Query psy967
Match_columns 82
No_of_seqs 123 out of 519
Neff 4.4
Searched_HMMs 46136
Date Sat Aug 17 01:38:06 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy967.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/967hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3840|consensus 99.2 1.7E-12 3.6E-17 103.2 1.3 32 44-75 143-174 (438)
2 KOG0441|consensus 99.1 1.4E-10 3E-15 83.2 6.0 47 4-50 2-51 (154)
3 PLN02386 superoxide dismutase 99.0 5.3E-10 1.2E-14 78.9 6.3 47 4-51 2-50 (152)
4 PLN02642 copper, zinc superoxi 99.0 8.4E-10 1.8E-14 79.3 6.1 47 4-51 8-56 (164)
5 PLN02957 copper, zinc superoxi 98.8 1.3E-08 2.7E-13 75.3 6.0 47 4-51 81-128 (238)
6 cd00305 Cu-Zn_Superoxide_Dismu 98.7 4.3E-08 9.3E-13 67.7 6.2 45 5-51 2-49 (144)
7 PF00080 Sod_Cu: Copper/zinc s 98.7 4.7E-08 1E-12 66.3 5.1 47 6-52 1-50 (142)
8 PRK15388 Cu/Zn superoxide dism 98.5 4.3E-07 9.3E-12 66.1 6.1 36 14-51 38-74 (177)
9 PRK10290 superoxide dismutase; 98.4 1.1E-06 2.5E-11 63.5 6.0 36 14-51 36-72 (173)
10 KOG4656|consensus 97.5 6.4E-05 1.4E-09 57.3 2.7 41 8-49 86-128 (247)
11 COG2032 SodC Cu/Zn superoxide 97.0 0.001 2.2E-08 48.9 4.4 44 5-50 30-76 (179)
12 PF02214 BTB_2: BTB/POZ domain 88.2 0.16 3.5E-06 31.7 0.2 24 49-72 49-73 (94)
13 KOG3713|consensus 83.8 0.59 1.3E-05 38.9 1.5 25 49-73 88-112 (477)
14 PLN02804 chalcone isomerase 79.8 4 8.6E-05 30.6 4.4 45 18-63 142-186 (206)
15 PF07452 CHRD: CHRD domain; I 77.3 9.8 0.00021 24.5 5.3 38 14-51 19-57 (119)
16 smart00754 CHRD A domain in th 69.9 18 0.00039 23.5 5.2 36 14-50 19-55 (118)
17 KOG4390|consensus 59.4 4.7 0.0001 34.1 1.1 21 50-70 88-108 (632)
18 PF07830 PP2C_C: Protein serin 52.3 6.2 0.00013 25.6 0.5 11 36-46 59-69 (81)
19 PF11789 zf-Nse: Zinc-finger o 49.1 11 0.00024 22.5 1.3 16 54-69 37-53 (57)
20 KOG3805|consensus 46.4 9.8 0.00021 30.9 0.9 18 52-69 329-346 (361)
21 smart00225 BTB Broad-Complex, 46.1 9.6 0.00021 21.4 0.7 22 49-70 47-68 (90)
22 PLN02559 chalcone--flavonone i 45.2 47 0.001 25.5 4.4 44 18-62 148-192 (230)
23 PTZ00415 transmission-blocking 43.6 14 0.00031 36.3 1.7 37 29-65 1930-1968(2849)
24 PF03201 HMD: H2-forming N5,N1 42.2 7.2 0.00016 26.4 -0.3 23 48-70 14-38 (98)
25 KOG3148|consensus 39.8 26 0.00056 27.1 2.3 28 35-66 35-62 (273)
26 PF14289 DUF4369: Domain of un 37.6 29 0.00063 21.1 1.9 16 28-43 11-26 (106)
27 PF08896 DUF1842: Domain of un 35.6 62 0.0013 22.1 3.4 12 14-25 32-43 (114)
28 smart00695 DUSP Domain in ubiq 33.1 33 0.00073 20.9 1.7 26 38-63 50-75 (86)
29 cd00525 AE_Prim_S_like AE_Prim 31.5 42 0.0009 21.7 2.0 27 43-74 98-127 (136)
30 KOG1332|consensus 30.1 29 0.00064 27.5 1.3 27 47-73 9-35 (299)
31 PF00791 ZU5: ZU5 domain; Int 28.8 41 0.00088 21.8 1.6 21 60-80 11-34 (103)
32 COG1993 PII-like signaling pro 26.6 15 0.00032 25.3 -0.8 18 49-66 39-56 (109)
33 PF00339 Arrestin_N: Arrestin 25.6 1.3E+02 0.0028 19.0 3.6 31 8-38 11-41 (149)
34 cd04487 RecJ_OBF2_like RecJ_OB 25.2 88 0.0019 19.1 2.6 16 30-45 1-16 (73)
35 KOG1545|consensus 24.4 16 0.00034 30.7 -1.2 24 49-72 109-133 (507)
36 PF04775 Bile_Hydr_Trans: Acyl 23.3 52 0.0011 22.1 1.4 12 32-43 5-16 (126)
37 PF02399 Herpes_ori_bp: Origin 23.1 38 0.00083 30.3 0.9 19 47-65 582-600 (824)
38 COG5485 Predicted ester cyclas 23.0 1.3E+02 0.0029 21.3 3.4 25 12-43 72-96 (131)
39 PF01599 Ribosomal_S27: Riboso 22.9 22 0.00047 21.0 -0.5 7 55-61 1-7 (47)
40 PF06337 DUSP: DUSP domain; I 21.8 64 0.0014 19.8 1.5 26 38-63 65-90 (99)
41 PF08462 Carmo_coat_C: Carmovi 21.2 2.7E+02 0.0059 18.8 4.5 29 9-40 49-77 (99)
42 PF13742 tRNA_anti_2: OB-fold 20.6 1.1E+02 0.0023 19.6 2.4 32 28-59 22-63 (99)
43 PF12816 Vps8: Golgi CORVET co 20.4 32 0.00068 24.9 -0.2 24 31-63 12-35 (196)
No 1
>KOG3840|consensus
Probab=99.24 E-value=1.7e-12 Score=103.17 Aligned_cols=32 Identities=44% Similarity=0.734 Sum_probs=29.3
Q ss_pred CCceeeehhhHHhhhhhhcceeeCCCCceecc
Q psy967 44 GLNLMNFTVFRAILDYYKGQVIKCPPSVSERA 75 (82)
Q Consensus 44 gfHih~~~~~~~~~~~~~~~~~~~~~~~~~~~ 75 (82)
-...++.+||||||||||+|+|+||++||||+
T Consensus 143 VAdGi~s~vFRAILdYYksG~iRCP~~vSvpE 174 (438)
T KOG3840|consen 143 VADGMTSSCFRAILDYYQSGTMRCPSSVSVSE 174 (438)
T ss_pred hhcchhHHHHHHHHHHHhcCceeCCCCCchHH
Confidence 45568899999999999999999999999987
No 2
>KOG0441|consensus
Probab=99.12 E-value=1.4e-10 Score=83.17 Aligned_cols=47 Identities=36% Similarity=0.633 Sum_probs=43.3
Q ss_pred eeEEEEecCC--CeEEEEEEEEcCCCCCeEEEEEEecCCCCc-CCceeee
Q psy967 4 IKAVCVLNNE--PVKGTIFFTQEHADSPVKVTGEIQGLEEDG-GLNLMNF 50 (82)
Q Consensus 4 ~kAVcVL~G~--~VsGtV~FtQ~~~~~~V~ItG~I~GL~Pg~-gfHih~~ 50 (82)
