Query psy11575
Match_columns 80
No_of_seqs 104 out of 224
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 22:01:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11575.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11575hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3668|consensus 100.0 9.5E-40 2.1E-44 243.6 9.2 80 1-80 189-268 (269)
2 cd08888 SRPBCC_PITPNA-B_like L 100.0 1.7E-39 3.7E-44 242.4 8.9 69 1-69 189-257 (258)
3 cd08890 SRPBCC_PITPNC1_like Li 100.0 5.5E-39 1.2E-43 238.9 8.2 69 1-69 181-249 (250)
4 cd07815 SRPBCC_PITP Lipid-bind 100.0 9.2E-39 2E-43 237.8 8.9 69 1-69 182-250 (251)
5 cd08889 SRPBCC_PITPNM1-2_like 100.0 1.5E-38 3.2E-43 237.6 8.1 69 1-69 190-259 (260)
6 PF02121 IP_trans: Phosphatidy 100.0 5.7E-38 1.2E-42 233.5 8.5 65 1-65 189-254 (254)
7 PF10698 DUF2505: Protein of u 87.9 1.6 3.4E-05 29.8 5.0 37 7-43 123-159 (159)
8 PF10544 T5orf172: T5orf172 do 63.3 12 0.00027 22.5 3.3 37 16-57 56-95 (100)
9 PF08671 SinI: Anti-repressor 60.6 6 0.00013 20.9 1.3 11 47-57 15-25 (30)
10 cd03495 SQR_TypeC_SdhD_like Su 56.7 16 0.00035 23.4 3.1 31 13-43 60-90 (100)
11 PF09510 Rtt102p: Rtt102p-like 53.2 6.8 0.00015 26.9 0.9 8 48-55 110-117 (130)
12 PF10471 APC_CDC26: Anaphase-p 51.2 3.8 8.3E-05 25.2 -0.5 21 47-67 9-29 (79)
13 PF05914 RIB43A: RIB43A; Inte 38.7 43 0.00093 26.5 3.5 21 43-63 271-291 (379)
14 PF04707 PRELI: PRELI-like fam 37.0 1E+02 0.0022 21.0 4.7 39 3-42 108-149 (157)
15 PF09278 MerR-DNA-bind: MerR, 36.6 23 0.00049 20.1 1.3 12 47-58 13-24 (65)
16 cd01104 HTH_MlrA-CarA Helix-Tu 36.1 52 0.0011 18.5 2.8 18 39-58 50-67 (68)
17 PF15581 Imm35: Immunity prote 32.4 27 0.00059 23.0 1.2 12 44-55 41-52 (93)
18 cd04763 HTH_MlrA-like Helix-Tu 32.3 61 0.0013 18.6 2.7 19 37-57 48-66 (68)
19 cd01388 SOX-TCF_HMG-box SOX-TC 31.5 88 0.0019 18.2 3.3 28 44-71 38-65 (72)
20 PF14045 YIEGIA: YIEGIA protei 29.6 43 0.00092 26.1 2.1 17 51-67 71-87 (285)
21 PF13455 MUG113: Meiotically u 29.4 40 0.00086 21.1 1.6 38 16-57 37-79 (83)
22 PF06868 DUF1257: Protein of u 28.4 51 0.0011 21.5 2.0 24 3-27 48-71 (105)
23 PF09346 SMI1_KNR4: SMI1 / KNR 27.9 45 0.00097 20.1 1.6 18 48-65 1-18 (130)
24 cd01389 MATA_HMG-box MATA_HMG- 27.7 1.2E+02 0.0025 17.9 3.4 27 44-70 38-64 (77)
25 PF11460 DUF3007: Protein of u 27.4 1.1E+02 0.0024 20.5 3.5 23 48-70 61-88 (104)
26 PF01486 K-box: K-box region; 27.2 83 0.0018 19.7 2.8 39 31-71 30-68 (100)
27 PF09011 HMG_box_2: HMG-box do 26.9 86 0.0019 18.3 2.7 25 43-67 40-64 (73)
28 PTZ00285 glucosamine-6-phospha 26.9 24 0.00053 25.6 0.3 32 34-65 62-93 (253)
29 TIGR00496 frr ribosome recycli 26.6 1E+02 0.0023 21.8 3.5 42 29-70 116-160 (176)
30 PF10666 Phage_Gp14: Phage pro 25.1 1.1E+02 0.0024 21.4 3.3 28 43-70 56-83 (140)
31 PF07078 FYTT: Forty-two-three 24.8 64 0.0014 25.5 2.3 20 44-64 27-46 (316)
32 KOG0717|consensus 23.7 2.1E+02 0.0045 24.1 5.1 39 9-49 136-175 (508)
33 cd04764 HTH_MlrA-like_sg1 Heli 23.6 1.1E+02 0.0023 17.4 2.7 18 38-57 48-65 (67)
34 PF01452 Rota_NSP4: Rotavirus 23.4 3E+02 0.0064 20.0 6.2 38 2-39 63-110 (173)
35 PF14048 MBD_C: C-terminal dom 23.0 1.2E+02 0.0027 19.6 3.1 20 46-65 70-89 (96)
36 PF00505 HMG_box: HMG (high mo 22.7 1.1E+02 0.0024 17.0 2.6 25 44-68 37-61 (69)
37 PF10642 Tom5: Mitochondrial i 22.3 1.7E+02 0.0038 16.9 3.4 21 49-69 9-29 (49)
38 COG0233 Frr Ribosome recycling 21.8 1.3E+02 0.0029 22.0 3.3 23 48-70 149-171 (187)
39 smart00760 Bac_DnaA_C Bacteria 21.5 80 0.0017 18.0 1.8 23 34-56 30-53 (60)
40 cd03081 TRX_Fd_NuoE_FDH_gamma 20.0 70 0.0015 19.3 1.4 14 44-57 62-76 (80)
No 1
>KOG3668|consensus
Probab=100.00 E-value=9.5e-40 Score=243.64 Aligned_cols=80 Identities=66% Similarity=1.145 Sum_probs=78.4
Q ss_pred CeeeeEeEEEeeccchhHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHHHHHHHHHHHhhcccccccCC
Q psy11575 1 MTCYKLVTAEFKWFGFQGRVENFIHKAERRLFTNFHRQVFCWIDRWHDLTMEDIRRIEEETKKELDRQRLEGEVRGMKAD 80 (80)
Q Consensus 1 M~~YKlv~v~f~~~Glq~~vE~~i~~~~r~i~~~~HRq~fcwiDeW~~lTmedIR~~E~et~~~l~~~~~~~~~~~~~~~ 80 (80)
|||||||+|+|+|||+|++||+|||++.+++|+++|||||||+|+||||||+|||++|++||..|+++++.++++|+.++
T Consensus 189 McaYKlvtvefk~wGmQ~~VE~fIhk~~~rv~~~~HRqafcw~D~W~gltm~diRe~E~~t~~~l~~~~~~~~~~~~~~~ 268 (269)
T KOG3668|consen 189 MCAYKLVTVEFKWWGMQTKVENFIHKVERRVFTRAHRQAFCWQDEWYGLTMEDIRELEDETQLELIKKRAKGEVRGMGAD 268 (269)
T ss_pred EEEeeEEEEEEEeehHHHHHHHHHHHHHHHHHHHHHHHHheehhhhhCccHHHHHHHHHHHHHHHHHHhccCCcccccCC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999998764
No 2
