Query 011181
Match_columns 491
No_of_seqs 124 out of 150
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 09:01:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011181.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011181hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08737 Rgp1: Rgp1; InterPro 100.0 1.2E-59 2.6E-64 483.6 30.2 300 53-435 99-414 (415)
2 KOG4469 Uncharacterized conser 100.0 1.1E-41 2.4E-46 331.6 16.4 278 49-472 83-377 (391)
3 PF02752 Arrestin_C: Arrestin 97.9 0.00064 1.4E-08 57.4 14.9 127 321-468 2-135 (136)
4 PF00339 Arrestin_N: Arrestin 96.4 0.0037 8.1E-08 53.9 3.9 105 327-432 2-126 (149)
5 PF00339 Arrestin_N: Arrestin 95.8 0.0073 1.6E-07 52.1 2.9 40 66-106 87-126 (149)
6 PF02752 Arrestin_C: Arrestin 93.9 0.19 4.1E-06 42.4 6.4 58 69-140 73-134 (136)
7 KOG3780 Thioredoxin binding pr 93.1 2.4 5.1E-05 43.8 14.1 134 313-465 177-316 (427)
8 PF07070 Spo0M: SpoOM protein; 85.1 8.4 0.00018 38.3 10.3 99 334-435 21-122 (218)
9 KOG3780 Thioredoxin binding pr 76.9 3.1 6.6E-05 43.0 4.3 57 51-108 79-140 (427)
10 PF13002 LDB19: Arrestin_N ter 66.5 13 0.00029 36.6 5.7 39 67-106 45-86 (191)
11 PF01835 A2M_N: MG2 domain; I 58.6 1.1E+02 0.0023 25.5 9.4 75 333-432 7-85 (99)
12 PF03643 Vps26: Vacuolar prote 57.2 1.7E+02 0.0037 30.1 11.9 106 318-434 160-272 (275)
13 PF08737 Rgp1: Rgp1; InterPro 51.7 78 0.0017 34.1 8.9 51 404-467 124-174 (415)
14 PF07070 Spo0M: SpoOM protein; 51.5 50 0.0011 33.0 6.9 40 63-102 76-115 (218)
15 cd05817 CBM20_DSP Dual-specifi 47.6 59 0.0013 27.8 6.0 64 49-119 11-79 (100)
16 PF10633 NPCBM_assoc: NPCBM-as 43.6 23 0.00049 28.7 2.7 23 68-90 45-67 (78)
17 cd05814 CBM20_Prei4 Prei4, N-t 39.2 93 0.002 27.4 6.1 50 49-105 13-69 (120)
18 cd05467 CBM20 The family 20 ca 35.3 1.3E+02 0.0028 24.6 6.0 51 49-104 11-67 (96)
19 PF02221 E1_DerP2_DerF2: ML do 31.8 1.7E+02 0.0036 25.3 6.4 23 68-90 87-109 (134)
20 PF03643 Vps26: Vacuolar prote 28.8 87 0.0019 32.2 4.7 37 68-107 92-129 (275)
21 cd05816 CBM20_DPE2_repeat2 Dis 28.3 2.1E+02 0.0045 24.4 6.2 50 49-104 12-66 (99)
22 PF00686 CBM_20: Starch bindin 25.7 3.6E+02 0.0077 22.5 7.2 63 48-119 12-83 (96)
23 PF02966 DIM1: Mitosis protein 24.9 36 0.00078 32.0 1.1 17 45-61 78-94 (133)
24 KOG3414 Component of the U4/U6 22.7 43 0.00093 31.7 1.2 20 42-61 78-97 (142)
25 PF06280 DUF1034: Fn3-like dom 21.3 71 0.0015 27.5 2.2 23 67-89 64-86 (112)
26 PLN03160 uncharacterized prote 20.5 7.1E+02 0.015 24.6 9.1 73 78-160 98-172 (219)
No 1
>PF08737 Rgp1: Rgp1; InterPro: IPR014848 Rgp1 forms heterodimer with Ric1 (IPR009771 from INTERPRO) which associates with Golgi membranes and functions as a guanyl-nucleotide exchange factor [].
Probab=100.00 E-value=1.2e-59 Score=483.58 Aligned_cols=300 Identities=25% Similarity=0.363 Sum_probs=239.0
Q ss_pred eeEeecCCcceeeeeeecCCCceeEEEEEecCCCCCCCCCcceEEEEEEEEeecccceeeeecCccccccccccceeeee
Q 011181 53 FAFLDISASKLISNQIVSSDATKSYVIRTELPSIIPPSYRGTTIRYLYYVKSTLSARWLILENGLTQRESKRDLTQVEAR 132 (491)
Q Consensus 53 ~~f~~~~~pslvs~~~l~~g~~ksy~~r~~LP~~lPpSy~G~~ir~~Y~l~~~~~~r~~~~~~g~~~~~~~~~~~~~~~~ 132 (491)
+-|+.+....|.+|++|+|||+|+|.|++.||++|||||||++|||.|+|. +|.|+ ++..++.+..++
T Consensus 99 ~p~~~t~~~iLf~dl~L~pge~k~f~~~~~lP~~lPPsy~g~~i~~~Y~l~-----------vg~~~-~~~~~~~~~~~~ 166 (415)
T PF08737_consen 99 IPIFSTPQSILFSDLRLAPGESKSFHFSFTLPKDLPPSYRGKAIKISYSLV-----------VGTQR-GSSVNSKVKSIR 166 (415)
T ss_pred ceEEecCCceEEEeeEECCCCcEEEEEEEeCCCCCCCCCcCcEEEEEEEEE-----------EEEEE-cCCCCcceEEEE
Confidence 457788888899999999999999999999999999999999999999998 89987 667788889999
Q ss_pred eeeEEEEeecCCccccccccCCCCcccccccceeeecccc--------------CCcccccccccchhhhcccccCcccc
Q 011181 133 LPLQIWVTQKGNGLLTEENQNDGIVPATTIQMDIYWKEMD--------------GDSEWSRANDIYDGVEEGYESSRDEI 198 (491)
Q Consensus 133 iP~~i~~~~~~~g~~~~~~~~~~~vp~~~~q~~i~~ke~~--------------~~s~w~~and~~~~veeg~~~~~d~~ 198 (491)
||||||.+|+++|.+++||+|.|++.+ .+++.+..++.+ ....|...+++++++++.+++..+..
T Consensus 167 ~Pi~v~~~v~~~g~~l~~dL~~p~i~l-~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fl~~~~~Ll~s~~~~~ 245 (415)
T PF08737_consen 167 VPIRVLPSVNSSGEQLQHDLMSPYIIL-RDEARVEVVDSDSKRPPSSFSISSFSSKKSESSKESFLQYVDELLESNSNNM 245 (415)
T ss_pred eCEEEeeeecCCccccccccCCCcccc-CccceEEccccccccccCcccccccccCCchhhHHHHHHHHHHHHhcccccc
Confidence 999999999999999999999999999 888886533321 23458888999999999988876531
Q ss_pred cccccCCcccccccccccccccccccccccCCCCCCccccccccccccCcCCcccceeccccCCCcccCCCccceeeccc
Q 011181 199 SSVSSYNPSKENLLKTFGSSLSLQSSTARSSTKDIPAFEGELMRLSSNVALPQLSAAEVLYDSSADVISPNKSAAVVSPS 278 (491)
Q Consensus 199 ~sv~s~~~~~~~~~~~~~ss~sl~s~~~r~s~~~~~~~~~~r~~~~~~~~~~~ls~~e~~~d~~~~~~~~~~~~a~~~~~ 278 (491)
...+.- .+ ++++.. .....+.+ ...+..++++.|+ .++ ++
T Consensus 246 ~~~~~~------~~--------~~~~s~--------~~~~~~~~----~~~~~~~~~~~I~------------~~~--~~ 285 (415)
T PF08737_consen 246 PDISTL------ED--------LLSPSQ--------FSMSSEDS----DSEPSYSYKDQIP------------SAI--SN 285 (415)
T ss_pred cccccc------cc--------cccccc--------CCcccccc----ccccccchhhhhh------------hhh--hh
Confidence 111111 00 001000 00000111 1112245566665 333 11
Q ss_pred ccccCCCCCCcCCCCCCCCCCcccccccccccccCcEEEEEeCCEEEEEEEccCCCCCcccCccEEEEEEecCCCCceeE
Q 011181 279 QQQKLTKPADDITGASPSPQAGVVEPAASEGFIRGRSYNIRMDDQVLLRFSPKNSESTYYFSDMIGGTLTFFHEEGARRC 358 (491)
Q Consensus 279 ~~~~~~~s~~~~~g~s~~~~~~~~e~~~~~~~~~~ksY~Inrngq~VarvsL~~pKpaYRLGEdI~Gt~DFt~s~a~irC 358 (491)
+.+. . .+++.|+|++||++||+|+|. ||+||+||||.|+|||++.+ .+||
T Consensus 286 ~~~~--------------------------~-~~~~~y~I~~n~~~va~~~Ls--K~~yrlGE~I~g~idf~~~~-~~~c 335 (415)
T PF08737_consen 286 LLSQ--------------------------S-RNPNSYNIRRNGQRVARLSLS--KPAYRLGEDIVGTIDFNDAS-TIPC 335 (415)
T ss_pred hccc--------------------------c-cCCcEEEEEECCeEEEEEEec--CCCcccCCeEEEEEEcCCCC-ccee
Confidence 1111 1 148999999999999999997 99999999999999997432 4999
Q ss_pred EEEEEEEEEeeeecCCccCCCCCC-CCceeeEEEeeeeeecccc-eeeEEecCCCCCCCceEeCceeEEEEEEEEEEec
Q 011181 359 LEVLITLETSETINRWFVHPSRRN-SPTITKIQSDHHEVVADLV-QTSFLFSIPMDGPMSFSTPYVSVQWALRFEFLTT 435 (491)
Q Consensus 359 ~qVSVSLESeE~Inp~~a~~S~~s-sr~trKVhAe~hE~cld~~-rT~FsL~IP~~ATPqF~TdiVsLKW~LRFEFVts 435 (491)
++|+|+||++|+|+++|++++..+ .++++++|+++||+|+|.+ +++|.|+||.++||+|.|++|+|||+||||||++
T Consensus 336 ~~v~~~LEs~E~v~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~f~l~IP~~~tp~F~T~~v~lkW~LrfeFv~~ 414 (415)
T PF08737_consen 336 YQVSASLESEETVNPSYAVRSSAKINRVTRKVHAEHHEICLDSRSRTSFSLPIPLSATPQFQTSGVSLKWRLRFEFVTS 414 (415)
T ss_pred EEEEEEEEEEEEeCchhcccccccccccEEEEEEEEeeeecCCcceEEEEeeCCCCCCCceEeCCEEEEEEEEEEEEec
Confidence 999999999999999998765544 6889999999999999999 9999999999999999999999999999999985
No 2
>KOG4469 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.1e-41 Score=331.62 Aligned_cols=278 Identities=26% Similarity=0.390 Sum_probs=212.8