++|+++|.|+ +|.|+|+|+|..++.+++|+++|+||+||. |||+|.+
T Consensus 2 ~~~~avl~g~~~~V~G~i~F~Q~~~~~~~~v~~~i~GL~pg~hgfHvHqf 51 (154)
T KOG0441|consen 2 AQAVAVLEGDEIQVIGVITFEQFLPGEPLRVSGEVTGLPPGKHGFHVHQF 51 (154)
T ss_pred cceEEEEecCCCCceeEEEEEEcCCCCcEEEEEEEecCCCceeeEEEEec
Confidence 5899999996 799999999987777999999999999995 9999986
No 3
>PLN02386 superoxide dismutase [Cu-Zn]
Probab=99.04 E-value=5.3e-10 Score=78.88 Aligned_cols=47 Identities=51% Similarity=0.786 Sum_probs=41.8
Q ss_pred eeEEEEecCC-CeEEEEEEEEcCCCCCeEEEEEEecCCCCc-CCceeeeh
Q psy967 4 IKAVCVLNNE-PVKGTIFFTQEHADSPVKVTGEIQGLEEDG-GLNLMNFT 51 (82)
Q Consensus 4 ~kAVcVL~G~-~VsGtV~FtQ~~~~~~V~ItG~I~GL~Pg~-gfHih~~~ 51 (82)
++|+|+|+++ .|.|+|+|+|.. .+++.|+++|+||+||. |||||..-
T Consensus 2 ~~a~a~~~~~~~v~G~v~f~q~~-~g~v~i~~~~~GL~pG~hg~HIHe~G 50 (152)
T PLN02386 2 VKAVAVLNSSEGVKGTIFFTQEG-DGPTTVTGSLSGLKPGLHGFHVHALG 50 (152)
T ss_pred ceEEEEEcCCCCCEEEEEEEEcC-CCCEEEEEEEeCCCCCceeEEEeCCC
Confidence 6899999987 799999999985 45799999999999995 99999654
No 4
>PLN02642 copper, zinc superoxide dismutase
Probab=99.00 E-value=8.4e-10 Score=79.29 Aligned_cols=47 Identities=30% Similarity=0.574 Sum_probs=41.7
Q ss_pred eeEEEEecCC-CeEEEEEEEEcCCCCCeEEEEEEecCCCCc-CCceeeeh
Q psy967 4 IKAVCVLNNE-PVKGTIFFTQEHADSPVKVTGEIQGLEEDG-GLNLMNFT 51 (82)
Q Consensus 4 ~kAVcVL~G~-~VsGtV~FtQ~~~~~~V~ItG~I~GL~Pg~-gfHih~~~ 51 (82)
.+|+|+|+++ .|.|+|+|+|..+ +.|.|+++|+||+||. |||||..-
T Consensus 8 ~~A~a~~~g~~~v~G~v~f~q~~~-g~v~I~~~v~GL~pG~HG~HIHe~G 56 (164)
T PLN02642 8 LRAVALIAGDNNVRGCLQFVQDIF-GTTHVTGKISGLSPGFHGFHIHSFG 56 (164)
T ss_pred eeEEEEEcCCCCcEEEEEEEECCC-CcEEEEEEEcCCCCCceeEEEcCCC
Confidence 5899999987 7999999999864 4699999999999995 99999865
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.79 E-value=1.3e-08 Score=75.33 Aligned_cols=47 Identities=17% Similarity=0.321 Sum_probs=41.4
Q ss_pred eeEEEEecCCCeEEEEEEEEcCCCCCeEEEEEEecCCCCc-CCceeeeh
Q psy967 4 IKAVCVLNNEPVKGTIFFTQEHADSPVKVTGEIQGLEEDG-GLNLMNFT 51 (82)
Q Consensus 4 ~kAVcVL~G~~VsGtV~FtQ~~~~~~V~ItG~I~GL~Pg~-gfHih~~~ 51 (82)
.+|+|.++|+.|+|+|+|+|..+ +.+.|+++|+||+||. |||||..-
T Consensus 81 ~~av~~~~g~~v~G~v~~~~~~~-~~v~i~~~~~GL~pg~hg~hiHe~G 128 (238)
T PLN02957 81 SAAVAEFKGPDIFGVVRFAQVSM-ELARIEAAFSGLSPGTHGWSINEYG 128 (238)
T ss_pred ceEEEEecCCceEEEEEEEEcCC-CCEEEEEEEcCCCCCcEEEEEcCCC
Confidence 46899999989999999999864 4699999999999994 99999764
No 6
>cd00305 Cu-Zn_Superoxide_Dismutase Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene causes familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Cytoplasmic and periplasmic SODs exist as dimers, whereas chloroplastic and extracellular enzymes exist as tetramers. Structure supports independent functional evolution in prokaryotes (P-class) and eukaryotes (E-class) [PMID:.8176730].
Probab=98.71 E-value=4.3e-08 Score=67.72 Aligned_cols=45 Identities=40% Similarity=0.625 Sum_probs=40.4
Q ss_pred eEEEEecCC--CeEEEEEEEEcCCCCCeEEEEEEecCCCCc-CCceeeeh
Q psy967 5 KAVCVLNNE--PVKGTIFFTQEHADSPVKVTGEIQGLEEDG-GLNLMNFT 51 (82)
Q Consensus 5 kAVcVL~G~--~VsGtV~FtQ~~~~~~V~ItG~I~GL~Pg~-gfHih~~~ 51 (82)
+|+|.|++. ++.|+|+|+|... .+.|+++++||+||. |||||..-
T Consensus 2 ~a~~~l~~~~g~v~G~v~f~q~~~--~v~v~~~l~GL~pG~hg~HIHe~G 49 (144)
T cd00305 2 SAVAVLKGPDGKVVGTVTFTQQSG--GVTITGELSGLTPGLHGFHIHEFG 49 (144)
T ss_pred cEEEEEECCCCceEEEEEEEECCC--CEEEEEEEECCCCCceeEEEEecC
Confidence 689999976 6999999999875 699999999999995 99999874
No 7
>PF00080 Sod_Cu: Copper/zinc superoxide dismutase (SODC); InterPro: IPR001424 Superoxide dismutases are ubiquitous metalloproteins that prevent damage by oxygen-mediated free radicals by catalysing the dismutation of superoxide into molecular oxygen and hydrogen peroxide []. Superoxide is a normal by-product of aerobic respiration and is produced by a number of reactions, including oxidative phosphorylation and photosynthesis. The dismutase enzymes have a very high catalytic efficiency due to the attraction of superoxide to the ions bound at the active site [, ]. There are three forms of superoxide dismutase, depending on the metal cofactor: Cu/Zn (which binds both copper and zinc), Fe and Mn types. The Fe and Mn forms are similar in their primary, secondary and tertiary structures, but are distinct from the Cu/Zn form []. Prokaryotes and protists contain Mn, Fe or both types, while most eukaryotic organisms utilise the Cu/Zn type.; GO: 0046872 metal ion binding, 0006801 superoxide metabolic process, 0055114 oxidation-reduction process; PDB: 2K4W_A 2APS_B 2WWN_B 2WWO_B 1ESO_A 2AQM_A 3F7L_A 3F7K_A 2E47_A 2E46_A ....
