Query 033184
Match_columns 125
No_of_seqs 51 out of 53
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 10:50:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033184.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033184hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07712 SURNod19: Stress up-r 100.0 1.3E-41 2.8E-46 290.1 6.9 73 1-73 309-381 (381)
2 PF01299 Lamp: Lysosome-associ 84.1 0.69 1.5E-05 37.8 2.0 17 105-123 290-306 (306)
3 cd06577 PASTA_pknB PASTA domai 72.0 6.1 0.00013 22.8 3.0 27 16-46 35-61 (62)
4 smart00740 PASTA PASTA domain. 71.5 6.5 0.00014 23.1 3.1 26 17-46 39-64 (66)
5 TIGR02657 amicyanin amicyanin. 71.1 8 0.00017 25.7 3.8 34 22-57 1-34 (83)
6 PF03793 PASTA: PASTA domain; 66.1 16 0.00035 22.5 4.2 31 13-47 32-62 (63)
7 cd06575 PASTA_Pbp2x-like_2 PAS 56.5 15 0.00033 20.8 2.7 25 18-46 29-53 (54)
8 PF13473 Cupredoxin_1: Cupredo 51.0 22 0.00048 24.2 3.2 39 20-58 23-61 (104)
9 PF00127 Copper-bind: Copper b 49.2 21 0.00046 24.3 2.9 30 28-59 13-42 (99)
10 cd06573 PASTA PASTA domain. Th 48.2 24 0.00052 19.9 2.6 24 18-45 28-52 (53)
11 PF03967 PRCH: Photosynthetic 45.7 30 0.00064 27.0 3.5 30 91-120 10-40 (136)
12 cd06576 PASTA_Pbp2x-like_1 PAS 40.4 28 0.00061 20.0 2.1 18 28-46 37-54 (55)
13 TIGR01167 LPXTG_anchor LPXTG-m 40.3 40 0.00087 18.8 2.7 18 96-113 13-31 (34)
14 PF08114 PMP1_2: ATPase proteo 38.1 19 0.00041 23.4 1.1 26 97-122 15-42 (43)
15 PRK02710 plastocyanin; Provisi 35.8 53 0.0011 23.4 3.3 40 16-57 27-70 (119)
16 PF01102 Glycophorin_A: Glycop 35.0 38 0.00082 25.5 2.5 20 97-116 73-95 (122)
17 TIGR02656 cyanin_plasto plasto 33.9 64 0.0014 22.0 3.4 28 28-57 13-40 (99)
18 TIGR02375 pseudoazurin pseudoa 32.8 41 0.00089 24.6 2.4 20 28-47 11-30 (116)
19 PRK06518 hypothetical protein; 32.7 31 0.00068 27.0 1.8 16 32-47 26-41 (177)
20 PF15330 SIT: SHP2-interacting 31.5 58 0.0012 23.9 2.9 11 107-117 19-29 (107)
21 COG3086 RseC Positive regulato 30.2 53 0.0011 26.1 2.7 30 95-124 108-138 (150)
22 cd00226 PRCH Photosynthetic re 30.1 57 0.0012 27.5 3.1 32 90-121 9-41 (246)
23 TIGR03096 nitroso_cyanin nitro 29.9 85 0.0018 24.1 3.7 34 27-60 56-89 (135)
24 PF12191 stn_TNFRSF12A: Tumour 28.9 19 0.0004 28.0 0.0 17 105-121 95-111 (129)
25 PRK15444 pduC propanediol dehy 27.9 39 0.00084 31.5 1.8 33 17-51 25-58 (554)
26 TIGR01150 puhA photosynthetic 27.1 72 0.0016 27.2 3.2 32 90-121 9-41 (252)
27 PF10017 Methyltransf_33: Hist 26.5 68 0.0015 23.2 2.6 35 18-52 60-98 (127)
28 PF08374 Protocadherin: Protoc 24.7 55 0.0012 27.4 2.0 16 107-122 59-74 (221)
29 cd03687 Dehydratase_LU Dehydra 24.4 48 0.001 30.9 1.8 33 17-51 18-51 (545)
30 smart00326 SH3 Src homology 3 24.4 1.4E+02 0.003 16.6 3.5 32 19-50 3-35 (58)
31 PF04246 RseC_MucC: Positive r 24.1 76 0.0017 22.8 2.5 18 34-51 50-67 (135)
32 PF03712 Cu2_monoox_C: Copper 23.7 57 0.0012 24.5 1.8 24 29-52 82-105 (156)
33 KOG4818 Lysosomal-associated m 23.6 65 0.0014 28.7 2.3 11 113-123 352-362 (362)
34 COG4807 Uncharacterized protei 23.3 22 0.00047 28.3 -0.5 30 94-123 23-52 (155)
35 PF14392 zf-CCHC_4: Zinc knuck 23.2 1.2E+02 0.0027 18.6 3.0 27 34-60 13-42 (49)
36 TIGR03102 halo_cynanin halocya 22.9 1.1E+02 0.0024 22.4 3.1 29 28-57 38-66 (115)
37 PF07653 SH3_2: Variant SH3 do 22.7 90 0.0019 19.0 2.3 25 21-45 2-27 (55)
38 COG1558 FlgC Flagellar basal b 22.3 49 0.0011 25.9 1.2 16 6-21 79-94 (137)
39 cd05762 Ig8_MLCK Eighth immuno 21.9 1.4E+02 0.003 20.1 3.3 25 30-54 6-30 (98)
40 PF08253 Leader_Erm: Erm Leade 21.0 22 0.00048 19.6 -0.6 13 58-70 1-13 (19)
41 PTZ00382 Variant-specific surf 20.4 58 0.0013 23.2 1.2 8 96-103 76-83 (96)
42 PF14874 PapD-like: Flagellar- 20.2 1.5E+02 0.0032 19.6 3.1 24 25-50 50-73 (102)
No 1
>PF07712 SURNod19: Stress up-regulated Nod 19; InterPro: IPR011692 This family of plant proteins have been implicated in nodule development [] in the legume Medicago truncatula (Barrel medic). MtN-19 was shown by Northern blot to be induced during nodulation []. The molecular function of these proteins is unknown.
Probab=100.00 E-value=1.3e-41 Score=290.11 Aligned_cols=73 Identities=70% Similarity=1.276 Sum_probs=71.5
Q ss_pred CcccCCCccCCCCCCCCcccEEEeeeeecCCCeeeeccCceEEEEEeecCCCCceehhhhhhhhhhccCCCCC
Q 033184 1 MCSSIPAYGNGKEAGNEAGYIVGMSTCYPKPGFLRITDKETLIVESNYSSSHDHTGVMGLFYILVADRVPESS 73 (125)
Q Consensus 1 iC~S~P~YG~G~eaGNE~GYvVGMStCyP~Pgs~kI~dGE~L~l~s~Ys~~~~hTGvMGlfyi~vAe~~p~~~ 73 (125)
||+|+|+||+|+|||||+|||||||||||+|||+||+|||+|||||+|||+++||||||||||+||||+|++.