Q ss_pred ccCceeEee-cCCc-ceeeeeeecCCCceeEEEEEecCCCCCCCCCcceEEEEEEEEeecccceeeeecCcccccccccc
Q 011181 49 FPGEFAFLD-ISAS-KLISNQIVSSDATKSYVIRTELPSIIPPSYRGTTIRYLYYVKSTLSARWLILENGLTQRESKRDL 126 (491)
Q Consensus 49 ~~ge~~f~~-~~~p-slvs~~~l~~g~~ksy~~r~~LP~~lPpSy~G~~ir~~Y~l~~~~~~r~~~~~~g~~~~~~~~~~ 126 (491)
.|||+--.- +++| .|.++++|.|||+|+|.|+-.||..=||||||.++||-|.|. +|-||-.+.-.+
T Consensus 83 hrgergqcilstppkilfcdlrldpgesksysysevlpiegppsfrgqsvkyvyklt-----------igcqrvnspitl 151 (391)
T KOG4469|consen 83 HRGERGQCILSTPPKILFCDLRLDPGESKSYSYSEVLPIEGPPSFRGQSVKYVYKLT-----------IGCQRVNSPITL 151 (391)
T ss_pred cCCcccceEecCCCceEEEEeecCCCccccccceeeeeccCCCccCCceeEEEEEEE-----------eeeEecCCcceE
Confidence 467653322 3334 467899999999999999999999999999999999999998 999987776666
Q ss_pred ceeeeeeeeEEEEeecCCccccccccCCCCcccccccceeeeccccCCcccccccccchhhhcccccCcccccccccCCc
Q 011181 127 TQVEARLPLQIWVTQKGNGLLTEENQNDGIVPATTIQMDIYWKEMDGDSEWSRANDIYDGVEEGYESSRDEISSVSSYNP 206 (491)
Q Consensus 127 ~~~~~~iP~~i~~~~~~~g~~~~~~~~~~~vp~~~~q~~i~~ke~~~~s~w~~and~~~~veeg~~~~~d~~~sv~s~~~ 206 (491)
. |+|+||.+--+-+..+ +..|++... +.. |+ ||.-.-.+|. +
T Consensus 152 l----rvplrvlvltglqdvr-----------fpqdeavap----ssp--------fl---eedeggkkds------w-- 193 (391)
T KOG4469|consen 152 L----RVPLRVLVLTGLQDVR-----------FPQDEAVAP----SSP--------FL---EEDEGGKKDS------W-- 193 (391)
T ss_pred E----eeceEEEEEecccccc-----------cCcccccCC----CCC--------cc---ccccCCccch------H--
Confidence 6 9999999866543333 112332211 111 32 2221113331 0
Q ss_pred ccccccccccccccccccccccCCCCCCccccccccccccCcCCcccceeccccCCCcccCCCccceeecccccccCCCC
Q 011181 207 SKENLLKTFGSSLSLQSSTARSSTKDIPAFEGELMRLSSNVALPQLSAAEVLYDSSADVISPNKSAAVVSPSQQQKLTKP 286 (491)
Q Consensus 207 ~~~~~~~~~~ss~sl~s~~~r~s~~~~~~~~~~r~~~~~~~~~~~ls~~e~~~d~~~~~~~~~~~~a~~~~~~~~~~~~s 286 (491)
.. .+.|+|- -++ + .|
T Consensus 194 ---------------la-----------elagerl-----------maa-------------------------t--sc- 208 (391)
T KOG4469|consen 194 ---------------LA-----------ELAGERL-----------MAA-------------------------T--SC- 208 (391)
T ss_pred ---------------HH-----------Hhhhhhh-----------hhh-------------------------c--cc-
Confidence 00 0111111 000 0 01
Q ss_pred CCcCCCCCCCCCCcccccccccccccCcEEEEEeCCEEEEEEEccCCCCCcccCccEEEEEEecCCCCceeEEEEEEEEE
Q 011181 287 ADDITGASPSPQAGVVEPAASEGFIRGRSYNIRMDDQVLLRFSPKNSESTYYFSDMIGGTLTFFHEEGARRCLEVLITLE 366 (491)
Q Consensus 287 ~~~~~g~s~~~~~~~~e~~~~~~~~~~ksY~Inrngq~VarvsL~~pKpaYRLGEdI~Gt~DFt~s~a~irC~qVSVSLE 366 (491)
-.-.-|+|+.+..+|+.|-++ |+.||+||||.|++++. ++++.|+|++++||
T Consensus 209 ------------------------rslhlynisdgrgkvgtfgif--ksvyrlgedvvgtlnlg--egtvaclqfsvslq 260 (391)
T KOG4469|consen 209 ------------------------RSLHLYNISDGRGKVGTFGIF--KSVYRLGEDVVGTLNLG--EGTVACLQFSVSLQ 260 (391)
T ss_pred ------------------------ceeeeEeecCCCccceeeehh--hhhhhcccceeeeeecC--CceEEEEEEEEeec
Confidence 035679999999999999999 99999999999999995 79999999999999
Q ss_pred EeeeecCCccCCCCCC-CC-ceeeEEEeeeeeecccceeeEEecCCCCCCCceEeCceeEEEEEEEEEEecCC-------
Q 011181 367 TSETINRWFVHPSRRN-SP-TITKIQSDHHEVVADLVQTSFLFSIPMDGPMSFSTPYVSVQWALRFEFLTTPK------- 437 (491)
Q Consensus 367 SeE~Inp~~a~~S~~s-sr-~trKVhAe~hE~cld~~rT~FsL~IP~~ATPqF~TdiVsLKW~LRFEFVts~~------- 437 (491)
++|.++|+|..+.++. .+ +..-.|+.|.|.|+++.+++|+|+||++.||.|+|.+|+|||+||||||++.+
T Consensus 261 teervqpeyqrrrgaggvpsvshvtharhqesclhttrtsfslpiplsstpgfctaivslkwrlhfefvtsrepglvllp 340 (391)
T KOG4469|consen 261 TEERVQPEYQRRRGAGGVPSVSHVTHARHQESCLHTTRTSFSLPIPLSSTPGFCTAIVSLKWRLHFEFVTSREPGLVLLP 340 (391)
T ss_pred hhhhcChHHHhhccCCCCCcchhhhhhhhhhhhhhcccceeeeccccCCCCccEeeEeeeeeEEEEEEEecCCCCeEecC
Confidence 9999999999876554 22 22224999999999999999999999999999999999999999999999754
Q ss_pred ------CcccccccCCCCcCCceEEEEEeeeEEeCCCCCCC
Q 011181 438 ------HVQWTRYEHPLLIEGRDKSEWVLPITVHAPPSGAP 472 (491)
Q Consensus 438 ------~~~wqa~Edp~~L~e~EtFeW~LPItVlPt~P~~~ 472 (491)
.+.|.++|+ + .+++|+|+|||+|+|++|.-+
T Consensus 341 pveqpepttwtgpeq---v-pvdtfswdlpikvlptsptla 377 (391)
T KOG4469|consen 341 PVEQPEPTTWTGPEQ---V-PVDTFSWDLPIKVLPTSPTLA 377 (391)
T ss_pred CcCCCCCccccCCcc---c-cccccccccceeeccCCcchh
Confidence 688999999 8 999999999999999999643
No 3
>PF02752 Arrestin_C: Arrestin (or S-antigen), C-terminal domain; InterPro: IPR011022 G protein-coupled receptors are a large family of signalling molecules that respond to a wide variety of extracellular stimuli. The receptors relay the information encoded by the ligand through the activation of heterotrimeric G proteins and intracellular effector molecules. To ensure the appropriate regulation of the signalling cascade, it is vital to properly inactivate the receptor. This inactivation is achieved, in part, by the binding of a soluble protein, arrestin, which uncouples the receptor from the downstream G protein after the receptors are phosphorylated by G protein-coupled receptor kinases. In addition to the inactivation of G protein-coupled receptors, arrestins have also been implicated in the endocytosis of receptors and cross talk with other signalling pathways. Arrestin (retinal S-antigen) is a major protein of the retinal rod outer segments. It interacts with photo-activated phosphorylated rhodopsin, inhibiting or 'arresting' its ability to interact with transducin []. The protein binds calcium, and shows similarity in its C terminus to alpha-transducin and other purine nucleotide-binding proteins. In mammals, arrestin is associated with autoimmune uveitis. Arrestins comprise a family of closely-related proteins that includes beta-arrestin-1 and -2, which regulate the function of beta-adrenergic receptors by binding to their phosphorylated forms, impairing their capacity to activate G(S) proteins; Cone photoreceptors C-arrestin (arrestin-X) [], which could bind to phosphorylated red/green opsins; and Drosophila phosrestins I and II, which undergo light-induced phosphorylation, and probably play a role in photoreceptor transduction [, , ]. The crystal structure of bovine retinal arrestin comprises two domains of antiparallel beta-sheets connected through a hinge region and one short alpha-helix on the back of the amino-terminal fold []. The binding region for phosphorylated light-activated rhodopsin is located at the N-terminal domain, as indicated by the docking of the photoreceptor to the three-dimensional structure of arrestin. The C-terminal domain consists of an immunoglobulin-like beta-sandwich structure. This entry represents proteins with immunoglobulin-like domains that are similar to those found in arrestin.; PDB: 1SUJ_A 3UGX_A 1CF1_B 1AYR_A 3UGU_A 3P2D_B 1ZSH_A 2WTR_B 3GC3_A 1G4R_A ....
