Query 024163
Match_columns 271
No_of_seqs 120 out of 130
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 02:32:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024163.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024163hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00037 photosystem II oxygen 100.0 6E-129 1E-133 894.4 24.7 256 15-270 58-313 (313)
2 PF01716 MSP: Manganese-stabil 100.0 1E-126 2E-131 858.1 17.8 235 34-270 1-245 (245)
3 TIGR02221 cas_TM1812 CRISPR-as 37.3 22 0.00048 32.7 1.9 17 254-270 159-175 (218)
4 PF06537 DUF1111: Protein of u 34.2 1.4E+02 0.0029 31.0 7.0 27 132-158 161-190 (499)
5 COG5515 Uncharacterized conser 33.0 40 0.00086 26.4 2.4 36 100-138 30-65 (70)
6 PF06999 Suc_Fer-like: Sucrase 31.1 25 0.00055 30.8 1.2 11 261-271 195-205 (230)
7 TIGR01564 S_layer_MJ S-layer p 29.8 38 0.00082 35.5 2.4 56 100-158 194-256 (571)
8 PF00394 Cu-oxidase: Multicopp 29.0 1.8E+02 0.004 24.1 5.9 33 123-155 91-126 (159)
9 KOG3245 Uncharacterized conser 27.8 20 0.00044 30.1 0.0 27 204-240 60-86 (106)
10 PF11138 DUF2911: Protein of u 25.7 3.5E+02 0.0076 23.6 7.2 74 38-113 34-112 (145)
11 PF01249 Ribosomal_S21e: Ribos 25.2 92 0.002 25.0 3.3 24 220-244 29-52 (81)
12 KOG0285 Pleiotropic regulator 24.9 1E+02 0.0022 31.5 4.2 76 68-144 319-405 (460)
13 cd03062 TRX_Fd_Sucrase TRX-lik 24.4 30 0.00066 27.2 0.5 11 261-271 62-72 (97)
No 1
>PLN00037 photosystem II oxygen-evolving enhancer protein 1; Provisional
Probab=100.00 E-value=5.7e-129 Score=894.40 Aligned_cols=256 Identities=84% Similarity=1.314 Sum_probs=249.5
Q ss_pred hhhccCCCCCCCCCccchhhhcccceeeeeceeecCCCCCcCCCCcceeecCCceeeeecccccceEEEEeeecCCCCCC
Q 024163 15 SSFRSGASAEGVPKRLTYDEIQSKTYMEVKGTGTANQCPTIDGGVDSFAFKPGKYQAKKFCLEPTSFTVKAESVNKNAPP 94 (271)
Q Consensus 15 ~~~~~~a~a~~~~~~lTyd~~~~ltY~qvkgTGlAN~CP~l~~~~~~i~l~~g~Y~l~~lClEPtsf~VkeE~~~k~~~~ 94 (271)
..++++|.|++++++|||||||+|||+||||||+||+||+++++.+.|++++|+|+|++||||||+|+||||+.+||+++
T Consensus 58 ~~~~~~~~a~~~~~~lt~~e~~~ltY~~vkgTG~AN~CP~l~~~~~~i~~~~g~y~l~~lClePtsf~VkeE~~~k~~~~ 137 (313)
T PLN00037 58 ALVASGASAEGVPKRLTYDEIQSLTYLEVKGTGTANQCPTVDGGDESFSFKPGKYALKKFCLEPTSFTVKAESVFKNGEP 137 (313)
T ss_pred HHHhccccccccccccchhhhcccchhhhcCceecccCCCcCCCcceecccCCceeeeeeccCCceEEEEecccCCcccc
Confidence 34567888888889999999999999999999999999999888888999999999999999999999999999999999
Q ss_pred ccccceeeeeeeeeeeeeeeeeEeCCCCCeeEEEecCeeeeeeEEecCCCceeeeEEEecceeeccCCcccceeeecccc