T Consensus 309 lCsS~P~YG~G~EaGNE~GYvVGMStCyP~pgsvkI~dGE~L~l~s~Ys~~~~HTGVMGlfyilvAe~~p~~~ 381 (381)
T PF07712_consen 309 LCSSIPQYGTGKEAGNEKGYVVGMSTCYPKPGSVKISDGETLTLESNYSNTQEHTGVMGLFYILVAEQLPHPE 381 (381)
T ss_pred eeccccccCCCCcCCcccceEEEeeeeecCCCCeEecCCCEEEEEEEecCCCCccchHHHHHHHHhhhcCCCC
Confidence 7999999999999999999999999999999999999999999999999999999999999999999999863
No 2
>PF01299 Lamp: Lysosome-associated membrane glycoprotein (Lamp); InterPro: IPR002000 Lysosome-associated membrane glycoproteins (lamp) [] are integral membrane proteins, specific to lysosomes, and whose exact biological function is not yet clear. Structurally, the lamp proteins consist of two internally homologous lysosome-luminal domains separated by a proline-rich hinge region; at the C-terminal extremity there is a transmembrane region (TM) followed by a very short cytoplasmic tail (C). In each of the duplicated domains, there are two conserved disulphide bonds. This structure is schematically represented in the figure below. +-----+ +-----+ +-----+ +-----+ | | | | | | | | xCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxxxCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxx +--------------------------++Hinge++--------------------------++TM++C+ In mammals, there are two closely related types of lamp: lamp-1 and lamp-2, which form major components of the lysosome membrane. In chicken lamp-1 is known as LEP100. Also included in this entry is the macrophage protein CD68 (or macrosialin) [] is a heavily glycosylated integral membrane protein whose structure consists of a mucin-like domain followed by a proline-rich hinge; a single lamp-like domain; a transmembrane region and a short cytoplasmic tail. Similar to CD68, mammalian lamp-3, which is expressed in lymphoid organs, dendritic cells and in lung, contains all the C-terminal regions but lacks the N-terminal lamp-like region []. In a lamp-family protein from nematodes [] only the part C-terminal to the hinge is conserved. ; GO: 0016020 membrane
Probab=84.12 E-value=0.69 Score=37.75 Aligned_cols=17 Identities=41% Similarity=0.397 Sum_probs=10.1
Q ss_pred HHHhhhhhhcccccCCccc
Q 033184 105 AAAVGYWRRNKYEDGYQPI 123 (125)
Q Consensus 105 vA~v~~~~k~~~~~gY~~l 123 (125)
||.+..||| .+.|||++
T Consensus 290 iaYli~Rrr--~~~gYq~~ 306 (306)
T PF01299_consen 290 IAYLIGRRR--SRAGYQSI 306 (306)
T ss_pred HhheeEecc--cccccccC
Confidence 555555444 33499986
No 3
>cd06577 PASTA_pknB PASTA domain of bacterial serine/threonine kinase pknB-like proteins. PknB is a member of a group of related transmembrane sensor kinases present in many gram positive bacteria, which has been shown to regulate cell shape in Mycobacterium tubercolosis. PknB is a receptor-like transmembrane protein with an extracellular signal sensor domain (containing multiple PASTA domains) and an intracellular, eukaryotic serine/threonine kinase-like domain. The PASTA domain is found at the C-termini of several Penicillin-binding proteins (PBPs) and bacterial serine/threonine kinases. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain.
Probab=72.05 E-value=6.1 Score=22.77 Aligned_cols=27 Identities=15% Similarity=0.336 Sum_probs=20.1
Q ss_pred CCcccEEEeeeeecCCCeeeeccCceEEEEE
Q 033184 16 NEAGYIVGMSTCYPKPGFLRITDKETLIVES 46 (125)
Q Consensus 16 NE~GYvVGMStCyP~Pgs~kI~dGE~L~l~s 46 (125)
.++|.|+.. .|.||+ ++..|+.++|..
T Consensus 35 ~~~g~V~~q---~p~~G~-~v~~~~~i~l~v 61 (62)
T cd06577 35 VPKGTVISQ---SPAAGT-KVKKGSTVTLTV 61 (62)
T ss_pred CCCCEEEEe---cCCCCC-ccCCCCEEEEEE
Confidence 357877765 599997 677788888754
No 4
>smart00740 PASTA PASTA domain.
Probab=71.46 E-value=6.5 Score=23.12 Aligned_cols=26 Identities=15% Similarity=0.332 Sum_probs=20.3
Q ss_pred CcccEEEeeeeecCCCeeeeccCceEEEEE
Q 033184 17 EAGYIVGMSTCYPKPGFLRITDKETLIVES 46 (125)
Q Consensus 17 E~GYvVGMStCyP~Pgs~kI~dGE~L~l~s 46 (125)
.+|.|+.. .|.||+ ++..|+.++|..
T Consensus 39 ~~g~V~~q---~p~~G~-~v~~~~~i~l~v 64 (66)
T smart00740 39 EEGTVIKQ---SPAAGT-TVKPGSKVTLTV 64 (66)
T ss_pred CCCEEEEe---CCCCCC-CcCCCCEEEEEE
Confidence 47788775 599998 688899888754
No 5
>TIGR02657 amicyanin amicyanin. Members of this family are amicyanin, a type I blue copper protein that accepts electrons from the tryptophan tryptophylquinone (TTQ) cofactor of the methylamine dehydrogenase light chain and then transfers them to the heme group of cytochrome c-551i. Amicyanin, methylamine dehydrogenase, and cytochrome c-551i are periplasmic and form a complex. This system has been studied primarily in Paracoccus denitrificans and Methylobacterium extorquens. Related type I blue copper proteins include plastocyanin, pseudoazurin, halocyanin, etc.
Probab=71.14 E-value=8 Score=25.72 Aligned_cols=34 Identities=12% Similarity=0.037 Sum_probs=25.6
Q ss_pred EEeeeeecCCCeeeeccCceEEEEEeecCCCCceeh
Q 033184 22 VGMSTCYPKPGFLRITDKETLIVESNYSSSHDHTGV 57 (125)
Q Consensus 22 VGMStCyP~Pgs~kI~dGE~L~l~s~Ys~~~~hTGv 57 (125)
|-+..|-..|..++|..|++++++-+ ....|+=.
T Consensus 1 v~i~~~~F~P~~i~v~~GdtVt~~N~--d~~~Hnv~ 34 (83)
T TIGR02657 1 VDIAKMKYETPELHVKVGDTVTWINR--EAMPHNVH 34 (83)
T ss_pred CEEEeeEEcCCEEEECCCCEEEEEEC--CCCCccEE
Confidence 35778999999999999999998532 23467643
No 6
>PF03793 PASTA: PASTA domain; InterPro: IPR005543 The PASTA domain is found at the C-termini of several Penicillin-binding proteins (PBP) and bacterial serine/threonine kinases. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. In PknB of Mycobacterium tuberculosis (P71584 from SWISSPROT), all of the extracellular portion is predicted to be made up of four PASTA domains, which strongly suggests that it is a signal-binding sensor domain. The domain has also been found in proteins involved in cell wall biosynthesis, where it is implicated in localizing the biosynthesis complex to unlinked peptidoglycan. PASTA is a small globular fold consisting of 3 beta-sheets and an alpha-helix, with a loop region of variable length between the first and second beta-strands. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain [].; GO: 0008658 penicillin binding; PDB: 2ZC3_C 1QME_A 1RP5_B 2Z2M_C 2Z2L_F 2ZC4_C 1QMF_A 3M9G_A 3PY9_A 1K25_B ....