Probab=97.91 E-value=0.00064 Score=57.43 Aligned_cols=127 Identities=13% Similarity=0.172 Sum_probs=77.6
Q ss_pred CCEEEEEEEccCCCCCcccCccEEEEEEecCCCCceeEEEEEEEEEEeeeecCCccCCCCCCCCceeeEEEeeeeeec--
Q 011181 321 DDQVLLRFSPKNSESTYYFSDMIGGTLTFFHEEGARRCLEVLITLETSETINRWFVHPSRRNSPTITKIQSDHHEVVA-- 398 (491)
Q Consensus 321 ngq~VarvsL~~pKpaYRLGEdI~Gt~DFt~s~a~irC~qVSVSLESeE~Inp~~a~~S~~ssr~trKVhAe~hE~cl-- 398 (491)
+|..-+.+.+. |.+|..||+|...+++.+ .+..++.++.++|.-.-.....-... ......++.++++..-.
T Consensus 2 ~g~i~~~~~i~--~~~~~~Ge~i~v~v~i~n-~s~~~i~~I~v~L~~~~~~~~~~~~~---~~~~~~~~v~~~~~~~~~~ 75 (136)
T PF02752_consen 2 SGKISLSISIP--RTAYVPGETIPVNVEIDN-QSKKKIKKIKVSLVERITYKAKGGKD---ESKSEKRVVAKSKNCGVDP 75 (136)
T ss_dssp TEEEEEEEEES---SEEETT--EEEEEEEEE--SSSEEEEEEEEEEEEEEE-SS-------S-EEEEEEEEEEECCEB-B
T ss_pred CCEEEEEEEEC--CCEECCCCEEEEEEEEEE-CCCCEEEEEEEEEEEEEEEEEeeccc---cceEEEEEEEEEecCCccC
Confidence 56777888884 999999999999999984 68899999999997766654332111 12333445555332222
Q ss_pred -cccee--eEEecCCCCCCCce--EeCceeEEEEEEEEEEecCCCcccccccCCCCcCCceEEEEEeeeEEeCCC
Q 011181 399 -DLVQT--SFLFSIPMDGPMSF--STPYVSVQWALRFEFLTTPKHVQWTRYEHPLLIEGRDKSEWVLPITVHAPP 468 (491)
Q Consensus 399 -d~~rT--~FsL~IP~~ATPqF--~TdiVsLKW~LRFEFVts~~~~~wqa~Edp~~L~e~EtFeW~LPItVlPt~ 468 (491)
....- ...|.+|.+.+|++ ..+.++++-.|++++.+.. ....+.+++||+|...+
T Consensus 76 ~~~~~~~~~~~l~lP~~~~~s~~~~~~~i~v~Y~l~v~~~~~~---------------~~~~~~~~~PI~I~~~p 135 (136)
T PF02752_consen 76 GSSGSFEFNIQLQLPSNLPPSTSTNSRLIQVEYQLEVTVKLSG---------------CTSDLRLELPITIGSSP 135 (136)
T ss_dssp -TTEEEEEEEEE-----B-----CGGGSEEEEEEEEEEEEEET---------------TSEEEEEEEEEEEEB-S
T ss_pred CCCceEEEEEEEcCCCccCcccccCCcEEEEEEEEEEEEEECC---------------ceeEEEEEccEEEEecC
Confidence 12212 37899999999988 6789999999999999862 23467899999998654
No 4
>PF00339 Arrestin_N: Arrestin (or S-antigen), N-terminal domain; InterPro: IPR011021 G protein-coupled receptors are a large family of signalling molecules that respond to a wide variety of extracellular stimuli. The receptors relay the information encoded by the ligand through the activation of heterotrimeric G proteins and intracellular effector molecules. To ensure the appropriate regulation of the signalling cascade, it is vital to properly inactivate the receptor. This inactivation is achieved, in part, by the binding of a soluble protein, arrestin, which uncouples the receptor from the downstream G protein after the receptors are phosphorylated by G protein-coupled receptor kinases. In addition to the inactivation of G protein-coupled receptors, arrestins have also been implicated in the endocytosis of receptors and cross talk with other signalling pathways. Arrestin (retinal S-antigen) is a major protein of the retinal rod outer segments. It interacts with photo-activated phosphorylated rhodopsin, inhibiting or 'arresting' its ability to interact with transducin []. The protein binds calcium, and shows similarity in its C terminus to alpha-transducin and other purine nucleotide-binding proteins. In mammals, arrestin is associated with autoimmune uveitis. Arrestins comprise a family of closely-related proteins that includes beta-arrestin-1 and -2, which regulate the function of beta-adrenergic receptors by binding to their phosphorylated forms, impairing their capacity to activate G(S) proteins; Cone photoreceptors C-arrestin (arrestin-X) [], which could bind to phosphorylated red/green opsins; and Drosophila phosrestins I and II, which undergo light-induced phosphorylation, and probably play a role in photoreceptor transduction [, , ]. The crystal structure of bovine retinal arrestin comprises two domains of antiparallel beta-sheets connected through a hinge region and one short alpha-helix on the back of the amino-terminal fold []. The binding region for phosphorylated light-activated rhodopsin is located at the N-terminal domain, as indicated by the docking of the photoreceptor to the three-dimensional structure of arrestin. The N-terminal domain consists of an immunoglobulin-like beta-sandwich structure. This entry represents proteins with immunoglobulin-like domains that are similar to those found in arrestin.; PDB: 1SUJ_A 3UGX_A 1CF1_B 1AYR_A 3UGU_A 3P2D_B 1ZSH_A 2WTR_B 3GC3_A 1G4R_A ....
Probab=96.38 E-value=0.0037 Score=53.89 Aligned_cols=105 Identities=13% Similarity=0.221 Sum_probs=60.6
Q ss_pred EEEccCCCCCcccCccEEEEEEecCCCCceeEEEEEEEEEEeeeecCCccCCCCCC-------------CCce----eeE
Q 011181 327 RFSPKNSESTYYFSDMIGGTLTFFHEEGARRCLEVLITLETSETINRWFVHPSRRN-------------SPTI----TKI 389 (491)
Q Consensus 327 rvsL~~pKpaYRLGEdI~Gt~DFt~s~a~irC~qVSVSLESeE~Inp~~a~~S~~s-------------sr~t----rKV 389 (491)
.+.|.++++.|..||.|.|.+.+.. ...+++-.+.+.|.-.+.+.-......... .... ..+
T Consensus 2 ~I~ld~~~~~y~~Ge~I~G~V~l~~-~~~~~i~~i~v~l~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 80 (149)
T PF00339_consen 2 EIELDNPKPVYFPGEVISGKVVLEL-SKPIKIKSIKVRLKGRAKTKWSESKSSGSTFRKQTTPKVQYSEKKEYFDHESQL 80 (149)
T ss_dssp EEEES-SEEEEESS--EEEEEEECT-TT-TTTSEEEEEEEEEEEESSSSTTSTTCEEEEEEESTSSS-SSSSSSHHHHHH
T ss_pred EEEECCCCCEECCCCEEEEEEEEEE-CCccceeEEEEEEEEEEEEEecCCCcceeeeeeEEecccccccceeeccceeEe
Confidence 4566678999999999999999963 567888889999999998753321111100 0000 000
Q ss_pred EEe-eeeee--cccceeeEEecCCCCCCCceEeCceeEEEEEEEEE
Q 011181 390 QSD-HHEVV--ADLVQTSFLFSIPMDGPMSFSTPYVSVQWALRFEF 432 (491)
Q Consensus 390 hAe-~hE~c--ld~~rT~FsL~IP~~ATPqF~TdiVsLKW~LRFEF 432 (491)
+.. ....+ .+...-+|.+.+|.+.+|+|.....+++|.|+-..
