Query psy14777
Match_columns 158
No_of_seqs 112 out of 130
Neff 3.3
Searched_HMMs 46136
Date Fri Aug 16 20:21:20 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14777.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14777hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05511 ATP-synt_F6: Mitochon 100.0 1E-45 2.3E-50 277.0 5.6 96 53-148 1-99 (99)
2 KOG4634|consensus 100.0 7.3E-40 1.6E-44 246.9 9.3 100 55-156 2-101 (105)
3 PF05511 ATP-synt_F6: Mitochon 99.8 2E-20 4.4E-25 140.7 0.7 59 1-59 1-60 (99)
4 KOG4634|consensus 99.6 1.2E-15 2.5E-20 115.8 4.2 50 2-52 1-50 (105)
5 PF10775 ATP_sub_h: ATP syntha 85.1 0.47 1E-05 33.9 1.2 27 72-102 1-27 (67)
6 cd07657 F-BAR_Fes_Fer The F-BA 77.5 4.8 0.0001 33.8 4.9 39 91-139 19-58 (237)
7 cd07654 F-BAR_FCHSD The F-BAR 73.3 5.2 0.00011 34.4 4.1 33 91-133 19-52 (264)
8 cd07678 F-BAR_FCHSD1 The F-BAR 64.9 11 0.00024 32.7 4.4 34 91-134 19-53 (263)
9 cd07656 F-BAR_srGAP The F-BAR 60.9 14 0.0003 31.3 4.1 36 89-134 17-53 (241)
10 cd07683 F-BAR_srGAP1 The F-BAR 58.4 19 0.00042 31.6 4.7 36 88-133 16-52 (253)
11 CHL00067 rps2 ribosomal protei 56.1 27 0.00058 29.4 5.1 60 85-146 106-166 (230)
12 cd07682 F-BAR_srGAP2 The F-BAR 56.0 22 0.00048 31.4 4.7 54 88-153 16-70 (263)
13 cd07686 F-BAR_Fer The F-BAR (F 52.5 27 0.00059 29.8 4.6 37 91-137 19-56 (234)
14 PLN02955 8-amino-7-oxononanoat 48.3 38 0.00082 31.8 5.2 43 85-127 117-160 (476)
15 PF00611 FCH: Fes/CIP4, and EF 48.1 41 0.00089 22.6 4.2 32 91-132 23-55 (91)
16 TIGR01011 rpsB_bact ribosomal 47.5 48 0.001 27.8 5.2 55 90-146 106-160 (225)
17 cd07684 F-BAR_srGAP3 The F-BAR 47.1 37 0.00081 29.8 4.7 36 88-133 16-52 (253)
18 cd00938 HisRS_RNA HisRS_RNA bi 46.6 58 0.0013 21.8 4.5 33 94-133 12-44 (45)
19 PRK05299 rpsB 30S ribosomal pr 42.5 55 0.0012 28.1 5.0 55 90-146 108-162 (258)
20 cd07677 F-BAR_FCHSD2 The F-BAR 42.0 36 0.00078 29.8 3.8 36 89-134 6-42 (260)
21 cd00552 RaiA RaiA ("ribosome-a 40.3 34 0.00074 23.5 2.8 27 106-132 6-32 (93)
22 cd07610 FCH_F-BAR The Extended 40.1 52 0.0011 25.1 4.1 33 91-133 14-47 (191)
23 PF10775 ATP_sub_h: ATP syntha 39.2 21 0.00046 25.5 1.7 21 32-52 9-29 (67)
24 PF09580 Spore_YhcN_YlaJ: Spor 38.5 43 0.00092 25.9 3.4 33 91-126 143-175 (177)
25 PF10303 DUF2408: Protein of u 35.7 1E+02 0.0022 24.1 5.1 22 91-112 45-67 (134)
26 PRK10324 translation inhibitor 35.6 45 0.00098 25.0 3.1 28 106-133 7-34 (113)
27 cd07675 F-BAR_FNBP1L The F-BAR 34.3 79 0.0017 27.3 4.7 36 91-136 19-55 (252)
28 PF08060 NOSIC: NOSIC (NUC001) 32.9 83 0.0018 20.7 3.7 25 113-144 10-34 (53)
29 COG1544 Ribosome-associated pr 30.3 52 0.0011 25.1 2.6 28 106-133 7-34 (110)
30 COG0052 RpsB Ribosomal protein 30.0 77 0.0017 27.9 3.9 77 62-146 85-161 (252)
31 PF02482 Ribosomal_S30AE: Sigm 29.6 51 0.0011 22.7 2.3 27 106-132 6-32 (97)
32 PF09779 Ima1_N: Ima1 N-termin 29.5 1.1E+02 0.0024 23.5 4.4 36 88-130 82-120 (131)
33 PRK12311 rpsB 30S ribosomal pr 29.4 1.2E+02 0.0027 27.2 5.2 60 85-146 97-157 (326)
34 smart00830 CM_2 Chorismate mut 27.0 1.3E+02 0.0028 20.1 3.9 38 92-132 21-58 (79)
35 smart00055 FCH Fes/CIP4 homolo 25.2 1.4E+02 0.0031 20.1 3.9 29 91-129 23-52 (87)
36 PF01817 CM_2: Chorismate muta 25.2 2.2E+02 0.0049 19.2 5.2 39 92-133 21-59 (81)
37 PRK10470 ribosome hibernation 23.7 92 0.002 22.0 2.8 28 106-133 7-34 (95)
38 COG2102 Predicted ATPases of P 23.6 52 0.0011 28.4 1.7 42 111-152 153-194 (223)
39 PF06877 RraB: Regulator of ri 23.4 1.1E+02 0.0024 21.7 3.2 25 109-133 74-98 (104)
40 PF11934 DUF3452: Domain of un 22.8 81 0.0017 24.3 2.5 32 92-131 29-60 (136)
41 KOG2269|consensus 22.3 68 0.0015 30.6 2.4 25 114-138 88-112 (531)
42 TIGR01795 CM_mono_cladeE monof 21.7 2.9E+02 0.0062 20.2 5.2 39 92-133 29-67 (94)
43 PF04368 DUF507: Protein of un 21.2 3.3E+02 0.0071 22.6 5.9 38 83-125 138-179 (183)
44 PF14824 Sirohm_synth_M: Siroh 21.1 98 0.0021 19.1 2.2 20 103-126 10-29 (30)
45 COG2952 Uncharacterized protei 20.7 1.2E+02 0.0026 25.6 3.2 35 86-125 141-179 (183)
46 TIGR00289 conserved hypothetic 20.3 56 0.0012 27.5 1.3 42 111-152 151-192 (222)
No 1
>PF05511 ATP-synt_F6: Mitochondrial ATP synthase coupling factor 6; InterPro: IPR008387 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit F6 (or coupling factor 6) found in the F0 complex of F-ATPases in mitochondria. The F6 subunit is part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In mitochondria, the peripheral stalk is composed of one copy each of subunits OSCP (oligomycin sensitivity conferral protein), F6, B and D []. There is no homologue of subunit F6 in bacterial or chloroplast F-ATPase, whose peripheral stalks are composed of one copy of the delta subunit (homologous to OSCP), and two copies of subunit B in bacteria, or one copy each of subunits B and B' in chloroplasts and photosynthetic bacteria. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0000276 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o); PDB: 2WSS_V 2CLY_C 1VZS_A.