>cd08888 SRPBCC_PITPNA-B_like Lipid-binding SRPBCC domain of mammalian PITPNA, -B, and related proteins (Class I PITPs). This subgroup includes the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of mammalian Class 1 phosphatidylinositol transfer proteins (PITPs), PITPNA/PITPalpha and PITPNB/PITPbeta, Drosophila vibrator, and related proteins. These are single domain proteins belonging to the PITP family of lipid transfer proteins, and to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. In vitro, PITPs bind phosphatidylinositol (PtdIns), as well as phosphatidylcholine (PtdCho) but with a lower affinity. They transfer these lipids from one membrane compartment to another. The cellular roles of PITPs include inositol lipid signaling, PtdIns metabolism, and membrane trafficking. In addition, PITPNB transfers sphingomyelin in vitro, with a low affinity. PITPNA is found chiefly in the nucleus and cy
Probab=100.00 E-value=1.7e-39 Score=242.40 Aligned_cols=69 Identities=75% Similarity=1.369 Sum_probs=67.9
Q ss_pred CeeeeEeEEEeeccchhHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHHHHHHHHHHH
Q psy11575 1 MTCYKLVTAEFKWFGFQGRVENFIHKAERRLFTNFHRQVFCWIDRWHDLTMEDIRRIEEETKKELDRQR 69 (80)
Q Consensus 1 M~~YKlv~v~f~~~Glq~~vE~~i~~~~r~i~~~~HRq~fcwiDeW~~lTmedIR~~E~et~~~l~~~~ 69 (80)
|||||||+|+|+|||||++||+|||+++|++|+++||||||||||||||||||||++|++||++|++.+
T Consensus 189 McaYKLv~v~f~~wG~q~rvE~fI~~~~r~~fl~~HRq~fcW~DeW~gltmedIR~~E~~t~~~l~~~~ 257 (258)
T cd08888 189 MCAYKLVTVEFKWWGLQNKVENFIQKQERRLFTNFHRQVFCWLDKWHGLTMDDIRRMEDETKKELDEMR 257 (258)
T ss_pred EEEeEEEEEEEeeecccHHHHHHHHHHHHHHHHHHHHHHhhhHHHHcCCCHHHHHHHHHHHHHHHHHhh
Confidence 899999999999999999999999999999999999999999999999999999999999999999875
No 3
>cd08890 SRPBCC_PITPNC1_like Lipid-binding SRPBCC domain of mammalian PITPNC1,and related proteins (Class IIB PITPs). This subgroup includes the N-terminal SRPBCC (START/RHO_alpha_C /PITP /Bet_v1/CoxG/CalC) domain of mammalian Class IIB phosphatidylinositol transfer protein (PITP), PITPNC1/RdgBbeta, and related proteins. These are metazoan proteins belonging to the PITP family of lipid transfer proteins, and to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. In vitro, PITPs bind phosphatidylinositol (PtdIns), as well as phosphatidylcholine (PtdCho) but with a lower affinity. They transfer these lipids from one membrane compartment to another. The cellular roles of PITPs include inositol lipid signaling, PtdIns metabolism, and membrane trafficking. Mammalian PITPNC1 contains an amino-terminal SRPBCC PITP-like domain and a short carboxyl-terminal domain. It is a cytoplasmic protein, and is ubiquitously
Probab=100.00 E-value=5.5e-39 Score=238.87 Aligned_cols=69 Identities=42% Similarity=0.808 Sum_probs=67.4
Q ss_pred CeeeeEeEEEeeccchhHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHHHHHHHHHHH
Q psy11575 1 MTCYKLVTAEFKWFGFQGRVENFIHKAERRLFTNFHRQVFCWIDRWHDLTMEDIRRIEEETKKELDRQR 69 (80)
Q Consensus 1 M~~YKlv~v~f~~~Glq~~vE~~i~~~~r~i~~~~HRq~fcwiDeW~~lTmedIR~~E~et~~~l~~~~ 69 (80)
|||||||+|+|+|||||++||+||++++|++|+++||||||||||||||||||||++|++||++|++++
T Consensus 181 McaYKLv~v~f~~wG~q~rvE~~I~~~~r~~~l~~HRq~fcW~DeW~gltmedIR~~E~e~~~~l~~k~ 249 (250)
T cd08890 181 MCSYKLVTVKFEVWGLQTRVEQFVHKVVRDILLLGHRQAFAWVDEWYDMTMDDVREYERTIQEKTNEKI 249 (250)
T ss_pred EEEEEEEEEEEeeecccHHHHHHHHHHHHHHHHHHHHHHheeHHHHcCCCHHHHHHHHHHHHHHHHhhc
Confidence 899999999999999999999999999999999999999999999999999999999999999999853
No 4
>cd07815 SRPBCC_PITP Lipid-binding SRPBCC domain of Class I and Class II Phosphatidylinositol Transfer Proteins. This family includes the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of the phosphatidylinositol transfer protein (PITP) family of lipid transfer proteins. This family of proteins includes Class 1 PITPs (PITPNA/PITPalpha and PITPNB/PITPbeta, Drosophila vibrator and related proteins), Class IIA PITPs (PITPNM1/PITPalphaI/Nir2, PITPNM2/PITPalphaII/Nir3, Drosophila RdgB, and related proteins), and Class IIB PITPs (PITPNC1/RdgBbeta and related proteins). The PITP family belongs to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. In vitro, PITPs bind phosphatidylinositol (PtdIns), as well as phosphatidylcholine (PtdCho) but with a lower affinity. They transfer these lipids from one membrane compartment to another. The cellular roles of PITPs include inositol lipid signaling, PtdIns
Probab=100.00 E-value=9.2e-39 Score=237.76 Aligned_cols=69 Identities=64% Similarity=1.157 Sum_probs=68.0
Q ss_pred CeeeeEeEEEeeccchhHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHHHHHHHHHHH
Q psy11575 1 MTCYKLVTAEFKWFGFQGRVENFIHKAERRLFTNFHRQVFCWIDRWHDLTMEDIRRIEEETKKELDRQR 69 (80)
Q Consensus 1 M~~YKlv~v~f~~~Glq~~vE~~i~~~~r~i~~~~HRq~fcwiDeW~~lTmedIR~~E~et~~~l~~~~ 69 (80)
|||||||+|+|+|||||++||+||++++|++|+++|||||||+||||||||||||++|++||++|++++
T Consensus 182 McaYKLv~v~f~~wG~q~rvE~~I~~~~r~~~l~~HRq~fcW~DeW~gltmedIR~~E~e~~~~L~~~~ 250 (251)
T cd07815 182 MCAYKLVTVDFPYWGLQNKVENFIQKVERDVFLNYHRQAFCWIDEWFDLTMEDIREFEEETKELLDAKR 250 (251)
T ss_pred EEEEEEEEEEeeeecccHHHHHHHHHHHHHHHHHHHHHHHhhHHHHcCCCHHHHHHHHHHHHHHHHHhh
