzyme acts with the assistance of a small flavin reductase domain protein (HpaC) to provide the cycle the flavin reductant for the reaction. This family of sequences is a member of a larger subfamily of monooxygenases (pfam03241).
Probab=82.97 E-value=1.6 Score=50.35 Aligned_cols=98 Identities=19% Similarity=0.326 Sum_probs=54.9
Q ss_pred ccccccccchhh---ceeecCcchhhhhhhhHHHhhcCCccccccccCccccHHHHHHHHhhhhhhHhhhcCCC-CCCCC
Q psy13311 476 VEGERYLDFLRF---CVWVNGESVEENANLVIRLLIRRPECLGPALRGEGEGLLQAIIEANKMSDRIAARRSII-PIDDG 551 (873)
Q Consensus 476 vegERyLdFLrf---~VwvnGEsveENanvv~RLLIrrPEClGpAlrgeG~gLl~a~~eaiklSe~~~~~~~~~-~~~~~ 551 (873)
..||.||+-||= .||++||-|+ |..-||.. | |..+++...-.+.-++...+.-+ +..+.
T Consensus 2 ~tg~eYlesL~~~~~~Vy~~Ge~V~-dvt~hPaf------------~----~~~~~~a~~YD~~~~~~~~~~~t~~~~g~ 64 (477)
T TIGR02309 2 RTGQEYIDALKTRPPNLYIKGERVE-DPTTHPVF------------R----GIVQSMAALYDLQHDPRYKEVLTYEEEGK 64 (477)
T ss_pred CCHHHHHHHHhcCCCeEEECCEEcc-CcCCChhh------------H----HHHHHHHHHHhhccCcccCceeeeCCCCC
Confidence 368999999998 7999999995 66667644 3 34555554444444444222211 11222
Q ss_pred CccCCCCCCCCCCchhhHhhhhhHHHHHHHHHHhhhcCCCCc
Q psy13311 552 VTDFDHPLPESEDDEDYIDTGAAILNFYCTLVDLLGRCAPDS 593 (873)
Q Consensus 552 ~~~~~~~l~~~e~~~d~i~~G~ail~FYs~LiDLLgrCAPd~ 593 (873)
... ..+-...+.+|++.=..++-.....--..+||| ||.
T Consensus 65 ~~~--~~~~~p~s~edL~~r~~~~~~~~~~~~g~~gR~-pD~ 103 (477)
T TIGR02309 65 RHG--MSFMIPKTKEDLKRRGEAYKLWADQNLGMMGRS-PDY 103 (477)
T ss_pred Eee--hhhcCCCCHHHHHHHHHHHHHHHHHcCCeeecC-hHH
Confidence 111 112223577888765555543322223458999 883
No 9
>PF13637 Ank_4: Ankyrin repeats (many copies); PDB: 3B95_A 3B7B_A 3F6Q_A 2KBX_A 3IXE_A 2DWZ_C 2DVW_A 3AJI_A 1S70_B 2HE0_A ....
