Query psy14169
Match_columns 97
No_of_seqs 54 out of 56
Neff 3.4
Searched_HMMs 46136
Date Fri Aug 16 21:11:08 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14169.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14169hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1925|consensus 100.0 8.3E-48 1.8E-52 329.8 8.3 95 1-95 585-679 (817)
2 smart00498 FH2 Formin Homology 98.7 1.7E-07 3.7E-12 76.3 10.0 86 1-92 315-400 (432)
3 PF02181 FH2: Formin Homology 97.9 3.5E-05 7.7E-10 60.5 6.4 57 1-60 314-370 (370)
4 KOG1922|consensus 68.3 50 0.0011 29.4 9.1 70 1-72 723-792 (833)
5 PF07568 HisKA_2: Histidine ki 60.7 33 0.00071 21.9 5.0 40 3-54 31-70 (76)
6 KOG4110|consensus 51.4 31 0.00068 25.3 4.1 38 54-93 58-95 (120)
7 KOG1924|consensus 48.9 1.5E+02 0.0033 28.5 9.0 53 1-56 934-986 (1102)
8 PF14726 RTTN_N: Rotatin, an a 47.2 30 0.00064 23.9 3.3 25 26-54 32-56 (98)
9 PF01627 Hpt: Hpt domain; Int 43.0 57 0.0012 19.4 3.9 36 2-37 4-50 (90)
10 PF02662 FlpD: Methyl-viologen 39.2 48 0.001 23.2 3.5 38 21-58 77-119 (124)
11 PF10147 CR6_interact: Growth 38.8 1.1E+02 0.0023 24.3 5.6 67 19-89 62-128 (217)
12 PF12927 DUF3835: Domain of un 37.6 33 0.00072 22.3 2.3 22 50-71 26-47 (79)
13 PF08397 IMD: IRSp53/MIM homol 37.2 73 0.0016 23.9 4.4 60 6-65 54-117 (219)
14 PF08355 EF_assoc_1: EF hand a 31.5 20 0.00044 23.7 0.5 12 27-38 40-51 (76)
15 KOG0180|consensus 31.1 44 0.00095 26.5 2.4 39 16-60 61-99 (204)
16 KOG1923|consensus 30.9 1.7E+02 0.0037 27.6 6.3 68 1-71 671-738 (830)
17 PF12834 Phage_int_SAM_2: Phag 30.8 84 0.0018 21.0 3.4 35 18-52 24-58 (91)
18 PF06777 DUF1227: Protein of u 30.0 61 0.0013 24.1 2.9 53 3-55 89-143 (146)
19 COG4024 Uncharacterized protei 27.6 30 0.00065 27.6 1.0 34 30-63 51-95 (218)
20 PF13426 PAS_9: PAS domain; PD 26.9 17 0.00036 21.4 -0.4 24 27-50 18-41 (104)
21 COG0663 PaaY Carbonic anhydras 25.4 66 0.0014 24.6 2.4 45 26-71 128-172 (176)
22 PF12958 DUF3847: Protein of u 24.8 95 0.0021 21.2 2.9 30 60-89 20-49 (86)
23 PF13384 HTH_23: Homeodomain-l 24.1 26 0.00056 19.8 0.0 22 34-55 17-41 (50)
24 CHL00027 rps15 ribosomal prote 23.9 1.3E+02 0.0028 20.7 3.5 39 7-57 46-84 (90)
25 PF06528 Phage_P2_GpE: Phage P 23.7 24 0.00053 21.1 -0.2 20 31-50 6-25 (39)
26 cd00642 GTP_cyclohydro1 GTP cy 22.5 1.4E+02 0.0029 22.8 3.6 40 21-61 5-46 (185)
27 PF12672 DUF3793: Protein of u 22.4 19 0.00042 26.8 -0.9 14 28-41 108-121 (176)
28 PF00656 Peptidase_C14: Caspas 21.9 77 0.0017 22.6 2.1 33 24-56 25-59 (248)
29 PF08447 PAS_3: PAS fold; Int 21.2 30 0.00064 20.6 -0.1 26 28-53 7-32 (91)
30 PF04884 DUF647: Vitamin B6 ph 20.2 1.2E+02 0.0025 24.3 3.0 41 17-57 8-48 (250)
No 1
>KOG1925|consensus
Probab=100.00 E-value=8.3e-48 Score=329.78 Aligned_cols=95 Identities=52% Similarity=0.805 Sum_probs=93.7
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhcCCCCCCCCCChhHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhhhhh
Q psy14169 1 MSEFLSDTAQRIIVLSIVHRRVLHRFHRFCLWLGVPLHRVPLTKPQDLARIISEFALEYRTTRERVIQTREKKASHRERN 80 (97)
Q Consensus 1 l~~FL~d~aeRI~iL~~VhrRv~NRF~~fLL~lG~s~~~~~~~k~~~fck~iSEFALEYRTtrervlqq~~K~a~~ReRn 80 (97)
|++||+||||||++||+||||++||||+||||||||+++++++.||+||+||+||||||||||||||||++|+|+|||||
T Consensus 585 ~~~fl~~cA~RI~~LKivhrr~~NRfHSFLLy~Gy~p~aIrev~iN~fc~~~~EFaLEYRTTRervLQQ~qk~A~~RERN 664 (817)
T KOG1925|consen 585 LTHFLDQCARRIAMLKIVHRRVCNRFHSFLLYLGYTPQAIREVRINQFCHTLREFALEYRTTRERVLQQQQKQATYRERN 664 (817)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCChhhhhhcCHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHhhc
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhchhHhhhhhccc
Q psy14169 81 KTRGKMITECEELSE 95 (97)
Q Consensus 81 KTrGKmit~~~~~s~ 95 (97)
||||||||+.|+||+
T Consensus 665 KTRGKmit~~Gkfs~ 679 (817)
T KOG1925|consen 665 KTRGKMITETGKFSG 679 (817)
T ss_pred ccccceeeecccccC
Confidence 999999999999984
No 2
>smart00498 FH2 Formin Homology 2 Domain. FH proteins control rearrangements of the actin cytoskeleton, especially in the context of cytokinesis and cell polarisation. Members of this family have been found to interact with Rho-GTPases, profilin and other actin-assoziated proteins. These interactions are mediated by the proline-rich FH1 domain, usually located in front of FH2 (but not listed in SMART). Despite this cytosolic function, vertebrate formins have been assigned functions within the nucleus. A set of Formin-Binding Proteins (FBPs) has been shown to bind FH1 with their WW domain.
