Query 030344
Match_columns 179
No_of_seqs 20 out of 22
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 12:18:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030344.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030344hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd07301 PX_SNX21 The phosphoin 41.7 76 0.0016 23.8 5.1 51 92-145 46-96 (112)
2 COG0598 CorA Mg2+ and Co2+ tra 38.5 25 0.00054 30.3 2.3 36 134-169 246-282 (322)
3 PF00690 Cation_ATPase_N: Cati 38.3 45 0.00099 22.2 3.1 41 131-171 26-67 (69)
4 PF08072 BDHCT: BDHCT (NUC031) 36.5 20 0.00044 24.4 1.1 10 127-136 30-39 (41)
5 PF15510 CENP-W: Centromere ki 36.5 19 0.00041 28.5 1.1 23 124-146 4-29 (102)
6 PF01366 PRTP: Herpesvirus pro 34.8 40 0.00086 33.2 3.3 20 127-146 452-471 (638)
7 PF05151 PsbM: Photosystem II 34.0 34 0.00074 22.0 1.8 26 146-172 4-29 (31)
8 TIGR00383 corA magnesium Mg(2+ 32.2 30 0.00064 28.8 1.7 37 135-171 243-280 (318)
9 PF09777 OSTMP1: Osteopetrosis 32.0 28 0.00061 29.7 1.6 47 125-171 159-212 (237)
10 PRK04989 psbM photosystem II r 28.9 30 0.00065 22.8 1.0 26 146-172 4-29 (35)
11 PLN00085 photosystem II reacti 27.4 26 0.00055 29.1 0.6 36 136-172 69-106 (149)
12 COG1862 YajC Preprotein transl 26.1 53 0.0012 25.1 2.0 22 127-149 29-50 (97)
13 KOG4782 Predicted membrane pro 25.3 42 0.0009 26.8 1.4 20 133-159 52-71 (108)
14 TIGR03038 PS_II_psbM photosyst 24.7 41 0.00088 22.0 1.0 26 146-172 4-29 (33)
15 PF06695 Sm_multidrug_ex: Puta 23.9 1E+02 0.0022 23.6 3.2 32 124-162 54-85 (121)
16 PF06796 NapE: Periplasmic nit 23.4 42 0.00092 23.8 1.0 16 156-174 25-40 (56)
17 KOG2745 Mitochondrial carrier 22.9 1.2E+02 0.0026 28.1 4.0 37 94-135 103-139 (321)
18 PF15341 SLX9: Ribosome biogen 21.7 87 0.0019 23.6 2.4 21 124-144 5-25 (121)
19 PF07957 DUF3294: Protein of u 21.2 40 0.00087 29.4 0.6 54 96-165 73-142 (216)
20 PF02870 Methyltransf_1N: 6-O- 20.6 37 0.00081 22.9 0.2 25 89-113 50-75 (77)
21 PRK14094 psbM photosystem II r 20.4 30 0.00065 24.4 -0.2 26 146-172 4-29 (50)
22 PF13207 AAA_17: AAA domain; P 20.4 70 0.0015 22.1 1.6 19 87-105 8-26 (121)
23 TIGR02972 TMAO_torE trimethyla 20.3 55 0.0012 22.7 1.0 16 156-174 17-32 (47)
No 1
>cd07301 PX_SNX21 The phosphoinositide binding Phox Homology domain of Sorting Nexin 21. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX21, also called SNX-L, is distinctly and highly-expressed in fetal liver and may be involved in protein sorting and degradation during embryonic liver development.