Q 024163 95 DFQNTKLMTRLTYTLDEIEGPFEVSPDGTIKFVEKDGIDYAAVTVQLPGGERVPFLFTIKQLVASGKPENFGGEFLVPSY 174 (271)
Q Consensus 95 eFv~tKLmTR~TyTLd~I~G~l~v~~dG~ltf~E~dGiDfa~iTVqlPGGErVPFLFTvK~L~A~~~~~~F~G~F~VPSY 174 (271)
|||++|||||+|||||+|+|+|++++||+|+|+|+|||||||||||||||||||||||||+|+|++++++|+|+|+||||
T Consensus 138 eFv~~KlmTR~TytLd~i~G~l~~~~dG~l~F~E~dGiDf~~~TVqlPGGErVPFlFTvK~LvA~~~~t~F~G~f~VPSY 217 (313)
T PLN00037 138 EFQNTKLMTRLTYTLDEIEGPLKVGSDGSVKFEEKDGIDYAAVTVQLPGGERVPFLFTIKELVATGKPESFGGDFLVPSY 217 (313)
T ss_pred ccccceEEEeeeeehhheeeeeEeCCCCcEEEEEeCCccceeEEEEcCCCceeeEEEEeecceeeccCccceeeEeCccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCCCCcccccceeccCCCCCChhHHhhhhcccccccceEEEEEEEeecCCCCeeeEEEeEeCCCCCCCCCC
Q 024163 175 RGSSFLDPKGRGGSTGYDNAIALPAGGRGDEEDLAKENIKNTSSSTGKITLSVTKSKPETGEVIGVFESLQPSDTDMGAK 254 (271)
Q Consensus 175 Rgs~FLDPKGRG~sTGYD~AvaLpa~g~~d~eeL~kEN~K~~~~~~G~i~l~V~kVd~~TGEiaGvF~S~QpSDTDmGak 254 (271)
|||+||||||||++|||||||||||.|++|+|||+|||+|++++++|+|+|+|+|||++||||||||+|+||||||||||
T Consensus 218 R~s~FLDPKGRG~~TGYD~AVaLpA~G~~d~eeL~kEN~K~~~~~~G~i~l~V~kVd~~TGEiaGvF~s~QpSDTDlGak 297 (313)
T PLN00037 218 RGSSFLDPKGRGGSTGYDNAVALPAGGRGDEEELAKENNKNTAASTGNITLSVAKSNPETGEIAGVFESIQPSDTDLGSK 297 (313)
T ss_pred cccCccCCCccCCccccccceeccccCCCCHHHHHhhhccccccccceEEEEEEeecCCCCeEEEEEEeeCCCCcccCCC
Confidence 99999999999999999999999998778999999999999999999999999999999999999999999999999999
Q ss_pred CCcceEEEEEEEEEec
Q 024163 255 VPKDVKIQGIWYAQLE 270 (271)
Q Consensus 255 ~PkdVki~GifYgrl~ 270 (271)
+||||||+|+|||||+
T Consensus 298 ~pkdVki~G~fYgrl~ 313 (313)
T PLN00037 298 VPKDVKIQGIWYAQLE 313 (313)
T ss_pred CCceEEEEEEEEEecC
Confidence 9999999999999985
No 2
>PF01716 MSP: Manganese-stabilising protein / photosystem II polypeptide; InterPro: IPR002628 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants []. This family represents the PSII OEC protein PsbO, which appears to be the most important extrinsic protein for oxygen evolution. PsbO lies closest to the Mn cluster where water oxidation occurs, and has a stabilising effect on the Mn cluster. As a result, PsbO is often referred to as the Mn-stabilising protein (MSP), although none of its amino acids are likely ligands for Mn. Calcium ions were found to modify the conformation of PsbO in solution [].; GO: 0005509 calcium ion binding, 0015979 photosynthesis, 0042549 photosystem II stabilization, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 3PRR_O 4FBY_f 3BZ1_O 3KZI_O 1S5L_o 2AXT_o 3BZ2_O 3PRQ_O 3ARC_O 3A0B_O ....
