Query 030417
Match_columns 177
No_of_seqs 31 out of 33
Neff 1.9
Searched_HMMs 46136
Date Fri Mar 29 13:24:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030417.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030417hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00054 photosystem I reactio 100.0 4.6E-42 9.9E-47 272.2 7.8 126 34-165 1-134 (139)
2 PF05479 PsaN: Photosystem I r 100.0 2.2E-38 4.8E-43 251.1 -2.6 96 38-136 8-109 (138)
3 PLN00078 photosystem I reactio 99.6 3.7E-17 8E-22 128.1 2.0 70 52-128 27-97 (122)
4 KOG3381 Uncharacterized conser 82.5 0.4 8.6E-06 40.0 -0.0 19 96-114 128-146 (161)
5 COG5133 Uncharacterized conser 73.5 1.3 2.8E-05 37.4 0.4 20 95-114 147-166 (181)
6 PF07172 GRP: Glycine rich pro 60.0 5.6 0.00012 29.7 1.5 14 94-107 32-45 (95)
7 PF05757 PsbQ: Oxygen evolving 47.0 5.1 0.00011 33.8 -0.6 26 41-70 15-40 (202)
8 PF13442 Cytochrome_CBB3: Cyto 42.6 3.2 6.9E-05 26.8 -1.9 19 113-131 1-19 (67)
9 PRK13697 cytochrome c6; Provis 39.4 15 0.00033 25.8 0.9 10 123-132 36-45 (111)
10 PF02167 Cytochrom_C1: Cytochr 38.9 6.8 0.00015 33.2 -1.0 21 115-135 15-35 (219)
11 PF01322 Cytochrom_C_2: Cytoch 37.0 4.1 8.8E-05 29.6 -2.3 20 113-132 101-120 (122)
12 TIGR02811 formate_TAT formate 36.7 47 0.001 23.5 3.1 16 55-70 5-20 (66)
13 PLN00042 photosystem II oxygen 36.7 47 0.001 29.5 3.7 53 43-103 39-93 (260)
14 PRK06835 DNA replication prote 33.8 15 0.00033 32.0 0.3 40 96-135 71-110 (329)
15 PLN00064 photosystem II protei 33.3 58 0.0012 27.5 3.6 44 52-96 27-70 (166)
16 TIGR02603 CxxCH_TIGR02603 puta 33.2 7 0.00015 29.3 -1.7 33 115-156 3-35 (133)
17 PRK11657 dsbG disulfide isomer 32.2 53 0.0011 27.3 3.2 65 86-150 81-154 (251)
18 PF12650 DUF3784: Domain of un 30.4 16 0.00035 25.9 -0.1 25 85-109 19-43 (97)
19 TIGR03044 PS_II_psb27 photosys 29.7 65 0.0014 26.2 3.2 33 63-98 11-43 (135)
20 PF10399 UCR_Fe-S_N: Ubiquitin 29.4 53 0.0011 21.6 2.2 20 56-75 6-25 (41)
21 KOG3052 Cytochrome c1 [Energy 28.3 10 0.00022 34.4 -1.7 50 113-162 93-150 (311)
22 PF14285 DUF4367: Domain of un 27.0 79 0.0017 23.1 3.0 31 60-90 2-32 (168)
23 PF02591 DUF164: Putative zinc 26.3 29 0.00063 22.7 0.6 14 120-133 19-32 (56)
24 PRK14139 heat shock protein Gr 22.7 26 0.00057 29.0 -0.2 23 94-116 43-66 (185)
25 PRK09133 hypothetical protein; 22.4 62 0.0013 28.2 2.0 26 65-90 12-37 (472)
26 PF11022 DUF2611: Protein of u 22.0 1.6E+02 0.0034 21.5 3.7 15 86-100 54-68 (71)
27 PF15240 Pro-rich: Proline-ric 21.6 57 0.0012 27.5 1.6 25 64-91 2-26 (179)
28 PRK07474 sulfur oxidation prot 21.3 1.4E+02 0.0031 24.3 3.7 37 59-95 8-44 (154)
29 TIGR03045 PS_II_C550 cytochrom 21.1 26 0.00056 28.5 -0.5 65 61-131 2-67 (159)
30 CHL00183 petJ cytochrome c553; 20.7 1.4E+02 0.003 21.2 3.2 9 124-132 35-43 (108)
31 COG3245 CycB Cytochrome c5 [En 20.4 52 0.0011 26.8 1.0 15 118-132 50-64 (126)
No 1
>PLN00054 photosystem I reaction center subunit N; Provisional
Probab=100.00 E-value=4.6e-42 Score=272.23 Aligned_cols=126 Identities=51% Similarity=0.581 Sum_probs=112.1
Q ss_pred Ccccccccceeeeccccc--cccccCCchhHHHHHHHHHHHHHhhhhccccccchhhHHHHHHHhhhhhhhhhhhhhccc
Q 030417 34 PAVHGHKMPVIRAQQVDV--SKESRGTDGRRAAMALLAVTLFTTATAAASSSANAGVIDEYLERSKANKELNDQKRLATS 111 (177)
Q Consensus 34 p~~~~~klPvIraqq~~~--~~~~~~~~gRRaal~~LAa~l~~tAa~a~a~~A~AgviedyL~KSkaNKELNDKKRLaTs 111 (177)
+++++.++|+|+||+++. +...++++|||++|++||++|++++ +.+++||||||+|||+|||+|||||||||||||
T Consensus 1 ~~~s~~~~~~ika~r~~~A~~~~~~~~~grraa~~~Laa~l~~~a--a~~~~AnAgv~~d~L~kS~aNKeLNDKKRlATS 78 (139)
T PLN00054 1 GAVSQMKMPVIKAQRVVRATGAVVDASDGRRAALVGLAATLFSTA--AAAASANAGVISDLLAKSKANKELNDKKRLATS 78 (139)
T ss_pred CccccccccccccccccccccchhccccchHHHHHHHHHHHHHHH--hcccccchhHHHHHHHHhhhhhhhhhHHhhhhc
Confidence 457889999999999884 7778999999999999999999987 888999999999999999999999999999999
Q ss_pred ccccchheeeeecccc------chhhhhhhhhcccccccccceEeeeecCCcccceeccc
Q 030417 112 GANFARAYTVQFGTCK------KCHSSRMIWNWSAKGKINTSVVPMFSGNGEVGQLISLN 165 (177)
Q Consensus 112 ~ANfaRayTV~fGtCk------~c~~~~~i~~~~~k~~~~ts~v~mfsgnge~~q~~~~n 165 (177)
+|||+|+||||||+|+ |||++.+.. |-+.-+..++|.....+...-.+-.
