Query 033561
Match_columns 116
No_of_seqs 95 out of 97
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 03:42:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033561.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033561hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00088 predicted protein; Pr 100.0 1.1E-33 2.5E-38 210.8 8.1 112 1-116 1-127 (127)
2 PF06596 PsbX: Photosystem II 99.8 8.1E-21 1.7E-25 118.2 2.2 38 79-116 1-39 (39)
3 CHL00114 psbX photosystem II p 99.8 2.6E-20 5.7E-25 116.1 4.2 38 79-116 1-39 (39)
4 PF14187 DUF4310: Domain of un 68.5 7.3 0.00016 31.9 3.7 34 77-110 101-134 (209)
5 TIGR03579 EF_0833 conserved hy 59.6 13 0.00028 30.5 3.6 33 77-109 99-131 (209)
6 PF12732 YtxH: YtxH-like prote 52.5 12 0.00026 24.4 2.0 15 86-100 1-15 (74)
7 PF09813 Coiled-coil_56: Coile 48.7 20 0.00044 26.4 2.9 30 82-111 48-77 (100)
8 PF04835 Pox_A9: A9 protein co 43.8 34 0.00073 22.9 3.0 33 82-114 21-53 (54)
9 PHA02680 ORF090 IMV phosphoryl 41.5 21 0.00045 26.1 1.9 28 82-109 6-35 (91)
10 PF05767 Pox_A14: Poxvirus vir 39.4 17 0.00037 26.6 1.2 30 81-110 5-36 (92)
11 PF07423 DUF1510: Protein of u 36.6 38 0.00083 27.3 2.9 25 85-109 13-38 (217)
12 PF13706 PepSY_TM_3: PepSY-ass 34.6 21 0.00046 21.0 0.9 26 88-115 11-37 (37)
13 PHA03048 IMV membrane protein; 33.7 23 0.00051 25.9 1.2 29 82-110 6-36 (93)
14 PHA02898 virion envelope prote 28.7 32 0.00069 25.2 1.2 30 82-111 6-37 (92)
15 TIGR03546 conserved hypothetic 28.3 66 0.0014 24.6 2.9 21 83-103 102-122 (154)
16 PF07123 PsbW: Photosystem II 27.9 2.3E+02 0.0051 22.0 5.8 9 1-9 1-9 (138)
17 PRK10927 essential cell divisi 27.9 60 0.0013 28.1 2.9 19 94-112 41-59 (319)
18 COG4062 MtrB Tetrahydromethano 27.5 54 0.0012 24.6 2.2 25 79-103 73-99 (108)
19 COG2354 Uncharacterized protei 25.0 72 0.0016 27.6 2.8 22 78-99 273-294 (303)
20 PF14575 EphA2_TM: Ephrin type 22.7 78 0.0017 21.3 2.1 22 87-108 3-24 (75)
21 TIGR02838 spore_V_AC stage V s 22.6 75 0.0016 24.5 2.3 21 79-99 13-33 (141)
22 PF06783 UPF0239: Uncharacteri 22.0 1E+02 0.0022 22.2 2.7 30 83-112 18-49 (85)
23 TIGR03319 YmdA_YtgF conserved 21.4 33 0.00071 30.4 0.1 12 104-115 246-257 (514)
24 PF05283 MGC-24: Multi-glycosy 20.8 40 0.00087 26.8 0.5 22 85-106 157-178 (186)
25 PF09835 DUF2062: Uncharacteri 20.3 98 0.0021 22.2 2.4 23 82-104 112-134 (154)
26 PF05440 MtrB: Tetrahydrometha 20.1 1.3E+02 0.0028 22.0 2.9 23 79-101 72-94 (97)
No 1
>PLN00088 predicted protein; Provisional
Probab=100.00 E-value=1.1e-33 Score=210.84 Aligned_cols=112 Identities=38% Similarity=0.511 Sum_probs=97.6
Q ss_pred Cccccc----cccchh-hhhhccc-CCCccccccCCC-CCCcchhhhcCCCCccceeEEech-hhhHHHHHHHHHHHHHH