Probab=100.00 E-value=1e-126 Score=858.05 Aligned_cols=235 Identities=68% Similarity=1.114 Sum_probs=194.2
Q ss_pred hhcccceeeeeceeecCCCCCcCCCCcc-eeecCCc-eeeeecccccceEEEEeeecCCCCCCccccceeeeeeeeeeee
Q 024163 34 EIQSKTYMEVKGTGTANQCPTIDGGVDS-FAFKPGK-YQAKKFCLEPTSFTVKAESVNKNAPPDFQNTKLMTRLTYTLDE 111 (271)
Q Consensus 34 ~~~~ltY~qvkgTGlAN~CP~l~~~~~~-i~l~~g~-Y~l~~lClEPtsf~VkeE~~~k~~~~eFv~tKLmTR~TyTLd~ 111 (271)
|||+|||+|||||||||+||+|++++++ |+|++|+ |+|++||||||+|+||||+++||+++|||+||||||+|||||+
T Consensus 1 e~~~ltY~qvkgTGlAN~CP~l~~~~~~~i~l~~g~~Y~~~~lClePtsf~VkeE~~~k~~~~eFv~tKlmTR~TytLd~ 80 (245)
T PF01716_consen 1 EIQSLTYDQVKGTGLANTCPTLSGGARGSISLKPGKSYKLKDLCLEPTSFQVKEEPANKRGEAEFVPTKLMTRQTYTLDQ 80 (245)
T ss_dssp ------HHHCTTTSGCCS-----ST-B--EESHSSSSEEEEEEEEEEEEEEEEE--SSSSSS-EEEEEEESSTS-SSEEE
T ss_pred CcccccceeeecceecccCCccCCCCCCceeeCCCCeeEeeeeeecCcEEEEEecccccCCcccceeeeEEeeeeeeehh
Confidence 5789999999999999999999998777 9999994 9999999999999999999999999999999999999999999
Q ss_pred eeeeeEeCCCCCeeEEEecCeeeeeeEEecCCCceeeeEEEecceeeccCCcc--------cceeeeccccCCCCCCCCC
Q 024163 112 IEGPFEVSPDGTIKFVEKDGIDYAAVTVQLPGGERVPFLFTIKQLVASGKPEN--------FGGEFLVPSYRGSSFLDPK 183 (271)
Q Consensus 112 I~G~l~v~~dG~ltf~E~dGiDfa~iTVqlPGGErVPFLFTvK~L~A~~~~~~--------F~G~F~VPSYRgs~FLDPK 183 (271)
|+|+|+|++||+|+|+|+|||||||||||||||||||||||||+|+|+++++. |+|+|+|||||||+|||||
T Consensus 81 i~G~l~v~~dG~ltf~E~dGiDfa~~TVqlPGGErVPFlFTvK~LvA~~~~~~~si~~stdf~G~f~VPSYRgs~FLDPK 160 (245)
T PF01716_consen 81 IEGDLKVGSDGSLTFKEKDGIDFAPITVQLPGGERVPFLFTVKELVAKGQPGGSSINPSTDFGGEFRVPSYRGSTFLDPK 160 (245)
T ss_dssp EEEEEEEETTSEEEEEEECEC-EEEEEEECSSS-EEEEEEE-CCEEEEE-SSSSEESTT-EEEEEEEEE-SS-TT-B-CC
T ss_pred eEEEEEECCCCcEEEEEeCCcceeeEEEecCCCcEeeEEEEehhhhccCCCCcccccccceeeeeEeccccccccccCCC
Confidence 99999999999999999999999999999999999999999999999998755 9999999999999999999
Q ss_pred CCCCCcccccceeccCCCCCChhHHhhhhcccccccceEEEEEEEeecCCCCeeeEEEeEeCCCCCCCCCCCCcceEEEE
Q 024163 184 GRGGSTGYDNAIALPAGGRGDEEDLAKENIKNTSSSTGKITLSVTKSKPETGEVIGVFESLQPSDTDMGAKVPKDVKIQG 263 (271)
Q Consensus 184 GRG~sTGYD~AvaLpa~g~~d~eeL~kEN~K~~~~~~G~i~l~V~kVd~~TGEiaGvF~S~QpSDTDmGak~PkdVki~G 263 (271)
|||++|||||||||||. +|+|||+|||+|++++++|+|+|+|+|||++||||||||+|+||||||||||+||||||+|
T Consensus 161 GRG~~TGYD~AvaLpa~--~d~eeL~keN~K~~~~~~G~i~l~V~kVd~~TGEiaGvF~s~QpSDTDlGak~pkdVki~G 238 (245)
T PF01716_consen 161 GRGGSTGYDNAVALPAA--GDDEELFKENNKRFDVGKGSISLSVAKVDPETGEIAGVFESIQPSDTDLGAKEPKDVKIKG 238 (245)
T ss_dssp SBBSSSSBSS-TTSTTS---STT-CHHHHS----EEEEEEEEEEEEEETTTTEEEEEEEEEEEB--TTTTS---EEEEEE
T ss_pred cccccccccchhhcccc--cchhhhhhhhccccccccceEEEEEEeECCCcCcEEEEEEeeCCCCccccCCCCceEEEEE
Confidence 99999999999999995 4999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEec
Q 024163 264 IWYAQLE 270 (271)
Q Consensus 264 ifYgrl~ 270 (271)
+|||||+
T Consensus 239 i~Y~rle 245 (245)
T PF01716_consen 239 IFYGRLE 245 (245)
T ss_dssp EEEEEEE
T ss_pred EEEEecC
Confidence 9999996
No 3
>TIGR02221 cas_TM1812 CRISPR-associated protein, TM1812 family. CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This family, represented by TM1812 of Thermotoga maritima, is found also in Vibrio vulnificus YJ016, Nitrosomonas europaea ATCC 19718, a large plasmid of Synechocystis sp. PCC 6803, and Fibrobacter succinogenes S85.