Probab=41.72 E-value=76 Score=23.79 Aligned_cols=51 Identities=22% Similarity=0.262 Sum_probs=31.4
Q ss_pred ccHHHHHHHHHcCcCCcccccccccccccccchhhHHHHHHHHHHHHHHHhhcc
Q 030344 92 LTIRDQLAQLVGDRDDEFSIPLGKNLKKVSEKFLTISQKRNIRRQAYLNEVSQR 145 (179)
Q Consensus 92 ~TIreQLaal~ge~~~eftiPlgk~lK~~a~~~lTiSQkRNikRQayL~~VsqR 145 (179)
...+++|..+++..-..+.+| +|++.. + +.-...++|..-=+.||+++.+-
T Consensus 46 ~~L~~~L~~~~~~~~~~~~~P-~K~~~~-~-~~~~~ie~Rr~~Le~fL~~i~~~ 96 (112)
T cd07301 46 ERLHRRLRRLFGGEMAGVSFP-RKRLRK-N-FTAETIAKRSRAFEQFLCHLHSL 96 (112)
T ss_pred HHHHHHHHHHCCCcCCCCCCC-CCcccC-C-CCHHHHHHHHHHHHHHHHHHhcC
Confidence 457889999998643334555 355432 2 23345566666667888888664
No 2
>COG0598 CorA Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]
Probab=38.49 E-value=25 Score=30.26 Aligned_cols=36 Identities=31% Similarity=0.470 Sum_probs=30.4
Q ss_pred HHHHHHHHhhcc-CCcchhhhhhhhhccchHHHHHHH
Q 030344 134 RRQAYLNEVSQR-NDSVFFATIGAFVILPPFIILGIA 169 (179)
Q Consensus 134 kRQayL~~VsqR-nDs~fFAtigaFvllPPliIL~iA 169 (179)
=.++|+..++.+ |+...+.|+-+.+++||-+|-++.
T Consensus 246 l~d~~~s~is~~~N~imk~LTi~s~iflPpTlIagiy 282 (322)
T COG0598 246 LLDAYLSLINNNQNEIMKILTIVSTIFLPPTLITGFY 282 (322)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHccc
Confidence 357888888876 888899999999999999987764
No 3
>PF00690 Cation_ATPase_N: Cation transporter/ATPase, N-terminus; InterPro: IPR004014 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+ (3.6.3.6 from EC), Na+ (3.6.3.7 from EC), Ca2+ (3.6.3.8 from EC), Na+/K+ (3.6.3.9 from EC), and H+/K+ (3.6.3.10 from EC). In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; PDB: 3KDP_C 3N2F_A 3B8E_A 3N23_A 2XZB_A 1MHS_B 3A3Y_A 2ZXE_A 3B8C_A 3B9B_A ....
Probab=38.34 E-value=45 Score=22.22 Aligned_cols=41 Identities=24% Similarity=0.298 Sum_probs=26.6
Q ss_pred HHHHHHHH-HHHhhccCCcchhhhhhhhhccchHHHHHHHHH
Q 030344 131 RNIRRQAY-LNEVSQRNDSVFFATIGAFVILPPFIILGIAVL 171 (179)
Q Consensus 131 RNikRQay-L~~VsqRnDs~fFAtigaFvllPPliIL~iAv~ 171 (179)
-..||+.| -|++....-..+|--+--.|.=|..+||.+|.+
T Consensus 26 v~~r~~~~G~N~l~~~~~~s~~~~~~~~f~~~~~~lL~~aai 67 (69)
T PF00690_consen 26 VEERRKKYGPNELPEPKKKSLWRIFLKQFKNPFIILLLIAAI 67 (69)
T ss_dssp HHHHHHHHSSSSTTTTTSSSHHHHHHHHTTSHHHHHHHHHHH
T ss_pred HHHHHHhcccccccccccCcHHHHHHHHHHhHHHHHHHHHHH
Confidence 34456666 677766666666666666667777777766653
No 4
>PF08072 BDHCT: BDHCT (NUC031) domain; InterPro: IPR012532 This is a C-terminal domain in Bloom's syndrome DEAD helicase subfamily []. The helicase articipates in DNA replication and repair, exhibiting a magnesium-dependent ATP-dependent DNA-helicase activity that unwinds single- and double-stranded DNA in a 3'-5' direction.; GO: 0003677 DNA binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006260 DNA replication, 0005634 nucleus
Probab=36.50 E-value=20 Score=24.39 Aligned_cols=10 Identities=50% Similarity=0.890 Sum_probs=8.6
Q ss_pred HHHHHHHHHH
Q 030344 127 ISQKRNIRRQ 136 (179)
Q Consensus 127 iSQkRNikRQ 136 (179)
-.|+||+||+
T Consensus 30 LlqqR~~Rrk 39 (41)
T PF08072_consen 30 LLQQRDIRRK 39 (41)
T ss_pred HHHHHHHHHh
Confidence 4699999997
No 5
>PF15510 CENP-W: Centromere kinetochore component W
Probab=36.47 E-value=19 Score=28.47 Aligned_cols=23 Identities=39% Similarity=0.668 Sum_probs=18.7
Q ss_pred hhhHHHHHHHHHHH---HHHHhhccC
Q 030344 124 FLTISQKRNIRRQA---YLNEVSQRN 146 (179)
Q Consensus 124 ~lTiSQkRNikRQa---yL~~VsqRn 146 (179)
+-|+|||.+|||++ +|..|..|.