Probab=100.00 E-value=1e-45 Score=277.04 Aligned_cols=96 Identities=56% Similarity=0.855 Sum_probs=52.8
Q ss_pred chhh-hhhhhhhhhhhhhhhhhhhhhHHHhhhcCChHHHHHHHHHHhh--hhcCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q psy14777 53 MLTP-QLFVCVRKNVSQNLTRNLATSYVALKNASDPIQQLFLDKLSEY--KSKSTGGKLVDPTPEIERELKADLSKTAKQ 129 (158)
Q Consensus 53 Mls~-~l~~~~r~a~~~~~rRnig~sA~a~~ka~DPIQkLFldKIREY--KsKs~gGklVDa~Pe~ekel~~el~kL~r~ 129 (158)
|+++ ++.+.+|++++++++||||+||++++|++|||||||||||||| |+|++||+|||+||||+|||++||+||+++
T Consensus 1 m~~~~~~~~~~~~~~s~~~~Rni~~sa~~~~k~~DPIQklFldKIREY~~Ksks~gGklVD~~Pe~~kel~eel~kL~r~ 80 (99)
T PF05511_consen 1 MALQRRLSSLLRSAVSVHLRRNIGTSAVAFNKALDPIQKLFLDKIREYNQKSKSSGGKLVDAGPEYEKELNEELEKLARQ 80 (99)
T ss_dssp --------------------------------S--TTTHHHHHHHHHHHHHHTTTSS-STT--THHHHHHHHHHHHHHHH
T ss_pred CchHHHHHHHHHHHHHHHHHHHhhhhHHHHhcccChHHHHHHHHHHHHHHHhccCCCCCCCCCHHHHHHHHHHHHHHHHH
Confidence 4444 4557889999999999999999999999999999999999999 888899999999999999999999999999
Q ss_pred hCCCCCCcCccCCCCcCCC
Q psy14777 130 YGGDGKEDMTKFPNFQFPE 148 (158)
Q Consensus 130 YGgg~~~DmtkFP~FkF~e 148 (158)
||||+|+||++||+|||+|
T Consensus 81 YG~g~~~Dm~kFP~FkF~d 99 (99)
T PF05511_consen 81 YGGGSGVDMTKFPTFKFED 99 (99)
T ss_dssp HHSS---TTTS-SS--SSS
T ss_pred hCCcccccHHhCCCCCCCC
Confidence 9999999999999999997
No 2
>KOG4634|consensus
Probab=100.00 E-value=7.3e-40 Score=246.94 Aligned_cols=100 Identities=43% Similarity=0.729 Sum_probs=89.0
Q ss_pred hhhhhhhhhhhhhhhhhhhhhhhHHHhhhcCChHHHHHHHHHHhhhhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhCCCC
Q psy14777 55 TPQLFVCVRKNVSQNLTRNLATSYVALKNASDPIQQLFLDKLSEYKSKSTGGKLVDPTPEIERELKADLSKTAKQYGGDG 134 (158)
Q Consensus 55 s~~l~~~~r~a~~~~~rRnig~sA~a~~ka~DPIQkLFldKIREYKsKs~gGklVDa~Pe~ekel~~el~kL~r~YGgg~ 134 (158)
++++++..++ ++..++|++|++|+|++|++|||||+|+||||||++||++|+|||++|||++||++||+||+.+|| +.
T Consensus 2 ~qrlfr~s~v-lrs~vs~~~gv~a~a~nk~~DpIqqlFldKvREy~~ks~~Gklvds~pe~e~eLk~el~rla~qfg-~~ 79 (105)
T KOG4634|consen 2 LQRLFRFSSV-LRSAVSVHLGVTATAFNKELDPIQQLFLDKVREYKKKSPAGKLVDSDPEYEQELKEELFRLAQQFG-LA 79 (105)
T ss_pred hHHHHHHHHH-HHHHHHHhhchhhhHHHhhhChHHHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhC-cc
Confidence 4666655444 444667788999999999999999999999999999999999999999999999999999999999 45
Q ss_pred CCcCccCCCCcCCCCCcccccC
Q psy14777 135 KEDMTKFPNFQFPEPKIEPQVS 156 (158)
Q Consensus 135 ~~DmtkFP~FkF~epk~d~i~~ 156 (158)
+.||.+||+||||+||+||+.+
T Consensus 80 ~~Dm~~fp~fkfed~kvdpV~~ 101 (105)
T KOG4634|consen 80 NADMLTFPPFKFEDPKVDPVIE 101 (105)
T ss_pred CchhhhCCCCCCCCCCcchHhh
Confidence 7899999999999999999643
No 3
>PF05511 ATP-synt_F6: Mitochondrial ATP synthase coupling factor 6; InterPro: IPR008387 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit F6 (or coupling factor 6) found in the F0 complex of F-ATPases in mitochondria. The F6 subunit is part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In mitochondria, the peripheral stalk is composed of one copy each of subunits OSCP (oligomycin sensitivity conferral protein), F6, B and D []. There is no homologue of subunit F6 in bacterial or chloroplast F-ATPase, whose peripheral stalks are composed of one copy of the delta subunit (homologous to OSCP), and two copies of subunit B in bacteria, or one copy each of subunits B and B' in chloroplasts and photosynthetic bacteria. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0000276 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o); PDB: 2WSS_V 2CLY_C 1VZS_A.
Probab=99.78 E-value=2e-20 Score=140.68 Aligned_cols=59 Identities=46% Similarity=0.591 Sum_probs=20.9
Q ss_pred CchhH-HHHHHhhhhhhhhhhhhhhhHHHhhhccChHHHHHHHHHhhhhccccchhhhhh
Q psy14777 1 MMTPQ-LFVCVRKNVSQNLTRNLATSYVALKNASDPIQQLFLDKLSEYKSKSAMLTPQLF 59 (158)
Q Consensus 1 m~~~~-l~~~~r~~~~~~~~rn~g~~~~~~~k~~dpiq~lf~dkirey~~ks~Mls~~l~ 59 (158)
|++++ +.+.+|++++++++||||++|++++|+.||||||||||||||++||+.-.-.++
T Consensus 1 m~~~~~~~~~~~~~~s~~~~Rni~~sa~~~~k~~DPIQklFldKIREY~~Ksks~gGklV 60 (99)
T PF05511_consen 1 MALQRRLSSLLRSAVSVHLRRNIGTSAVAFNKALDPIQKLFLDKIREYNQKSKSSGGKLV 60 (99)
T ss_dssp --------------------------------S--TTTHHHHHHHHHHHHHHTTTSS-ST
T ss_pred CchHHHHHHHHHHHHHHHHHHHhhhhHHHHhcccChHHHHHHHHHHHHHHHhccCCCCCC
Confidence 55555 446899999999999999999999999999999999999999888775444443
No 4
>KOG4634|consensus
Probab=99.58 E-value=1.2e-15 Score=115.85 Aligned_cols=50 Identities=42% Similarity=0.557 Sum_probs=43.2
Q ss_pred chhHHHHHHhhhhhhhhhhhhhhhHHHhhhccChHHHHHHHHHhhhhcccc
Q psy14777 2 MTPQLFVCVRKNVSQNLTRNLATSYVALKNASDPIQQLFLDKLSEYKSKSA 52 (158)
Q Consensus 2 ~~~~l~~~~r~~~~~~~~rn~g~~~~~~~k~~dpiq~lf~dkirey~~ks~ 52 (158)
|+|++++.+++.++. +++|+|++|+++||+.|||||||+||||||++||.
T Consensus 1 ~~qrlfr~s~vlrs~-vs~~~gv~a~a~nk~~DpIqqlFldKvREy~~ks~ 50 (105)
T KOG4634|consen 1 MLQRLFRFSSVLRSA-VSVHLGVTATAFNKELDPIQQLFLDKVREYKKKSP 50 (105)
T ss_pred ChHHHHHHHHHHHHH-HHHhhchhhhHHHhhhChHHHHHHHHHHHHHhcCC
Confidence 578888876655554 66889999999999999999999999999999965
No 5
>PF10775 ATP_sub_h: ATP synthase complex subunit h; InterPro: IPR019711 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit H found in the F0 complex of F-ATPases from fungal mitochondria. Subunit H is homologous to the mammalian factor F6, and is essential for the correct assembly and/or functioning of F-ATPases, since yeast cells lacking it are not able to grow on non-fermentable carbon sources. Subunit H occupies a central place in the peripheral stalk between the F1 sector and the membrane [].
Probab=85.08 E-value=0.47 Score=33.87 Aligned_cols=27 Identities=33% Similarity=0.551 Sum_probs=21.2
Q ss_pred hhhhhhHHHhhhcCChHHHHHHHHHHhhhhc
Q psy14777 72 RNLATSYVALKNASDPIQQLFLDKLSEYKSK 102 (158)
Q Consensus 72 Rnig~sA~a~~ka~DPIQkLFldKIREYKsK 102 (158)
|+|++ ++ . -.|.||-|+|.-||.||-.
T Consensus 1 R~Fst-~~-~--r~d~VQDLYLkELKayKp~ 27 (67)
T PF10775_consen 1 RSFST-TP-R--RADLVQDLYLKELKAYKPP 27 (67)
T ss_pred Ccccc-cc-c--cccHHHHHHHHHHHhcCCC
Confidence 67777 33 2 3699999999999999655
No 6
>cd07657 F-BAR_Fes_Fer The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Fes (feline sarcoma) and Fer (Fes related) tyrosine kinases. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Fes (feline sarcoma), also called Fps (Fujinami poultry sarcoma), and Fer (Fes related) are cytoplasmic (or nonreceptor) tyrosine kinases that play roles in haematopoiesis, inflammation and immunity, growth factor signaling, cytoskeletal regulation, cell migration and adhesion, and the regulation of cell-cell interactions. Although Fes and Fer show redundancy in their biological functions, they show differences in their expression patterns. Fer is ubiquitously expressed while Fes is expressed predominantly in myeloid and endothelial cells. Fes and Fer contain an N-terminal F-BAR domain, an SH2 domain, and a C-terminal catalytic kinase domain. F-BAR domains form banana-shaped dimers with a posit
Probab=77.49 E-value=4.8 Score=33.84 Aligned_cols=39 Identities=21% Similarity=0.228 Sum_probs=32.0
Q ss_pred HHHHHHHhh-hhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhCCCCCCcCc
Q psy14777 91 LFLDKLSEY-KSKSTGGKLVDPTPEIERELKADLSKTAKQYGGDGKEDMT 139 (158)
Q Consensus 91 LFldKIREY-KsKs~gGklVDa~Pe~ekel~~el~kL~r~YGgg~~~Dmt 139 (158)
-||+.|+.| +.+ .++++||...|.+|.++|..++..|++
T Consensus 19 ~lLe~i~~F~reR----------a~iE~EYA~~L~~L~kq~~k~~~~~~~ 58 (237)
T cd07657 19 RLLETMKKYMAKR----------AKSDREYASTLGSLANQGLKIEAGDDL 58 (237)
T ss_pred HHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHhhCcCCCcccC
Confidence 478999999 666 579999999999999999877544544
No 7
>cd07654 F-BAR_FCHSD The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of FCH and double SH3 domains proteins (FCHSD). F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. This subfamily is composed of FCH and double SH3 domain (FCHSD) proteins, so named as they contain an N-terminal F-BAR domain and two SH3 domains at the C-terminus. Vertebrates harbor two subfamily members, FCHSD1 and FCHSD2, which have been characterized only in silico. Their biological function is still unknown. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.