Q 033561 1 MASVSM----AMPLSS-ATQNRLI-QPSSESFLKPLP-VRPSKAARFLGKPKSRARLQVQAS-LKEKAVTGLTAAALTAS 72 (116)
Q Consensus 1 MAS~Sm----a~pl~~-at~~~~~-~pss~~~~~Plp-~r~s~~~~~~~~~~~~~r~~~~as-~k~k~v~~ltaaa~~as 72 (116)
|||++| +.++++ ++|.|+. .++.|+|-.--| .||+++... .+|+|+|++++ +|||+++|+|++|++|+
T Consensus 1 ma~~~~~s~~~a~~~~~~t~~~~~k~~~~~g~~l~~p~~~~~~~~~~----~n~~r~~~~as~~~ekav~gltaaAl~As 76 (127)
T PLN00088 1 MACAAMASVSSAATAPLATLVWEAKLLSRQGLALAAPSGKKQVSVAI----SNRSRVVMSLPAKEDHNVASLTSLALLAA 76 (127)
T ss_pred CchHHHHHhhccccchhhHhhhhhhhhccccceecCCCCccchhhhh----cccceeEEecchHHHHHHHHHHHHHHHHH
Confidence 788775 357777 8899988 899999875445 677777754 34799999998 89999999999999999
Q ss_pred hh------hc-CCCChhHHHHHHHHHHHHHHHHHHhhheeeeeccCcccCC
Q 033561 73 MA------AG-SGLSPSLKNFLLSIVAGGVVLAAIVGAVIGVANFDPVKRT 116 (116)
Q Consensus 73 ~v------Aa-~~mTPSL~NFl~SLvaG~vVv~~i~~Ali~VSq~D~V~R~ 116 (116)
|+ || +||||||+||||||+|||+|+++|+++||||||||||+|+
T Consensus 77 mv~pevAeAA~~gvTPSLsNFL~SLvaGgvVv~pI~~Ali~VSq~D~V~R~ 127 (127)
T PLN00088 77 AVVPEIAEAAQPGVSPSLKNLLLSVVAGGVVITVIGVAVAGVSTFDPVKRK 127 (127)
T ss_pred hhCHHHHHhccCCCChhHHHHHHHHHhhhhhhhhhheeeEEEeccCccccC
Confidence 98 55 7899999999999999999999999999999999999996
No 2
>PF06596 PsbX: Photosystem II reaction centre X protein (PsbX); InterPro: IPR009518 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 []. The low molecular weight transmembrane protein PsbX found in PSII is associated with the oxygen-evolving complex. Its expression is light-regulated. PsbX appears to be involved in the regulation of the amount of PSII [], and may be involved in the binding or turnover of quinone molecules at the Qb (PsbA) site [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0016020 membrane; PDB: 3ARC_x 3A0H_X 3A0B_X 3PRR_X 1S5L_x 4FBY_j 3PRQ_X 3KZI_X 3BZ2_X 3BZ1_X.
Probab=99.81 E-value=8.1e-21 Score=118.17 Aligned_cols=38 Identities=58% Similarity=0.922 Sum_probs=29.6
Q ss_pred CChhHHHHHHHHHHHH-HHHHHHhhheeeeeccCcccCC
Q 033561 79 LSPSLKNFLLSIVAGG-VVLAAIVGAVIGVANFDPVKRT 116 (116)
Q Consensus 79 mTPSL~NFl~SLvaG~-vVv~~i~~Ali~VSq~D~V~R~ 116 (116)
|||||+|||+||+||+ +|+++|+++|++|||+||++|+
T Consensus 1 mTpSL~nfl~Sl~aG~~iVv~~i~~ali~VSq~D~v~R~ 39 (39)
T PF06596_consen 1 MTPSLSNFLLSLVAGAVIVVIPIAGALIFVSQFDRVKRS 39 (39)
T ss_dssp --HHHHHHHHHHHHHH-HHHHHHHHHHHHHHCCS-----
T ss_pred CCHhHHHHHHHHHhhhhhhhhhhhhheEEEeccCccccC
Confidence 8999999999999999 6678899999999999999996
No 3
>CHL00114 psbX photosystem II protein X; Reviewed
Probab=99.81 E-value=2.6e-20 Score=116.10 Aligned_cols=38 Identities=29% Similarity=0.511 Sum_probs=36.2
