Query psy12678
Match_columns 80
No_of_seqs 112 out of 1060
Neff 7.6
Searched_HMMs 46136
Date Fri Aug 16 16:41:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12678.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12678hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PHA02713 hypothetical protein; 99.6 1.4E-15 2.9E-20 112.7 4.3 58 14-71 3-61 (557)
2 KOG4441|consensus 99.6 3E-15 6.5E-20 111.3 5.2 65 8-72 8-72 (571)
3 PF00651 BTB: BTB/POZ domain; 99.3 1.6E-12 3.5E-17 77.0 3.5 43 27-69 1-44 (111)
4 PHA02790 Kelch-like protein; P 99.3 3.1E-12 6.6E-17 93.3 3.7 47 25-72 11-57 (480)
5 KOG4350|consensus 99.1 1.7E-11 3.7E-16 88.8 2.1 61 15-75 23-83 (620)
6 PHA03098 kelch-like protein; P 99.1 3.5E-11 7.7E-16 87.9 3.1 39 33-71 6-46 (534)
7 smart00225 BTB Broad-Complex, 98.8 4E-09 8.7E-14 59.0 2.6 34 38-71 1-34 (90)
8 KOG4591|consensus 98.5 9E-08 1.9E-12 64.4 2.6 52 16-69 46-100 (280)
9 KOG0783|consensus 98.3 7.7E-07 1.7E-11 69.3 4.7 52 23-74 541-596 (1267)
10 KOG2075|consensus 98.1 2.9E-06 6.2E-11 62.6 3.7 60 13-72 91-155 (521)
11 KOG2838|consensus 97.4 5.7E-05 1.2E-09 53.1 1.0 53 20-72 114-166 (401)
12 KOG0783|consensus 97.1 0.00018 4E-09 56.6 1.3 32 38-69 712-744 (1267)
13 KOG4682|consensus 96.8 0.0015 3.3E-08 47.9 3.6 44 27-71 60-103 (488)
14 KOG2838|consensus 95.5 0.0038 8.2E-08 44.1 0.1 47 21-67 220-282 (401)
15 KOG0511|consensus 78.9 0.15 3.2E-06 37.7 -3.2 31 35-65 148-179 (516)
16 KOG3863|consensus 78.2 0.25 5.3E-06 38.0 -2.3 40 25-69 3-42 (604)
17 KOG2716|consensus 72.7 3.5 7.7E-05 28.2 2.3 32 39-70 7-38 (230)
18 PF02214 BTB_2: BTB/POZ domain 70.8 1.2 2.7E-05 25.4 -0.2 31 39-69 1-32 (94)
19 KOG0511|consensus 67.1 1.2 2.7E-05 33.0 -0.8 41 28-68 169-210 (516)
20 KOG1987|consensus 58.6 4.2 9.1E-05 27.7 0.6 26 45-70 109-134 (297)
21 KOG3342|consensus 58.0 3.8 8.3E-05 26.7 0.3 19 36-54 80-100 (180)
22 PF04343 DUF488: Protein of un 54.2 6.6 0.00014 23.6 0.9 19 39-57 101-120 (122)
23 PF03931 Skp1_POZ: Skp1 family 53.1 31 0.00068 18.2 3.4 33 39-72 3-36 (62)
24 PF11822 DUF3342: Domain of un 50.4 14 0.0003 26.5 2.1 34 46-79 14-52 (317)
25 COG1576 Uncharacterized conser 42.7 44 0.00095 21.6 3.3 26 19-46 81-106 (155)
26 PF13180 PDZ_2: PDZ domain; PD 42.7 57 0.0012 17.7 3.7 36 36-78 34-69 (82)
27 COG1531 Uncharacterized protei 34.2 49 0.0011 19.0 2.3 16 40-55 48-63 (77)
28 TIGR02370 pyl_corrinoid methyl 33.9 55 0.0012 21.4 2.9 34 15-48 144-177 (197)
29 COG0350 Ada Methylated DNA-pro 33.2 21 0.00045 23.0 0.8 12 48-59 137-148 (168)
30 PF10905 DUF2695: Protein of u 30.9 60 0.0013 17.2 2.2 20 24-43 33-52 (53)
31 PF14615 Rsa3: Ribosome-assemb 30.3 61 0.0013 16.7 2.1 20 20-39 11-30 (47)
32 TIGR00589 ogt O-6-methylguanin 28.7 22 0.00047 20.2 0.3 12 47-58 50-61 (80)
33 cd00758 MoCF_BD MoCF_BD: molyb 26.4 1E+02 0.0022 18.6 3.0 29 15-46 40-68 (133)
34 cd02070 corrinoid_protein_B12- 25.3 90 0.002 20.3 2.8 34 16-49 143-176 (201)
35 PF11265 Med25_VWA: Mediator c 25.1 59 0.0013 22.2 1.9 24 33-65 10-33 (226)
36 PRK00901 methylated-DNA--prote 24.7 30 0.00065 22.1 0.4 12 47-58 121-132 (155)
37 PF11995 DUF3490: Domain of un 24.4 58 0.0012 21.2 1.6 21 60-80 24-44 (161)
38 PF01848 HOK_GEF: Hok/gef fami 22.2 1.2E+02 0.0027 15.2 2.8 22 30-51 19-40 (43)
39 PF05582 Peptidase_U57: YabG p 22.0 2.9E+02 0.0064 19.7 4.9 41 18-69 180-220 (287)
40 PF11889 DUF3409: Domain of un 21.0 82 0.0018 16.8 1.5 18 35-52 34-51 (56)
41 TIGR02855 spore_yabG sporulati 20.0 3.4E+02 0.0073 19.4 5.0 41 18-69 179-219 (283)
No 1
>PHA02713 hypothetical protein; Provisional
Probab=99.58 E-value=1.4e-15 Score=112.68 Aligned_cols=58 Identities=28% Similarity=0.400 Sum_probs=53.8
Q ss_pred eeechhHHHHHHHHHHHhhCCCceeEEEEeC-CeEEeceeeeecccCHHHHHhhcCCCC
Q psy12678 14 LRWNDFQTSILSSFRHLRDEEDFVDVTLACD-GCSFTAHKVVLSACSPYFKTLLKSIDG 71 (80)
Q Consensus 14 ~~~~~~~~~~~~~l~~~~~~~~~~Dv~l~v~-g~~~~~Hk~vLaa~S~~F~~~f~~~~~ 71 (80)
+....|+..+++.|++||+++.+|||+|.++ |+.|+|||+|||++|+|||+||+++..