T Consensus 81 ~~~~~~~~~l~~G~~~fpF~f~LP~~lP~S~~~~~g~I~Y~l~a~l 126 (149)
T PF00339_consen 81 WGSEDGPNILPPGEYEFPFEFQLPSNLPSSFEGSHGSIRYKLKATL 126 (149)
T ss_dssp HHH--------C-TTEEEEEE---TTS--SEEEE-SEEEEEEEEEE
T ss_pred eeeccceecccCCCEEEEEEEECCCCCCceEeccCcCEEEEEEEEE
Confidence 100 00122 23444599999999999999999889999998876
No 5
>PF00339 Arrestin_N: Arrestin (or S-antigen), N-terminal domain; InterPro: IPR011021 G protein-coupled receptors are a large family of signalling molecules that respond to a wide variety of extracellular stimuli. The receptors relay the information encoded by the ligand through the activation of heterotrimeric G proteins and intracellular effector molecules. To ensure the appropriate regulation of the signalling cascade, it is vital to properly inactivate the receptor. This inactivation is achieved, in part, by the binding of a soluble protein, arrestin, which uncouples the receptor from the downstream G protein after the receptors are phosphorylated by G protein-coupled receptor kinases. In addition to the inactivation of G protein-coupled receptors, arrestins have also been implicated in the endocytosis of receptors and cross talk with other signalling pathways. Arrestin (retinal S-antigen) is a major protein of the retinal rod outer segments. It interacts with photo-activated phosphorylated rhodopsin, inhibiting or 'arresting' its ability to interact with transducin []. The protein binds calcium, and shows similarity in its C terminus to alpha-transducin and other purine nucleotide-binding proteins. In mammals, arrestin is associated with autoimmune uveitis. Arrestins comprise a family of closely-related proteins that includes beta-arrestin-1 and -2, which regulate the function of beta-adrenergic receptors by binding to their phosphorylated forms, impairing their capacity to activate G(S) proteins; Cone photoreceptors C-arrestin (arrestin-X) [], which could bind to phosphorylated red/green opsins; and Drosophila phosrestins I and II, which undergo light-induced phosphorylation, and probably play a role in photoreceptor transduction [, , ]. The crystal structure of bovine retinal arrestin comprises two domains of antiparallel beta-sheets connected through a hinge region and one short alpha-helix on the back of the amino-terminal fold []. The binding region for phosphorylated light-activated rhodopsin is located at the N-terminal domain, as indicated by the docking of the photoreceptor to the three-dimensional structure of arrestin. The N-terminal domain consists of an immunoglobulin-like beta-sandwich structure. This entry represents proteins with immunoglobulin-like domains that are similar to those found in arrestin.; PDB: 1SUJ_A 3UGX_A 1CF1_B 1AYR_A 3UGU_A 3P2D_B 1ZSH_A 2WTR_B 3GC3_A 1G4R_A ....
Probab=95.78 E-value=0.0073 Score=52.10 Aligned_cols=40 Identities=28% Similarity=0.474 Sum_probs=25.5
Q ss_pred eeeecCCCceeEEEEEecCCCCCCCCCcceEEEEEEEEeec
Q 011181 66 NQIVSSDATKSYVIRTELPSIIPPSYRGTTIRYLYYVKSTL 106 (491)
Q Consensus 66 ~~~l~~g~~ksy~~r~~LP~~lPpSy~G~~ir~~Y~l~~~~ 106 (491)
...|.+|+ -+|-|.+.||..||+||+|.--++.|.|++++
T Consensus 87 ~~~l~~G~-~~fpF~f~LP~~lP~S~~~~~g~I~Y~l~a~l 126 (149)
T PF00339_consen 87 PNILPPGE-YEFPFEFQLPSNLPSSFEGSHGSIRYKLKATL 126 (149)
T ss_dssp -----C-T-TEEEEEE---TTS--SEEEE-SEEEEEEEEEE
T ss_pred eecccCCC-EEEEEEEECCCCCCceEeccCcCEEEEEEEEE
Confidence 57888995 67999999999999999999899999999776
No 6
>PF02752 Arrestin_C: Arrestin (or S-antigen), C-terminal domain; InterPro: IPR011022 G protein-coupled receptors are a large family of signalling molecules that respond to a wide variety of extracellular stimuli. The receptors relay the information encoded by the ligand through the activation of heterotrimeric G proteins and intracellular effector molecules. To ensure the appropriate regulation of the signalling cascade, it is vital to properly inactivate the receptor. This inactivation is achieved, in part, by the binding of a soluble protein, arrestin, which uncouples the receptor from the downstream G protein after the receptors are phosphorylated by G protein-coupled receptor kinases. In addition to the inactivation of G protein-coupled receptors, arrestins have also been implicated in the endocytosis of receptors and cross talk with other signalling pathways. Arrestin (retinal S-antigen) is a major protein of the retinal rod outer segments. It interacts with photo-activated phosphorylated rhodopsin, inhibiting or 'arresting' its ability to interact with transducin []. The protein binds calcium, and shows similarity in its C terminus to alpha-transducin and other purine nucleotide-binding proteins. In mammals, arrestin is associated with autoimmune uveitis. Arrestins comprise a family of closely-related proteins that includes beta-arrestin-1 and -2, which regulate the function of beta-adrenergic receptors by binding to their phosphorylated forms, impairing their capacity to activate G(S) proteins; Cone photoreceptors C-arrestin (arrestin-X) [], which could bind to phosphorylated red/green opsins; and Drosophila phosrestins I and II, which undergo light-induced phosphorylation, and probably play a role in photoreceptor transduction [, , ]. The crystal structure of bovine retinal arrestin comprises two domains of antiparallel beta-sheets connected through a hinge region and one short alpha-helix on the back of the amino-terminal fold []. The binding region for phosphorylated light-activated rhodopsin is located at the N-terminal domain, as indicated by the docking of the photoreceptor to the three-dimensional structure of arrestin. The C-terminal domain consists of an immunoglobulin-like beta-sandwich structure. This entry represents proteins with immunoglobulin-like domains that are similar to those found in arrestin.; PDB: 1SUJ_A 3UGX_A 1CF1_B 1AYR_A 3UGU_A 3P2D_B 1ZSH_A 2WTR_B 3GC3_A 1G4R_A ....
Probab=93.89 E-value=0.19 Score=42.45 Aligned_cols=58 Identities=24% Similarity=0.410 Sum_probs=34.5
Q ss_pred ecCCCceeEE--EEEecCCCCCCCC--CcceEEEEEEEEeecccceeeeecCccccccccccceeeeeeeeEEEEe
Q 011181 69 VSSDATKSYV--IRTELPSIIPPSY--RGTTIRYLYYVKSTLSARWLILENGLTQRESKRDLTQVEARLPLQIWVT 140 (491)
Q Consensus 69 l~~g~~ksy~--~r~~LP~~lPpSy--~G~~ir~~Y~l~~~~~~r~~~~~~g~~~~~~~~~~~~~~~~iP~~i~~~ 140 (491)
+.+++..+|. ..+.||..+|||. .|.-|++.|.|+ +....+ .....+.+++|+.|...
T Consensus 73 ~~~~~~~~~~~~~~l~lP~~~~~s~~~~~~~i~v~Y~l~-------v~~~~~-------~~~~~~~~~~PI~I~~~ 134 (136)
T PF02752_consen 73 VDPGSSGSFEFNIQLQLPSNLPPSTSTNSRLIQVEYQLE-------VTVKLS-------GCTSDLRLELPITIGSS 134 (136)
T ss_dssp B-B-TTEEEEEEEEE-----B-----CGGGSEEEEEEEE-------EEEEEE-------TTSEEEEEEEEEEEEB-
T ss_pred ccCCCCceEEEEEEEcCCCccCcccccCCcEEEEEEEEE-------EEEEEC-------CceeEEEEEccEEEEec
Confidence 4778888888 9999999999998 999999999998 222222 12456778999998653
No 7
>KOG3780 consensus Thioredoxin binding protein TBP-2/VDUP1 [General function prediction only]
Probab=93.09 E-value=2.4 Score=43.79 Aligned_cols=134 Identities=18% Similarity=0.166 Sum_probs=86.7
Q ss_pred CcEEEEEeCCEEEEEEEccCCCCCcccCccEEEEEEecCCCCceeEEEEEEEEEEeeeecCCccC---CCCCCCCceeeE
Q 011181 313 GRSYNIRMDDQVLLRFSPKNSESTYYFSDMIGGTLTFFHEEGARRCLEVLITLETSETINRWFVH---PSRRNSPTITKI 389 (491)
Q Consensus 313 ~ksY~Inrngq~VarvsL~~pKpaYRLGEdI~Gt~DFt~s~a~irC~qVSVSLESeE~Inp~~a~---~S~~ssr~trKV 389 (491)
...+..-.+|..+..+.+ ||.+|..||.|...+++.+. ....+..+.+.|-..+.....-.. ..+.......+
T Consensus 177 ~~~~~~~~~g~v~~~~~i--p~~~~~~ge~i~~~~~i~n~-ss~~~~~~~~~l~q~~~~~~~~~~~~~~~~~~~~~~~~- 252 (427)
T KOG3780|consen 177 KLGCVCFSSGPVSLELTI--PKTGYVPGETIPVTLEIENK-SSRTIKKVKAKLIQKISYLAFSYGEHTKTKKSEKTLIK- 252 (427)
T ss_pred eeeEEEecCCcEEEEEEc--ccccCcCCccEEEEEEEecC-CCCcceeeEEEEEEEEEEEeecCCccccceeeeeEEee-
Confidence 344467788999999999 59999999999999999853 677777777777776665332110 00000111111
Q ss_pred EEeeeeeeccccee-eEEecCCCCCCCceE--eCceeEEEEEEEEEEecCCCcccccccCCCCcCCceEEEEEeeeEEe
Q 011181 390 QSDHHEVVADLVQT-SFLFSIPMDGPMSFS--TPYVSVQWALRFEFLTTPKHVQWTRYEHPLLIEGRDKSEWVLPITVH 465 (491)
Q Consensus 390 hAe~hE~cld~~rT-~FsL~IP~~ATPqF~--TdiVsLKW~LRFEFVts~~~~~wqa~Edp~~L~e~EtFeW~LPItVl 465 (491)
+.....+....... ...|.||... |+|. +.+++++-.|++.+.+... + .....+.+||.|.
