Query psy13005
Match_columns 130
No_of_seqs 101 out of 183
Neff 5.5
Searched_HMMs 46136
Date Fri Aug 16 16:43:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13005.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13005hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08510 PIG-P: PIG-P; InterP 100.0 1.1E-49 2.3E-54 292.1 11.6 115 10-125 1-126 (126)
2 KOG2257|consensus 100.0 1.1E-42 2.4E-47 256.7 9.6 123 6-129 1-130 (135)
3 PF07297 DPM2: Dolichol phosph 97.8 0.00014 3.1E-09 49.9 7.1 63 14-81 5-72 (78)
4 KOG3488|consensus 95.2 0.092 2E-06 35.8 5.9 66 14-82 7-75 (81)
5 TIGR01332 cyt_b559_alpha cytoc 80.3 0.33 7.2E-06 33.3 -1.0 37 51-89 16-55 (80)
6 PRK02557 psbE cytochrome b559 79.6 0.33 7.2E-06 33.4 -1.2 37 51-89 17-56 (81)
7 CHL00064 psbE photosystem II p 79.1 0.31 6.8E-06 33.6 -1.4 38 51-90 17-57 (83)
8 PF05545 FixQ: Cbb3-type cytoc 66.9 8.1 0.00017 23.5 2.9 27 13-39 8-34 (49)
9 PF03475 3-alpha: 3-alpha doma 58.4 7 0.00015 23.5 1.5 16 113-128 1-16 (47)
10 KOG4455|consensus 56.2 15 0.00032 26.8 3.0 43 13-62 48-90 (110)
11 PRK10633 hypothetical protein; 47.3 70 0.0015 21.9 5.2 55 21-87 17-76 (80)
12 PF06916 DUF1279: Protein of u 46.9 27 0.00059 23.8 3.2 30 49-79 6-35 (91)
13 PF00283 Cytochrom_B559: Cytoc 40.9 23 0.00049 20.0 1.6 14 51-64 12-28 (29)
14 PF09930 DUF2162: Predicted tr 40.3 79 0.0017 25.5 5.3 56 14-72 65-120 (224)
15 cd01324 cbb3_Oxidase_CcoQ Cyto 37.9 48 0.001 20.3 2.9 17 23-39 19-35 (48)
16 PF04341 DUF485: Protein of un 35.9 49 0.0011 22.6 3.1 22 14-35 57-78 (91)
17 PF11874 DUF3394: Domain of un 34.0 25 0.00054 27.6 1.5 19 49-68 155-173 (183)
18 PF07853 DUF1648: Protein of u 33.4 1E+02 0.0022 18.5 3.9 38 25-62 7-49 (51)
19 PF14163 SieB: Superinfection 32.8 2E+02 0.0042 21.0 6.3 18 35-52 14-31 (151)
20 PF14089 KbaA: KinB-signalling 31.9 1.1E+02 0.0023 24.2 4.7 44 14-66 38-82 (180)
21 COG4988 CydD ABC-type transpor 26.7 38 0.00082 31.0 1.6 36 48-85 117-152 (559)
22 PRK14750 kdpF potassium-transp 26.2 65 0.0014 18.1 1.9 16 62-78 10-25 (29)
23 PF15102 TMEM154: TMEM154 prot 26.1 84 0.0018 24.0 3.1 26 104-129 115-140 (146)
24 PF13687 DUF4153: Domain of un 24.5 2.7E+02 0.0058 21.5 5.8 24 43-68 150-173 (217)
25 PRK12438 hypothetical protein; 24.3 4.9E+02 0.011 25.7 8.5 39 39-80 44-82 (991)
26 PF03994 DUF350: Domain of Unk 24.1 77 0.0017 19.3 2.2 31 61-94 1-31 (54)
27 PF09591 DUF2463: Protein of u 23.0 2.6E+02 0.0056 22.6 5.5 26 47-72 172-204 (210)
28 PRK12721 secretion system appa 22.9 1.2E+02 0.0025 26.0 3.7 24 1-24 1-38 (349)
29 PF05817 Ribophorin_II: Oligos 22.3 3.6E+02 0.0078 25.0 7.0 71 6-83 541-611 (636)
30 PRK06298 type III secretion sy 21.6 1.3E+02 0.0028 25.8 3.8 23 1-23 1-37 (356)
31 PF11014 DUF2852: Protein of u 20.7 1.3E+02 0.0027 22.1 3.1 21 14-34 16-36 (115)
No 1
>PF08510 PIG-P: PIG-P; InterPro: IPR013717 PIG-P (phosphatidylinositol N-acetylglucosaminyltransferase subunit P) is an enzyme involved in GPI anchor biosynthesis [].