Q ss_pred CChhHHHHHHHHHHHHHHHH-HHhhheeeeeccCcccCC
Q 033561 79 LSPSLKNFLLSIVAGGVVLA-AIVGAVIGVANFDPVKRT 116 (116)
Q Consensus 79 mTPSL~NFl~SLvaG~vVv~-~i~~Ali~VSq~D~V~R~ 116 (116)
|||||+|||+||+||++|++ +|++||+||||+|+++|+
T Consensus 1 MTpSLsnF~~SL~~Ga~ivvipi~~aLifvSq~D~v~R~ 39 (39)
T CHL00114 1 MTPSLSAFINSLLLGAIIVVIPITLALLFVSQKDRTTRN 39 (39)
T ss_pred CChhHHHHHHHHHHHHHHhHHHhhhheEEEeccceeccC
Confidence 99999999999999999976 599999999999999996
No 4
>PF14187 DUF4310: Domain of unknown function (DUF4310)
Probab=68.47 E-value=7.3 Score=31.90 Aligned_cols=34 Identities=29% Similarity=0.518 Sum_probs=29.4
Q ss_pred CCCChhHHHHHHHHHHHHHHHHHHhhheeeeecc
Q 033561 77 SGLSPSLKNFLLSIVAGGVVLAAIVGAVIGVANF 110 (116)
Q Consensus 77 ~~mTPSL~NFl~SLvaG~vVv~~i~~Ali~VSq~ 110 (116)
.+.+-.++||-+||+-|+++=.+|+..+|++-++
T Consensus 101 ~Gi~~p~~~F~laLl~G~~iG~~iG~iIi~iRK~ 134 (209)
T PF14187_consen 101 AGITAPLENFPLALLTGAVIGLIIGYIIILIRKF 134 (209)
T ss_pred ccccchHHHhHHHHHHHHHHHHHHhheeEEEEee
Confidence 5888999999999999999988888888887653
No 5
>TIGR03579 EF_0833 conserved hypothetical protein EF_0833/AHA_3914. Members of this family of relatively rare proteins are found in both Gram-positive (e.g. Enterococcus faecalis) and Gram-negative (e.g. Aeromonas hydrophila) bacteria, as part of a cluster of conserved proteins. The function is unknown.
Probab=59.62 E-value=13 Score=30.46 Aligned_cols=33 Identities=27% Similarity=0.425 Sum_probs=28.0
Q ss_pred CCCChhHHHHHHHHHHHHHHHHHHhhheeeeec
Q 033561 77 SGLSPSLKNFLLSIVAGGVVLAAIVGAVIGVAN 109 (116)
Q Consensus 77 ~~mTPSL~NFl~SLvaG~vVv~~i~~Ali~VSq 109 (116)
.+++-.++||-+||+-|+++=++|+..+|++-+
T Consensus 99 ~G~~~pv~nF~lsL~tG~~lG~~iG~iIi~~RK 131 (209)
T TIGR03579 99 AGIVAPVENFGLSLLTGAVLGLAVGYVIILIRK 131 (209)
T ss_pred ccccccHHHHHHHHHHHHHHHHHhheeEEEEEe
Confidence 588999999999999999987778777777554
No 6
>PF12732 YtxH: YtxH-like protein; InterPro: IPR024623 This family of uncharacterised proteins is found in bacteria. Proteins in this family are typically between 100 and 143 amino acids in length. The N-terminal region is the most conserved.
Probab=52.51 E-value=12 Score=24.35 Aligned_cols=15 Identities=47% Similarity=0.612 Sum_probs=10.8
Q ss_pred HHHHHHHHHHHHHHH
Q 033561 86 FLLSIVAGGVVLAAI 100 (116)
Q Consensus 86 Fl~SLvaG~vVv~~i 100 (116)
|++++++|+++-+++
T Consensus 1 F~~g~l~Ga~~Ga~~ 15 (74)
T PF12732_consen 1 FLLGFLAGAAAGAAA 15 (74)
T ss_pred CHHHHHHHHHHHHHH
Confidence 788888888765443
No 7
>PF09813 Coiled-coil_56: Coiled-coil domain-containing protein 56; InterPro: IPR018628 Members of this family of proteins have no known function.