Probab=37.30 E-value=22 Score=32.67 Aligned_cols=17 Identities=35% Similarity=0.792 Sum_probs=14.5
Q ss_pred CCCcceEEEEEEEEEec
Q 024163 254 KVPKDVKIQGIWYAQLE 270 (271)
Q Consensus 254 k~PkdVki~GifYgrl~ 270 (271)
|.-|.|+|+|+|||.++
T Consensus 159 k~~k~v~i~~I~YGa~e 175 (218)
T TIGR02221 159 RYVKNVKVEGVLYGALD 175 (218)
T ss_pred HHhcCceEeeEEEeeec
Confidence 55689999999999875
No 4
>PF06537 DUF1111: Protein of unknown function (DUF1111); InterPro: IPR010538 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=34.24 E-value=1.4e+02 Score=31.02 Aligned_cols=27 Identities=26% Similarity=0.367 Sum_probs=23.1
Q ss_pred eeeeeeEEecCCCcee---eeEEEecceee
Q 024163 132 IDYAAVTVQLPGGERV---PFLFTIKQLVA 158 (271)
Q Consensus 132 iDfa~iTVqlPGGErV---PFLFTvK~L~A 158 (271)
|+|..++|++|+|+.| .=.|.|+++..
T Consensus 161 i~y~~~~v~~~dG~~v~Lr~p~~~~~~~~~ 190 (499)
T PF06537_consen 161 ISYEEETVTFADGTTVTLRKPTYSVTQPYY 190 (499)
T ss_pred EEEEeeEEeeCCCCEEEeeCCeEEeecccc
Confidence 7999999999999998 55788888754
No 5
>COG5515 Uncharacterized conserved small protein [Function unknown]
Probab=33.04 E-value=40 Score=26.42 Aligned_cols=36 Identities=31% Similarity=0.421 Sum_probs=28.0
Q ss_pred eeeeeeeeeeeeeeeeeEeCCCCCeeEEEecCeeeeeeE
Q 024163 100 KLMTRLTYTLDEIEGPFEVSPDGTIKFVEKDGIDYAAVT 138 (271)
Q Consensus 100 KLmTR~TyTLd~I~G~l~v~~dG~ltf~E~dGiDfa~iT 138 (271)
||--.-||+.+.-.+.+.+ |.-..+|.|||||-|-|
T Consensus 30 ~LyGsPtyafn~~~~~m~c---gQaVVkdvdg~dy~pd~ 65 (70)
T COG5515 30 KLYGSPTYAFNAETKTMIC---GQAVVKDVDGIDYGPDT 65 (70)
T ss_pred eEecCcceeecCCCceEEe---cceEEEeccccccCCCc
Confidence 4555667888887788887 45788999999998865
No 6
>PF06999 Suc_Fer-like: Sucrase/ferredoxin-like; InterPro: IPR009737 This family contains a number of bacterial and eukaryotic proteins approximately 400 residues long that resemble ferredoxin and appear to have sucrolytic activity [].
Probab=31.10 E-value=25 Score=30.80 Aligned_cols=11 Identities=36% Similarity=1.042 Sum_probs=9.4
Q ss_pred EEEEEEEEecC
Q 024163 261 IQGIWYAQLEQ 271 (271)
Q Consensus 261 i~GifYgrl~~ 271 (271)
-.|+|||||.+
T Consensus 195 p~g~wyGrv~p 205 (230)
T PF06999_consen 195 PDGIWYGRVTP 205 (230)
T ss_pred CcEEEEEeeCH
Confidence 57999999964
No 7
>TIGR01564 S_layer_MJ S-layer protein, MJ0822 family. This model represents one of several families of proteins associated with the formation of prokaryotic S-layers. Members of this family are found in archaeal species, including Pyrococcus horikoshii (split into two tandem reading frames), Methanococcus jannaschii, and related species. Some local similarity can be found to other S-layer protein families.