T Consensus 253 ~~~~~~v~~~~~~~~~~~~~iP~~~-Ps~~~~~~~i~v~y~l~v~~~~~~~---~-----------~~~~~l~~pi~ig 316 (427)
T KOG3780|consen 253 SRGSLEVAPRSEDKFEKELRIPPVP-PSILPDTPIIRVEYELKVTLKTSSL---R-----------HSELALELPIIIG 316 (427)
T ss_pred eccccccCCCCccccceEEEcCCCC-CccCCCCceEEEEEEEEEEEecCcc---c-----------ccceeeeeceEEe
Confidence 22333344433332 5666689888 4666 6999999999999988651 1 1234566788887
No 8
>PF07070 Spo0M: SpoOM protein; InterPro: IPR009776 This family consists of several bacterial SpoOM proteins which are thought to control sporulation in Bacillus subtilis.Spo0M exerts certain negative effects on sporulation and its gene expression is controlled by sigmaH [].
Probab=85.12 E-value=8.4 Score=38.29 Aligned_cols=99 Identities=10% Similarity=0.096 Sum_probs=60.7
Q ss_pred CCCcccCccEEEEEEecCCCCceeEEEEEEEEEEeeeecCCccCCCCCC-CCceee-EEEeeeeeeccccee-eEEecCC
Q 011181 334 ESTYYFSDMIGGTLTFFHEEGARRCLEVLITLETSETINRWFVHPSRRN-SPTITK-IQSDHHEVVADLVQT-SFLFSIP 410 (491)
Q Consensus 334 KpaYRLGEdI~Gt~DFt~s~a~irC~qVSVSLESeE~Inp~~a~~S~~s-sr~trK-VhAe~hE~cld~~rT-~FsL~IP 410 (491)
++.|+.||+|.|++.+...+..-++-++.+.|.+.=..... +.... ....-+ ..++-..+=.+..+. +|.+++|
T Consensus 21 ~~~~~pGe~v~G~V~i~GG~v~Q~I~~I~l~L~t~~~~e~~---d~~~~~~~~~~~~~v~~~f~I~~ge~~~iPF~~~lP 97 (218)
T PF07070_consen 21 KPSVRPGETVRGEVHIKGGSVDQEIDRIYLELVTRYEVESD---DKEYTQEVELARVRVSGPFTIEPGEEKEIPFSFPLP 97 (218)
T ss_pred CCCccCCCEEEEEEEEEeCCcceEEeEEEEEEEEEEEEecC---CCeEEEEEEEEEEEeCCCEEECCCCEEEEeEEEECC
Confidence 99999999999999998545566778888888775333211 00000 001111 011222222233333 9999999
Q ss_pred CCCCCceEeCceeEEEEEEEEEEec
Q 011181 411 MDGPMSFSTPYVSVQWALRFEFLTT 435 (491)
Q Consensus 411 ~~ATPqF~TdiVsLKW~LRFEFVts 435 (491)
.+.+.+-....|.|+=.|.++--+-
T Consensus 98 ~etPiT~~~~~v~l~T~LdI~~avD 122 (218)
T PF07070_consen 98 WETPITEGGMRVWLRTGLDIAGAVD 122 (218)
T ss_pred CCCCccCCCcEEEEEEEEEeCCCCC
Confidence 9988877666677777776665553
No 9
>KOG3780 consensus Thioredoxin binding protein TBP-2/VDUP1 [General function prediction only]
Probab=76.86 E-value=3.1 Score=42.98 Aligned_cols=57 Identities=23% Similarity=0.417 Sum_probs=42.9
Q ss_pred CceeEeecCCcceee----ee-eecCCCceeEEEEEecCCCCCCCCCcceEEEEEEEEeeccc
Q 011181 51 GEFAFLDISASKLIS----NQ-IVSSDATKSYVIRTELPSIIPPSYRGTTIRYLYYVKSTLSA 108 (491)
Q Consensus 51 ge~~f~~~~~pslvs----~~-~l~~g~~ksy~~r~~LP~~lPpSy~G~~ir~~Y~l~~~~~~ 108 (491)
|+-.++|+......+ +. .+.|| .-+|.|++.||..+|+||.|+-=-+.|.|+.++-.
T Consensus 79 ~~~~y~~~~~~~~~~~~g~~~~~l~~G-~~~~pF~~~LP~~~P~Sfeg~~G~irY~vk~~idr 140 (427)
T KOG3780|consen 79 AKETYLDSKTILWTSSNGSNSRVLPPG-NYEFPFSFTLPLNLPPSFEGKFGHVRYFVKAEIDR 140 (427)
T ss_pred ceEEEeeeeeEEeeccCCCCceecCCC-ceEEeEeccCCCCCCCceeeCCceEEEEEEEEEec
Confidence 555666666665552 23 35566 56899999999999999999999999999865544
No 10
>PF13002 LDB19: Arrestin_N terminal like; InterPro: IPR024391 This entry represents a predicted Ig-like beta sandwich domain found towards the N terminus of protein LDB19 []. It is also found in other sequences and is related to the arrestin N-terminal fold [].
Probab=66.51 E-value=13 Score=36.58 Aligned_cols=39 Identities=13% Similarity=0.290 Sum_probs=34.6
Q ss_pred eeecCCCceeEEEEEecCCCCCCCCC---cceEEEEEEEEeec
Q 011181 67 QIVSSDATKSYVIRTELPSIIPPSYR---GTTIRYLYYVKSTL 106 (491)
Q Consensus 67 ~~l~~g~~ksy~~r~~LP~~lPpSy~---G~~ir~~Y~l~~~~ 106 (491)
.-|.+|. .+|=|+..||--||+|-. +.-..+.|+|+++.
T Consensus 45 t~l~~G~-h~fPFS~LiPG~LPaS~~lgs~~l~~I~Yel~A~a 86 (191)
T PF13002_consen 45 TTLTKGS-HAFPFSYLIPGHLPASMDLGSTPLVSIKYELKAEA 86 (191)
T ss_pred cccCCCc-ccCCeeEECCCCCccccccCCCCcEEEEEEEEEEE
Confidence 4588895 899999999999999999 99999999998554
No 11
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) [] are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2B39_B 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 4ACQ_C 2P9R_B ....
Probab=58.57 E-value=1.1e+02 Score=25.45 Aligned_cols=75 Identities=12% Similarity=0.081 Sum_probs=38.2
Q ss_pred CCCCcccCccEEEEEEecCCCC---ceeEEEEEEEEEEeeeecCCccCCCCCCCCceeeEEEeeee-eecccceeeEEec
Q 011181 333 SESTYYFSDMIGGTLTFFHEEG---ARRCLEVLITLETSETINRWFVHPSRRNSPTITKIQSDHHE-VVADLVQTSFLFS 408 (491)
Q Consensus 333 pKpaYRLGEdI~Gt~DFt~s~a---~irC~qVSVSLESeE~Inp~~a~~S~~ssr~trKVhAe~hE-~cld~~rT~FsL~ 408 (491)
.|+.||.||+|...+-+...++ ...-..+++.|.. |. + +...+... .........+.+.
T Consensus 7 Dr~iYrPGetV~~~~~~~~~~~~~~~~~~~~~~v~i~d-----p~-----g-------~~v~~~~~~~~~~~G~~~~~~~ 69 (99)
T PF01835_consen 7 DRPIYRPGETVHFRAIVRDLDNDFKPPANSPVTVTIKD-----PS-----G-------NEVFRWSVNTTNENGIFSGSFQ 69 (99)
T ss_dssp SSSEE-TTSEEEEEEEEEEECTTCSCESSEEEEEEEEE-----TT-----S-------EEEEEEEEEETTCTTEEEEEEE
T ss_pred CccCcCCCCEEEEEEEEeccccccccccCCceEEEEEC-----CC-----C-------CEEEEEEeeeeCCCCEEEEEEE
Confidence 4999999999988776543222 2223344444433 21 1 11222222 2344555688899
Q ss_pred CCCCCCCceEeCceeEEEEEEEEE
Q 011181 409 IPMDGPMSFSTPYVSVQWALRFEF 432 (491)
Q Consensus 409 IP~~ATPqF~TdiVsLKW~LRFEF 432 (491)
||.++... .|.|+.+.