Probab=98.68 E-value=1.7e-07 Score=76.29 Aligned_cols=86 Identities=26% Similarity=0.353 Sum_probs=74.1
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhcCCCCCCCCCChhHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhhhhh
Q psy14169 1 MSEFLSDTAQRIIVLSIVHRRVLHRFHRFCLWLGVPLHRVPLTKPQDLARIISEFALEYRTTRERVIQTREKKASHRERN 80 (97)
Q Consensus 1 l~~FL~d~aeRI~iL~~VhrRv~NRF~~fLL~lG~s~~~~~~~k~~~fck~iSEFALEYRTtrervlqq~~K~a~~ReRn 80 (97)
|.+|+.+|..++..|+..+..+.+.|.+++.|||.++.. .+|++||.++++|..+|..+++.-+ ++++...+|.
T Consensus 315 m~~F~~~a~~~~~~l~~~~~~~~~~~~~~~~yfge~~~~---~~~~efF~~f~~F~~~f~ka~~en~---~~~~~e~~~~ 388 (432)
T smart00498 315 MKPFLKAAKEKYDKLQKDLSDLKTRFEKLVEYYGEDPKD---TSPEEFFKDFNEFLKEFSKAAEENI---KKEEEEEERR 388 (432)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCC---CCHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHH
Confidence 568999999999999999999999999999999999995 7999999999999999999988743 3334556788
Q ss_pred hhhchhHhhhhh
Q psy14169 81 KTRGKMITECEE 92 (97)
Q Consensus 81 KTrGKmit~~~~ 92 (97)
+.+.|.+++-..
T Consensus 389 ~~~~~~~~~~~~ 400 (432)
T smart00498 389 KQLVKETTEYEQ 400 (432)
T ss_pred HHHHHHHHhhhh
Confidence 888887776433
No 3
>PF02181 FH2: Formin Homology 2 Domain; InterPro: IPR015425 Formin homology (FH) proteins play a crucial role in the reorganisation of the actin cytoskeleton, which mediates various functions of the cell cortex including motility, adhesion, and cytokinesis []. Formins are multidomain proteins that interact with diverse signalling molecules and cytoskeletal proteins, although some formins have been assigned functions within the nucleus. Formins are characterised by the presence of three FH domains (FH1, FH2 and FH3), although members of the formin family do not necessarily contain all three domains []. The proline-rich FH1 domain mediates interactions with a variety of proteins, including the actin-binding protein profilin, SH3 (Src homology 3) domain proteins, and WW domain proteins. The FH2 domain is required for the self-association of formin proteins through the ability of FH2 domains to directly bind each other [], and may also act to inhibit actin polymerisation []. The FH3 domain (IPR010472 from INTERPRO) is less well conserved and may be important for determining intracellular localisation of formin family proteins. In addition, some formins can contain a GTPase-binding domain (GBD) (IPR010473 from INTERPRO) required for binding to Rho small GTPases, and a C-terminal conserved Dia-autoregulatory domain (DAD). This entry represents the FH2 domain, which was shown by X-ray crystallography to have an elongated, crescent shape containing three helical subdomains [].; PDB: 1Y64_B 1UX4_A 1UX5_A 3O4X_H 3OBV_E 1V9D_D 2Z6E_B 2J1D_G.
Probab=97.89 E-value=3.5e-05 Score=60.46 Aligned_cols=57 Identities=19% Similarity=0.410 Sum_probs=51.9
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhcCCCCCCCCCChhHHHHHHHHHHHHHH
Q psy14169 1 MSEFLSDTAQRIIVLSIVHRRVLHRFHRFCLWLGVPLHRVPLTKPQDLARIISEFALEYR 60 (97)
Q Consensus 1 l~~FL~d~aeRI~iL~~VhrRv~NRF~~fLL~lG~s~~~~~~~k~~~fck~iSEFALEYR 60 (97)
|.+|+.+|..++..|+.-+.++.+.|..++.|||-.++ +.+|++|+.++++|+.+|.
T Consensus 314 ~~~f~~~~~~~~~~l~~~~~~~~~~~~~~~~yfge~~~---~~~~~~ff~~l~~F~~~fk 370 (370)
T PF02181_consen 314 MKEFLEEAETKLDELQELYEELEEAFKQLLQYFGEDPK---KMSPEEFFKILSQFIDMFK 370 (370)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--TT---CCHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCC---CCCHHHHHHHHHHHHHHhC
Confidence 46899999999999999999999999999999998887 8889999999999999884
No 4
>KOG1922|consensus
Probab=68.33 E-value=50 Score=29.36 Aligned_cols=70 Identities=20% Similarity=0.327 Sum_probs=57.9
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhcCCCCCCCCCChhHHHHHHHHHHHHHHhHHHHHHHHHHH
Q psy14169 1 MSEFLSDTAQRIIVLSIVHRRVLHRFHRFCLWLGVPLHRVPLTKPQDLARIISEFALEYRTTRERVIQTREK 72 (97)
Q Consensus 1 l~~FL~d~aeRI~iL~~VhrRv~NRF~~fLL~lG~s~~~~~~~k~~~fck~iSEFALEYRTtrervlqq~~K 72 (97)
|.+|+.-+.+-+.-+.-=.++++.-+.++..|||..+. .+..+.+++.++.+|-.-+--.-+-+-.+.+|
T Consensus 723 ~~~fl~~ae~ev~~l~~~~~~~~~~~~~~~~yf~~~~~--~~~~~~~~f~~~r~fl~~~~~~~~e~~~~~~k 792 (833)
T KOG1922|consen 723 KKEFLSSAEKEVKLLISEEREVRESVKKTAKYFGEDPK--EEITPEQVFSILRDFLRTFDKAHEENKKAEEK 792 (833)
T ss_pred hhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhccCcc--ccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 57899999999999999999999999999999999998 88888889999988877666544444444433
No 5
>PF07568 HisKA_2: Histidine kinase; InterPro: IPR011495 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This is the dimerisation and phosphoacceptor domain of a subfamily of histidine kinases. It shares sequence similarity with IPR003661 from INTERPRO and IPR011102 from INTERPRO. It is usually found adjacent to a C-terminal ATPase domain (IPR003594 from INTERPRO). This domain is found in a wide range of bacteria and also several archaea.