Probab=48.74 E-value=20 Score=26.40 Aligned_cols=30 Identities=20% Similarity=0.294 Sum_probs=25.5
Q ss_pred hHHHHHHHHHHHHHHHHHHhhheeeeeccC
Q 033561 82 SLKNFLLSIVAGGVVLAAIVGAVIGVANFD 111 (116)
Q Consensus 82 SL~NFl~SLvaG~vVv~~i~~Ali~VSq~D 111 (116)
.-+|-+.++..|++|+++-+--+..|+|-|
T Consensus 48 R~rN~~Tgl~L~~~v~gIY~YTi~sV~Qe~ 77 (100)
T PF09813_consen 48 RRRNLLTGLALGAFVVGIYAYTIYSVKQED 77 (100)
T ss_pred hhhhHHHHHHHHHHHHHHHhheeeeechhh
Confidence 458999999999999999888888888865
No 8
>PF04835 Pox_A9: A9 protein conserved region; InterPro: IPR006920 This entry represents a family of Chordopoxvirus A9 proteins. Chordopoxvirus belongs to the family Poxviridae and is the cause of vertebrate infections [].
Probab=43.76 E-value=34 Score=22.93 Aligned_cols=33 Identities=18% Similarity=0.108 Sum_probs=24.3
Q ss_pred hHHHHHHHHHHHHHHHHHHhhheeeeeccCccc
Q 033561 82 SLKNFLLSIVAGGVVLAAIVGAVIGVANFDPVK 114 (116)
Q Consensus 82 SL~NFl~SLvaG~vVv~~i~~Ali~VSq~D~V~ 114 (116)
|+.+-+.=++.+-++-.+++++|+.+|+.|..+
T Consensus 21 sF~fViik~vismimylilGi~L~yis~~~~~~ 53 (54)
T PF04835_consen 21 SFWFVIIKSVISMIMYLILGIALIYISSNDDKK 53 (54)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhhccCcccc
Confidence 445555556667677788999999999988653
No 9
>PHA02680 ORF090 IMV phosphorylated membrane protein; Provisional
Probab=41.48 E-value=21 Score=26.10 Aligned_cols=28 Identities=25% Similarity=0.419 Sum_probs=21.4
Q ss_pred hHHHHHHHHHHHHHHHHH--Hhhheeeeec
Q 033561 82 SLKNFLLSIVAGGVVLAA--IVGAVIGVAN 109 (116)
Q Consensus 82 SL~NFl~SLvaG~vVv~~--i~~Ali~VSq 109 (116)
-++|+..+++.||+++++ ...|.+=.|+
T Consensus 6 ~i~ny~s~vli~GIiLL~~ACIFAfidFSK 35 (91)
T PHA02680 6 TLKSYYSGVLICGVLLLTAACVFAFVDFSK 35 (91)
T ss_pred HHHHhccHHHHHHHHHHHHHHHHhhhhhhc
Confidence 479999999999999866 4456655555
No 10
>PF05767 Pox_A14: Poxvirus virion envelope protein A14; InterPro: IPR008785 This family consists of several Poxvirus virion envelope protein A14-like sequences. A14 is a component of the virion membrane and has been found to be an H1 phosphatase substrate in vivo and in vitro. A14 is hyperphosphorylated on serine residues in the absence of H1 expression [].; GO: 0019031 viral envelope
Probab=39.37 E-value=17 Score=26.55 Aligned_cols=30 Identities=23% Similarity=0.409 Sum_probs=21.9
Q ss_pred hhHHHHHHHHHHHHHHHHH--Hhhheeeeecc
Q 033561 81 PSLKNFLLSIVAGGVVLAA--IVGAVIGVANF 110 (116)
Q Consensus 81 PSL~NFl~SLvaG~vVv~~--i~~Ali~VSq~ 110 (116)
--|+|+..+++.||+++++ +..|.+=.|+.