Probab=66.09 E-value=16 Score=22.48 Aligned_cols=31 Identities=13% Similarity=0.369 Sum_probs=22.9
Q ss_pred CCCCCcccEEEeeeeecCCCeeeeccCceEEEEEe
Q 033184 13 EAGNEAGYIVGMSTCYPKPGFLRITDKETLIVESN 47 (125)
Q Consensus 13 eaGNE~GYvVGMStCyP~Pgs~kI~dGE~L~l~s~ 47 (125)
....++|.|+.. .|.||+ ++..|..++|..+
T Consensus 32 ~~~~~~g~V~~Q---~P~~G~-~v~~~~~I~l~vs 62 (63)
T PF03793_consen 32 SDSVPKGTVISQ---SPAPGT-KVKKGSKITLTVS 62 (63)
T ss_dssp ESSSSTTSEEEE---SSCTTS-EEETTSEEEEEEE
T ss_pred cCCCCCCEEEEE---ECCCCC-CcCCCCEEEEEEe
Confidence 344567777654 699998 7788999988753
No 7
>cd06575 PASTA_Pbp2x-like_2 PASTA domain of PBP2x-like proteins, second repeat. Penicillin-binding proteins (PBPs) are the major targets for beta-lactam antibiotics, like penicillins and cephalosporins. Beta-lactam antibiotics specifically inhibit transpeptidase activity by acylating the active site serine. PBPs catalyze key steps in the synthesis of the peptidoglycan, such as the interconnecting of glycan chains (polymers of N-glucosamine and N-acetylmuramic acid residues) and the cross-linking (transpeptidation) of short stem peptides, which are attached to glycan chains. Peptidoglycan is essential in cell division and protects bacteria from osmotic shock and lysis. PBP2x is one of the two monofunctional high molecular mass PBPs in Streptococcus pneumoniae and has been seen as the primary PBP target in beta-lactam-resistant strains. The PASTA domain is found at the C-termini of several PBPs and bacterial serine/threonine kinases. The name PASTA is derived from PBP and Serine/Threonine
Probab=56.55 E-value=15 Score=20.79 Aligned_cols=25 Identities=28% Similarity=0.510 Sum_probs=18.9
Q ss_pred cccEEEeeeeecCCCeeeeccCceEEEEE
Q 033184 18 AGYIVGMSTCYPKPGFLRITDKETLIVES 46 (125)
Q Consensus 18 ~GYvVGMStCyP~Pgs~kI~dGE~L~l~s 46 (125)
+|.|+. ..|.||+ ++..|++++|..
T Consensus 29 ~g~v~~---q~p~~g~-~v~~~~~v~l~v 53 (54)
T cd06575 29 SGYVVS---QSIAPGT-KVKKGTTITVTL 53 (54)
T ss_pred ceEEEE---ecCCCCC-CCCCCCEEEEEE
Confidence 566644 6899997 588899988864
No 8
>PF13473 Cupredoxin_1: Cupredoxin-like domain; PDB: 1IBZ_D 1IC0_E 1IBY_D.
Probab=50.98 E-value=22 Score=24.19 Aligned_cols=39 Identities=10% Similarity=0.140 Sum_probs=22.4
Q ss_pred cEEEeeeeecCCCeeeeccCceEEEEEeecCCCCceehh
Q 033184 20 YIVGMSTCYPKPGFLRITDKETLIVESNYSSSHDHTGVM 58 (125)
Q Consensus 20 YvVGMStCyP~Pgs~kI~dGE~L~l~s~Ys~~~~hTGvM 58 (125)
.-|-++.=...|..++++.|+.++|+..-.++..|.=+.
T Consensus 23 v~I~~~~~~f~P~~i~v~~G~~v~l~~~N~~~~~h~~~i 61 (104)
T PF13473_consen 23 VTITVTDFGFSPSTITVKAGQPVTLTFTNNDSRPHEFVI 61 (104)
T ss_dssp -------EEEES-EEEEETTCEEEEEEEE-SSS-EEEEE
T ss_pred ccccccCCeEecCEEEEcCCCeEEEEEEECCCCcEEEEE
Confidence 455566666778899999999999988666555665443
No 9
>PF00127 Copper-bind: Copper binding proteins, plastocyanin/azurin family; InterPro: IPR000923 Blue (type 1) copper proteins are small proteins which bind a single copper atom and which are characterised by an intense electronic absorption band near 600 nm [, ]. The most well known members of this class of proteins are the plant chloroplastic plastocyanins, which exchange electrons with cytochrome c6, and the distantly related bacterial azurins, which exchange electrons with cytochrome c551. This family of proteins also includes amicyanin from bacteria such as Methylobacterium extorquens or Paracoccus versutus (Thiobacillus versutus) that can grow on methylamine; auracyanins A and B from Chloroflexus aurantiacus []; blue copper protein from Alcaligenes faecalis; cupredoxin (CPC) from Cucumis sativus (Cucumber) peelings []; cusacyanin (basic blue protein; plantacyanin, CBP) from cucumber; halocyanin from Natronomonas pharaonis (Natronobacterium pharaonis) [], a membrane associated copper-binding protein; pseudoazurin from Pseudomonas; rusticyanin from Thiobacillus ferrooxidans []; stellacyanin from Rhus vernicifera (Japanese lacquer tree); umecyanin from the roots of Armoracia rusticana (Horseradish); and allergen Ra3 from ragweed. This pollen protein is evolutionary related to the above proteins, but seems to have lost the ability to bind copper. Although there is an appreciable amount of divergence in the sequences of all these proteins, the copper ligand sites are conserved.; GO: 0005507 copper ion binding, 0009055 electron carrier activity; PDB: 1UAT_A 1CUO_A 1PLC_A 4PCY_A 3PCY_A 1PND_A 1PNC_A 1JXG_A 6PCY_A 1TKW_A ....
Probab=49.21 E-value=21 Score=24.26 Aligned_cols=30 Identities=20% Similarity=0.201 Sum_probs=22.8
Q ss_pred ecCCCeeeeccCceEEEEEeecCCCCceehhh
Q 033184 28 YPKPGFLRITDKETLIVESNYSSSHDHTGVMG 59 (125)
Q Consensus 28 yP~Pgs~kI~dGE~L~l~s~Ys~~~~hTGvMG 59 (125)
...|-.++|+.|++++++-+ +..+|+=+..
T Consensus 13 ~F~P~~i~V~~G~tV~~~n~--~~~~Hnv~~~ 42 (99)
T PF00127_consen 13 AFDPSEITVKAGDTVTFVNN--DSMPHNVVFV 42 (99)
T ss_dssp SEESSEEEEETTEEEEEEEE--SSSSBEEEEE
T ss_pred EEeCCEEEECCCCEEEEEEC--CCCCceEEEe
Confidence 46788999999999998877 4456765543
No 10
>cd06573 PASTA PASTA domain. This domain is found at the C-termini of several Penicillin-binding proteins (PBPs) and bacterial serine/threonine kinases. It is a small globular fold consisting of 3 beta-sheets and an alpha-helix. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain.
Probab=48.22 E-value=24 Score=19.94 Aligned_cols=24 Identities=21% Similarity=0.451 Sum_probs=17.5
Q ss_pred ccc-EEEeeeeecCCCeeeeccCceEEEE
Q 033184 18 AGY-IVGMSTCYPKPGFLRITDKETLIVE 45 (125)
Q Consensus 18 ~GY-vVGMStCyP~Pgs~kI~dGE~L~l~ 45 (125)
+|+ |+. -.|.||+ ++..|++++|.
