Query 019870
Match_columns 334
No_of_seqs 120 out of 142
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 05:11:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019870.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019870hhsearch_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 1E-138 3E-143 979.7 26.5 312 22-333 2-313 (313)
2 PF01716 MSP: Manganese-stabil 100.0 3E-124 8E-129 860.7 16.4 235 97-333 1-245 (245)
3 PF07467 BLIP: Beta-lactamase 39.4 6.1 0.00013 36.8 -1.3 29 89-117 27-60 (183)
4 TIGR02221 cas_TM1812 CRISPR-as 35.7 24 0.00053 33.3 1.9 17 317-333 159-175 (218)
5 PF06537 DUF1111: Protein of u 34.8 1.3E+02 0.0027 32.1 7.1 27 195-221 161-190 (499)
6 COG5515 Uncharacterized conser 34.2 36 0.00078 27.4 2.4 36 163-201 30-65 (70)
7 PLN00092 photosystem I reactio 34.0 17 0.00037 32.6 0.6 48 38-86 31-81 (137)
8 PLN00037 photosystem II oxygen 28.9 57 0.0012 32.8 3.3 37 65-101 51-89 (313)
9 PF06999 Suc_Fer-like: Sucrase 28.8 29 0.00062 31.3 1.2 11 324-334 195-205 (230)
10 PRK10564 maltose regulon perip 28.6 6.2E+02 0.013 25.5 11.0 38 279-316 196-233 (303)
11 KOG3245 Uncharacterized conser 28.2 20 0.00043 31.0 0.0 27 267-303 60-86 (106)
12 PF00394 Cu-oxidase: Multicopp 26.7 1.6E+02 0.0035 25.2 5.3 33 186-218 91-126 (159)
13 KOG0285 Pleiotropic regulator 25.2 92 0.002 32.6 4.1 76 131-207 319-405 (460)
14 TIGR01564 S_layer_MJ S-layer p 25.1 60 0.0013 35.0 2.9 55 163-220 194-255 (571)
15 PF11138 DUF2911: Protein of u 24.8 3.1E+02 0.0067 24.6 6.8 71 102-174 35-110 (145)
16 cd03062 TRX_Fd_Sucrase TRX-lik 22.6 34 0.00075 27.7 0.5 11 324-334 62-72 (97)
17 PF07162 B9-C2: Ciliary basal 21.2 69 0.0015 28.2 2.1 62 124-190 100-163 (168)
18 COG4704 Uncharacterized protei 20.4 51 0.0011 30.1 1.1 27 109-135 63-92 (151)
19 PF01249 Ribosomal_S21e: Ribos 20.1 1.3E+02 0.0028 24.9 3.3 24 283-307 29-52 (81)
No 1
>PLN00037 photosystem II oxygen-evolving enhancer protein 1; Provisional
Probab=100.00 E-value=1.4e-138 Score=979.69 Aligned_cols=312 Identities=82% Similarity=1.260 Sum_probs=305.7
Q ss_pred CCccccccccccchhcccccccCCceeEEeeccchhHHHHHhhhhHHHHHHHHHHhhhhccCCcCCCCCCccchhhhccc
Q 019870 22 ARSSSLQLRSSQSVSKAFGVDSAGARISCSLNNDLKDLAQKCVDATKIAGFALATSALVVSGASAEGVPKRLTYDEIQSK 101 (334)
Q Consensus 22 ~~~~~~~~~~~~~~~~~fg~~~~~~~~~~s~~~~~~~~~~~~~~~~~~a~~~la~~a~~~~~a~A~~~~~~lTyd~~~~l 101 (334)
+++.+.++|++++++|+||++++.++++|+++.+++.++.||+++++++++++++++++++++.|++++++||||||++|
T Consensus 2 ~~~~~~~~~~sasvskafgv~~a~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~lt~~e~~~l 81 (313)
