Query psy1485
Match_columns 252
No_of_seqs 258 out of 1002
Neff 5.0
Searched_HMMs 46136
Date Fri Aug 16 22:20:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1485.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1485hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0695|consensus 100.0 2.9E-32 6.2E-37 256.3 0.4 138 43-193 40-185 (593)
2 KOG0696|consensus 99.9 3.1E-24 6.7E-29 206.0 0.8 99 125-229 33-131 (683)
3 KOG0694|consensus 99.8 3.5E-20 7.5E-25 185.0 1.6 115 125-241 146-264 (694)
4 KOG4236|consensus 99.6 2.1E-16 4.6E-21 155.7 0.8 125 70-195 194-324 (888)
5 KOG4236|consensus 99.6 1.6E-16 3.5E-21 156.5 -2.4 109 134-243 142-303 (888)
6 PF00130 C1_1: Phorbol esters/ 99.4 2E-13 4.3E-18 95.1 4.0 52 138-190 1-52 (53)
7 cd00029 C1 Protein kinase C co 99.3 2.7E-12 5.9E-17 87.4 2.5 50 138-188 1-50 (50)
8 smart00109 C1 Protein kinase C 99.1 2.2E-11 4.8E-16 82.1 2.3 49 138-188 1-49 (49)
9 cd06404 PB1_aPKC PB1 domain is 99.1 1.2E-11 2.5E-16 95.4 0.9 52 44-106 26-82 (83)
10 KOG0696|consensus 98.7 2.1E-09 4.5E-14 104.6 -0.3 72 116-193 94-165 (683)
11 KOG1011|consensus 98.6 1.1E-09 2.4E-14 110.2 -4.5 87 134-221 169-268 (1283)
12 KOG4239|consensus 98.5 4.1E-08 8.9E-13 91.6 1.7 112 131-246 45-171 (348)
13 KOG0694|consensus 97.9 2.9E-06 6.3E-11 86.2 -0.2 63 132-195 225-287 (694)
14 KOG2996|consensus 97.4 3.9E-05 8.4E-10 77.2 -0.3 54 134-189 520-573 (865)
15 KOG3564|consensus 97.2 5.8E-05 1.2E-09 74.5 -1.0 99 135-242 284-384 (604)
16 KOG0193|consensus 96.9 0.0005 1.1E-08 69.8 2.1 54 135-192 176-229 (678)
17 cd06402 PB1_p62 The PB1 domain 96.6 0.00063 1.4E-08 53.1 0.2 39 43-86 32-75 (87)
18 cd06396 PB1_NBR1 The PB1 domai 95.8 0.0018 4E-08 50.0 -0.7 41 44-91 28-72 (81)
19 cd06408 PB1_NoxR The PB1 domai 95.5 0.004 8.6E-08 48.6 0.3 37 43-86 27-67 (86)
20 PF03107 C1_2: C1 domain; Int 94.8 0.018 4E-07 36.1 1.8 29 150-181 2-30 (30)
21 KOG1453|consensus 94.4 0.0082 1.8E-07 63.8 -1.0 58 132-194 539-598 (918)
22 PF07649 C1_3: C1-like domain; 93.0 0.031 6.8E-07 34.8 0.2 29 150-181 2-30 (30)
23 KOG1169|consensus 92.7 0.054 1.2E-06 55.5 1.5 60 132-191 93-154 (634)
24 cd06407 PB1_NLP A PB1 domain i 89.9 0.086 1.9E-06 40.5 -0.2 37 44-87 26-69 (82)
25 PF00130 C1_1: Phorbol esters/ 86.2 0.38 8.3E-06 32.9 1.2 31 209-239 1-32 (53)
26 KOG3532|consensus 84.9 0.19 4E-06 52.4 -1.3 48 135-185 744-791 (1051)
27 KOG3532|consensus 81.6 0.22 4.8E-06 51.8 -2.2 50 134-186 69-118 (1051)
28 smart00109 C1 Protein kinase C 77.5 1.6 3.4E-05 28.6 1.7 31 209-239 1-31 (49)