Confidence 899999999999999999999999999999999999999999999999999999999999999999876
No 5
>cd08889 SRPBCC_PITPNM1-2_like Lipid-binding SRPBCC domain of mammalian PITPNM1-2 and related proteins (Class IIA PITPs). This subgroup includes an N-terminal SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of mammalian Class II phosphatidylinositol transfer protein (PITPs), PITPNM1/PITPalphaI/Nir2 (PYK2 N-terminal domain-interacting receptor2) and PITPNM2/PITPalphaII/Nir3), Drosophila RdgB, and related proteins. These are membrane associated multidomain proteins belonging to the PITP family of lipid transfer proteins, and to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. In vitro, PITPs bind phosphatidylinositol (PtdIns), as well as phosphatidylcholine (PtdCho) but with a lower affinity. They transfer these lipids from one membrane compartment to another. The cellular roles of PITPs include inositol lipid signaling, PtdIns metabolism, and membrane trafficking. Ablation of the mouse gene en
Probab=100.00 E-value=1.5e-38 Score=237.61 Aligned_cols=69 Identities=46% Similarity=0.938 Sum_probs=67.1
Q ss_pred CeeeeEeEEEeeccchhHHHHHHHHHHH-HHHHHHHHHHHHHHhhcccCCCHHHHHHHHHHHHHHHHHHH
Q psy11575 1 MTCYKLVTAEFKWFGFQGRVENFIHKAE-RRLFTNFHRQVFCWIDRWHDLTMEDIRRIEEETKKELDRQR 69 (80)
Q Consensus 1 M~~YKlv~v~f~~~Glq~~vE~~i~~~~-r~i~~~~HRq~fcwiDeW~~lTmedIR~~E~et~~~l~~~~ 69 (80)
|||||||+|+|+|||||++||+|||++. |++|+++|||||||+||||||||||||++|++||++|++.+
T Consensus 190 McaYKLv~v~f~~wG~q~rvE~fI~~~~lr~~~l~~HRq~fcW~DeW~gltmedIR~~E~etq~~L~~k~ 259 (260)
T cd08889 190 MCAYKLCKVEFRYWGMQTKIERFIHDVALRKVMLRAHRQAWCWQDEWYGLTMEDIRKLEEETQLALAQKM 259 (260)
T ss_pred EEEeEEEEEEEeeecchHHHHHHHHHhhhHHHHHHHHHHHheeHHHHcCCCHHHHHHHHHHHHHHHHhhc
Confidence 8999999999999999999999999997 99999999999999999999999999999999999999853
No 6
>PF02121 IP_trans: Phosphatidylinositol transfer protein; InterPro: IPR001666 Phosphatidylinositol transfer protein (PITP) is a ubiquitous cytosolic protein, thought to be involved in transport of phospholipids from their site of synthesis in the endoplasmic reticulum and Golgi to other cell membranes []. More recently, PITP has been shown to be an essential component of the polyphosphoinositide synthesis machinery and is hence required for proper signalling by epidermal growth factor and f-Met-Leu-Phe, as well as for exocytosis. The role of PITP in polyphosphoinositide synthesis may also explain its involvement in intracellular vesicular traffic [].; GO: 0006810 transport, 0005622 intracellular; PDB: 1T27_A 1KCM_A 2A1L_A 1UW5_C.
Probab=100.00 E-value=5.7e-38 Score=233.52 Aligned_cols=65 Identities=72% Similarity=1.329 Sum_probs=60.1
Q ss_pred CeeeeEeEEEeeccchhHHHHHHHHHHH-HHHHHHHHHHHHHHhhcccCCCHHHHHHHHHHHHHHH
Q psy11575 1 MTCYKLVTAEFKWFGFQGRVENFIHKAE-RRLFTNFHRQVFCWIDRWHDLTMEDIRRIEEETKKEL 65 (80)
Q Consensus 1 M~~YKlv~v~f~~~Glq~~vE~~i~~~~-r~i~~~~HRq~fcwiDeW~~lTmedIR~~E~et~~~l 65 (80)
|||||||+|+|+|||||++||+||++++ |++|+++|||||||+||||||||||||++|++||++|
T Consensus 189 Mc~YKlv~v~f~~~GlQ~~vE~~I~~~~~r~i~~~~HRq~fcw~DeW~glTmedIR~~E~et~~~L 254 (254)
T PF02121_consen 189 MCCYKLVTVEFKWWGLQTKVENFIHKQILRRIFLNFHRQAFCWIDEWYGLTMEDIRELEEETQEEL 254 (254)
T ss_dssp EEEEEEEEEEE--TTTHHHHHHHHHHHH-HHHHHHHHHHHHHTHHHHTT--HHHHHHHHHHHHHHH
T ss_pred EEEEEEEEEEeeeechHHHHHHHHHHhhhhHHHHHHHHHHheehhhhcCCCHHHHHHHHHHHHhcC
Confidence 8999999999999999999999999998 9999999999999999999999999999999999987
No 7
>PF10698 DUF2505: Protein of unknown function (DUF2505); InterPro: IPR019639 This entry represents proteins found Actinobacteria and Proteobacteria. The function is not known.
Probab=87.92 E-value=1.6 Score=29.77 Aligned_cols=37 Identities=16% Similarity=0.220 Sum_probs=32.1
Q ss_pred eEEEeeccchhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy11575 7 VTAEFKWFGFQGRVENFIHKAERRLFTNFHRQVFCWI 43 (80)
Q Consensus 7 v~v~f~~~Glq~~vE~~i~~~~r~i~~~~HRq~fcwi 43 (80)
.+|+++++.++.++|++|...+.+.+-.-++.+=.||
T Consensus 123 g~v~v~VPlvGgkiE~~v~~~~~~~~~~e~~~~~~wl 159 (159)
T PF10698_consen 123 GEVKVKVPLVGGKIEKAVAENLRKLLEAEQEFTAEWL 159 (159)
T ss_pred EEEEEEEccccHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 5788889999999999999999999988888776664
No 8
>PF10544 T5orf172: T5orf172 domain; InterPro: IPR018306 This entry represents a DNA-binding domain found in bacteriophage T5, ORF172 []. The domain is related to the Bro-N and KilA-N domains that are widespread in large-DNA viruses infecting bacteria and eukaryotes [].
Probab=63.28 E-value=12 Score=22.47 Aligned_cols=37 Identities=24% Similarity=0.382 Sum_probs=25.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHH---HhhcccCCCHHHHHHH
Q psy11575 16 FQGRVENFIHKAERRLFTNFHRQVFC---WIDRWHDLTMEDIRRI 57 (80)
Q Consensus 16 lq~~vE~~i~~~~r~i~~~~HRq~fc---wiDeW~~lTmedIR~~ 57 (80)
-...+|+.||+.+++ ||.-+- =--|||.++.+++++.