T Consensus 5 ~~~~n~~S~vli~GiiLL~~aCIfAfidfsK~ 36 (92)
T PF05767_consen 5 GFLSNYFSGVLIGGIILLIAACIFAFIDFSKN 36 (92)
T ss_pred HHHHhccchHHHHHHHHHHHHHHHHhhhhccC
Confidence 3589999999999999866 44455555544
No 11
>PF07423 DUF1510: Protein of unknown function (DUF1510); InterPro: IPR009988 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=36.59 E-value=38 Score=27.33 Aligned_cols=25 Identities=32% Similarity=0.279 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHH-Hhhheeeeec
Q 033561 85 NFLLSIVAGGVVLAA-IVGAVIGVAN 109 (116)
Q Consensus 85 NFl~SLvaG~vVv~~-i~~Ali~VSq 109 (116)
|-++=++.|-|+|++ |.+.-+|+.+
T Consensus 13 N~iLNiaI~IV~lLIiiva~~lf~~~ 38 (217)
T PF07423_consen 13 NKILNIAIGIVSLLIIIVAYQLFFGG 38 (217)
T ss_pred hhhHHHHHHHHHHHHHHHhhhheecC
Confidence 556667777777666 4444555533
No 12
>PF13706 PepSY_TM_3: PepSY-associated TM helix
Probab=34.59 E-value=21 Score=20.99 Aligned_cols=26 Identities=27% Similarity=0.514 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHH-HhhheeeeeccCcccC
Q 033561 88 LSIVAGGVVLAA-IVGAVIGVANFDPVKR 115 (116)
Q Consensus 88 ~SLvaG~vVv~~-i~~Ali~VSq~D~V~R 115 (116)
.+|+.|.++++. ++|++... .|.++|
T Consensus 11 ~Gl~~g~~l~~~~~tG~~~~f--~~ei~r 37 (37)
T PF13706_consen 11 LGLILGLLLFVIFLTGAVMVF--RDEIDR 37 (37)
T ss_pred HHHHHHHHHHHHHHHhHHHHH--HHhhcC
Confidence 567777776655 55555443 444444
No 13
>PHA03048 IMV membrane protein; Provisional
Probab=33.71 E-value=23 Score=25.92 Aligned_cols=29 Identities=21% Similarity=0.438 Sum_probs=21.5
Q ss_pred hHHHHHHHHHHHHHHHHH--Hhhheeeeecc
Q 033561 82 SLKNFLLSIVAGGVVLAA--IVGAVIGVANF 110 (116)
Q Consensus 82 SL~NFl~SLvaG~vVv~~--i~~Ali~VSq~ 110 (116)
-++|+...++.||+++++ ...|.+=.|+.
T Consensus 6 ~~~ny~S~vli~GIiLL~~aCIfAfidfsK~ 36 (93)
T PHA03048 6 MISNYFSTALIGGIILLAASCIFAFVDFSKN 36 (93)
T ss_pred HhhcccchHHHHHHHHHHHHHHHhhhhhhcC
Confidence 489999999999999866 44455555554
No 14
>PHA02898 virion envelope protein; Provisional
Probab=28.66 E-value=32 Score=25.20 Aligned_cols=30 Identities=27% Similarity=0.260 Sum_probs=22.0
Q ss_pred hHHHHHHHHHHHHHHHHH--HhhheeeeeccC
Q 033561 82 SLKNFLLSIVAGGVVLAA--IVGAVIGVANFD 111 (116)
Q Consensus 82 SL~NFl~SLvaG~vVv~~--i~~Ali~VSq~D 111 (116)
-++|...+++.+|++|++ ...|.+=.|+..
T Consensus 6 ~~~N~~s~vli~GIiLL~~ACIfAfidfSK~~ 37 (92)
T PHA02898 6 FFKNRPSYVVAFGIILLIVACICAYIELSKSE 37 (92)
T ss_pred hhhcCcchHHHHHHHHHHHHHHHheehhhcCC
Confidence 368999999999999866 445666556543
No 15
>TIGR03546 conserved hypothetical protein TIGR03546. Members of this family are uncharacterized proteins, usually encoded by a gene adjacent to a member of family TIGR03545, which is also uncharacterized.
Probab=28.34 E-value=66 Score=24.58 Aligned_cols=21 Identities=33% Similarity=0.420 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhh
Q 033561 83 LKNFLLSIVAGGVVLAAIVGA 103 (116)
Q Consensus 83 L~NFl~SLvaG~vVv~~i~~A 103 (116)
+..|..+++.|+++++.|.+.