T Consensus 28 ~g~~v~~---q~p~~g~-~v~~~~~i~l~ 52 (53)
T cd06573 28 SGNKVVK---QSPEAGT-KVAEGSTIRIY 52 (53)
T ss_pred CCCEEEE---eCCCCCC-CcCCCCEEEEE
Confidence 467 544 4689997 68888988874
No 11
>PF03967 PRCH: Photosynthetic reaction centre, H-chain N-terminal region; InterPro: IPR015810 The photosynthetic apparatus in non-oxygenic bacteria consists of light-harvesting (LH) protein-pigment complexes LH1 and LH2, which use carotenoid and bacteriochlorophyll as primary donors []. LH1 acts as the energy collection hub, temporarily storing it before its transfer to the photosynthetic reaction centre (RC) []. Electrons are transferred from the primary donor via an intermediate acceptor (bacteriopheophytin) to the primary acceptor (quinine Qa), and finally to the secondary acceptor (quinone Qb), resulting in the formation of ubiquinol QbH2. RC uses the excitation energy to shuffle electrons across the membrane, transferring them via ubiquinol to the cytochrome bc1 complex in order to establish a proton gradient across the membrane, which is used by ATP synthetase to form ATP [, , ]. The core complex is anchored in the cell membrane, consisting of one unit of RC surrounded by LH1; in some species there may be additional subunits []. RC consists of three subunits: L (light), M (medium), and H (heavy). Subunits L and M provide the scaffolding for the chromophore, while subunit H contains a cytoplasmic domain []. In Rhodopseudomonas viridis, there is also a non-membranous tetrahaem cytochrome (4Hcyt) subunit on the periplasmic surface. This entry represents the N-terminal domain of the photosynthetic reaction centre H subunit, which includes the transmembrane domain and part of the cytoplasmic domain [].; GO: 0045156 electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity, 0019684 photosynthesis, light reaction, 0030077 plasma membrane light-harvesting complex; PDB: 1RZZ_H 1PST_H 2J8D_H 3DUQ_H 1FNP_H 1KBY_H 1E14_H 2HG3_H 1UMX_H 1YST_H ....
Probab=45.74 E-value=30 Score=27.04 Aligned_cols=30 Identities=33% Similarity=0.435 Sum_probs=23.9
Q ss_pred ehhhHHHHHHHHHHHH-HhhhhhhcccccCC
Q 033184 91 FVWGAFVLAGVAITAA-AVGYWRRNKYEDGY 120 (125)
Q Consensus 91 ~~~~~v~v~g~a~~vA-~v~~~~k~~~~~gY 120 (125)
.-++-++|+..-+-.| .|.|.+|-++||||
T Consensus 10 ~DvAql~lyaFwiFFagLi~YLrrEdkREGY 40 (136)
T PF03967_consen 10 FDVAQLVLYAFWIFFAGLIYYLRREDKREGY 40 (136)
T ss_dssp CCHHHHHHHHHHHHHHHHHHHHHHHTTSSST
T ss_pred ccHHHHHHHHHHHHHHHHHHHHhccccccCC
Confidence 3456777777777766 88899999999999
No 12
>cd06576 PASTA_Pbp2x-like_1 PASTA domain of PBP2x-like proteins, first repeat. Penicillin-binding proteins (PBPs) are the major targets for beta-lactam antibiotics, like penicillins and cephalosporins. Beta-lactam antibiotics specifically inhibit transpeptidase activity by acylating the active site serine. PBPs catalyze key steps in the synthesis of the peptidoglycan, such as the interconnecting of glycan chains (polymers of N-glucosamine and N-acetylmuramic acid residues) and the cross-linking (transpeptidation) of short stem peptides, which are connected to glycan chains. Peptidoglycan is essential in cell division and protects bacteria from osmotic shock and lysis. PBP2x is one of the two monofunctional high molecular mass PBPs in Streptococcus pneumoniae and has been seen as the primary PBP target in beta-lactam-resistant strains. The PASTA domain is found at the C-termini of several PBPs and bacterial serine/threonine kinases. The name PASTA is derived from PBP and Serine/Threonine
Probab=40.42 E-value=28 Score=19.97 Aligned_cols=18 Identities=22% Similarity=0.571 Sum_probs=15.0
Q ss_pred ecCCCeeeeccCceEEEEE
Q 033184 28 YPKPGFLRITDKETLIVES 46 (125)
Q Consensus 28 yP~Pgs~kI~dGE~L~l~s 46 (125)
.|.||+ ++..|++++|.+
T Consensus 37 ~p~~g~-~v~~~~~i~l~~ 54 (55)
T cd06576 37 SPKPGE-KVLEGSKVLLYT 54 (55)
T ss_pred cCCCCC-EeCCCCEEEEec
Confidence 799997 788999988854
No 13
>TIGR01167 LPXTG_anchor LPXTG-motif cell wall anchor domain. A common feature of this proteins containing this domain appears to be a high proportion of charged and zwitterionic residues immediatedly upstream of the LPXTG motif. This model differs from other descriptions of the LPXTG region by including a portion of that upstream charged region.
Probab=40.27 E-value=40 Score=18.78 Aligned_cols=18 Identities=17% Similarity=0.340 Sum_probs=7.2
Q ss_pred HHHHHHHHH-HHHhhhhhh
Q 033184 96 FVLAGVAIT-AAAVGYWRR 113 (125)
Q Consensus 96 v~v~g~a~~-vA~v~~~~k 113 (125)
.+++|+++. ++.+.+++|
T Consensus 13 ~~~~G~~l~~~~~~~~~~r 31 (34)
T TIGR01167 13 LLLLGLLLLGLGGLLLRKR 31 (34)
T ss_pred HHHHHHHHHHHHHHHheec
Confidence 344444333 344444333
No 14
>PF08114 PMP1_2: ATPase proteolipid family; InterPro: IPR012589 This family consists of small proteolipids associated with the plasma membrane H+ ATPase. Two proteolipids (PMP1 and PMP2) are associated with the ATPase and both genes are similarly expressed in the wild-type strain of yeast. No modification of the level of transcription of one PMP gene is detected in a strain deleted of the other. Though both proteolipids show similarity with other small proteolipids associated with other cation -transporting ATPases, their functions remain unclear [].
Probab=38.10 E-value=19 Score=23.42 Aligned_cols=26 Identities=19% Similarity=0.174 Sum_probs=14.9
Q ss_pred HHHHHHHH--HHHhhhhhhcccccCCcc
Q 033184 97 VLAGVAIT--AAAVGYWRRNKYEDGYQP 122 (125)
Q Consensus 97 ~v~g~a~~--vA~v~~~~k~~~~~gY~~ 122 (125)
.++|++.+ +|++.||+-+.+.++-|+
T Consensus 15 ~lVglv~i~iva~~iYRKw~aRkr~l~r 42 (43)
T PF08114_consen 15 CLVGLVGIGIVALFIYRKWQARKRALQR 42 (43)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34444433 668888655666655554
No 15
>PRK02710 plastocyanin; Provisional
Probab=35.77 E-value=53 Score=23.38 Aligned_cols=40 Identities=23% Similarity=0.189 Sum_probs=27.2
Q ss_pred CCcccEEEeee----eecCCCeeeeccCceEEEEEeecCCCCceeh
Q 033184 16 NEAGYIVGMST----CYPKPGFLRITDKETLIVESNYSSSHDHTGV 57 (125)
Q Consensus 16 NE~GYvVGMSt----CyP~Pgs~kI~dGE~L~l~s~Ys~~~~hTGv 57 (125)
..+-+-|-|.+ =...|..++|..|++++++-+ +..+|+-+
T Consensus 27 ~a~~~~V~~~~~~~~~~F~P~~i~v~~Gd~V~~~N~--~~~~H~v~ 70 (119)
T PRK02710 27 SAETVEVKMGSDAGMLAFEPSTLTIKAGDTVKWVNN--KLAPHNAV 70 (119)
T ss_pred ccceEEEEEccCCCeeEEeCCEEEEcCCCEEEEEEC--CCCCceEE
Confidence 34445566642 367888999999999998632 34578754
No 16
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=34.99 E-value=38 Score=25.54 Aligned_cols=20 Identities=30% Similarity=0.127 Sum_probs=7.9
Q ss_pred HHHHHHHH---HHHhhhhhhccc
Q 033184 97 VLAGVAIT---AAAVGYWRRNKY 116 (125)
Q Consensus 97 ~v~g~a~~---vA~v~~~~k~~~ 116 (125)
|++|++.. |+.+..|+||+.