Probab=66.61 E-value=5.1 Score=32.06 Aligned_cols=40 Identities=25% Similarity=0.325 Sum_probs=26.8
Q ss_pred HHHHHHHHhcccccccCCCCCCCCccccccccccCchHHHHHH
Q psy13311 24 FDHLSFLLENSNILLSRPSLRGSTPLDVAYSSVMENTELALAL 66 (873)
Q Consensus 24 ~dh~~~Ll~~~~~~~~~~s~~gstPlDVa~a~~~dn~pLlKL~ 66 (873)
.|-+.||++. ++.+......|.|||+.|. ...|..++|++
T Consensus 14 ~~~~~~Ll~~-~~din~~d~~g~t~lh~A~--~~g~~~~~~~L 53 (54)
T PF13637_consen 14 LEIVKLLLEH-GADINAQDEDGRTPLHYAA--KNGNIDIVKFL 53 (54)
T ss_dssp HHHHHHHHHT-TSGTT-B-TTS--HHHHHH--HTT-HHHHHHH
T ss_pred HHHHHHHHHC-CCCCCCCCCCCCCHHHHHH--HccCHHHHHHH
Confidence 4568899987 6777666788999999966 55688887765
No 10
>PF11794 HpaB_N: 4-hydroxyphenylacetate 3-hydroxylase N terminal; InterPro: IPR024674 This domain is found in the N terminus of HpaB, which encodes part of the 4-hydroxyphenylacetate 3-hydroxylase from Escherichia coli []. The enzyme is NADH-dependent and uses FAD as the redox chromophore. The domain is also found in pyoverdin chromophore biosynthetic protein (PvcC), which may play a role in one of the proposed hydroxylation steps of pyoverdine chromophore biosynthesis [] and in 4-hydroxybutyryl-CoA dehydratase (4-BUDH), a key enzyme in the metabolism of gamma-aminobutyrate [].; PDB: 3HWC_D 1U8V_D 2YYM_A 2YYI_A 2YYJ_A 2YYL_A 2YYG_A 2YYK_A.
Probab=54.77 E-value=2.7 Score=45.59 Aligned_cols=96 Identities=25% Similarity=0.370 Sum_probs=49.9
Q ss_pred cccccccchh---hceeecCcchhhhhhhhHHHhhcCCccccccccCccccHHHHHHHHhhhhhhHhhhcCC---CCCCC
Q psy13311 477 EGERYLDFLR---FCVWVNGESVEENANLVIRLLIRRPECLGPALRGEGEGLLQAIIEANKMSDRIAARRSI---IPIDD 550 (873)
Q Consensus 477 egERyLdFLr---f~VwvnGEsveENanvv~RLLIrrPEClGpAlrgeG~gLl~a~~eaiklSe~~~~~~~~---~~~~~ 550 (873)
.||.||.-|| -.||++||-|+ |...|| |+| |.++++.+.-.+..++...+.- ++..+
T Consensus 1 Tg~eYlesL~d~r~~Vy~~Ge~V~-dvt~HP------------af~----~~i~~~A~lYD~~~~p~~~d~~t~~s~~~g 63 (264)
T PF11794_consen 1 TGEEYLESLRDGRPEVYIDGERVE-DVTTHP------------AFR----GAIRSIARLYDLQHDPEHQDLLTYVSPETG 63 (264)
T ss_dssp -HHHHHHHHCCS--EEEETTEEES-TTTTST------------TTH----HHHHHHHHHHHHTTSTTTHHHHEEE-TTTT
T ss_pred CHHHHHHHHhcCCCeEEECCEEcc-CCCCCh------------hhH----HHHHHHHHHHHhccCcccccceEEEecCCC
Confidence 4788988885 48999999999 766775 444 4666666665665544433211 11111
Q ss_pred CCccCCCCCCCCCCchhhHhhhhhHHHHHHHHHHhhhcCCCC
Q psy13311 551 GVTDFDHPLPESEDDEDYIDTGAAILNFYCTLVDLLGRCAPD 592 (873)
Q Consensus 551 ~~~~~~~~l~~~e~~~d~i~~G~ail~FYs~LiDLLgrCAPd 592 (873)
..... .+-...+.+|++.=..++-......-..+|| .||
T Consensus 64 ~~v~~--~~~~p~s~eDL~~rr~~~~~~a~~t~G~~gR-~pD 102 (264)
T PF11794_consen 64 ERVSR--SFHIPRSKEDLVKRRKAIREWARYTGGCMGR-SPD 102 (264)
T ss_dssp CEEEG--GG----SHHHHHHHHHHHHHHHHHCCC--ST-CHH
T ss_pred chhhh--hcccCCCHHHHHHHHHHHHHHHHHcCceeec-Chh
Confidence 11111 1112347778776555555333333335555 555
No 11
>TIGR02310 HpaB-2 4-hydroxyphenylacetate 3-monooxygenase, oxygenase component. This gene for this monooxygenase is found within apparent operons for the degradation of 4-hydroxyphenylacetic acid in Shigella, Photorhabdus and Pasteurella. The family modelled by this alignment is narrowly limited to gammaproteobacteria to exclude other aromatic hydroxylases involved in various secondary metabolic pathways. Generally, this enzyme acts with the assistance of a small flavin reductase domain protein (HpaC) to provide the cycle the flavin reductant for the reaction. This family of sequences is a member of a larger subfamily of monooxygenases (pfam03241).