Probab=29.83 E-value=38 Score=35.53 Aligned_cols=56 Identities=21% Similarity=0.301 Sum_probs=39.3
Q ss_pred eeeeeeeeeeeeeeeeeEeCCCC----CeeEEEecCeeeeeeEEecCCCceeeeE---EEecceee
Q 024163 100 KLMTRLTYTLDEIEGPFEVSPDG----TIKFVEKDGIDYAAVTVQLPGGERVPFL---FTIKQLVA 158 (271)
Q Consensus 100 KLmTR~TyTLd~I~G~l~v~~dG----~ltf~E~dGiDfa~iTVqlPGGErVPFL---FTvK~L~A 158 (271)
=+|+|++|+.. ..++.|.+++ +|.|++ +.-+|++-+..|..|-|+||| .++..|.+
T Consensus 194 i~~~~~~~~~~--~~~~~v~~~~~~y~sl~~~~-~~~~~~~~~~~l~~G~~ipfLG~e~~~v~ld~ 256 (571)
T TIGR01564 194 ITMAVYNWTKT--KAKDTVTGVTTLYASIAYKD-DLENFQPATYSISEGTRSPFLGEEVTLVVFDK 256 (571)
T ss_pred EEEEEEeccCc--CccceecCccceEEEEEeec-cccccCCCceeccCCCCccccccceEEEEecC
Confidence 37889999865 5667777765 344565 334777778899889999999 44444433
No 8
>PF00394 Cu-oxidase: Multicopper oxidase; InterPro: IPR001117 Copper is one of the most prevalent transition metals in living organisms and its biological function is intimately related to its redox properties. Since free copper is toxic, even at very low concentrations, its homeostasis in living organisms is tightly controlled by subtle molecular mechanisms. In eukaryotes, before being transported inside the cell via the high-affinity copper transporters of the CTR family, the copper (II) ion is reduced to copper (I). In blue copper proteins such as cupredoxin, the copper (I) ion form is stabilised by a constrained His2Cys coordination environment. Multicopper oxidases oxidise their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre; dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water []. There are three spectroscopically different copper centres found in multicopper oxidases: type 1 (or blue), type 2 (or normal) and type 3 (or coupled binuclear) [, ]. Multicopper oxidases consist of 2, 3 or 6 of these homologous domains, which also share homology to the cupredoxins azurin and plastocyanin. Structurally, these domains consist of a cupredoxin-like fold, a beta-sandwich consisting of 7 strands in 2 beta-sheets, arranged in a Greek-key beta-barrel []. Multicopper oxidases include: Ceruloplasmin (1.16.3.1 from EC) (ferroxidase), a 6-domain enzyme found in the serum of mammals and birds that oxidizes different inorganic and organic substances; exhibits internal sequence homology that appears to have evolved from the triplication of a Cu-binding domain similar to that of laccase and ascorbate oxidase. Laccase (1.10.3.2 from EC) (urishiol oxidase), a 3-domain enzyme found in fungi and plants, which oxidizes different phenols and diamines. CueO is a laccase found in Escherichia coli that is involved in copper-resistance []. Ascorbate oxidase (1.10.3.3 from EC), a 3-domain enzyme found in higher plants. Nitrite reductase (1.7.2.1 from EC), a 2-domain enzyme containing type-1 and type-2 copper centres [, ]. In addition to the above enzymes there are a number of other proteins that are similar to the multi-copper oxidases in terms of structure and sequence, some of which have lost the ability to bind copper. These include: copper resistance protein A (copA) from a plasmid in Pseudomonas syringae; domain A of (non-copper binding) blood coagulation factors V (Fa V) and VIII (Fa VIII) []; yeast FET3 required for ferrous iron uptake []; yeast hypothetical protein YFL041w; and the fission yeast homologue SpAC1F7.08. This entry represents multicopper oxidase type 1 (blue) domains. These domains are also present in proteins that have lost the ability to bind copper.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1RZP_A 2AVF_D 1NIA_A 1KCB_A 2NRD_A 1NIB_A 2BW4_A 1RZQ_C 2BWD_A 2BWI_A ....