Probab=60.71 E-value=33 Score=21.91 Aligned_cols=40 Identities=20% Similarity=0.340 Sum_probs=30.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhcCCCCCCCCCChhHHHHHHHH
Q psy14169 3 EFLSDTAQRIIVLSIVHRRVLHRFHRFCLWLGVPLHRVPLTKPQDLARIISE 54 (97)
Q Consensus 3 ~FL~d~aeRI~iL~~VhrRv~NRF~~fLL~lG~s~~~~~~~k~~~fck~iSE 54 (97)
+-|.+++.||..+..||+.+. .......+.+.+|..-+.+
T Consensus 31 ~~L~~~~~RI~aia~vh~~L~------------~~~~~~~v~l~~yl~~L~~ 70 (76)
T PF07568_consen 31 EALEDAQNRIQAIALVHEQLY------------QSEDLSEVDLREYLEELCE 70 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHh------------cCCCCCeecHHHHHHHHHH
Confidence 468999999999999999863 4456667777777665543
No 6
>KOG4110|consensus
Probab=51.38 E-value=31 Score=25.30 Aligned_cols=38 Identities=32% Similarity=0.464 Sum_probs=31.6
Q ss_pred HHHHHHHhHHHHHHHHHHHHHhhhhhhhhhchhHhhhhhc
Q psy14169 54 EFALEYRTTRERVIQTREKKASHRERNKTRGKMITECEEL 93 (97)
Q Consensus 54 EFALEYRTtrervlqq~~K~a~~ReRnKTrGKmit~~~~~ 93 (97)
|-|+||+--.|=|+-|++++-.+--|| -|.|+|.+ |++
T Consensus 58 eC~ie~~dFqECv~~qKqmrra~aiR~-qr~Kl~le-Gk~ 95 (120)
T KOG4110|consen 58 ECAIEYDDFQECVLMQKQMRRAHAIRK-QRYKLILE-GKY 95 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHc-CCc
Confidence 668999999999999999998887775 57888887 444
No 7
>KOG1924|consensus
Probab=48.92 E-value=1.5e+02 Score=28.54 Aligned_cols=53 Identities=13% Similarity=0.176 Sum_probs=47.8
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhcCCCCCCCCCChhHHHHHHHHHH
Q psy14169 1 MSEFLSDTAQRIIVLSIVHRRVLHRFHRFCLWLGVPLHRVPLTKPQDLARIISEFA 56 (97)
Q Consensus 1 l~~FL~d~aeRI~iL~~VhrRv~NRF~~fLL~lG~s~~~~~~~k~~~fck~iSEFA 56 (97)
|+.|-.+|-|....|...|--+.+=|.++--|+-+.+. +.++++|+-=|..|.
T Consensus 934 M~~F~e~a~eq~~~ls~M~~~M~~lye~L~eYyaFd~k---kysmEEFFaDi~tFr 986 (1102)
T KOG1924|consen 934 MTSFHEKAREQYSKLSSMHGNMEKLYESLGEYYAFDPK---KYSMEEFFADIRTFR 986 (1102)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHeecCcc---cCcHHHHHHHHHHHH
Confidence 67899999999999999999999999999999988774 678899998888883
No 8
>PF14726 RTTN_N: Rotatin, an armadillo repeat protein, centriole functioning
Probab=47.19 E-value=30 Score=23.93 Aligned_cols=25 Identities=8% Similarity=0.364 Sum_probs=19.7
Q ss_pred HHHHHHHhcCCCCCCCCCChhHHHHHHHH
Q psy14169 26 FHRFCLWLGVPLHRVPLTKPQDLARIISE 54 (97)
Q Consensus 26 F~~fLL~lG~s~~~~~~~k~~~fck~iSE 54 (97)
|..+|-|||+|+.. -.+++..++++
T Consensus 32 l~~LleWFnf~~~~----~~~~VL~Ll~~ 56 (98)
T PF14726_consen 32 LKQLLEWFNFPPVP----MKEEVLALLLR 56 (98)
T ss_pred HHHHHHHhCCCCCc----cHHHHHHHHHH
Confidence 57889999999987 34667777777
No 9
>PF01627 Hpt: Hpt domain; InterPro: IPR008207 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents a domain present at the N terminus in proteins which undergo autophosphorylation. The group includes, the gliding motility regulatory protein from Myxococcus xanthus and a number of bacterial chemotaxis proteins.; GO: 0004871 signal transducer activity, 0000160 two-component signal transduction system (phosphorelay); PDB: 3KYJ_A 3KYI_A 3IQT_A 1Y6D_A 2LD6_A 1TQG_A 2R25_A 1OXB_A 1QSP_B 1C03_B ....
Probab=43.01 E-value=57 Score=19.43 Aligned_cols=36 Identities=28% Similarity=0.383 Sum_probs=31.2
Q ss_pred chHHHHHHHHHHHHHHHH-----------HHHHhhHHHHHHHhcCCC
Q psy14169 2 SEFLSDTAQRIIVLSIVH-----------RRVLHRFHRFCLWLGVPL 37 (97)
Q Consensus 2 ~~FL~d~aeRI~iL~~Vh-----------rRv~NRF~~fLL~lG~s~ 37 (97)
..|+.++.+.+..|+... +|..++.+.-.-.+|.+.