T Consensus 102 l~~f~~tl~~Gg~l~Gli~~~ 122 (154)
T TIGR03546 102 LARFNNTIVMGSFVVGLILLP 122 (154)
T ss_pred HHHHHHHHHHhhHHHHHHHHH
Confidence 778888999999999876554
No 16
>PF07123 PsbW: Photosystem II reaction centre W protein (PsbW); InterPro: IPR009806 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 PsbW found in PSII, where it is a subunit of the oxygen-evolving complex. PsbW appears to have several roles, including guiding PSII biogenesis and assembly, stabilising dimeric PSII [], and facilitating PSII repair after photo-inhibition []. There appears to be two classes of PsbW, class 1 being found predominantly in algae and cyanobacteria, and class 2 being found predominantly in plants. This entry represents class 2 PsbW.; GO: 0015979 photosynthesis, 0009507 chloroplast, 0009523 photosystem II
Probab=27.94 E-value=2.3e+02 Score=21.97 Aligned_cols=9 Identities=22% Similarity=0.464 Sum_probs=5.9
Q ss_pred Ccccccccc
Q 033561 1 MASVSMAMP 9 (116)
Q Consensus 1 MAS~Sma~p 9 (116)
||+++++.+
T Consensus 1 MAti~a~~~ 9 (138)
T PF07123_consen 1 MATIAASAS 9 (138)
T ss_pred Cceeeeccc
Confidence 677776555
No 17
>PRK10927 essential cell division protein FtsN; Provisional
Probab=27.92 E-value=60 Score=28.08 Aligned_cols=19 Identities=16% Similarity=0.361 Sum_probs=13.8
Q ss_pred HHHHHHHhhheeeeeccCc
Q 033561 94 GVVLAAIVGAVIGVANFDP 112 (116)
Q Consensus 94 ~vVv~~i~~Ali~VSq~D~ 112 (116)
..||++.+|+|.||++..+
T Consensus 41 vavlv~fiGGLyFith~k~ 59 (319)
T PRK10927 41 AAVLVTFIGGLYFITHHKK 59 (319)
T ss_pred HHHHHHHhhheEEEecCCC
Confidence 4456667778999998664
No 18
>COG4062 MtrB Tetrahydromethanopterin S-methyltransferase, subunit B [Coenzyme metabolism]
Probab=27.53 E-value=54 Score=24.62 Aligned_cols=25 Identities=24% Similarity=0.230 Sum_probs=18.0
Q ss_pred CChhHHHHHHHHHHHHHH--HHHHhhh
Q 033561 79 LSPSLKNFLLSIVAGGVV--LAAIVGA 103 (116)
Q Consensus 79 mTPSL~NFl~SLvaG~vV--v~~i~~A 103 (116)
|.--|+||+++++.|-.| ++++..+
T Consensus 73 ~aG~~tna~yGfviGl~i~aLlAlil~ 99 (108)
T COG4062 73 TAGYLTNAFYGFVIGLGIMALLALILG 99 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445689999999999888 4444433
No 19
>COG2354 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.03 E-value=72 Score=27.59 Aligned_cols=22 Identities=45% Similarity=0.606 Sum_probs=19.3
Q ss_pred CCChhHHHHHHHHHHHHHHHHH
Q 033561 78 GLSPSLKNFLLSIVAGGVVLAA 99 (116)
Q Consensus 78 ~mTPSL~NFl~SLvaG~vVv~~ 99 (116)
-..|++-|+...+++|+++++.
T Consensus 273 w~~~t~~~~v~g~v~G~vvv~~ 294 (303)
T COG2354 273 WLVPTLLNAVLGLVIGAVVVAL 294 (303)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3679999999999999998865
No 20
>PF14575 EphA2_TM: Ephrin type-A receptor 2 transmembrane domain; PDB: 3KUL_A 2XVD_A 2VX1_A 2VWV_A 2VX0_A 2VWY_A 2VWZ_A 2VWW_A 2VWU_A 2VWX_A ....
Probab=22.67 E-value=78 Score=21.26 Aligned_cols=22 Identities=32% Similarity=0.357 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHHhhheeeee
Q 033561 87 LLSIVAGGVVLAAIVGAVIGVA 108 (116)
Q Consensus 87 l~SLvaG~vVv~~i~~Ali~VS 108 (116)
+++++.|.++++++.+.++++.