Probab=28.97 E-value=1.8e+02 Score=24.10 Aligned_cols=33 Identities=24% Similarity=0.412 Sum_probs=26.5
Q ss_pred CeeEEEecCeeeeeeE---EecCCCceeeeEEEecc
Q 024163 123 TIKFVEKDGIDYAAVT---VQLPGGERVPFLFTIKQ 155 (271)
Q Consensus 123 ~ltf~E~dGiDfa~iT---VqlPGGErVPFLFTvK~ 155 (271)
+++..+.||.+..|.+ +.|+-|||+=+|++.++
T Consensus 91 ~~~Via~DG~~v~p~~~~~l~l~~G~R~dvlv~~~~ 126 (159)
T PF00394_consen 91 PMTVIAADGVPVEPYKVDTLVLAPGQRYDVLVTADQ 126 (159)
T ss_dssp CEEEEEETTEEEEEEEESBEEE-TTEEEEEEEEECS
T ss_pred ceeEeeeccccccccccceEEeeCCeEEEEEEEeCC
Confidence 5777888888877764 57999999999999976
No 9
>KOG3245 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.76 E-value=20 Score=30.08 Aligned_cols=27 Identities=33% Similarity=0.423 Sum_probs=19.7
Q ss_pred ChhHHhhhhcccccccceEEEEEEEeecCCCCeeeEE
Q 024163 204 DEEDLAKENIKNTSSSTGKITLSVTKSKPETGEVIGV 240 (271)
Q Consensus 204 d~eeL~kEN~K~~~~~~G~i~l~V~kVd~~TGEiaGv 240 (271)
-.++|.||-.|-+- +.||+-||||+|-
T Consensus 60 ~~~~~Ekepl~~~p----------~~vNp~TgEiGGp 86 (106)
T KOG3245|consen 60 HPSHLEKEPLKPWP----------NDVNPYTGEIGGP 86 (106)
T ss_pred ChhhhhcccCCCCc----------ccCCccccccCCC
Confidence 35666777776543 5799999999983
No 10
>PF11138 DUF2911: Protein of unknown function (DUF2911); InterPro: IPR021314 This bacterial family of proteins has no known function.
Probab=25.74 E-value=3.5e+02 Score=23.56 Aligned_cols=74 Identities=23% Similarity=0.245 Sum_probs=47.6
Q ss_pred cceeeeeceeecCCCCCcCCCCcc----eeecCCceeeeecccccceEEEEeeecCCC-CCCccccceeeeeeeeeeeee
Q 024163 38 KTYMEVKGTGTANQCPTIDGGVDS----FAFKPGKYQAKKFCLEPTSFTVKAESVNKN-APPDFQNTKLMTRLTYTLDEI 112 (271)
Q Consensus 38 ltY~qvkgTGlAN~CP~l~~~~~~----i~l~~g~Y~l~~lClEPtsf~VkeE~~~k~-~~~eFv~tKLmTR~TyTLd~I 112 (271)
.-|-+|=-|| ||.|-++.-..+= ..|++|+|.|.-+= .+++++|---..... +..+|-+.+-+-|.+-+....
T Consensus 34 vPygkvWRtG-AN~aT~i~f~~dv~igGk~l~AG~Ysl~tiP-~~~~WtvI~n~~~~~wG~~~Y~~~~Dv~rv~v~~~~~ 111 (145)
T PF11138_consen 34 VPYGKVWRTG-ANEATTITFSKDVTIGGKKLKAGTYSLFTIP-GEDEWTVIFNKDTDQWGAYNYDPSKDVLRVTVPPQKL 111 (145)
T ss_pred ccCCCeecCC-CCcceEEEECCCeEECCEEcCCeeEEEEEec-CCCeEEEEEECCCCccCccccCchheEEEEEeeeecC
Confidence 3455599999 9999999644432 46999999987653 445688854333332 234677777776766555444
Q ss_pred e
Q 024163 113 E 113 (271)
Q Consensus 113 ~ 113 (271)
.