T Consensus 79 ~ANfaRa~TV~~G~C~FP~Nf~GCqdlA~~k----~V~flsdDl~iECEGkd~~~CgS~~ 134 (139)
T PLN00054 79 GANFARSRTVQDGTCKFPENFTGCEDLAKQK----KVPFISEDLALECEGKDKKKCGSKV 134 (139)
T ss_pred chhhhhheeeecccccCCcccccHHHHHhcC----CCCccccccceeecCCccceecccc
Confidence 9999999999999999 999999876 5667777888888777665544443
No 2
>PF05479 PsaN: Photosystem I reaction centre subunit N (PSAN or PSI-N); InterPro: IPR008796 This family contains several Photosystem I reaction centre subunit N (PSI-N) proteins. The protein has no known function although it is localised in the thylakoid lumen []. PSI-N is a small extrinsic subunit at the lumen side and is very likely involved in the docking of plastocyanin.; GO: 0005516 calmodulin binding, 0015979 photosynthesis, 0009522 photosystem I, 0042651 thylakoid membrane; PDB: 2WSE_N 2WSC_N 2WSF_N 2O01_N.
Probab=100.00 E-value=2.2e-38 Score=251.07 Aligned_cols=96 Identities=58% Similarity=0.779 Sum_probs=41.6
Q ss_pred ccccceeeeccccccccccCCchhHHHHHHHHHHHHHhhhhccccccchhhHHHHHHHhhhhhhhhhhhhhcccccccch
Q 030417 38 GHKMPVIRAQQVDVSKESRGTDGRRAAMALLAVTLFTTATAAASSSANAGVIDEYLERSKANKELNDQKRLATSGANFAR 117 (177)
Q Consensus 38 ~~klPvIraqq~~~~~~~~~~~gRRaal~~LAa~l~~tAa~a~a~~A~AgviedyL~KSkaNKELNDKKRLaTs~ANfaR 117 (177)
..++|+|++++.+ ....+.+++||+++++|+++|++|| +.+++||+|||||||+|||+||||||||||+||++||+|
T Consensus 8 sa~~qai~~~ka~-~~~~~~~~~~Raall~Laa~l~~tA--a~a~~A~A~l~~dyL~KSkaNKelNDKkRlaTs~aNfaR 84 (138)
T PF05479_consen 8 SAKVQAIRAAKAK-RVVVRASDGRRAALLGLAAVLAATA--ASASSARAGLLEDYLEKSKANKELNDKKRLATSYANFAR 84 (138)
T ss_dssp ---------------------------------------------------SSSSS-SSHSSSSSTTTSS-TSSSSSSTS
T ss_pred hcccchhhhccCC-CcccccCccchHHHHHHHHHHHHHh--hcCcchhhHHHHHHHHHhHhhhhhhhHHHhhhhhhhhhh
Confidence 4588999999887 4456778899999999999999887 677999999999999999999999999999999999999
Q ss_pred heeeeecccc------chhhhhhhh
Q 030417 118 AYTVQFGTCK------KCHSSRMIW 136 (177)
Q Consensus 118 ayTV~fGtCk------~c~~~~~i~ 136 (177)
+||||||+|+ |||++.+..