T Consensus 4 s~tv~qrk~ikrkaPrgfLkrv~Kr~ 29 (102)
T PF15510_consen 4 STTVSQRKHIKRKAPRGFLKRVFKRQ 29 (102)
T ss_pred chhhhHHHHHHHhCchHHHHHHHHhc
Confidence 46999999999986 777777754
No 6
>PF01366 PRTP: Herpesvirus processing and transport protein; InterPro: IPR000501 The members of this family are associated with capsid intermediates during packaging of dsDNA viruses with no RNA stage in their replication cycle []. The protein may affect translocation of the virus glycoproteins to membranes, and is involved in capsid maturation.; GO: 0008565 protein transporter activity, 0016485 protein processing, 0019069 viral capsid assembly
Probab=34.82 E-value=40 Score=33.21 Aligned_cols=20 Identities=30% Similarity=0.684 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHhhccC
Q 030344 127 ISQKRNIRRQAYLNEVSQRN 146 (179)
Q Consensus 127 iSQkRNikRQayL~~VsqRn 146 (179)
+.+-=+.||++||+|||.|-
T Consensus 452 v~~Da~~RK~aYl~KlSk~g 471 (638)
T PF01366_consen 452 VLSDAHVRKRAYLQKLSKRG 471 (638)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 44445678999999999874
No 7
>PF05151 PsbM: Photosystem II reaction centre M protein (PsbM); InterPro: IPR007826 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 []. This family represents the low molecular weight transmembrane protein PsbM found in PSII. PsbM is one of the most hydrophobic proteins in the thylakoid membrane. The function of this protein is unknown.; GO: 0015979 photosynthesis, 0019684 photosynthesis, light reaction, 0009523 photosystem II, 0016021 integral to membrane; PDB: 3A0H_m 3ARC_m 3A0B_M 3PRR_M 3PRQ_M 1S5L_M 4FBY_e 3BZ2_M 3BZ1_M 2AXT_M ....
Probab=34.03 E-value=34 Score=22.03 Aligned_cols=26 Identities=23% Similarity=0.429 Sum_probs=17.6
Q ss_pred CCcchhhhhhhhhccchHHHHHHHHHh
Q 030344 146 NDSVFFATIGAFVILPPFIILGIAVLT 172 (179)
Q Consensus 146 nDs~fFAtigaFvllPPliIL~iAv~t 172 (179)
|+-.|- .++.|+++|-...+.+.+.|
T Consensus 4 n~l~fi-AtaLfi~iPt~FLiilyvqT 29 (31)
T PF05151_consen 4 NILAFI-ATALFILIPTAFLIILYVQT 29 (31)
T ss_dssp -TTHHH-HHHHHHHHHHHHHHHHHHHH
T ss_pred chhhHH-HHHHHHHHHHHHHhheEeee
Confidence 455554 45789999987777776655
No 8
>TIGR00383 corA magnesium Mg(2+) and cobalt Co(2+) transport protein (corA). The article in Microb Comp Genomics 1998;3(3):151-69 (Medline:98448512) discusses this family and suggests that some members may have functions other than Mg2+ transport.
Probab=32.19 E-value=30 Score=28.85 Aligned_cols=37 Identities=24% Similarity=0.373 Sum_probs=29.5
Q ss_pred HHHHHHHhhcc-CCcchhhhhhhhhccchHHHHHHHHH
Q 030344 135 RQAYLNEVSQR-NDSVFFATIGAFVILPPFIILGIAVL 171 (179)
Q Consensus 135 RQayL~~VsqR-nDs~fFAtigaFvllPPliIL~iAv~ 171 (179)
..+|++.++.| |..--+.|+-+.+++||-+|-|+.-.