Probab=100.00 E-value=1.1e-49 Score=292.08 Aligned_cols=115 Identities=42% Similarity=0.784 Sum_probs=107.1
Q ss_pred CCchhhHHHHHHHHHHHHHHHHHhhccChHHHHHcCccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCc
Q psy13005 10 PSRANNGFVLYLASTIMFVVYLIWAFIPDSILYYFGLTYLPQKYWAIAVPIYGMVLLFVFVMFFYPCINMSLTPVRDSPN 89 (130)
Q Consensus 10 ~~re~yGFv~~i~s~~~~~lyl~Wa~lP~~~L~~lgity~P~kyWalaiP~~~l~~~~~~~~~~y~~~n~~~T~plds~~ 89 (130)
|+||+|||++|++|+++|++|++||++||++||++|+|||||||||+|+|+|++|+++++|++ |.++|+++|+|+||++
T Consensus 1 p~~e~YGFv~~i~s~~~~~lyl~Wa~lP~~~L~~lgity~P~kyWAlaiP~~~l~~~l~~~~~-y~~~N~~~T~pld~~~ 79 (126)
T PF08510_consen 1 PSREYYGFVLYILSTVAFVLYLLWAFLPDEWLHSLGITYYPDKYWALAIPSWLLMAMLFTYVG-YPAYNLVLTPPLDSLR 79 (126)
T ss_pred CCceeeehHHHHHHHHHHHHHHHHHhcCHHHHHhcCccccCcchHHHHHHHHHHHHHHHHHHH-HHHHHHhcCCCCCccc
Confidence 799999999999999999999999999999999999999999999999999999999999999 9999999999999999
Q ss_pred ccccCCCccc-c-------CCCCC---CCCCCcccCCHHHHHHHHhc
Q psy13005 90 VMIDSFSLSD-K-------KETVP---GGIPSACDIPISTVCEMLYL 125 (130)
Q Consensus 90 tI~D~~a~~~-~-------~~~~~---~~ip~i~DlPi~~Vn~~LY~ 125 (130)
||+|++++.. . ++... +++|+++||||++|||+||+
T Consensus 80 ti~D~~~~~~~~~~~~~~~~~~~~~~~~~ip~i~Dlpi~~Vn~~Ly~ 126 (126)
T PF08510_consen 80 TITDEYARVPDEDDDSSFEDENAFKEKKPIPPIRDLPITEVNRVLYG 126 (126)
T ss_pred eeeccccccccccccccccccccccccCCCCCCccCCHHHHHHHHcC
Confidence 9999999876 1 11111 46999999999999999996
No 2
>KOG2257|consensus
Probab=100.00 E-value=1.1e-42 Score=256.67 Aligned_cols=123 Identities=39% Similarity=0.646 Sum_probs=115.8
Q ss_pred CCCCCCchhhHHHHHHHHHHHHHHHHHhhccChHHHHHcCccccccchhHHHHHHHHHHHHHHHHHHHHHHHHh-hcCCC
Q psy13005 6 PSPTPSRANNGFVLYLASTIMFVVYLIWAFIPDSILYYFGLTYLPQKYWAIAVPIYGMVLLFVFVMFFYPCINM-SLTPV 84 (130)
Q Consensus 6 p~p~~~re~yGFv~~i~s~~~~~lyl~Wa~lP~~~L~~lgity~P~kyWalaiP~~~l~~~~~~~~~~y~~~n~-~~T~p 84 (130)
|.|.|+||+||||+|+.++++|++|++||++|+++|+++||+|+||||||+|+|+|++|++++++++ +.++|. ..|+|
T Consensus 1 ~~~~~t~e~YgF~~yiv~~~~~ViylIWai~P~~~l~~~gi~y~Psk~WalAip~~l~v~~l~~~v~-ll~~N~e~tt~p 79 (135)
T KOG2257|consen 1 PGPHPTREYYGFVLYIVSWTLFVIYLIWAITPVPILESLGITYYPSKYWALAIPTYLLVAVLLAYVF-LLGYNFESTTKP 79 (135)
T ss_pred CCCCCcceehhhHHHHHHHHHHHHHHHhhcccHHHHhhcCceeehHHHHHHHHHHHHHHHHHHHHHH-HHhcCccccCCC
Confidence 5688999999999999999999999999999999999999999999999999999999999999999 999998 56669
Q ss_pred CCCCcccccCCCccc------cCCCCCCCCCCcccCCHHHHHHHHhccCCC
Q psy13005 85 RDSPNVMIDSFSLSD------KKETVPGGIPSACDIPISTVCEMLYLKNKK 129 (130)
Q Consensus 85 lds~~tI~D~~a~~~------~~~~~~~~ip~i~DlPi~~Vn~~LY~~~~~ 129 (130)
+||++|++|+++++. .++..+++++++.|+.+++|||.+|..+++
T Consensus 80 l~Sl~ti~D~y~r~~~e~~v~~kk~~~~a~~~i~Di~isevn~l~~~s~~~ 130 (135)
T KOG2257|consen 80 LDSLNTITDSYAREIQEFAVKMKKGEDRAIDGISDIRISEVNQLQLNSGDL 130 (135)
T ss_pred CcchhhhhhhhhhccchhHHHHhhcccCcCCCcccccHHHHHHHHHhcccc
Confidence 999999999999985 467889999999999999999999987654
No 3
>PF07297 DPM2: Dolichol phosphate-mannose biosynthesis regulatory protein (DPM2); InterPro: IPR009914 This family consists of several eukaryotic dolichol phosphate-mannose biosynthesis regulatory (DPM2) proteins. Biosynthesis of glycosylphosphatidylinositol and N-glycan precursor is dependent upon a mannosyl donor, dolichol phosphate-mannose (DPM). DPM2, an 84 amino acid membrane protein expressed in the endoplasmic reticulum (ER), makes a complex with DPM1 that is essential for the ER localisation and stable expression of DPM1. Moreover, DPM2 enhances binding of dolichol phosphate, a substrate of DPM synthase. Biosynthesis of DPM in mammalian cells is regulated by DPM2 [].; GO: 0009059 macromolecule biosynthetic process, 0030176 integral to endoplasmic reticulum membrane
Probab=97.78 E-value=0.00014 Score=49.85 Aligned_cols=63 Identities=22% Similarity=0.430 Sum_probs=48.0
Q ss_pred hhHHHHHHHHHHHHHHHHHhhc-cC----hHHHHHcCccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy13005 14 NNGFVLYLASTIMFVVYLIWAF-IP----DSILYYFGLTYLPQKYWAIAVPIYGMVLLFVFVMFFYPCINMSL 81 (130)
Q Consensus 14 ~yGFv~~i~s~~~~~lyl~Wa~-lP----~~~L~~lgity~P~kyWalaiP~~~l~~~~~~~~~~y~~~n~~~ 81 (130)
.=|++.-..+++.|+-|.+|.+ +| |+.+|+ |+|.|.||+.+|..+++..+ ..++.+.++-+..