T Consensus 56 ~~~~~E~~ih~~l~~-----~~~~~~~~~~~~E~F~~~~~~~~~~ 95 (100)
T PF10544_consen 56 DARKVERLIHRELKD-----YRYRIPCPDGHTEWFKLDPEEVRAV 95 (100)
T ss_pred CHHHHHHHHHHHHHH-----hCccccCCCCCCEEEECCHHHHHHH
Confidence 357899999987665 222210 0469999999988864
No 9
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=60.58 E-value=6 Score=20.92 Aligned_cols=11 Identities=36% Similarity=0.619 Sum_probs=7.7
Q ss_pred cCCCHHHHHHH
Q psy11575 47 HDLTMEDIRRI 57 (80)
Q Consensus 47 ~~lTmedIR~~ 57 (80)
-|+|.||||++
T Consensus 15 ~Gls~eeir~F 25 (30)
T PF08671_consen 15 SGLSKEEIREF 25 (30)
T ss_dssp TT--HHHHHHH
T ss_pred cCCCHHHHHHH
Confidence 48999999986
No 10
>cd03495 SQR_TypeC_SdhD_like Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit-like; composed of predominantly uncharacterized bacterial proteins with similarity to the E. coli SdhD subunit. One characterized protein is the respiratory Complex II SdhD subunit of the only eukaryotic member, Reclinomonas americana. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. It is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. E. coli SQR is classified as Type C SQRs because it contains two transmembrane subunits and one heme group. The SdhD and SdhC subunits are membrane anchor subunits containing heme and quinone binding sites. The two-electron oxidation of succinate in the flavoprotein active site is
Probab=56.69 E-value=16 Score=23.39 Aligned_cols=31 Identities=23% Similarity=0.377 Sum_probs=24.3
Q ss_pred ccchhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy11575 13 WFGFQGRVENFIHKAERRLFTNFHRQVFCWI 43 (80)
Q Consensus 13 ~~Glq~~vE~~i~~~~r~i~~~~HRq~fcwi 43 (80)
+-|+|..+|++||+..-|..+..=-..||+.
T Consensus 60 ~~Gm~~IieDYV~~~~~R~~l~~~~~~~~~~ 90 (100)
T cd03495 60 RLGMQVVIEDYVHSEGLRLALIIAVKLFAIA 90 (100)
T ss_pred HHHHHHHHHHHhCchHHHHHHHHHHHHHHHH
Confidence 4589999999999887677777666777763
No 11
>PF09510 Rtt102p: Rtt102p-like transcription regulator protein; InterPro: IPR018304 Rtt102p (Regulator of Ty1 Transposition Protein 102) is a transcription regulator protein found in fungi that appears to be integrally associated with both the Swi-Snf and the RSC chromatin remodelling complexes, []. RSC is involved in transcription regulation and nucleosome positioning, and is responsible for the transfer of a histone octamer from a nucleosome core particle to naked DNA. The reaction requires ATP and involves an activated RSC-nucleosome intermediate. Remodelling reaction also involves DNA translocation, DNA twist and conformational change. As a reconfigurer of centromeric and flanking nucleosomes, RSC complex is required both for proper kinetochore function in chromosome segregation and, via a PKC1-dependent signalling pathway, for organisation of the cellular cytoskeleton. It is a probable component of the SWI/SNF complex, an ATP-dependent chromatin-remodelling complex, is required for the positive and negative regulation of gene expression of a large number of genes. It changes chromatin structure by altering DNA-histone contacts within a nucleosome, leading eventually to a change in nucleosome position, thus facilitating or repressing binding of gene-specific transcription factors.
Probab=53.24 E-value=6.8 Score=26.92 Aligned_cols=8 Identities=63% Similarity=1.028 Sum_probs=7.3
Q ss_pred CCCHHHHH
Q psy11575 48 DLTMEDIR 55 (80)
Q Consensus 48 ~lTmedIR 55 (80)
+|||+|||
T Consensus 110 ~LT~dDIR 117 (130)
T PF09510_consen 110 SLTVDDIR 117 (130)
T ss_pred CCCHHHhh
Confidence 69999999
No 12
>PF10471 APC_CDC26: Anaphase-promoting complex APC subunit 1; InterPro: IPR018860 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents subunit CDC26, whose exact function is not known [].; GO: 0030071 regulation of mitotic metaphase/anaphase transition, 0031145 anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process, 0005680 anaphase-promoting complex; PDB: 2XPI_E 3HYM_A.
Probab=51.21 E-value=3.8 Score=25.21 Aligned_cols=21 Identities=33% Similarity=0.465 Sum_probs=11.9
Q ss_pred cCCCHHHHHHHHHHHHHHHHH
Q psy11575 47 HDLTMEDIRRIEEETKKELDR 67 (80)
Q Consensus 47 ~~lTmedIR~~E~et~~~l~~ 67 (80)
+-||.|||-+||+..++...+
T Consensus 9 I~Lt~eDi~eye~~~~~~~~~ 29 (79)
T PF10471_consen 9 IELTLEDIAEYEDRRKEQKLQ 29 (79)
T ss_dssp ----CHHHHHHCCCHHH----
T ss_pred EEecHHHHHHHHHHHHHHHHH
Confidence 458999999999988777533
No 13
>PF05914 RIB43A: RIB43A; InterPro: IPR008805 This family consists of several RIB43A-like eukaryotic proteins. Ciliary and flagellar microtubules contain a specialised set of protofilaments, termed ribbons, that are composed of tubulin and several associated proteins. RIB43A was first characterised in the unicellular biflagellate, Chlamydomonas reinhardtii although highly related sequences are present in several higher eukaryotes including humans. The function of this protein is unknown although the structure of RIB43A and its association with the specialised protofilament ribbons and with basal bodies is relevant to the proposed role of ribbons in forming and stabilising doublet and triplet microtubules and in organising their three-dimensional structure. Human RIB43A homologues could represent a structural requirement in centriole replication in dividing cells [].
Probab=38.73 E-value=43 Score=26.54 Aligned_cols=21 Identities=29% Similarity=0.692 Sum_probs=16.0
Q ss_pred hhcccCCCHHHHHHHHHHHHH
Q psy11575 43 IDRWHDLTMEDIRRIEEETKK 63 (80)
Q Consensus 43 iDeW~~lTmedIR~~E~et~~ 63 (80)
-|.|.|||.+++..+-..-..
T Consensus 271 ~d~wKGMs~eQl~~i~~~Q~~ 291 (379)
T PF05914_consen 271 PDRWKGMSPEQLEEIRKEQEQ 291 (379)
T ss_pred CcccCCCCHHHHHHHHHHHHH
Confidence 489999999988877654433
No 14
>PF04707 PRELI: PRELI-like family; InterPro: IPR006797 These proteins contain a conserved region found in the yeast YLR168C gene MSF1 product. The function of this protein is unknown, though it is thought to be involved in intra-mitochondrial protein sorting. GFP-tagged MSF1 localizes to mitochondria and is required for wild-type respiratory growth []. This region is also found in a number of other eukaryotic proteins. The PRELI/MSF1 domain is an eukaryotic protein module which occurs in stand-alone form in several proteins, including the human PRELI protein and the yeast MSF1 protein, and as an amino-terminal domain in an orthologous group of proteins typified by human SEC14L1, which is conserved in all animals. In this group of proteins, the PRELI/MSF1 domain co-occurs with the CRAL-TRIO (see PDOC50191 from PROSITEDOC) and the GOLD domains (see PDOC50866 from PROSITEDOC). The PRELI/MSF1 domain is approximately 170 residues long and is predicted to assume a globular alpha + beta fold with six beta strands and four alpha helices. It has been suggested that the PRELI/MSF1 domain may have a function associated with cellular membrane [].