T Consensus 3 ~~~~~h~~~~l~~l~~lr~~~~l~DV~L~v~~~~~f~~Hr~vLaa~S~YF~amF~~~~~ 61 (557)
T PHA02713 3 IDDIKHNRRVVSNISNLLDDDILCDVIITIGDGEEIKAHKTILAAGSKYFRTLFTTPMI 61 (557)
T ss_pred cchhhhhHHHHHHHHHHHhCCCCCCEEEEeCCCCEEeehHHHHhhcCHHHHHHhcCCch
Confidence 4567889999999999999999999999997 899999999999999999999998754
No 2
>KOG4441|consensus
Probab=99.57 E-value=3e-15 Score=111.35 Aligned_cols=65 Identities=32% Similarity=0.498 Sum_probs=59.0
Q ss_pred CCceeEeeechhHHHHHHHHHHHhhCCCceeEEEEeCCeEEeceeeeecccCHHHHHhhcCCCCC
Q psy12678 8 VDQQFALRWNDFQTSILSSFRHLRDEEDFVDVTLACDGCSFTAHKVVLSACSPYFKTLLKSIDGR 72 (80)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~Dv~l~v~g~~~~~Hk~vLaa~S~~F~~~f~~~~~~ 72 (80)
......+....|...+++.|+.+|+++.+|||+|.+++++|+|||+|||++|+|||+||+++..+
T Consensus 8 ~~~~~~~~~~~h~~~~l~~l~~lr~~~~lcDv~L~v~~~~~~aHR~VLAa~S~YFraMFt~~l~e 72 (571)
T KOG4441|consen 8 FNSTSEFTDPSHSKFLLQGLNELREEGLLCDVTLLVGDREFPAHRVVLAACSPYFRAMFTSGLKE 72 (571)
T ss_pred cccccccccHHHHHHHHHHHHHHHHhCCCceEEEEECCeeechHHHHHHhccHHHHHHhcCCccc
Confidence 34456678889999999999999999999999999999999999999999999999999987543
No 3
>PF00651 BTB: BTB/POZ domain; InterPro: IPR013069 The BTB (for BR-C, ttk and bab) [] or POZ (for Pox virus and Zinc finger) [] domain is present near the N terminus of a fraction of zinc finger (IPR007087 from INTERPRO) proteins and in proteins that contain the IPR006652 from INTERPRO motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation []. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule []. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT [, , ]. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.; GO: 0005515 protein binding; PDB: 3M5B_A 1R28_B 3LBZ_A 3E4U_F 3BIM_B 1R2B_A 1R29_A 2VPK_A 2YY9_B 3GA1_A ....
Probab=99.31 E-value=1.6e-12 Score=76.96 Aligned_cols=43 Identities=37% Similarity=0.682 Sum_probs=38.3
Q ss_pred HHHHhhCCCceeEEEEeC-CeEEeceeeeecccCHHHHHhhcCC
Q psy12678 27 FRHLRDEEDFVDVTLACD-GCSFTAHKVVLSACSPYFKTLLKSI 69 (80)
Q Consensus 27 l~~~~~~~~~~Dv~l~v~-g~~~~~Hk~vLaa~S~~F~~~f~~~ 69 (80)
|+++++++.++|++|.++ ++.|++||.||+++|+||+.+|.+.
T Consensus 1 ~~~~~~~~~~~D~~i~v~d~~~~~vhk~iL~~~S~~F~~~~~~~ 44 (111)
T PF00651_consen 1 LNDLFNSNEFSDVTIRVGDGKTFYVHKNILAARSPYFRNLFEGS 44 (111)
T ss_dssp HHHHHHHTTS--EEEEETTTEEEEE-HHHHHHHBHHHHHHHTTT
T ss_pred ChHHHcCCCCCCEEEEECCCEEEeechhhhhccchhhhhccccc
Confidence 578999999999999999 8999999999999999999999998
No 4
>PHA02790 Kelch-like protein; Provisional
Probab=99.27 E-value=3.1e-12 Score=93.33 Aligned_cols=47 Identities=23% Similarity=0.383 Sum_probs=40.1
Q ss_pred HHHHHHhhCCCceeEEEEeCCeEEeceeeeecccCHHHHHhhcCCCCC
Q psy12678 25 SSFRHLRDEEDFVDVTLACDGCSFTAHKVVLSACSPYFKTLLKSIDGR 72 (80)
Q Consensus 25 ~~l~~~~~~~~~~Dv~l~v~g~~~~~Hk~vLaa~S~~F~~~f~~~~~~ 72 (80)
+.+-.+|.++.+|||++++|+ +|+|||+|||++|+|||+||+++..+
T Consensus 11 ~~~~~~~~~~~~~~~~~~~~~-~~~~HR~VLAa~S~YFraMF~~~~~E 57 (480)
T PHA02790 11 KNILALSMTKKFKTIIEAIGG-NIIVNSTILKKLSPYFRTHLRQKYTK 57 (480)
T ss_pred hhHHHHHhhhhhceEEEEcCc-EEeeehhhhhhcCHHHHHHhcCCccc
Confidence 455678889999998877665 79999999999999999999988643
No 5
>KOG4350|consensus
Probab=99.14 E-value=1.7e-11 Score=88.83 Aligned_cols=61 Identities=31% Similarity=0.439 Sum_probs=51.8
Q ss_pred eechhHHHHHHHHHHHhhCCCceeEEEEeCCeEEeceeeeecccCHHHHHhhcCCCCCceE
Q psy12678 15 RWNDFQTSILSSFRHLRDEEDFVDVTLACDGCSFTAHKVVLSACSPYFKTLLKSIDGRRLC 75 (80)
Q Consensus 15 ~~~~~~~~~~~~l~~~~~~~~~~Dv~l~v~g~~~~~Hk~vLaa~S~~F~~~f~~~~~~~~~ 75 (80)
+.-.-...+.+.+.+++.+..++||+++|++++|+|||+|||++|.|||+++-++..+..+
T Consensus 23 ~~~~i~~~fS~~~~~l~~~e~y~DVtfvve~~rfpAHRvILAaRs~yFRAlLYgGm~Es~q 83 (620)
T KOG4350|consen 23 ESAAISNNFSQSFDELFTSEDYSDVTFVVEDTRFPAHRVILAARSSYFRALLYGGMQESHQ 83 (620)
T ss_pred hhhhhccchhHHHHHHhhcCcccceEEEEeccccchhhhhHHHHHHHHHHHHhhhhhhhhh
Confidence 3334555677889999999999999999999999999999999999999999887654433
No 6
>PHA03098 kelch-like protein; Provisional
Probab=99.12 E-value=3.5e-11 Score=87.93 Aligned_cols=39 Identities=31% Similarity=0.503 Sum_probs=36.9
Q ss_pred CCCceeEEEEe--CCeEEeceeeeecccCHHHHHhhcCCCC
Q psy12678 33 EEDFVDVTLAC--DGCSFTAHKVVLSACSPYFKTLLKSIDG 71 (80)
Q Consensus 33 ~~~~~Dv~l~v--~g~~~~~Hk~vLaa~S~~F~~~f~~~~~ 71 (80)
++.+|||+|.+ +|++|+|||.||+++|+||++||+++..