T Consensus 5 ~vG~~~l~~a~~vF~YYt~WvlllPFvd~d~~i~~----~F~Pr~yAi~lP~~lll~~~-~~vg~f~g~vmik 72 (78)
T PF07297_consen 5 LVGLLMLAVALSVFTYYTIWVLLLPFVDEDHPIHS----FFPPREYAIILPIFLLLLGL-SGVGTFLGYVMIK 72 (78)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcccCCCchHHH----cCCCHHHHHHHHHHHHHHHH-HHHHHHHHHHHhh
Confidence 3589999999999999999985 43 346664 79999999999999887655 4444366665544
No 4
>KOG3488|consensus
Probab=95.15 E-value=0.092 Score=35.77 Aligned_cols=66 Identities=21% Similarity=0.468 Sum_probs=43.4
Q ss_pred hhHHHHHHHHHHHHHHHHHhhc-cChHHHHHcCc--cccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Q psy13005 14 NNGFVLYLASTIMFVVYLIWAF-IPDSILYYFGL--TYLPQKYWAIAVPIYGMVLLFVFVMFFYPCINMSLT 82 (130)
Q Consensus 14 ~yGFv~~i~s~~~~~lyl~Wa~-lP~~~L~~lgi--ty~P~kyWalaiP~~~l~~~~~~~~~~y~~~n~~~T 82 (130)
.-|--.--.|...|.-|-+|.. +| +.++..+ .|+-+|.||+++|.......++. ++.+.++-+..+
T Consensus 7 ~vgl~lv~iSl~iFtYYT~WViilP--FvDs~hiihKyFLpr~yAi~iPvaagl~ll~l-ig~Fis~vMlKs 75 (81)
T KOG3488|consen 7 VVGLMLVYISLAIFTYYTIWVIILP--FVDSMHIIHKYFLPREYAITIPVAAGLFLLCL-IGTFISLVMLKS 75 (81)
T ss_pred hhhHHHHHHHHHHHHHHHHHHhhhc--ccchhHHHHHHhcChhHHhhhHHHHHHHHHHH-HHHHHHHHhhhc
Confidence 3455566678888999999987 45 3333222 38889999999998876655533 333555555443
No 5
>TIGR01332 cyt_b559_alpha cytochrome b559, alpha subunit. Sequences scoring between trusted and noise cutoffs are fragments.
Probab=80.35 E-value=0.33 Score=33.30 Aligned_cols=37 Identities=16% Similarity=0.223 Sum_probs=29.4
Q ss_pred cchh---HHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCc
Q psy13005 51 QKYW---AIAVPIYGMVLLFVFVMFFYPCINMSLTPVRDSPN 89 (130)
Q Consensus 51 ~kyW---alaiP~~~l~~~~~~~~~~y~~~n~~~T~plds~~ 89 (130)
-||| +|.||++++.+.+|...+ .+|+..-||..|..-
T Consensus 16 iRYWvIHsITIPsLFiaGwLFVstG--LAYdvFGtPrpneYf 55 (80)
T TIGR01332 16 IRYWVIHSITIPMLFIAGWLFVSTG--LAYDAFGTPRPNEYF 55 (80)
T ss_pred eeEEEEEeechhHHHhhhhheeecC--cceeccCCCCccccc
Confidence 3788 479999999999988776 678788888876543
No 6
>PRK02557 psbE cytochrome b559 subunit alpha; Provisional
Probab=79.60 E-value=0.33 Score=33.37 Aligned_cols=37 Identities=22% Similarity=0.228 Sum_probs=29.3
Q ss_pred cchh---HHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCc
Q psy13005 51 QKYW---AIAVPIYGMVLLFVFVMFFYPCINMSLTPVRDSPN 89 (130)
Q Consensus 51 ~kyW---alaiP~~~l~~~~~~~~~~y~~~n~~~T~plds~~ 89 (130)
-||| +|.||++++.+.+|...+ .+|+..-||..|..-
T Consensus 17 iRYWvIHsITIPsLFiaGwLFVstG--LAYdvFGtPrpneYf 56 (81)
T PRK02557 17 IRYWVIHAITIPALFIAGWLFVSTG--LAYDAFGTPRPDEYF 56 (81)
T ss_pred eeEEEEEeechhHHHhhhhheeecC--ceeeccCCCCccccc
Confidence 3888 479999999999988776 677778888876543
No 7
>CHL00064 psbE photosystem II protein V
Probab=79.13 E-value=0.31 Score=33.65 Aligned_cols=38 Identities=13% Similarity=0.191 Sum_probs=29.9
Q ss_pred cchh---HHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCcc
Q psy13005 51 QKYW---AIAVPIYGMVLLFVFVMFFYPCINMSLTPVRDSPNV 90 (130)
Q Consensus 51 ~kyW---alaiP~~~l~~~~~~~~~~y~~~n~~~T~plds~~t 90 (130)
-||| +|.||++++.+.+|...+ .+|+..-||..|..-+
T Consensus 17 iRYWvIHsITIPslFiaGwLFVstG--LAYdvFGtPrpneYft 57 (83)
T CHL00064 17 IRYWVIHSITIPSLFIAGWLFVSTG--LAYDVFGSPRPNEYFT 57 (83)
T ss_pred eeeEEEEeechhHHHhhchheeecC--cceeccCCCCcccccc
Confidence 3888 479999999999988776 6788888888765433
No 8
>PF05545 FixQ: Cbb3-type cytochrome oxidase component FixQ; InterPro: IPR008621 This family consists of several Cbb3-type cytochrome oxidase components (FixQ/CcoQ). FixQ is found in nitrogen fixing bacteria. Since nitrogen fixation is an energy-consuming process, effective symbioses depend on operation of a respiratory chain with a high affinity for O2, closely coupled to ATP production. This requirement is fulfilled by a special three-subunit terminal oxidase (cytochrome terminal oxidase cbb3), which was first identified in Bradyrhizobium japonicum as the product of the fixNOQP operon [].