T Consensus 85 ~~tv~fg~c~fP~n~~gc~~la~~~ 109 (138)
T PF05479_consen 85 AYTVQFGTCKFPENFTGCQDLAKQK 109 (138)
T ss_dssp GTT--TSTSSSSS-SSSSSSS-STT
T ss_pred heeeecccccCCccchhhHHHHHcC
Confidence 9999999999 999998754
No 3
>PLN00078 photosystem I reaction center subunit N (PsaN); Provisional
Probab=99.65 E-value=3.7e-17 Score=128.08 Aligned_cols=70 Identities=33% Similarity=0.503 Sum_probs=65.2
Q ss_pred cccccCCchhHHHHHHHHHHHHHhhhhc-cccccchhhHHHHHHHhhhhhhhhhhhhhcccccccchheeeeeccccc
Q 030417 52 SKESRGTDGRRAAMALLAVTLFTTATAA-ASSSANAGVIDEYLERSKANKELNDQKRLATSGANFARAYTVQFGTCKK 128 (177)
Q Consensus 52 ~~~~~~~~gRRaal~~LAa~l~~tAa~a-~a~~A~AgviedyL~KSkaNKELNDKKRLaTs~ANfaRayTV~fGtCk~ 128 (177)
...+|||.+||++|++|.+ ||||+ .++.++..+||+||+||++|||.|||+|| +++|+|+|++||++-+|
T Consensus 27 ~~a~rng~srr~llt~l~s----taaip~~~~~Sr~~liq~llkkSeeNKakndkERL---DdYYKRNykDYF~fveG 97 (122)
T PLN00078 27 MLAQRNGISRRCLLTFLTS----TAAIPEAGSESRKALLQEYLKKSEENKEKNDKERL---DDYYKRNYKDYFGLIEG 97 (122)
T ss_pred HHHHhcchhHHHHHHHHHh----hccCCCCcCchHHHHHHHHHHHhHHhHHHhHHHHH---HHHHHHhHHHHHHHhcc
Confidence 4578999999999999998 88888 77889999999999999999999999999 99999999999999883
No 4
>KOG3381 consensus Uncharacterized conserved protein [Function unknown]
Probab=82.53 E-value=0.4 Score=39.98 Aligned_cols=19 Identities=42% Similarity=0.594 Sum_probs=14.5
Q ss_pred hhhhhhhhhhhhhcccccc
Q 030417 96 SKANKELNDQKRLATSGAN 114 (177)
Q Consensus 96 SkaNKELNDKKRLaTs~AN 114 (177)
..-||.||||+|.|..-.|
T Consensus 128 ~~vNKQLnDKERVaAA~EN 146 (161)
T KOG3381|consen 128 EAVNKQLNDKERVAAALEN 146 (161)
T ss_pred HHHHhhhccHHHHHHHhcC
Confidence 3469999999999765433
No 5
>COG5133 Uncharacterized conserved protein [Function unknown]
Probab=73.48 E-value=1.3 Score=37.43 Aligned_cols=20 Identities=40% Similarity=0.635 Sum_probs=15.4
Q ss_pred Hhhhhhhhhhhhhhcccccc
Q 030417 95 RSKANKELNDQKRLATSGAN 114 (177)
Q Consensus 95 KSkaNKELNDKKRLaTs~AN 114 (177)
.+.-||.||||+|.|..-.|
T Consensus 147 e~qvNKQLnDKeRVaAAcEN 166 (181)
T COG5133 147 ERQVNKQLNDKERVAAACEN 166 (181)
T ss_pred HHHHhhhhchHHHHHHhhch
Confidence 35679999999999765433
No 6
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=59.97 E-value=5.6 Score=29.71 Aligned_cols=14 Identities=29% Similarity=0.537 Sum_probs=8.5
Q ss_pred HHhhhhhhhhhhhh
Q 030417 94 ERSKANKELNDQKR 107 (177)
Q Consensus 94 ~KSkaNKELNDKKR 107 (177)
+|..+.++.+|.|.
T Consensus 32 ~~~~~~~~v~~~~~ 45 (95)
T PF07172_consen 32 EKEEEENEVQDDKY 45 (95)
T ss_pred cccccCCCCCcccc
Confidence 55566666666653
No 7
>PF05757 PsbQ: Oxygen evolving enhancer protein 3 (PsbQ); InterPro: IPR008797 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 PsbQ. Both PsbQ and PsbP (IPR002683 from INTERPRO) are regulators that are necessary for the biogenesis of optically active PSII. The crystal structure of PsbQ from spinach revealed a 4-helical bundle polypeptide. The distribution of positive and negative charges on the protein surface might explain the ability of PsbQ to increase the binding of chloride and calcium ions and make them available to PSII [].; GO: 0005509 calcium ion binding, 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 1VYK_A 1NZE_A 3LS1_A 3LS0_A.
Probab=47.03 E-value=5.1 Score=33.76 Aligned_cols=26 Identities=31% Similarity=0.371 Sum_probs=0.0
Q ss_pred cceeeeccccccccccCCchhHHHHHHHHH
Q 030417 41 MPVIRAQQVDVSKESRGTDGRRAAMALLAV 70 (177)
Q Consensus 41 lPvIraqq~~~~~~~~~~~gRRaal~~LAa 70 (177)
-+++|||| .......+||++|.+|++
T Consensus 15 ~~~vra~~----~~~~~~~~RRa~l~~l~a 40 (202)
T PF05757_consen 15 GVVVRASQ----SPAQQQTSRRAVLGSLLA 40 (202)
T ss_dssp ------------------------------
T ss_pred cceecccc----CcccccccHHHHHHHHHH
Confidence 35688887 223445789999884443
No 8
>PF13442 Cytochrome_CBB3: Cytochrome C oxidase, cbb3-type, subunit III ; PDB: 1KB0_A 2DGE_D 2CE1_A 2CE0_A 2V07_A 1W2L_A 2ZOO_A 2ZBO_G 1DVV_A 2EXV_A ....
Probab=42.57 E-value=3.2 Score=26.84 Aligned_cols=19 Identities=26% Similarity=0.548 Sum_probs=14.7
Q ss_pred cccchheeeeeccccchhh
Q 030417 113 ANFARAYTVQFGTCKKCHS 131 (177)
Q Consensus 113 ANfaRayTV~fGtCk~c~~ 131 (177)
||.++-..+|...|..||.