T Consensus 243 ~d~~~~~~s~~~N~~mk~LTvvt~IflP~t~IaGiyGM 280 (318)
T TIGR00383 243 MDLYLSLVNNKMNEIMKILTVVSTIFIPLTFIAGIYGM 280 (318)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 46777888776 66777899999999999999887543
No 9
>PF09777 OSTMP1: Osteopetrosis-associated transmembrane protein 1 precursor; InterPro: IPR019172 Osteopetrosis-associated transmembrane protein 1 (OSTM1) is required for osteoclast and melanocyte maturation and function. Mutations in OSTM1 give rise to autosomal recessive osteopetrosis, also called autosomal recessive Albers-Schonberg disease [, ].
Probab=31.99 E-value=28 Score=29.69 Aligned_cols=47 Identities=13% Similarity=0.225 Sum_probs=31.5
Q ss_pred hhHHHHHHHHHHHHHH-------HhhccCCcchhhhhhhhhccchHHHHHHHHH
Q 030344 125 LTISQKRNIRRQAYLN-------EVSQRNDSVFFATIGAFVILPPFIILGIAVL 171 (179)
Q Consensus 125 lTiSQkRNikRQayL~-------~VsqRnDs~fFAtigaFvllPPliIL~iAv~ 171 (179)
+.+.=.=|+-|+.+=+ ....|.+..+|.+|+.||+++|++.-+.+++
T Consensus 159 ~DveD~MN~Tr~lWs~~~~C~~~~~~~~~~~~~~i~v~~~vl~lpv~FY~~s~~ 212 (237)
T PF09777_consen 159 FDVEDAMNRTRHLWSKTFNCSVPCKDEVPSETAVIAVSVFVLFLPVLFYLSSYL 212 (237)
T ss_pred hhHHHHHHHHHHHhcccccCCCcccccccchhHHHHHHHHHHHHHHHHHHhhee
Confidence 3445555777777655 3344455668999999999888776655543
No 10
>PRK04989 psbM photosystem II reaction center protein M; Provisional
Probab=28.92 E-value=30 Score=22.84 Aligned_cols=26 Identities=31% Similarity=0.446 Sum_probs=17.8
Q ss_pred CCcchhhhhhhhhccchHHHHHHHHHh
Q 030344 146 NDSVFFATIGAFVILPPFIILGIAVLT 172 (179)
Q Consensus 146 nDs~fFAtigaFvllPPliIL~iAv~t 172 (179)
||-.|-| .+.|+++|-...|.+++.|
T Consensus 4 N~lgfiA-t~Lfi~iPt~FLlilYvqT 29 (35)
T PRK04989 4 NDLGFVA-SLLFVLVPTVFLIILYIQT 29 (35)
T ss_pred hHHHHHH-HHHHHHHHHHHHHHHheec
Confidence 5556655 4689999977777666554
No 11
>PLN00085 photosystem II reaction center protein M (PsbM); Provisional
Probab=27.41 E-value=26 Score=29.13 Aligned_cols=36 Identities=28% Similarity=0.346 Sum_probs=25.8
Q ss_pred HHHHHHh--hccCCcchhhhhhhhhccchHHHHHHHHHh
Q 030344 136 QAYLNEV--SQRNDSVFFATIGAFVILPPFIILGIAVLT 172 (179)
Q Consensus 136 QayL~~V--sqRnDs~fFAtigaFvllPPliIL~iAv~t 172 (179)
++-||+| .+=||-.|-|| ..|+++|-...|.+++.|
T Consensus 69 ~e~l~qval~EVNiLgfIAt-aLFIlIPTaFLLILYVkT 106 (149)
T PLN00085 69 AEELNQVALADVNILGVIAT-ALFIIIPTSFLIILYVKS 106 (149)
T ss_pred HHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHheeee
Confidence 4556665 36788888876 588999877777666654
No 12
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=26.09 E-value=53 Score=25.13 Aligned_cols=22 Identities=32% Similarity=0.421 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHHHhhccCCcc
Q 030344 127 ISQKRNIRRQAYLNEVSQRNDSV 149 (179)
Q Consensus 127 iSQkRNikRQayL~~VsqRnDs~ 149 (179)
.-|||..+||++|+.+- +.|.+
T Consensus 29 PQrKr~K~~~~ml~sL~-kGD~V 50 (97)
T COG1862 29 PQRKRMKEHQELLNSLK-KGDEV 50 (97)
T ss_pred HHHHHHHHHHHHHHhcc-CCCEE
Confidence 46899999999999985 55544
No 13
>KOG4782 consensus Predicted membrane protein [Function unknown]
Probab=25.25 E-value=42 Score=26.76 Aligned_cols=20 Identities=55% Similarity=0.788 Sum_probs=13.9
Q ss_pred HHHHHHHHHhhccCCcchhhhhhhhhc
Q 030344 133 IRRQAYLNEVSQRNDSVFFATIGAFVI 159 (179)
Q Consensus 133 ikRQayL~~VsqRnDs~fFAtigaFvl 159 (179)
|+|+.|-|.|| |++||+.||
T Consensus 52 ~~aknykN~is-------~a~i~alVi 71 (108)
T KOG4782|consen 52 IFAKNYKNHIS-------FAGIGALVI 71 (108)
T ss_pred HHHhhhhhhhh-------hHHHHHHHH
Confidence 55666666554 899998764
No 14
>TIGR03038 PS_II_psbM photosystem II reaction center protein PsbM. Members of this protein family are the photosystem II reaction center M protein, product of the psbM gene, in Cyanobacteria and their derived organelles in plants. This model resembles Pfam model pfam05151 but has cutoffs set to avoid false-positive matches to similar (not necessarily homologous) sequences in species that are not photosynthetic.