Probab=66.94 E-value=8.1 Score=23.47 Aligned_cols=27 Identities=19% Similarity=0.369 Sum_probs=19.7
Q ss_pred hhhHHHHHHHHHHHHHHHHHhhccChH
Q psy13005 13 ANNGFVLYLASTIMFVVYLIWAFIPDS 39 (130)
Q Consensus 13 e~yGFv~~i~s~~~~~lyl~Wa~lP~~ 39 (130)
+......=++..+.|+.+++|++-|.+
T Consensus 8 ~~~~~~~~v~~~~~F~gi~~w~~~~~~ 34 (49)
T PF05545_consen 8 GFARSIGTVLFFVFFIGIVIWAYRPRN 34 (49)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcccc
Confidence 444555556667778888999999984
No 9
>PF03475 3-alpha: 3-alpha domain; InterPro: IPR005163 This small triple helical domain has been predicted to assume a topology similar to helix-turn-helix domains. These domains are found at the C terminus of proteins related to the YiiM protein (P32157 from SWISSPROT) from Escherichia coli.; PDB: 1O67_C 1O65_C.
Probab=58.38 E-value=7 Score=23.50 Aligned_cols=16 Identities=19% Similarity=0.385 Sum_probs=12.1
Q ss_pred cCCHHHHHHHHhccCC
Q psy13005 113 DIPISTVCEMLYLKNK 128 (130)
Q Consensus 113 DlPi~~Vn~~LY~~~~ 128 (130)
|++|..||+.+|.+..
T Consensus 1 ~~tV~~~~~~~~~~~~ 16 (47)
T PF03475_consen 1 EWTVARVNRLLYHDRL 16 (47)
T ss_dssp S-BHHHHHHHHHTS--
T ss_pred CCCHHHHHHHHhCCCC
Confidence 6899999999999763
No 10
>KOG4455|consensus
Probab=56.17 E-value=15 Score=26.81 Aligned_cols=43 Identities=14% Similarity=0.314 Sum_probs=26.0
Q ss_pred hhhHHHHHHHHHHHHHHHHHhhccChHHHHHcCccccccchhHHHHHHHH
Q psy13005 13 ANNGFVLYLASTIMFVVYLIWAFIPDSILYYFGLTYLPQKYWAIAVPIYG 62 (130)
Q Consensus 13 e~yGFv~~i~s~~~~~lyl~Wa~lP~~~L~~lgity~P~kyWalaiP~~~ 62 (130)
.++||+.|+++.+...++++|--= -+|. .||++|+ -+-.-.++
T Consensus 48 g~~GFi~Y~l~~~i~~il~~~K~~-~~~~-----kyf~s~~-~~f~~~f~ 90 (110)
T KOG4455|consen 48 GLHGFIFYFLSVLILSILLVLKAG-GQWG-----KYFQSRR-NLFTESFL 90 (110)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHC-CCHH-----hhcCchh-HHHHHHHh
Confidence 579999999996665555554210 0111 3788887 55554444
No 11
>PRK10633 hypothetical protein; Provisional
Probab=47.28 E-value=70 Score=21.94 Aligned_cols=55 Identities=9% Similarity=0.220 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHhhccChHHHHHcCccccccchhHHHHHHHHHHHHHHHHHH----HHHHHHh-hcCCCCCC
Q psy13005 21 LASTIMFVVYLIWAFIPDSILYYFGLTYLPQKYWAIAVPIYGMVLLFVFVMF----FYPCINM-SLTPVRDS 87 (130)
Q Consensus 21 i~s~~~~~lyl~Wa~lP~~~L~~lgity~P~kyWalaiP~~~l~~~~~~~~~----~y~~~n~-~~T~plds 87 (130)
.++.+-|+.+.+.||+|++-. | ..-+|.|+.++++...++ ++..... ..--||||
T Consensus 17 ~L~l~y~~~W~~~aY~~~~~~---~---------i~GlP~WF~~sCi~~p~lfi~l~~~~Vk~vFkDi~Ld~ 76 (80)
T PRK10633 17 GLTLLYLAAWLVAAYLPGNAP---G---------FTGLPHWFEMACLLLPLLFILLCWLMVKFIFRDIPLED 76 (80)
T ss_pred HHHHHHHHHHHHHHhccCCCC---c---------ccCCcHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCC
Confidence 345556677788888887632 2 345677777766543222 1333333 45556654
No 12
>PF06916 DUF1279: Protein of unknown function (DUF1279); InterPro: IPR009688 This entry represents the C terminus (approx. 120 residues) of a number of eukaryotic proteins of unknown function.