Probab=98.66 E-value=4.7e-08 Score=66.29 Aligned_cols=47 Identities=36% Similarity=0.446 Sum_probs=41.7
Q ss_pred EEEEecCC--CeEEEEEEEEcCCCCCeEEEEEEecCCCCc-CCceeeehh
Q psy967 6 AVCVLNNE--PVKGTIFFTQEHADSPVKVTGEIQGLEEDG-GLNLMNFTV 52 (82)
Q Consensus 6 AVcVL~G~--~VsGtV~FtQ~~~~~~V~ItG~I~GL~Pg~-gfHih~~~~ 52 (82)
|+|+|++. .|+|+|+|+|..++..+.|+.++.||+||. ++|||..-+
T Consensus 1 a~a~l~~~~~~v~G~v~f~q~~~~~~~~v~~~~~GL~~g~~~~hIH~~g~ 50 (142)
T PF00080_consen 1 AVAVLKGAGGKVKGTVTFTQVSDGDGVQVTVSLNGLPPGQHGYHIHENGD 50 (142)
T ss_dssp EEEEEBETSSSEEEEEEEEEETTTTEEEEEEEEESSSSEEEEEEEESSST
T ss_pred CEEEEeCCCCCeEEEEEEEEeCCCCCEEEEEEEECCCCCCceEEEEeccc
Confidence 79999953 899999999999776799999999999985 999998654
No 8
>PRK15388 Cu/Zn superoxide dismutase; Provisional
Probab=98.47 E-value=4.3e-07 Score=66.11 Aligned_cols=36 Identities=17% Similarity=0.227 Sum_probs=31.9
Q ss_pred CeEEEEEEEEcCCCCCeEEEEEEecCCCC-cCCceeeeh
Q psy967 14 PVKGTIFFTQEHADSPVKVTGEIQGLEED-GGLNLMNFT 51 (82)
Q Consensus 14 ~VsGtV~FtQ~~~~~~V~ItG~I~GL~Pg-~gfHih~~~ 51 (82)
++.|+|+|+|.. ++ ++|+++++||+|| +|||||..-
T Consensus 38 ~~~G~v~f~~~~-~g-v~I~~~l~GL~pG~HGfHIHe~G 74 (177)
T PRK15388 38 ENIGEITVSETP-YG-LLFTPHLNGLTPGIHGFHVHTNP 74 (177)
T ss_pred ceEEEEEEEEcC-Cc-EEEEEEEcCCCCcceEEEEccCC
Confidence 899999999986 33 9999999999999 499999864
No 9
>PRK10290 superoxide dismutase; Provisional
Probab=98.35 E-value=1.1e-06 Score=63.55 Aligned_cols=36 Identities=11% Similarity=0.261 Sum_probs=32.0
Q ss_pred CeEEEEEEEEcCCCCCeEEEEEEecCCCC-cCCceeeeh
Q psy967 14 PVKGTIFFTQEHADSPVKVTGEIQGLEED-GGLNLMNFT 51 (82)
Q Consensus 14 ~VsGtV~FtQ~~~~~~V~ItG~I~GL~Pg-~gfHih~~~ 51 (82)
++.|+++|+|... .|+|+++++||+|| +|||||..-
T Consensus 36 ~~~G~v~f~~~~~--gv~i~~~l~GL~pG~HGfHIHe~G 72 (173)
T PRK10290 36 QSIGSVTITETDK--GLEFSPDLKALPPGEHGFHIHAKG 72 (173)
T ss_pred ceEEEEEEEEcCC--cEEEEEEEcCCCCCceEEEEeCCC
Confidence 8999999999863 39999999999999 499999864
No 10
>KOG4656|consensus
Probab=97.52 E-value=6.4e-05 Score=57.27 Aligned_cols=41 Identities=22% Similarity=0.450 Sum_probs=35.0
Q ss_pred EEecCC-CeEEEEEEEEcCCCCCeEEEEEEecCCCC-cCCceee
Q psy967 8 CVLNNE-PVKGTIFFTQEHADSPVKVTGEIQGLEED-GGLNLMN 49 (82)
Q Consensus 8 cVL~G~-~VsGtV~FtQ~~~~~~V~ItG~I~GL~Pg-~gfHih~ 49 (82)
+.+.|+ .|.|.|+|.|-.++ .+.|.|.+.||+|| +|.|||.
T Consensus 86 a~~~~~~~v~GvvRf~qvt~e-k~lid~tvdGlspG~h~~~Ihe 128 (247)
T KOG4656|consen 86 AKYTGPQAVQGVVRFVQVTEE-KTLIDGTVDGLSPGLHGLHIHE 128 (247)
T ss_pred HHhcCCccceeEEEEEEeccc-cEEEEEEecCCCCcccceeEee
Confidence 444566 89999999999976 69999999999999 4899985
No 11
>COG2032 SodC Cu/Zn superoxide dismutase [Inorganic ion transport and metabolism]
Probab=97.03 E-value=0.001 Score=48.90 Aligned_cols=44 Identities=25% Similarity=0.289 Sum_probs=35.5
Q ss_pred eEEEEecC-C-CeEEEEEEEEcCCCCCeEEEEEEecCCCCc-CCceeee
Q psy967 5 KAVCVLNN-E-PVKGTIFFTQEHADSPVKVTGEIQGLEEDG-GLNLMNF 50 (82)
Q Consensus 5 kAVcVL~G-~-~VsGtV~FtQ~~~~~~V~ItG~I~GL~Pg~-gfHih~~ 50 (82)
++.+++.. + ++-|+|+++|...+ +.++-.+.||+||. |||||..
T Consensus 30 ~~~~~~~~~~G~~vG~vt~~e~~~g--~~~~~~~~~L~pg~hGfHIHe~ 76 (179)
T COG2032 30 KANAVLVDGTGKDVGTVTITETGYG--LLFTPALGGLPPGEHGFHIHEK 76 (179)
T ss_pred cceeeccCCCCceeEEEEEeecCCc--eEEeecccCCCCcceeEEeccc
Confidence 55556653 2 77899999998743 99999999999995 9999964
No 12
>PF02214 BTB_2: BTB/POZ domain; InterPro: IPR003131 Potassium channels are the most diverse group of the ion channel family [, ]. They are important in shaping the action potential, and in neuronal excitability and plasticity []. The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups []: the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group. These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K+ channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers []. In eukaryotic cells, K+ channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes []. In prokaryotic cells, they play a role in the maintenance of ionic homeostasis []. All K+ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K+ selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K+ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K+ channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K+ channels; and three types of calcium (Ca)-activated K+ channels (BK, IK and SK) []. The 2TM domain family comprises inward-rectifying K+ channels. In addition, there are K+ channel alpha-subunits that possess two P-domains. These are usually highly regulated K+ selective leak channels. The Kv family can be divided into several subfamilies on the basis of sequence similarity and function. Four of these subfamilies, Kv1 (Shaker), Kv2 (Shab), Kv3 (Shaw) and Kv4 (Shal), consist of pore-forming alpha subunits that associate with different types of beta subunit. Each alpha subunit comprises six hydrophobic TM domains with a P-domain between the fifth and sixth, which partially resides in the membrane. The fourth TM domain has positively charged residues at every third residue and acts as a voltage sensor, which triggers the conformational change that opens the channel pore in response to a displacement in membrane potential []. More recently, 4 new electrically-silent alpha subunits have been cloned: Kv5 (KCNF), Kv6 (KCNG), Kv8 and Kv9 (KCNS). These subunits do not themselves possess any functional activity, but appear to form heteromeric channels with Kv2 subunits, and thus modulate Shab channel activity []. When highly expressed, they inhibit channel activity, but at lower levels show more specific modulatory actions. The N-terminal, cytoplasmic tetramerization domain (T1) of voltage-gated potassium channels encodes molecular determinants for subfamily-specific assembly of alpha-subunits into functional tetrameric channels []. This domain is found in a subset of a larger group of proteins that contain the BTB/POZ domain.; GO: 0005249 voltage-gated potassium channel activity, 0006813 potassium ion transport, 0008076 voltage-gated potassium channel complex, 0016020 membrane; PDB: 1NN7_A 3KVT_A 1EXB_E 1QDV_A 1DSX_E 1QDW_F 3LUT_B 3LNM_B 2A79_B 3DRY_C ....