T Consensus 70 lp~~~~~G--------~y~i~~~~ 85 (99)
T PF01835_consen 70 LPDDAPLG--------TYTIRVKT 85 (99)
T ss_dssp --SS---E--------EEEEEEEE
T ss_pred CCCCCCCE--------eEEEEEEE
Confidence 99987543 57777764
No 12
>PF03643 Vps26: Vacuolar protein sorting-associated protein 26 ; InterPro: IPR005377 The movement of lipid and protein components between intracellular organelles requires the regulated interactions of many molecules. Vacuolar protein sorting-associated protein (Vps)5 is a yeast protein that is a subunit of a large multimeric complex, termed the retromer complex, involved in retrograde transport of proteins from endosomes to the trans-Golgi network. Sorting nexin (SNX) 1 and SNX2 are its mammalian orthologs []. To carry out its biological functions, Vps5 forms the retromer complex with at least four other proteins: Vps17, Vps26, Vps29, and Vps35 []. This family of Vps26-proteins also contains Down syndrome critical region 3/A.; GO: 0007034 vacuolar transport, 0030904 retromer complex; PDB: 3LHA_A 3LH9_A 2R51_A 3LH8_B 2FAU_A.
Probab=57.16 E-value=1.7e+02 Score=30.13 Aligned_cols=106 Identities=16% Similarity=0.226 Sum_probs=60.8
Q ss_pred EEeCCEEEEEEEccCCCCCcccCccEEEEEEecCCCCceeEEEEEEEEEEeeeecCCccCCCCCCCCceeeEEEeeeeee
Q 011181 318 IRMDDQVLLRFSPKNSESTYYFSDMIGGTLTFFHEEGARRCLEVLITLETSETINRWFVHPSRRNSPTITKIQSDHHEVV 397 (491)
Q Consensus 318 Inrngq~VarvsL~~pKpaYRLGEdI~Gt~DFt~s~a~irC~qVSVSLESeE~Inp~~a~~S~~ssr~trKVhAe~hE~c 397 (491)
+...+-.-..+.+. |+.|.|.|.|.|.+.|- -..++...+-+.|-.-|++.. +.+ ..+-..--...|+.
T Consensus 160 vgie~~lhief~~~--k~~~~l~d~i~G~i~f~--lv~~kIk~~elqLiR~Et~g~------~~~-~~~e~t~i~~~eIm 228 (275)
T PF03643_consen 160 VGIEDCLHIEFEYD--KSKYHLKDVITGKIYFL--LVRIKIKSMELQLIRVETCGC------GEN-YAKESTEIQKIEIM 228 (275)
T ss_dssp ECETTTEEEEEEES---SEEETT-EEEEEEEEE--EESS-EEEEEEEEEEEEEECE------CCC-EEEEEEEEEEEEEE
T ss_pred cCCCccEEEEEEEc--ccceECCCCEEEEEEEE--EEeecceEEEEEEEEEEEEec------CCc-ccccceEEEEEEee
Confidence 33334344567776 99999999999999995 356888888888988888732 111 00011112223333
Q ss_pred cccce----eeEEecCC-CCCCCceEe--CceeEEEEEEEEEEe
Q 011181 398 ADLVQ----TSFLFSIP-MDGPMSFST--PYVSVQWALRFEFLT 434 (491)
Q Consensus 398 ld~~r----T~FsL~IP-~~ATPqF~T--diVsLKW~LRFEFVt 434 (491)
-+... -+|.+-+| +..+|++.| +.|+++..|++-.+.
T Consensus 229 DG~p~rge~IPirl~l~~l~l~Pt~~~~~~~FsV~y~lnlvlid 272 (275)
T PF03643_consen 229 DGAPCRGESIPIRLFLPRLFLCPTYKNVNNKFSVEYELNLVLID 272 (275)
T ss_dssp SS---TT-EEEEEEECCCT-----EEEECTTEEEEEEEEEEEEE
T ss_pred cCCccccceeeEEEEcCCcccCCcchhcCCcEEEEEEEEEEEEc
Confidence 33322 26665554 568899995 679999999987664
No 13
>PF08737 Rgp1: Rgp1; InterPro: IPR014848 Rgp1 forms heterodimer with Ric1 (IPR009771 from INTERPRO) which associates with Golgi membranes and functions as a guanyl-nucleotide exchange factor [].
Probab=51.70 E-value=78 Score=34.08 Aligned_cols=51 Identities=20% Similarity=0.327 Sum_probs=37.4
Q ss_pred eEEecCCCCCCCceEeCceeEEEEEEEEEEecCCCcccccccCCCCcCCceEEEEEeeeEEeCC
Q 011181 404 SFLFSIPMDGPMSFSTPYVSVQWALRFEFLTTPKHVQWTRYEHPLLIEGRDKSEWVLPITVHAP 467 (491)
Q Consensus 404 ~FsL~IP~~ATPqF~TdiVsLKW~LRFEFVts~~~~~wqa~Edp~~L~e~EtFeW~LPItVlPt 467 (491)
.|++.+|.+.+|+|+...|+....|.+-.-- ..+ . ........+||+|+|.
T Consensus 124 ~~~~~lP~~lPPsy~g~~i~~~Y~l~vg~~~---------~~~---~-~~~~~~~~~Pi~v~~~ 174 (415)
T PF08737_consen 124 HFSFTLPKDLPPSYRGKAIKISYSLVVGTQR---------GSS---V-NSKVKSIRVPIRVLPS 174 (415)
T ss_pred EEEEeCCCCCCCCCcCcEEEEEEEEEEEEEE---------cCC---C-CcceEEEEeCEEEeee
Confidence 8899999999999998887777766544333 111 1 3345688999999976
No 14
>PF07070 Spo0M: SpoOM protein; InterPro: IPR009776 This family consists of several bacterial SpoOM proteins which are thought to control sporulation in Bacillus subtilis.Spo0M exerts certain negative effects on sporulation and its gene expression is controlled by sigmaH [].
Probab=51.48 E-value=50 Score=32.99 Aligned_cols=40 Identities=13% Similarity=0.067 Sum_probs=32.0
Q ss_pred eeeeeeecCCCceeEEEEEecCCCCCCCCCcceEEEEEEE
Q 011181 63 LISNQIVSSDATKSYVIRTELPSIIPPSYRGTTIRYLYYV 102 (491)
Q Consensus 63 lvs~~~l~~g~~ksy~~r~~LP~~lPpSy~G~~ir~~Y~l 102 (491)
+-....|.|||+|++-|++.||-.+|-|-.|..+-+.=.|
T Consensus 76 v~~~f~I~~ge~~~iPF~~~lP~etPiT~~~~~v~l~T~L 115 (218)
T PF07070_consen 76 VSGPFTIEPGEEKEIPFSFPLPWETPITEGGMRVWLRTGL 115 (218)
T ss_pred eCCCEEECCCCEEEEeEEEECCCCCCccCCCcEEEEEEEE
Confidence 4445899999999999999999999999977654443333
No 15
>cd05817 CBM20_DSP Dual-specificity phosphatase (DSP), N-terminal CBM20 (carbohydrate-binding module, family 20) domain. This CBM20 domain is located at the N-terminus of a protein tyrosine phosphatase of unknown function found in slime molds and ciliated protozoans. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific recognition of appropriate regions of starch.
Probab=47.56 E-value=59 Score=27.77 Aligned_cols=64 Identities=16% Similarity=0.273 Sum_probs=41.9
Q ss_pred ccCceeEeecCCcceeee-----eeecCCCceeEEEEEecCCCCCCCCCcceEEEEEEEEeecccceeeeecCccc
Q 011181 49 FPGEFAFLDISASKLISN-----QIVSSDATKSYVIRTELPSIIPPSYRGTTIRYLYYVKSTLSARWLILENGLTQ 119 (491)
Q Consensus 49 ~~ge~~f~~~~~pslvs~-----~~l~~g~~ksy~~r~~LP~~lPpSy~G~~ir~~Y~l~~~~~~r~~~~~~g~~~ 119 (491)
-.||.++|--+.|.|-+= +.+.....-.....+.||. |..+.|+|.++.--.|..+.-|.|..|
T Consensus 11 ~~Ge~l~v~Gs~~~LG~W~~~~a~~m~~~~~~~W~~~v~lp~-------~~~veYKY~i~~~~~~~~~~WE~g~nr 79 (100)
T cd05817 11 QFGEAVYISGNCNQLGNWNPSKAKRMQWNEGDLWTVDVGIPE-------SVYIEYKYFVSNYDDPNTVLWESGPNR 79 (100)
T ss_pred CCCCEEEEEeCcHHHCCCCccccCcccCCCCCCEEEEEEECC-------CCcEEEEEEEEecCCCCCeEecCCCCE
Confidence 469999998888877641 3444444456777888875 556999999964332334455666443
No 16
>PF10633 NPCBM_assoc: NPCBM-associated, NEW3 domain of alpha-galactosidase; InterPro: IPR018905 This domain has been named NEW3, but its function is not known. It is found on proteins which are bacterial galactosidases [].; PDB: 1EUT_A 2BZD_A 1WCQ_C 2BER_A 1W8O_A 1EUU_A 1W8N_A.