T Consensus 73 v~aGvIg~Illi~y~irR~~Kk~ 95 (122)
T PF01102_consen 73 VMAGVIGIILLISYCIRRLRKKS 95 (122)
T ss_dssp HHHHHHHHHHHHHHHHHHHS---
T ss_pred HHHHHHHHHHHHHHHHHHHhccC
Confidence 44454443 444444444443
No 17
>TIGR02656 cyanin_plasto plastocyanin. Members of this family are plastocyanin, a blue copper protein related to pseudoazurin, halocyanin, amicyanin, etc. This protein, located in the thylakoid luman, performs electron transport to photosystem I in Cyanobacteria and chloroplasts.
Probab=33.85 E-value=64 Score=22.02 Aligned_cols=28 Identities=21% Similarity=0.197 Sum_probs=20.4
Q ss_pred ecCCCeeeeccCceEEEEEeecCCCCceeh
Q 033184 28 YPKPGFLRITDKETLIVESNYSSSHDHTGV 57 (125)
Q Consensus 28 yP~Pgs~kI~dGE~L~l~s~Ys~~~~hTGv 57 (125)
...|..+.|+.|+++++.-+ ...+|+=+
T Consensus 13 ~F~P~~i~v~~G~~V~~~N~--~~~~H~~~ 40 (99)
T TIGR02656 13 VFEPAKISIAAGDTVEWVNN--KGGPHNVV 40 (99)
T ss_pred eEeCCEEEECCCCEEEEEEC--CCCCceEE
Confidence 47788999999999998721 23567544
No 18
>TIGR02375 pseudoazurin pseudoazurin. Pseudoazurin, also called cupredoxin, is a small, blue periplasmic protein with a single bound copper atom. Pseudoazurin is related plastocyanins. Several examples of pseudoazurin are encoded by a neighboring gene for, or have been shown to transfer electrons to, copper-containing nitrite reductases (TIGR02376) of the same species.
Probab=32.75 E-value=41 Score=24.64 Aligned_cols=20 Identities=15% Similarity=0.343 Sum_probs=18.0
Q ss_pred ecCCCeeeeccCceEEEEEe
Q 033184 28 YPKPGFLRITDKETLIVESN 47 (125)
Q Consensus 28 yP~Pgs~kI~dGE~L~l~s~ 47 (125)
.+.|..++|+.||+++++-+
T Consensus 11 ~F~P~~v~V~~GdTV~f~n~ 30 (116)
T TIGR02375 11 VFEPAYIRAAPGDTVTFVPT 30 (116)
T ss_pred EEeCCEEEECCCCEEEEEEC
Confidence 57899999999999999875
No 19
>PRK06518 hypothetical protein; Provisional
Probab=32.65 E-value=31 Score=27.05 Aligned_cols=16 Identities=19% Similarity=0.243 Sum_probs=13.7
Q ss_pred CeeeeccCceEEEEEe
Q 033184 32 GFLRITDKETLIVESN 47 (125)
Q Consensus 32 gs~kI~dGE~L~l~s~ 47 (125)
|.++|.||+||+|..+
T Consensus 26 G~v~V~DGDTl~l~~~ 41 (177)
T PRK06518 26 GRAQVTSGVTFKLIAD 41 (177)
T ss_pred ceEEEEcCCEEEEeec
Confidence 6789999999999653
No 20
>PF15330 SIT: SHP2-interacting transmembrane adaptor protein, SIT
Probab=31.52 E-value=58 Score=23.86 Aligned_cols=11 Identities=0% Similarity=0.229 Sum_probs=4.7
Q ss_pred Hhhhhhhcccc
Q 033184 107 AVGYWRRNKYE 117 (125)
Q Consensus 107 ~v~~~~k~~~~ 117 (125)
.+.||.++++.
T Consensus 19 l~~wr~~~rq~ 29 (107)
T PF15330_consen 19 LLAWRMKQRQK 29 (107)
T ss_pred HHHHHHHhhhc
Confidence 44444444333
No 21
>COG3086 RseC Positive regulator of sigma E activity [Signal transduction mechanisms]
Probab=30.21 E-value=53 Score=26.10 Aligned_cols=30 Identities=23% Similarity=0.322 Sum_probs=21.9
Q ss_pred HHHHHHHHHH-HHHhhhhhhcccccCCcccC
Q 033184 95 AFVLAGVAIT-AAAVGYWRRNKYEDGYQPIM 124 (125)
Q Consensus 95 ~v~v~g~a~~-vA~v~~~~k~~~~~gY~~ll 124 (125)
+.+++|.+.. +.+..|.||.+.+..|||.+
T Consensus 108 ~~~~lg~~l~fl~~r~ysRkl~~~~~~QpVi 138 (150)
T COG3086 108 FGAFLGLALGFLLARRYSRKLAKRTEWQPVI 138 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhcccCCCeE
Confidence 3355555555 55788889999999999975
No 22
>cd00226 PRCH Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to produce ATP by ATP synthase. Subunit H is positioned mainly in the cytoplasm with one transmembrane alpha helix. Provides proton transfer pathway (water channels) connecting the terminal quinone electron acceptor of RC, to the aqueous phase. Found in photosynthetic bacteria: alpha, beta, and gamma proteobacteria.
Probab=30.12 E-value=57 Score=27.51 Aligned_cols=32 Identities=28% Similarity=0.414 Sum_probs=24.8
Q ss_pred eehhhHHHHHHHHHHHH-HhhhhhhcccccCCc
Q 033184 90 AFVWGAFVLAGVAITAA-AVGYWRRNKYEDGYQ 121 (125)
Q Consensus 90 ~~~~~~v~v~g~a~~vA-~v~~~~k~~~~~gY~ 121 (125)
..-++-++|+..-+..| .|.|.+|-++||||-
T Consensus 9 ~~D~A~~~l~~Fw~ffa~Li~YL~~E~~REGYP 41 (246)
T cd00226 9 YFDLAQLVIYAFWIFFAGLIYYLRRENMREGYP 41 (246)
T ss_pred eccHHHHHHHHHHHHHHHHHHHHhccccccCCC
Confidence 34557777887777766 888888889999994
No 23
>TIGR03096 nitroso_cyanin nitrosocyanin. Nitrosocyanin, as described from the obligate chemolithoautotroph Nitrosomonas europaea, is a red copper protein of unknown function with sequence similarity to a number of blue copper redox proteins.