Probab=39.99 E-value=24 Score=41.85 Aligned_cols=31 Identities=32% Similarity=0.537 Sum_probs=25.1
Q ss_pred Cccccccccchhh--ceeecCcchhhhhhhhHHH
Q psy13311 475 PVEGERYLDFLRF--CVWVNGESVEENANLVIRL 506 (873)
Q Consensus 475 PvegERyLdFLrf--~VwvnGEsveENanvv~RL 506 (873)
|..||.||+-||= .||++||-|+ |...||..
T Consensus 12 ~~TG~eYlesLrd~r~Vyi~Ge~V~-dVt~HPaf 44 (519)
T TIGR02310 12 PFTGEEYLASLRDGREIYIYGERVK-DVTTHPAF 44 (519)
T ss_pred CcCHHHHHHHhcCCCeEEECCEEcc-CcCCChhh
Confidence 6789999999976 5999999996 66666633
No 12
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=28.85 E-value=37 Score=38.88 Aligned_cols=46 Identities=24% Similarity=0.437 Sum_probs=25.1
Q ss_pred hhhhhhhHhhcchh---hHHHHHHHHHHHHhccc---------ccccCCCCCCCCccc
Q psy13311 5 CCRFLCYFCRTSRQ---NQKAMFDHLSFLLENSN---------ILLSRPSLRGSTPLD 50 (873)
Q Consensus 5 cc~flc~f~~~s~q---nq~a~~dh~~~Ll~~~~---------~~~~~~s~~gstPlD 50 (873)
-|++.|.||.+... ....+-+-+..|.++=. ..+.+.-..|-||.-
T Consensus 59 fC~~~C~yC~~~~~~~~~~~~~~~y~~~L~~Ei~~~~~~~~~~~~v~~i~fgGGTPs~ 116 (453)
T PRK13347 59 FCRSLCWFCGCNTIITQRDAPVEAYVAALIREIRLVAASLPQRRRVSQLHWGGGTPTI 116 (453)
T ss_pred CccccCCCCCCcCcCccccchHHHHHHHHHHHHHHHHHhcCCCCeEEEEEEcCccccc
Confidence 39999999976532 22223333444444411 233445566777754
No 13
>COG0240 GpsA Glycerol-3-phosphate dehydrogenase [Energy production and conversion]
Probab=25.62 E-value=73 Score=36.09 Aligned_cols=95 Identities=24% Similarity=0.302 Sum_probs=55.0
Q ss_pred HHHHHHHHhhhhhH--HHhhhhc--c-CCCCCCCccccccccchHH-------Hhhh--------------HHHHHHHHH
Q psy13311 624 QNMAERLAENSHDI--WAKKKKE--E-SGGSVHPQLVPYDLLTDKE-------KKKD--------------RERSQEFLK 677 (873)
Q Consensus 624 ~~mve~lAeN~Hnv--WAkkr~~--~-~~~~~hP~LVPYd~Lt~~e-------K~~d--------------Re~aqe~lk 677 (873)
.+|+..||+|.|+| |+++... + .-+++||...|--.|.+-. +..+ |+.++.+ |
T Consensus 14 TALA~~la~ng~~V~lw~r~~~~~~~i~~~~~N~~yLp~i~lp~~l~at~Dl~~a~~~ad~iv~avPs~~~r~v~~~l-~ 92 (329)
T COG0240 14 TALAKVLARNGHEVRLWGRDEEIVAEINETRENPKYLPGILLPPNLKATTDLAEALDGADIIVIAVPSQALREVLRQL-K 92 (329)
T ss_pred HHHHHHHHhcCCeeEEEecCHHHHHHHHhcCcCccccCCccCCcccccccCHHHHHhcCCEEEEECChHHHHHHHHHH-h
Confidence 47899999999986 8886542 2 2337788888754444422 2222 4444444 2
Q ss_pred HHHHccceeeeccccCcchhh-HHHHHHhhcccccchhhhcccc