Probab=37.01 E-value=1e+02 Score=21.02 Aligned_cols=39 Identities=23% Similarity=0.370 Sum_probs=24.3
Q ss_pred eeeE-eEEEe--eccchhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy11575 3 CYKL-VTAEF--KWFGFQGRVENFIHKAERRLFTNFHRQVFCW 42 (80)
Q Consensus 3 ~YKl-v~v~f--~~~Glq~~vE~~i~~~~r~i~~~~HRq~fcw 42 (80)
.|+. .+|++ .++||++++|+++.+....-..++ |+++-|
T Consensus 108 ~~~q~a~i~~~~~~~~~~~~iE~~~~~~f~~na~kg-r~~~e~ 149 (157)
T PF04707_consen 108 LFKQEATISIKGSFSGFSSRIEKFSVSRFKSNAKKG-REGMEW 149 (157)
T ss_pred eEEEEEEEEEeCchhhHhHHHHHHHHHHHHHHHHHH-HHHHHH
Confidence 3444 44555 569999999999988765543333 344333
No 15
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=36.61 E-value=23 Score=20.13 Aligned_cols=12 Identities=25% Similarity=0.553 Sum_probs=8.6
Q ss_pred cCCCHHHHHHHH
Q psy11575 47 HDLTMEDIRRIE 58 (80)
Q Consensus 47 ~~lTmedIR~~E 58 (80)
.|+|.++||++=
T Consensus 13 lGfsL~eI~~~l 24 (65)
T PF09278_consen 13 LGFSLEEIRELL 24 (65)
T ss_dssp TT--HHHHHHHH
T ss_pred cCCCHHHHHHHH
Confidence 799999999874
No 16
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=36.10 E-value=52 Score=18.53 Aligned_cols=18 Identities=0% Similarity=0.065 Sum_probs=13.1
Q ss_pred HHHHhhcccCCCHHHHHHHH
Q psy11575 39 VFCWIDRWHDLTMEDIRRIE 58 (80)
Q Consensus 39 ~fcwiDeW~~lTmedIR~~E 58 (80)
+.+..+ .|+|+++|+++.
T Consensus 50 i~~l~~--~g~~l~~i~~~~ 67 (68)
T cd01104 50 IRRLTS--EGVRISQAAALA 67 (68)
T ss_pred HHHHHH--CCCCHHHHHHHh
Confidence 344444 799999999874
No 17
>PF15581 Imm35: Immunity protein 35
Probab=32.36 E-value=27 Score=22.99 Aligned_cols=12 Identities=25% Similarity=0.645 Sum_probs=9.9
Q ss_pred hcccCCCHHHHH
Q psy11575 44 DRWHDLTMEDIR 55 (80)
Q Consensus 44 DeW~~lTmedIR 55 (80)
-||-||+|++|.
T Consensus 41 ~eWRGl~~~qV~ 52 (93)
T PF15581_consen 41 HEWRGLPEEQVL 52 (93)
T ss_pred HHHcCCCHHHHH
Confidence 379999988874
No 18
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=32.35 E-value=61 Score=18.56 Aligned_cols=19 Identities=16% Similarity=0.644 Sum_probs=14.1
Q ss_pred HHHHHHhhcccCCCHHHHHHH
Q psy11575 37 RQVFCWIDRWHDLTMEDIRRI 57 (80)
Q Consensus 37 Rq~fcwiDeW~~lTmedIR~~ 57 (80)
+++-|..| .|+|+++|+++
T Consensus 48 ~~i~~l~~--~g~~l~~i~~~ 66 (68)
T cd04763 48 LEIKRWID--NGVQVSKVKKL 66 (68)
T ss_pred HHHHHHHH--cCCCHHHHHHH
Confidence 34556667 89999999874
No 19
>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.
Probab=31.46 E-value=88 Score=18.22 Aligned_cols=28 Identities=32% Similarity=0.394 Sum_probs=23.0
Q ss_pred hcccCCCHHHHHHHHHHHHHHHHHHHhh
Q psy11575 44 DRWHDLTMEDIRRIEEETKKELDRQRLE 71 (80)
Q Consensus 44 DeW~~lTmedIR~~E~et~~~l~~~~~~ 71 (80)
..|-.||-++-..+.++..+..++-..+
T Consensus 38 ~~Wk~ls~~eK~~y~~~a~~~k~~y~~~ 65 (72)
T cd01388 38 DRWKALSNEEKQPYYEEAKKLKELHMKL 65 (72)
T ss_pred HHHHcCCHHHHHHHHHHHHHHHHHHHHH
Confidence 5799999999999999988877765543
No 20
>PF14045 YIEGIA: YIEGIA protein
Probab=29.57 E-value=43 Score=26.09 Aligned_cols=17 Identities=35% Similarity=0.655 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy11575 51 MEDIRRIEEETKKELDR 67 (80)
Q Consensus 51 medIR~~E~et~~~l~~ 67 (80)
--|||++|++|-++|++
T Consensus 71 FRdVR~mER~tL~~le~ 87 (285)
T PF14045_consen 71 FRDVRNMERETLTNLEE 87 (285)
T ss_pred HHHHHHHHHHHHHhhhh
Confidence 36999999999999875
No 21
>PF13455 MUG113: Meiotically up-regulated gene 113
Probab=29.36 E-value=40 Score=21.09 Aligned_cols=38 Identities=24% Similarity=0.275 Sum_probs=25.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHhh-----cccCCCHHHHHHH
Q psy11575 16 FQGRVENFIHKAERRLFTNFHRQVFCWID-----RWHDLTMEDIRRI 57 (80)
Q Consensus 16 lq~~vE~~i~~~~r~i~~~~HRq~fcwiD-----eW~~lTmedIR~~ 57 (80)
...++|+.||..+.+.-... -+=-| |||.++.+++.+.
T Consensus 37 ~~~rvErliH~eL~~~r~~~----~~c~~C~~~HEwF~v~~~~~~~v 79 (83)
T PF13455_consen 37 HVHRVERLIHLELADKRLRG----GECDDCGKRHEWFEVEAEDVKEV 79 (83)
T ss_pred cHHHHHHHHHHHHHhcccCc----ccCCCCCceeeEEeeCHHHHHHH
Confidence 56889999998887722211 11112 9999998887754
No 22
>PF06868 DUF1257: Protein of unknown function (DUF1257); InterPro: IPR009666 This family represents Ycf35, which is encoded in algal chloroplast and in cyanobacteria. The function of these proteins are unknown. As the family is exclusively found in phototrophic organisms it may play a role in photosynthesis.
Probab=28.38 E-value=51 Score=21.52 Aligned_cols=24 Identities=29% Similarity=0.595 Sum_probs=20.4
Q ss_pred eeeEeEEEeeccchhHHHHHHHHHH
Q psy11575 3 CYKLVTAEFKWFGFQGRVENFIHKA 27 (80)
Q Consensus 3 ~YKlv~v~f~~~Glq~~vE~~i~~~ 27 (80)
+|-||. +.-+|+-...+|.|+.+.