Probab=29.89 E-value=85 Score=24.08 Aligned_cols=34 Identities=12% Similarity=0.065 Sum_probs=26.0
Q ss_pred eecCCCeeeeccCceEEEEEeecCCCCceehhhh
Q 033184 27 CYPKPGFLRITDKETLIVESNYSSSHDHTGVMGL 60 (125)
Q Consensus 27 CyP~Pgs~kI~dGE~L~l~s~Ys~~~~hTGvMGl 60 (125)
-+.+|..|+++.|+++++...=.+...|+-.+.-
T Consensus 56 ~~~~P~~I~VkaGD~Vtl~vtN~d~~~H~f~i~~ 89 (135)
T TIGR03096 56 VLNEPEALVVKKGTPVKVTVENKSPISEGFSIDA 89 (135)
T ss_pred eEEcCCEEEECCCCEEEEEEEeCCCCccceEECC
Confidence 4678889999999999998764444578766644
No 24
>PF12191 stn_TNFRSF12A: Tumour necrosis factor receptor stn_TNFRSF12A_TNFR domain; InterPro: IPR022316 The tumour necrosis factor (TNF) receptor (TNFR) superfamily comprises more than 20 type-I transmembrane proteins. Family members are defined based on similarity in their extracellular domain - a region that contains many cysteine residues arranged in a specific repetitive pattern []. The cysteines allow formation of an extended rod-like structure, responsible for ligand binding []. Upon receptor activation, different intracellular signalling complexes are assembled for different members of the TNFR superfamily, depending on their intracellular domains and sequences []. Activation of TNFRs can therefore induce a range of disparate effects, including cell proliferation, differentiation, survival, or apoptotic cell death, depending upon the receptor involved []. TNFRs are widely distributed and play important roles in many crucial biological processes, such as lymphoid and neuronal development, innate and adaptive immunity, and maintenance of cellular homeostasis []. Drugs that manipulate their signalling have potential roles in the prevention and treatment of many diseases, such as viral infections, coronary heart disease, transplant rejection, and immune disease []. TNF receptor 12 (also known as TWEAK receptor, and fibroblast growth factor-inducible-14 (Fn14)) has been implicated in endothelial cell growth and migration []. The receptor may also play a role in cell-matrix interactions [].; PDB: 2KN0_A 2RPJ_A 2KMZ_A 2EQP_A.
Probab=28.89 E-value=19 Score=28.00 Aligned_cols=17 Identities=18% Similarity=0.487 Sum_probs=0.0
Q ss_pred HHHhhhhhhcccccCCc
Q 033184 105 AAAVGYWRRNKYEDGYQ 121 (125)
Q Consensus 105 vA~v~~~~k~~~~~gY~ 121 (125)
+|-+.+|||+++++-+.
T Consensus 95 lsg~lv~rrcrrr~~~t 111 (129)
T PF12191_consen 95 LSGFLVWRRCRRREKFT 111 (129)
T ss_dssp -----------------
T ss_pred HHHHHHHhhhhccccCC
Confidence 45666778877776553
No 25
>PRK15444 pduC propanediol dehydratase large subunit; Provisional
Probab=27.92 E-value=39 Score=31.50 Aligned_cols=33 Identities=21% Similarity=0.438 Sum_probs=21.6
Q ss_pred CcccEEEee-eeecCCCeeeeccCceEEEEEeecCC
Q 033184 17 EAGYIVGMS-TCYPKPGFLRITDKETLIVESNYSSS 51 (125)
Q Consensus 17 E~GYvVGMS-tCyP~Pgs~kI~dGE~L~l~s~Ys~~ 51 (125)
|.|. |.|. ---|+| ||||.||.++.+-..-..+
T Consensus 25 e~Gl-iAm~sp~DPkP-sikienG~vvElDGk~r~d 58 (554)
T PRK15444 25 EEGL-IAMESPNDPKP-SIKIENGKVVELDGKPRED 58 (554)
T ss_pred ccce-eeccCCCCCCC-ceEeeCCeEEeccCcchHh
Confidence 3443 4554 455777 6999999998876544333
No 26
>TIGR01150 puhA photosynthetic reaction center, subunit H, bacterial. This model describes the photosynthetic reaction center H subunit in non-oxygenic photosynthetic bacteria. The reaction center is an integral membrane pigment-protein that carries out light-driven electron transfer reactions. At the core of reaction center is a collection light-harvesting cofactors and closely associated polypeptides. The core protein complex is made of L, M and H subunits. The common cofactors include bacterichlorophyll, bacteriopheophytins, ubiquinone and no-heme ferrous iron. The net result of electron tranfer reactions is the establishment of proton electrochemical gradient and production of reducing equivalents in the form of NADH. Ultimately, the process results in the reduction of C02 to carbohydrates(C6H12O6) In non-oxygenic organisms, the electron donor is an organic acid rather than water. Much of our current functional understanding of photosynthesis comes from the structural determination
Probab=27.10 E-value=72 Score=27.23 Aligned_cols=32 Identities=28% Similarity=0.420 Sum_probs=24.7
Q ss_pred eehhhHHHHHHHHHHHH-HhhhhhhcccccCCc
Q 033184 90 AFVWGAFVLAGVAITAA-AVGYWRRNKYEDGYQ 121 (125)
Q Consensus 90 ~~~~~~v~v~g~a~~vA-~v~~~~k~~~~~gY~ 121 (125)
..-++-++|+..-+..| .|.|.+|-++||||-
T Consensus 9 ~~DvAq~~ly~FwiFFA~Li~YLrrEd~REGYP 41 (252)
T TIGR01150 9 HFDLAQLVIYAFWIFLAGLIYYLRREDRREGYP 41 (252)
T ss_pred eccHHHHHHHHHHHHHHHHHHHHhccccccCCC
Confidence 34457777887777766 888988889999994
No 27
>PF10017 Methyltransf_33: Histidine-specific methyltransferase, SAM-dependent; InterPro: IPR019257 This domain is found in methyltransferases and various hypothetical proteins.
Probab=26.47 E-value=68 Score=23.18 Aligned_cols=35 Identities=17% Similarity=0.231 Sum_probs=25.2
Q ss_pred cccEEE---eeeeecCCC-eeeeccCceEEEEEeecCCC
Q 033184 18 AGYIVG---MSTCYPKPG-FLRITDKETLIVESNYSSSH 52 (125)
Q Consensus 18 ~GYvVG---MStCyP~Pg-s~kI~dGE~L~l~s~Ys~~~ 52 (125)
+-|++. .+...+.++ .|.++.||.+.+|.+|+-+.
T Consensus 60 e~~l~~~~~~~v~i~~~~~~i~~~~GE~I~~e~S~Ky~~ 98 (127)
T PF10017_consen 60 EMYLVAKRDQTVRIGGLDLTIHFKEGERIHTENSYKYSP 98 (127)
T ss_pred EEEEEeCCcEEEEEcCCCceeEECCCCEEEEEEeeCcCH
Confidence 345544 334455555 58999999999999999874
No 28
>PF08374 Protocadherin: Protocadherin; InterPro: IPR013585 The structure of protocadherins is similar to that of classic cadherins (IPR002126 from INTERPRO), but they also have some unique features associated with the cytoplasmic domains. They are expressed in a variety of organisms and are found in high concentrations in the brain where they seem to be localised mainly at cell-cell contact sites. Their expression seems to be developmentally regulated [].