T Consensus 6 ~~~~~Dv~l~~~~~~~~~~~Hk~vLaa~S~yF~~mf~~~~~ 46 (534)
T PHA03098 6 LQKFCDESIIIVNGGGIIKVHKIILSSSSEYFKKMFKNNFK 46 (534)
T ss_pred cCCCCCEEEEEEcCCEEEEeHHHHHHhhhHHHHHHHhCCCC
Confidence 78999999998 9999999999999999999999998865
No 7
>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=98.79 E-value=4e-09 Score=58.97 Aligned_cols=34 Identities=56% Similarity=0.837 Sum_probs=31.6
Q ss_pred eEEEEeCCeEEeceeeeecccCHHHHHhhcCCCC
Q psy12678 38 DVTLACDGCSFTAHKVVLSACSPYFKTLLKSIDG 71 (80)
Q Consensus 38 Dv~l~v~g~~~~~Hk~vLaa~S~~F~~~f~~~~~ 71 (80)
|+++.++|+.|++||.+|+++|+||+.+|.++..
T Consensus 1 dv~i~v~~~~~~~h~~iL~~~s~~f~~~~~~~~~ 34 (90)
T smart00225 1 DVTLVVGGKKFKAHKAVLAACSPYFKALFSGDFK 34 (90)
T ss_pred CeEEEECCEEEehHHHHHhhcCHHHHHHHcCCCc
Confidence 6889999999999999999999999999998754
No 8
>KOG4591|consensus
Probab=98.48 E-value=9e-08 Score=64.35 Aligned_cols=52 Identities=29% Similarity=0.434 Sum_probs=46.1
Q ss_pred echhHHHHHHHHHHHhhCCCceeEEEEeCC---eEEeceeeeecccCHHHHHhhcCC
Q psy12678 16 WNDFQTSILSSFRHLRDEEDFVDVTLACDG---CSFTAHKVVLSACSPYFKTLLKSI 69 (80)
Q Consensus 16 ~~~~~~~~~~~l~~~~~~~~~~Dv~l~v~g---~~~~~Hk~vLaa~S~~F~~~f~~~ 69 (80)
..++++.++....+++++.+|+|+++.++| +.++|||.|||++|++++ |.+.
T Consensus 46 ~dSF~SRLLaitadL~Ek~qfSDlk~K~~gns~k~i~AHKfVLAARsD~Wk--faN~ 100 (280)
T KOG4591|consen 46 PDSFISRLLAITADLLEKEQFSDLKFKFAGNSDKHIPAHKFVLAARSDFWK--FANG 100 (280)
T ss_pred chhHHHHHHHHHHHHhhcccccceeEEecCCccccCchhhhhhhhhcchhh--hccC
Confidence 346888999999999999999999999985 779999999999999997 6554
No 9
>KOG0783|consensus
Probab=98.33 E-value=7.7e-07 Score=69.34 Aligned_cols=52 Identities=31% Similarity=0.452 Sum_probs=41.2
Q ss_pred HHHHHHHHhh----CCCceeEEEEeCCeEEeceeeeecccCHHHHHhhcCCCCCce
Q psy12678 23 ILSSFRHLRD----EEDFVDVTLACDGCSFTAHKVVLSACSPYFKTLLKSIDGRRL 74 (80)
Q Consensus 23 ~~~~l~~~~~----~~~~~Dv~l~v~g~~~~~Hk~vLaa~S~~F~~~f~~~~~~~~ 74 (80)
+...+..+.. ...+.|||+.||++.|+|||.||+++|++||.+|-......+
T Consensus 541 fe~sf~kLl~e~~~~ds~hDVtf~vg~~~F~aHKfIl~~rs~flrkL~l~~~~~s~ 596 (1267)
T KOG0783|consen 541 FEGSFPKLLSEENYKDSFHDVTFYVGTSMFHAHKFILCARSSFLRKLLLQKKKSSV 596 (1267)
T ss_pred chhhhHHHhhccccccccceEEEEecCeecccceEEEEeccHHHHHHHHhhccccc
Confidence 4445555544 457888999999999999999999999999999976655433
No 10
>KOG2075|consensus
Probab=98.11 E-value=2.9e-06 Score=62.55 Aligned_cols=60 Identities=20% Similarity=0.248 Sum_probs=51.9
Q ss_pred EeeechhHHHHHHHHHHHhhCCCceeEEEEeCC-----eEEeceeeeecccCHHHHHhhcCCCCC
Q psy12678 13 ALRWNDFQTSILSSFRHLRDEEDFVDVTLACDG-----CSFTAHKVVLSACSPYFKTLLKSIDGR 72 (80)
Q Consensus 13 ~~~~~~~~~~~~~~l~~~~~~~~~~Dv~l~v~g-----~~~~~Hk~vLaa~S~~F~~~f~~~~~~ 72 (80)
-+.|..-...+......++++...+|+.++||+ +.|||||.|||..|+.|.+||.++...
T Consensus 91 ~~nwq~~~~t~~er~~~l~~n~~~adv~fivg~~~~~~q~~paHk~vla~gS~VFdaMf~g~~a~ 155 (521)
T KOG2075|consen 91 IPNWQAQKETMRERQAALFNNELLADVHFIVGEEDGGSQRIPAHKLVLADGSDVFDAMFYGGLAE 155 (521)
T ss_pred CcccccchhhHHHhhHhhccCcccceeEEEeccCCCcccccchhhhhhhcchHHHHHHhccCccc
Confidence 456666677888889999999999999999973 579999999999999999999887543
No 11
>KOG2838|consensus
Probab=97.41 E-value=5.7e-05 Score=53.10 Aligned_cols=53 Identities=26% Similarity=0.392 Sum_probs=46.7
Q ss_pred HHHHHHHHHHHhhCCCceeEEEEeCCeEEeceeeeecccCHHHHHhhcCCCCC
Q psy12678 20 QTSILSSFRHLRDEEDFVDVTLACDGCSFTAHKVVLSACSPYFKTLLKSIDGR 72 (80)
Q Consensus 20 ~~~~~~~l~~~~~~~~~~Dv~l~v~g~~~~~Hk~vLaa~S~~F~~~f~~~~~~ 72 (80)
...++..+.+.++...+.|+-+......|++||++|+++|++|+.+.+++++.