Probab=43.64 E-value=23 Score=28.68 Aligned_cols=23 Identities=9% Similarity=0.234 Sum_probs=16.7
Q ss_pred eecCCCceeEEEEEecCCCCCCC
Q 011181 68 IVSSDATKSYVIRTELPSIIPPS 90 (491)
Q Consensus 68 ~l~~g~~ksy~~r~~LP~~lPpS 90 (491)
.|.||+++++.|+++.|.+.+|-
T Consensus 45 ~l~pG~s~~~~~~V~vp~~a~~G 67 (78)
T PF10633_consen 45 SLPPGESVTVTFTVTVPADAAPG 67 (78)
T ss_dssp -B-TTSEEEEEEEEEE-TT--SE
T ss_pred cCCCCCEEEEEEEEECCCCCCCc
Confidence 78999999999999999998873
No 17
>cd05814 CBM20_Prei4 Prei4, N-terminal CBM20 (carbohydrate-binding module, family 20) domain. Preimplantation protein 4 (Prei4) is a protein of unknown function that is expressed during mouse preimplantation embryogenesis. In addition to the N-terminal CBM20 domain, Prei4 contains a C-terminal glycerophosphoryl diester phosphodiesterase (GDPD) domain. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific recognition of appropriate regions of starch.
Probab=39.19 E-value=93 Score=27.42 Aligned_cols=50 Identities=24% Similarity=0.323 Sum_probs=36.5
Q ss_pred ccCceeEeecCCcceeee-----eeecCC--CceeEEEEEecCCCCCCCCCcceEEEEEEEEee
Q 011181 49 FPGEFAFLDISASKLISN-----QIVSSD--ATKSYVIRTELPSIIPPSYRGTTIRYLYYVKST 105 (491)
Q Consensus 49 ~~ge~~f~~~~~pslvs~-----~~l~~g--~~ksy~~r~~LP~~lPpSy~G~~ir~~Y~l~~~ 105 (491)
-+||.+++--+.|.|-+- +.+... ....+...+.||. |+.|.|+|.+...
T Consensus 13 ~~ge~v~v~G~~~~LG~W~~~~a~~l~~~~~~~~~W~~~v~lp~-------~~~veYkY~~~~~ 69 (120)
T cd05814 13 APGEVVAVVGSLPVLGNWQPEKAVPLEKEDDDCNLWKASIELPR-------GVDFQYRYFVAVV 69 (120)
T ss_pred CCCCEEEEEeChHHhCCCCHHhCeeCccCCCcCCccEEEEEECC-------CCeEEEEEEEEEe
Confidence 369999998888877642 345544 4466888888886 5579999999743
No 18
>cd05467 CBM20 The family 20 carbohydrate-binding module (CBM20), also known as the starch-binding domain, is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific recognition of appropriate regions of starch.
Probab=35.26 E-value=1.3e+02 Score=24.60 Aligned_cols=51 Identities=20% Similarity=0.286 Sum_probs=36.6
Q ss_pred ccCceeEeecCCcceee----e-eeecCCC-ceeEEEEEecCCCCCCCCCcceEEEEEEEEe
Q 011181 49 FPGEFAFLDISASKLIS----N-QIVSSDA-TKSYVIRTELPSIIPPSYRGTTIRYLYYVKS 104 (491)
Q Consensus 49 ~~ge~~f~~~~~pslvs----~-~~l~~g~-~ksy~~r~~LP~~lPpSy~G~~ir~~Y~l~~ 104 (491)
-+||.+++--+.|.|-. + +.+.... .-.+...+.||. | .|..+.|+|.++.
T Consensus 11 ~~Ge~l~v~G~~~~LG~W~~~~a~~m~~~~~~~~W~~~v~~~~--~---~~~~~~yKy~~~~ 67 (96)
T cd05467 11 QFGQSVYVVGSHPELGNWDPAKALRLNTSNSYPLWTGEIPLPA--P---EGQVIEYKYVIVD 67 (96)
T ss_pred CCCCEEEEEeCcHHhCCcChhcCccccCCCCCCcEEEEEEecC--C---CCCeEEEEEEEEC
Confidence 47999999888887754 2 4455554 455777777775 2 5789999999973
No 19
>PF02221 E1_DerP2_DerF2: ML domain; InterPro: IPR003172 The MD-2-related lipid-recognition (ML) domain is implicated in lipid recognition, particularly in the recognition of pathogen related products. It has an immunoglobulin-like beta-sandwich fold similar to that of E-set Ig domains. This domain is present in the following proteins: Epididymal secretory protein E1 (also known as Niemann-Pick C2 protein), which is known to bind cholesterol. Niemann-Pick disease type C2 is a fatal hereditary disease characterised by accumulation of low-density lipoprotein-derived cholesterol in lysosomes []. House-dust mite allergen proteins such as Der f 2 from Dermatophagoides farinae and Der p 2 from Dermatophagoides pteronyssinus []. ; PDB: 2AG9_B 1G13_B 2AG2_B 2AG4_A 1TJJ_C 1PU5_C 1PUB_A 2AF9_A 3T6Q_D 3M7O_B ....
Probab=31.77 E-value=1.7e+02 Score=25.27 Aligned_cols=23 Identities=22% Similarity=0.501 Sum_probs=20.4
Q ss_pred eecCCCceeEEEEEecCCCCCCC
Q 011181 68 IVSSDATKSYVIRTELPSIIPPS 90 (491)
Q Consensus 68 ~l~~g~~ksy~~r~~LP~~lPpS 90 (491)
-+.+|+.-+|.+.+.+|..+|+-
T Consensus 87 Pi~~G~~~~~~~~~~i~~~~p~~ 109 (134)
T PF02221_consen 87 PIKAGEYYTYTYTIPIPKIYPPG 109 (134)
T ss_dssp TBTTTEEEEEEEEEEESTTSSSE
T ss_pred ccCCCcEEEEEEEEEcccceeeE
Confidence 48999999999999999999874
No 20
>PF03643 Vps26: Vacuolar protein sorting-associated protein 26 ; InterPro: IPR005377 The movement of lipid and protein components between intracellular organelles requires the regulated interactions of many molecules. Vacuolar protein sorting-associated protein (Vps)5 is a yeast protein that is a subunit of a large multimeric complex, termed the retromer complex, involved in retrograde transport of proteins from endosomes to the trans-Golgi network. Sorting nexin (SNX) 1 and SNX2 are its mammalian orthologs []. To carry out its biological functions, Vps5 forms the retromer complex with at least four other proteins: Vps17, Vps26, Vps29, and Vps35 []. This family of Vps26-proteins also contains Down syndrome critical region 3/A.; GO: 0007034 vacuolar transport, 0030904 retromer complex; PDB: 3LHA_A 3LH9_A 2R51_A 3LH8_B 2FAU_A.
Probab=28.83 E-value=87 Score=32.20 Aligned_cols=37 Identities=16% Similarity=0.363 Sum_probs=21.3
Q ss_pred eecCCCceeEEEEEec-CCCCCCCCCcceEEEEEEEEeecc
Q 011181 68 IVSSDATKSYVIRTEL-PSIIPPSYRGTTIRYLYYVKSTLS 107 (491)
Q Consensus 68 ~l~~g~~ksy~~r~~L-P~~lPpSy~G~~ir~~Y~l~~~~~ 107 (491)
.|..|.+ |-|.|.+ |+. =.||+|..+++.|+|+.+..
T Consensus 92 ~l~~~~t--~pFeF~~~~k~-yETY~G~~v~i~Y~lrv~v~ 129 (275)
T PF03643_consen 92 KLPEGKT--FPFEFPLVEKP-YETYHGVNVNIRYFLRVTVK 129 (275)
T ss_dssp EE-S-EE--EEEEE-SB----S--EE-SSEEEEEEEEEEE-
T ss_pred ccCCCcE--EeeEeCCCCCC-CccEeeeEEEEEEEEEEEEE
Confidence 4445544 8888866 333 68999999999999996654
No 21
>cd05816 CBM20_DPE2_repeat2 Disproportionating enzyme 2 (DPE2), N-terminal CBM20 (carbohydrate-binding module, family 20) domain, repeat 2. DPE2 is a transglucosidase that is essential for the cytosolic metabolism of maltose in plant leaves at night. Maltose is an intermediate on the pathway from starch to sucrose and DPE2 is thought to metabolize the maltose that is exported from the chloroplast. DPE2 has two N-terminal CBM20 domains as well as a C-terminal amylomaltase (4-alpha-glucanotransferase) catalytic domain. DPE1, the plastid version of this enzyme, has a transglucosidase domain that is similar to that of DPE2 but lacks the N-terminal CBM20 domains. Included in this group are PDE2-like proteins from Dictyostelium, Entamoeba, and Bacteroides. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in star
Probab=28.27 E-value=2.1e+02 Score=24.36 Aligned_cols=50 Identities=12% Similarity=0.143 Sum_probs=34.7
Q ss_pred ccCceeEeecCCcceee-----eeeecCCCceeEEEEEecCCCCCCCCCcceEEEEEEEEe
Q 011181 49 FPGEFAFLDISASKLIS-----NQIVSSDATKSYVIRTELPSIIPPSYRGTTIRYLYYVKS 104 (491)
Q Consensus 49 ~~ge~~f~~~~~pslvs-----~~~l~~g~~ksy~~r~~LP~~lPpSy~G~~ir~~Y~l~~ 104 (491)
.+||+++|--+.|.|-. -+.+.....-.+...+.+|.. +.+|.|+|.++.