Probab=46.88 E-value=27 Score=23.80 Aligned_cols=30 Identities=20% Similarity=0.246 Sum_probs=24.0
Q ss_pred cccchhHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy13005 49 LPQKYWAIAVPIYGMVLLFVFVMFFYPCINM 79 (130)
Q Consensus 49 ~P~kyWalaiP~~~l~~~~~~~~~~y~~~n~ 79 (130)
+=.|||.++++.++.+..+.+..+ |.+...
T Consensus 6 l~k~YG~~~l~vy~~~s~~~~~~~-y~~v~~ 35 (91)
T PF06916_consen 6 LFKKYGYVALGVYLGLSFISLGSC-YLAVSS 35 (91)
T ss_pred HHHHhCHhHHHHHHHHHHHHHHHH-HHHHHh
Confidence 346899999999999998877666 776644
No 13
>PF00283 Cytochrom_B559: Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits; InterPro: IPR013081 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 []. Cytochrome b559, which forms part of the reaction centre core of PSII is a heterodimer composed of one alpha subunit (PsbE), one beta (PsbF) subunit, and a haem cofactor. Two histidine residues from each subunit coordinate the haem. Although cytochrome b559 is a redox-active protein, it is unlikely to be involved in the primary electron transport in PSII due to its very slow photo-oxidation and photo-reduction kinetics. Instead, cytochrome b559 could participate in a secondary electron transport pathway that helps protect PSII from photo-damage. Cytochrome b559 is essential for PSII assembly []. This domain occurs in both the alpha and beta subunits of cytochrome B559. In the alpha sbunit it occurs together with a lumenal domain (IPR013082 from INTERPRO), while in the beta subunit it occurs on its own.; GO: 0046872 metal ion binding, 0015979 photosynthesis, 0009523 photosystem II, 0009536 plastid, 0009579 thylakoid, 0016021 integral to membrane; PDB: 3ARC_f 3A0H_f 3A0B_f 1W5C_K 1S5L_e 3BZ2_E 3PRQ_E 1IZL_P 2AXT_E 4FBY_R ....
Probab=40.92 E-value=23 Score=20.01 Aligned_cols=14 Identities=21% Similarity=0.774 Sum_probs=9.4
Q ss_pred cchhH---HHHHHHHHH
Q psy13005 51 QKYWA---IAVPIYGMV 64 (130)
Q Consensus 51 ~kyWa---laiP~~~l~ 64 (130)
-|||+ +++|+.++.
T Consensus 12 vR~~~IH~l~iPtvf~~ 28 (29)
T PF00283_consen 12 VRWWAIHALTIPTVFFL 28 (29)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred EeeeeeeecccceEEec
Confidence 37775 578887654
No 14
>PF09930 DUF2162: Predicted transporter (DUF2162); InterPro: IPR017199 This group represents a predicted membrane transporter, MTH672 type.
Probab=40.27 E-value=79 Score=25.46 Aligned_cols=56 Identities=14% Similarity=0.253 Sum_probs=40.4
Q ss_pred hhHHHHHHHHHHHHHHHHHhhccChHHHHHcCccccccchhHHHHHHHHHHHHHHHHHH
Q psy13005 14 NNGFVLYLASTIMFVVYLIWAFIPDSILYYFGLTYLPQKYWAIAVPIYGMVLLFVFVMF 72 (130)
Q Consensus 14 ~yGFv~~i~s~~~~~lyl~Wa~lP~~~L~~lgity~P~kyWalaiP~~~l~~~~~~~~~ 72 (130)
-||++.|++-.+..+.+=+|.. ++|-+. |=+.-....||+.+||=.+.+.+++-..
T Consensus 65 ~yg~~~h~imal~li~~Gi~ti--~~W~~~-~~~~s~~t~lal~~PCPvCl~Ai~~S~~ 120 (224)
T PF09930_consen 65 RYGMVIHLIMALLLIYAGIYTI--KKWKKS-GKDSSRRTFLALSLPCPVCLTAIFFSIM 120 (224)
T ss_pred HHhHHHHHHHHHHHHHHHHHHH--HHHccc-CCCCcccchhhhhcCchHHHHHHHHHHH
Confidence 4888888888777777666666 677554 5566677789999999777766644333
No 15
>cd01324 cbb3_Oxidase_CcoQ Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. Found exclusively in proteobacteria, cbb3 is believed to be a modern enzyme that has evolved independently to perform a specialized function in microaerobic energy metabolism. The cbb3 operon contains four genes (ccoNOQP or fixNOQP), with ccoN coding for subunit I. Instead of a CuA-containing subunit II analogous to other cytochrome oxidases, cbb3 utilizes subunits ccoO and ccoP, which contain one and two hemes, respectively, to transfer electrons to the binuclear center. ccoQ, the fourth subunit, is a single transmembrane helix protein. It has been shown to protect the core complex from proteolytic degradation by serine proteases. See cd00919, cd01322
Probab=37.90 E-value=48 Score=20.35 Aligned_cols=17 Identities=29% Similarity=0.802 Sum_probs=13.1
Q ss_pred HHHHHHHHHHhhccChH
Q psy13005 23 STIMFVVYLIWAFIPDS 39 (130)
Q Consensus 23 s~~~~~lyl~Wa~lP~~ 39 (130)
..+.|+.-++|||-|.+
T Consensus 19 ~~~~Figiv~wa~~p~~ 35 (48)
T cd01324 19 LALFFLGVVVWAFRPGR 35 (48)
T ss_pred HHHHHHHHHHHHhCCCc
Confidence 35677778899999974
No 16
>PF04341 DUF485: Protein of unknown function, DUF485; InterPro: IPR007436 This family includes several putative integral membrane proteins.