Probab=73.25 E-value=5.2 Score=34.41 Aligned_cols=33 Identities=33% Similarity=0.461 Sum_probs=29.2
Q ss_pred HHHHHHHhh-hhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhCCC
Q psy14777 91 LFLDKLSEY-KSKSTGGKLVDPTPEIERELKADLSKTAKQYGGD 133 (158)
Q Consensus 91 LFldKIREY-KsKs~gGklVDa~Pe~ekel~~el~kL~r~YGgg 133 (158)
-||+.|++| +.+ .++|+||...|.+|+++|..-
T Consensus 19 ~lLedi~~F~reR----------a~IE~EYa~~L~kLakky~~K 52 (264)
T cd07654 19 DLLEDIRTYSQKK----------AAIEREYGQALQKLASQFLKR 52 (264)
T ss_pred HHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHhcc
Confidence 488999999 777 589999999999999999763
No 8
>cd07678 F-BAR_FCHSD1 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of FCH and double SH3 domains 1 (FCHSD1). F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. FCH and double SH3 domains 1 (FCHSD1) contains an N-terminal F-BAR domain and two SH3 domains at the C-terminus. It has been characterized only in silico, and its biological function is still unknown. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.
Probab=64.95 E-value=11 Score=32.73 Aligned_cols=34 Identities=29% Similarity=0.471 Sum_probs=29.6
Q ss_pred HHHHHHHhh-hhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhCCCC
Q psy14777 91 LFLDKLSEY-KSKSTGGKLVDPTPEIERELKADLSKTAKQYGGDG 134 (158)
Q Consensus 91 LFldKIREY-KsKs~gGklVDa~Pe~ekel~~el~kL~r~YGgg~ 134 (158)
-||+.|++| +.+ .++++||...|.+|.++|.+..
T Consensus 19 ~~le~~~~f~k~R----------~~iE~eYa~~L~~L~k~~~~k~ 53 (263)
T cd07678 19 ELLEDIRSYSKQR----------AAIEREYGQALQRLASQFLKRD 53 (263)
T ss_pred HHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHcccc
Confidence 478999999 666 5899999999999999998765
No 9
>cd07656 F-BAR_srGAP The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase Activating Proteins. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Slit-Robo GTPase Activating Proteins (srGAPs) are Rho GAPs that interact with Robo1, the transmembrane receptor of Slit proteins. Slit proteins are secreted proteins that control axon guidance and the migration of neurons and leukocytes. Vertebrates contain three isoforms of srGAPs, all of which are expressed during embryonic and early development in the nervous system but with different localization and timing. srGAPs contain an N-terminal F-BAR domain, a Rho GAP domain, and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.
Probab=60.85 E-value=14 Score=31.28 Aligned_cols=36 Identities=31% Similarity=0.502 Sum_probs=30.7
Q ss_pred HHHHHHHHHhh-hhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhCCCC
Q psy14777 89 QQLFLDKLSEY-KSKSTGGKLVDPTPEIERELKADLSKTAKQYGGDG 134 (158)
Q Consensus 89 QkLFldKIREY-KsKs~gGklVDa~Pe~ekel~~el~kL~r~YGgg~ 134 (158)
+--||+.|++| +.+ .++|+||...|.+|.++|....
T Consensus 17 ~i~lLed~~~F~r~R----------aeIE~EYs~~L~kL~k~~~~K~ 53 (241)
T cd07656 17 QVQLLADLQDYFRRR----------AEIELEYSRSLEKLADRFSSKH 53 (241)
T ss_pred HHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHhcccc
Confidence 34589999999 666 5899999999999999998764
No 10
>cd07683 F-BAR_srGAP1 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase Activating Protein 1. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Slit-Robo GTPase Activating Proteins (srGAPs) are Rho GAPs that interact with Robo1, the transmembrane receptor of Slit proteins. Slit proteins are secreted proteins that control axon guidance and the migration of neurons and leukocytes. Vertebrates contain three isoforms of srGAPs. srGAP1, also called Rho GTPase-Activating Protein 13 (ARHGAP13), is a Cdc42- and RhoA-specific GAP and is expressed later in the development of CNS (central nervous system) tissues. It is an important downstream signaling molecule of Robo1. srGAP1 contains an N-terminal F-BAR domain, a Rho GAP domain, and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-cha
Probab=58.40 E-value=19 Score=31.57 Aligned_cols=36 Identities=28% Similarity=0.526 Sum_probs=31.6
Q ss_pred HHHHHHHHHHhh-hhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhCCC
Q psy14777 88 IQQLFLDKLSEY-KSKSTGGKLVDPTPEIERELKADLSKTAKQYGGD 133 (158)
Q Consensus 88 IQkLFldKIREY-KsKs~gGklVDa~Pe~ekel~~el~kL~r~YGgg 133 (158)
+|.-+|.-|+|| +.+ .|+|+||..-|+||+..|-.-
T Consensus 16 ~~~~lLqDlqdF~RrR----------AeIE~EYS~~L~KLa~~f~~K 52 (253)
T cd07683 16 MRVQLLQDLQDFFRKK----------AEIESEYSRNLEKLAERFMAK 52 (253)
T ss_pred HHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHhc
Confidence 566788899999 666 689999999999999999875
No 11
>CHL00067 rps2 ribosomal protein S2
Probab=56.14 E-value=27 Score=29.36 Aligned_cols=60 Identities=25% Similarity=0.298 Sum_probs=43.3
Q ss_pred CChHH-HHHHHHHHhhhhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhCCCCCCcCccCCCCcC
Q psy14777 85 SDPIQ-QLFLDKLSEYKSKSTGGKLVDPTPEIERELKADLSKTAKQYGGDGKEDMTKFPNFQF 146 (158)
Q Consensus 85 ~DPIQ-kLFldKIREYKsKs~gGklVDa~Pe~ekel~~el~kL~r~YGgg~~~DmtkFP~FkF 146 (158)
.++.+ +.++.+++++......|.+-+-+....-.+..|..||.+.|||- .+|.+.|++=|
T Consensus 106 TN~~~i~~~i~~~~~l~~~~~~~~~~~~~kk~~~~~~~~~~kl~k~~~Gi--~~m~~~P~~ii 166 (230)
T CHL00067 106 TNWSTTKTRLQKLRDLRMEEKTGLFNRLPKKEAAILKRQLSRLEKYLGGI--KYMTKLPDIVI 166 (230)
T ss_pred cCHHHHHHHHHHHHHHHHHhhccchhcccHhHHHHHHHHHHHHHHhhccc--cccccCCCEEE
Confidence 34443 56788888775444445455566666777888999999999985 58999998644
No 12
>cd07682 F-BAR_srGAP2 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase Activating Protein 2. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Slit-Robo GTPase Activating Proteins (srGAPs) are Rho GAPs that interact with Robo1, the transmembrane receptor of Slit proteins. Slit proteins are secreted proteins that control axon guidance and the migration of neurons and leukocytes. Vertebrates contain three isoforms of srGAPs. srGAP2 is expressed in zones of neuronal differentiation. It plays a role in the regeneration of neurons and axons. srGAP2 contains an N-terminal F-BAR domain, a Rho GAP domain, and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.