29 PF08746 zf-RING-like: RING-li 75.9 0.81 1.8E-05 31.0 -0.1 28 151-183 1-30 (43)
30 PF13901 DUF4206: Domain of un 75.5 2.5 5.3E-05 37.4 2.7 40 148-190 152-194 (202)
31 KOG0612|consensus 75.1 0.53 1.1E-05 51.5 -1.8 55 134-190 1206-1260(1317)
32 cd00029 C1 Protein kinase C co 74.8 1.6 3.4E-05 29.0 1.0 22 209-230 1-22 (50)
33 PF14446 Prok-RING_1: Prokaryo 72.4 1.8 4E-05 31.1 1.0 35 148-184 5-39 (54)
34 PF00628 PHD: PHD-finger; Int 65.1 5 0.00011 27.0 1.9 31 150-183 1-31 (51)
35 PF13831 PHD_2: PHD-finger; PD 56.5 3.2 6.9E-05 27.1 -0.3 20 165-184 3-22 (36)
36 PF02318 FYVE_2: FYVE-type zin 46.0 15 0.00033 29.5 2.1 36 147-183 53-88 (118)
37 cd02340 ZZ_NBR1_like Zinc fing 43.0 17 0.00037 24.5 1.6 30 150-183 2-32 (43)
38 KOG3362|consensus 40.7 10 0.00022 32.7 0.2 37 138-181 106-145 (156)
39 KOG0955|consensus 39.4 23 0.00049 39.0 2.7 39 145-184 216-254 (1051)
40 COG1571 Predicted DNA-binding 37.7 21 0.00047 35.4 2.0 40 137-178 340-379 (421)
41 PF10367 Vps39_2: Vacuolar sor 37.4 25 0.00054 26.6 2.0 33 146-182 76-108 (109)
42 smart00249 PHD PHD zinc finger 33.0 32 0.00068 21.6 1.6 31 150-183 1-31 (47)
43 smart00661 RPOL9 RNA polymeras 32.9 32 0.0007 23.1 1.8 27 150-176 2-30 (52)
44 KOG1170|consensus 32.8 26 0.00056 37.8 1.8 60 133-192 103-162 (1099)
45 KOG1170|consensus 31.6 20 0.00044 38.5 0.8 67 172-241 68-137 (1099)
46 PF07282 OrfB_Zn_ribbon: Putat 28.5 45 0.00097 23.8 2.0 32 147-178 27-58 (69)
47 KOG0612|consensus 28.5 8.3 0.00018 42.7 -2.7 54 136-196 892-945 (1317)
48 PF14471 DUF4428: Domain of un 28.5 19 0.00042 25.2 0.0 21 150-172 1-26 (51)
49 PF13824 zf-Mss51: Zinc-finger 27.8 43 0.00093 24.2 1.7 25 150-177 1-25 (55)
50 KOG4323|consensus 26.4 23 0.00051 35.5 0.2 35 151-186 171-205 (464)
51 KOG2807|consensus 25.4 56 0.0012 31.7 2.5 78 148-238 263-348 (378)
52 PF09297 zf-NADH-PPase: NADH p 25.0 42 0.00091 20.9 1.1 27 148-174 3-29 (32)
53 PF14569 zf-UDP: Zinc-binding 24.2 31 0.00066 26.8 0.4 35 147-183 8-45 (80)
54 TIGR01384 TFS_arch transcripti 24.1 49 0.0011 25.6 1.6 27 150-178 2-28 (104)
55 PF04571 Lipin_N: lipin, N-ter 23.7 42 0.00091 27.5 1.2 21 226-246 30-50 (110)
56 cd02249 ZZ Zinc finger, ZZ typ 23.6 48 0.001 22.2 1.3 29 150-182 2-31 (46)
57 KOG1169|consensus 22.7 18 0.00039 37.6 -1.4 84 136-225 32-115 (634)
58 PF02150 RNA_POL_M_15KD: RNA p 22.6 40 0.00087 21.8 0.7 28 149-176 2-30 (35)
59 PRK00432 30S ribosomal protein 22.4 55 0.0012 22.8 1.4 27 148-176 20-47 (50)