T PLN00037 2 PSRASAQLRSSASVSKAFGLEPASARLTCSLQSDLKDFADKCVDAGKAAGFALAASALVASGASAEGVPKRLTYDEIQSL 81 (313)
T ss_pred cccchhhhhhhhhhHhhcCCchhhhhhhhhhhhhhHHHhhhhhhhHHHHHHHHHHHHHHhccccccccccccchhhhccc
Confidence 45677889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeeeeceeecCCCCCcCCCCcceeecCCceeeeccccccceEEEeeeecCCCCCCCcccceeeeeeeeeccceeeeeee
Q 019870 102 TYMEVKGTGTANQCPTIDGGVDSFAFKPGKYQAKKFCLEPTSFTVKAESVNKNAPPDFQNTKLMTRLTYTLDEIEGPFEV 181 (334)
Q Consensus 102 tY~qVkgTGlAN~CP~l~~~~~~i~l~~G~Y~l~~lClEPtsf~VkeE~~~K~~~~eFv~tKLmTR~TyTLd~I~G~l~v 181 (334)
||+||||||+||+||+++++.++|++++|+|+|+|||||||+|+||||+.+||+++|||++|||||+|||||+|+|+|++
T Consensus 82 tY~~vkgTG~AN~CP~l~~~~~~i~~~~g~y~l~~lClePtsf~VkeE~~~k~~~~eFv~~KlmTR~TytLd~i~G~l~~ 161 (313)
T PLN00037 82 TYLEVKGTGTANQCPTVDGGDESFSFKPGKYALKKFCLEPTSFTVKAESVFKNGEPEFQNTKLMTRLTYTLDEIEGPLKV 161 (313)
T ss_pred chhhhcCceecccCCCcCCCcceecccCCceeeeeeccCCceEEEEecccCCccccccccceEEEeeeeehhheeeeeEe
Confidence 99999999999999999888889999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeeEEEecCeeeeeeeeecCCCceeeeEEEecceeeccCCccccceeeccccCCCCCCCCCCCCCCcccccceecc
Q 019870 182 SPDGTIKFVEKDGIDYAAVTVQLPGGERVPFLFTIKQLVASGKPENFGGEFLVPSYRGSSFLDPKGRGGSTGYDNAIALP 261 (334)
Q Consensus 182 ~~dG~ltF~E~dGiDya~iTVQlPGGErVPFLFTvK~LvA~~~~~~F~G~F~VPSYRgs~FLDPKGRG~sTGYD~AvaLp 261 (334)
++||+|+|+|+|||||||||||||||||||||||||+|+|++++++|+|+|+||||||++||||||||++||||||||||
T Consensus 162 ~~dG~l~F~E~dGiDf~~~TVqlPGGErVPFlFTvK~LvA~~~~t~F~G~f~VPSYR~s~FLDPKGRG~~TGYD~AVaLp 241 (313)
T PLN00037 162 GSDGSVKFEEKDGIDYAAVTVQLPGGERVPFLFTIKELVATGKPESFGGDFLVPSYRGSSFLDPKGRGGSTGYDNAVALP 241 (313)
T ss_pred CCCCcEEEEEeCCccceeEEEEcCCCceeeEEEEeecceeeccCccceeeEeCccccccCccCCCccCCccccccceecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCChhHHhhhhcccccccceeEEEEEEeecCCCceeeEEEeEeCCCCCCCCCCCCcceEEEEEEEEEec
Q 019870 262 AGGRGDEEDLAKENIKNTSSSTGKITLSVTKSKPETGEVIGVFESLQPSDTDMGAKVPKDVKIQGIWYAQLE 333 (334)
Q Consensus 262 a~g~~d~eeL~kEN~K~~~~~~G~i~l~V~kVd~~TGEiaGvF~S~QpSDTDmGaK~PkdVki~GifYgrl~ 333 (334)
|.|++|+|||+|||+|++++++|+|+|+|+|||++||||+|||||+||||||||+|+||||||+|+|||||+
T Consensus 242 A~G~~d~eeL~kEN~K~~~~~~G~i~l~V~kVd~~TGEiaGvF~s~QpSDTDlGak~pkdVki~G~fYgrl~ 313 (313)
T PLN00037 242 AGGRGDEEELAKENNKNTAASTGNITLSVAKSNPETGEIAGVFESIQPSDTDLGSKVPKDVKIQGIWYAQLE 313 (313)
T ss_pred ccCCCCHHHHHhhhccccccccceEEEEEEeecCCCCeEEEEEEeeCCCCcccCCCCCceEEEEEEEEEecC
Confidence 987789999999999999999999999999999999999999999999999999999999999999999995
