Query psy1854
Match_columns 110
No_of_seqs 140 out of 1164
Neff 6.2
Searched_HMMs 46136
Date Fri Aug 16 17:59:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1854.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1854hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PHA02713 hypothetical protein; 99.5 2.6E-14 5.7E-19 119.6 3.8 57 50-106 3-60 (557)
2 KOG4441|consensus 99.4 6.5E-14 1.4E-18 117.9 2.9 61 45-105 9-69 (571)
3 PHA02790 Kelch-like protein; P 99.2 1.6E-11 3.5E-16 101.0 3.5 46 60-106 10-55 (480)
4 PF00651 BTB: BTB/POZ domain; 99.1 4.4E-11 9.6E-16 78.7 1.9 43 63-105 1-44 (111)
5 PHA03098 kelch-like protein; P 98.9 4.1E-10 9E-15 92.6 1.9 38 69-106 6-45 (534)
6 KOG4350|consensus 98.8 9.4E-10 2E-14 90.5 1.3 51 56-106 28-78 (620)
7 smart00225 BTB Broad-Complex, 98.5 5.4E-08 1.2E-12 60.1 1.6 34 74-107 1-34 (90)
8 KOG2075|consensus 97.9 7E-06 1.5E-10 68.5 2.8 58 48-105 90-152 (521)
9 KOG0783|consensus 97.7 5.3E-05 1.1E-09 67.2 4.3 45 59-103 541-589 (1267)
10 KOG4591|consensus 97.6 3.1E-05 6.7E-10 59.2 1.7 47 53-99 47-96 (280)
11 KOG0783|consensus 96.6 0.00092 2E-08 59.6 1.5 33 71-103 709-742 (1267)
12 KOG4682|consensus 96.6 0.0025 5.3E-08 52.9 3.6 43 62-105 59-101 (488)
13 KOG2838|consensus 95.1 0.0054 1.2E-07 49.0 -0.2 52 55-106 113-164 (401)
14 KOG2838|consensus 92.6 0.022 4.8E-07 45.5 -1.0 44 59-102 222-281 (401)
15 KOG3863|consensus 71.0 0.52 1.1E-05 40.8 -2.4 37 61-102 3-39 (604)
16 PF02214 BTB_2: BTB/POZ domain 63.7 2.4 5.2E-05 27.1 0.1 31 75-105 1-32 (94)
17 KOG0511|consensus 54.3 2.4 5.3E-05 35.5 -1.3 30 74-103 180-209 (516)
18 KOG0511|consensus 49.8 1.1 2.4E-05 37.5 -4.0 29 72-100 149-178 (516)
19 KOG1987|consensus 49.6 6.8 0.00015 29.9 0.5 25 81-105 109-133 (297)
20 KOG2716|consensus 47.1 17 0.00038 28.0 2.4 31 75-105 7-37 (230)
21 PF03931 Skp1_POZ: Skp1 family 35.9 37 0.00079 20.2 2.2 29 75-104 3-32 (62)
22 KOG3342|consensus 35.5 11 0.00024 27.8 -0.2 19 72-90 80-100 (180)
23 COG0350 Ada Methylated DNA-pro 25.4 33 0.00072 24.8 0.8 13 83-95 136-148 (168)
24 PF07977 FabA: FabA-like domai 25.1 97 0.0021 20.9 3.1 38 71-109 8-51 (138)
25 PF04343 DUF488: Protein of un 22.9 33 0.00072 23.0 0.4 19 75-93 101-120 (122)
No 1
>PHA02713 hypothetical protein; Provisional
Probab=99.47 E-value=2.6e-14 Score=119.61 Aligned_cols=57 Identities=28% Similarity=0.451 Sum_probs=53.0
Q ss_pred eecCCcHHHHHHHHHhhhcCCCcceEEEEeC-CeEEEeEEEeeccCCHHHHHhhCCCC