60 PF01363 FYVE: FYVE zinc finge 21.7 57 0.0012 23.2 1.4 33 148-182 9-41 (69)
61 KOG1829|consensus 20.6 47 0.001 34.3 1.0 64 148-218 325-395 (580)
62 PF07754 DUF1610: Domain of un 20.5 75 0.0016 19.2 1.5 23 151-174 1-24 (24)
No 1
>KOG0695|consensus
Probab=99.97 E-value=2.9e-32 Score=256.29 Aligned_cols=138 Identities=25% Similarity=0.420 Sum_probs=128.0
Q ss_pred hHHHHHHHh-----HhhhhhhccCCCCCCCCCCCCCcccchhhhhccccCCccccccccccceeeeeccCCcccccccCC
Q psy1485 43 RVDLIRSAC-----QVYLMVFVLNDHCSSVGPLREGSARSSLSEASGVSGASTRTYFNEASTLVLETLENGVKKHYLIPL 117 (252)
Q Consensus 43 ~~~~~~~~~-----~~~~~~~~~~d~~~~~~~~~~~s~~~~Lseas~~s~~~~~~~~~~~s~L~le~~~~~~~~~~~vp~ 117 (252)
-.+|+|+|| |++||+||||| |+|.++|+++||+||.++.. +.++++|+||+++ +.|+.|.+||
T Consensus 40 ~~~~vrd~c~~h~~q~~t~kwidee-----gdp~tv~sqmeleea~r~~~------~~~d~el~ihvf~-~~pe~pglpc 107 (593)
T KOG0695|consen 40 LCEEVRDMCRLHQQQPLTLKWIDEE-----GDPCTVSSQMELEEAFRLAR------QCRDEELIIHVFP-STPEQPGLPC 107 (593)
T ss_pred HHHHHHHHHHHhhcCCceeEeecCC-----CCcceechhhhHHHHHHHHH------hccccceEEEEcc-CCCCCCCCCC
Confidence 358999999 78999999955 55557999999999999998 8899999999997 5999999999
Q ss_pred cccccc---cccccCcceeecCCCeEEEEecCCCCcCCCCCCcccccccccccccCCccccccccccccccccCCCCcc
Q psy1485 118 SLAQKN---RWSKKGTKLHIFNDHTFIAKHLPGGTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRTETTCPHSTI 193 (252)
Q Consensus 118 ~~~~r~---~~~~k~~klh~~~gH~F~a~~f~~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V~~~C~~~s~ 193 (252)
++++|+ +++++|+|++.++||.|+++.|.+..+|..|.+.|| |+++|||+|.+|++.+|||||..|+..|+....
T Consensus 108 ~gedksiyrrgarrwrkly~~ngh~fqakr~nrr~~c~ic~d~iw-glgrqgyrcinckl~vhkkch~~v~~~cg~~~~ 185 (593)
T KOG0695|consen 108 PGEDKSIYRRGARRWRKLYRANGHLFQAKRFNRRAYCGICSDRIW-GLGRQGYRCINCKLLVHKKCHGLVPLTCGKHMD 185 (593)
T ss_pred CCCcchHHHhHHHHHHHHHhhcCcchhhhhhccceeeeechhhhh-hcccccceeecceeehhhhhcccccchhhhhcc
Confidence 999998 678899999999999999999999999999999997 999999999999999999999999999987654
No 2
>KOG0696|consensus
Probab=99.88 E-value=3.1e-24 Score=206.02 Aligned_cols=99 Identities=25% Similarity=0.469 Sum_probs=89.7
Q ss_pred ccccCcceeecCCCeEEEEecCCCCcCCCCCCcccccccccccccCCccccccccccccccccCCCCcccccccchhhhc
Q psy1485 125 WSKKGTKLHIFNDHTFIAKHLPGGTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRTETTCPHSTIQHLELNKDRIE 204 (252)
Q Consensus 125 ~~~k~~klh~~~gH~F~a~~f~~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V~~~C~~~s~~~~el~~~r~~ 204 (252)
++-|.+.+|++++|.|.+.+|++||||++|.+||| |+++||+||+.|.+++||+||..|+..|++... +.+...