T Consensus 114 a~sf~kD~ad~ye~k~c~dldiiFkeTcfpahRA~laaRCpffK~l~nsd~e~ 166 (401)
T KOG2838|consen 114 ANSFLKDFADGYERKVCGDLDIIFKETCFPAHRAFLAARCPFFKILANSDEEP 166 (401)
T ss_pred hhHHHHHHhhhhheeeeccceeeeeeccchHHHHHHHhhCcchhhhccCCCCc
Confidence 45678888888889999999999999999999999999999999988877654
No 12
>KOG0783|consensus
Probab=97.14 E-value=0.00018 Score=56.58 Aligned_cols=32 Identities=34% Similarity=0.560 Sum_probs=26.7
Q ss_pred eEEEEe-CCeEEeceeeeecccCHHHHHhhcCC
Q psy12678 38 DVTLAC-DGCSFTAHKVVLSACSPYFKTLLKSI 69 (80)
Q Consensus 38 Dv~l~v-~g~~~~~Hk~vLaa~S~~F~~~f~~~ 69 (80)
|+.+++ +|+.|+|||++|++|.+||..||..-
T Consensus 712 d~~i~~KDGkvl~aHkc~L~aRlEYF~smf~~~ 744 (1267)
T KOG0783|consen 712 DTVIKLKDGKVLKAHKCFLSARLEYFSSMFQFV 744 (1267)
T ss_pred eEEEEecCCcCcccceeEeeeHHHHHHHHHHHH
Confidence 444443 88999999999999999999999654
No 13
>KOG4682|consensus
Probab=96.80 E-value=0.0015 Score=47.86 Aligned_cols=44 Identities=27% Similarity=0.359 Sum_probs=39.1
Q ss_pred HHHHhhCCCceeEEEEeCCeEEeceeeeecccCHHHHHhhcCCCC
Q psy12678 27 FRHLRDEEDFVDVTLACDGCSFTAHKVVLSACSPYFKTLLKSIDG 71 (80)
Q Consensus 27 l~~~~~~~~~~Dv~l~v~g~~~~~Hk~vLaa~S~~F~~~f~~~~~ 71 (80)
++.++.++.-+||++.+-|+.|+.||.-|.. |+||++||++...
T Consensus 60 yq~lf~q~enSDv~l~alg~eWrlHk~yL~Q-S~yf~smf~Gtw~ 103 (488)
T KOG4682|consen 60 YQNLFLQGENSDVILEALGFEWRLHKPYLFQ-SEYFKSMFSGTWK 103 (488)
T ss_pred HHHHHhcCCCcceehhhccceeeeeeeeeec-cHHHHHHhccccC
Confidence 5568889999999999999999999999976 5899999998744
No 14
>KOG2838|consensus
Probab=95.52 E-value=0.0038 Score=44.10 Aligned_cols=47 Identities=28% Similarity=0.383 Sum_probs=34.2
Q ss_pred HHHHHHHHHHhhCCCceeEEEE--eCCe--------------EEeceeeeecccCHHHHHhhc
Q psy12678 21 TSILSSFRHLRDEEDFVDVTLA--CDGC--------------SFTAHKVVLSACSPYFKTLLK 67 (80)
Q Consensus 21 ~~~~~~l~~~~~~~~~~Dv~l~--v~g~--------------~~~~Hk~vLaa~S~~F~~~f~ 67 (80)
..+-..++.++++....|+.+. ++|+ .++||++|.+++|++||.++.
T Consensus 220 kkLd~Dmkglfd~~c~~d~li~~ssD~elveafggeeNc~deeikahkai~aaRS~ffRnLL~ 282 (401)
T KOG2838|consen 220 KKLDEDMKGLFDQDCKHDDLIIESSDGELVEAFGGEENCEDEEIKAHKAIAAARSKFFRNLLL 282 (401)
T ss_pred hhhhHHHHHHHHhhcccCcEEEEeccchhhhhcCCcccchhHHHHHHHHHHHhhhHHHHHHHH
Confidence 3445566777777766665553 3432 589999999999999999873
No 15
>KOG0511|consensus
Probab=78.94 E-value=0.15 Score=37.66 Aligned_cols=31 Identities=29% Similarity=0.397 Sum_probs=21.6
Q ss_pred CceeEEEEe-CCeEEeceeeeecccCHHHHHh
Q psy12678 35 DFVDVTLAC-DGCSFTAHKVVLSACSPYFKTL 65 (80)
Q Consensus 35 ~~~Dv~l~v-~g~~~~~Hk~vLaa~S~~F~~~ 65 (80)
...|+++.. +|+.|.|||..|+++|++|..-
T Consensus 148 ~~~di~f~~q~g~~f~ahkfll~arSs~~~~k 179 (516)
T KOG0511|consen 148 CCHDIDFLQQEGANFDAHKFLLEARSSNYFPK 179 (516)
T ss_pred cccchHHHhhccccccHHHHHHHhhhcccCch
Confidence 455666654 6777888888888888776443
No 16
>KOG3863|consensus
Probab=78.22 E-value=0.25 Score=37.99 Aligned_cols=40 Identities=30% Similarity=0.510 Sum_probs=33.3
Q ss_pred HHHHHHhhCCCceeEEEEeCCeEEeceeeeecccCHHHHHhhcCC
Q psy12678 25 SSFRHLRDEEDFVDVTLACDGCSFTAHKVVLSACSPYFKTLLKSI 69 (80)
Q Consensus 25 ~~l~~~~~~~~~~Dv~l~v~g~~~~~Hk~vLaa~S~~F~~~f~~~ 69 (80)
..++..|++...||+++.+.++.|.+|+ +++||..-.-+.