Q psy1854 50 LKWNNHCNTLLQVFGNLLKTETLVDCTIGAD-GQYLKAHKVVVSACSPYFQVSWDVVF 106 (110)
Q Consensus 50 ~~~~~h~~~~l~~l~~lr~~~~~~DV~l~v~-g~~f~aHk~VLAa~S~yFr~mf~~~p 106 (110)
+.+..|...+++.|++||+++.+|||+|.++ |++|+|||.||||+|+|||+||++++
T Consensus 3 ~~~~~h~~~~l~~l~~lr~~~~l~DV~L~v~~~~~f~~Hr~vLaa~S~YF~amF~~~~ 60 (557)
T PHA02713 3 IDDIKHNRRVVSNISNLLDDDILCDVIITIGDGEEIKAHKTILAAGSKYFRTLFTTPM 60 (557)
T ss_pred cchhhhhHHHHHHHHHHHhCCCCCCEEEEeCCCCEEeehHHHHhhcCHHHHHHhcCCc
Confidence 3456899999999999999999999999997 89999999999999999999999864
No 2
>KOG4441|consensus
Probab=99.42 E-value=6.5e-14 Score=117.91 Aligned_cols=61 Identities=30% Similarity=0.449 Sum_probs=57.0
Q ss_pred CceeEeecCCcHHHHHHHHHhhhcCCCcceEEEEeCCeEEEeEEEeeccCCHHHHHhhCCC
Q psy1854 45 DQQFRLKWNNHCNTLLQVFGNLLKTETLVDCTIGADGQYLKAHKVVVSACSPYFQVSWDVV 105 (110)
Q Consensus 45 ~~~~~~~~~~h~~~~l~~l~~lr~~~~~~DV~l~v~g~~f~aHk~VLAa~S~yFr~mf~~~ 105 (110)
.....+.+..|...+++.|+.+|+++.+|||+|.+++++|+|||+||||+|+|||+||++.
T Consensus 9 ~~~~~~~~~~h~~~~l~~l~~lr~~~~lcDv~L~v~~~~~~aHR~VLAa~S~YFraMFt~~ 69 (571)
T KOG4441|consen 9 NSTSEFTDPSHSKFLLQGLNELREEGLLCDVTLLVGDREFPAHRVVLAACSPYFRAMFTSG 69 (571)
T ss_pred ccccccccHHHHHHHHHHHHHHHHhCCCceEEEEECCeeechHHHHHHhccHHHHHHhcCC
Confidence 3556788889999999999999999999999999999999999999999999999999975
No 3
>PHA02790 Kelch-like protein; Provisional
Probab=99.17 E-value=1.6e-11 Score=101.00 Aligned_cols=46 Identities=15% Similarity=0.229 Sum_probs=39.5
Q ss_pred HHHHHhhhcCCCcceEEEEeCCeEEEeEEEeeccCCHHHHHhhCCCC
Q psy1854 60 LQVFGNLLKTETLVDCTIGADGQYLKAHKVVVSACSPYFQVSWDVVF 106 (110)
Q Consensus 60 l~~l~~lr~~~~~~DV~l~v~g~~f~aHk~VLAa~S~yFr~mf~~~p 106 (110)
.+.+-.+|.++.||||++++|+ +|+|||+||||+|+|||+||++++
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~-~~~~HR~VLAa~S~YFraMF~~~~ 55 (480)
T PHA02790 10 CKNILALSMTKKFKTIIEAIGG-NIIVNSTILKKLSPYFRTHLRQKY 55 (480)
T ss_pred hhhHHHHHhhhhhceEEEEcCc-EEeeehhhhhhcCHHHHHHhcCCc
Confidence 3455668999999998877655 899999999999999999999864
No 4
>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=99.08 E-value=4.4e-11 Score=78.73 Aligned_cols=43 Identities=28% Similarity=0.530 Sum_probs=37.8
Q ss_pred HHhhhcCCCcceEEEEeC-CeEEEeEEEeeccCCHHHHHhhCCC
Q psy1854 63 FGNLLKTETLVDCTIGAD-GQYLKAHKVVVSACSPYFQVSWDVV 105 (110)
Q Consensus 63 l~~lr~~~~~~DV~l~v~-g~~f~aHk~VLAa~S~yFr~mf~~~ 105 (110)
|+++++++.++|++|.++ |+.|+|||.||+++|+||++||.+.