T Consensus 33 GAlrqKnvhevk~HkF~aRFFKqPTfCsHCkDFiw-GfgKQGfQCqvC~fvvHkrChefVtF~CPGadk-----g~dtDd 106 (683)
T KOG0696|consen 33 GALRQKNVHEVKSHKFIARFFKQPTFCSHCKDFIW-GFGKQGFQCQVCCFVVHKRCHEFVTFSCPGADK-----GPDTDD 106 (683)
T ss_pred hhhhhcchhhhccceeeehhccCCchhhhhhhhee-ccccCceeeeEEeehhhhhhcceEEEECCCCCC-----CCCCCC
Confidence 33355789999999999999999999999999998 999999999999999999999999999999765 456667
Q ss_pred cccccccccCCcccccccccccccc
Q psy1485 205 LRQQNRWSKKGTKLHIFNDHTFIAK 229 (252)
Q Consensus 205 ir~PHrf~~~~y~sptFCdHCF~ak 229 (252)
++..|.|++++|.+|||||||+...
T Consensus 107 pr~kHkf~~~tYssPTFCDhCGsLL 131 (683)
T KOG0696|consen 107 PRSKHKFKIHTYSSPTFCDHCGSLL 131 (683)
T ss_pred cccccceeeeecCCCchhhhHHHHH
Confidence 8899999999999999999998643
No 3
>KOG0694|consensus
Probab=99.78 E-value=3.5e-20 Score=185.02 Aligned_cols=115 Identities=28% Similarity=0.388 Sum_probs=100.6
Q ss_pred ccccCcceeecCCCeEEEEecCCCCcCCCCCCcccccccccccccCCccccccccccccccccCCCCcccc-cc--cchh
Q psy1485 125 WSKKGTKLHIFNDHTFIAKHLPGGTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRTETTCPHSTIQH-LE--LNKD 201 (252)
Q Consensus 125 ~~~k~~klh~~~gH~F~a~~f~~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V~~~C~~~s~~~-~e--l~~~ 201 (252)
++.+..|+|++.||.|.++.+++|++|++|.+||| ||++|||||++|...|||+|+.++.+.|.....++ .+ ....
T Consensus 146 ga~~~~kVhei~gH~F~aT~l~Qpt~Cs~C~kFi~-gL~kqGyQCqvC~~vvHKkCh~kvv~~C~~~~~~n~e~q~~~~~ 224 (694)
T KOG0694|consen 146 GAISQSKVHEIDGHKFGATSLRQPTFCSWCQKFIW-GLRKQGYQCQVCWRVVHKKCHVKVVTLCDFLDNLNSEPQGFLFE 224 (694)
T ss_pred cccccceeEEeeCcEEEEeeccCcchhhhhhhhee-ccCCCceEEeeeeehHhhhhHHHHHHhccCcCccCcCCcccccc
Confidence 44466789999999999999999999999999997 99999999999999999999999999999877632 22 3455
Q ss_pred hhccccccccccCCcccccccccccc-ccccCCcccccCCc
Q psy1485 202 RIELRQQNRWSKKGTKLHIFNDHTFI-AKHLPGTLYTNSPF 241 (252)
Q Consensus 202 r~~ir~PHrf~~~~y~sptFCdHCF~-ak~L~g~~~~~~~~ 241 (252)
+++++||+|..++|.+||||+||+- ...++.++++++..