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=3.5e-124 Score=860.70 Aligned_cols=235 Identities=68% Similarity=1.117 Sum_probs=194.0
Q ss_pred hhcccceeeeeceeecCCCCCcCCCCc-ceeecCCc-eeeeccccccceEEEeeeecCCCCCCCcccceeeeeeeeeccc
Q 019870 97 EIQSKTYMEVKGTGTANQCPTIDGGVD-SFAFKPGK-YQAKKFCLEPTSFTVKAESVNKNAPPDFQNTKLMTRLTYTLDE 174 (334)
Q Consensus 97 ~~~~ltY~qVkgTGlAN~CP~l~~~~~-~i~l~~G~-Y~l~~lClEPtsf~VkeE~~~K~~~~eFv~tKLmTR~TyTLd~ 174 (334)
|||+|||+|||||||||+||+|+++++ +|+|++|+ |+|++||||||+|+||||+.+||+++|||+||||||+|||||+
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 588999999999999999999998866 89999995 9999999999999999999999999999999999999999999
Q ss_pred eeeeeeeCCCCCeeEEEecCeeeeeeeeecCCCceeeeEEEecceeeccCCcc--------ccceeeccccCCCCCCCCC
Q 019870 175 IEGPFEVSPDGTIKFVEKDGIDYAAVTVQLPGGERVPFLFTIKQLVASGKPEN--------FGGEFLVPSYRGSSFLDPK 246 (334)
Q Consensus 175 I~G~l~v~~dG~ltF~E~dGiDya~iTVQlPGGErVPFLFTvK~LvA~~~~~~--------F~G~F~VPSYRgs~FLDPK 246 (334)
|+|+|+|++||+|+|+|+|||||||||||||||||||||||||+|+|+++++. |+|+|+||||||++|||||
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 99999999999999999999999999999999999999999999999998765 9999999999999999999
Q ss_pred CCCCCcccccceeccCCCCCChhHHhhhhcccccccceeEEEEEEeecCCCceeeEEEeEeCCCCCCCCCCCCcceEEEE
Q 019870 247 GRGGSTGYDNAIALPAGGRGDEEDLAKENIKNTSSSTGKITLSVTKSKPETGEVIGVFESLQPSDTDMGAKVPKDVKIQG 326 (334)
Q Consensus 247 GRG~sTGYD~AvaLpa~g~~d~eeL~kEN~K~~~~~~G~i~l~V~kVd~~TGEiaGvF~S~QpSDTDmGaK~PkdVki~G 326 (334)
|||++|||||||||||. +|+|||+|||+|++++++|+|+|+|+|||++||||+|||||+||||||||||+||||||+|
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 019870 327 IWYAQLE 333 (334)
Q Consensus 327 ifYgrl~ 333 (334)
+|||||+
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
>PF07467 BLIP: Beta-lactamase inhibitor (BLIP); InterPro: IPR009099 The beta-lactamase-inhibitor protein (BLIP) is produced by Streptomyces species. BLIP acts as a potent inhibitor of beta-lactamases such as TEM-1, which is the most widespread resistance enzyme to penicillin antibiotics. BLIP binds competitively to TEM-1 and makes direct contacts with TEM-1 active site residues. BLIP is able to inhibit a variety of class A beta-lactamases, possibly through flexibility of its two domains. The two tandemly repeated domains of BLIP have an alpha(2)-beta(4) structure, the beta-hairpin loop from domain 1 inserting into the active site of beta-lactamase []. BLIP shows no sequence similarity with BLIP-II, even though both bind to and inhibit TEM-1 [].; PDB: 3GMY_B 3GMX_B 3C4O_B 1XXM_C 1S0W_D 3N4I_B 3C7U_B 2G2W_B 3C7V_D 3E2K_C ....