Probab=56.00 E-value=22 Score=31.41 Aligned_cols=54 Identities=24% Similarity=0.432 Sum_probs=38.0
Q ss_pred HHHHHHHHHHhh-hhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhCCCCCCcCccCCCCcCCCCCccc
Q psy14777 88 IQQLFLDKLSEY-KSKSTGGKLVDPTPEIERELKADLSKTAKQYGGDGKEDMTKFPNFQFPEPKIEP 153 (158)
Q Consensus 88 IQkLFldKIREY-KsKs~gGklVDa~Pe~ekel~~el~kL~r~YGgg~~~DmtkFP~FkF~epk~d~ 153 (158)
+|--+|.-|+|| +.+ .|+|+||..-|+||+..|-.-.. -++=+-++=++|.+-|
T Consensus 16 ~~i~lLqDLqdFyRrR----------AeIE~EYS~~L~KLA~~f~~K~~--~~~~~~s~~d~~~~Sp 70 (263)
T cd07682 16 LRVQLLQDLQDFFRKK----------AEIEMDYSRNLEKLAERFLAKTR--STKDQQFKKDQNVLSP 70 (263)
T ss_pred HHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHhccc--ccccccccCCCCccCH
Confidence 456688899999 666 68999999999999999987521 1222334445555544
No 13
>cd07686 F-BAR_Fer The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Fer (Fes related) tyrosine kinase. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Fer (Fes related) is a cytoplasmic (or nonreceptor) tyrosine kinase expressed in a wide variety of tissues, and is found to reside in both the cytoplasm and the nucleus. It plays important roles in neuronal polarization and neurite development, cytoskeletal reorganization, cell migration, growth factor signaling, and the regulation of cell-cell interactions mediated by adherens junctions and focal adhesions. Fer kinase also regulates cell cycle progression in malignant cells. It contains an N-terminal F-BAR domain, an SH2 domain, and a C-terminal catalytic kinase domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membran
Probab=52.51 E-value=27 Score=29.82 Aligned_cols=37 Identities=11% Similarity=0.292 Sum_probs=30.2
Q ss_pred HHHHHHHhh-hhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhCCCCCCc
Q psy14777 91 LFLDKLSEY-KSKSTGGKLVDPTPEIERELKADLSKTAKQYGGDGKED 137 (158)
Q Consensus 91 LFldKIREY-KsKs~gGklVDa~Pe~ekel~~el~kL~r~YGgg~~~D 137 (158)
-+|+.|+.| +.+ .++++||...|.+|.++|..+...+
T Consensus 19 ~lLE~i~~f~~eR----------akiEkEYA~~L~~L~kq~~kk~~~~ 56 (234)
T cd07686 19 RLLETVKKFMALR----------VKSDKEYASTLQNLCNQVDKESTSQ 56 (234)
T ss_pred HHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHhcccCccc
Confidence 589999999 666 4689999999999999997654333
No 14
>PLN02955 8-amino-7-oxononanoate synthase
Probab=48.28 E-value=38 Score=31.76 Aligned_cols=43 Identities=23% Similarity=0.302 Sum_probs=34.7
Q ss_pred CCh-HHHHHHHHHHhhhhcCCCCCCCCCCHHHHHHHHHHHHHHH
Q psy14777 85 SDP-IQQLFLDKLSEYKSKSTGGKLVDPTPEIERELKADLSKTA 127 (158)
Q Consensus 85 ~DP-IQkLFldKIREYKsKs~gGklVDa~Pe~ekel~~el~kL~ 127 (158)
.|| |++.+.+.|++|-.-+.|-.++.....+..+++++|.++-
T Consensus 117 ~~p~v~~a~~~ai~~yG~g~~gSrl~~G~~~~h~~LE~~LA~f~ 160 (476)
T PLN02955 117 SHPTISNAAANAAKEYGMGPKGSALICGYTTYHRLLESSLADLK 160 (476)
T ss_pred CCHHHHHHHHHHHHHcCCCCCCcCccccChHHHHHHHHHHHHHH
Confidence 567 7999999999997655566788888999999998776553
No 15
>PF00611 FCH: Fes/CIP4, and EFC/F-BAR homology domain; InterPro: IPR001060 The FCH domain is a short conserved region of around 60 amino acids first described as a region of homology between FER and CIP4 proteins []. Many proteins containing an FCH domain are involved in the regulation of cytoskeletal rearrangements, vesicular transport and endocytosis. In the CIP4 protein the FCH domain binds to microtubules []. The FCH domain is always found N-terminally and is followed by a coiled-coil region. Proteins containing an FCH domain can be divided in 3 classes []: A subfamily of protein kinases usually associated with an SH2 domain: Fps/fes (Fujimani poultry sarcoma/feline sarcoma) proto-oncogenes. They are non-receptor protein-tyrosine kinases preferentially expressed in myeloid lineage. The viral oncogene has an unregulated kinase activity which abrogates the need for cytokines and influences differentiation of haematopoietic progenitor cells. Fes related protein (fer). It is an ubiquitously expressed homologue of Fes. Adaptor proteins usually associated with a C-terminal SH3 domain: Schizosaccharomyces pombe CDC15 protein. It mediates cytoskeletal rearrangements required for cytokinesis. It is essential for viability. CD2 cytoplasmic domain binding protein. Mammalian Cdc42-interacting protein 4 (CIP4). It may act as a link between Cdc42 signaling and regulation of the actin cytoskeleton. Mammalian PACSIN proteins. A family of cytoplasmic phosphoproteins playing a role in vesicle formation and transport. A subfamily of Rho-GAP proteins: Mammalian RhoGAP4 proteins. They may down-regulate Rho-like GTPases in hematopoietic cells. Yeast hypothetical protein YBR260C. Caenorhabditis elegans hypothetical protein ZK669.1. ; PDB: 2EFK_A 2EFL_A 2X3W_A 2X3X_C 2X3V_C 3I2W_A 3ABH_B 3Q0K_B 3HAJ_A 3ACO_B ....
Probab=48.13 E-value=41 Score=22.57 Aligned_cols=32 Identities=28% Similarity=0.532 Sum_probs=27.0
Q ss_pred HHHHHHHhh-hhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhCC
Q psy14777 91 LFLDKLSEY-KSKSTGGKLVDPTPEIERELKADLSKTAKQYGG 132 (158)
Q Consensus 91 LFldKIREY-KsKs~gGklVDa~Pe~ekel~~el~kL~r~YGg 132 (158)
.+++.|++| +.+ .++|++|...|.||.++|..
T Consensus 23 ~~~~~l~~~~keR----------a~lE~~Yak~L~kl~~~~~~ 55 (91)
T PF00611_consen 23 KLLEELASFFKER----------ASLEEEYAKSLQKLAKKFKK 55 (91)
T ss_dssp HHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHhc
Confidence 478888888 666 57999999999999999974
No 16
>TIGR01011 rpsB_bact ribosomal protein S2, bacterial type. TIGR01012 describes the archaeal and cytosolic forms.
Probab=47.49 E-value=48 Score=27.76 Aligned_cols=55 Identities=27% Similarity=0.393 Sum_probs=35.4
Q ss_pred HHHHHHHHhhhhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhCCCCCCcCccCCCCcC
Q psy14777 90 QLFLDKLSEYKSKSTGGKLVDPTPEIERELKADLSKTAKQYGGDGKEDMTKFPNFQF 146 (158)
Q Consensus 90 kLFldKIREYKsKs~gGklVDa~Pe~ekel~~el~kL~r~YGgg~~~DmtkFP~FkF 146 (158)
+..+.+++++.+....|..=.-+-...-.+..+.+||.+.|||- -+|.++|+.=|
T Consensus 106 ~~~i~~l~~l~~~~~~~~f~~~~kke~~~~~k~~~kl~k~~~Gi--~~m~~~Pd~vi 160 (225)
T TIGR01011 106 RKSIKKLKKLEKMEEDGTFDDLTKKEALMLSREKEKLEKSLGGI--KDMKKLPDLLF 160 (225)
T ss_pred HHHHHHHHHHHHHHhcCccccccHHHHHHHHHHHHHHHHhccCc--cccccCCCEEE
Confidence 45666777664433223222333334456788899999999986 58999998644
No 17
>cd07684 F-BAR_srGAP3 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase Activating Protein 3. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Slit-Robo GTPase Activating Proteins (srGAPs) are Rho GAPs that interact with Robo1, the transmembrane receptor of Slit proteins. Slit proteins are secreted proteins that control axon guidance and the migration of neurons and leukocytes. Vertebrates contain three isoforms of srGAPs. srGAP3, also called MEGAP (MEntal disorder associated GTPase-Activating Protein), is a Rho GAP with activity towards Rac1 and Cdc42. It impacts cell migration by regulating actin and microtubule cytoskeletal dynamics. The association between srGAP3 haploinsufficiency and mental retardation is under debate. srGAP3 contains an N-terminal F-BAR domain, a Rho GAP domain, and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers wit
Probab=47.11 E-value=37 Score=29.84 Aligned_cols=36 Identities=31% Similarity=0.492 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhh-hhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhCCC
Q psy14777 88 IQQLFLDKLSEY-KSKSTGGKLVDPTPEIERELKADLSKTAKQYGGD 133 (158)
Q Consensus 88 IQkLFldKIREY-KsKs~gGklVDa~Pe~ekel~~el~kL~r~YGgg 133 (158)
++--+|.-|+|| +.+ .|+|+||..-|+||+..|-.-
T Consensus 16 ~~i~~LqDLqdFyRrR----------AeIE~EYS~~L~KLA~~f~~K 52 (253)
T cd07684 16 SRLQLLQDLQEFFRRK----------AEIELEYSRSLEKLAERFSSK 52 (253)
T ss_pred HHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHhh
Confidence 456678889999 766 689999999999999999764
No 18
>cd00938 HisRS_RNA HisRS_RNA binding domain. This short RNA-binding domain is found at the N-terminus of HisRS in several higher eukaryote aminoacyl-tRNA synthetases (aaRSs). This domain consists of a helix- turn- helix structure, which is similar to other RNA-binding proteins. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions, which are important for the formation of aaRSs into multienzyme complexes.