Probab=35.95 E-value=49 Score=22.58 Aligned_cols=22 Identities=14% Similarity=0.043 Sum_probs=20.2
Q ss_pred hhHHHHHHHHHHHHHHHHHhhc
Q psy13005 14 NNGFVLYLASTIMFVVYLIWAF 35 (130)
Q Consensus 14 ~yGFv~~i~s~~~~~lyl~Wa~ 35 (130)
.+|++.++.+++...+|..||=
T Consensus 57 ~~g~~~~~~~~~l~~~Yv~~An 78 (91)
T PF04341_consen 57 VLGLGQIVFAWVLTWLYVRRAN 78 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHHHc
Confidence 5999999999999999999884
No 17
>PF11874 DUF3394: Domain of unknown function (DUF3394); InterPro: IPR021814 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 190 amino acids in length. This domain is found associated with PF06808 from PFAM.
Probab=33.98 E-value=25 Score=27.63 Aligned_cols=19 Identities=26% Similarity=0.539 Sum_probs=15.9
Q ss_pred cccchhHHHHHHHHHHHHHH
Q psy13005 49 LPQKYWAIAVPIYGMVLLFV 68 (130)
Q Consensus 49 ~P~kyWalaiP~~~l~~~~~ 68 (130)
=|.|+| +.+|++++.+++.
T Consensus 155 rp~ke~-~yiPAlLLL~lv~ 173 (183)
T PF11874_consen 155 RPPKEW-VYIPALLLLGLVA 173 (183)
T ss_pred CCCcce-EeHHHHHHHHHHH
Confidence 488999 9999999888763
No 18
>PF07853 DUF1648: Protein of unknown function (DUF1648); InterPro: IPR012867 This entry contains hypothetical proteins expressed by either bacterial or archaeal species. Some of these are annotated as being transmembrane proteins, and many contain a high proportion of hydrophobic residues.
Probab=33.40 E-value=1e+02 Score=18.49 Aligned_cols=38 Identities=16% Similarity=0.253 Sum_probs=24.5
Q ss_pred HHHHHHHHhhccChHHHHHcCccc----cccch-hHHHHHHHH
Q psy13005 25 IMFVVYLIWAFIPDSILYYFGLTY----LPQKY-WAIAVPIYG 62 (130)
Q Consensus 25 ~~~~lyl~Wa~lP~~~L~~lgity----~P~ky-WalaiP~~~ 62 (130)
........|..+||+.--..|..- +=+|. ....+|...
T Consensus 7 ~~i~~~~~y~~LP~~ip~H~~~~G~~d~~~~K~~~~~~~p~l~ 49 (51)
T PF07853_consen 7 PLIITLIFYPQLPDQIPTHFNANGEPDGWGSKSFGIFLLPVLM 49 (51)
T ss_pred HHHHHHHHHHHCChhhceeeCCCCCccccccHHHHHHHHHHHH
Confidence 344455789999999776566544 44555 566666554
No 19
>PF14163 SieB: Superinfection exclusion protein B
Probab=32.79 E-value=2e+02 Score=21.00 Aligned_cols=18 Identities=33% Similarity=0.696 Sum_probs=14.4
Q ss_pred ccChHHHHHcCccccccc
Q psy13005 35 FIPDSILYYFGLTYLPQK 52 (130)
Q Consensus 35 ~lP~~~L~~lgity~P~k 52 (130)
|+|+++++.+|++-+-++
T Consensus 14 f~P~~~~~~l~l~~~~~~ 31 (151)
T PF14163_consen 14 FLPESLLEWLNLDKFEIK 31 (151)
T ss_pred HCCHHHHHHhCcchHHHh
Confidence 899999999998654443
No 20
>PF14089 KbaA: KinB-signalling pathway activation in sporulation
Probab=31.93 E-value=1.1e+02 Score=24.17 Aligned_cols=44 Identities=30% Similarity=0.545 Sum_probs=33.7
Q ss_pred hhHHHHHHHHHHHHHHHHHhhccChHHHHHcCccccccch-hHHHHHHHHHHHH
Q psy13005 14 NNGFVLYLASTIMFVVYLIWAFIPDSILYYFGLTYLPQKY-WAIAVPIYGMVLL 66 (130)
Q Consensus 14 ~yGFv~~i~s~~~~~lyl~Wa~lP~~~L~~lgity~P~ky-WalaiP~~~l~~~ 66 (130)
..|+...+.|-.+|.-|+ .+|++|+..+.++. |- +++..+++.+
T Consensus 38 ~~G~~~SviSQMGFFAYL--------t~h~~glgiFRs~~lWn-~vQ~~li~fv 82 (180)
T PF14089_consen 38 GVGFTFSVISQMGFFAYL--------TVHRFGLGIFRSKSLWN-AVQLVLIAFV 82 (180)
T ss_pred HHHHHHHHHHHHHHHHHH--------HHHHHHHHHhccHhHHH-HHHHHHHHHH
Confidence 467888888888888887 68999999999996 75 4565554433
No 21
>COG4988 CydD ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]
Probab=26.70 E-value=38 Score=30.97 Aligned_cols=36 Identities=25% Similarity=0.492 Sum_probs=28.5
Q ss_pred ccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCC
Q psy13005 48 YLPQKYWAIAVPIYGMVLLFVFVMFFYPCINMSLTPVR 85 (130)
Q Consensus 48 y~P~kyWalaiP~~~l~~~~~~~~~~y~~~n~~~T~pl 85 (130)
|+||++-++.+|..+++.++++.+. .++-++.|.|+
T Consensus 117 yLPq~~~~~ivp~~i~i~v~~~~w~--aalIllit~Pl 152 (559)
T COG4988 117 YLPQMFLSAIVPLLILIAIFFFNWA--AALILLITAPL 152 (559)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhHH--HHHHHHHHHHH
Confidence 8999999999999999988877665 44445666664
No 22
>PRK14750 kdpF potassium-transporting ATPase subunit F; Provisional
Probab=26.20 E-value=65 Score=18.12 Aligned_cols=16 Identities=31% Similarity=0.451 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy13005 62 GMVLLFVFVMFFYPCIN 78 (130)
Q Consensus 62 ~l~~~~~~~~~~y~~~n 78 (130)
+++.++..|+. |..+|
T Consensus 10 llv~lLl~YLv-YAL~n 25 (29)
T PRK14750 10 LLVLLLLGYLV-YALFN 25 (29)
T ss_pred HHHHHHHHHHH-HHHcC
Confidence 44555666666 66665
No 23
>PF15102 TMEM154: TMEM154 protein family
Probab=26.11 E-value=84 Score=23.95 Aligned_cols=26 Identities=15% Similarity=0.259 Sum_probs=21.7
Q ss_pred CCCCCCCcccCCHHHHHHHHhccCCC
Q psy13005 104 VPGGIPSACDIPISTVCEMLYLKNKK 129 (130)
Q Consensus 104 ~~~~ip~i~DlPi~~Vn~~LY~~~~~ 129 (130)
-++.+|.+..|-..+.-+=+++.+|.