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 578899999999999999 8999999999999999999999887
No 5
>PHA03098 kelch-like protein; Provisional
Probab=98.91 E-value=4.1e-10 Score=92.62 Aligned_cols=38 Identities=29% Similarity=0.507 Sum_probs=35.9
Q ss_pred CCCcceEEEEe--CCeEEEeEEEeeccCCHHHHHhhCCCC
Q psy1854 69 TETLVDCTIGA--DGQYLKAHKVVVSACSPYFQVSWDVVF 106 (110)
Q Consensus 69 ~~~~~DV~l~v--~g~~f~aHk~VLAa~S~yFr~mf~~~p 106 (110)
++.||||+|.+ +|++|+|||.|||++|+||++||++++
T Consensus 6 ~~~~~Dv~l~~~~~~~~~~~Hk~vLaa~S~yF~~mf~~~~ 45 (534)
T PHA03098 6 LQKFCDESIIIVNGGGIIKVHKIILSSSSEYFKKMFKNNF 45 (534)
T ss_pred cCCCCCEEEEEEcCCEEEEeHHHHHHhhhHHHHHHHhCCC
Confidence 78999999998 999999999999999999999998864
No 6
>KOG4350|consensus
Probab=98.83 E-value=9.4e-10 Score=90.48 Aligned_cols=51 Identities=27% Similarity=0.398 Sum_probs=46.0
Q ss_pred HHHHHHHHHhhhcCCCcceEEEEeCCeEEEeEEEeeccCCHHHHHhhCCCC
Q psy1854 56 CNTLLQVFGNLLKTETLVDCTIGADGQYLKAHKVVVSACSPYFQVSWDVVF 106 (110)
Q Consensus 56 ~~~~l~~l~~lr~~~~~~DV~l~v~g~~f~aHk~VLAa~S~yFr~mf~~~p 106 (110)
...+.+.+..+..+.+++||++++++++|||||+|||++|.|||+|+-+.+
T Consensus 28 ~~~fS~~~~~l~~~e~y~DVtfvve~~rfpAHRvILAaRs~yFRAlLYgGm 78 (620)
T KOG4350|consen 28 SNNFSQSFDELFTSEDYSDVTFVVEDTRFPAHRVILAARSSYFRALLYGGM 78 (620)
T ss_pred ccchhHHHHHHhhcCcccceEEEEeccccchhhhhHHHHHHHHHHHHhhhh
Confidence 445577888999999999999999999999999999999999999997754
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=98.49 E-value=5.4e-08 Score=60.13 Aligned_cols=34 Identities=44% Similarity=0.747 Sum_probs=31.5
Q ss_pred eEEEEeCCeEEEeEEEeeccCCHHHHHhhCCCCc
Q psy1854 74 DCTIGADGQYLKAHKVVVSACSPYFQVSWDVVFC 107 (110)
Q Consensus 74 DV~l~v~g~~f~aHk~VLAa~S~yFr~mf~~~p~ 107 (110)
|+++.++|+.|++||.+|++.|+||++||.+.+.