T Consensus 4 ~~f~~~~~~~~~~l~~~~~~~~~~d~~~l~~~~H~lkG~a~~~g~~~ 50 (90)
T PF01627_consen 4 DIFLEEAPEDLEQLEQALQALEQEDWEELRRLAHRLKGSAGNLGAPR 50 (90)
T ss_dssp HHHHHHHHHHHHHHHHHHCSSHHCHHHHHHHHHHHHHHHHHHTTCHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHhHhhHHHHHHHHHHHhhhHHhcCHHH
Confidence 469999999999998877 788889999999999864
No 10
>PF02662 FlpD: Methyl-viologen-reducing hydrogenase, delta subunit; InterPro: IPR003813 Methyl-viologen-reducing hydrogenase (MVH) is one of the enzymes involved in methanogenesis and coded in the mth-flp-mvh-mrt cluster of methane genes in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) []. No specific functions have been assigned to the delta subunit.; GO: 0015948 methanogenesis, 0055114 oxidation-reduction process
Probab=39.21 E-value=48 Score=23.19 Aligned_cols=38 Identities=24% Similarity=0.406 Sum_probs=29.8
Q ss_pred HHHhhHHHHHHHhcCCCCCCC-----CCChhHHHHHHHHHHHH
Q psy14169 21 RVLHRFHRFCLWLGVPLHRVP-----LTKPQDLARIISEFALE 58 (97)
Q Consensus 21 Rv~NRF~~fLL~lG~s~~~~~-----~~k~~~fck~iSEFALE 58 (97)
+-+.+..+.|.-+|++|..+. -.....|..++.||+=+
T Consensus 77 ~Rv~~~k~~L~~~Gi~~eRv~~~~~~~~~~~~fa~~~~~f~~~ 119 (124)
T PF02662_consen 77 KRVERLKKLLEELGIEPERVRLYWISAPEGKRFAEIVNEFTER 119 (124)
T ss_pred HHHHHHHHHHHHcCCChhHeEEEEeCcccHHHHHHHHHHHHHH
Confidence 445677889999999998866 45667899999999743
No 11
>PF10147 CR6_interact: Growth arrest and DNA-damage-inducible proteins-interacting protein 1; InterPro: IPR018472 Members of this family of proteins act as negative regulators of G1 to S cell cycle phase progression by inhibiting cyclin-dependent kinases. Inhibitory effects are additive with GADD45 proteins but occur also in the absence of GADD45 proteins. Furthermore, they act as a repressor of the orphan nuclear receptor NR4A1 by inhibiting AB domain-mediated transcriptional activity []. They may be involved in the hormone-mediated regulation of NR4A1 transcriptional activity.; GO: 0007049 cell cycle, 0005634 nucleus
Probab=38.79 E-value=1.1e+02 Score=24.27 Aligned_cols=67 Identities=24% Similarity=0.193 Sum_probs=42.1
Q ss_pred HHHHHhhHHHHHHHhcCCCCCCCCCChhHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhhhhhhhhchhHhh
Q psy14169 19 HRRVLHRFHRFCLWLGVPLHRVPLTKPQDLARIISEFALEYRTTRERVIQTREKKASHRERNKTRGKMITE 89 (97)
Q Consensus 19 hrRv~NRF~~fLL~lG~s~~~~~~~k~~~fck~iSEFALEYRTtrervlqq~~K~a~~ReRnKTrGKmit~ 89 (97)
.|++.-||+.- -|++|...+++. .+...+.-|=-.=|.|..+.+=....+++...+...+|=+.|..
T Consensus 62 ~Rk~fGRYG~a---SgV~P~~lwPt~-eelee~e~Ee~~~~~sl~em~k~~~~~~~~k~~k~~~Rek~Ia~ 128 (217)
T PF10147_consen 62 KRKLFGRYGLA---SGVDPGILWPTP-EELEEQEYEEVEWPPSLQEMLKELREKKEEKEEKRLAREKEIAK 128 (217)
T ss_pred HHHHHHhhhhh---cCCChhhhCCCH-HHHHHHHHHHHcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666677665 899999999998 77777655422234555555444455555555555566555554
No 12
>PF12927 DUF3835: Domain of unknown function (DUF3835); InterPro: IPR024325 This domain is found in a number of fungal proteins whose function is unknown.
Probab=37.65 E-value=33 Score=22.30 Aligned_cols=22 Identities=32% Similarity=0.469 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHhHHHHHHHHHH
Q psy14169 50 RIISEFALEYRTTRERVIQTRE 71 (97)
Q Consensus 50 k~iSEFALEYRTtrervlqq~~ 71 (97)
.+--|-|+||.-.|++++++..
T Consensus 26 ~~~~eia~ey~~~R~~~i~~~~ 47 (79)
T PF12927_consen 26 LLQREIAEEYHRLRNKIIQQEG 47 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHcc
Confidence 4557899999999999999876
No 13
>PF08397 IMD: IRSp53/MIM homology domain; InterPro: IPR013606 The IMD (IRSp53 and MIM (missing in metastases) homology) domain is a BAR-like domain of approximately 250 amino acids found at the N-terminal in the insulin receptor tyrosine kinase substrate p53 (IRSp53) and in the evolutionarily related IRSp53/MIM family. In IRSp53, a ubiquitous regulator o the actin cytoskeleton, the IMD domain acts as conserved F-actin bundling domain involved in filopodium formation. Filopodium-inducing IMD activity is regulated by Cdc42 and Rac1 (Rho-family GTPases) and is SH3-independent [, , ]. The IRSp53/MIM family is a novel F-actin bundling protein family that includes invertebrate relatives: Vertebrate MIM (missing in metastasis), an actin-binding scaffold protein that may be involved in cancer metastasis. Vertebrate ABBA-1, a MIM-related protein. Vertebrate brain-specific angiogenesis inhibitor 1-associated protein 2 (BAI1-associated protein 2) or insulin receptor tyrosine kinase substrate p53 (IRSp53), a multifunctional adaptor protein that links Rac1 with a Wiskott-Aldrich syndrome family verprolin-homologous protein 2 (WAVE2) to induce lamellipodia or Cdc42 with Mena to induce filopodia []. Vertebrate brain-specific angiogenesis inhibitor 1-associated protein 2-like proteins 1 and 2 (BAI1-associated protein 2-like proteins 1 and 2). Drosophila melanogaster (Fruit fly) CG32082-PA. Caenorhabditis elegans M04F3.5 protein. The vertebrate IRSp53/MIM family is divided into two major groups: the IRSp53 subfamily and the MIM/ABBA subfamily. The putative invertebrate homologues are positioned between them. The IRSp53 subfamily members contain an SH3 domain, and the MIM/ABBA subfamily proteins contain a WH2 (WASP-homology 2) domain. The vertebrate SH3-containing subfamily is further divided into three groups according to the presence or absence of the WWB and the half-CRIB motif. The IMD domain can bind to and bundle actin filaments, bind to membranes and interact with the small GTPase Rac [, ]. The IMD domain folds as a coiled coil of three extended alpha-helices and a shorter C-terminal helix. Helix 4 packs tightly against the other three helices, and thus represents an integral part of the domain. The fold of the IMD domain closely resembles that of the BAR (Bin-Amphiphysin-RVS) domain, a functional module serving both as a sensor and inducer of membrane curvature []. The WH2 domain performs a scaffolding function [].; GO: 0008093 cytoskeletal adaptor activity, 0017124 SH3 domain binding, 0007165 signal transduction, 0046847 filopodium assembly; PDB: 2D1L_A 3OK8_B 1WDZ_B 1Y2O_A 2YKT_A.