T Consensus 115 FEedtpsvmeiEmeeldkwm~s~n~n 140 (146)
T PF15102_consen 115 FEEDTPSVMEIEMEELDKWMNSMNRN 140 (146)
T ss_pred cccCCcchhhhhHHHHHhHHHhhccC
Confidence 35889999999999999888887664
No 24
>PF13687 DUF4153: Domain of unknown function (DUF4153)
Probab=24.54 E-value=2.7e+02 Score=21.52 Aligned_cols=24 Identities=29% Similarity=0.775 Sum_probs=17.8
Q ss_pred HcCccccccchhHHHHHHHHHHHHHH
Q psy13005 43 YFGLTYLPQKYWAIAVPIYGMVLLFV 68 (130)
Q Consensus 43 ~lgity~P~kyWalaiP~~~l~~~~~ 68 (130)
+-|+| |+|||++++=.+.....+.
T Consensus 150 qYGlT--~~R~~~~~~~~~~~~~~l~ 173 (217)
T PF13687_consen 150 QYGLT--PNRYYALLLAIFLLIYALY 173 (217)
T ss_pred HHCCC--HHHHHHHHHHHHHHHHHHH
Confidence 35666 9999999988777665543
No 25
>PRK12438 hypothetical protein; Provisional
Probab=24.29 E-value=4.9e+02 Score=25.70 Aligned_cols=39 Identities=5% Similarity=-0.037 Sum_probs=26.3
Q ss_pred HHHHHcCccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy13005 39 SILYYFGLTYLPQKYWAIAVPIYGMVLLFVFVMFFYPCINMS 80 (130)
Q Consensus 39 ~~L~~lgity~P~kyWalaiP~~~l~~~~~~~~~~y~~~n~~ 80 (130)
-|.+++| |-+=+|...+.-+.++...+..+++....|+.
T Consensus 44 lWf~~lg---y~~Vf~t~l~tr~~Lf~~~~~~~~~~v~~~~~ 82 (991)
T PRK12438 44 LWFGEVG---FRSVWITVLLTRLALFAAVALVVGGIVLAALL 82 (991)
T ss_pred HHHHhCC---CceehhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4778888 67788888887777766555555544555654
No 26
>PF03994 DUF350: Domain of Unknown Function (DUF350) ; InterPro: IPR007140 This motif occurs in a small set of bacterial proteins. It has two transmembrane regions, and often occurs as tandem repeats. The are no conserved catalytic residues.
Probab=24.11 E-value=77 Score=19.26 Aligned_cols=31 Identities=23% Similarity=0.473 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCCCCCcccccC
Q psy13005 61 YGMVLLFVFVMFFYPCINMSLTPVRDSPNVMIDS 94 (130)
Q Consensus 61 ~~l~~~~~~~~~~y~~~n~~~T~plds~~tI~D~ 94 (130)
|.+++++...++ +..++. .|| .|.-+.|.+.
T Consensus 1 y~~~g~~l~~~~-~~~~~~-~tp-~~~~~eI~~~ 31 (54)
T PF03994_consen 1 YGLVGIVLLLLG-FFVFDL-LTP-YDLREEIKKG 31 (54)
T ss_pred CHHHHHHHHHHH-HHHHHH-hcC-CChHHHHhCC
Confidence 345666666566 666666 887 7777777665
No 27
>PF09591 DUF2463: Protein of unknown function (DUF2463); InterPro: IPR019081 This protein is found in eukaryotic, parasitic microsporidia. Its function is unknown.