Probab=24.71 E-value=41 Score=21.98 Aligned_cols=26 Identities=27% Similarity=0.376 Sum_probs=17.1
Q ss_pred CCcchhhhhhhhhccchHHHHHHHHHh
Q 030344 146 NDSVFFATIGAFVILPPFIILGIAVLT 172 (179)
Q Consensus 146 nDs~fFAtigaFvllPPliIL~iAv~t 172 (179)
|+-.|-| .+.|+++|-...|...+.|
T Consensus 4 n~l~fiA-t~Lfi~iPt~FLiilYvqT 29 (33)
T TIGR03038 4 NILGFIA-TLLFILVPTVFLLILYIQT 29 (33)
T ss_pred cHHHHHH-HHHHHHHHHHHHHHHheec
Confidence 4555544 5689999977666665544
No 15
>PF06695 Sm_multidrug_ex: Putative small multi-drug export protein; InterPro: IPR009577 This family contains a small number of putative small multi-drug export proteins.
Probab=23.91 E-value=1e+02 Score=23.57 Aligned_cols=32 Identities=19% Similarity=0.387 Sum_probs=24.9
Q ss_pred hhhHHHHHHHHHHHHHHHhhccCCcchhhhhhhhhccch
Q 030344 124 FLTISQKRNIRRQAYLNEVSQRNDSVFFATIGAFVILPP 162 (179)
Q Consensus 124 ~lTiSQkRNikRQayL~~VsqRnDs~fFAtigaFvllPP 162 (179)
...-..+|-.|+++++++-. |.++..||.+|.
T Consensus 54 ~~~~~~~k~~~~~~~i~kyg-------~~GL~lFVaIPl 85 (121)
T PF06695_consen 54 FYEWLEKKAEKKSKKIEKYG-------FWGLALFVAIPL 85 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHh-------HHHHHHHHhCCC
Confidence 45566777777888888875 888999998874
No 16
>PF06796 NapE: Periplasmic nitrate reductase protein NapE; InterPro: IPR010649 This family consists of several bacterial periplasmic nitrate reductase NapE proteins. Seven genes, napKEFDABC, encoding the periplasmic nitrate reductase system were cloned from the denitrifying phototrophic bacterium Rhodobacter sphaeroides. NapE is thought to be a transmembrane protein [].