Probab=88.16 E-value=0.16 Score=31.65 Aligned_cols=24 Identities=21% Similarity=0.468 Sum_probs=16.2
Q ss_pred eehhhHHhhhhhhc-ceeeCCCCce
Q psy967 49 NFTVFRAILDYYKG-QVIKCPPSVS 72 (82)
Q Consensus 49 ~~~~~~~~~~~~~~-~~~~~~~~~~ 72 (82)
+...|+.||+||++ +.+..|+.+.
T Consensus 49 dp~~F~~IL~ylr~~~~l~~~~~~~ 73 (94)
T PF02214_consen 49 DPELFEYILNYLRTGGKLPIPDEIC 73 (94)
T ss_dssp -HHHHHHHHHHHHHTSSB---TTS-
T ss_pred ChhhhhHHHHHHhhcCccCCCCchh
Confidence 45799999999999 7777776554
No 13
>KOG3713|consensus
Probab=83.84 E-value=0.59 Score=38.94 Aligned_cols=25 Identities=20% Similarity=0.487 Sum_probs=21.7
Q ss_pred eehhhHHhhhhhhcceeeCCCCcee
Q psy967 49 NFTVFRAILDYYKGQVIKCPPSVSE 73 (82)
Q Consensus 49 ~~~~~~~~~~~~~~~~~~~~~~~~~ 73 (82)
+..+|+.||+||.+|.+.||..+-.
T Consensus 88 ~P~~F~~Vl~fYrtGkLH~p~~vC~ 112 (477)
T KOG3713|consen 88 HPGAFAYVLNFYRTGKLHVPADVCP 112 (477)
T ss_pred ChHHHHHHHHHHhcCeeccccccch
Confidence 4578999999999999999987643
No 14
>PLN02804 chalcone isomerase
Probab=79.76 E-value=4 Score=30.56 Aligned_cols=45 Identities=22% Similarity=0.353 Sum_probs=35.5
Q ss_pred EEEEEEcCCCCCeEEEEEEecCCCCcCCceeeehhhHHhhhhhhcc
Q psy967 18 TIFFTQEHADSPVKVTGEIQGLEEDGGLNLMNFTVFRAILDYYKGQ 63 (82)
Q Consensus 18 tV~FtQ~~~~~~V~ItG~I~GL~Pg~gfHih~~~~~~~~~~~~~~~ 63 (82)
.|.|+|....+.+.|.....| +.-...-|.|..+-+|+||.|=+|
T Consensus 142 ~I~ft~~~~~g~l~Isfs~dg-~e~~~~~Ienk~l~~avl~~yi~G 186 (206)
T PLN02804 142 IITYHFPATSGIVEISFSTEG-KEESKLTVENANVVEMIQKWYLGG 186 (206)
T ss_pred EEEEEecCCCCeEEEEEecCC-cccceeEEecHHHHHHHHHHHhcC
Confidence 579999753456889999888 433455699999999999999866
No 15
>PF07452 CHRD: CHRD domain; InterPro: IPR010895 CHRD (after SWISS-PROT abbreviation for chordin) is a novel domain identified in chordin, an inhibitor of bone morphogenetic proteins. This family includes bacterial homologues. It is anticipated to have an immunoglobulin-like beta-barrel structure based on limited similarity to superoxide dismutases but, as yet, no clear functional prediction can be made [].
Probab=77.27 E-value=9.8 Score=24.46 Aligned_cols=38 Identities=16% Similarity=0.289 Sum_probs=28.9
Q ss_pred CeEEEEEEEEcCCCCCeEEEEEEecCCCC-cCCceeeeh
Q psy967 14 PVKGTIFFTQEHADSPVKVTGEIQGLEED-GGLNLMNFT 51 (82)
Q Consensus 14 ~VsGtV~FtQ~~~~~~V~ItG~I~GL~Pg-~gfHih~~~ 51 (82)
..+|...|+=+.+...+..+..+.||+.. ...|||.+.
T Consensus 19 ~a~G~a~~~l~~~~~~l~y~i~~~gl~~~~~~~hih~~~ 57 (119)
T PF07452_consen 19 SASGTAWFTLDDDGNTLHYSITLSGLSSPPTAAHIHQGA 57 (119)
T ss_pred CCEEEEEEEEECCCCEEEEEEEEeCCCCCcEEEEEEcCC
Confidence 46799988888765578889999999333 479998643
No 16
>smart00754 CHRD A domain in the BMP inhibitor chordin and in microbial proteins.
Probab=69.93 E-value=18 Score=23.46 Aligned_cols=36 Identities=17% Similarity=0.267 Sum_probs=28.6
Q ss_pred CeEEEEEEEEcCCCCCeEEEEEEecCCCCc-CCceeee
Q psy967 14 PVKGTIFFTQEHADSPVKVTGEIQGLEEDG-GLNLMNF 50 (82)
Q Consensus 14 ~VsGtV~FtQ~~~~~~V~ItG~I~GL~Pg~-gfHih~~ 50 (82)
+..|...|+-+. +..+..+..+.||+.-. ..|||.+
T Consensus 19 ~a~G~a~~~l~~-~~~l~y~i~~~gl~~~~~~~hih~~ 55 (118)
T smart00754 19 GAVGGAWFTLDD-DGSLHYQVTLSGLSGPETAAHIHEG 55 (118)
T ss_pred CcEEEEEEEECC-CCEEEEEEEEcccCCCceeeeEecc
Confidence 668999998885 45788889999998754 7899863
No 17
>KOG4390|consensus
Probab=59.45 E-value=4.7 Score=34.10 Aligned_cols=21 Identities=24% Similarity=0.646 Sum_probs=18.5
Q ss_pred ehhhHHhhhhhhcceeeCCCC
Q psy967 50 FTVFRAILDYYKGQVIKCPPS 70 (82)
Q Consensus 50 ~~~~~~~~~~~~~~~~~~~~~ 70 (82)
-.+||-||.||.+|-+.||--
T Consensus 88 PdiFRhvLnFYRTGkLHyPR~ 108 (632)
T KOG4390|consen 88 PDIFRHVLNFYRTGKLHYPRH 108 (632)
T ss_pred hHHHHHHHHHhhcCcccCchH
Confidence 358999999999999999953
No 18
>PF07830 PP2C_C: Protein serine/threonine phosphatase 2C, C-terminal domain; InterPro: IPR012911 Protein phosphatase 2C (PP2C) is involved in regulating cellular responses to stress in various eukaryotes. It consists of two domains: an N-terminal catalytic domain and a C-terminal domain characteristic of mammalian PP2Cs. This domain consists of three antiparallel alpha helices, one of which packs against two corresponding alpha-helices of the N-terminal domain. The C-terminal domain does not seem to play a role in catalysis, but it may provide protein substrate specificity due to the cleft that is created between it and the catalytic domain []. ; GO: 0000287 magnesium ion binding, 0004721 phosphoprotein phosphatase activity, 0030145 manganese ion binding; PDB: 2P8E_A 3FXL_A 3FXO_A 1A6Q_A 3FXK_A 3FXM_A 3FXJ_A.