Probab=46.58 E-value=58 Score=21.80 Aligned_cols=33 Identities=27% Similarity=0.450 Sum_probs=20.3
Q ss_pred HHHHhhhhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhCCC
Q psy14777 94 DKLSEYKSKSTGGKLVDPTPEIERELKADLSKTAKQYGGD 133 (158)
Q Consensus 94 dKIREYKsKs~gGklVDa~Pe~ekel~~el~kL~r~YGgg 133 (158)
|++|+-|+..+.- ..+..|. ..|-.|..+||++
T Consensus 12 e~VRkLKa~KA~k------~~i~~eV-~~LL~LKaqlg~~ 44 (45)
T cd00938 12 ELVRKLKAEKASK------EQIAEEV-AKLLELKAQLGGD 44 (45)
T ss_pred HHHHHHHHccCCH------HHHHHHH-HHHHHHHHHhCCC
Confidence 7888887764432 2233333 3455689999996
No 19
>PRK05299 rpsB 30S ribosomal protein S2; Provisional
Probab=42.47 E-value=55 Score=28.11 Aligned_cols=55 Identities=25% Similarity=0.363 Sum_probs=35.9
Q ss_pred HHHHHHHHhhhhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhCCCCCCcCccCCCCcC
Q psy14777 90 QLFLDKLSEYKSKSTGGKLVDPTPEIERELKADLSKTAKQYGGDGKEDMTKFPNFQF 146 (158)
Q Consensus 90 kLFldKIREYKsKs~gGklVDa~Pe~ekel~~el~kL~r~YGgg~~~DmtkFP~FkF 146 (158)
+-.+.+++++.+....|..=.-+-...-.+..+.+||.+.|||- -+|.++|++=|
T Consensus 108 ~~~i~~l~~l~~~~~~~~~~~~~kke~~~~~k~~~kl~k~~~Gi--~~m~~~Pd~ii 162 (258)
T PRK05299 108 RKSIKRLKELEKMEEDGTFEKLTKKEALMLTRELEKLEKSLGGI--KDMGGLPDALF 162 (258)
T ss_pred HHHHHHHHHHHHHHhcCcccccCHHHHHHHHHHHHHHHHhccCc--cccccCCCEEE
Confidence 44677777775443333221222233445688999999999996 68999998754
No 20
>cd07677 F-BAR_FCHSD2 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of FCH and double SH3 domains 2 (FCHSD2). F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. FCH and double SH3 domains 2 (FCHSD2) contains an N-terminal F-BAR domain and two SH3 domains at the C-terminus. It has been characterized only in silico, and its biological function is still unknown. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.
Probab=41.98 E-value=36 Score=29.83 Aligned_cols=36 Identities=19% Similarity=0.164 Sum_probs=30.0
Q ss_pred HHHHHHHHHhh-hhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhCCCC
Q psy14777 89 QQLFLDKLSEY-KSKSTGGKLVDPTPEIERELKADLSKTAKQYGGDG 134 (158)
Q Consensus 89 QkLFldKIREY-KsKs~gGklVDa~Pe~ekel~~el~kL~r~YGgg~ 134 (158)
|--+|+-|++| +.+ .++|+||...|.+|++.|+...
T Consensus 6 e~~~LqDiqqFyreR----------s~IEkEYS~kL~kL~kky~~Kk 42 (260)
T cd07677 6 QMTKLQAKHQAECKL----------LEDEREFSQKIAAIESEYAQKE 42 (260)
T ss_pred HHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHhh
Confidence 45678899998 555 2899999999999999999754
No 21
>cd00552 RaiA RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site. RaiA is also thought to counteract miscoding at the A site thus reducing translation errors. The RaiA fold structurally resembles the double-stranded RNA-binding domain (dsRBD).
Probab=40.28 E-value=34 Score=23.53 Aligned_cols=27 Identities=19% Similarity=0.351 Sum_probs=23.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHhCC
Q psy14777 106 GKLVDPTPEIERELKADLSKTAKQYGG 132 (158)
Q Consensus 106 GklVDa~Pe~ekel~~el~kL~r~YGg 132 (158)
|+-+|.+++++.-.++.+++|.+.|..
T Consensus 6 ~r~~~~t~al~~~i~~k~~kl~r~~~~ 32 (93)
T cd00552 6 GRNIEVTDALREYVEEKLEKLEKYFDR 32 (93)
T ss_pred EEcccCCHHHHHHHHHHHHHHHHhcCC
Confidence 456999999999999999999999853
No 22
>cd07610 FCH_F-BAR The Extended FES-CIP4 Homology (FCH) or F-BAR (FCH and Bin/Amphiphysin/Rvs) domain, a dimerization module that binds and bends membranes. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. F-BAR domain containing proteins, also known as Pombe Cdc15 homology (PCH) family proteins, include Fes and Fer tyrosine kinases, PACSINs/Syndapins, FCHO, PSTPIP, CIP4-like proteins and srGAPs. Many members also contain an SH3 domain and play roles in endocytosis. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. These tubules have diameters larger than those observed with N-BARs. The F-BAR domains of some members such as NOSTRIN and Rgd1 are important for the subcellular localization of the protein.
Probab=40.14 E-value=52 Score=25.15 Aligned_cols=33 Identities=33% Similarity=0.535 Sum_probs=27.4
Q ss_pred HHHHHHHhh-hhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhCCC
Q psy14777 91 LFLDKLSEY-KSKSTGGKLVDPTPEIERELKADLSKTAKQYGGD 133 (158)
Q Consensus 91 LFldKIREY-KsKs~gGklVDa~Pe~ekel~~el~kL~r~YGgg 133 (158)
.+++.|++| +.+ .++|++|...|.+|++.|.++
T Consensus 14 ~~~~e~~~f~keR----------a~iE~eYak~L~kLak~~~~~ 47 (191)
T cd07610 14 DLLKDLREFLKKR----------AAIEEEYAKNLQKLAKKFSKK 47 (191)
T ss_pred HHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHhhcc
Confidence 366777887 555 579999999999999999876
No 23
>PF10775 ATP_sub_h: ATP synthase complex subunit h; InterPro: IPR019711 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit H found in the F0 complex of F-ATPases from fungal mitochondria. Subunit H is homologous to the mammalian factor F6, and is essential for the correct assembly and/or functioning of F-ATPases, since yeast cells lacking it are not able to grow on non-fermentable carbon sources. Subunit H occupies a central place in the peripheral stalk between the F1 sector and the membrane [].
Probab=39.25 E-value=21 Score=25.46 Aligned_cols=21 Identities=33% Similarity=0.618 Sum_probs=18.3
Q ss_pred ccChHHHHHHHHHhhhhcccc
Q psy14777 32 ASDPIQQLFLDKLSEYKSKSA 52 (158)
Q Consensus 32 ~~dpiq~lf~dkirey~~ks~ 52 (158)
-.|.||-|+|.-|+.||-...
T Consensus 9 r~d~VQDLYLkELKayKp~p~ 29 (67)
T PF10775_consen 9 RADLVQDLYLKELKAYKPPPI 29 (67)
T ss_pred cccHHHHHHHHHHHhcCCCCC
Confidence 359999999999999987764
No 24
>PF09580 Spore_YhcN_YlaJ: Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ); InterPro: IPR019076 This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Probab=38.48 E-value=43 Score=25.92 Aligned_cols=33 Identities=15% Similarity=0.331 Sum_probs=26.5
Q ss_pred HHHHHHHhhhhcCCCCCCCCCCHHHHHHHHHHHHHH
Q psy14777 91 LFLDKLSEYKSKSTGGKLVDPTPEIERELKADLSKT 126 (158)
Q Consensus 91 LFldKIREYKsKs~gGklVDa~Pe~ekel~~el~kL 126 (158)
-|++.|++|..+...|+++ .++.+|+++-+.|+
T Consensus 143 ~~~~ri~~~~~~~~~g~~~---~~~~~~~~~i~~r~ 175 (177)
T PF09580_consen 143 DIFDRIRNLANRIRNGRPV---SGFNDEIKEIVRRM 175 (177)
T ss_pred HHHHHHHHHHHHHHCCCCh---HHHHHHHHHHHHhh
Confidence 4788999997776667777 78888888888776
No 25
>PF10303 DUF2408: Protein of unknown function (DUF2408); InterPro: IPR018810 This entry represents a family of proteins conserved in fungi whose function is unknown.