Q psy13311 678 YLQYQGYKLRSIARRGKNESL-RARAILRSLVPLEDLQGVLSLR 720 (873)
Q Consensus 678 ~Lq~~GY~v~~~~~~~~~e~l-rara~~~rl~r~edL~~V~Sl~ 720 (873)
-+..-+=.+..++++.-.+.. +.-.++.+.++-.. .+|+|||
T Consensus 93 ~~l~~~~~iv~~sKGie~~t~~l~seii~e~l~~~~-~~vLSGP 135 (329)
T COG0240 93 PLLLKDAIIVSATKGLEPETGRLLSEIIEEELPDNP-IAVLSGP 135 (329)
T ss_pred hhccCCCeEEEEeccccCCCcchHHHHHHHHcCCCe-EEEEECc
Confidence 222344445556655443333 45555666666444 8899987
No 14
>PF13857 Ank_5: Ankyrin repeats (many copies); PDB: 1SW6_A 3EHR_B 3EHQ_A.
Probab=24.76 E-value=32 Score=28.17 Aligned_cols=35 Identities=29% Similarity=0.318 Sum_probs=13.5
Q ss_pred HHhcccccccCCCCCCCCccccccccccCchHHHHHH
Q psy13311 30 LLENSNILLSRPSLRGSTPLDVAYSSVMENTELALAL 66 (873)
Q Consensus 30 Ll~~~~~~~~~~s~~gstPlDVa~a~~~dn~pLlKL~ 66 (873)
||++...........|.|||-+|+. ..+.++++++
T Consensus 1 LL~~~~~~~n~~d~~G~T~LH~A~~--~g~~~~v~~L 35 (56)
T PF13857_consen 1 LLEHGPADVNAQDKYGNTPLHWAAR--YGHSEVVRLL 35 (56)
T ss_dssp -----T--TT---TTS--HHHHHHH--HT-HHHHHHH
T ss_pred CCccCcCCCcCcCCCCCcHHHHHHH--cCcHHHHHHH
Confidence 3444444555556677888887665 4555555544
No 15
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=23.19 E-value=79 Score=24.99 Aligned_cols=29 Identities=45% Similarity=0.693 Sum_probs=21.2
Q ss_pred HHHhhccccc----hhhHHhhcCCCCCCCCccccccccchhhceeecCcchhh
Q psy13311 450 IYLSRCGLQS----NSELVEKGYPDLGWDPVEGERYLDFLRFCVWVNGESVEE 498 (873)
Q Consensus 450 ~yLa~cglqs----~~~li~kGypdigW~PvegERyLdFLrf~VwvnGEsveE 498 (873)
.+|+.+|+.+ ...+|..| .|+|||+.+.+
T Consensus 5 ~~L~~~~~~~sr~~a~~~I~~g--------------------~V~VNg~~v~~ 37 (48)
T PF01479_consen 5 KFLSRLGLASSRSEARRLIKQG--------------------RVKVNGKVVKD 37 (48)
T ss_dssp HHHHHTTSSSSHHHHHHHHHTT--------------------TEEETTEEESS
T ss_pred HHHHHcCCcCCHHHHHHhcCCC--------------------EEEECCEEEcC
Confidence 4567777765 33477778 79999999874
No 16
>KOG4825|consensus
Probab=21.13 E-value=2.3e+02 Score=33.99 Aligned_cols=83 Identities=17% Similarity=0.231 Sum_probs=59.7
Q ss_pred HHHHhhhcCCCCchhhhhccCC-CCCCCCCCCccc--ccccccHHHHHHHHHHHhhhhhHHHhhhhccCCCCCCCccccc
Q psy13311 581 TLVDLLGRCAPDSTVIAQDMGS-GPGNYHPNPIDM--TNLTLSREMQNMAERLAENSHDIWAKKKKEESGGSVHPQLVPY 657 (873)