Probab=52.26 E-value=6.2 Score=25.61 Aligned_cols=11 Identities=55% Similarity=0.921 Sum_probs=6.7
Q ss_pred EecCCCCcCCc
Q psy967 36 IQGLEEDGGLN 46 (82)
Q Consensus 36 I~GL~Pg~gfH 46 (82)
|-|||||+|+|
T Consensus 59 ip~LPPGGGl~ 69 (81)
T PF07830_consen 59 IPGLPPGGGLA 69 (81)
T ss_dssp -SS--TTTTCG
T ss_pred CCCCcCCcCHH
Confidence 77999998775
No 19
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=49.10 E-value=11 Score=22.47 Aligned_cols=16 Identities=38% Similarity=0.787 Sum_probs=11.6
Q ss_pred HHhhhhh-hcceeeCCC
Q psy967 54 RAILDYY-KGQVIKCPP 69 (82)
Q Consensus 54 ~~~~~~~-~~~~~~~~~ 69 (82)
.+|++|+ +.+..+||-
T Consensus 37 ~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 37 EAILQYIQRNGSKRCPV 53 (57)
T ss_dssp HHHHHHCTTTS-EE-SC
T ss_pred HHHHHHHHhcCCCCCCC
Confidence 5889999 778999995
No 20
>KOG3805|consensus
Probab=46.40 E-value=9.8 Score=30.85 Aligned_cols=18 Identities=39% Similarity=0.696 Sum_probs=15.0
Q ss_pred hhHHhhhhhhcceeeCCC
Q psy967 52 VFRAILDYYKGQVIKCPP 69 (82)
Q Consensus 52 ~~~~~~~~~~~~~~~~~~ 69 (82)
.=|+|-.|||.|+|+=|.
T Consensus 329 lsRslRqYyKkGiikK~e 346 (361)
T KOG3805|consen 329 LSRSLRQYYKKGIIKKPE 346 (361)
T ss_pred HHHHHHHHhhcCccccch
Confidence 348999999999998654
No 21
>smart00225 BTB Broad-Complex, Tramtrack and Bric a brac. Domain in Broad-Complex, Tramtrack and Bric a brac. Also known as POZ (poxvirus and zinc finger) domain. Known to be a protein-protein interaction motif found at the N-termini of several C2H2-type transcription factors as well as Shaw-type potassium channels. Known structure reveals a tightly intertwined dimer formed via interactions between N-terminal strand and helix structures. However in a subset of BTB/POZ domains, these two secondary structures appear to be missing. Be aware SMART predicts BTB/POZ domains without the beta1- and alpha1-secondary structures.
Probab=46.05 E-value=9.6 Score=21.42 Aligned_cols=22 Identities=23% Similarity=0.395 Sum_probs=18.9
Q ss_pred eehhhHHhhhhhhcceeeCCCC
Q psy967 49 NFTVFRAILDYYKGQVIKCPPS 70 (82)
Q Consensus 49 ~~~~~~~~~~~~~~~~~~~~~~ 70 (82)
+...|+.+|+|..++.+..|++
T Consensus 47 ~~~~f~~~l~~ly~~~~~~~~~ 68 (90)
T smart00225 47 SPEDFRALLEFLYTGKLDLPEE 68 (90)
T ss_pred CHHHHHHHHHeecCceeecCHH
Confidence 5678999999999998887765
No 22
>PLN02559 chalcone--flavonone isomerase
Probab=45.18 E-value=47 Score=25.46 Aligned_cols=44 Identities=23% Similarity=0.299 Sum_probs=33.2
Q ss_pred EEEEEEcCCCCCeEEEEEEec-CCCCcCCceeeehhhHHhhhhhhc
Q psy967 18 TIFFTQEHADSPVKVTGEIQG-LEEDGGLNLMNFTVFRAILDYYKG 62 (82)
Q Consensus 18 tV~FtQ~~~~~~V~ItG~I~G-L~Pg~gfHih~~~~~~~~~~~~~~ 62 (82)
.|.|+|.. .+...|+-.=.| +|.....-|-|..+-+|+||.|=|
T Consensus 148 ~I~ft~sp-~g~L~isfs~dg~ipe~~~~~Ienk~l~eAv~e~~IG 192 (230)
T PLN02559 148 SILFTHSP-TGSLTVAFSKDSSVPEVGNAVIENKLLCEAVLESIIG 192 (230)
T ss_pred EEEEEECC-CCcEEEEEecCCCCCccceEEEechHHHHHHHHHHcc
Confidence 57999985 456766655444 455567789999999999999974
No 23
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=43.63 E-value=14 Score=36.30 Aligned_cols=37 Identities=35% Similarity=0.711 Sum_probs=30.5
Q ss_pred CeEE-EEEEecCCCCcCCceeeehhhHHh-hhhhhccee
Q psy967 29 PVKV-TGEIQGLEEDGGLNLMNFTVFRAI-LDYYKGQVI 65 (82)
Q Consensus 29 ~V~I-tG~I~GL~Pg~gfHih~~~~~~~~-~~~~~~~~~ 65 (82)
.|+| .|.|-|++=--||-+.+-.||..+ |||||+.+-
T Consensus 1930 ~v~i~kgd~fg~~cpkgf~~~p~~cfs~v~l~yyk~~~~ 1968 (2849)
T PTZ00415 1930 SVKIAKGDIFGIKCPKGFAIFPEACFSNVLLDYYKGDLE 1968 (2849)
T ss_pred EEEeecCceeeeecCCccEECchHhhhhhhHHHhccchh
Confidence 3566 789999887679999999999875 799998653
No 24
>PF03201 HMD: H2-forming N5,N10-methylene-tetrahydromethanopterin dehydrogenase; InterPro: IPR004889 This entry represents the C-terminal domain of H2-forming N5,N10-methylene-tetrahydromethanopterin dehydrogenases. The N(5),N(10)-methylenetetrahydromethanopterin dehydrogenase system of methanogenic archaea is composed of H2-forming methylenetetrahydromethanopterin dehydrogenase (Hmd, represented by this entry) and F420-dependent methylenetetrahydromethanopterin dehydrogenase (IPR002844 from INTERPRO) [, ]. Hmd is an iron-sulphur-cluster-free enzyme that contains an intrinsic CO ligand bound to iron []. This domain is found at the C terminus of two distinct subgroups: one has been experimentally characterised as H2-forming N(5),N(10)-methenyltetrahydromethanopterin dehydrogenase (Hmd or HmdI), and the other one contains isozymes that have not been experimentally characterised (HmdII and HmdIII). Because all three isozyme forms are present in each of the corresponding sequenced genomes, it has been suggested that HmdII and HmdIII may not exhibit Hmd activity and may have a different biological function [].; GO: 0018537 coenzyme F420-dependent N5,N10-methenyltetrahydromethanopterin reductase activity, 0047068 N5,N10-methenyltetrahydromethanopterin hydrogenase activity, 0015948 methanogenesis, 0055114 oxidation-reduction process; PDB: 3F46_A 2B0J_A 3DAG_A 3DAF_A 3H65_A 3F47_A.
Probab=42.17 E-value=7.2 Score=26.41 Aligned_cols=23 Identities=26% Similarity=0.660 Sum_probs=15.7
Q ss_pred eeehhhHHhhhhhhc--ceeeCCCC
Q psy967 48 MNFTVFRAILDYYKG--QVIKCPPS 70 (82)
Q Consensus 48 h~~~~~~~~~~~~~~--~~~~~~~~ 70 (82)
.+|.+|-.|||||.. .+++-|..