T Consensus 1 a~~~~G~~ly~~~C~~CH~ 19 (67)
T PF13442_consen 1 ADAAKGKALYEQNCASCHG 19 (67)
T ss_dssp -HHHHHHHHHHHHTHHHHG
T ss_pred CcHHHHHHHHHhHhHHhcC
Confidence 4556667778889999998
No 9
>PRK13697 cytochrome c6; Provisional
Probab=39.44 E-value=15 Score=25.81 Aligned_cols=10 Identities=30% Similarity=0.946 Sum_probs=7.8
Q ss_pred eccccchhhh
Q 030417 123 FGTCKKCHSS 132 (177)
Q Consensus 123 fGtCk~c~~~ 132 (177)
...|-.||..
T Consensus 36 ~~~C~~CHg~ 45 (111)
T PRK13697 36 SANCASCHAG 45 (111)
T ss_pred HHHHHHhCCC
Confidence 3569999984
No 10
>PF02167 Cytochrom_C1: Cytochrome C1 family; InterPro: IPR002326 Cytochrome bc1 complex (ubiquinol:ferricytochrome c oxidoreductase) is found in mitochondria, photosynthetic bacteria and other prokaryotes. It is minimally composed of three subunits: cytochrome b, carrying a low- and a high-potential haem group; cytochrome c1 (cyt c1); and a high-potential Rieske iron-sulphur protein. The general function of the complex is electron transfer between two mobile redox carriers, ubiquinol and cytochrome c; the electron transfer is coupled with proton translocation across the membrane, thus generating proton-motive force in the form of an electrochemical potential that can drive ATP synthesis. In its structure and functions, the cytochrome bc1 complex bears extensive analogy to the cytochrome b6f complex of chloroplasts and cyanobacteria; cyt c1 plays an analogous role to cytochrome f, in spite of their different structures [].; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding; PDB: 1P84_D 2IBZ_D 1EZV_D 3CX5_O 3CXH_O 1KB9_D 1KYO_D 1ZRT_Q 2CA4_B 2C9X_B ....
Probab=38.87 E-value=6.8 Score=33.22 Aligned_cols=21 Identities=29% Similarity=0.662 Sum_probs=17.9
Q ss_pred cchheeeeeccccchhhhhhh
Q 030417 115 FARAYTVQFGTCKKCHSSRMI 135 (177)
Q Consensus 115 faRayTV~fGtCk~c~~~~~i 135 (177)
..|=+.||-..|-.||++.-+
T Consensus 15 lqRG~qvy~~~C~~CHsl~~~ 35 (219)
T PF02167_consen 15 LQRGAQVYMEVCASCHSLKYV 35 (219)
T ss_dssp HHHHHHHHHHTGGGTSBCTTC
T ss_pred HHHHHHHHHHHHhhccccccc
Confidence 378999999999999998543
No 11
>PF01322 Cytochrom_C_2: Cytochrome C'; InterPro: IPR002321 Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes. Ambler [] recognised four classes of cytC. Class II includes the high-spin cytC' and a number of low-spin cytochromes, e.g. cyt c-556. The haem-attachment site is close to the C terminus. The cytC' are capable of binding such ligands as CO, NO or CN(-), albeit with rate and equilibrium constants 100 to 1,000,000-fold smaller than other high-spin haemoproteins []. This, coupled with its relatively low redox potential, makes it unlikely that cytC' is a terminal oxidase. Thus cytC' probably functions as an electron transfer protein []. The 3D structures of a number of cytC' have been determined. The molecule usually exists as a dimer, each monomer folding as a four-alpha-helix bundle incorporating a covalently-bound haem group at the core []. The Chromatium vinosum cytC' exhibits dimer dissociation upon ligand binding [].; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding, 0005746 mitochondrial respiratory chain; PDB: 1BBH_A 2J9B_B 2J8W_A 1JAF_B 3ZTM_A 2XLD_A 2XL6_A 1E86_A 2YLD_A 2YKZ_A ....
Probab=37.00 E-value=4.1 Score=29.65 Aligned_cols=20 Identities=30% Similarity=0.562 Sum_probs=15.8
Q ss_pred cccchheeeeeccccchhhh
Q 030417 113 ANFARAYTVQFGTCKKCHSS 132 (177)
Q Consensus 113 ANfaRayTV~fGtCk~c~~~ 132 (177)
+.+.+++..--.+|+.||+.
T Consensus 101 ~~~~~a~~~v~~~C~aCH~~ 120 (122)
T PF01322_consen 101 AAIKAAFGEVGKSCKACHDA 120 (122)
T ss_dssp HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 34677777788899999974
No 12
>TIGR02811 formate_TAT formate dehydrogenase region TAT target. Members of this uncharacterized protein family are all small, extending 70 or fewer residues from their respective likely start codons. All have the twin-arginine-dependent tranport (TAT) signal sequence at the N-terminus and a conserved 20-residue C-terminal region that includes the motif Y-[HRK]-X-[TS]-X-H-[IV]-X-X-[YF]-Y. The TAT signal sequence suggests a bound cofactor. All members are encoded near genes for subunits of formate dehydrogenase, and may themselves be a subunit or accessory protein.