Probab=37.23 E-value=73 Score=23.88 Aligned_cols=60 Identities=17% Similarity=0.337 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHHHh----cCCCCCCCCCChhHHHHHHHHHHHHHHhHHHH
Q psy14169 6 SDTAQRIIVLSIVHRRVLHRFHRFCLWL----GVPLHRVPLTKPQDLARIISEFALEYRTTRER 65 (97)
Q Consensus 6 ~d~aeRI~iL~~VhrRv~NRF~~fLL~l----G~s~~~~~~~k~~~fck~iSEFALEYRTtrer 65 (97)
.|.++-+.-+-.+||++-+..+.+.-.| -.|...--+.-...+-..--+|.-||+--++.
T Consensus 54 ~~lG~~L~~~s~~~r~i~~~~~~~~~~~~~~li~pLe~~~e~d~k~i~~~~K~y~ke~k~~~~~ 117 (219)
T PF08397_consen 54 KELGDALMQISEVHRRIENELEEVFKAFHSELIQPLEKKLEEDKKYITQLEKDYEKEYKRKRDE 117 (219)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 4667777888889999998887777664 23333222222222334444677777765554
No 14
>PF08355 EF_assoc_1: EF hand associated; InterPro: IPR013566 This region typically appears on the C terminus of EF hands in GTP-binding proteins such as Arht/Rhot (may be involved in mitochondrial homeostasis and apoptosis[]). The EF hand associated region is found in yeast, vertebrates and plants.
Probab=31.50 E-value=20 Score=23.73 Aligned_cols=12 Identities=25% Similarity=0.440 Sum_probs=9.9
Q ss_pred HHHHHHhcCCCC
Q psy14169 27 HRFCLWLGVPLH 38 (97)
Q Consensus 27 ~~fLL~lG~s~~ 38 (97)
=..|.|||||..
T Consensus 40 le~L~YLGy~~~ 51 (76)
T PF08355_consen 40 LEYLAYLGYPGL 51 (76)
T ss_pred HHHHhhcCCCCc
Confidence 358999999994
No 15
>KOG0180|consensus
Probab=31.08 E-value=44 Score=26.46 Aligned_cols=39 Identities=21% Similarity=0.322 Sum_probs=27.8
Q ss_pred HHHHHHHHhhHHHHHHHhcCCCCCCCCCChhHHHHHHHHHHHHHH
Q psy14169 16 SIVHRRVLHRFHRFCLWLGVPLHRVPLTKPQDLARIISEFALEYR 60 (97)
Q Consensus 16 ~~VhrRv~NRF~~fLL~lG~s~~~~~~~k~~~fck~iSEFALEYR 60 (97)
+++.+|++ |++.| |-...-++++|..|..+||.+.-|-|
T Consensus 61 qtl~~~~~--fr~nL----y~lre~R~i~P~~~s~mvS~~lYekR 99 (204)
T KOG0180|consen 61 QTLLERLR--FRKNL----YELREEREIKPETFSSMVSSLLYEKR 99 (204)
T ss_pred HHHHHHHH--HHHhH----HHhhhhcccCcHHHHHHHHHHHHHhh
Confidence 34555554 44444 23456789999999999999988765
No 16
>KOG1923|consensus
Probab=30.91 E-value=1.7e+02 Score=27.64 Aligned_cols=68 Identities=19% Similarity=0.349 Sum_probs=48.4
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhcCCCCCCCCCChhHHHHHHHHHHHHHHhHHHHHHHHHH
Q psy14169 1 MSEFLSDTAQRIIVLSIVHRRVLHRFHRFCLWLGVPLHRVPLTKPQDLARIISEFALEYRTTRERVIQTRE 71 (97)
Q Consensus 1 l~~FL~d~aeRI~iL~~VhrRv~NRF~~fLL~lG~s~~~~~~~k~~~fck~iSEFALEYRTtrervlqq~~ 71 (97)
|++|+.+.-.-..-|+.--+-..-=|...-.|||=++. .+.|..|+..++-|---|..+++-.=+.++
T Consensus 671 L~~F~~n~~~kmkkl~~~~k~A~~af~~~~~y~Gespk---~tppt~ff~~f~~F~~~~k~~~~ene~k~~ 738 (830)
T KOG1923|consen 671 LSEFLDNNKPKMKKLRKDFKDAAEAFEDVVEYFGESPK---TTPPTVFFQLFVRFVRAYKMARQENEQKKK 738 (830)
T ss_pred HHHHHhcccHHHHHHHHHHHHHHHHHHhHhHhhCCCCC---CCCCCccHHHHHHHHHHHHhhhhhhhhhhh
Confidence 45666665555555555555555667788899997763 567788999999999999999965544444
No 17
>PF12834 Phage_int_SAM_2: Phage integrase, N-terminal; InterPro: IPR024457 Phage integrase proteins cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [, ]. This entry represents the N-terminal predicted alpha-helical domain found in a family of putative prophage DNA-binding integrases.