Probab=39.37 E-value=6.1 Score=36.83 Aligned_cols=29 Identities=38% Similarity=0.643 Sum_probs=17.1
Q ss_pred CCCccc---hhhhc-ccceeeeece-eecCCCCC
Q 019870 89 VPKRLT---YDEIQ-SKTYMEVKGT-GTANQCPT 117 (334)
Q Consensus 89 ~~~~lT---yd~~~-~ltY~qVkgT-GlAN~CP~ 117 (334)
+...|| |++|| .|||.||... |-++.|-+
T Consensus 27 a~s~lT~EkY~kIqfGMt~~EV~~ilGa~~~Cse 60 (183)
T PF07467_consen 27 ACSKLTAEKYEKIQFGMTYDEVWDILGAEDNCSE 60 (183)
T ss_dssp ---SS-HHHHHHS-TT-BHHHHHHHHTHHHHEEE
T ss_pred cccccCHHHhhhHhcCCCHHHHHHHhCCcCcccc
Confidence 345576 88887 7999999875 55557843
No 4
>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=35.68 E-value=24 Score=33.34 Aligned_cols=17 Identities=35% Similarity=0.792 Sum_probs=14.4
Q ss_pred CCCcceEEEEEEEEEec
Q 019870 317 KVPKDVKIQGIWYAQLE 333 (334)
Q Consensus 317 K~PkdVki~GifYgrl~ 333 (334)
|.-|.|+|+|+|||.++
T Consensus 159 k~~k~v~i~~I~YGa~e 175 (218)
T TIGR02221 159 RYVKNVKVEGVLYGALD 175 (218)
T ss_pred HHhcCceEeeEEEeeec
Confidence 45689999999999875
No 5
>PF06537 DUF1111: Protein of unknown function (DUF1111); InterPro: IPR010538 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=34.83 E-value=1.3e+02 Score=32.11 Aligned_cols=27 Identities=26% Similarity=0.367 Sum_probs=23.3
Q ss_pred eeeeeeeeecCCCcee---eeEEEecceee
Q 019870 195 IDYAAVTVQLPGGERV---PFLFTIKQLVA 221 (334)
Q Consensus 195 iDya~iTVQlPGGErV---PFLFTvK~LvA 221 (334)
|+|..++|++|+|+.| +=.|.|+++..
T Consensus 161 i~y~~~~v~~~dG~~v~Lr~p~~~~~~~~~ 190 (499)
T PF06537_consen 161 ISYEEETVTFADGTTVTLRKPTYSVTQPYY 190 (499)
T ss_pred EEEEeeEEeeCCCCEEEeeCCeEEeecccc
Confidence 7899999999999998 55788888754
No 6
>COG5515 Uncharacterized conserved small protein [Function unknown]
Probab=34.18 E-value=36 Score=27.43 Aligned_cols=36 Identities=31% Similarity=0.421 Sum_probs=27.8
Q ss_pred eeeeeeeeeccceeeeeeeCCCCCeeEEEecCeeeeeee
Q 019870 163 KLMTRLTYTLDEIEGPFEVSPDGTIKFVEKDGIDYAAVT 201 (334)
Q Consensus 163 KLmTR~TyTLd~I~G~l~v~~dG~ltF~E~dGiDya~iT 201 (334)
||--.-||+.+.-.+.+.+ |.-..+|.|||||-|-|
T Consensus 30 ~LyGsPtyafn~~~~~m~c---gQaVVkdvdg~dy~pd~ 65 (70)
T COG5515 30 KLYGSPTYAFNAETKTMIC---GQAVVKDVDGIDYGPDT 65 (70)
T ss_pred eEecCcceeecCCCceEEe---cceEEEeccccccCCCc
Confidence 4555667888777777776 56788999999999865
No 7
>PLN00092 photosystem I reaction center subunit V (PsaG); Provisional
Probab=34.01 E-value=17 Score=32.56 Aligned_cols=48 Identities=21% Similarity=0.329 Sum_probs=23.4
Q ss_pred cccccc---CCceeEEeeccchhHHHHHhhhhHHHHHHHHHHhhhhccCCcC
Q 019870 38 AFGVDS---AGARISCSLNNDLKDLAQKCVDATKIAGFALATSALVVSGASA 86 (334)
Q Consensus 38 ~fg~~~---~~~~~~~s~~~~~~~~~~~~~~~~~~a~~~la~~a~~~~~a~A 86 (334)
..||.. -..|+.|+++.+-.. -....+.+..|.+.+|+.++.+++..|
T Consensus 31 vlGLPam~~~~g~v~Cs~e~k~~~-~~~~~~~g~~asl~Aaa~a~a~~a~PA 81 (137)
T PLN00092 31 VLGLPAMAKKKGRVRCSMEEKPSV-QDKSSNMGMGASLMAAACAVAMSASPA 81 (137)
T ss_pred ccCCchhcccCceeEEecccCccc-cccccccchhHHHHHHHHHHHhhcCcH
Confidence 477764 234899999654211 122333344444444444444443333
No 8
>PLN00037 photosystem II oxygen-evolving enhancer protein 1; Provisional