T Consensus 3 ~~~~~qr~~~~~~~~~~~~~~~~f~~~~-----~~e~~~~~~~G~ 42 (604)
T KOG3863|consen 3 LSLNDQRKKDVLCDVTAFVERQGFRAHR-----CSEYFTSRIVGQ 42 (604)
T ss_pred ccccccccccccchhHHHHhccccccee-----ccchhhhhhccc
Confidence 3567889999999999999999999999 888886555443
No 17
>KOG2716|consensus
Probab=72.73 E-value=3.5 Score=28.20 Aligned_cols=32 Identities=31% Similarity=0.461 Sum_probs=28.9
Q ss_pred EEEEeCCeEEeceeeeecccCHHHHHhhcCCC
Q psy12678 39 VTLACDGCSFTAHKVVLSACSPYFKTLLKSID 70 (80)
Q Consensus 39 v~l~v~g~~~~~Hk~vLaa~S~~F~~~f~~~~ 70 (80)
|.|-|||..|.-.+.-|.-...+|++||..+-
T Consensus 7 vkLnvGG~~F~Tsk~TLtk~dg~fk~m~e~~i 38 (230)
T KOG2716|consen 7 VKLNVGGTIFKTSKSTLTKFDGFFKTMLETDI 38 (230)
T ss_pred EEEecCCeEEEeehhhhhhhhhHHHHHhhcCC
Confidence 45779999999999999999999999998874
No 18
>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=70.82 E-value=1.2 Score=25.36 Aligned_cols=31 Identities=19% Similarity=0.288 Sum_probs=25.9
Q ss_pred EEEEeCCeEEeceeeeec-ccCHHHHHhhcCC
Q psy12678 39 VTLACDGCSFTAHKVVLS-ACSPYFKTLLKSI 69 (80)
Q Consensus 39 v~l~v~g~~~~~Hk~vLa-a~S~~F~~~f~~~ 69 (80)
|.|-|||+.|..-+..|. ....+|.+++...
T Consensus 1 V~lNVGG~~f~~~~~tL~~~~~s~l~~~~~~~ 32 (94)
T PF02214_consen 1 VRLNVGGTIFETSRSTLTRYPDSLLARLFSGE 32 (94)
T ss_dssp EEEEETTEEEEEEHHHHHTSTTSTTTSHHHTG
T ss_pred CEEEECCEEEEEcHHHHhhCCCChhhhHHhhc
Confidence 678899999999999998 5667888888754
No 19
>KOG0511|consensus
Probab=67.11 E-value=1.2 Score=32.97 Aligned_cols=41 Identities=34% Similarity=0.458 Sum_probs=32.0
Q ss_pred HHHhhCC-CceeEEEEeCCeEEeceeeeecccCHHHHHhhcC
Q psy12678 28 RHLRDEE-DFVDVTLACDGCSFTAHKVVLSACSPYFKTLLKS 68 (80)
Q Consensus 28 ~~~~~~~-~~~Dv~l~v~g~~~~~Hk~vLaa~S~~F~~~f~~ 68 (80)
-.+|.+. .--||.+-+.|++|-+||+++.+.+++|+-+|-.
T Consensus 169 l~arSs~~~~k~v~~~~~~heI~~~~v~~~~f~~flk~lyl~ 210 (516)
T KOG0511|consen 169 LEARSSNYFPKDVMFYVQGHEIEAHRVILSAFSPFLKQLYLN 210 (516)
T ss_pred HHhhhcccCchhhhhccccCchhhhhhhHhhhhHHHHHHHHh
Confidence 3444443 2346788899999999999999999999988754
No 20
>KOG1987|consensus
Probab=58.64 E-value=4.2 Score=27.74 Aligned_cols=26 Identities=38% Similarity=0.310 Sum_probs=22.8
Q ss_pred CeEEeceeeeecccCHHHHHhhcCCC
Q psy12678 45 GCSFTAHKVVLSACSPYFKTLLKSID 70 (80)
Q Consensus 45 g~~~~~Hk~vLaa~S~~F~~~f~~~~ 70 (80)
+..+.+|+++++++++.|+.++..+.
T Consensus 109 ~g~~~~~~~~~~a~~~V~~~~~~~d~ 134 (297)
T KOG1987|consen 109 NGFLVAHKLVLVARSEVFEAMGKSDV 134 (297)
T ss_pred CcEEEcCceEEEeeecceeeeccccc
Confidence 55699999999999999999987664
No 21
>KOG3342|consensus
Probab=58.00 E-value=3.8 Score=26.72 Aligned_cols=19 Identities=21% Similarity=0.522 Sum_probs=14.4
Q ss_pred ceeEEE-EeCCeEEe-ceeee
Q psy12678 36 FVDVTL-ACDGCSFT-AHKVV 54 (80)
Q Consensus 36 ~~Dv~l-~v~g~~~~-~Hk~v 54 (80)
--|+++ .++||++| +||+|
T Consensus 80 vGdivVf~vegR~IPiVHRvi 100 (180)
T KOG3342|consen 80 VGDIVVFKVEGREIPIVHRVI 100 (180)
T ss_pred eccEEEEEECCccCchhHHHH
Confidence 345554 78999999 78877
No 22
>PF04343 DUF488: Protein of unknown function, DUF488; InterPro: IPR007438 This family includes several proteins of uncharacterised function.
Probab=54.21 E-value=6.6 Score=23.60 Aligned_cols=19 Identities=26% Similarity=0.452 Sum_probs=14.6
Q ss_pred EEEEeCC-eEEeceeeeecc
Q psy12678 39 VTLACDG-CSFTAHKVVLSA 57 (80)
Q Consensus 39 v~l~v~g-~~~~~Hk~vLaa 57 (80)
++|.+.. -...|||.||+.
T Consensus 101 v~LlC~e~dp~~CHR~iLa~ 120 (122)
T PF04343_consen 101 VALLCAEKDPERCHRRILAE 120 (122)
T ss_pred eEEEEEecChhcCcHHHHHH
Confidence 8888744 457899999874
No 23
>PF03931 Skp1_POZ: Skp1 family, tetramerisation domain; InterPro: IPR016073 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a POZ domain with a core structure consisting of beta(2)/alpha(2)/beta(2)/alpha(2) in two layers, alpha/beta. This domain is found at the N-terminal of SKP1 proteins [] as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. ; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 1LM8_C 2XAI_E 1VCB_E 3ZRC_K 3ZRF_E 3DCG_B 2C9W_C 1LQB_B 2IZV_C 1HV2_A ....
Probab=53.13 E-value=31 Score=18.20 Aligned_cols=33 Identities=24% Similarity=0.378 Sum_probs=24.1
Q ss_pred EEEEe-CCeEEeceeeeecccCHHHHHhhcCCCCC
Q psy12678 39 VTLAC-DGCSFTAHKVVLSACSPYFKTLLKSIDGR 72 (80)
Q Consensus 39 v~l~v-~g~~~~~Hk~vLaa~S~~F~~~f~~~~~~ 72 (80)
++|+. +|+.|.+.+.+.. .|..++.|+.+....