Probab=30.76 E-value=84 Score=20.97 Aligned_cols=35 Identities=29% Similarity=0.528 Sum_probs=29.6
Q ss_pred HHHHHHhhHHHHHHHhcCCCCCCCCCChhHHHHHH
Q psy14169 18 VHRRVLHRFHRFCLWLGVPLHRVPLTKPQDLARII 52 (97)
Q Consensus 18 VhrRv~NRF~~fLL~lG~s~~~~~~~k~~~fck~i 52 (97)
...+++.||-.+|.=+||-+..+..+++..+-..|
T Consensus 24 ~R~~~~~~~~~~L~~~g~~i~~~~~lk~kHI~~lv 58 (91)
T PF12834_consen 24 DRMRILKRFARFLRELGFQIRSIRNLKPKHIEALV 58 (91)
T ss_pred HHHHHHHHHHHHHHHCCCCcCCHHHhhHHHHHHHH
Confidence 44577899999998899999999999998776555
No 18
>PF06777 DUF1227: Protein of unknown function (DUF1227); InterPro: IPR010643 This domain represents a conserved region within a number of eukaryotic DNA repair helicases.; GO: 0005634 nucleus
Probab=30.03 E-value=61 Score=24.15 Aligned_cols=53 Identities=17% Similarity=0.171 Sum_probs=34.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhcCCCC-C-CCCCChhHHHHHHHHH
Q psy14169 3 EFLSDTAQRIIVLSIVHRRVLHRFHRFCLWLGVPLH-R-VPLTKPQDLARIISEF 55 (97)
Q Consensus 3 ~FL~d~aeRI~iL~~VhrRv~NRF~~fLL~lG~s~~-~-~~~~k~~~fck~iSEF 55 (97)
.||+++.+.+-|=...-|=.-.|-++++-=|+++.. . .+-..+-+||.+||-+
T Consensus 89 sFL~~~~~~~~id~k~LrFc~eRL~sLl~TLei~d~~df~~L~~Va~FaTLv~tY 143 (146)
T PF06777_consen 89 SFLQHLKDETFIDRKPLRFCSERLSSLLRTLEITDIDDFSALQLVADFATLVSTY 143 (146)
T ss_pred HHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHCCCcHhhhhHHHHHHHHHHHHHHh
Confidence 588888887776666666677788899999997741 1 1123345566666543
No 19
>COG4024 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.62 E-value=30 Score=27.56 Aligned_cols=34 Identities=29% Similarity=0.514 Sum_probs=30.6
Q ss_pred HHHhcCCCCCCCCCChhHHHH-----------HHHHHHHHHHhHH
Q psy14169 30 CLWLGVPLHRVPLTKPQDLAR-----------IISEFALEYRTTR 63 (97)
Q Consensus 30 LL~lG~s~~~~~~~k~~~fck-----------~iSEFALEYRTtr 63 (97)
.||-..|.+..+.-..++||+ ++..|..|.+|-|
T Consensus 51 ~Ly~saP~HeL~gE~A~EfcrklIa~~e~l~~ILa~fGveee~~~ 95 (218)
T COG4024 51 ALYESAPEHELRGERAQEFCRKLIALDEILRSILALFGVEEETER 95 (218)
T ss_pred HHHhcCchhhhccHhHHHHHHHHHHHHHHHHHHHHHcCcchhccc
Confidence 578899999999999999999 7789999999855
No 20
>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A ....
Probab=26.93 E-value=17 Score=21.41 Aligned_cols=24 Identities=13% Similarity=0.030 Sum_probs=18.3
Q ss_pred HHHHHHhcCCCCCCCCCChhHHHH
Q psy14169 27 HRFCLWLGVPLHRVPLTKPQDLAR 50 (97)
Q Consensus 27 ~~fLL~lG~s~~~~~~~k~~~fck 50 (97)
.+|+-++||++..+-..++.+|+.
T Consensus 18 ~~~~~~~g~~~~~~~g~~~~~~~~ 41 (104)
T PF13426_consen 18 PAFERLFGYSREELIGKSISDFFP 41 (104)
T ss_dssp HHHHHHHTS-HHHHTTSBGGGGCS
T ss_pred HHHHHHHCcCHHHHcCCCcccccC
Confidence 467889999999988888777664
No 21
>COG0663 PaaY Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]
Probab=25.36 E-value=66 Score=24.64 Aligned_cols=45 Identities=18% Similarity=0.161 Sum_probs=37.0
Q ss_pred HHHHHHHhcCCCCCCCCCChhHHHHHHHHHHHHHHhHHHHHHHHHH
Q psy14169 26 FHRFCLWLGVPLHRVPLTKPQDLARIISEFALEYRTTRERVIQTRE 71 (97)
Q Consensus 26 F~~fLL~lG~s~~~~~~~k~~~fck~iSEFALEYRTtrervlqq~~ 71 (97)
+-...|++|-|...+++....+ -.-+.++|-+|-...++-+...+
T Consensus 128 ~p~~~L~~G~Pak~~r~l~~~~-~~~~~~~a~~Yv~~~~~~~~~~~ 172 (176)
T COG0663 128 IPGGSLVVGSPAKVVRPLDDEE-LAWLRENAENYVKLADRYLAGLK 172 (176)
T ss_pred CCCCeEeecCcceeeecCChhH-hhhhhHhHHHHHHHHHHHhhhhh
Confidence 4456789999999999999999 77789999999988877665543
No 22
>PF12958 DUF3847: Protein of unknown function (DUF3847); InterPro: IPR024215 This entry represents a family of uncharacterised proteins that were found by clustering human gut metagenomic sequences [].