T Consensus 14 vTAv~~agiL~Y~~v~t~il~AP~~ 38 (98)
T PF03201_consen 14 VTAVTYAGILDYYDVGTKILGAPAD 38 (98)
T ss_dssp HHHHHHHHHHHHHHHHHHTS---HH
T ss_pred HHHHHHHHHHHHHHHHHHHhcChHH
Confidence 367889999999998 46666643
No 25
>KOG3148|consensus
Probab=39.77 E-value=26 Score=27.11 Aligned_cols=28 Identities=18% Similarity=0.555 Sum_probs=21.6
Q ss_pred EEecCCCCcCCceeeehhhHHhhhhhhcceee
Q psy967 35 EIQGLEEDGGLNLMNFTVFRAILDYYKGQVIK 66 (82)
Q Consensus 35 ~I~GL~Pg~gfHih~~~~~~~~~~~~~~~~~~ 66 (82)
-+.|||-|+ -+--+|..+++|||.|.+.
T Consensus 35 f~lglptgs----tplg~ykklie~~k~g~~s 62 (273)
T KOG3148|consen 35 FVLGLPTGS----TPLGMYKKLIEFYKNGVLS 62 (273)
T ss_pred EEEecCCCC----CchhHHHHHHHHHhcCceE
Confidence 446888875 2456999999999999864
No 26
>PF14289 DUF4369: Domain of unknown function (DUF4369)
Probab=37.60 E-value=29 Score=21.11 Aligned_cols=16 Identities=25% Similarity=0.613 Sum_probs=13.1
Q ss_pred CCeEEEEEEecCCCCc
Q psy967 28 SPVKVTGEIQGLEEDG 43 (82)
Q Consensus 28 ~~V~ItG~I~GL~Pg~ 43 (82)
...+|+|+|.|++.|.
T Consensus 11 ~~~~I~G~i~~~~~~~ 26 (106)
T PF14289_consen 11 KQFTIEGKIKGLPDGD 26 (106)
T ss_pred CcEEEEEEEcCCCCCC
Confidence 4689999999997764
No 27
>PF08896 DUF1842: Domain of unknown function (DUF1842); InterPro: IPR014992 This domain is found at the N terminus of proteins that are functionally uncharacterised.
Probab=35.56 E-value=62 Score=22.09 Aligned_cols=12 Identities=33% Similarity=0.340 Sum_probs=7.2
Q ss_pred CeEEEEEEEEcC
Q psy967 14 PVKGTIFFTQEH 25 (82)
Q Consensus 14 ~VsGtV~FtQ~~ 25 (82)
.|+|....+|..
T Consensus 32 ~VsG~a~ItQat 43 (114)
T PF08896_consen 32 SVSGRARITQAT 43 (114)
T ss_pred EEEeEEEEEEec
Confidence 566666666643
No 28
>smart00695 DUSP Domain in ubiquitin-specific proteases.
Probab=33.12 E-value=33 Score=20.88 Aligned_cols=26 Identities=19% Similarity=0.385 Sum_probs=22.4
Q ss_pred cCCCCcCCceeeehhhHHhhhhhhcc
Q psy967 38 GLEEDGGLNLMNFTVFRAILDYYKGQ 63 (82)
Q Consensus 38 GL~Pg~gfHih~~~~~~~~~~~~~~~ 63 (82)
+|..+..|-+.+..+|+.+..+|.+|
T Consensus 50 ~l~~~~dy~~V~~~vW~~l~~~YGgg 75 (86)
T smart00695 50 HLVEGEDYVLIPEELWNKLVSWYGGG 75 (86)
T ss_pred ccccCCCEEEeCHHHHHHHHHHHCCC
Confidence 45555689999999999999999998
No 29
>cd00525 AE_Prim_S_like AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In eukaryotes, this small catalytically active primase subunit (p50) and a larger primase subunit (p60), referred to jointly as the core primase, associate with the B subunit and the DNA polymerase alpha subunit in a complex, called Pol alpha-pri. In addition to its catalytic role in replication, eukaryotic DNA primase may play a role in coupling replication to DNA damage repair and in checkpoint control during S phase. Pfu41 and Pfu46 comprise the primase complex of the archaea Pyrococcus furiosus; these proteins have sequence identity to the eukaryotic p50 and p60 primase proteins respectively. Pfu41 preferentially uses dNTPs as substrate. Pfu46 regulates the pri
Probab=31.48 E-value=42 Score=21.66 Aligned_cols=27 Identities=33% Similarity=0.560 Sum_probs=21.2
Q ss_pred cCCceeeehhhHHhhhhhh---cceeeCCCCceec
Q psy967 43 GGLNLMNFTVFRAILDYYK---GQVIKCPPSVSER 74 (82)
Q Consensus 43 ~gfHih~~~~~~~~~~~~~---~~~~~~~~~~~~~ 74 (82)
.|+|+.-.- +|+-. ++.+.+|+|+--.
T Consensus 98 ~G~H~~~~~-----iDi~~~~~~~~~v~p~S~~~~ 127 (136)
T cd00525 98 RGLHVYVRL-----IDIRVNARGRLLVAPPSVHPR 127 (136)
T ss_pred CEEEEEEEe-----cceeccCCCCeEEcCCCcCCC
Confidence 578876544 99988 4999999998774
No 30
>KOG1332|consensus
Probab=30.09 E-value=29 Score=27.54 Aligned_cols=27 Identities=22% Similarity=0.370 Sum_probs=22.7
Q ss_pred eeeehhhHHhhhhhhcceeeCCCCcee
Q psy967 47 LMNFTVFRAILDYYKGQVIKCPPSVSE 73 (82)
Q Consensus 47 ih~~~~~~~~~~~~~~~~~~~~~~~~~ 73 (82)
.|.-++-.+.||||..-+-.|-+.=+|
T Consensus 9 ~H~D~IHda~lDyygkrlATcsSD~tV 35 (299)
T KOG1332|consen 9 QHEDMIHDAQLDYYGKRLATCSSDGTV 35 (299)
T ss_pred hhhhhhhHhhhhhhcceeeeecCCccE
Confidence 578889999999999999999875444
No 31
>PF00791 ZU5: ZU5 domain; InterPro: IPR000906 This is a domain of unknown function, present in ZO-1 and Unc5-like netrin receptors. It is also found in different variants of ankyrin, which are responsible for attaching integral membrane proteins to cytoskeletal elements.; PDB: 4D8O_A 3G5B_A 3UD2_C 3KBT_D 3UD1_A 3KBU_D 3F59_A 2KXS_A 2KXR_A.
Probab=28.77 E-value=41 Score=21.83 Aligned_cols=21 Identities=29% Similarity=0.450 Sum_probs=15.2
Q ss_pred hhcceeeCCC---CceeccCcccC
Q psy967 60 YKGQVIKCPP---SVSERAGALSD 80 (82)
Q Consensus 60 ~~~~~~~~~~---~~~~~~~~~~~ 80 (82)
..||.+++|. ++.+|+||+..
T Consensus 11 ~~GG~L~l~~~gv~L~IPpGAv~~ 34 (103)
T PF00791_consen 11 HEGGRLRLPESGVSLSIPPGAVPK 34 (103)
T ss_dssp TT-EEEESTTTTEEEEE-TTSSST
T ss_pred CCCcEEEeCCCCEEEEECCCcCCC
Confidence 3688899888 68899999864
No 32
>COG1993 PII-like signaling protein [Signal transduction mechanisms]
Probab=26.57 E-value=15 Score=25.30 Aligned_cols=18 Identities=33% Similarity=0.379 Sum_probs=15.5
Q ss_pred eehhhHHhhhhhhcceee
Q psy967 49 NFTVFRAILDYYKGQVIK 66 (82)
Q Consensus 49 ~~~~~~~~~~~~~~~~~~ 66 (82)
-|||||.|.-|++++.+.