Probab=36.72 E-value=47 Score=23.46 Aligned_cols=16 Identities=25% Similarity=0.353 Sum_probs=11.1
Q ss_pred ccCCchhHHHHHHHHH
Q 030417 55 SRGTDGRRAAMALLAV 70 (177)
Q Consensus 55 ~~~~~gRRaal~~LAa 70 (177)
...+.+||-+|-+|+.
T Consensus 5 ~~~~~sRR~Flk~lg~ 20 (66)
T TIGR02811 5 QKADPSRRDLLKGLGV 20 (66)
T ss_pred ccCCccHHHHHHHHHH
Confidence 3445789998876555
No 13
>PLN00042 photosystem II oxygen-evolving enhancer protein 2; Provisional
Probab=36.68 E-value=47 Score=29.48 Aligned_cols=53 Identities=38% Similarity=0.364 Sum_probs=29.8
Q ss_pred eeeeccccccccccCCchhHHHHHHHHHHHHHhhhhccccccchhhHHH--HHHHhhhhhhhh
Q 030417 43 VIRAQQVDVSKESRGTDGRRAAMALLAVTLFTTATAAASSSANAGVIDE--YLERSKANKELN 103 (177)
Q Consensus 43 vIraqq~~~~~~~~~~~gRRaal~~LAa~l~~tAa~a~a~~A~Agvied--yL~KSkaNKELN 103 (177)
+-|||... ....+||.+|++++.++... +...+|++..=|+ -.-|.|.++.-.
T Consensus 39 ~~~~~~~~-----~~~~srr~~l~~~~ga~a~~---~~~~pa~aay~~~anvfg~~k~~~gF~ 93 (260)
T PLN00042 39 VCRAQEED-----NSAVSRRAALALLAGAAAAG---AKVSPANAAYGESANVFGKPKTNTGFL 93 (260)
T ss_pred eeeccccc-----cccccHHHHHHHHHHHHHhh---cccCchhhhhcchhhccCCCCCCCCCe
Confidence 55666322 23468999988888753322 5556666655443 234555555443
No 14
>PRK06835 DNA replication protein DnaC; Validated
Probab=33.78 E-value=15 Score=32.03 Aligned_cols=40 Identities=20% Similarity=0.305 Sum_probs=32.5
Q ss_pred hhhhhhhhhhhhhcccccccchheeeeeccccchhhhhhh
Q 030417 96 SKANKELNDQKRLATSGANFARAYTVQFGTCKKCHSSRMI 135 (177)
Q Consensus 96 SkaNKELNDKKRLaTs~ANfaRayTV~fGtCk~c~~~~~i 135 (177)
.+++++|..+|+-.-....|.-.|-...-.|.+|+|---|
T Consensus 71 ~~~~~~l~~~~~~lL~~~g~~~dyl~~~y~Cp~C~dtG~i 110 (329)
T PRK06835 71 KEKITDLRVKKAELLVSNGYPPDYLEMKYTCPKCKDTGFI 110 (329)
T ss_pred HHHHHHHHHHHHHHHHHcCCChhhcCCCCCCCCCCCCCCc
Confidence 4568899999888788889999998888899988876544
No 15
>PLN00064 photosystem II protein Psb27; Provisional
Probab=33.28 E-value=58 Score=27.51 Aligned_cols=44 Identities=20% Similarity=0.218 Sum_probs=25.4
Q ss_pred cccccCCchhHHHHHHHHHHHHHhhhhccccccchhhHHHHHHHh
Q 030417 52 SKESRGTDGRRAAMALLAVTLFTTATAAASSSANAGVIDEYLERS 96 (177)
Q Consensus 52 ~~~~~~~~gRRaal~~LAa~l~~tAa~a~a~~A~AgviedyL~KS 96 (177)
+...++..+||.+|.+.++++.+. ..-+..+|.++-..||.+..
T Consensus 27 ~~~~~~~~~rr~~~~~~~~~~~~~-~~~~~~~a~a~~~g~Y~~DT 70 (166)
T PLN00064 27 PPPRRNHLLRREFLSLATTILTSA-ALLPVAPAFAASDEEYVKET 70 (166)
T ss_pred CchhhhhhHHHHHHHHHHHHHHHH-HhccCcchhhccCCChHHHH
Confidence 344566678999988665544432 23344446565556665543
No 16
>TIGR02603 CxxCH_TIGR02603 putative heme-binding domain, Pirellula/Verrucomicrobium type. This model represents a domain limited to very few species but expanded into large paralogous families in some species that conain it. We find it in over 20 copies each in Pirellula sp. strain 1 (phylum Planctomycetes) and Verrucomicrobium spinosum DSM 4136 (phylum Verrucomicrobia), and no matches above trusted cutoff an any other species so far. This domain, about 140 amino acids long, contains an absolutely conserved motif CxxCH, the cytochrome c family heme-binding site signature (PS00190).