T Consensus 1 dv~i~v~~~~~~~h~~iL~~~s~~f~~~~~~~~~ 34 (90)
T smart00225 1 DVTLVVGGKKFKAHKAVLAACSPYFKALFSGDFK 34 (90)
T ss_pred CeEEEECCEEEehHHHHHhhcCHHHHHHHcCCCc
Confidence 7889999999999999999999999999998653
No 8
>KOG2075|consensus
Probab=97.91 E-value=7e-06 Score=68.50 Aligned_cols=58 Identities=22% Similarity=0.237 Sum_probs=52.0
Q ss_pred eEeecCCcHHHHHHHHHhhhcCCCcceEEEEeCC-----eEEEeEEEeeccCCHHHHHhhCCC
Q psy1854 48 FRLKWNNHCNTLLQVFGNLLKTETLVDCTIGADG-----QYLKAHKVVVSACSPYFQVSWDVV 105 (110)
Q Consensus 48 ~~~~~~~h~~~~l~~l~~lr~~~~~~DV~l~v~g-----~~f~aHk~VLAa~S~yFr~mf~~~ 105 (110)
-.+.|..-...+......+++++..+|+.+++|+ ++|||||.|||.+|..|.+||.+.
T Consensus 90 ~~~nwq~~~~t~~er~~~l~~n~~~adv~fivg~~~~~~q~~paHk~vla~gS~VFdaMf~g~ 152 (521)
T KOG2075|consen 90 GIPNWQAQKETMRERQAALFNNELLADVHFIVGEEDGGSQRIPAHKLVLADGSDVFDAMFYGG 152 (521)
T ss_pred cCcccccchhhHHHhhHhhccCcccceeEEEeccCCCcccccchhhhhhhcchHHHHHHhccC
Confidence 3566777888899999999999999999999973 789999999999999999999875
No 9
>KOG0783|consensus
Probab=97.65 E-value=5.3e-05 Score=67.17 Aligned_cols=45 Identities=22% Similarity=0.307 Sum_probs=37.6
Q ss_pred HHHHHHhhhc----CCCcceEEEEeCCeEEEeEEEeeccCCHHHHHhhC
Q psy1854 59 LLQVFGNLLK----TETLVDCTIGADGQYLKAHKVVVSACSPYFQVSWD 103 (110)
Q Consensus 59 ~l~~l~~lr~----~~~~~DV~l~v~g~~f~aHk~VLAa~S~yFr~mf~ 103 (110)
+.+.+..|.. .+.+.|||+.||++.|+|||.||+++|++||.+|-
T Consensus 541 fe~sf~kLl~e~~~~ds~hDVtf~vg~~~F~aHKfIl~~rs~flrkL~l 589 (1267)
T KOG0783|consen 541 FEGSFPKLLSEENYKDSFHDVTFYVGTSMFHAHKFILCARSSFLRKLLL 589 (1267)
T ss_pred chhhhHHHhhccccccccceEEEEecCeecccceEEEEeccHHHHHHHH
Confidence 4555666644 45778899999999999999999999999999983
No 10
>KOG4591|consensus
Probab=97.59 E-value=3.1e-05 Score=59.17 Aligned_cols=47 Identities=28% Similarity=0.472 Sum_probs=43.0
Q ss_pred CCcHHHHHHHHHhhhcCCCcceEEEEeCC---eEEEeEEEeeccCCHHHH
Q psy1854 53 NNHCNTLLQVFGNLLKTETLVDCTIGADG---QYLKAHKVVVSACSPYFQ 99 (110)
Q Consensus 53 ~~h~~~~l~~l~~lr~~~~~~DV~l~v~g---~~f~aHk~VLAa~S~yFr 99 (110)
.++++.++.....+.++.+|+|+++.++| +.+||||.||||+|.++.
T Consensus 47 dSF~SRLLaitadL~Ek~qfSDlk~K~~gns~k~i~AHKfVLAARsD~Wk 96 (280)
T KOG4591|consen 47 DSFISRLLAITADLLEKEQFSDLKFKFAGNSDKHIPAHKFVLAARSDFWK 96 (280)
T ss_pred hhHHHHHHHHHHHHhhcccccceeEEecCCccccCchhhhhhhhhcchhh
Confidence 46888999999999999999999999985 779999999999999986
No 11
>KOG0783|consensus
Probab=96.59 E-value=0.00092 Score=59.59 Aligned_cols=33 Identities=39% Similarity=0.560 Sum_probs=27.3
Q ss_pred CcceEEEEe-CCeEEEeEEEeeccCCHHHHHhhC
Q psy1854 71 TLVDCTIGA-DGQYLKAHKVVVSACSPYFQVSWD 103 (110)
Q Consensus 71 ~~~DV~l~v-~g~~f~aHk~VLAa~S~yFr~mf~ 103 (110)
..-|+.|.+ +|++|+|||.+|+|+++||..||.