T Consensus 225 -~~~~~Phrf~~~~~q~ptFc~hCGs~L~r~~qqGlkCs~C 264 (694)
T KOG0694|consen 225 -FTFRNPHRFVKLNRQRPTFCDHCGSVLYRLRQQGLKCSTC 264 (694)
T ss_pred -ccccCCCcchhhhccCccHHHhcchhhhhhcccCeeehhh
Confidence 8999999999999999999999954 77778888887753
No 4
>KOG4236|consensus
Probab=99.59 E-value=2.1e-16 Score=155.67 Aligned_cols=125 Identities=29% Similarity=0.446 Sum_probs=91.3
Q ss_pred CCCCcccchhhhhccccCCcccccccccccee-----eeeccCCccc-ccccCCcccccccccccCcceeecCCCeEEEE
Q psy1485 70 LREGSARSSLSEASGVSGASTRTYFNEASTLV-----LETLENGVKK-HYLIPLSLAQKNRWSKKGTKLHIFNDHTFIAK 143 (252)
Q Consensus 70 ~~~~s~~~~Lseas~~s~~~~~~~~~~~s~L~-----le~~~~~~~~-~~~vp~~~~~r~~~~~k~~klh~~~gH~F~a~ 143 (252)
-+.++|+++|+.++-....|.|.-+...+.+- +.+.+-+.++ .+.....+.+|+.|..|..-.....+|+|+.+
T Consensus 194 NCsG~r~rr~sa~~l~~~~s~~l~~s~~~p~~p~~~~~pst~~~~~~~p~~~~~S~sgrpi~~ek~~~~rvkvPHTf~vH 273 (888)
T KOG4236|consen 194 NCSGVRKRRLSAVSLQPSRSNRLNLSPSSPLEPLLPARPSTELGGPREPSSAILSWSGRPIWMEKMLMSRVKVPHTFIVH 273 (888)
T ss_pred CCCcccccCCCCCCCCCCCccccccCCCCCCCccccCCCcccccCCCCCCcccccccCCCchhhhhhhhcccCCeeEEEe
Confidence 34599999999988433444443222222211 1111112232 24445668899999877654445589999999
Q ss_pred ecCCCCcCCCCCCcccccccccccccCCccccccccccccccccCCCCcccc
Q psy1485 144 HLPGGTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRTETTCPHSTIQH 195 (252)
Q Consensus 144 ~f~~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V~~~C~~~s~~~ 195 (252)
+|.+||.|.+|.+++ .||.+||+||+||+++|||||+.+|+.+|.+.....
T Consensus 274 SY~rpTVCq~CkkLL-kGL~rQGlqCkDCk~NcHkrCa~~v~~dClge~~~n 324 (888)
T KOG4236|consen 274 SYTRPTVCQYCKKLL-KGLFRQGLQCKDCKFNCHKRCAMKVPNDCLGEVTAN 324 (888)
T ss_pred eccCchHHHHHHHHH-HHHHhcCcccccCCcchhhhhhhhcccccccceeec
Confidence 999999999999998 599999999999999999999999999999876654
No 5
>KOG4236|consensus
Probab=99.56 E-value=1.6e-16 Score=156.54 Aligned_cols=109 Identities=18% Similarity=0.313 Sum_probs=84.8
Q ss_pred ecCCCeEEEEecCCCCcCCCCCCcccccccccccccCCccccccccccccccccCCCCccc--------c----------
Q psy1485 134 IFNDHTFIAKHLPGGTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRTETTCPHSTIQ--------H---------- 195 (252)
Q Consensus 134 ~~~gH~F~a~~f~~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V~~~C~~~s~~--------~---------- 195 (252)
.+.+|....++|+.||||++|++++| ||.+||++|..|+.+.||+|+.++++.|.+.... +
T Consensus 142 ~i~PH~l~vhSY~~PtFCD~CGEmL~-GLvrQGlKC~gCglNyHKRCa~kipNNCsG~r~rr~sa~~l~~~~s~~l~~s~ 220 (888)
T KOG4236|consen 142 QIRPHTLFVHSYKAPTFCDFCGEMLF-GLVRQGLKCEGCGLNYHKRCAFKIPNNCSGVRKRRLSAVSLQPSRSNRLNLSP 220 (888)
T ss_pred eeecceeeeecccCchHHHHHHHHHH-HHHHccccccCCCCcHhhhhhhcCCCCCCcccccCCCCCCCCCCCccccccCC
Confidence 56899999999999999999999997 9999999999999999999999999999652110 0
Q ss_pred -------------ccc------------------chhh---hccccccccccCCccccccccccc-cccccCCcccccCC
Q psy1485 196 -------------LEL------------------NKDR---IELRQQNRWSKKGTKLHIFNDHTF-IAKHLPGTLYTNSP 240 (252)
Q Consensus 196 -------------~el------------------~~~r---~~ir~PHrf~~~~y~sptFCdHCF-~ak~L~g~~~~~~~ 240 (252)
.++ ..+. ..+.+||.|.+|+|..||+|.+|- ..+.|..++++|-|
T Consensus 221 ~~p~~p~~~~~pst~~~~~~~p~~~~~S~sgrpi~~ek~~~~rvkvPHTf~vHSY~rpTVCq~CkkLLkGL~rQGlqCkD 300 (888)
T KOG4236|consen 221 SSPLEPLLPARPSTELGGPREPSSAILSWSGRPIWMEKMLMSRVKVPHTFIVHSYTRPTVCQYCKKLLKGLFRQGLQCKD 300 (888)
T ss_pred CCCCCccccCCCcccccCCCCCCcccccccCCCchhhhhhhhcccCCeeEEEeeccCchHHHHHHHHHHHHHhcCccccc
Confidence 000 0011 144589999999999999999994 24555556666666
Q ss_pred cee
Q psy1485 241 FYF 243 (252)
Q Consensus 241 ~~~ 243 (252)
--|
T Consensus 301 Ck~ 303 (888)
T KOG4236|consen 301 CKF 303 (888)
T ss_pred CCc
Confidence 444
No 6
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=99.40 E-value=2e-13 Score=95.12 Aligned_cols=52 Identities=37% Similarity=0.826 Sum_probs=47.1
Q ss_pred CeEEEEecCCCCcCCCCCCcccccccccccccCCccccccccccccccccCCC
Q psy1485 138 HTFIAKHLPGGTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRTETTCPH 190 (252)
Q Consensus 138 H~F~a~~f~~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V~~~C~~ 190 (252)
|.|+...|..|++|++|+++|| |+++|||+|.+|++.+|++|..+++..|+.