Probab=33.18 E-value=7 Score=29.35 Aligned_cols=33 Identities=27% Similarity=0.443 Sum_probs=20.1
Q ss_pred cchheeeeeccccchhhhhhhhhcccccccccceEeeeecCC
Q 030417 115 FARAYTVQFGTCKKCHSSRMIWNWSAKGKINTSVVPMFSGNG 156 (177)
Q Consensus 115 faRayTV~fGtCk~c~~~~~i~~~~~k~~~~ts~v~mfsgng 156 (177)
.+|-..+++..|..||...- ++ ..+.|-.+|.|
T Consensus 3 ~~~G~~~f~~~C~~CH~~~g------~g---~~~gP~L~~~~ 35 (133)
T TIGR02603 3 AEKGKAVYAQRCYVCHRIGG------EG---VDVGPDLTGVG 35 (133)
T ss_pred HHHHHHHHHhHHHHhCCCCC------CC---CccCCCccccc
Confidence 34445566667999998742 22 13457777755
No 17
>PRK11657 dsbG disulfide isomerase/thiol-disulfide oxidase; Provisional
Probab=32.16 E-value=53 Score=27.32 Aligned_cols=65 Identities=17% Similarity=0.325 Sum_probs=39.4
Q ss_pred hhhHHHHHHHh-------hhhhhhhhhhhhcccccccch-heeeeeccccchhhhhhh-hhcccccccccceEe
Q 030417 86 AGVIDEYLERS-------KANKELNDQKRLATSGANFAR-AYTVQFGTCKKCHSSRMI-WNWSAKGKINTSVVP 150 (177)
Q Consensus 86 AgviedyL~KS-------kaNKELNDKKRLaTs~ANfaR-ayTV~fGtCk~c~~~~~i-~~~~~k~~~~ts~v~ 150 (177)
..|+++.+++. +.=++|++...+.....|=+| -|-..|-.|.-||.+..- ..|+.++++.--.+|
T Consensus 81 ~nlT~~~~~~~~~~~~~~~~~~~l~~~~~i~~g~~~ak~~I~vFtDp~CpyC~kl~~~l~~~~~~g~V~v~~ip 154 (251)
T PRK11657 81 ENLSEALLEKEVYAPMGREMWQRLEQSHWILDGKADAPRIVYVFADPNCPYCKQFWQQARPWVDSGKVQLRHIL 154 (251)
T ss_pred CccCHHHHHHHhcCCccHHHHHHhhccCCccccCCCCCeEEEEEECCCChhHHHHHHHHHHHhhcCceEEEEEe
Confidence 36666666652 223466666666555556555 344567789999987544 457766655544554
No 18
>PF12650 DUF3784: Domain of unknown function (DUF3784); InterPro: IPR017259 This group represents an uncharacterised conserved protein.
Probab=30.41 E-value=16 Score=25.91 Aligned_cols=25 Identities=36% Similarity=0.360 Sum_probs=21.8
Q ss_pred chhhHHHHHHHhhhhhhhhhhhhhc
Q 030417 85 NAGVIDEYLERSKANKELNDQKRLA 109 (177)
Q Consensus 85 ~AgviedyL~KSkaNKELNDKKRLa 109 (177)
..-++..|=-.||+.||.=|||+|.
T Consensus 19 ~~~LIaGyntms~eEk~~~D~~~l~ 43 (97)
T PF12650_consen 19 GYFLIAGYNTMSKEEKEKYDKKKLC 43 (97)
T ss_pred cccchhhcccCCHHHHHHhhHHHHH
Confidence 3468889999999999999999994
No 19
>TIGR03044 PS_II_psb27 photosystem II protein Psb27. Members of this family are the Psb27 protein of the cyanobacterial photosynthetic supracomplex, photosystem II. Although most protein components of both cyanobacterial and chloroplast versions of photosystem II are closely related and described together by single model families, this family is strictly bacterial. Some uncharacterized proteins with highly divergent sequences, from Arabidopsis, score between trusted and noise cutoffs for this model but are not at this time assigned as functionally equivalent photosystem II proteins.
Probab=29.69 E-value=65 Score=26.22 Aligned_cols=33 Identities=30% Similarity=0.427 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHhhhhccccccchhhHHHHHHHhhh
Q 030417 63 AAMALLAVTLFTTATAAASSSANAGVIDEYLERSKA 98 (177)
Q Consensus 63 aal~~LAa~l~~tAa~a~a~~A~AgviedyL~KSka 98 (177)
++.++|..+|+.++ .++++..++..||.+.+.+
T Consensus 11 ~lal~L~~~l~l~~---c~~~~~~~Ltg~Y~~DT~~ 43 (135)
T TIGR03044 11 ALALVLGLCLLLTA---CSGAAKTRLTGDYVEDTLA 43 (135)
T ss_pred HHHHHHHHHHHHhc---ccCCCcccccchHHHHHHH
Confidence 35566666677773 4456789999999887643
No 20
>PF10399 UCR_Fe-S_N: Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; InterPro: IPR019470 This entry represents the TAT-signal region found in the iron-sulphur subunit of Ubiquinol-cytochrome C reductase (also known as the cytochrome bc1 complex). This enzymex is an oligomeric membrane protein complex that is a component of respiratory and photosynthetic electron transfer chains. It couples the transfer of electrons from ubiquinol to cytochrome c with the generation of a protein gradient across the membrane []. This entry is associated with IPR017941 from INTERPRO, IPR004192 from INTERPRO and IPR015248 from INTERPRO. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0055114 oxidation-reduction process; PDB: 1ZRT_R 2QJY_R 2FYN_L 2QJK_O 2QJP_I 2YIU_F.