Probab=35.71 E-value=1e+02 Score=24.13 Aligned_cols=22 Identities=32% Similarity=0.523 Sum_probs=15.5
Q ss_pred HHHHHHHhhhhcC-CCCCCCCCC
Q psy14777 91 LFLDKLSEYKSKS-TGGKLVDPT 112 (158)
Q Consensus 91 LFldKIREYKsKs-~gGklVDa~ 112 (158)
-|-++++|..++. .+||.|+++
T Consensus 45 ~lq~qL~eIe~~R~~DGKF~~~~ 67 (134)
T PF10303_consen 45 PLQEQLKEIESMRDVDGKFVSPD 67 (134)
T ss_pred HHHHHHHHHHHhccCCCCeeCCC
Confidence 3567788886665 677777777
No 26
>PRK10324 translation inhibitor protein RaiA; Provisional
Probab=35.62 E-value=45 Score=24.97 Aligned_cols=28 Identities=25% Similarity=0.242 Sum_probs=25.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHhCCC
Q psy14777 106 GKLVDPTPEIERELKADLSKTAKQYGGD 133 (158)
Q Consensus 106 GklVDa~Pe~ekel~~el~kL~r~YGgg 133 (158)
|+-|+.||+++.-.++.++||.+-|+.-
T Consensus 7 gr~v~~tdalr~~ie~Kl~kL~k~~~~i 34 (113)
T PRK10324 7 SKQMEITPAIRQHVADRLAKLEKWQTHL 34 (113)
T ss_pred EEcCcCCHHHHHHHHHHHHHHHHhcCCC
Confidence 5679999999999999999999999753
No 27
>cd07675 F-BAR_FNBP1L The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Formin Binding Protein 1-Like. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. FormiN Binding Protein 1-Like (FNBP1L), also known as Toca-1 (Transducer of Cdc42-dependent actin assembly), forms a complex with neural Wiskott-Aldrich syndrome protein (N-WASP). The FNBP1L/N-WASP complex induces the formation of filopodia and endocytic vesicles. FNBP1L is required for Cdc42-induced actin assembly and is essential for autophagy of intracellular pathogens. It contains an N-terminal F-BAR domain, a central Cdc42-binding HR1 domain, and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules.
Probab=34.34 E-value=79 Score=27.33 Aligned_cols=36 Identities=25% Similarity=0.458 Sum_probs=29.6
Q ss_pred HHHHHHHhh-hhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhCCCCCC
Q psy14777 91 LFLDKLSEY-KSKSTGGKLVDPTPEIERELKADLSKTAKQYGGDGKE 136 (158)
Q Consensus 91 LFldKIREY-KsKs~gGklVDa~Pe~ekel~~el~kL~r~YGgg~~~ 136 (158)
-|++.|..| +.+ .++|+||...|-+|.+.|++-.+.
T Consensus 19 ~~l~~~~~F~keR----------a~IE~eYakkL~~L~Kky~~KK~~ 55 (252)
T cd07675 19 DFLERYAKFVKER----------LEIEQNYAKQLRNLVKKYCPKRSS 55 (252)
T ss_pred HHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHhccccCC
Confidence 477888887 555 579999999999999999987553
No 28
>PF08060 NOSIC: NOSIC (NUC001) domain; InterPro: IPR012976 This is the central domain in Nop56/SIK1-like proteins [].; PDB: 3PLA_K 3ICX_B 3ID6_A 3ID5_E 3NVM_A 3NMU_B 2NNW_C 3NVI_A 3NVK_A 2OZB_E ....
Probab=32.93 E-value=83 Score=20.74 Aligned_cols=25 Identities=20% Similarity=0.424 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCcCccCCCC
Q psy14777 113 PEIERELKADLSKTAKQYGGDGKEDMTKFPNF 144 (158)
Q Consensus 113 Pe~ekel~~el~kL~r~YGgg~~~DmtkFP~F 144 (158)
.++++|++.--.++...||- +||+.
T Consensus 10 ~~id~ei~~~~~~lre~Y~~-------~FPEL 34 (53)
T PF08060_consen 10 DDIDKEINLLHMRLREWYSW-------HFPEL 34 (53)
T ss_dssp HHHHHHHHHHHHHHHHHHTT-------TSTTH
T ss_pred HHHHHHHHHHHHHHHHHHHc-------cchhH
Confidence 57889999999999999998 57774
No 29
>COG1544 Ribosome-associated protein Y (PSrp-1) [Translation, ribosomal structure and biogenesis]
Probab=30.29 E-value=52 Score=25.10 Aligned_cols=28 Identities=25% Similarity=0.328 Sum_probs=25.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHhCCC
Q psy14777 106 GKLVDPTPEIERELKADLSKTAKQYGGD 133 (158)
Q Consensus 106 GklVDa~Pe~ekel~~el~kL~r~YGgg 133 (158)
|+-|+-||.+....++.|+||.+.|--.
T Consensus 7 G~nieit~a~r~~Ve~Kl~kl~r~~~~~ 34 (110)
T COG1544 7 GKNVEITEAIREYVEEKLAKLERYFDDI 34 (110)
T ss_pred eeeeeeCHHHHHHHHHHHHHHHhhhccC
Confidence 7789999999999999999999999754
No 30
>COG0052 RpsB Ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=30.00 E-value=77 Score=27.90 Aligned_cols=77 Identities=23% Similarity=0.273 Sum_probs=48.4
Q ss_pred hhhhhhhhhhhhhhhhHHHhhhcCChHHHHHHHHHHhhhhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhCCCCCCcCccC
Q psy14777 62 VRKNVSQNLTRNLATSYVALKNASDPIQQLFLDKLSEYKSKSTGGKLVDPTPEIERELKADLSKTAKQYGGDGKEDMTKF 141 (158)
Q Consensus 62 ~r~a~~~~~rRnig~sA~a~~ka~DPIQkLFldKIREYKsKs~gGklVDa~Pe~ekel~~el~kL~r~YGgg~~~DmtkF 141 (158)
-|+....+..|-+|=+ +.| --||++. ++++++-.....+| .-+-+-.-.-.+..|++||.+-+||= -||...
T Consensus 85 ~r~g~~yV~~RwLgG~--LTN--~~ti~~s-i~rl~~lE~~~~~~-~~~~tKkE~l~l~re~~kL~k~lgGI--k~m~~~ 156 (252)
T COG0052 85 ERTGAYYVNGRWLGGM--LTN--FKTIRKS-IKRLKELEKMEEDG-FDGLTKKEALMLTRELEKLEKSLGGI--KDMKGL 156 (252)
T ss_pred HHhCCceecCcccCcc--ccC--chhHHHH-HHHHHHHHHHhhcc-cccccHHHHHHHHHHHHHHHHhhcch--hhccCC
Confidence 3444555566666633 111 2266652 23344332223455 55556666678999999999999996 699999
Q ss_pred CCCcC
Q psy14777 142 PNFQF 146 (158)
Q Consensus 142 P~FkF 146 (158)
|+.=|
T Consensus 157 Pd~l~ 161 (252)
T COG0052 157 PDVLF 161 (252)
T ss_pred CCEEE
Confidence 99766
No 31
>PF02482 Ribosomal_S30AE: Sigma 54 modulation protein / S30EA ribosomal protein; InterPro: IPR003489 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the sigma-54 modulation protein family and the S30Ae family of ribosomal proteins which includes the light-repressed protein (lrtA) [].; GO: 0005488 binding, 0044238 primary metabolic process; PDB: 1L4S_A 1VOX_a 1VOV_a 3V2E_Y 3V2C_Y 1N3G_A 1VOS_a 1VOZ_a 1VOQ_a 1IMU_A ....
Probab=29.57 E-value=51 Score=22.69 Aligned_cols=27 Identities=15% Similarity=0.316 Sum_probs=20.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHhCC
Q psy14777 106 GKLVDPTPEIERELKADLSKTAKQYGG 132 (158)
Q Consensus 106 GklVDa~Pe~ekel~~el~kL~r~YGg 132 (158)
|+-++.+++++.-.++.+++|.+.+..