T Consensus 39 GATVlRGI~GfG~~~~~h 56 (109)
T COG1993 39 GATVLRGIAGFGKDGKIH 56 (109)
T ss_pred ceeeeeeeeccCCCCccc
Confidence 489999999999998653
No 33
>PF00339 Arrestin_N: Arrestin (or S-antigen), N-terminal domain; InterPro: IPR011021 G protein-coupled receptors are a large family of signalling molecules that respond to a wide variety of extracellular stimuli. The receptors relay the information encoded by the ligand through the activation of heterotrimeric G proteins and intracellular effector molecules. To ensure the appropriate regulation of the signalling cascade, it is vital to properly inactivate the receptor. This inactivation is achieved, in part, by the binding of a soluble protein, arrestin, which uncouples the receptor from the downstream G protein after the receptors are phosphorylated by G protein-coupled receptor kinases. In addition to the inactivation of G protein-coupled receptors, arrestins have also been implicated in the endocytosis of receptors and cross talk with other signalling pathways. Arrestin (retinal S-antigen) is a major protein of the retinal rod outer segments. It interacts with photo-activated phosphorylated rhodopsin, inhibiting or 'arresting' its ability to interact with transducin []. The protein binds calcium, and shows similarity in its C terminus to alpha-transducin and other purine nucleotide-binding proteins. In mammals, arrestin is associated with autoimmune uveitis. Arrestins comprise a family of closely-related proteins that includes beta-arrestin-1 and -2, which regulate the function of beta-adrenergic receptors by binding to their phosphorylated forms, impairing their capacity to activate G(S) proteins; Cone photoreceptors C-arrestin (arrestin-X) [], which could bind to phosphorylated red/green opsins; and Drosophila phosrestins I and II, which undergo light-induced phosphorylation, and probably play a role in photoreceptor transduction [, , ]. The crystal structure of bovine retinal arrestin comprises two domains of antiparallel beta-sheets connected through a hinge region and one short alpha-helix on the back of the amino-terminal fold []. The binding region for phosphorylated light-activated rhodopsin is located at the N-terminal domain, as indicated by the docking of the photoreceptor to the three-dimensional structure of arrestin. The N-terminal domain consists of an immunoglobulin-like beta-sandwich structure. This entry represents proteins with immunoglobulin-like domains that are similar to those found in arrestin.; PDB: 1SUJ_A 3UGX_A 1CF1_B 1AYR_A 3UGU_A 3P2D_B 1ZSH_A 2WTR_B 3GC3_A 1G4R_A ....
Probab=25.62 E-value=1.3e+02 Score=19.00 Aligned_cols=31 Identities=10% Similarity=0.217 Sum_probs=17.8
Q ss_pred EEecCCCeEEEEEEEEcCCCCCeEEEEEEec
Q psy967 8 CVLNNEPVKGTIFFTQEHADSPVKVTGEIQG 38 (82)
Q Consensus 8 cVL~G~~VsGtV~FtQ~~~~~~V~ItG~I~G 38 (82)
....|+.|+|.|.+.-..+-.--.|.-.+.|
T Consensus 11 ~y~~Ge~I~G~V~l~~~~~~~i~~i~v~l~G 41 (149)
T PF00339_consen 11 VYFPGEVISGKVVLELSKPIKIKSIKVRLKG 41 (149)
T ss_dssp EEESS--EEEEEEECTTT-TTTSEEEEEEEE
T ss_pred EECCCCEEEEEEEEEECCccceeEEEEEEEE
Confidence 4556789999999966554343445555555
No 34
>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.
Probab=25.24 E-value=88 Score=19.12 Aligned_cols=16 Identities=25% Similarity=0.588 Sum_probs=10.2
Q ss_pred eEEEEEEecCCCCcCC
Q psy967 30 VKVTGEIQGLEEDGGL 45 (82)
Q Consensus 30 V~ItG~I~GL~Pg~gf 45 (82)
+.|+|+|.+++..+|+
T Consensus 1 v~v~GeVs~~~~~~GH 16 (73)
T cd04487 1 VHIEGEVVQIKQTSGP 16 (73)
T ss_pred CEEEEEEeccccCCCC
Confidence 3577888887763344
No 35
>KOG1545|consensus
Probab=24.41 E-value=16 Score=30.66 Aligned_cols=24 Identities=38% Similarity=0.588 Sum_probs=18.1
Q ss_pred eehhhHHhhhhhhcc-eeeCCCCce
Q psy967 49 NFTVFRAILDYYKGQ-VIKCPPSVS 72 (82)
Q Consensus 49 ~~~~~~~~~~~~~~~-~~~~~~~~~ 72 (82)
+-.-|.+||-|||+| -+|=|-.|.
T Consensus 109 nRpSFdaILYyYQSGGRlrRPvnVP 133 (507)
T KOG1545|consen 109 NRPSFDAILYYYQSGGRLRRPVNVP 133 (507)
T ss_pred CCCccceEEEEeecCceecCCcccc
Confidence 456799999999964 677776553
No 36
>PF04775 Bile_Hydr_Trans: Acyl-CoA thioester hydrolase/BAAT N-terminal region; InterPro: IPR006862 This entry presents the N-termini of acyl-CoA thioester hydrolase and bile acid-CoA:amino acid N-acetyltransferase (BAAT) []. This region is not thought to contain the active site of either enzyme. Thioesterase isoforms have been identified in peroxisomes, cytoplasm and mitochondria, where they are thought to have distinct functions in lipid metabolism []. For example, in peroxisomes, the hydrolase acts on bile-CoA esters [].; GO: 0016290 palmitoyl-CoA hydrolase activity, 0006629 lipid metabolic process; PDB: 3HLK_B 3K2I_B.
Probab=23.31 E-value=52 Score=22.09 Aligned_cols=12 Identities=25% Similarity=0.315 Sum_probs=5.7
Q ss_pred EEEEEecCCCCc
Q psy967 32 VTGEIQGLEEDG 43 (82)
Q Consensus 32 ItG~I~GL~Pg~ 43 (82)
+.-.|+||+||.