Probab=29.37 E-value=53 Score=21.57 Aligned_cols=20 Identities=10% Similarity=0.056 Sum_probs=10.3
Q ss_pred cCCchhHHHHHHHHHHHHHh
Q 030417 56 RGTDGRRAAMALLAVTLFTT 75 (177)
Q Consensus 56 ~~~~gRRaal~~LAa~l~~t 75 (177)
....+||-.|...++++++.
T Consensus 6 ~~~~~RRdFL~~at~~~gav 25 (41)
T PF10399_consen 6 PVDPTRRDFLTIATSAVGAV 25 (41)
T ss_dssp ----HHHHHHHHHHHHHHHH
T ss_pred CCCchHHHHHHHHHHHHHHH
Confidence 33467888876666555443
No 21
>KOG3052 consensus Cytochrome c1 [Energy production and conversion]
Probab=28.33 E-value=10 Score=34.41 Aligned_cols=50 Identities=24% Similarity=0.427 Sum_probs=33.1
Q ss_pred cccchheeeeeccccchhhhhhhhhcccc--------cccccceEeeeecCCccccee
Q 030417 113 ANFARAYTVQFGTCKKCHSSRMIWNWSAK--------GKINTSVVPMFSGNGEVGQLI 162 (177)
Q Consensus 113 ANfaRayTV~fGtCk~c~~~~~i~~~~~k--------~~~~ts~v~mfsgnge~~q~~ 162 (177)
+-..|-|+||--.|--||++.-|---+.- +|.-..-+-+-.|-.|++..|
T Consensus 93 aSiRRGyqVYkqVCaaCHSm~~iayR~lVgv~~Te~EaKa~A~eiev~Dgpdd~G~~~ 150 (311)
T KOG3052|consen 93 ASIRRGYQVYKQVCAACHSMDLIAYRHLVGVCYTEEEAKAMAAEIEVVDGPDDEGEMF 150 (311)
T ss_pred HHHhhhHHHHHHHHHHhhhhHHHHHHhhhhhhccHHHHHHhhhheeeccCCCCCCCcc
Confidence 45689999999999999999877433322 233334455556665655444
No 22
>PF14285 DUF4367: Domain of unknown function (DUF4367)
Probab=27.03 E-value=79 Score=23.08 Aligned_cols=31 Identities=26% Similarity=0.314 Sum_probs=15.9
Q ss_pred hhHHHHHHHHHHHHHhhhhccccccchhhHH
Q 030417 60 GRRAAMALLAVTLFTTATAAASSSANAGVID 90 (177)
Q Consensus 60 gRRaal~~LAa~l~~tAa~a~a~~A~Agvie 90 (177)
.||.|++++|+.+...++...+...+..+++
T Consensus 2 ~~r~a~~~~a~~i~~~~~~~t~~a~~~~~~~ 32 (168)
T PF14285_consen 2 RKRAAVAAAAVIILVFAASMTVQAVREKVYN 32 (168)
T ss_pred hHHHHHHHHHHHHHHHhHhEEehHHhHHHHh
Confidence 3566666665555544444444433455554
No 23
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=26.27 E-value=29 Score=22.71 Aligned_cols=14 Identities=43% Similarity=0.795 Sum_probs=11.2
Q ss_pred eeeeccccchhhhh
Q 030417 120 TVQFGTCKKCHSSR 133 (177)
Q Consensus 120 TV~fGtCk~c~~~~ 133 (177)
.|..|+|.+||-..
T Consensus 19 ~v~~~~C~gC~~~l 32 (56)
T PF02591_consen 19 RVEGGTCSGCHMEL 32 (56)
T ss_pred EeeCCccCCCCEEc
Confidence 57889999999643
No 24
>PRK14139 heat shock protein GrpE; Provisional
Probab=22.71 E-value=26 Score=29.04 Aligned_cols=23 Identities=26% Similarity=0.276 Sum_probs=10.2
Q ss_pred HHhhhhhhhhhh-hhhcccccccc
Q 030417 94 ERSKANKELNDQ-KRLATSGANFA 116 (177)
Q Consensus 94 ~KSkaNKELNDK-KRLaTs~ANfa 116 (177)
+.-+..+||.|+ .|+..--.||.
T Consensus 43 ~le~e~~elkd~~lR~~AefeN~r 66 (185)
T PRK14139 43 EAEAKAAELQDSFLRAKAETENVR 66 (185)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334445555444 34444444443
No 25
>PRK09133 hypothetical protein; Provisional
Probab=22.36 E-value=62 Score=28.21 Aligned_cols=26 Identities=38% Similarity=0.331 Sum_probs=11.2
Q ss_pred HHHHHHHHHHhhhhccccccchhhHH
Q 030417 65 MALLAVTLFTTATAAASSSANAGVID 90 (177)
Q Consensus 65 l~~LAa~l~~tAa~a~a~~A~Agvie 90 (177)
|.+||++..+.|+++.++.+.+.--+
T Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 (472)
T PRK09133 12 LALLAAAAATGAAAAAAPAAPTADQQ 37 (472)
T ss_pred HHHhhccchhhhhhhcCCCCcchhHH
Confidence 34444444444444444444443333
No 26
>PF11022 DUF2611: Protein of unknown function (DUF2611); InterPro: IPR021278 This family is conserved in the Dikarya of Fungi. The function is not known.