Probab=28.92 E-value=57 Score=32.82 Aligned_cols=37 Identities=19% Similarity=0.099 Sum_probs=21.0
Q ss_pred hhHHHHHHHHHHhhhhccCCc--CCCCCCccchhhhccc
Q 019870 65 DATKIAGFALATSALVVSGAS--AEGVPKRLTYDEIQSK 101 (334)
Q Consensus 65 ~~~~~a~~~la~~a~~~~~a~--A~~~~~~lTyd~~~~l 101 (334)
.++.+++++++.++..++.++ .-....+|||+||.+-
T Consensus 51 ~~~~~~~~~~~~~~~a~~~~~~lt~~e~~~ltY~~vkgT 89 (313)
T PLN00037 51 GFALAASALVASGASAEGVPKRLTYDEIQSLTYLEVKGT 89 (313)
T ss_pred HHHHHHHHHHhccccccccccccchhhhcccchhhhcCc
Confidence 444445555555555543222 2233577999999883
No 9
>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=28.79 E-value=29 Score=31.31 Aligned_cols=11 Identities=36% Similarity=1.042 Sum_probs=9.3
Q ss_pred EEEEEEEEecC
Q 019870 324 IQGIWYAQLEQ 334 (334)
Q Consensus 324 i~GifYgrl~~ 334 (334)
-.|+|||||.+
T Consensus 195 p~g~wyGrv~p 205 (230)
T PF06999_consen 195 PDGIWYGRVTP 205 (230)
T ss_pred CcEEEEEeeCH
Confidence 57999999964
No 10
>PRK10564 maltose regulon periplasmic protein; Provisional
Probab=28.57 E-value=6.2e+02 Score=25.49 Aligned_cols=38 Identities=18% Similarity=0.309 Sum_probs=25.2
Q ss_pred ccccceeEEEEEEeecCCCceeeEEEeEeCCCCCCCCC
Q 019870 279 TSSSTGKITLSVTKSKPETGEVIGVFESLQPSDTDMGA 316 (334)
Q Consensus 279 ~~~~~G~i~l~V~kVd~~TGEiaGvF~S~QpSDTDmGa 316 (334)
--...|+|+|.|...+..+.=|+-.|.+-.+..+-.|.
T Consensus 196 ~Hs~~G~l~l~v~~~~~~~~~ig~~f~~~~~~~v~v~~ 233 (303)
T PRK10564 196 RHTTDGTLKLKVKTESSGNVLIGPLFGSSAPAPVTVGN 233 (303)
T ss_pred ccCCCceEEEEEEecCCCceeeecccCCCCCccccccc
Confidence 34568999999988887333333347776666655555
No 11
>KOG3245 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.22 E-value=20 Score=31.00 Aligned_cols=27 Identities=33% Similarity=0.423 Sum_probs=20.0
Q ss_pred ChhHHhhhhcccccccceeEEEEEEeecCCCceeeEE
Q 019870 267 DEEDLAKENIKNTSSSTGKITLSVTKSKPETGEVIGV 303 (334)
Q Consensus 267 d~eeL~kEN~K~~~~~~G~i~l~V~kVd~~TGEiaGv 303 (334)
-.++|.||-.|-+- +.||+-||||+|-
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 12
>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=26.68 E-value=1.6e+02 Score=25.17 Aligned_cols=33 Identities=24% Similarity=0.412 Sum_probs=26.5
Q ss_pred CeeEEEecCeeeeeee---eecCCCceeeeEEEecc
Q 019870 186 TIKFVEKDGIDYAAVT---VQLPGGERVPFLFTIKQ 218 (334)
Q Consensus 186 ~ltF~E~dGiDya~iT---VQlPGGErVPFLFTvK~ 218 (334)
+++..+.||.+..|.+ +.|+-|||+=+|++.++
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 67999999999999976
No 13
>KOG0285 consensus Pleiotropic regulator 1 [RNA processing and modification]
Probab=25.21 E-value=92 Score=32.60 Aligned_cols=76 Identities=24% Similarity=0.389 Sum_probs=39.4
Q ss_pred ceeeeccccccceEEEeeeecCCCCCCCcccceeeee---ee---eeccce-eeeeeeCC-CCCeeEEE-ecCeeeeee-
Q 019870 131 KYQAKKFCLEPTSFTVKAESVNKNAPPDFQNTKLMTR---LT---YTLDEI-EGPFEVSP-DGTIKFVE-KDGIDYAAV- 200 (334)
Q Consensus 131 ~Y~l~~lClEPtsf~VkeE~~~K~~~~eFv~tKLmTR---~T---yTLd~I-~G~l~v~~-dG~ltF~E-~dGiDya~i- 200 (334)
+-...-+|++|+.|.+-.-+.+--..-.|-.+..|.- .+ -||.-- .|-+.+++ +|.+-|-. ++|-.||..