T Consensus 48 sYeLVa-Dl~~W~q~~~~e~fl~kl 71 (105)
T PF06868_consen 48 SYELVA-DLQFWQQPYSVERFLNKL 71 (105)
T ss_pred cEEEEe-ehhhhcccCCHHHHHHHH
Confidence 588887 888999778899999875
No 23
>PF09346 SMI1_KNR4: SMI1 / KNR4 family (SUKH-1); InterPro: IPR018958 Proteins in this family are involved in the regulation of 1,3-beta-glucan synthase activity and cell-wall formation [, ]. Yeast members of this family are involved in the regulation of cell wall assembly. Saccharomyces cerevisiae (Baker's yeast) protein KNR4 (SMI1) has a regulatory role in chitin deposition and in cell wall assembly []. It was originally identified as a regulator of chitin synthase expression (acting as a repressor) [] and of 1,3-beta-glucan synthase levels []. It was shown to localise in patches at presumptive bud sites in unbudded cells and at the incipient bud site during bud emergence []. KNR4 is believed to connect the PKC1-SLT2 MAPK pathway with cell proliferation. It has been shown to interact with BCK2, a gene involved in cell cycle progression in S. cerevisiae (forming a complex) to allow PKC1 to coordinate the cell cycle (cell proliferation) with cell wall integrity [, ]. PKC1 plays an essential role in cell wall integrity and cell proliferation through a bifurcated PKC1/mitogen-activated protein (MAP) kinase pathway. KNR4 also interacts with the tyrosine-tRNA synthetase protein encoded by TYS1 and is involved in sporulation process []. Note: previously reported evidence that KNR4 may interact with nuclear matrix-association region [] may be due to an artefact [].; PDB: 3D5P_A 2ICG_A.
Probab=27.94 E-value=45 Score=20.08 Aligned_cols=18 Identities=33% Similarity=0.414 Sum_probs=11.9
Q ss_pred CCCHHHHHHHHHHHHHHH
Q psy11575 48 DLTMEDIRRIEEETKKEL 65 (80)
Q Consensus 48 ~lTmedIR~~E~et~~~l 65 (80)
++|-++|+++|++..-.|
T Consensus 1 p~t~~~I~~~E~~lg~~L 18 (130)
T PF09346_consen 1 PATEEEIQELEEKLGVRL 18 (130)
T ss_dssp ---HHHHHHHHHHHTS--
T ss_pred CCCHHHHHHHHHHhCCCC
Confidence 468899999999987665
No 24
>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include the fungal mating type gene products MC, MATA1 and Ste11.
Probab=27.74 E-value=1.2e+02 Score=17.86 Aligned_cols=27 Identities=19% Similarity=0.217 Sum_probs=22.1
Q ss_pred hcccCCCHHHHHHHHHHHHHHHHHHHh
Q psy11575 44 DRWHDLTMEDIRRIEEETKKELDRQRL 70 (80)
Q Consensus 44 DeW~~lTmedIR~~E~et~~~l~~~~~ 70 (80)
+.|..||-++=..+++...++.++..+
T Consensus 38 ~~Wk~ls~eeK~~y~~~A~~~k~~~~~ 64 (77)
T cd01389 38 RMWRSESPEVKAYYKELAEEEKERHAR 64 (77)
T ss_pred HHHhhCCHHHHHHHHHHHHHHHHHHHH
Confidence 679999999999999988777665544
No 25
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=27.42 E-value=1.1e+02 Score=20.46 Aligned_cols=23 Identities=26% Similarity=0.420 Sum_probs=15.2
Q ss_pred CCC-HHHHHHHHHHH----HHHHHHHHh
Q psy11575 48 DLT-MEDIRRIEEET----KKELDRQRL 70 (80)
Q Consensus 48 ~lT-medIR~~E~et----~~~l~~~~~ 70 (80)
+|| |++.|.||+.. ++++++.+.
T Consensus 61 ~MTy~~Q~k~Ye~a~~~~~~~~lqkRle 88 (104)
T PF11460_consen 61 KMTYMQQRKDYEEAVDQLTNEELQKRLE 88 (104)
T ss_pred CCcHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence 577 78888888876 444544443
No 26
>PF01486 K-box: K-box region; InterPro: IPR002487 MADS genes in plants encode key developmental regulators of vegetative and reproductive development. The majority of the plant MADS proteins share a stereotypical MIKC structure. It comprises (from N- to C-terminal) an N-terminal domain, which is, however, present only in a minority of proteins; a MADS domain (see PDOC00302 from PROSITEDOC, IPR002100 from INTERPRO), which is the major determinant of DNA-binding but which also performs dimerisation and accessory factor binding functions; a weakly conserved intervening (I) domain, which constitutes a key molecular determinant for the selective formation of DNA-binding dimers; a keratin-like (K-box) domain, which promotes protein dimerisation; and a C-terminal (C) domain, which is involved in transcriptional activation or in the formation of ternary or quaternary protein complexes. The 80-amino acid K-box domain was originally identified as a region with low but significant similarity to a region of keratin, which is part of the coiled-coil sequence constituting the central rod-shaped domain of keratin [, , ]. The K-box protein-protein interaction domain which mediates heterodimerization of MIKC-type MADS proteins contains several heptad repeats in which the first and the fourth positions are occupied by hydrophobic amino acids suggesting that the K-box domain forms three amphipathic alpha-helices referred to as K1, K2, and K3 [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=27.18 E-value=83 Score=19.73 Aligned_cols=39 Identities=15% Similarity=0.350 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHhhcccCCCHHHHHHHHHHHHHHHHHHHhh
Q psy11575 31 LFTNFHRQVFCWIDRWHDLTMEDIRRIEEETKKELDRQRLE 71 (80)
Q Consensus 31 i~~~~HRq~fcwiDeW~~lTmedIR~~E~et~~~l~~~~~~ 71 (80)
.+-..+|++- =+.=-+||++|+-.+|......|.+.+..
T Consensus 30 ~L~~~~R~~~--GedL~~Ls~~eL~~LE~~Le~aL~~VR~r 68 (100)
T PF01486_consen 30 SLQKELRHLM--GEDLESLSLKELQQLEQQLESALKRVRSR 68 (100)
T ss_pred HHHHHHhccc--cccccccchHHHHHHHHhhhhhHHHHHHH
Confidence 3344445442 13345599999999999999888777653
No 27
>PF09011 HMG_box_2: HMG-box domain; InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins. It has no known function. ; GO: 0005634 nucleus; PDB: 2EQZ_A 1V64_A 2CTO_A 1H5P_A 3TQ6_A 3FGH_A 3TMM_A 1J3X_A 2YRQ_A 1AAB_A ....
Probab=26.94 E-value=86 Score=18.31 Aligned_cols=25 Identities=32% Similarity=0.641 Sum_probs=19.7
Q ss_pred hhcccCCCHHHHHHHHHHHHHHHHH
Q psy11575 43 IDRWHDLTMEDIRRIEEETKKELDR 67 (80)
Q Consensus 43 iDeW~~lTmedIR~~E~et~~~l~~ 67 (80)
-++|-.||-++=..|++..++.-++
T Consensus 40 ~~~Wk~Ls~~EK~~Y~~~A~~~k~~ 64 (73)
T PF09011_consen 40 SERWKSLSEEEKEPYEERAKEDKER 64 (73)
T ss_dssp HHHHHHS-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHhcCHHHHHHHHHHHHHHHHH
Confidence 4789999999999999987766443
No 28
>PTZ00285 glucosamine-6-phosphate isomerase; Provisional
Probab=26.91 E-value=24 Score=25.65 Aligned_cols=32 Identities=16% Similarity=0.180 Sum_probs=24.9
Q ss_pred HHHHHHHHHhhcccCCCHHHHHHHHHHHHHHH
Q psy11575 34 NFHRQVFCWIDRWHDLTMEDIRRIEEETKKEL 65 (80)
Q Consensus 34 ~~HRq~fcwiDeW~~lTmedIR~~E~et~~~l 65 (80)
.+.|=-|.|+|||+|+..++-.....-.++.|
T Consensus 62 ~w~~v~if~~DEr~~Vp~~~~~Sn~~~~~~~l 93 (253)
T PTZ00285 62 SFSNVVTFNMDEYVGLPRDHPQSYHYFMKENF 93 (253)
T ss_pred chhHeEEECCcEEecCCCCchHHHHHHHHHHH
Confidence 44555678899999999998887777777665
No 29
>TIGR00496 frr ribosome recycling factor. This model finds only eubacterial proteins. Mitochondrial and/or chloroplast forms might be expected but are not currently known. This protein was previously called ribosome releasing factor. By releasing ribosomes from mRNA at the end of protein biosynthesis, it prevents inappropriate translation from 3-prime regions of the mRNA and frees the ribosome for new rounds of translation. EGAD|53116|YHR038W is part of the frr superfamily.