T Consensus 12 ~~Ge~v~i~Gs~~~LG~W~~~~a~~l~~~~~~~W~~~v~~p~~------~~~ieYKyvi~~ 66 (99)
T cd05816 12 PKGQSVYVTGSSPELGNWDPQKALKLSDVGFPIWEADIDISKD------SFPFEYKYIIAN 66 (99)
T ss_pred CCCCEEEEEEChHHhCCCCccccccCCCCCCCcEEEEEEeCCC------CccEEEEEEEEe
Confidence 58999999888887654 134455555556677776631 348999999973
No 22
>PF00686 CBM_20: Starch binding domain; InterPro: IPR002044 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This domain binds to starch, and is found often at the C terminus of a variety of glycosyl hydrolases acting on polysaccharides more rapidly than on oligosaccharides. Reations include: the hydrolysis of terminal 1,4-linked alpha-D-glucose residues successively from non-reducing ends of the chains with release of beta-D-glucose, the degradation of starch to cyclodextrins by formation of a 1,4-alpha-D-glucosidic bond, and hydrolysis of 1,4-alpha-glucosidic linkages in polysaccharides to remove successive maltose units from the non-reducing ends of the chains.; GO: 0003824 catalytic activity, 0005975 carbohydrate metabolic process; PDB: 1KUL_A 1ACZ_A 1AC0_A 1KUM_A 2Z0B_C 9CGT_A 3CGT_A 6CGT_A 4CGT_A 1CGT_A ....
Probab=25.75 E-value=3.6e+02 Score=22.53 Aligned_cols=63 Identities=24% Similarity=0.366 Sum_probs=42.2
Q ss_pred cccCceeEeecCCccee----ee-eeecC----CCceeEEEEEecCCCCCCCCCcceEEEEEEEEeecccceeeeecCcc
Q 011181 48 FFPGEFAFLDISASKLI----SN-QIVSS----DATKSYVIRTELPSIIPPSYRGTTIRYLYYVKSTLSARWLILENGLT 118 (491)
Q Consensus 48 ~~~ge~~f~~~~~pslv----s~-~~l~~----g~~ksy~~r~~LP~~lPpSy~G~~ir~~Y~l~~~~~~r~~~~~~g~~ 118 (491)
.-+||.+++--+.|.|= .+ +.|.. +....+...+.||. |..+.|+|.++.. .| .++.|.|..
T Consensus 12 ~~~ge~v~i~Gs~~~LG~W~~~~a~~l~~~~~~~~~~~W~~~v~lp~-------~~~~eYKy~i~~~-~g-~~~WE~g~n 82 (96)
T PF00686_consen 12 TQPGESVYIVGSCPELGNWDPKKAVPLQWNEGTENYPIWSATVDLPA-------GTPFEYKYVIKDA-DG-NVIWESGEN 82 (96)
T ss_dssp --TTEEEEEEESSGGGTTTSGGGSBESEBESSSSTTTSEEEEEEEET-------TSEEEEEEEEEET-TS-EEEE-SSSE
T ss_pred CCCCCEEEEEECcHHhCCCChHhccccccccCCCCCCeEEEEEECcC-------CCEEEEEEEEEeC-CC-CEEECCCCC
Confidence 35799999999999762 22 44443 36678888888886 5699999999632 22 556666654
Q ss_pred c
Q 011181 119 Q 119 (491)
Q Consensus 119 ~ 119 (491)
|
T Consensus 83 R 83 (96)
T PF00686_consen 83 R 83 (96)
T ss_dssp E
T ss_pred E
Confidence 4
No 23
>PF02966 DIM1: Mitosis protein DIM1; InterPro: IPR004123 Thioredoxins [, , , ] are small disulphide-containing redox proteins that have been found in all the kingdoms of living organisms. Thioredoxin serves as a general protein disulphide oxidoreductase. It interacts with a broad range of proteins by a redox mechanism based on reversible oxidation of 2 cysteine thiol groups to a disulphide, accompanied by the transfer of 2 electrons and 2 protons. The net result is the covalent interconversion of a disulphide and a dithiol. Compared to human thioredoxin, human U5 snRNP-specific protein U5-15kDa contains 37 additional residues that may cause structural changes which most likely form putative binding sites for other spliceosomal proteins or RNA. Although U5-15kDa apparently lacks protein disulphide isomerase activity, it is strictly required for pre-mRNA splicing [].; GO: 0007067 mitosis, 0005681 spliceosomal complex; PDB: 1SYX_E 1PQN_A 1QGV_A 2AV4_A 1XBS_A 3GIX_A.
Probab=24.88 E-value=36 Score=31.98 Aligned_cols=17 Identities=24% Similarity=0.706 Sum_probs=15.4
Q ss_pred hhhcccCceeEeecCCc
Q 011181 45 LLFFFPGEFAFLDISAS 61 (491)
Q Consensus 45 ~~~~~~ge~~f~~~~~p 61 (491)
++|||||.|+-+|+.++
T Consensus 78 vmFF~rnkhm~vD~Gtg 94 (133)
T PF02966_consen 78 VMFFFRNKHMMVDFGTG 94 (133)
T ss_dssp EEEEETTEEEEEESSSS
T ss_pred EEEEecCeEEEEEecCC
Confidence 57888999999999987
No 24
>KOG3414 consensus Component of the U4/U6.U5 snRNP/mitosis protein DIM1 [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=22.65 E-value=43 Score=31.69 Aligned_cols=20 Identities=20% Similarity=0.471 Sum_probs=17.2
Q ss_pred hhhhhhcccCceeEeecCCc
Q 011181 42 FVELLFFFPGEFAFLDISAS 61 (491)
Q Consensus 42 ~~~~~~~~~ge~~f~~~~~p 61 (491)
++-..|||++.|+-+||.++
T Consensus 78 p~tvmfFfn~kHmkiD~gtg 97 (142)
T KOG3414|consen 78 PPTVMFFFNNKHMKIDLGTG 97 (142)
T ss_pred CceEEEEEcCceEEEeeCCC
Confidence 34567999999999999987
No 25
>PF06280 DUF1034: Fn3-like domain (DUF1034); InterPro: IPR010435 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain of unknown function is present in bacterial and plant peptidases belonging to MEROPS peptidase family S8 (subfamily S8A subtilisin, clan SB). It is C-terminal to and adjacent to the S8 peptidase domain and can be found in conjunction with the PA (Protease associated) domain (IPR003137 from INTERPRO) and additionally in Gram-positive bacteria with the surface protein anchor domain (IPR001899 from INTERPRO).; GO: 0004252 serine-type endopeptidase activity, 0005618 cell wall, 0016020 membrane; PDB: 3EIF_A 1XF1_B.
Probab=21.34 E-value=71 Score=27.51 Aligned_cols=23 Identities=17% Similarity=0.225 Sum_probs=19.0
Q ss_pred eeecCCCceeEEEEEecCCCCCC
Q 011181 67 QIVSSDATKSYVIRTELPSIIPP 89 (491)
Q Consensus 67 ~~l~~g~~ksy~~r~~LP~~lPp 89 (491)
+.|.||+++++.|.+.+|.++.+
T Consensus 64 vTV~ag~s~~v~vti~~p~~~~~ 86 (112)
T PF06280_consen 64 VTVPAGQSKTVTVTITPPSGLDA 86 (112)
T ss_dssp EEE-TTEEEEEEEEEE--GGGHH
T ss_pred EEECCCCEEEEEEEEEehhcCCc
Confidence 88999999999999999999887
No 26
>PLN03160 uncharacterized protein; Provisional
Probab=20.54 E-value=7.1e+02 Score=24.58 Aligned_cols=73 Identities=12% Similarity=0.173 Sum_probs=36.3
Q ss_pred EEEEecCCCCCCCCCcceEEEEEEEEeecccceeeeecCccccccccccceeeeeeeeEEEEee--cCCccccccccCCC
Q 011181 78 VIRTELPSIIPPSYRGTTIRYLYYVKSTLSARWLILENGLTQRESKRDLTQVEARLPLQIWVTQ--KGNGLLTEENQNDG 155 (491)
Q Consensus 78 ~~r~~LP~~lPpSy~G~~ir~~Y~l~~~~~~r~~~~~~g~~~~~~~~~~~~~~~~iP~~i~~~~--~~~g~~~~~~~~~~ 155 (491)
.++.+=|-...=.|.+.++.+.|.=. .-|. ..+..|.|++..+ ..+.+. +.+-... .+.+ +.+|+..|
T Consensus 98 ~v~v~NPN~~~~~Y~~~~~~v~Y~g~--~vG~-a~~p~g~~~ar~T---~~l~~t--v~~~~~~~~~~~~--L~~D~~~G 167 (219)
T PLN03160 98 DVSVKNPNVASFKYSNTTTTIYYGGT--VVGE-ARTPPGKAKARRT---MRMNVT--VDIIPDKILSVPG--LLTDISSG 167 (219)
T ss_pred EEEEECCCceeEEEcCeEEEEEECCE--EEEE-EEcCCcccCCCCe---EEEEEE--EEEEeceeccchh--HHHHhhCC
Confidence 33455577766677777777766322 2222 1234555543322 211222 2222111 1222 45679999
Q ss_pred Ccccc
Q 011181 156 IVPAT 160 (491)
Q Consensus 156 ~vp~~ 160 (491)
.+|+.
T Consensus 168 ~v~l~ 172 (219)
T PLN03160 168 LLNMN 172 (219)
T ss_pred eEEEE
Confidence 99995
Done!