T Consensus 5 ~~I~v~GL~p~~ 16 (126)
T PF04775_consen 5 VDIRVSGLPPGQ 16 (126)
T ss_dssp -EEEEES--TT-
T ss_pred eEEEEeCCCCCC
Confidence 345567999986
No 37
>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein. It functions as a docking protein to recruit essential components of the viral replication machinery to viral DNA origins. In the presence of the major DNA-binding protein, it opens dsDNA which leads to a conformational change in the origin that facilitates DNA unwinding and subsequent replication [].; GO: 0003688 DNA replication origin binding, 0005524 ATP binding, 0006260 DNA replication
Probab=23.13 E-value=38 Score=30.30 Aligned_cols=19 Identities=42% Similarity=0.583 Sum_probs=16.7
Q ss_pred eeeehhhHHhhhhhhccee
Q psy967 47 LMNFTVFRAILDYYKGQVI 65 (82)
Q Consensus 47 ih~~~~~~~~~~~~~~~~~ 65 (82)
+++..+|+.+.|||++|.+
T Consensus 582 ~~s~~vf~~~y~~y~sg~v 600 (824)
T PF02399_consen 582 LESEEVFRRIYDHYASGVV 600 (824)
T ss_pred cccHHHHHHHHHHHhcCCc
Confidence 3678999999999999966
No 38
>COG5485 Predicted ester cyclase [General function prediction only]
Probab=23.02 E-value=1.3e+02 Score=21.30 Aligned_cols=25 Identities=28% Similarity=0.553 Sum_probs=19.6
Q ss_pred CCCeEEEEEEEEcCCCCCeEEEEEEecCCCCc
Q psy967 12 NEPVKGTIFFTQEHADSPVKVTGEIQGLEEDG 43 (82)
Q Consensus 12 G~~VsGtV~FtQ~~~~~~V~ItG~I~GL~Pg~ 43 (82)
|+.|.-.++|.-.. +|+|-|||||+
T Consensus 72 ~~~vaarl~Fdctp-------~G~i~Gip~nG 96 (131)
T COG5485 72 GDRVAARLTFDCTP-------SGEIMGIPPNG 96 (131)
T ss_pred CCceEEEEEEccCc-------CceEeccCCCC
Confidence 55888888997332 68999999987
No 39
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=22.88 E-value=22 Score=21.00 Aligned_cols=7 Identities=71% Similarity=1.369 Sum_probs=2.3
Q ss_pred Hhhhhhh
Q psy967 55 AILDYYK 61 (82)
Q Consensus 55 ~~~~~~~ 61 (82)
|+|.|||
T Consensus 1 AvlkyYk 7 (47)
T PF01599_consen 1 AVLKYYK 7 (47)
T ss_dssp S----CE
T ss_pred CcceEEE
Confidence 6889997
No 40
>PF06337 DUSP: DUSP domain; InterPro: IPR006615 Deubiquitinating enzymes (DUB) form a large family of cysteine protease that can deconjugate ubiquitin or ubiquitin-like proteins (see PDOC00271 from PROSITEDOC) from ubiquitin-conjugated proteins. All DUBs contain a catalytic domain surrounded by one or more subdomains, some of which contribute to target recognition. The ~120-residue DUSP (domain present in ubiquitin-specific proteases) domain is one of these specific subdomains. Single or tandem DUSP domains are located both N- and C-terminal to the ubiquitin carboxyl-terminal hydrolase catalytic core domain (see PDOC00750 from PROSITEDOC) []. The DUSP domain displays a tripod-like AB3 fold with a three-helix bundle and a three-stranded anti-parallel beta-sheet resembling the legs and seat of the tripod. Conserved residues are predominantly involved in hydrophobic packing interactions within the three alpha-helices. The most conserved DUSP residues, forming the PGPI motif, are flanked by two long loops that vary both in length and sequence. The PGPI motif packs against the three-helix bundle and is highly ordered []. The function of the DUSP domain is unknown but it may play a role in protein/protein interaction or substrate recognition. This domain is associated with ubiquitin carboxyl-terminal hydrolase family 2 (IPR001394 from INTERPRO, MEROPS peptidase family C19). They are a family 100 to 200 kDa peptides which includes the Ubp1 ubiquitin peptidase from yeast; others include: Mammalian ubiquitin carboxyl-terminal hydrolase 4 (USP4), Mammalian ubiquitin carboxyl-terminal hydrolase 11 (USP11), Mammalian ubiquitin carboxyl-terminal hydrolase 15 (USP15), Mammalian ubiquitin carboxyl-terminal hydrolase 20 (USP20), Mammalian ubiquitin carboxyl-terminal hydrolase 32 (USP32), Vertebrate ubiquitin carboxyl-terminal hydrolase 33 (USP33), Vertebrate ubiquitin carboxyl-terminal hydrolase 48 (USP48). ; GO: 0004221 ubiquitin thiolesterase activity; PDB: 4A3O_B 3PPA_A 3LMN_A 1W6V_A 3T9L_A 4A3P_A 3PV1_A 3JYU_B.
Probab=21.84 E-value=64 Score=19.84 Aligned_cols=26 Identities=23% Similarity=0.392 Sum_probs=20.0
Q ss_pred cCCCCcCCceeeehhhHHhhhhhhcc
Q psy967 38 GLEEDGGLNLMNFTVFRAILDYYKGQ 63 (82)
Q Consensus 38 GL~Pg~gfHih~~~~~~~~~~~~~~~ 63 (82)
+|..+..|=+.+..+++.+.++|.+|
T Consensus 65 ~l~~~~Dy~~v~~~~W~~l~~~Yggg 90 (99)
T PF06337_consen 65 NLQEGVDYELVPEEVWDYLHSWYGGG 90 (99)
T ss_dssp S--CTTTEEEEEHHHHHHHHHHH-T-
T ss_pred cccCCCCEEEECHHHHHHHHHHcCCC
Confidence 67777789999999999999999754
No 41
>PF08462 Carmo_coat_C: Carmovirus coat protein; InterPro: IPR013669 This domain is found to the C terminus of the IPR000937 from INTERPRO domain in Carmoviruses. The coat protein of the Turnip crinkle virus (TCV; Tombusviridae) is a suppressor of RNA silencing and is required for cell to cell movement in its host []. The plant cellular trafficking machinery could hijack functional viral proteins to permit cell-to-cell movement of RNA silencing []. The 3'-proximal coat protein is coded by ORF4 [].; PDB: 1OPO_B.
Probab=21.22 E-value=2.7e+02 Score=18.83 Aligned_cols=29 Identities=14% Similarity=0.311 Sum_probs=22.0
Q ss_pred EecCCCeEEEEEEEEcCCCCCeEEEEEEecCC
Q psy967 9 VLNNEPVKGTIFFTQEHADSPVKVTGEIQGLE 40 (82)
Q Consensus 9 VL~G~~VsGtV~FtQ~~~~~~V~ItG~I~GL~ 40 (82)
+|.|.+.+|.|...-. .++.+.-.|+.|+
T Consensus 49 ti~GsGaSG~V~y~S~---~~~aV~~vvtnlp 77 (99)
T PF08462_consen 49 TIIGSGASGDVDYESA---RPIAVCEVVTNLP 77 (99)
T ss_dssp EEESTTEEEEEEEETT---TTEEEEEEEESST
T ss_pred eeecCCccceEEEeeC---CceEeeeeeccCC
Confidence 3456689999998654 4788888888774
No 42
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=20.60 E-value=1.1e+02 Score=19.59 Aligned_cols=32 Identities=28% Similarity=0.401 Sum_probs=22.0
Q ss_pred CCeEEEEEEecCCC-CcCCcee---------eehhhHHhhhh
Q psy967 28 SPVKVTGEIQGLEE-DGGLNLM---------NFTVFRAILDY 59 (82)
Q Consensus 28 ~~V~ItG~I~GL~P-g~gfHih---------~~~~~~~~~~~ 59 (82)
..+-|.|+|+++.. +.|+-.+ ++++|+.-+..
T Consensus 22 ~~vwV~GEIs~~~~~~~gh~YftLkD~~a~i~~~~~~~~~~~ 63 (99)
T PF13742_consen 22 PNVWVEGEISNLKRHSSGHVYFTLKDEEASISCVIFRSRARR 63 (99)
T ss_pred CCEEEEEEEeecEECCCceEEEEEEcCCcEEEEEEEHHHHhh
Confidence 46899999999998 4444443 46667665543
No 43
>PF12816 Vps8: Golgi CORVET complex core vacuolar protein 8
Probab=20.38 E-value=32 Score=24.90 Aligned_cols=24 Identities=29% Similarity=0.663 Sum_probs=18.9
Q ss_pred EEEEEEecCCCCcCCceeeehhhHHhhhhhhcc
Q psy967 31 KVTGEIQGLEEDGGLNLMNFTVFRAILDYYKGQ 63 (82)
Q Consensus 31 ~ItG~I~GL~Pg~gfHih~~~~~~~~~~~~~~~ 63 (82)
...|+|+.||| ++|.++++||+..
T Consensus 12 Il~~~i~~lpp---------~v~k~lv~~y~~~ 35 (196)
T PF12816_consen 12 ILSGKIKSLPP---------EVFKALVEHYASK 35 (196)
T ss_pred HHcCCCCCCCH---------HHHHHHHHHHHHC
Confidence 35677888866 8999999999753
Done!