Probab=23.40 E-value=42 Score=23.81 Aligned_cols=16 Identities=50% Similarity=0.989 Sum_probs=10.0
Q ss_pred hhhccchHHHHHHHHHhcc
Q 030344 156 AFVILPPFIILGIAVLTGY 174 (179)
Q Consensus 156 aFvllPPliIL~iAv~tGY 174 (179)
+|||.| ||.|++..||
T Consensus 25 ~~~l~P---iL~v~~Vg~Y 40 (56)
T PF06796_consen 25 AVVLFP---ILAVAFVGGY 40 (56)
T ss_pred HHHHHH---HHHHHHHHHH
Confidence 567888 4555555555
No 17
>KOG2745 consensus Mitochondrial carrier protein [General function prediction only]
Probab=22.94 E-value=1.2e+02 Score=28.10 Aligned_cols=37 Identities=27% Similarity=0.302 Sum_probs=30.4
Q ss_pred HHHHHHHHHcCcCCcccccccccccccccchhhHHHHHHHHH
Q 030344 94 IRDQLAQLVGDRDDEFSIPLGKNLKKVSEKFLTISQKRNIRR 135 (179)
Q Consensus 94 IreQLaal~ge~~~eftiPlgk~lK~~a~~~lTiSQkRNikR 135 (179)
+++++.+.+++.+-+-..|+|...|| +..|=||+|||
T Consensus 103 ~~~rv~q~l~~~~p~~~~~~~~~~kE-----~~~sF~~vik~ 139 (321)
T KOG2745|consen 103 VSDRVLQYLDEYYPNEGGPLGNQDKE-----DAESFKKVIKR 139 (321)
T ss_pred HhhHHHHHhhhhCcCcCcccccchhH-----HHHHHHHHHHH
Confidence 45677788888777667889988888 77899999999
No 18
>PF15341 SLX9: Ribosome biogenesis protein SLX9
Probab=21.66 E-value=87 Score=23.63 Aligned_cols=21 Identities=29% Similarity=0.638 Sum_probs=17.6
Q ss_pred hhhHHHHHHHHHHHHHHHhhc
Q 030344 124 FLTISQKRNIRRQAYLNEVSQ 144 (179)
Q Consensus 124 ~lTiSQkRNikRQayL~~Vsq 144 (179)
.+|--+||.+||.++|++|..
T Consensus 5 ~~sKkeKr~~K~~~fl~Ki~~ 25 (121)
T PF15341_consen 5 RLSKKEKRKLKREAFLQKIED 25 (121)
T ss_pred ccCHHHHHHHHHHHHHHHHHH
Confidence 367789999999999998853
No 19
>PF07957 DUF3294: Protein of unknown function (DUF3294); InterPro: IPR012917 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 [, ]. This is a family of mitochondrial ribosomal proteins, which appears to be fungal specific [].
Probab=21.15 E-value=40 Score=29.44 Aligned_cols=54 Identities=30% Similarity=0.449 Sum_probs=38.6
Q ss_pred HHHHHHHcCcCCcccccccccccccccchhhHHHHHHHHHH---------HHHHHhhccC-------Ccchhhhhhhhhc
Q 030344 96 DQLAQLVGDRDDEFSIPLGKNLKKVSEKFLTISQKRNIRRQ---------AYLNEVSQRN-------DSVFFATIGAFVI 159 (179)
Q Consensus 96 eQLaal~ge~~~eftiPlgk~lK~~a~~~lTiSQkRNikRQ---------ayL~~VsqRn-------Ds~fFAtigaFvl 159 (179)
|-|.+|+||=|+. |...+.|+|||= +.|.-+..+| |..|=+|++-|-=
T Consensus 73 eDLVQLV~ELQgQ----------------Ld~lEeRsiRR~~NS~~~~~~d~laPlpn~DGe~P~~~~~~fP~TL~eF~~ 136 (216)
T PF07957_consen 73 EDLVQLVGELQGQ----------------LDNLEERSIRRTVNSTKTDDDDLLAPLPNADGEIPPGKDFLFPKTLKEFKN 136 (216)
T ss_pred hhHHHHHHHHHHH----------------HHHHHHHHHHHHHhcccCCcccccccCCCCCCCCCCCCcccChhhHHHHHh
Confidence 4688999987776 899999999993 4555555555 6677788887765
Q ss_pred cchHHH
Q 030344 160 LPPFII 165 (179)
Q Consensus 160 lPPliI 165 (179)
+.=.-+
T Consensus 137 l~~~~l 142 (216)
T PF07957_consen 137 LDDVKL 142 (216)
T ss_pred ccHHHH
Confidence 543333
No 20
>PF02870 Methyltransf_1N: 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; InterPro: IPR008332 Synonym(s): 6-O-methylguanine-DNA methyltransferase, O-6-methylguanine-DNA-alkyltransferase The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (2.1.1.63 from EC). The major mutagenic and carcinogenic effect of methylating agents in DNA is the formation of O6-alkylguanine. The alkyl group at the O-6 position is transferred to a cysteine residue in the enzyme []. This is a suicide reaction since the enzyme is irreversibly inactivated and the methylated protein accumulates as a dead-end product. Most, but not all of the methyltransferases are also able to repair O-4-methylthymine. DNA-[protein]-cysteine S-methyltransferases are widely distributed and are found in various prokaryotic and eukaryotic sources []. This group of proteins are characterised by having an N-terminal ribonuclease-like domain associated with 6-O-methylguanine DNA methyltransferase activity (IPR001497 from INTERPRO).; GO: 0003908 methylated-DNA-[protein]-cysteine S-methyltransferase activity, 0006281 DNA repair; PDB: 1SFE_A 1T39_B 1T38_A 1EH7_A 1EH6_A 1YFH_C 1EH8_A 1QNT_A.