Q Consensus 581 ~LiDLLgrCAPd~~~i~~~~~~-~~~gy~P~P~D~--s~v~L~~~~~~mve~lAeN~HnvWAkkr~~~~~~~~hP~LVPY 657 (873)
.+||+.|..-|+..-|. ++ ..-.++|-|+|= -.+.-+++++.|.-++-||-..--|
T Consensus 127 kdidhfgghlpeDeaiE---adparkddkigilddlafDhkqdkElaaiIgaidenKqeAVa------------------ 185 (666)
T KOG4825|consen 127 KDIDHFGGHLPEDEAIE---ADPARKDDKIGILDDLAFDHKQDKELAAIIGAIDENKQEAVA------------------ 185 (666)
T ss_pred hHHHHhccCCCCCcccc---CCcccccCCCCchhhcCcccccCHHHHHHHHHHHhhHHHHHh------------------
Confidence 46888888888865554 22 123677777763 2456789999999999999864444
Q ss_pred cccchHHHhhhHHHHHHHHHHHHHccceeeec
Q psy13311 658 DLLTDKEKKKDRERSQEFLKYLQYQGYKLRSI 689 (873)
Q Consensus 658 d~Lt~~eK~~dRe~aqe~lk~Lq~~GY~v~~~ 689 (873)
+|.-.--.+||-+++-|+..|-.++..
T Consensus 186 -----kEdfdlAKkaklAiaDLkKsgeeleel 212 (666)
T KOG4825|consen 186 -----KEDFDLAKKAKLAIADLKKSGEELEEL 212 (666)
T ss_pred -----hhhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 444455678999999999999877663
No 17
>PF09827 CRISPR_Cas2: CRISPR associated protein Cas2; InterPro: IPR019199 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. Members of this family of bacterial proteins comprise various hypothetical proteins, as well as CRISPR (clustered regularly interspaced short palindromic repeats) associated proteins, conferring resistance to infection by certain bacteriophages. ; PDB: 3EXC_X 2I0X_A 3OQ2_B 3UI3_A 1ZPW_X 2I8E_A 2IVY_A.
Probab=20.53 E-value=1.2e+02 Score=26.49 Aligned_cols=53 Identities=26% Similarity=0.378 Sum_probs=34.5
Q ss_pred CccccccccchHHHhhhHHHHHHHHHHHHHccceeeeccccCc---chhhHHHHHHhhccccc
Q psy13311 652 PQLVPYDLLTDKEKKKDRERSQEFLKYLQYQGYKLRSIARRGK---NESLRARAILRSLVPLE 711 (873)
Q Consensus 652 P~LVPYd~Lt~~eK~~dRe~aqe~lk~Lq~~GY~v~~~~~~~~---~e~lrara~~~rl~r~e 711 (873)
..+|-||+ +++.....+.|+|..+|+.++-=.=++. .+....++.+.+++.-+
T Consensus 3 ~~lv~YDi-------~~~k~~~kv~k~L~~~g~~iQ~SVf~~~~~~~~~~~l~~~l~~~i~~~ 58 (78)
T PF09827_consen 3 LYLVAYDI-------SDNKRRNKVRKILKSYGTRIQYSVFEGNLTNAELRKLRRELEKLIDPD 58 (78)
T ss_dssp EEEEEEEE-------HSHHHHHHHHHHHHHTTEEEETTEEEEEE-HHHHHHHHHHHHHHSCTT
T ss_pred EEEEEEEC-------CCcHHHHHHHHHHHHhCccccceEEEEEcCHHHHHHHHHHHHhhCCCC
Confidence 35788999 5556778899999999988876211111 22224666666666644
Done!