T Consensus 1 H~f~~~~~~~~~~C~~C~~~i~-g~~~~g~~C~~C~~~~H~~C~~~~~~~C~~ 52 (53)
T PF00130_consen 1 HHFVPTTFSKPTYCDVCGKFIW-GLGKQGYRCSWCGLVCHKKCLSKVPPSCGC 52 (53)
T ss_dssp -EEEEEESSSTEB-TTSSSBEC-SSSSCEEEETTTT-EEETTGGCTSSSBSST
T ss_pred CeEEEccCCCCCCCcccCcccC-CCCCCeEEECCCCChHhhhhhhhcCCCCCC
Confidence 8999999999999999999997 899999999999999999999999999874
No 7
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=99.25 E-value=2.7e-12 Score=87.40 Aligned_cols=50 Identities=40% Similarity=0.822 Sum_probs=47.5
Q ss_pred CeEEEEecCCCCcCCCCCCcccccccccccccCCccccccccccccccccC
Q psy1485 138 HTFIAKHLPGGTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRTETTC 188 (252)
Q Consensus 138 H~F~a~~f~~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V~~~C 188 (252)
|.|....+.++++|++|.+.|| |+.++||+|.+|++++|++|..+|+.+|
T Consensus 1 H~f~~~~~~~~~~C~~C~~~i~-~~~~~~~~C~~C~~~~H~~C~~~v~~~C 50 (50)
T cd00029 1 HRFVRKSFFKPTFCDVCRKSIW-GLFKQGLRCSWCKVKCHKKCADKVPPSC 50 (50)
T ss_pred CccEEeeCCCCCChhhcchhhh-ccccceeEcCCCCCchhhhhhccCCCCC
Confidence 8899999999999999999997 7789999999999999999999999877
No 8
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=99.13 E-value=2.2e-11 Score=82.11 Aligned_cols=49 Identities=35% Similarity=0.758 Sum_probs=45.5
Q ss_pred CeEEEEecCCCCcCCCCCCcccccccccccccCCccccccccccccccccC
Q psy1485 138 HTFIAKHLPGGTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRTETTC 188 (252)
Q Consensus 138 H~F~a~~f~~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V~~~C 188 (252)
|.|....+.++++|++|++.|| ++. +||+|.+|++.+|++|..+|+.+|
T Consensus 1 H~~~~~~~~~~~~C~~C~~~i~-~~~-~~~~C~~C~~~~H~~C~~~v~~~C 49 (49)
T smart00109 1 HHFVERTFKKPTKCCVCRKSIW-GSF-QGLRCSWCKVKCHKKCAEKVPQPC 49 (49)
T ss_pred CceEEeccCCCCCccccccccC-cCC-CCcCCCCCCchHHHHHHhhcCCCC
Confidence 7899999999999999999997 655 899999999999999999999877
No 9
>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells. PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi,
Probab=99.13 E-value=1.2e-11 Score=95.36 Aligned_cols=52 Identities=21% Similarity=0.333 Sum_probs=46.6
Q ss_pred HHHHHHHh-----HhhhhhhccCCCCCCCCCCCCCcccchhhhhccccCCccccccccccceeeeecc
Q psy1485 44 VDLIRSAC-----QVYLMVFVLNDHCSSVGPLREGSARSSLSEASGVSGASTRTYFNEASTLVLETLE 106 (252)
Q Consensus 44 ~~~~~~~~-----~~~~~~~~~~d~~~~~~~~~~~s~~~~Lseas~~s~~~~~~~~~~~s~L~le~~~ 106 (252)