T Consensus 3 i~~~~~g~~~ll~~v~~~~~~~ 24 (75)
T PF14575_consen 3 IASIIVGVLLLLVLVIIVIVCF 24 (75)
T ss_dssp HHHHHHHHHHHHHHHHHHHCCC
T ss_pred EehHHHHHHHHHHhheeEEEEE
Confidence 4566667666655444444443
No 21
>TIGR02838 spore_V_AC stage V sporulation protein AC. This model describes stage V sporulation protein AC, a paralog of stage V sporulation protein AE. Both are proteins found to present in a species if and only if that species is one of the Firmicutes capable of endospore formation, as of the time of the publication of the genome of Carboxydothermus hydrogenoformans. Mutants in spoVAC have a stage V sproulation defect.
Probab=22.58 E-value=75 Score=24.50 Aligned_cols=21 Identities=29% Similarity=0.594 Sum_probs=17.8
Q ss_pred CChhHHHHHHHHHHHHHHHHH
Q 033561 79 LSPSLKNFLLSIVAGGVVLAA 99 (116)
Q Consensus 79 mTPSL~NFl~SLvaG~vVv~~ 99 (116)
=.|.++|+++..+.||+|-++
T Consensus 13 k~~~~~n~l~AFlvGG~IC~i 33 (141)
T TIGR02838 13 KPPYLKNCVMAFLVGGLICLI 33 (141)
T ss_pred CCcHHHHHHHHHHhCcHHHHH
Confidence 367899999999999998654
No 22
>PF06783 UPF0239: Uncharacterised protein family (UPF0239); InterPro: IPR009621 This is a group of transmembrane proteins of unknown function.; GO: 0016021 integral to membrane
Probab=21.98 E-value=1e+02 Score=22.20 Aligned_cols=30 Identities=13% Similarity=0.390 Sum_probs=19.5
Q ss_pred HHHHH-HHHHHHHHHHHH-HhhheeeeeccCc
Q 033561 83 LKNFL-LSIVAGGVVLAA-IVGAVIGVANFDP 112 (116)
Q Consensus 83 L~NFl-~SLvaG~vVv~~-i~~Ali~VSq~D~ 112 (116)
+.|+| ++|..|++.=.+ |..+++-+++.|.
T Consensus 18 ~e~llRYGLf~GAIFQliCilAiI~~~~~s~~ 49 (85)
T PF06783_consen 18 FENLLRYGLFVGAIFQLICILAIILPISKSHE 49 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHheeeecCCccC
Confidence 44554 789999998444 5555666666654
No 23
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=21.39 E-value=33 Score=30.39 Aligned_cols=12 Identities=42% Similarity=0.891 Sum_probs=9.9
Q ss_pred eeeeeccCcccC
Q 033561 104 VIGVANFDPVKR 115 (116)
Q Consensus 104 li~VSq~D~V~R 115 (116)
.|.+|.||||+|
T Consensus 246 ~v~ls~fdp~rr 257 (514)
T TIGR03319 246 AVILSGFDPVRR 257 (514)
T ss_pred eEEecCCchHHH
Confidence 566899999988
No 24
>PF05283 MGC-24: Multi-glycosylated core protein 24 (MGC-24); InterPro: IPR007947 CD164 is a mucin-like receptor, or sialomucin, with specificity in receptor/ ligand interactions that depends on the structural characteristics of the mucin-like receptor. Its functions include mediating, or regulating, haematopoietic progenitor cell adhesion and the negative regulation of their growth and/or-differentiation. It exists in the native state as a disulphide- linked homodimer of two 80-85kDa subunits. It is usually expressed by CD34+ and CD341o/- haematopoietic stem cells and associated microenvironmental cells. It contains, in its extracellular region, two mucin domains (I and II) linked by a non-mucin domain, which has been predicted to contain intra- disulphide bridges. This receptor may play a key role in haematopoiesis by facilitating the adhesion of human CD34+ cells to bone marrow stroma and by negatively regulating CD34+ CD341o/- haematopoietic progenitor cell proliferation. These effects involve the CD164 class I and/or II epitopes recognised by the monoclonal antibodies (mAbs) 105A5 and 103B2/9E10. These epitopes are carbohydrate-dependent and are located on the N-terminal mucin domain I [, ]. It has been found that murine MGC-24v and rat endolyn share significant sequence similarities with human CD164. However, CD164 lacks the consensus glycosaminoglycan (GAG)-attachment site found in MGC-24; it is possible that GAG-association is responsible for the high molecular weight of the epithelial-derived MGC-24 glycoprotein []. Genomic structure studies