Probab=24.65 E-value=55 Score=27.38 Aligned_cols=16 Identities=38% Similarity=0.654 Sum_probs=8.1
Q ss_pred HhhhhhhcccccCCcc
Q 033184 107 AVGYWRRNKYEDGYQP 122 (125)
Q Consensus 107 ~v~~~~k~~~~~gY~~ 122 (125)
.+.++|...+..|||.
T Consensus 59 ~vR~CRq~~~k~g~Qa 74 (221)
T PF08374_consen 59 LVRYCRQSPHKKGYQA 74 (221)
T ss_pred HHHHHhhccccchhhh
Confidence 3333343556667763
No 29
>cd03687 Dehydratase_LU Dehydratase large subunit. This family contains the large (alpha) subunit of B12-dependent glycerol dehydratases (GDHs) and B12-dependent diol dehydratases (DDHs). GDH is isofunctional with DDH. These enzymes can each catalyze the conversion of 1,2-propanediol, glycerol, and 1,2-ethanediol to the corresponding aldehydes via a coenzyme B12 (adenosylcobalamin)-dependent radical mechanism. Both enzymes exhibit a subunit composition of alpha2beta2gamma2. The enzymes differ in substrate specificity; glycerol is the preferred substrate for GDH and 1,2-propanediol for DDH. GDH shows almost equal affinity for both (R) and (S)-isomers while DDH prefers the (S) isomer. GDH plays a key role in the dihydroxyacetone (DHA) pathway and DDH in the anaerobic degradation of 1,2-diols. The radical mechanism has been well studied for Klebsiella oxytoca DDH and involves binding of 1,2-propanediol to the enzyme to induce hemolytic cleavage of the Co-C5' bond of the coenzyme to form co
Probab=24.43 E-value=48 Score=30.90 Aligned_cols=33 Identities=21% Similarity=0.446 Sum_probs=21.7
Q ss_pred CcccEEEeee-eecCCCeeeeccCceEEEEEeecCC
Q 033184 17 EAGYIVGMST-CYPKPGFLRITDKETLIVESNYSSS 51 (125)
Q Consensus 17 E~GYvVGMSt-CyP~Pgs~kI~dGE~L~l~s~Ys~~ 51 (125)
|.|. |.|.+ --|+| ||||.||.++.+-..-..+
T Consensus 18 e~Gl-iAm~sp~DPkP-SikienG~vvEmDgk~~~d 51 (545)
T cd03687 18 EEGL-IAMESPNDPKP-SIKIVNGRVVELDGKPVAD 51 (545)
T ss_pred hcce-eeccCCCCCCC-ceEeecCeEEeccCcchHh
Confidence 3443 45554 45666 7999999998886654443
No 30
>smart00326 SH3 Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
Probab=24.36 E-value=1.4e+02 Score=16.60 Aligned_cols=32 Identities=6% Similarity=0.038 Sum_probs=23.8
Q ss_pred ccEEEeeeeecCC-CeeeeccCceEEEEEeecC
Q 033184 19 GYIVGMSTCYPKP-GFLRITDKETLIVESNYSS 50 (125)
Q Consensus 19 GYvVGMStCyP~P-gs~kI~dGE~L~l~s~Ys~ 50 (125)
.+++.+-.+.++. +.+.+..||.+.+....++
T Consensus 3 ~~~~a~~~~~~~~~~~l~~~~Gd~v~v~~~~~~ 35 (58)
T smart00326 3 PQVRALYDYTAQDPDELSFKKGDIITVLEKSDD 35 (58)
T ss_pred cEEEEeeeeCCCCCCCCCCCCCCEEEEEEcCCC
Confidence 4567777777755 5688999999999876533
No 31
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=24.12 E-value=76 Score=22.78 Aligned_cols=18 Identities=22% Similarity=0.051 Sum_probs=12.6
Q ss_pred eeeccCceEEEEEeecCC
Q 033184 34 LRITDKETLIVESNYSSS 51 (125)
Q Consensus 34 ~kI~dGE~L~l~s~Ys~~ 51 (125)
+..+-||.++++..-++-
T Consensus 50 ~~~~~GD~V~v~i~~~~~ 67 (135)
T PF04246_consen 50 IGAKVGDRVEVEIPESSL 67 (135)
T ss_pred CCCCCCCEEEEEeccchH
Confidence 456678899888865543
No 32
>PF03712 Cu2_monoox_C: Copper type II ascorbate-dependent monooxygenase, C-terminal domain; PDB: 1YI9_A 3MLL_A 1SDW_A 3MID_A 1YIP_A 3PHM_A 3MIC_A 3MIB_A 1OPM_A 3MIG_A ....
Probab=23.75 E-value=57 Score=24.45 Aligned_cols=24 Identities=29% Similarity=0.376 Sum_probs=16.9
Q ss_pred cCCCeeeeccCceEEEEEeecCCC
Q 033184 29 PKPGFLRITDKETLIVESNYSSSH 52 (125)
Q Consensus 29 P~Pgs~kI~dGE~L~l~s~Ys~~~ 52 (125)
+-+..++|..|++|..+-.|+|+.
T Consensus 82 ~l~~~v~i~~GD~l~~~C~Ydns~ 105 (156)
T PF03712_consen 82 PLKEPVTIPPGDTLRTECTYDNSD 105 (156)
T ss_dssp EEEEEEEE-TT-EEEEEEEEE-TT
T ss_pred ECCCceEecCCCEEEEEEEEeCCC
Confidence 333468999999999999999953
No 33
>KOG4818 consensus Lysosomal-associated membrane protein [General function prediction only]
Probab=23.57 E-value=65 Score=28.74 Aligned_cols=11 Identities=45% Similarity=0.845 Sum_probs=8.3
Q ss_pred hcccccCCccc
Q 033184 113 RNKYEDGYQPI 123 (125)
Q Consensus 113 k~~~~~gY~~l 123 (125)
|+.++.|||++
T Consensus 352 rr~~~~gYq~i 362 (362)
T KOG4818|consen 352 RRRSHSGYQTI 362 (362)
T ss_pred heecccccccC
Confidence 34589999985
No 34
>COG4807 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.26 E-value=22 Score=28.33 Aligned_cols=30 Identities=27% Similarity=0.420 Sum_probs=21.9
Q ss_pred hHHHHHHHHHHHHHhhhhhhcccccCCccc
Q 033184 94 GAFVLAGVAITAAAVGYWRRNKYEDGYQPI 123 (125)
Q Consensus 94 ~~v~v~g~a~~vA~v~~~~k~~~~~gY~~l 123 (125)
-++++.++-++.+-|.-|.||+.|+|||..