Probab=20.59 E-value=37 Score=22.87 Aligned_cols=25 Identities=24% Similarity=0.428 Sum_probs=17.8
Q ss_pred CccccHHHHHHHHHcCcCC-cccccc
Q 030344 89 SRKLTIRDQLAQLVGDRDD-EFSIPL 113 (179)
Q Consensus 89 ~~~~TIreQLaal~ge~~~-eftiPl 113 (179)
.....+++||.+-+..+-. +|+|||
T Consensus 50 ~~~~~~~~qL~eYF~G~r~~~F~lPl 75 (77)
T PF02870_consen 50 PLLAEAKQQLDEYFAGERTPEFDLPL 75 (77)
T ss_dssp CCHHHHHHHHHHHHHHHHS--B-SHC
T ss_pred ccHHHHHHHHHHHHcCCCCCCCcCCc
Confidence 3456788999988877666 999998
No 21
>PRK14094 psbM photosystem II reaction center protein M; Provisional
Probab=20.45 E-value=30 Score=24.43 Aligned_cols=26 Identities=27% Similarity=0.415 Sum_probs=16.9
Q ss_pred CCcchhhhhhhhhccchHHHHHHHHHh
Q 030344 146 NDSVFFATIGAFVILPPFIILGIAVLT 172 (179)
Q Consensus 146 nDs~fFAtigaFvllPPliIL~iAv~t 172 (179)
|+-.|-| .+.|+++|-...|++.+.|
T Consensus 4 N~lgfiA-taLFi~iPT~FLlilYVkT 29 (50)
T PRK14094 4 TNFGFVA-SLLFVGVPTIFLIGLFIST 29 (50)
T ss_pred hHHHHHH-HHHHHHHHHHHhhheeEEe
Confidence 5555555 4689999877666665543
No 22
>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A ....
Probab=20.35 E-value=70 Score=22.13 Aligned_cols=19 Identities=32% Similarity=0.298 Sum_probs=16.3
Q ss_pred CCCccccHHHHHHHHHcCc
Q 030344 87 GSSRKLTIRDQLAQLVGDR 105 (179)
Q Consensus 87 ~s~~~~TIreQLaal~ge~ 105 (179)
.+++++|+..+|+..+|-.
T Consensus 8 ~gsGKST~a~~La~~~~~~ 26 (121)
T PF13207_consen 8 PGSGKSTLAKELAERLGFP 26 (121)
T ss_dssp TTSSHHHHHHHHHHHHTCE
T ss_pred CCCCHHHHHHHHHHHHCCe
Confidence 4789999999999999753
No 23
>TIGR02972 TMAO_torE trimethylamine N-oxide reductase system, TorE protein. Members of this small, apparent transmembrane protein are designated TorE and occur in operons for the trimethylamine N-oxide (TMAO) reductase system. Members are closely related to the NapE protein of the related periplasmic nitrate reductase system. It may be that TorE is an integral membrane subunit of a complex with the reductase TorA.
Probab=20.30 E-value=55 Score=22.68 Aligned_cols=16 Identities=44% Similarity=0.870 Sum_probs=10.0
Q ss_pred hhhccchHHHHHHHHHhcc
Q 030344 156 AFVILPPFIILGIAVLTGY 174 (179)
Q Consensus 156 aFvllPPliIL~iAv~tGY 174 (179)
+++|.| ||.++...||
T Consensus 17 ~v~l~P---iLsV~~Vg~Y 32 (47)
T TIGR02972 17 IVVLFP---ILSVAGIGGY 32 (47)
T ss_pred HHHHHH---HHHHHHHHHH
Confidence 567778 4555555565
Done!