Probab=26.59 E-value=1e+02 Score=21.75 Aligned_cols=42 Identities=19% Similarity=0.269 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHHHhhcc---cCCCHHHHHHHHHHHHHHHHHHHh
Q psy11575 29 RRLFTNFHRQVFCWIDRW---HDLTMEDIRRIEEETKKELDRQRL 70 (80)
Q Consensus 29 r~i~~~~HRq~fcwiDeW---~~lTmedIR~~E~et~~~l~~~~~ 70 (80)
+--+.+..|.+.--+... .++|-||++.+|.+.|+..++..+
T Consensus 116 Kv~iRniRr~~~~~iKk~~k~~~iseD~~k~~~~~iQkltd~~i~ 160 (176)
T TIGR00496 116 KVAVRNVRRDANDKVKKLEKDKEISEDEERRLQEEIQKLTDEYIK 160 (176)
T ss_pred HHHHHHHHHHHHHHHHHHhhcCCCChhHHHHHHHHHHHHHHHHHH
Confidence 344556666666666655 469999999999999988766554
No 30
>PF10666 Phage_Gp14: Phage protein Gp14; InterPro: IPR018923 This Listeria phage Gp14 protein family is of unknown function but is expressed from within a cluster of tail- and base plate genes [].
Probab=25.15 E-value=1.1e+02 Score=21.45 Aligned_cols=28 Identities=25% Similarity=0.374 Sum_probs=22.7
Q ss_pred hhcccCCCHHHHHHHHHHHHHHHHHHHh
Q psy11575 43 IDRWHDLTMEDIRRIEEETKKELDRQRL 70 (80)
Q Consensus 43 iDeW~~lTmedIR~~E~et~~~l~~~~~ 70 (80)
||.=-.||.+|.+.+|.+..+.|...+.
T Consensus 56 id~~~EmS~e~~~aLe~~~re~L~ea~~ 83 (140)
T PF10666_consen 56 IDFDREMSSEEYRALEEQQREALKEAIE 83 (140)
T ss_pred ccchhhcCHHHHHHHHHHHHHHHHHHHH
Confidence 4555679999999999999998877653
No 31
>PF07078 FYTT: Forty-two-three protein; InterPro: IPR009782 This family consists of several hypothetical mammalian proteins of around 320 residues in length. The function of this family is unknown although several of the family members are annotated as putative 40-2-3 proteins.
Probab=24.79 E-value=64 Score=25.49 Aligned_cols=20 Identities=25% Similarity=0.677 Sum_probs=15.2
Q ss_pred hcccCCCHHHHHHHHHHHHHH
Q psy11575 44 DRWHDLTMEDIRRIEEETKKE 64 (80)
Q Consensus 44 DeW~~lTmedIR~~E~et~~~ 64 (80)
|+ +|||+|||-+|-.+-+.+
T Consensus 27 DK-IDMSLDDIIKLNKKE~kk 46 (316)
T PF07078_consen 27 DK-IDMSLDDIIKLNKKEQKK 46 (316)
T ss_pred cc-ccccHHHHHHhhhhhhhh
Confidence 44 899999999887665443
No 32
>KOG0717|consensus
Probab=23.68 E-value=2.1e+02 Score=24.11 Aligned_cols=39 Identities=18% Similarity=0.390 Sum_probs=27.9
Q ss_pred EEeeccch-hHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCC
Q psy11575 9 AEFKWFGF-QGRVENFIHKAERRLFTNFHRQVFCWIDRWHDL 49 (80)
Q Consensus 9 v~f~~~Gl-q~~vE~~i~~~~r~i~~~~HRq~fcwiDeW~~l 49 (80)
.-.++||. -+..+.++ -....=....-+.-|||.|+ |+.
T Consensus 136 ~~ap~fg~~~t~ye~~~-~fY~~W~afsT~Ksf~W~d~-Ydv 175 (508)
T KOG0717|consen 136 LLYPLFGYSTTDYEQVV-PFYQFWLAFSTKKSFEWLDE-YDV 175 (508)
T ss_pred cccccccCCCCcHHHHH-HHHHHHHhhhhhhhHHhhhh-hhh
Confidence 45688997 46688877 55555556667888999999 444
No 33
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=23.63 E-value=1.1e+02 Score=17.36 Aligned_cols=18 Identities=17% Similarity=0.543 Sum_probs=12.3
Q ss_pred HHHHHhhcccCCCHHHHHHH
Q psy11575 38 QVFCWIDRWHDLTMEDIRRI 57 (80)
Q Consensus 38 q~fcwiDeW~~lTmedIR~~ 57 (80)
.+-+..+ .|+|+++|+++
T Consensus 48 ~i~~l~~--~g~~l~~i~~~ 65 (67)
T cd04764 48 KIKTLLE--KGLSIKEIKEI 65 (67)
T ss_pred HHHHHHH--CCCCHHHHHHH
Confidence 3444555 78899998864
No 34
>PF01452 Rota_NSP4: Rotavirus non structural protein; InterPro: IPR002107 This entry contains rotaviral non-structural protein 4 (NSP4) as well as related proteins: NSP5, NS28, and NCVP5. The final steps in the assembly of rotavirus occur in the lumen of the endoplasmic reticulum (ER). Targeting of the immature inner capsid particle (ICP) to this compartment is mediated by the cytoplasmic tail of NSP4, located in the ER membrane [, ].; PDB: 2O1J_D 1G1J_B 1G1I_B 2O1K_B 3MIW_A.
Probab=23.40 E-value=3e+02 Score=20.00 Aligned_cols=38 Identities=26% Similarity=0.414 Sum_probs=13.6
Q ss_pred eeeeEeEE--------Eeeccch--hHHHHHHHHHHHHHHHHHHHHHH
Q psy11575 2 TCYKLVTA--------EFKWFGF--QGRVENFIHKAERRLFTNFHRQV 39 (80)
Q Consensus 2 ~~YKlv~v--------~f~~~Gl--q~~vE~~i~~~~r~i~~~~HRq~ 39 (80)
|+||++.+ -.+.+|. |-.-++-|.+++-++.-..-||+
T Consensus 63 csYKViky~ivTI~N~llklaGykeqittkDeie~qmdrivkemrrQl 110 (173)
T PF01452_consen 63 CSYKVIKYCIVTIFNTLLKLAGYKEQITTKDEIEKQMDRIVKEMRRQL 110 (173)
T ss_dssp --------------------------------HHHHHHHHHHHHHHHH
T ss_pred ccceEEEEEEEeehhhHHHHhcccccCCcHHHHHHHHHHHHHHHHHHH
Confidence 78988654 4567787 55567778888888888888886
No 35
>PF14048 MBD_C: C-terminal domain of methyl-CpG binding protein 2 and 3; PDB: 2L2L_B.