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 3456789999999988433322112223333333332 11 111111 12233333 36677755 889999987
Q ss_pred -eeecCCC
Q 019870 201 -TVQLPGG 207 (334)
Q Consensus 201 -TVQlPGG 207 (334)
-|| ||.
T Consensus 399 t~vq-pGS 405 (460)
T KOG0285|consen 399 TIVQ-PGS 405 (460)
T ss_pred cccc-CCc
Confidence 555 653
No 14
>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=25.12 E-value=60 Score=35.04 Aligned_cols=55 Identities=24% Similarity=0.315 Sum_probs=39.0
Q ss_pred eeeeeeeeeccceeeeeeeCCCCC----eeEEEecCeeeeeeeeecCCCceeeeE---EEeccee
Q 019870 163 KLMTRLTYTLDEIEGPFEVSPDGT----IKFVEKDGIDYAAVTVQLPGGERVPFL---FTIKQLV 220 (334)
Q Consensus 163 KLmTR~TyTLd~I~G~l~v~~dG~----ltF~E~dGiDya~iTVQlPGGErVPFL---FTvK~Lv 220 (334)
=+|+|++|+.. ..++.+.+++- |.|.+ +.-+|++-+..|..|-|+||| .++..|.
T Consensus 194 i~~~~~~~~~~--~~~~~v~~~~~~y~sl~~~~-~~~~~~~~~~~l~~G~~ipfLG~e~~~v~ld 255 (571)
T TIGR01564 194 ITMAVYNWTKT--KAKDTVTGVTTLYASIAYKD-DLENFQPATYSISEGTRSPFLGEEVTLVVFD 255 (571)
T ss_pred EEEEEEeccCc--CccceecCccceEEEEEeec-cccccCCCceeccCCCCccccccceEEEEec
Confidence 47889999965 56677777663 34455 334777778899999999999 4444443
No 15
>PF11138 DUF2911: Protein of unknown function (DUF2911); InterPro: IPR021314 This bacterial family of proteins has no known function.
Probab=24.79 E-value=3.1e+02 Score=24.61 Aligned_cols=71 Identities=24% Similarity=0.284 Sum_probs=46.2
Q ss_pred ceeeeeceeecCCCCCcCCCCc-ce---eecCCceeeeccccccceEEEeeeecCCC-CCCCcccceeeeeeeeeccc
Q 019870 102 TYMEVKGTGTANQCPTIDGGVD-SF---AFKPGKYQAKKFCLEPTSFTVKAESVNKN-APPDFQNTKLMTRLTYTLDE 174 (334)
Q Consensus 102 tY~qVkgTGlAN~CP~l~~~~~-~i---~l~~G~Y~l~~lClEPtsf~VkeE~~~K~-~~~eFv~tKLmTR~TyTLd~ 174 (334)
-|-+|=-|| ||.|-++.-..+ .| .|++|+|.|.-+= .+++|+|---..... +..+|-+.+-+-|.+-+...