T Consensus 6 ~~~~~~t~~l~~~i~~kl~kl~~~~~~ 32 (97)
T PF02482_consen 6 GRNFELTDALREYIEEKLEKLERFFDD 32 (97)
T ss_dssp ECSS---HHHHHHHHHHHHHHHTTSSC
T ss_pred EEcccCCHHHHHHHHHHHHHHHhhcCC
Confidence 456899999999999999999988754
No 32
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=29.48 E-value=1.1e+02 Score=23.51 Aligned_cols=36 Identities=25% Similarity=0.336 Sum_probs=22.4
Q ss_pred HHHHHHHHHHhhhhcCCCCCCCCCCHHH---HHHHHHHHHHHHHHh
Q psy14777 88 IQQLFLDKLSEYKSKSTGGKLVDPTPEI---ERELKADLSKTAKQY 130 (158)
Q Consensus 88 IQkLFldKIREYKsKs~gGklVDa~Pe~---ekel~~el~kL~r~Y 130 (158)
=|.|++++|.+|- |-+-.|+| ++|+.+=-.+|.+.|
T Consensus 82 NQ~L~~~~LA~f~-------P~~e~p~y~~~~~e~~~Yr~~LE~rY 120 (131)
T PF09779_consen 82 NQHLKINQLASFL-------PDPEDPEYANYEEELPEYRRSLEQRY 120 (131)
T ss_pred HHHHHHHHHHhcC-------CCCCCccHHHHHHHHHHHHHHHHHHh
Confidence 3999999999992 33334444 444444445566666
No 33
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=29.42 E-value=1.2e+02 Score=27.16 Aligned_cols=60 Identities=18% Similarity=0.259 Sum_probs=40.4
Q ss_pred CChHH-HHHHHHHHhhhhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhCCCCCCcCccCCCCcC
Q psy14777 85 SDPIQ-QLFLDKLSEYKSKSTGGKLVDPTPEIERELKADLSKTAKQYGGDGKEDMTKFPNFQF 146 (158)
Q Consensus 85 ~DPIQ-kLFldKIREYKsKs~gGklVDa~Pe~ekel~~el~kL~r~YGgg~~~DmtkFP~FkF 146 (158)
.++.+ +-.+.++++|.+....|.+-.-+....-.+..|.+||.+.|||= -+|.+.|+.=|
T Consensus 97 TN~~ti~~si~~l~~l~~~~~~~~~~~~~kke~~~~~r~~~kl~k~l~Gi--~~m~~~Pd~vi 157 (326)
T PRK12311 97 TNWKTISGSIQRLRKLDEVLSSGEANGYTKKERLTLQRERDKLDRALGGI--KDMGGLPDLLF 157 (326)
T ss_pred CCHHHHHHHHHHHHHHHHHhhcCccccCCHHHHHHHHHHHHHHHHhccch--hhcccCCCEEE
Confidence 34443 44678888885554444333344444556788999999999975 58999998644
No 34
>smart00830 CM_2 Chorismate mutase type II. Chorismate mutase, catalyses the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine PUBMED:9642265, PUBMED:9497350.
Probab=26.96 E-value=1.3e+02 Score=20.05 Aligned_cols=38 Identities=29% Similarity=0.349 Sum_probs=23.7
Q ss_pred HHHHHHhhhhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhCC
Q psy14777 92 FLDKLSEYKSKSTGGKLVDPTPEIERELKADLSKTAKQYGG 132 (158)
Q Consensus 92 FldKIREYKsKs~gGklVDa~Pe~ekel~~el~kL~r~YGg 132 (158)
+.++|-+||.. .|..+.| |+=++.+-+.+...+..+|.
T Consensus 21 l~~~i~~~K~~-~~~~i~d--~~Re~~vl~~~~~~a~~~~l 58 (79)
T smart00830 21 LAREVARLKAK-NGLPIYD--PEREAEVLERLRALAEGPGL 58 (79)
T ss_pred HHHHHHHHHHH-CCCCCCC--hHHHHHHHHHHHHHcccCCc
Confidence 55667777766 3443344 66677776666666666664
No 35
>smart00055 FCH Fes/CIP4 homology domain. Alignment extended from original report. Highly alpha-helical. Also known as the RAEYL motif or the S. pombe Cdc15 N-terminal domain.
Probab=25.24 E-value=1.4e+02 Score=20.09 Aligned_cols=29 Identities=28% Similarity=0.549 Sum_probs=23.4
Q ss_pred HHHHHHHhh-hhcCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q psy14777 91 LFLDKLSEY-KSKSTGGKLVDPTPEIERELKADLSKTAKQ 129 (158)
Q Consensus 91 LFldKIREY-KsKs~gGklVDa~Pe~ekel~~el~kL~r~ 129 (158)
.+++-|..| +.+ .++|+||...|.+|+++
T Consensus 23 ~~~~~~~~f~~~R----------a~iE~eYak~L~kL~~~ 52 (87)
T smart00055 23 RLLEDLKKFIRER----------AKIEEEYAKKLQKLSKK 52 (87)
T ss_pred HHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHh
Confidence 457777777 555 57899999999999987
No 36
>PF01817 CM_2: Chorismate mutase type II; InterPro: IPR020822 Chorismate mutase, 5.4.99.5 from EC, catalyses the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine [, ]. Prephenate dehydratase (IPR001086 from INTERPRO, 4.2.1.51 from EC, PDT) catalyses the decarboxylation of prephenate into phenylpyruvate. In microorganisms PDT is involved in the terminal pathway of the biosynthesis of phenylalanine. In some bacteria, such as Escherichia coli, PDT is part of a bifunctional enzyme (P-protein) that also catalyzes the transformation of chorismate into prephenate (chorismate mutase) while in other bacteria it is a monofunctional enzyme. The sequence of monofunctional chorismate mutase aligns well with the N-terminal part of P-proteins [].; GO: 0046417 chorismate metabolic process; PDB: 1YBZ_A 2GTV_X 2FP1_B 2F6L_B 2FP2_B 2AO2_A 3HGW_C 3HGX_B 2H9C_A 3RET_B ....
Probab=25.23 E-value=2.2e+02 Score=19.24 Aligned_cols=39 Identities=33% Similarity=0.543 Sum_probs=27.9
Q ss_pred HHHHHHhhhhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhCCC
Q psy14777 92 FLDKLSEYKSKSTGGKLVDPTPEIERELKADLSKTAKQYGGD 133 (158)
Q Consensus 92 FldKIREYKsKs~gGklVDa~Pe~ekel~~el~kL~r~YGgg 133 (158)
.+.+|-+||.+. |....| |+-++++-+.+..++..+|..
T Consensus 21 l~~~i~~~K~~~-~~~i~d--~~RE~~v~~~~~~~~~~~~l~ 59 (81)
T PF01817_consen 21 LVRKIAEYKKEN-GLPIFD--PDREEEVLERLRELAEEGGLD 59 (81)
T ss_dssp HHHHHHHHHHHT-TCCSST--HHHHHHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHhC-CCCCCC--cHHHHHHHHHHHHHhHhCCCC
Confidence 456788887773 333455 888888888888888877763
No 37
>PRK10470 ribosome hibernation promoting factor HPF; Provisional
Probab=23.71 E-value=92 Score=21.97 Aligned_cols=28 Identities=18% Similarity=0.233 Sum_probs=24.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHhCCC
Q psy14777 106 GKLVDPTPEIERELKADLSKTAKQYGGD 133 (158)
Q Consensus 106 GklVDa~Pe~ekel~~el~kL~r~YGgg 133 (158)
|+-+|.+++++.-.++.++||.+.|..-
T Consensus 7 ~r~i~~t~al~~~v~~kl~kL~r~~~~i 34 (95)
T PRK10470 7 GHNVEITEALREFVTAKFAKLEQYFDRI 34 (95)
T ss_pred EEeeccCHHHHHHHHHHHHHHHHhcCCC
Confidence 4568999999999999999999999754
No 38
>COG2102 Predicted ATPases of PP-loop superfamily [General function prediction only]
Probab=23.64 E-value=52 Score=28.40 Aligned_cols=42 Identities=19% Similarity=0.349 Sum_probs=36.7
Q ss_pred CCHHHHHHHHHHHHHHHHHhCCCCCCcCccCCCCcCCCCCcc
Q psy14777 111 PTPEIERELKADLSKTAKQYGGDGKEDMTKFPNFQFPEPKIE 152 (158)
Q Consensus 111 a~Pe~ekel~~el~kL~r~YGgg~~~DmtkFP~FkF~epk~d 152 (158)
.|-.+.++..+++.+|.+.||-.....=-+|-||-+..|-++
T Consensus 153 lGr~i~~~~~e~l~~l~~~ygi~~~GEgGEfeT~VldaP~F~ 194 (223)
T COG2102 153 LGRRIDREFLEELKSLNRRYGIHPAGEGGEFETLVLDAPLFK 194 (223)
T ss_pred hCCccCHHHHHHHHHHHHhcCCCccCCCcceEEEEecccccc
Confidence 567888999999999999999877777789999999888776
No 39
>PF06877 RraB: Regulator of ribonuclease activity B; InterPro: IPR009671 This entry occurs in several hypothetical bacterial proteins of around 120 residues in length. The function of these proteins is unknown. The protein structure has been determined for one member of this group, the hypothetical protein VCO424 from Vibrio cholerae; it has an alpha+beta sandwich fold.; PDB: 1NXI_A.