T Consensus 709 e~~d~~i~~KDGkvl~aHkc~L~aRlEYF~smf~ 742 (1267)
T KOG0783|consen 709 ETMDTVIKLKDGKVLKAHKCFLSARLEYFSSMFQ 742 (1267)
T ss_pred cceeEEEEecCCcCcccceeEeeeHHHHHHHHHH
Confidence 333555555 889999999999999999999995
No 12
>KOG4682|consensus
Probab=96.56 E-value=0.0025 Score=52.87 Aligned_cols=43 Identities=23% Similarity=0.297 Sum_probs=38.8
Q ss_pred HHHhhhcCCCcceEEEEeCCeEEEeEEEeeccCCHHHHHhhCCC
Q psy1854 62 VFGNLLKTETLVDCTIGADGQYLKAHKVVVSACSPYFQVSWDVV 105 (110)
Q Consensus 62 ~l~~lr~~~~~~DV~l~v~g~~f~aHk~VLAa~S~yFr~mf~~~ 105 (110)
.++.++.++.-+||.+.+-|++|+.||.-|.. |+||.+||+|.
T Consensus 59 iyq~lf~q~enSDv~l~alg~eWrlHk~yL~Q-S~yf~smf~Gt 101 (488)
T KOG4682|consen 59 IYQNLFLQGENSDVILEALGFEWRLHKPYLFQ-SEYFKSMFSGT 101 (488)
T ss_pred HHHHHHhcCCCcceehhhccceeeeeeeeeec-cHHHHHHhccc
Confidence 35677889999999999999999999999986 88999999875
No 13
>KOG2838|consensus
Probab=95.10 E-value=0.0054 Score=48.98 Aligned_cols=52 Identities=19% Similarity=0.271 Sum_probs=44.1
Q ss_pred cHHHHHHHHHhhhcCCCcceEEEEeCCeEEEeEEEeeccCCHHHHHhhCCCC
Q psy1854 55 HCNTLLQVFGNLLKTETLVDCTIGADGQYLKAHKVVVSACSPYFQVSWDVVF 106 (110)
Q Consensus 55 h~~~~l~~l~~lr~~~~~~DV~l~v~g~~f~aHk~VLAa~S~yFr~mf~~~p 106 (110)
....+++.+...++.....|+-|+....-|||||.+||+++|+|+.+.++.|
T Consensus 113 ea~sf~kD~ad~ye~k~c~dldiiFkeTcfpahRA~laaRCpffK~l~nsd~ 164 (401)
T KOG2838|consen 113 EANSFLKDFADGYERKVCGDLDIIFKETCFPAHRAFLAARCPFFKILANSDE 164 (401)
T ss_pred chhHHHHHHhhhhheeeeccceeeeeeccchHHHHHHHhhCcchhhhccCCC
Confidence 3455677777777778888999999999999999999999999998887765
No 14
>KOG2838|consensus
Probab=92.60 E-value=0.022 Score=45.55 Aligned_cols=44 Identities=30% Similarity=0.363 Sum_probs=31.7
Q ss_pred HHHHHHhhhcCCCcceEEEE--eCC--------------eEEEeEEEeeccCCHHHHHhh
Q psy1854 59 LLQVFGNLLKTETLVDCTIG--ADG--------------QYLKAHKVVVSACSPYFQVSW 102 (110)
Q Consensus 59 ~l~~l~~lr~~~~~~DV~l~--v~g--------------~~f~aHk~VLAa~S~yFr~mf 102 (110)
+-..+..|+++...-|++|+ ++| .+++||+.|.|++|++||.++
T Consensus 222 Ld~Dmkglfd~~c~~d~li~~ssD~elveafggeeNc~deeikahkai~aaRS~ffRnLL 281 (401)