T Consensus 35 PygkvWRtG-AN~aT~i~f~~dv~igGk~l~AG~Ysl~tiP-~~~~WtvI~n~~~~~wG~~~Y~~~~Dv~rv~v~~~~ 110 (145)
T PF11138_consen 35 PYGKVWRTG-ANEATTITFSKDVTIGGKKLKAGTYSLFTIP-GEDEWTVIFNKDTDQWGAYNYDPSKDVLRVTVPPQK 110 (145)
T ss_pred cCCCeecCC-CCcceEEEECCCeEECCEEcCCeeEEEEEec-CCCeEEEEEECCCCccCccccCchheEEEEEeeeec
Confidence 455599999 999999976666 44 6999999987653 445688854333332 22466666666666554433
No 16
>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=22.61 E-value=34 Score=27.70 Aligned_cols=11 Identities=36% Similarity=0.984 Sum_probs=9.1
Q ss_pred EEEEEEEEecC
Q 019870 324 IQGIWYAQLEQ 334 (334)
Q Consensus 324 i~GifYgrl~~ 334 (334)
..|+||+++++
T Consensus 62 ~~g~wy~~v~p 72 (97)
T cd03062 62 GDGIWYGRVTP 72 (97)
T ss_pred CCeeEEeecCH
Confidence 58999999864
No 17
>PF07162 B9-C2: Ciliary basal body-associated, B9 protein; InterPro: IPR010796 Proteins in this entry include the MSK1 protein (Q9NXB0 from SWISSPROT) and other known or predicted flagellar basal body proteome components [] or cilia-containing species. Although the function is unknown, a cilia-specific role has been suggested for the poorly characterised B9 domain [, , ]. Mutations in MSK1 have been shown to cause Meckel syndrome type 1, a severe foetal development disorder that has been reported in most populations.
Probab=21.16 E-value=69 Score=28.16 Aligned_cols=62 Identities=15% Similarity=0.295 Sum_probs=38.1
Q ss_pred ceeecCCceeeeccccccceEEEeeee--cCCCCCCCcccceeeeeeeeeccceeeeeeeCCCCCeeEE
Q 019870 124 SFAFKPGKYQAKKFCLEPTSFTVKAES--VNKNAPPDFQNTKLMTRLTYTLDEIEGPFEVSPDGTIKFV 190 (334)
Q Consensus 124 ~i~l~~G~Y~l~~lClEPtsf~VkeE~--~~K~~~~eFv~tKLmTR~TyTLd~I~G~l~v~~dG~ltF~ 190 (334)
.|++.||.|+++=-|..|.+=...++- -+-++.+|+++-+++.. -++=+| |...+.|+|+++
T Consensus 100 ~lP~~pG~h~~~v~~wrP~~~s~~~~l~~~f~G~~pel~d~~~~~~----~~~R~~-l~t~s~G~V~v~ 163 (168)
T PF07162_consen 100 HLPTQPGRHEVEVPTWRPVSGSIRQELRSFFVGGRPELVDPDFIAS----GESRFG-LRTESSGSVKVR 163 (168)
T ss_pred EeCCCCceEEEEEEEEeecCCCHHHHhhhheecCCceEcCcchhcC----cccccC-cEEEeeeEEEEE
Confidence 567789999999999999322222221 12356789999887765 222222 444556766554
No 18
>COG4704 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.37 E-value=51 Score=30.07 Aligned_cols=27 Identities=37% Similarity=0.703 Sum_probs=18.2
Q ss_pred eeecCCCCCcCCCCc--ce-eecCCceeee
Q 019870 109 TGTANQCPTIDGGVD--SF-AFKPGKYQAK 135 (334)
Q Consensus 109 TGlAN~CP~l~~~~~--~i-~l~~G~Y~l~ 135 (334)
.=.++.|-.+.+..- ++ .|+||+|.+.
T Consensus 63 ~~f~ractsit~dpv~~~f~~Lk~G~YAva 92 (151)
T COG4704 63 SRFQRACTSITGDPVSKSFYGLKPGKYAVA 92 (151)
T ss_pred hHHhhhcccccCCchhheeecCCCccEEEE
Confidence 345788888866554 33 3789988765
No 19
>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=20.12 E-value=1.3e+02 Score=24.91 Aligned_cols=24 Identities=17% Similarity=0.457 Sum_probs=19.1
Q ss_pred ceeEEEEEEeecCCCceeeEEEeEe
Q 019870 283 TGKITLSVTKSKPETGEVIGVFESL 307 (334)
Q Consensus 283 ~G~i~l~V~kVd~~TGEiaGvF~S~ 307 (334)
.++|.+.|.+||+. |.+.|-|...
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
Done!