Probab=23.04 E-value=2.6e+02 Score=22.56 Aligned_cols=26 Identities=27% Similarity=0.628 Sum_probs=21.9
Q ss_pred cccccch-------hHHHHHHHHHHHHHHHHHH
Q psy13005 47 TYLPQKY-------WAIAVPIYGMVLLFVFVMF 72 (130)
Q Consensus 47 ty~P~ky-------WalaiP~~~l~~~~~~~~~ 72 (130)
.|.|+|. |.+++-..++...+++|.+
T Consensus 172 k~~Ps~kss~pta~wRv~ifvlILil~~~iY~~ 204 (210)
T PF09591_consen 172 KYFPSKKSSLPTAPWRVAIFVLILILAIFIYGF 204 (210)
T ss_pred ccCCCCCCCCCcchHHHHHHHHHHHHHHHHHHH
Confidence 6888887 9999999998888877665
No 28
>PRK12721 secretion system apparatus protein SsaU; Reviewed
Probab=22.90 E-value=1.2e+02 Score=25.96 Aligned_cols=24 Identities=29% Similarity=0.196 Sum_probs=17.5
Q ss_pred CCCCCCCCCCCc--------------hhhHHHHHHHHH
Q psy13005 1 MVESTPSPTPSR--------------ANNGFVLYLAST 24 (130)
Q Consensus 1 m~~~~p~p~~~r--------------e~yGFv~~i~s~ 24 (130)
|.|+|..|+|.| |.-+++..+...
T Consensus 1 MaeKTE~pT~kkl~dARkkGqV~kS~el~~a~~ll~~~ 38 (349)
T PRK12721 1 MSEKTEKPTEKKLRDARKKGQVVKSVEITSGVQLAALL 38 (349)
T ss_pred CCCCCCCCChHHHHHHHHcCCCcchhhHHHHHHHHHHH
Confidence 889999999876 666666654433
No 29
>PF05817 Ribophorin_II: Oligosaccharyltransferase subunit Ribophorin II; InterPro: IPR008814 This family consists of several eukaryotic Ribophorin II (RPN2) proteins. The mammalian oligosaccharyltransferase (OST) is a protein complex that effects the cotranslational N-glycosylation of newly synthesised polypeptides, and is composed of at least four rough ER-specific membrane proteins: ribophorins I and II (RI and RII), OST48, and Dadl. The mechanism(s) by which the subunits of this complex are retained in the ER are not well understood [].; GO: 0004579 dolichyl-diphosphooligosaccharide-protein glycotransferase activity, 0018279 protein N-linked glycosylation via asparagine, 0005789 endoplasmic reticulum membrane, 0008250 oligosaccharyltransferase complex
Probab=22.32 E-value=3.6e+02 Score=24.97 Aligned_cols=71 Identities=17% Similarity=0.199 Sum_probs=37.4
Q ss_pred CCCCCCchhhHHHHHHHHHHHHHHHHHhhccChHHHHHcCccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhcCC
Q psy13005 6 PSPTPSRANNGFVLYLASTIMFVVYLIWAFIPDSILYYFGLTYLPQKYWAIAVPIYGMVLLFVFVMFFYPCINMSLTP 83 (130)
Q Consensus 6 p~p~~~re~yGFv~~i~s~~~~~lyl~Wa~lP~~~L~~lgity~P~kyWalaiP~~~l~~~~~~~~~~y~~~n~~~T~ 83 (130)
|.++|.+-+--...-+.....+++.+.|..+--. ++ -+|.--.++.+=.. +.++...|+.-|..+|+.-|-
T Consensus 541 ~eK~pp~~vS~~F~~~vlapl~~Ll~~W~~lG~N-l~-----~l~~~~~~~~F~~~-l~ai~glf~~Yw~~l~lFqTL 611 (636)
T PF05817_consen 541 PEKRPPKIVSLVFTGLVLAPLLVLLILWLKLGAN-LS-----NLPFSPSAILFHGG-LGAIEGLFFLYWLGLNLFQTL 611 (636)
T ss_pred CCCCCchHHHHHHHHHHHHHHHHHHHHHHHcCcc-hh-----hCCCCchHHHHHHH-HHHHHHHHHHHHHhccHHHHH
Confidence 3344444554444444555568888999988643 22 23443335544443 334444444425678876443
No 30
>PRK06298 type III secretion system protein; Validated
Probab=21.55 E-value=1.3e+02 Score=25.76 Aligned_cols=23 Identities=30% Similarity=0.404 Sum_probs=17.3
Q ss_pred CCCCCCCCCCCc--------------hhhHHHHHHHH
Q psy13005 1 MVESTPSPTPSR--------------ANNGFVLYLAS 23 (130)
Q Consensus 1 m~~~~p~p~~~r--------------e~yGFv~~i~s 23 (130)
|.|+|..|+|.| |.-+++..+.+
T Consensus 1 M~eKTE~pT~kkl~~ARekGqV~kS~el~~a~~ll~~ 37 (356)
T PRK06298 1 MGEKTEKATPKRLRDARKKGQVAKSQDFPSAITFIVS 37 (356)
T ss_pred CCCCCCCCChhHHHHHHHcCCCccchhHHHHHHHHHH
Confidence 889999999876 66666665543
No 31
>PF11014 DUF2852: Protein of unknown function (DUF2852); InterPro: IPR021273 This bacterial family of proteins has no known function.
Probab=20.72 E-value=1.3e+02 Score=22.09 Aligned_cols=21 Identities=24% Similarity=0.795 Sum_probs=17.7
Q ss_pred hhHHHHHHHHHHHHHHHHHhh
Q psy13005 14 NNGFVLYLASTIMFVVYLIWA 34 (130)
Q Consensus 14 ~yGFv~~i~s~~~~~lyl~Wa 34 (130)
+-||+.|--.-+++..|++|.
T Consensus 16 VlGFi~fWPlGla~Lay~iw~ 36 (115)
T PF11014_consen 16 VLGFIVFWPLGLALLAYMIWG 36 (115)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 678888888888888888887
Done!