T KOG2838|consen 222 LDEDMKGLFDQDCKHDDLIIESSDGELVEAFGGEENCEDEEIKAHKAIAAARSKFFRNLL 281 (401)
T ss_pred hhHHHHHHHHhhcccCcEEEEeccchhhhhcCCcccchhHHHHHHHHHHHhhhHHHHHHH
Confidence 33445566666666665554 233 368999999999999999987
No 15
>KOG3863|consensus
Probab=71.00 E-value=0.52 Score=40.85 Aligned_cols=37 Identities=30% Similarity=0.458 Sum_probs=32.1
Q ss_pred HHHHhhhcCCCcceEEEEeCCeEEEeEEEeeccCCHHHHHhh
Q psy1854 61 QVFGNLLKTETLVDCTIGADGQYLKAHKVVVSACSPYFQVSW 102 (110)
Q Consensus 61 ~~l~~lr~~~~~~DV~l~v~g~~f~aHk~VLAa~S~yFr~mf 102 (110)
..++..|+....||+++.+.++.|.+|+ +|.||..-.
T Consensus 3 ~~~~~qr~~~~~~~~~~~~~~~~f~~~~-----~~e~~~~~~ 39 (604)
T KOG3863|consen 3 LSLNDQRKKDVLCDVTAFVERQGFRAHR-----CSEYFTSRI 39 (604)
T ss_pred ccccccccccccchhHHHHhccccccee-----ccchhhhhh
Confidence 4567789999999999999999999999 899996544
No 16
>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=63.67 E-value=2.4 Score=27.06 Aligned_cols=31 Identities=3% Similarity=0.109 Sum_probs=26.5
Q ss_pred EEEEeCCeEEEeEEEeec-cCCHHHHHhhCCC
Q psy1854 75 CTIGADGQYLKAHKVVVS-ACSPYFQVSWDVV 105 (110)
Q Consensus 75 V~l~v~g~~f~aHk~VLA-a~S~yFr~mf~~~ 105 (110)
|.|-|||+.|..-+..|. ...++|.+||.+.
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 678999999999999998 6678998888753
No 17
>KOG0511|consensus
Probab=54.33 E-value=2.4 Score=35.47 Aligned_cols=30 Identities=30% Similarity=0.548 Sum_probs=20.0
Q ss_pred eEEEEeCCeEEEeEEEeeccCCHHHHHhhC
Q psy1854 74 DCTIGADGQYLKAHKVVVSACSPYFQVSWD 103 (110)
Q Consensus 74 DV~l~v~g~~f~aHk~VLAa~S~yFr~mf~ 103 (110)
||.+-+.|++|-+||+++.+.|++|+-+|.
T Consensus 180 ~v~~~~~~heI~~~~v~~~~f~~flk~lyl 209 (516)
T KOG0511|consen 180 DVMFYVQGHEIEAHRVILSAFSPFLKQLYL 209 (516)
T ss_pred hhhhccccCchhhhhhhHhhhhHHHHHHHH
Confidence 555666677777777777777777766553
No 18
>KOG0511|consensus
Probab=49.80 E-value=1.1 Score=37.49 Aligned_cols=29 Identities=24% Similarity=0.281 Sum_probs=24.2
Q ss_pred cceEEEEe-CCeEEEeEEEeeccCCHHHHH
Q psy1854 72 LVDCTIGA-DGQYLKAHKVVVSACSPYFQV 100 (110)
Q Consensus 72 ~~DV~l~v-~g~~f~aHk~VLAa~S~yFr~ 100 (110)
..|+++.. +|+.|.|||..|+++|++|..