Probab=24.76 E-value=95 Score=21.24 Aligned_cols=30 Identities=20% Similarity=0.424 Sum_probs=21.1
Q ss_pred HhHHHHHHHHHHHHHhhhhhhhhhchhHhh
Q psy14169 60 RTTRERVIQTREKKASHRERNKTRGKMITE 89 (97)
Q Consensus 60 RTtrervlqq~~K~a~~ReRnKTrGKmit~ 89 (97)
=.-+.++|+++.|...+.||.+..-++|+-
T Consensus 20 ~e~~~k~L~nr~k~l~k~eRK~RtHRLi~r 49 (86)
T PF12958_consen 20 AEHKIKQLENRKKKLEKKERKERTHRLIER 49 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345678999999988877776655555544
No 23
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=24.14 E-value=26 Score=19.82 Aligned_cols=22 Identities=14% Similarity=0.285 Sum_probs=11.0
Q ss_pred cCCCCCCC---CCChhHHHHHHHHH
Q psy14169 34 GVPLHRVP---LTKPQDLARIISEF 55 (97)
Q Consensus 34 G~s~~~~~---~~k~~~fck~iSEF 55 (97)
|+|...|. .++++.+.+.+..|
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT--
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 66665554 56667777776665
No 24
>CHL00027 rps15 ribosomal protein S15
Probab=23.89 E-value=1.3e+02 Score=20.75 Aligned_cols=39 Identities=18% Similarity=0.329 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHHHHHhhHHHHHHHhcCCCCCCCCCChhHHHHHHHHHHH
Q psy14169 7 DTAQRIIVLSIVHRRVLHRFHRFCLWLGVPLHRVPLTKPQDLARIISEFAL 57 (97)
Q Consensus 7 d~aeRI~iL~~VhrRv~NRF~~fLL~lG~s~~~~~~~k~~~fck~iSEFAL 57 (97)
|-+-+--.++.|++| +++|-|| +...+..+..+|+++-|
T Consensus 46 D~~s~RgL~~lv~kR-----krLL~YL-------~r~d~~~Y~~li~~Lgl 84 (90)
T CHL00027 46 DYSSQRGLRKILGKR-----QRLLAYL-------SKKNRVRYKKLISQLGI 84 (90)
T ss_pred cchhHHHHHHHHHHH-----HHHHHHH-------HhCCHHHHHHHHHHhCC
Confidence 444455555555554 6788887 56677778888777644
No 25
>PF06528 Phage_P2_GpE: Phage P2 GpE; InterPro: IPR009493 This entry is represented by Burkholderia phage phiE202, Gp27. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage and bacterial proteins which are closely related to the GpE tail protein from Phage P2.
Probab=23.74 E-value=24 Score=21.09 Aligned_cols=20 Identities=10% Similarity=0.064 Sum_probs=16.8
Q ss_pred HHhcCCCCCCCCCChhHHHH
Q psy14169 31 LWLGVPLHRVPLTKPQDLAR 50 (97)
Q Consensus 31 L~lG~s~~~~~~~k~~~fck 50 (97)
.+||.||+.+-.+++.|+..
T Consensus 6 ~~FhW~Pse~~~m~l~El~~ 25 (39)
T PF06528_consen 6 WVFHWPPSEMDAMSLDELMD 25 (39)
T ss_pred eecCCCHHHHhcCCHHHHHH
Confidence 47899999999999988753
No 26
>cd00642 GTP_cyclohydro1 GTP cyclohydrolase I (GTP-CH-I) catalyzes the conversion of GTP into dihydroneopterin triphosphate. The enzyme product is the precursor of tetrahydrofolate in eubacteria, fungi, and plants and of the folate analogs in methanogenic bacteria. In vertebrates and insects it is the biosynthtic precursor of tetrahydrobiopterin (BH4) which is involved in the formation of catacholamines, nitric oxide, and the stimulation of T lymphocytes. The biosynthetic reaction of BH4 is controlled by a regulatory protein GFRP which mediates feedback inhibition of GTP-CH-I by BH4. This inhibition is reversed by phenylalanine. The decameric GTP-CH-I forms a complex with two pentameric GFRP in the presence of phenylalanine or a combination of GTP and BH4, respectively.
Probab=22.49 E-value=1.4e+02 Score=22.83 Aligned_cols=40 Identities=20% Similarity=0.297 Sum_probs=31.2
Q ss_pred HHHhhHHHHHHHhcCCCCC--CCCCChhHHHHHHHHHHHHHHh
Q psy14169 21 RVLHRFHRFCLWLGVPLHR--VPLTKPQDLARIISEFALEYRT 61 (97)
Q Consensus 21 Rv~NRF~~fLL~lG~s~~~--~~~~k~~~fck~iSEFALEYRT 61 (97)
++..-++.+|.++|-.++. ..+| |..+.++..|+---|+.
T Consensus 5 ~~e~av~~lL~alGeD~~regL~~T-P~Rva~~~~e~~~G~~~ 46 (185)
T cd00642 5 KIAAAVREILELLGEDPNREGLLET-PERVAKAYQEITSGYDQ 46 (185)
T ss_pred HHHHHHHHHHHHhCCCCCccchhhH-HHHHHHHHHHHhcCcCC
Confidence 3566788999999998877 4555 89999999887555654
No 27
>PF12672 DUF3793: Protein of unknown function (DUF3793); InterPro: IPR024523 This family of bacterial proteins is functionally uncharacterised. The proteins in this family contain two conserved sequence motifs: PHE and LGYP.
Probab=22.39 E-value=19 Score=26.76 Aligned_cols=14 Identities=36% Similarity=0.710 Sum_probs=10.9
Q ss_pred HHHHHhcCCCCCCC
Q psy14169 28 RFCLWLGVPLHRVP 41 (97)
Q Consensus 28 ~fLL~lG~s~~~~~ 41 (97)
=.=+|||||...|.