Probab=23.00 E-value=1.2e+02 Score=19.63 Aligned_cols=20 Identities=45% Similarity=0.418 Sum_probs=13.0
Q ss_pred ccCCCHHHHHHHHHHHHHHH
Q psy11575 46 WHDLTMEDIRRIEEETKKEL 65 (80)
Q Consensus 46 W~~lTmedIR~~E~et~~~l 65 (80)
.+-.|-+|||+=|+++++.=
T Consensus 70 ~~~VT~eDIr~QE~rVk~aR 89 (96)
T PF14048_consen 70 QFVVTEEDIRRQERRVKKAR 89 (96)
T ss_dssp -----HHHHHHHHHHHHHHH
T ss_pred CCccCHHHHHHHHHHHHHHH
Confidence 45578999999999988763
No 36
>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin. HMG1 (also called HMG-T in fish) and HMG2 are two highly related proteins that bind single-stranded DNA preferentially and unwind double-stranded DNA. Although they have no sequence specificity, they have a high affinity for bent or distorted DNA, and bend linear DNA. HMG1 and HMG2 contain two DNA-binding HMG-box domains (A and B) that show structural and functional differences, and have a long acidic C-terminal domain rich in aspartic and glutamic acid residues. The acidic tail modulates the affinity of the tandem HMG boxes in HMG1 and 2 for a variety of DNA targets. HMG1 and 2 appear to play important architectural roles in the assembly of nucleoprotein complexes in a variety of biological processes, for example V(D)J recombination, the initiation of transcription, and DNA repair []. The profile in this entry describing the HMG-domains is much more general than the signature. In addition to the HMG1 and HMG2 proteins, HMG-domains occur in single or multiple copies in the following protein classes; the SOX family of transcription factors; SRY sex determining region Y protein and related proteins []; LEF1 lymphoid enhancer binding factor 1 []; SSRP recombination signal recognition protein; MTF1 mitochondrial transcription factor 1; UBF1/2 nucleolar transcription factors; Abf2 yeast ARS-binding factor []; and Saccharomyces cerevisiae transcription factors Ixr1, Rox1, Nhp6a, Nhp6b and Spp41.; GO: 0003677 DNA binding; PDB: 1I11_A 1J3C_A 1J3D_A 1WZ6_A 1WGF_A 2D7L_A 1GT0_D 3U2B_C 2CRJ_A 2CS1_A ....
Probab=22.72 E-value=1.1e+02 Score=17.00 Aligned_cols=25 Identities=28% Similarity=0.538 Sum_probs=20.0
Q ss_pred hcccCCCHHHHHHHHHHHHHHHHHH
Q psy11575 44 DRWHDLTMEDIRRIEEETKKELDRQ 68 (80)
Q Consensus 44 DeW~~lTmedIR~~E~et~~~l~~~ 68 (80)
..|.+||-++-..+.++..+...+-
T Consensus 37 ~~W~~l~~~eK~~y~~~a~~~~~~y 61 (69)
T PF00505_consen 37 QMWKNLSEEEKAPYKEEAEEEKERY 61 (69)
T ss_dssp HHHHCSHHHHHHHHHHHHHHHHHHH
T ss_pred HHHhcCCHHHHHHHHHHHHHHHHHH
Confidence 4699999999999988877766543
No 37
>PF10642 Tom5: Mitochondrial import receptor subunit or translocase; InterPro: IPR019603 This entry represents a short family of yeast proteins. Tom5 is one of three very small translocases of the mitochondrial outer membrane. Tom5 links mitochondrial preprotein receptors to the general import pore []. Although Tom5 has allegedly been identified in vertebrates this could not be confirmed.
Probab=22.27 E-value=1.7e+02 Score=16.91 Aligned_cols=21 Identities=14% Similarity=0.222 Sum_probs=17.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHH
Q psy11575 49 LTMEDIRRIEEETKKELDRQR 69 (80)
Q Consensus 49 lTmedIR~~E~et~~~l~~~~ 69 (80)
.|-|+|+..|.++...++...
T Consensus 9 pS~eE~k~~e~~A~~Tvk~a~ 29 (49)
T PF10642_consen 9 PSEEEIKAAEAQANFTVKNAA 29 (49)
T ss_pred CCHHHHHHHHHHHHHHHHHHH
Confidence 588999999999988876654
No 38
>COG0233 Frr Ribosome recycling factor [Translation, ribosomal structure and biogenesis]
Probab=21.82 E-value=1.3e+02 Score=21.97 Aligned_cols=23 Identities=22% Similarity=0.404 Sum_probs=19.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHh
Q psy11575 48 DLTMEDIRRIEEETKKELDRQRL 70 (80)
Q Consensus 48 ~lTmedIR~~E~et~~~l~~~~~ 70 (80)
..|.||.|..|++.|...++..+
T Consensus 149 ~isEDe~k~~e~~iQKlTd~yi~ 171 (187)
T COG0233 149 EISEDEVKKAEEEIQKLTDEYIK 171 (187)
T ss_pred CcchHHHHHHHHHHHHHHHHHHH
Confidence 37999999999999988766554
No 39
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=21.49 E-value=80 Score=17.96 Aligned_cols=23 Identities=26% Similarity=0.492 Sum_probs=17.9
Q ss_pred HHHHHHHHHhhcc-cCCCHHHHHH
Q psy11575 34 NFHRQVFCWIDRW-HDLTMEDIRR 56 (80)
Q Consensus 34 ~~HRq~fcwiDeW-~~lTmedIR~ 56 (80)
..=||+.+|+-.. .|+|+.+|=+
T Consensus 30 ~~aR~iamyla~~~~~~sl~~Ig~ 53 (60)
T smart00760 30 VLARQIAMYLARELTDLSLPEIGK 53 (60)
T ss_pred hHHHHHHHHHHHHHHCCCHHHHHH
Confidence 4468888888877 8899888853
No 40
>cd03081 TRX_Fd_NuoE_FDH_gamma TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, NAD-dependent formate dehydrogenase (FDH) gamma subunit; composed of proteins similar to the gamma subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD+ to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH gamma subunit is closely related to NuoE, which is part of a multisubunit complex (Nuo) catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE. Similarly, the FDH gamma subunit is hypothesized to be involved in an electron transport chain involving other FDH subunits, upon the oxidat
Probab=20.02 E-value=70 Score=19.29 Aligned_cols=14 Identities=14% Similarity=0.240 Sum_probs=10.0
Q ss_pred hccc-CCCHHHHHHH
Q psy11575 44 DRWH-DLTMEDIRRI 57 (80)
Q Consensus 44 DeW~-~lTmedIR~~ 57 (80)
|+|| ++|.++|+++
T Consensus 62 ~~~~~~~~~e~i~~i 76 (80)
T cd03081 62 GEVHGRVDPEKFDAL 76 (80)
T ss_pred CEEECCCCHHHHHHH
Confidence 4577 6788888764
Done!