T Consensus 149 ~~di~f~~q~g~~f~ahkfll~arSs~~~~ 178 (516)
T KOG0511|consen 149 CHDIDFLQQEGANFDAHKFLLEARSSNYFP 178 (516)
T ss_pred ccchHHHhhccccccHHHHHHHhhhcccCc
Confidence 45777765 788999999999999998854
No 19
>KOG1987|consensus
Probab=49.61 E-value=6.8 Score=29.89 Aligned_cols=25 Identities=32% Similarity=0.337 Sum_probs=22.1
Q ss_pred CeEEEeEEEeeccCCHHHHHhhCCC
Q psy1854 81 GQYLKAHKVVVSACSPYFQVSWDVV 105 (110)
Q Consensus 81 g~~f~aHk~VLAa~S~yFr~mf~~~ 105 (110)
+..+.+|++++++.|+.|++|+...
T Consensus 109 ~g~~~~~~~~~~a~~~V~~~~~~~d 133 (297)
T KOG1987|consen 109 NGFLVAHKLVLVARSEVFEAMGKSD 133 (297)
T ss_pred CcEEEcCceEEEeeecceeeecccc
Confidence 5669999999999999999998654
No 20
>KOG2716|consensus
Probab=47.14 E-value=17 Score=27.98 Aligned_cols=31 Identities=13% Similarity=0.319 Sum_probs=27.7
Q ss_pred EEEEeCCeEEEeEEEeeccCCHHHHHhhCCC
Q psy1854 75 CTIGADGQYLKAHKVVVSACSPYFQVSWDVV 105 (110)
Q Consensus 75 V~l~v~g~~f~aHk~VLAa~S~yFr~mf~~~ 105 (110)
|.|-|||..|.-.+.-|.--..||++||.+.
T Consensus 7 vkLnvGG~~F~Tsk~TLtk~dg~fk~m~e~~ 37 (230)
T KOG2716|consen 7 VKLNVGGTIFKTSKSTLTKFDGFFKTMLETD 37 (230)
T ss_pred EEEecCCeEEEeehhhhhhhhhHHHHHhhcC
Confidence 4578999999999999999999999999764
No 21
>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=35.88 E-value=37 Score=20.22 Aligned_cols=29 Identities=14% Similarity=0.134 Sum_probs=22.3
Q ss_pred EEEEe-CCeEEEeEEEeeccCCHHHHHhhCC
Q psy1854 75 CTIGA-DGQYLKAHKVVVSACSPYFQVSWDV 104 (110)
Q Consensus 75 V~l~v-~g~~f~aHk~VLAa~S~yFr~mf~~ 104 (110)
|+|+. +|+.|.+-+.+.. .|..+++||.+
T Consensus 3 v~L~SsDg~~f~V~~~~a~-~S~~i~~ml~~ 32 (62)
T PF03931_consen 3 VKLVSSDGQEFEVSREAAK-QSKTIKNMLED 32 (62)
T ss_dssp EEEEETTSEEEEEEHHHHT-TSHHHHHHHHC
T ss_pred EEEEcCCCCEEEeeHHHHH-HhHHHHHHHhh
Confidence 55655 7888988887655 78999999864
No 22
>KOG3342|consensus
Probab=35.50 E-value=11 Score=27.79 Aligned_cols=19 Identities=21% Similarity=0.487 Sum_probs=14.1
Q ss_pred cceEE-EEeCCeEEE-eEEEe
Q psy1854 72 LVDCT-IGADGQYLK-AHKVV 90 (110)
Q Consensus 72 ~~DV~-l~v~g~~f~-aHk~V 90 (110)
--|++ +.++|+++| +||+|
T Consensus 80 vGdivVf~vegR~IPiVHRvi 100 (180)
T KOG3342|consen 80 VGDIVVFKVEGREIPIVHRVI 100 (180)
T ss_pred eccEEEEEECCccCchhHHHH
Confidence 34544 478999999 78876
No 23
>COG0350 Ada Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=25.39 E-value=33 Score=24.82 Aligned_cols=13 Identities=15% Similarity=0.340 Sum_probs=10.2
Q ss_pred EEEeEEEeeccCC
Q psy1854 83 YLKAHKVVVSACS 95 (110)