Probab=23.39 E-value=1.1e+02 Score=21.67 Aligned_cols=25 Identities=24% Similarity=0.372 Sum_probs=19.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHhCCC
Q psy14777 109 VDPTPEIERELKADLSKTAKQYGGD 133 (158)
Q Consensus 109 VDa~Pe~ekel~~el~kL~r~YGgg 133 (158)
..++++...++..+|..|++.|||.
T Consensus 74 ~~~~~~~I~~~~~~l~~lA~~~~g~ 98 (104)
T PF06877_consen 74 MVLDYEDINAITQELEDLAKEFGGE 98 (104)
T ss_dssp E-S-HHHHHHHHHHHHHHHHHHT-E
T ss_pred cCCCHHHHHHHHHHHHHHHHHhCcE
Confidence 4566888999999999999999983
No 40
>PF11934 DUF3452: Domain of unknown function (DUF3452); InterPro: IPR024599 This domain is found in proteins of the retinoblastoma protein family. It is found in association with Pfam:PF01858 and Pfam:PF01857. This domain is typically between 124 to 150 amino acids in length and has a single completely conserved residue W that may be functionally important.; PDB: 2QDJ_A 4ELJ_A.
Probab=22.76 E-value=81 Score=24.31 Aligned_cols=32 Identities=19% Similarity=0.475 Sum_probs=16.9
Q ss_pred HHHHHHhhhhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhC
Q psy14777 92 FLDKLSEYKSKSTGGKLVDPTPEIERELKADLSKTAKQYG 131 (158)
Q Consensus 92 FldKIREYKsKs~gGklVDa~Pe~ekel~~el~kL~r~YG 131 (158)
|.+|++++- ++.++.-.+.+.+++++|++.|+
T Consensus 29 Ff~~l~~~~--------~~m~~~~~~~~~~~~~~L~~~f~ 60 (136)
T PF11934_consen 29 FFKKLKKWA--------VDMANILSKRFRAQVKELERNFV 60 (136)
T ss_dssp HHHHHCCS----------------HHHHHH-HHHHHHHHH
T ss_pred HHHHHHHHH--------HHhccCcHHHHHHHHHHHHHHHH
Confidence 888898773 34444455666667777777665
No 41
>KOG2269|consensus
Probab=22.35 E-value=68 Score=30.59 Aligned_cols=25 Identities=16% Similarity=0.381 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCcC
Q psy14777 114 EIERELKADLSKTAKQYGGDGKEDM 138 (158)
Q Consensus 114 e~ekel~~el~kL~r~YGgg~~~Dm 138 (158)
+|.+|+++||-|..|++|+.+++-.
T Consensus 88 ~fDrEydeeLRR~er~~n~~SkV~~ 112 (531)
T KOG2269|consen 88 HFDREYDEELRRVERAVNSSSKVHF 112 (531)
T ss_pred HhhhhhhHHHHHHHHHhCCCCcEEe
Confidence 4678999999999999999877544
No 42
>TIGR01795 CM_mono_cladeE monofunctional chorismate mutase, alpha proteobacterial type. The alpha proteobacterial members are trusted because the pathways of CM are evident and there is only one plausible CM in the genome. In S. coelicolor, however, there is another aparrent monofunctional CM.
Probab=21.74 E-value=2.9e+02 Score=20.21 Aligned_cols=39 Identities=26% Similarity=0.224 Sum_probs=30.2
Q ss_pred HHHHHHhhhhcCCCCCCCCCCHHHHHHHHHHHHHHHHHhCCC
Q psy14777 92 FLDKLSEYKSKSTGGKLVDPTPEIERELKADLSKTAKQYGGD 133 (158)
Q Consensus 92 FldKIREYKsKs~gGklVDa~Pe~ekel~~el~kL~r~YGgg 133 (158)
+.++|-+||.+. |..+.| |+=++++-+.+..++..+|..
T Consensus 29 ~~~~ia~~K~~~-~~~v~d--p~Re~~vl~~~~~~a~~~gl~ 67 (94)
T TIGR01795 29 CTSQVGVLKANA-GLAPAD--PAREDYQIARLRRLAIDAGLD 67 (94)
T ss_pred HHHHHHHHHHhC-CCCCCC--HHHHHHHHHHHHHHHHHCCCC
Confidence 567788887764 333444 889999999999999999986
No 43
>PF04368 DUF507: Protein of unknown function (DUF507); InterPro: IPR007463 This entry represents a bacterial protein of unknown function.
Probab=21.16 E-value=3.3e+02 Score=22.61 Aligned_cols=38 Identities=26% Similarity=0.430 Sum_probs=29.4
Q ss_pred hcCChHHHHHHHHHHhhhhcCCCCCCCCCCHHH----HHHHHHHHHH
Q psy14777 83 NASDPIQQLFLDKLSEYKSKSTGGKLVDPTPEI----ERELKADLSK 125 (158)
Q Consensus 83 ka~DPIQkLFldKIREYKsKs~gGklVDa~Pe~----ekel~~el~k 125 (158)
+..+-|-+.=.+||+-|+.| +|..|||+ +|-|++|+.|
T Consensus 138 ~~~~eid~~Vr~ki~~y~r~-----~i~Gt~e~~ily~k~yeeel~k 179 (183)
T PF04368_consen 138 KEEEEIDDEVREKIKSYKRK-----IIPGTEEWDILYEKLYEEELRK 179 (183)
T ss_pred HHHHHHHHHHHHHHHhhCcC-----CCCCCHHHHHHHHHHHHHHHHH
Confidence 45677888888999999877 88889995 5666666654
No 44
>PF14824 Sirohm_synth_M: Sirohaem biosynthesis protein central; PDB: 1KYQ_B.
Probab=21.07 E-value=98 Score=19.07 Aligned_cols=20 Identities=25% Similarity=0.625 Sum_probs=15.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHH
Q psy14777 103 STGGKLVDPTPEIERELKADLSKT 126 (158)
Q Consensus 103 s~gGklVDa~Pe~ekel~~el~kL 126 (158)
|++| .+|.+-+.+.+|++++
T Consensus 10 STnG----~sP~la~~iR~~ie~~ 29 (30)
T PF14824_consen 10 STNG----KSPRLARLIRKEIERL 29 (30)
T ss_dssp EESS----S-HHHHHHHHHHHHHH
T ss_pred ECCC----CChHHHHHHHHHHHHh
Confidence 4566 6899999999999874
No 45
>COG2952 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.69 E-value=1.2e+02 Score=25.60 Aligned_cols=35 Identities=31% Similarity=0.438 Sum_probs=24.4
Q ss_pred ChHHHHHHHHHHhhhhcCCCCCCCCCCHHHH----HHHHHHHHH
Q psy14777 86 DPIQQLFLDKLSEYKSKSTGGKLVDPTPEIE----RELKADLSK 125 (158)
Q Consensus 86 DPIQkLFldKIREYKsKs~gGklVDa~Pe~e----kel~~el~k 125 (158)
.-|-+---.||..|+.| |...+|||+ +-|++||.|
T Consensus 141 E~iE~eV~ekIk~Ykrk-----l~~GS~Ey~liferlYeeELrK 179 (183)
T COG2952 141 ESIENEVHEKIKHYKRK-----LPVGSDEYELVFERLYEEELRK 179 (183)
T ss_pred HHHHHHHHHHHHhcccC-----CCCCChHHHHHHHHHHHHHHHH
Confidence 34445555788888766 677789975 677787754
No 46
>TIGR00289 conserved hypothetical protein TIGR00289. Homologous proteins related to MJ0570 of Methanococcus jannaschii include both the apparent orthologs found by this model above the trusted cutoff, the much longer protein YLR143W from Saccharomyces cerevisiae, and second homologous proteins from Archaeoglobus fulgidus and Pyrococcus horikoshii that appear to represent a second orthologous group.
Probab=20.31 E-value=56 Score=27.49 Aligned_cols=42 Identities=17% Similarity=0.207 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHHHHHHHhCCCCCCcCccCCCCcCCCCCcc
Q psy14777 111 PTPEIERELKADLSKTAKQYGGDGKEDMTKFPNFQFPEPKIE 152 (158)
Q Consensus 111 a~Pe~ekel~~el~kL~r~YGgg~~~DmtkFP~FkF~epk~d 152 (158)
.|-++..++-++|.+|.++||-.....=-+|-||-+..|-+.
T Consensus 151 LGr~id~~~~~~L~~l~~~~gid~~GEgGEyhT~V~d~PlF~ 192 (222)
T TIGR00289 151 LGRRIDKECIDDLKRLNEKYGIHLAFEGGEAETLVLDAPLFK 192 (222)
T ss_pred cCCccCHHHHHHHHHHHhhcCccccCCCceEEEEEEeccccC
Confidence 456677888889999999999877778889999998888653
Done!