T Consensus 3 v~L~SsDg~~f~V~~~~a~-~S~~i~~ml~~~~~~ 36 (62)
T PF03931_consen 3 VKLVSSDGQEFEVSREAAK-QSKTIKNMLEDLGDE 36 (62)
T ss_dssp EEEEETTSEEEEEEHHHHT-TSHHHHHHHHCTCCC
T ss_pred EEEEcCCCCEEEeeHHHHH-HhHHHHHHHhhhccc
Confidence 45544 7788988888765 678999999766443
No 24
>PF11822 DUF3342: Domain of unknown function (DUF3342); InterPro: IPR021777 This family of proteins are functionally uncharacterised. This family is found in bacteria. This presumed domain is typically between 170 to 303 amino acids in length. The N-terminal half of this family is a BTB-like domain.
Probab=50.44 E-value=14 Score=26.53 Aligned_cols=34 Identities=21% Similarity=0.249 Sum_probs=27.0
Q ss_pred eEEeceeeeecccCHHHHHhhc-----CCCCCceEEeee
Q psy12678 46 CSFTAHKVVLSACSPYFKTLLK-----SIDGRRLCVDTA 79 (80)
Q Consensus 46 ~~~~~Hk~vLaa~S~~F~~~f~-----~~~~~~~~~~v~ 79 (80)
+.|.|.+-+|-..=.||+.++. +...+++.|.|.
T Consensus 14 rdF~C~~~lL~~~M~YF~~~l~~~~~~~~~~~~idisVh 52 (317)
T PF11822_consen 14 RDFTCPRDLLVSEMRYFAEYLSRYINDSQRWEEIDISVH 52 (317)
T ss_pred eeeeccHHHHHHhhHHHHHHHhhcccccCcCCCcceEEe
Confidence 5799999999999999999993 445566666663
No 25
>COG1576 Uncharacterized conserved protein [Function unknown]
Probab=42.71 E-value=44 Score=21.62 Aligned_cols=26 Identities=19% Similarity=0.354 Sum_probs=21.2
Q ss_pred hHHHHHHHHHHHhhCCCceeEEEEeCCe
Q psy12678 19 FQTSILSSFRHLRDEEDFVDVTLACDGC 46 (80)
Q Consensus 19 ~~~~~~~~l~~~~~~~~~~Dv~l~v~g~ 46 (80)
.+..+.+.+++++..+ .|+++++||-
T Consensus 81 sSe~fA~~l~~~~~~G--~~i~f~IGG~ 106 (155)
T COG1576 81 SSEEFADFLERLRDDG--RDISFLIGGA 106 (155)
T ss_pred ChHHHHHHHHHHHhcC--CeEEEEEeCc
Confidence 3556778888888888 9999999984
No 26
>PF13180 PDZ_2: PDZ domain; PDB: 2L97_A 1Y8T_A 2Z9I_A 1LCY_A 2PZD_B 2P3W_A 1VCW_C 1TE0_B 1SOZ_C 1SOT_C ....
Probab=42.65 E-value=57 Score=17.73 Aligned_cols=36 Identities=19% Similarity=0.240 Sum_probs=22.4
Q ss_pred ceeEEEEeCCeEEeceeeeecccCHHHHHhhcCCCCCceEEee
Q psy12678 36 FVDVTLACDGCSFTAHKVVLSACSPYFKTLLKSIDGRRLCVDT 78 (80)
Q Consensus 36 ~~Dv~l~v~g~~~~~Hk~vLaa~S~~F~~~f~~~~~~~~~~~v 78 (80)
--|+++.++|+.+ ....++-+.+....+.+.+.+.|
T Consensus 34 ~GD~I~~ing~~v-------~~~~~~~~~l~~~~~g~~v~l~v 69 (82)
T PF13180_consen 34 PGDIILAINGKPV-------NSSEDLVNILSKGKPGDTVTLTV 69 (82)
T ss_dssp TTEEEEEETTEES-------SSHHHHHHHHHCSSTTSEEEEEE
T ss_pred CCcEEEEECCEEc-------CCHHHHHHHHHhCCCCCEEEEEE
Confidence 4588999999866 22334444454566666666654
No 27
>COG1531 Uncharacterized protein conserved in archaea [Function unknown]
Probab=34.22 E-value=49 Score=18.95 Aligned_cols=16 Identities=25% Similarity=0.351 Sum_probs=12.7
Q ss_pred EEEeCCeEEeceeeee
Q psy12678 40 TLACDGCSFTAHKVVL 55 (80)
Q Consensus 40 ~l~v~g~~~~~Hk~vL 55 (80)
.+..+|..+|-||.|-
T Consensus 48 ~~~~~~~~IP~HRIve 63 (77)
T COG1531 48 YLLYQGTYIPYHRIVE 63 (77)
T ss_pred EEEecCceeeeEEEEE
Confidence 5566888999999874
No 28
>TIGR02370 pyl_corrinoid methyltransferase cognate corrinoid proteins, Methanosarcina family. This model describes a subfamily of the B12 binding domain (pfam02607, pfam02310) proteins. Members of the seed alignment include corrinoid proteins specific to four different, mutally non-homologous enzymes of the genus Methanosarcina. Three of the four cognate enzymes (trimethylamine, dimethylamine, and monomethylamine methyltransferases) all have the unusual, ribosomally incorporated amino acid pyrrolysine at the active site. All act in systems in which a methyl group is transferred to the corrinoid protein to create methylcobalamin, from which the methyl group is later transferred elsewhere.
Probab=33.85 E-value=55 Score=21.37 Aligned_cols=34 Identities=12% Similarity=0.010 Sum_probs=27.1
Q ss_pred eechhHHHHHHHHHHHhhCCCceeEEEEeCCeEE
Q psy12678 15 RWNDFQTSILSSFRHLRDEEDFVDVTLACDGCSF 48 (80)
Q Consensus 15 ~~~~~~~~~~~~l~~~~~~~~~~Dv~l~v~g~~~ 48 (80)
....+...+.+.++.+++.+...++.+.+||..|
T Consensus 144 ~~~~~~~~~~~~i~~l~~~~~~~~v~i~vGG~~~ 177 (197)
T TIGR02370 144 LMTTTMYGQKDINDKLKEEGYRDSVKFMVGGAPV 177 (197)
T ss_pred ccccCHHHHHHHHHHHHHcCCCCCCEEEEEChhc
Confidence 3445566777888888888888899999999866
No 29
>COG0350 Ada Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=33.19 E-value=21 Score=23.05 Aligned_cols=12 Identities=17% Similarity=0.326 Sum_probs=9.4
Q ss_pred EeceeeeecccC
Q psy12678 48 FTAHKVVLSACS 59 (80)
Q Consensus 48 ~~~Hk~vLaa~S 59 (80)
+||||+|=+..+
T Consensus 137 IPCHRVig~~G~ 148 (168)
T COG0350 137 IPCHRVIGADGD 148 (168)
T ss_pred ecCeEeEcCCCC
Confidence 999999966643
No 30
>PF10905 DUF2695: Protein of unknown function (DUF2695); InterPro: IPR024248 This bacterial family of proteins has no known function.