T Consensus 112 ~ 112 (145)
T PF11138_consen 112 P 112 (145)
T ss_pred C
Confidence 3
No 11
>PF01249 Ribosomal_S21e: Ribosomal protein S21e ; InterPro: IPR001931 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 [, ]. A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities. These proteins have 82 to 87 amino acids. The amino termini are all N alpha-acetylated. The N-terminal halves of the protein molecules are highly conserved in contrast to the carboxy-terminal parts [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3U5G_V 3U5C_V 3IZB_T 2XZN_Z 2XZM_Z 3IZ6_T.
Probab=25.19 E-value=92 Score=25.04 Aligned_cols=24 Identities=17% Similarity=0.457 Sum_probs=19.1
Q ss_pred ceEEEEEEEeecCCCCeeeEEEeEe
Q 024163 220 TGKITLSVTKSKPETGEVIGVFESL 244 (271)
Q Consensus 220 ~G~i~l~V~kVd~~TGEiaGvF~S~ 244 (271)
.++|.+.|.+||+. |.+.|-|...
T Consensus 29 HaSvQinv~~vd~~-G~~~g~~~t~ 52 (81)
T PF01249_consen 29 HASVQINVADVDEN-GRFTGQFKTY 52 (81)
T ss_dssp TTSEEEEEEEE-SS-S-EEEEEEEE
T ss_pred ceeEEEEeeeecCc-ccCcCCceEE
Confidence 46799999999999 9999998764
No 12
>KOG0285 consensus Pleiotropic regulator 1 [RNA processing and modification]
Probab=24.92 E-value=1e+02 Score=31.48 Aligned_cols=76 Identities=24% Similarity=0.389 Sum_probs=39.3
Q ss_pred ceeeeecccccceEEEEeeecCCCCCCccccceeeee---ee---eeeeee-eeeeEeCC-CCCeeEEE-ecCeeeeee-
Q 024163 68 KYQAKKFCLEPTSFTVKAESVNKNAPPDFQNTKLMTR---LT---YTLDEI-EGPFEVSP-DGTIKFVE-KDGIDYAAV- 137 (271)
Q Consensus 68 ~Y~l~~lClEPtsf~VkeE~~~k~~~~eFv~tKLmTR---~T---yTLd~I-~G~l~v~~-dG~ltf~E-~dGiDfa~i- 137 (271)
+-...-+|++|+.|.+---+.+--..-.+-.+..|.- .+ -||.-- .|-+.+++ +|.+-|-. ++|-.||..
T Consensus 319 kksvral~lhP~e~~fASas~dnik~w~~p~g~f~~nlsgh~~iintl~~nsD~v~~~G~dng~~~fwdwksg~nyQ~~~ 398 (460)
T KOG0285|consen 319 KKSVRALCLHPKENLFASASPDNIKQWKLPEGEFLQNLSGHNAIINTLSVNSDGVLVSGGDNGSIMFWDWKSGHNYQRGQ 398 (460)
T ss_pred cceeeEEecCCchhhhhccCCccceeccCCccchhhccccccceeeeeeeccCceEEEcCCceEEEEEecCcCccccccc
Confidence 3456789999999988433322111222333333332 11 112111 12233333 36677755 889999977
Q ss_pred -EEecCCC
Q 024163 138 -TVQLPGG 144 (271)
Q Consensus 138 -TVqlPGG 144 (271)
-|| ||.
T Consensus 399 t~vq-pGS 405 (460)
T KOG0285|consen 399 TIVQ-PGS 405 (460)
T ss_pred cccc-CCc
Confidence 455 553
No 13
>cd03062 TRX_Fd_Sucrase TRX-like [2Fe-2S] Ferredoxin (Fd) family, Sucrase subfamily; composed of proteins with similarity to a novel plant enzyme, isolated from potato, which contains a Fd-like domain and exhibits sucrolytic activity. The putative active site of the Fd-like domain of the enzyme contains two cysteines and two histidines for possible binding to iron-sulfur clusters, compared to four cysteines present in the active site of Fd.
Probab=24.39 E-value=30 Score=27.23 Aligned_cols=11 Identities=36% Similarity=0.984 Sum_probs=9.3
Q ss_pred EEEEEEEEecC
Q 024163 261 IQGIWYAQLEQ 271 (271)
Q Consensus 261 i~GifYgrl~~ 271 (271)
..|+||+++++
T Consensus 62 ~~g~wy~~v~p 72 (97)
T cd03062 62 GDGIWYGRVTP 72 (97)
T ss_pred CCeeEEeecCH
Confidence 58999999864
Done!