have placed CD164 within the mucin-subgroup that comprises multiple exons, and demonstrate the diverse chromosomal distribution of this family of molecules. Molecules with such multiple exons may have sophisticated regulatory mechanisms that involve not only post-translational modifications of the oligosaccharide side chains, but also differential exon usage. Although differences in the intron and exon sizes are seen between the mouse and human genes, the predicted proteins are similar in size and structure, maintaining functionally important motifs that regulate cell proliferation or subcellular distribution []. CD164 is a gene whose expression depends on differential usage of poly- adenylation sites within the 3'-UTR. The conserved distribution of the 3.2- and 1.2-kb CD164 transcripts between mouse and human suggests that (i) a mechanism may exist to regulate tissue-specific polyadenylation, and (ii) differences in polyadenylation are important for the expression and function of CD164 in different tissues. Two other aspects of the structure of CD164 are of particular interest. First, it shares one of several conserved features of a cytokine-binding pocket - in this respect, it is notable that evidence exists for a class of cell-surface sialomucin modulators that directly interact with growth factor receptors to regulate their response to physiological ligands. Second, its cytoplasmic tail contains a C-terminal YHTL motif found in many endocytic membrane proteins or receptors. These Tyr-based motifs bind to adaptor proteins, which mediate the sorting of membrane proteins into transport vesicles from the plasma membrane to the endosomes, and between intracellular compartments.
Probab=20.75 E-value=40 Score=26.76 Aligned_cols=22 Identities=36% Similarity=0.347 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHHHhhheee
Q 033561 85 NFLLSIVAGGVVLAAIVGAVIG 106 (116)
Q Consensus 85 NFl~SLvaG~vVv~~i~~Ali~ 106 (116)
-|=-.=+.||+||+.-..+++|
T Consensus 157 ~FD~~SFiGGIVL~LGv~aI~f 178 (186)
T PF05283_consen 157 TFDAASFIGGIVLTLGVLAIIF 178 (186)
T ss_pred CCchhhhhhHHHHHHHHHHHHH
Confidence 4655667788888664444444
No 25
>PF09835 DUF2062: Uncharacterized protein conserved in bacteria (DUF2062); InterPro: IPR018639 This domain, found in various prokaryotic proteins, has no known function. It is found at the C-terminal of family 2 glycosyltransferase proteins, in addition to proteins of unknown function.
Probab=20.32 E-value=98 Score=22.15 Aligned_cols=23 Identities=30% Similarity=0.603 Sum_probs=18.0
Q ss_pred hHHHHHHHHHHHHHHHHHHhhhe
Q 033561 82 SLKNFLLSIVAGGVVLAAIVGAV 104 (116)
Q Consensus 82 SL~NFl~SLvaG~vVv~~i~~Al 104 (116)
.+.++++.++.|++|++++.+.+
T Consensus 112 ~~~~~~~~~~~G~~i~~~v~~~i 134 (154)
T PF09835_consen 112 SLWEFGLPFLLGSLILGIVLGII 134 (154)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 57778999999999987765543
No 26
>PF05440 MtrB: Tetrahydromethanopterin S-methyltransferase subunit B; InterPro: IPR008690 The N5-methyltetrahydromethanopterin: coenzyme M (2.1.1.86 from EC) of Methanosarcina mazei Go1 is a membrane-associated, corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump [].; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0015948 methanogenesis, 0016021 integral to membrane
Probab=20.13 E-value=1.3e+02 Score=22.01 Aligned_cols=23 Identities=13% Similarity=0.345 Sum_probs=16.9
Q ss_pred CChhHHHHHHHHHHHHHHHHHHh
Q 033561 79 LSPSLKNFLLSIVAGGVVLAAIV 101 (116)
Q Consensus 79 mTPSL~NFl~SLvaG~vVv~~i~ 101 (116)
+.--++|++++++.|.++.+.++
T Consensus 72 ~AG~~tn~fyGf~igL~i~~lva 94 (97)
T PF05440_consen 72 IAGIFTNMFYGFIIGLVIAGLVA 94 (97)
T ss_pred ehhhhhhHHHHHHHHHHHHHHHH
Confidence 44467899999999988865543
Done!