Probab=30.88 E-value=60 Score=17.18 Aligned_cols=20 Identities=15% Similarity=0.330 Sum_probs=15.4
Q ss_pred HHHHHHHhhCCCceeEEEEe
Q psy12678 24 LSSFRHLRDEEDFVDVTLAC 43 (80)
Q Consensus 24 ~~~l~~~~~~~~~~Dv~l~v 43 (80)
-+.+..++++|-+||..|..
T Consensus 33 ~~vl~~l~~nGg~CDCEVl~ 52 (53)
T PF10905_consen 33 EDVLEWLRENGGYCDCEVLY 52 (53)
T ss_pred HHHHHHHHHcCCCcceeeec
Confidence 45567788899999987764
No 31
>PF14615 Rsa3: Ribosome-assembly protein 3
Probab=30.34 E-value=61 Score=16.68 Aligned_cols=20 Identities=25% Similarity=0.390 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHhhCCCceeE
Q psy12678 20 QTSILSSFRHLRDEEDFVDV 39 (80)
Q Consensus 20 ~~~~~~~l~~~~~~~~~~Dv 39 (80)
...+.+.|+++|+.+.|.+-
T Consensus 11 t~efgdDLd~lR~~~dF~~~ 30 (47)
T PF14615_consen 11 TDEFGDDLDELRKAPDFTDK 30 (47)
T ss_pred HHHHHHHHHHHhcCCCCCch
Confidence 45678899999999998773
No 32
>TIGR00589 ogt O-6-methylguanine DNA methyltransferase. All proteins in this family for which functions are known are involved alkyl-DNA transferases which remove alkyl groups from DNA as part of alkylation DNA repair. Some of the proteins in this family are also transcription regulators and have a distinct transcription regulatory domain. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.67 E-value=22 Score=20.19 Aligned_cols=12 Identities=17% Similarity=0.202 Sum_probs=9.8
Q ss_pred EEeceeeeeccc
Q psy12678 47 SFTAHKVVLSAC 58 (80)
Q Consensus 47 ~~~~Hk~vLaa~ 58 (80)
.+||||+|-+..
T Consensus 50 ~iPcHRVv~s~G 61 (80)
T TIGR00589 50 LVPCHRVIGKNG 61 (80)
T ss_pred CCCCceeECCCC
Confidence 589999997765
No 33
>cd00758 MoCF_BD MoCF_BD: molybdenum cofactor (MoCF) binding domain (BD). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. The domain is presumed to bind molybdopterin.
Probab=26.41 E-value=1e+02 Score=18.58 Aligned_cols=29 Identities=24% Similarity=0.226 Sum_probs=21.8
Q ss_pred eechhHHHHHHHHHHHhhCCCceeEEEEeCCe
Q psy12678 15 RWNDFQTSILSSFRHLRDEEDFVDVTLACDGC 46 (80)
Q Consensus 15 ~~~~~~~~~~~~l~~~~~~~~~~Dv~l~v~g~ 46 (80)
..++....+.+.+.++.++ +|+++..||-
T Consensus 40 ~v~Dd~~~i~~~i~~~~~~---~DlvittGG~ 68 (133)
T cd00758 40 VVPDDADSIRAALIEASRE---ADLVLTTGGT 68 (133)
T ss_pred ecCCCHHHHHHHHHHHHhc---CCEEEECCCC
Confidence 3456677788888887665 8999999874
No 34
>cd02070 corrinoid_protein_B12-BD B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or monomethylamine, which is initiated by a series of corrinoid-dependent methyltransferases.
Probab=25.35 E-value=90 Score=20.28 Aligned_cols=34 Identities=9% Similarity=0.077 Sum_probs=25.4
Q ss_pred echhHHHHHHHHHHHhhCCCceeEEEEeCCeEEe
Q psy12678 16 WNDFQTSILSSFRHLRDEEDFVDVTLACDGCSFT 49 (80)
Q Consensus 16 ~~~~~~~~~~~l~~~~~~~~~~Dv~l~v~g~~~~ 49 (80)
...+...+...++.+++.+...|+.+.+||..+.
T Consensus 143 ~~~~~~~~~~~i~~lr~~~~~~~~~i~vGG~~~~ 176 (201)
T cd02070 143 MTTTMGGMKEVIEALKEAGLRDKVKVMVGGAPVN 176 (201)
T ss_pred ccccHHHHHHHHHHHHHCCCCcCCeEEEECCcCC
Confidence 3455666777788888887667999999997543
No 35
>PF11265 Med25_VWA: Mediator complex subunit 25 von Willebrand factor type A; InterPro: IPR021419 The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain which is this one, an SD2 domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This VWA or von Willebrand factor type A domain when bound to RAR and the histone acetyltransferase CBP is responsible for recruiting Med1 to the rest of the Mediator complex [].
Probab=25.10 E-value=59 Score=22.23 Aligned_cols=24 Identities=29% Similarity=0.583 Sum_probs=18.9
Q ss_pred CCCceeEEEEeCCeEEeceeeeecccCHHHHHh
Q psy12678 33 EEDFVDVTLACDGCSFTAHKVVLSACSPYFKTL 65 (80)
Q Consensus 33 ~~~~~Dv~l~v~g~~~~~Hk~vLaa~S~~F~~~ 65 (80)
++...||+++|+|. |+-++||..+
T Consensus 10 ~~~~~~vVfvvEgT---------Aalgpy~~~L 33 (226)
T PF11265_consen 10 QPPQAQVVFVVEGT---------AALGPYWNTL 33 (226)
T ss_pred cCccceEEEEEecc---------hhhhhhHHHH
Confidence 36788999999998 6777787655
No 36
>PRK00901 methylated-DNA--protein-cysteine methyltransferase; Provisional
Probab=24.67 E-value=30 Score=22.11 Aligned_cols=12 Identities=17% Similarity=0.235 Sum_probs=9.1
Q ss_pred EEeceeeeeccc
Q psy12678 47 SFTAHKVVLSAC 58 (80)
Q Consensus 47 ~~~~Hk~vLaa~ 58 (80)
.+||||+|=+..
T Consensus 121 iIPCHRVv~~~G 132 (155)
T PRK00901 121 FIPCHRVIGANG 132 (155)
T ss_pred ccCCceEECCCC
Confidence 478999996654
No 37
>PF11995 DUF3490: Domain of unknown function (DUF3490); InterPro: IPR021881 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 160 amino acids in length. This domain is found associated with PF00225 from PFAM. This domain is found associated with PF00225 from PFAM. This domain has two conserved sequence motifs: EVE and ESA.