T Consensus 23 ~i~~~~n~~~t~edv~~yLkKedeeGfq~c 52 (155)
T COG4807 23 RILALGNVEATAEDVAVYLKKEDEEGFQRC 52 (155)
T ss_pred HHHHhcCcccCHHHHHHHHHHhhHhHHhhC
Confidence 455666666667755566899999999964
No 35
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=23.17 E-value=1.2e+02 Score=18.65 Aligned_cols=27 Identities=22% Similarity=0.425 Sum_probs=19.3
Q ss_pred eeeccCceEEEEEeecCCC---Cceehhhh
Q 033184 34 LRITDKETLIVESNYSSSH---DHTGVMGL 60 (125)
Q Consensus 34 ~kI~dGE~L~l~s~Ys~~~---~hTGvMGl 60 (125)
+++.+||.+++...|-.-. .|-|.+|+
T Consensus 13 v~~~~g~~~~~~v~YE~lp~~C~~C~~~gH 42 (49)
T PF14392_consen 13 VKFPEGESFWVKVKYERLPRFCFHCGRIGH 42 (49)
T ss_pred EEeCCCcEEEEEEEECCcChhhcCCCCcCc
Confidence 4556899999999998744 45555554
No 36
>TIGR03102 halo_cynanin halocyanin domain. Halocyanins are blue (type I) copper redox proteins found in halophilic archaea such as Natronobacterium pharaonis. This model represents a domain duplicated in some halocyanins, while appearing once in others. This domain includes the characteristic copper ligand residues. This family does not include plastocyanins, and does not include certain divergent paralogs of halocyanin.
Probab=22.86 E-value=1.1e+02 Score=22.41 Aligned_cols=29 Identities=21% Similarity=0.167 Sum_probs=21.8
Q ss_pred ecCCCeeeeccCceEEEEEeecCCCCceeh
Q 033184 28 YPKPGFLRITDKETLIVESNYSSSHDHTGV 57 (125)
Q Consensus 28 yP~Pgs~kI~dGE~L~l~s~Ys~~~~hTGv 57 (125)
-++|..++|+.|++++.+-+- ...+|+=+
T Consensus 38 ~F~P~~ltV~~GdTVtw~~~~-d~~~HnV~ 66 (115)
T TIGR03102 38 AFDPPAIRVDPGTTVVWEWTG-EGGGHNVV 66 (115)
T ss_pred eEeCCEEEECCCCEEEEEECC-CCCCEEEE
Confidence 478889999999999987542 23568754
No 37
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=22.70 E-value=90 Score=18.98 Aligned_cols=25 Identities=12% Similarity=0.111 Sum_probs=16.6
Q ss_pred EEEeeeeec-CCCeeeeccCceEEEE
Q 033184 21 IVGMSTCYP-KPGFLRITDKETLIVE 45 (125)
Q Consensus 21 vVGMStCyP-~Pgs~kI~dGE~L~l~ 45 (125)
.+.+..+.+ .|+.+.++.||++++.
T Consensus 2 ~~a~~d~~~~~~~~Ls~~~Gd~i~v~ 27 (55)
T PF07653_consen 2 YRAIFDYVAEDPDELSFKKGDVIEVL 27 (55)
T ss_dssp EEESSSBESSSTTB-EB-TTEEEEEE
T ss_pred EEEeEEECCCCCCceEEecCCEEEEE
Confidence 344445544 5677999999999998
No 38
>COG1558 FlgC Flagellar basal body rod protein [Cell motility and secretion]
Probab=22.26 E-value=49 Score=25.86 Aligned_cols=16 Identities=25% Similarity=0.646 Sum_probs=14.6
Q ss_pred CCccCCCCCCCCcccE
Q 033184 6 PAYGNGKEAGNEAGYI 21 (125)
Q Consensus 6 P~YG~G~eaGNE~GYv 21 (125)
.+|-.|++.-||+|||
T Consensus 79 ~~YdP~hP~Ad~~GYV 94 (137)
T COG1558 79 LVYDPGHPDADAKGYV 94 (137)
T ss_pred eeeCCCCCCccccCce
Confidence 4799999999999997
No 39
>cd05762 Ig8_MLCK Eighth immunoglobulin (Ig)-like domain of human myosin light-chain kinase (MLCK). Ig8_MLCK: the eighth immunoglobulin (Ig)-like domain of human myosin light-chain kinase (MLCK). MLCK is a key regulator of different forms of cell motility involving actin and myosin II. Agonist stimulation of smooth muscle cells increases cytosolic Ca2+, which binds calmodulin. This Ca2+-calmodulin complex in turn binds to and activates MLCK. Activated MLCK leads to the phosphorylation of the 20 kDa myosin regulatory light chain (RLC) of myosin II and the stimulation of actin-activated myosin MgATPase activity. MLCK is widely present in vertebrate tissues; it phosphorylates the 20 kDa RLC of both smooth and nonmuscle myosin II. Phosphorylation leads to the activation of the myosin motor domain and altered structural properties of myosin II. In smooth muscle MLCK it is involved in initiating contraction. In nonmuscle cells, MLCK may participate in cell division and cell motility; it has
Probab=21.90 E-value=1.4e+02 Score=20.06 Aligned_cols=25 Identities=8% Similarity=0.130 Sum_probs=19.7
Q ss_pred CCCeeeeccCceEEEEEeecCCCCc
Q 033184 30 KPGFLRITDKETLIVESNYSSSHDH 54 (125)
Q Consensus 30 ~Pgs~kI~dGE~L~l~s~Ys~~~~h 54 (125)
.|-++++..|+.++|...++...+.
T Consensus 6 ~p~~~~v~~G~~v~l~C~~~G~p~p 30 (98)
T cd05762 6 FPEDMKVRAGESVELFCKVTGTQPI 30 (98)
T ss_pred CCcCEEEECCCEEEEEEEEcccCCC
Confidence 4557889999999999998876543
No 40
>PF08253 Leader_Erm: Erm Leader peptide ; InterPro: IPR013204 These short proteins are leader peptides (15-19 amino acids) of erm genes that code for resistance determinants in Staphylococcus aureus [].
Probab=20.98 E-value=22 Score=19.63 Aligned_cols=13 Identities=46% Similarity=0.812 Sum_probs=10.2
Q ss_pred hhhhhhhhhccCC
Q 033184 58 MGLFYILVADRVP 70 (125)
Q Consensus 58 MGlfyi~vAe~~p 70 (125)
||.|.|+|-+...
T Consensus 1 MG~fSiFVI~~vh 13 (19)
T PF08253_consen 1 MGMFSIFVINTVH 13 (19)
T ss_pred CceEEEEEEEeec
Confidence 8899998887644
No 41
>PTZ00382 Variant-specific surface protein (VSP); Provisional
Probab=20.44 E-value=58 Score=23.16 Aligned_cols=8 Identities=13% Similarity=0.306 Sum_probs=3.0
Q ss_pred HHHHHHHH
Q 033184 96 FVLAGVAI 103 (125)
Q Consensus 96 v~v~g~a~ 103 (125)
++++++++
T Consensus 76 ~~~v~~lv 83 (96)
T PTZ00382 76 VAVVGGLV 83 (96)
T ss_pred hhHHHHHH
Confidence 33333333
No 42
>PF14874 PapD-like: Flagellar-associated PapD-like
Probab=20.20 E-value=1.5e+02 Score=19.58 Aligned_cols=24 Identities=21% Similarity=0.351 Sum_probs=20.2
Q ss_pred eeeecCCCeeeeccCceEEEEEeecC
Q 033184 25 STCYPKPGFLRITDKETLIVESNYSS 50 (125)
Q Consensus 25 StCyP~Pgs~kI~dGE~L~l~s~Ys~ 50 (125)
-++.|++| ++..|+..+++..+..
T Consensus 50 ~~v~~~~g--~l~PG~~~~~~V~~~~ 73 (102)
T PF14874_consen 50 FSVEPPSG--FLAPGESVELEVTFSP 73 (102)
T ss_pred EEEECCCC--EECCCCEEEEEEEEEe
Confidence 36678888 7999999999999984
Done!