T Consensus 108 EIGiFLGYPleDV~ 121 (176)
T PF12672_consen 108 EIGIFLGYPLEDVK 121 (176)
T ss_pred hhHhccCCCHHHHH
Confidence 34689999998765
No 28
>PF00656 Peptidase_C14: Caspase domain; InterPro: IPR011600 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of sequences represent the p20 (20kDa) and p10 (10kDa) subunits of caspases, which together form the catalytic domain of the caspase and are derived from the p45 (45 kDa) precursor (IPR002398 from INTERPRO) []. Caspases (Cysteine-dependent ASPartyl-specific proteASE) are cysteine peptidases that belong to the MEROPS peptidase family C14 (caspase family, clan CD) based on the architecture of their catalytic dyad or triad []. Caspases are tightly regulated proteins that require zymogen activation to become active, and once active can be regulated by caspase inhibitors. Activated caspases act as cysteine proteases, using the sulphydryl group of a cysteine side chain for catalysing peptide bond cleavage at aspartyl residues in their substrates. The catalytic cysteine and histidine residues are on the p20 subunit after cleavage of the p45 precursor. Caspases are mainly involved in mediating cell death (apoptosis) [, , ]. They have two main roles within the apoptosis cascade: as initiators that trigger the cell death process, and as effectors of the process itself. Caspase-mediated apoptosis follows two main pathways, one extrinsic and the other intrinsic or mitochondrial-mediated. The extrinsic pathway involves the stimulation of various TNF (tumour necrosis factor) cell surface receptors on cells targeted to die by various TNF cytokines that are produced by cells such as cytotoxic T cells. The activated receptor transmits the signal to the cytoplasm by recruiting FADD, which forms a death-inducing signalling complex (DISC) with caspase-8. The subsequent activation of caspase-8 initiates the apoptosis cascade involving caspases 3, 4, 6, 7, 9 and 10. The intrinsic pathway arises from signals that originate within the cell as a consequence of cellular stress or DNA damage. The stimulation or inhibition of different Bcl-2 family receptors results in the leakage of cytochrome c from the mitochondria, and the formation of an apoptosome composed of cytochrome c, Apaf1 and caspase-9. The subsequent activation of caspase-9 initiates the apoptosis cascade involving caspases 3 and 7, among others. At the end of the cascade, caspases act on a variety of signal transduction proteins, cytoskeletal and nuclear proteins, chromatin-modifying proteins, DNA repair proteins and endonucleases that destroy the cell by disintegrating its contents, including its DNA. The different caspases have different domain architectures depending upon where they fit into the apoptosis cascades, however they all carry the catalytic p10 and p20 subunits. Caspases can have roles other than in apoptosis, such as caspase-1 (interleukin-1 beta convertase) (3.4.22.36 from EC), which is involved in the inflammatory process. The activation of apoptosis can sometimes lead to caspase-1 activation, providing a link between apoptosis and inflammation, such as during the targeting of infected cells. Caspases may also be involved in cell differentiation [].; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 1M72_C 2NN3_C 3V4L_A 3IBF_B 2QLF_D 2QLB_C 3IBC_B 2QL9_A 3R5K_B 3H1P_A ....
Probab=21.86 E-value=77 Score=22.55 Aligned_cols=33 Identities=9% Similarity=0.155 Sum_probs=27.1
Q ss_pred hhHHHHHHHhcCCCCC--CCCCChhHHHHHHHHHH
Q psy14169 24 HRFHRFCLWLGVPLHR--VPLTKPQDLARIISEFA 56 (97)
Q Consensus 24 NRF~~fLL~lG~s~~~--~~~~k~~~fck~iSEFA 56 (97)
+++.++|..+|+++.. ..+.+..++-+.|.+|.
T Consensus 25 ~~~~~~L~~~gf~~~~~l~~~~t~~~i~~~l~~l~ 59 (248)
T PF00656_consen 25 EAMAEALEKLGFDVENILIDNATRANILKALRELL 59 (248)
T ss_dssp HHHHHHHHHTTEEEEEEEEESSSHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCceeeccccchHHHHHHHHHhhhh
Confidence 4677888999999999 77878888888887775
No 29
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.
Probab=21.21 E-value=30 Score=20.61 Aligned_cols=26 Identities=12% Similarity=0.119 Sum_probs=16.5
Q ss_pred HHHHHhcCCCCCCCCCChhHHHHHHH
Q psy14169 28 RFCLWLGVPLHRVPLTKPQDLARIIS 53 (97)
Q Consensus 28 ~fLL~lG~s~~~~~~~k~~~fck~iS 53 (97)
.|+-.|||+++.+....++.+...|.
T Consensus 7 ~~~~i~G~~~~~~~~~~~~~~~~~ih 32 (91)
T PF08447_consen 7 NFYEIFGYSPEEIGKPDFEEWLERIH 32 (91)
T ss_dssp HHHHHHTS-HHHHTCBEHHHHHHHB-
T ss_pred HHHHHhCCCHHHhccCCHHHHHhhcC
Confidence 57788999998884445555555543
No 30
>PF04884 DUF647: Vitamin B6 photo-protection and homoeostasis; InterPro: IPR006968 This is a family of proteins of unknown function, restricted to eukaryotes.
Probab=20.25 E-value=1.2e+02 Score=24.31 Aligned_cols=41 Identities=20% Similarity=0.160 Sum_probs=36.1
Q ss_pred HHHHHHHhhHHHHHHHhcCCCCCCCCCChhHHHHHHHHHHH
Q psy14169 17 IVHRRVLHRFHRFCLWLGVPLHRVPLTKPQDLARIISEFAL 57 (97)
Q Consensus 17 ~VhrRv~NRF~~fLL~lG~s~~~~~~~k~~~fck~iSEFAL 57 (97)
.-++.+.+++..++|==|||.|.-+|--+-.....+..|+-
T Consensus 8 ~~~~~~~~~l~~~fLP~GyP~SVs~dY~~y~~w~~~q~~~s 48 (250)
T PF04884_consen 8 RRSRSLQQRLRDVFLPAGYPDSVSPDYLRYQIWDFLQAFAS 48 (250)
T ss_pred hhhhHHHHHHHHHhCCCCCCCCcCchhHhHHHHHHHHHHHH
Confidence 45788999999999999999999999988888888888864
Done!