Probab=24.36 E-value=58 Score=21.23 Aligned_cols=21 Identities=24% Similarity=0.414 Sum_probs=18.1
Q ss_pred HHHHHhhcCCCCCceEEeeeC
Q psy12678 60 PYFKTLLKSIDGRRLCVDTAL 80 (80)
Q Consensus 60 ~~F~~~f~~~~~~~~~~~v~l 80 (80)
.||--+|.+++.+.+-+.|.+
T Consensus 24 TyFfLLFkGdpaD~iYmEVEl 44 (161)
T PF11995_consen 24 TYFFLLFKGDPADSIYMEVEL 44 (161)
T ss_pred hhhhheecCCcccceEEEeeh
Confidence 588899999999999888864
No 38
>PF01848 HOK_GEF: Hok/gef family; InterPro: IPR000021 The hok/gef family of Gram-negative bacterial proteins are toxic to cells when over-expressed, killing the cells from within by interfering with a vital function in the cell membrane []. Some family members (flm) increase the stability of unstable RNA [], some (pnd) induce the degradation of stable RNA at higher than optimum growth temperatures [], while others affect the release of cellular magnesium by membrane alterations []. The proteins are short (50-70 residues), consisting of an N-terminal hydrophobic (possibly membrane spanning) domain, and a C-terminal periplasmic region, which contains the toxic domain. The C-terminal region contains a conserved cysteine residue that mediates homo-dimerisation in the gef protein, although dimerisation is not necessary for the toxic effect [].; GO: 0016020 membrane
Probab=22.24 E-value=1.2e+02 Score=15.24 Aligned_cols=22 Identities=5% Similarity=0.144 Sum_probs=18.2
Q ss_pred HhhCCCceeEEEEeCCeEEece
Q psy12678 30 LRDEEDFVDVTLACDGCSFTAH 51 (80)
Q Consensus 30 ~~~~~~~~Dv~l~v~g~~~~~H 51 (80)
+...+.+|.+.+..|+.++.|.
T Consensus 19 ~l~r~sLCEl~i~~g~~evaA~ 40 (43)
T PF01848_consen 19 WLTRDSLCELRIKDGNTEVAAF 40 (43)
T ss_pred HHhccCcEEEEEecCCEEEEEE
Confidence 4556889999999999988764
No 39
>PF05582 Peptidase_U57: YabG peptidase U57; InterPro: IPR008764 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. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This is a group of peptidases belong to MEROPS peptidase family U57 (clan U-). The type example is the YabG protein of Bacillus subtilis. This is a protease involved in the synthesis and maturation of the spore coat proteins SpoIVA and YrbA of B. subtilis [].
Probab=21.99 E-value=2.9e+02 Score=19.68 Aligned_cols=41 Identities=22% Similarity=0.319 Sum_probs=29.1
Q ss_pred hhHHHHHHHHHHHhhCCCceeEEEEeCCeEEeceeeeecccCHHHHHhhcCC
Q psy12678 18 DFQTSILSSFRHLRDEEDFVDVTLACDGCSFTAHKVVLSACSPYFKTLLKSI 69 (80)
Q Consensus 18 ~~~~~~~~~l~~~~~~~~~~Dv~l~v~g~~~~~Hk~vLaa~S~~F~~~f~~~ 69 (80)
.++..+.+..+.+|+-..--|=.+...| ||-++|++++..+
T Consensus 180 rnSkyFVeaV~~aR~~ep~~D~LVIfAG-----------ACQS~fEall~AG 220 (287)
T PF05582_consen 180 RNSKYFVEAVKEARKYEPNLDDLVIFAG-----------ACQSHFEALLEAG 220 (287)
T ss_pred hccHHHHHHHHHHHhcCCCcccEEEEcc-----------hhHHHHHHHHHcC
Confidence 5677788999999987655554443333 6778999998665
No 40
>PF11889 DUF3409: Domain of unknown function (DUF3409); InterPro: IPR021824 This domain is functionally uncharacterised. This domain is found in viruses. This presumed domain is about 60 amino acids in length. This domain is found associated with PF00271 from PFAM, PF05550 from PFAM, PF05578 from PFAM. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0004252 serine-type endopeptidase activity, 0016817 hydrolase activity, acting on acid anhydrides, 0017111 nucleoside-triphosphatase activity, 0070008 serine-type exopeptidase activity
Probab=20.97 E-value=82 Score=16.83 Aligned_cols=18 Identities=28% Similarity=0.473 Sum_probs=13.2
Q ss_pred CceeEEEEeCCeEEecee
Q psy12678 35 DFVDVTLACDGCSFTAHK 52 (80)
Q Consensus 35 ~~~Dv~l~v~g~~~~~Hk 52 (80)
.-.|.||+|+|..+.+-+
T Consensus 34 kPPdativv~GvKYQVkK 51 (56)
T PF11889_consen 34 KPPDATIVVDGVKYQVKK 51 (56)
T ss_pred CCCCceEEEeeeEEEEee
Confidence 446889999998776543
No 41
>TIGR02855 spore_yabG sporulation peptidase YabG. Members of this family are the protein YabG, demonstrated for Bacillus subtilis to be an endopeptidase able to release N-terminal peptides from a number of sporulation proteins, including CotT, CotF, and SpoIVA. It appears to be expressed under control of sigma-K.
Probab=20.03 E-value=3.4e+02 Score=19.36 Aligned_cols=41 Identities=20% Similarity=0.342 Sum_probs=28.8
Q ss_pred hhHHHHHHHHHHHhhCCCceeEEEEeCCeEEeceeeeecccCHHHHHhhcCC
Q psy12678 18 DFQTSILSSFRHLRDEEDFVDVTLACDGCSFTAHKVVLSACSPYFKTLLKSI 69 (80)
Q Consensus 18 ~~~~~~~~~l~~~~~~~~~~Dv~l~v~g~~~~~Hk~vLaa~S~~F~~~f~~~ 69 (80)
.|+..+.+..+.+|+...--|=.+...| ||-++|++++..+
T Consensus 179 rnSkyFVeaVk~aR~y~~~~D~LVIFAG-----------ACQS~yEall~AG 219 (283)
T TIGR02855 179 RHSKYFVETVREARKYVPSLDQLVIFAG-----------ACQSHFESLIRAG 219 (283)
T ss_pred hhhHHHHHHHHHHHhcCCCcccEEEEcc-----------hhHHHHHHHHHcC
Confidence 5777888999999997655453333332 6778999998665
Done!