Q Consensus 83 ~f~aHk~VLAa~S 95 (110)
.|||||+|=+..+
T Consensus 136 iIPCHRVig~~G~ 148 (168)
T COG0350 136 IIPCHRVIGADGD 148 (168)
T ss_pred EecCeEeEcCCCC
Confidence 3999999976654
No 24
>PF07977 FabA: FabA-like domain; InterPro: IPR013114 Fatty acids biosynthesis occurs by two distinct pathways: in fungi, mammals and mycobacteria, type I or associative fatty-acid biosynthesis (type I FAS) is accomplished by multifunctional proteins in which distinct domains catalyse specific reactions; in plants and most bacteria, type II or dissociative fatty-acid biosynthesis (type II FAS) is accomplished by distinct enzymes []. Both FabZ and FabA catalyse the dehydration of beta-hydroxyacyl acyl carrier protein (ACP) to trans 2-enoyl ACP. However, FabZ and FabA display subtle differences in substrate specificities, whereby FabA is most effective on acyl ACPs of 9-11 carbon atoms in length, while FabZ is less specific. Unlike FabA, FabZ does not function as an isomerase and cannot initiate unsaturated fatty acid biosynthesis. However, only FabZ can act during the elongation of unsaturated fatty acid chains. This enzyme domain has a HotDog fold.; PDB: 3D6X_F 2GLV_J 2GLM_E 2GLP_E 2GLL_C 1U1Z_F 3ESI_A 3AZB_T 3AZA_M 3AZ9_U ....
Probab=25.08 E-value=97 Score=20.86 Aligned_cols=38 Identities=29% Similarity=0.326 Sum_probs=23.6
Q ss_pred CcceEEEEeC--CeE----EEeEEEeeccCCHHHHHhhCCCCccc
Q psy1854 71 TLVDCTIGAD--GQY----LKAHKVVVSACSPYFQVSWDVVFCML 109 (110)
Q Consensus 71 ~~~DV~l~v~--g~~----f~aHk~VLAa~S~yFr~mf~~~p~~~ 109 (110)
.+-|=++.++ |+. +.|.+.|=. ..+||+..|.++|++-
T Consensus 8 llvD~v~~v~~~g~~~~g~~~a~~~v~~-~~~~f~gHFp~~Pv~P 51 (138)
T PF07977_consen 8 LLVDRVLEVDPPGGSHGGRIVARKNVTP-DEPFFDGHFPGDPVMP 51 (138)
T ss_dssp ---SEEEEEETTTTETTEEEEEEEEE-T-TSGGGGCSTTTS--B-
T ss_pred EEEEEEEEEEcCCCeEEEEEEEEEEeCC-CCCEEEcCCCCCCCCC
Confidence 3456555554 666 888887754 4899999999999863
No 25
>PF04343 DUF488: Protein of unknown function, DUF488; InterPro: IPR007438 This family includes several proteins of uncharacterised function.
Probab=22.87 E-value=33 Score=22.97 Aligned_cols=19 Identities=5% Similarity=0.212 Sum_probs=14.6
Q ss_pred EEEEe-CCeEEEeEEEeecc
Q psy1854 75 CTIGA-DGQYLKAHKVVVSA 93 (110)
Q Consensus 75 V~l~v-~g~~f~aHk~VLAa 93 (110)
|+|.+ +.....|||.||+.
T Consensus 101 v~LlC~e~dp~~CHR~iLa~ 120 (122)
T PF04343_consen 101 VALLCAEKDPERCHRRILAE 120 (122)
T ss_pred eEEEEEecChhcCcHHHHHH
Confidence 78877 55567899999874
Done!