Probab=21.97 E-value=1.6e+02 Score=21.50 Aligned_cols=15 Identities=20% Similarity=0.457 Sum_probs=11.0
Q ss_pred hhhHHHHHHHhhhhh
Q 030417 86 AGVIDEYLERSKANK 100 (177)
Q Consensus 86 AgviedyL~KSkaNK 100 (177)
...|+|||++-++-+
T Consensus 54 E~fIk~fl~~~~~e~ 68 (71)
T PF11022_consen 54 EKFIKEFLKEHEKEE 68 (71)
T ss_pred HHHHHHHHHHHHHhh
Confidence 468999998876543
No 27
>PF15240 Pro-rich: Proline-rich
Probab=21.63 E-value=57 Score=27.54 Aligned_cols=25 Identities=28% Similarity=0.465 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHhhhhccccccchhhHHH
Q 030417 64 AMALLAVTLFTTATAAASSSANAGVIDE 91 (177)
Q Consensus 64 al~~LAa~l~~tAa~a~a~~A~Agvied 91 (177)
||+||.+||++- .+|-..+-+|..|
T Consensus 2 LlVLLSvALLAL---SSAQ~~dEdv~~e 26 (179)
T PF15240_consen 2 LLVLLSVALLAL---SSAQSTDEDVSQE 26 (179)
T ss_pred hhHHHHHHHHHh---hhccccccccccc
Confidence 677777777754 4555566666543
No 28
>PRK07474 sulfur oxidation protein SoxY; Provisional
Probab=21.33 E-value=1.4e+02 Score=24.29 Aligned_cols=37 Identities=24% Similarity=0.291 Sum_probs=18.2
Q ss_pred chhHHHHHHHHHHHHHhhhhccccccchhhHHHHHHH
Q 030417 59 DGRRAAMALLAVTLFTTATAAASSSANAGVIDEYLER 95 (177)
Q Consensus 59 ~gRRaal~~LAa~l~~tAa~a~a~~A~AgviedyL~K 95 (177)
-+||.+|.+.++.+..++..+....|.+.=++|.++.
T Consensus 8 ~~rr~~l~~~~~~~~~~~~~~~~~~a~~~~~~~a~~~ 44 (154)
T PRK07474 8 LSRRQALALGGGALAAAVLPPRAAPARAAAVDAAIRK 44 (154)
T ss_pred cCHHHHHHHHHHHHHHHhccccccccchhhHHHHHHH
Confidence 5788887776554444432222224443333444443
No 29
>TIGR03045 PS_II_C550 cytochrome c-550. Members of this protein family are cytochrome c-550, the PsbV extrinsic protein of photosystem II, from both Cyanobacteria and chloroplasts. A paralog to this protein, PsbV2, is found in some species in addition to PsbV itself.
Probab=21.06 E-value=26 Score=28.50 Aligned_cols=65 Identities=23% Similarity=0.375 Sum_probs=33.9
Q ss_pred hHHHHHHHHHHHHHhhhhccccccchhhHHHHHHHhhhhhhhhhh-hhhcccccccchheeeeeccccchhh
Q 030417 61 RRAAMALLAVTLFTTATAAASSSANAGVIDEYLERSKANKELNDQ-KRLATSGANFARAYTVQFGTCKKCHS 131 (177)
Q Consensus 61 RRaal~~LAa~l~~tAa~a~a~~A~AgviedyL~KSkaNKELNDK-KRLaTs~ANfaRayTV~fGtCk~c~~ 131 (177)
||.+...++..++.-. ...++|.|.-++| .+.. =.||+. +-..-|..+.++=..++.-.|..||.
T Consensus 2 ~~~~~~~~~~~~~~~~--~~~~~~~a~~~~~---~~~t-~~~~~~g~~~~~~~~~~~~Gk~lF~~~Ca~CH~ 67 (159)
T TIGR03045 2 RKSFWRLLALLLLLIQ--LNVGPAQAAELDE---ETRT-VPLNSTGETVTLTEEQVKRGKRLFNTACGTCHV 67 (159)
T ss_pred hhHHHHHHHHHHHHHH--HccchHHHHhccc---ccce-eeecCCCCeEEeChHhHHHHHHHHHHHHHHhCC
Confidence 3444444444333332 2345555554444 1111 123443 44444566677777776678999995
No 30
>CHL00183 petJ cytochrome c553; Provisional
Probab=20.69 E-value=1.4e+02 Score=21.15 Aligned_cols=9 Identities=33% Similarity=1.136 Sum_probs=7.0
Q ss_pred ccccchhhh
Q 030417 124 GTCKKCHSS 132 (177)
Q Consensus 124 GtCk~c~~~ 132 (177)
-.|..||..
T Consensus 35 ~~Ca~CHg~ 43 (108)
T CHL00183 35 ANCAACHAG 43 (108)
T ss_pred HHHHHHCCC
Confidence 359999973
No 31
>COG3245 CycB Cytochrome c5 [Energy production and conversion]
Probab=20.36 E-value=52 Score=26.77 Aligned_cols=15 Identities=33% Similarity=0.673 Sum_probs=12.3
Q ss_pred heeeeeccccchhhh
Q 030417 118 AYTVQFGTCKKCHSS 132 (177)
Q Consensus 118 ayTV~fGtCk~c~~~ 132 (177)
--+||.-+|+-||.-
T Consensus 50 Gk~vy~~tC~~CHa~ 64 (126)
T COG3245 50 GKKVYGATCQACHAA 64 (126)
T ss_pred cchhHhhhhhHhccC
Confidence 346889999999974
Done!