.++||++| |+|||+|+||| |+|.++|+++||.||+++++ ++++|+|+||.++
T Consensus 26 ~~~v~~~c~~~~~q~ft~kw~DEE-----GDp~tiSS~~EL~EA~rl~~------~n~~~~l~ihvfp 82 (83)
T cd06404 26 CNEVRDMCRFHNDQPFTLKWIDEE-----GDPCTISSQMELEEAFRLYE------LNKDSELNIHVFP 82 (83)
T ss_pred HHHHHHHhCCCCCCcEEEEEECCC-----CCceeecCHHHHHHHHHHHH------hcCcccEEEEecC
Confidence 57899999 79999999954 44448999999999999999 9999999999986
No 10
>KOG0696|consensus
Probab=98.71 E-value=2.1e-09 Score=104.58 Aligned_cols=72 Identities=22% Similarity=0.399 Sum_probs=59.9
Q ss_pred CCcccccccccccCcceeecCCCeEEEEecCCCCcCCCCCCcccccccccccccCCccccccccccccccccCCCCcc
Q psy1485 116 PLSLAQKNRWSKKGTKLHIFNDHTFIAKHLPGGTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRTETTCPHSTI 193 (252)
Q Consensus 116 p~~~~~r~~~~~k~~klh~~~gH~F~a~~f~~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V~~~C~~~s~ 193 (252)
.|++.++-.... -....|.|..++|..||||++|+.+++ |+..||++|..|.+++|++|...||.-|+....
T Consensus 94 ~CPGadkg~dtD-----dpr~kHkf~~~tYssPTFCDhCGsLLy-Gl~HQGmKC~~C~mNVH~rCv~nVPslCG~Dht 165 (683)
T KOG0696|consen 94 SCPGADKGPDTD-----DPRSKHKFKIHTYSSPTFCDHCGSLLY-GLIHQGMKCDTCDMNVHHRCVENVPSLCGTDHT 165 (683)
T ss_pred ECCCCCCCCCCC-----CcccccceeeeecCCCchhhhHHHHHH-HHHhcccccccccchHHHHHhhcCCcccCCcch
Confidence 566555543321 234579999999999999999999998 999999999999999999999999999986543
No 11
>KOG1011|consensus
Probab=98.65 E-value=1.1e-09 Score=110.21 Aligned_cols=87 Identities=24% Similarity=0.468 Sum_probs=72.6
Q ss_pred ecCCCeEEEEecCCCCcCCCCCCcccccccccccccCCccccccccccccccccCCCCcccccc-------------cch
Q psy1485 134 IFNDHTFIAKHLPGGTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRTETTCPHSTIQHLE-------------LNK 200 (252)
Q Consensus 134 ~~~gH~F~a~~f~~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V~~~C~~~s~~~~e-------------l~~ 200 (252)
...+|.|..++|..||||.-|.+++| |+.+||++|..|++.||.+|..++.++|...++.... ...
T Consensus 169 ~ttphnf~~~t~~tpt~cyecegllw-glarqglrctqc~vk~hdkc~ell~adclqraaeks~khg~~drtq~lv~~ir 247 (1283)
T KOG1011|consen 169 ATTPHNFATTTFQTPTFCYECEGLLW-GLARQGLRCTQCQVKVHDKCRELLSADCLQRAAEKSTKHGEADRTQSLVNVIR 247 (1283)
T ss_pred cCCCCceeeeeccCCchhhhhhhHHH-HHhhcccchhhccccHHHHHHHHhhhHHHHHHHHhhccccchhhHHHHHHHHH
Confidence 46899999999999999999999997 9999999999999999999999999999887765421 136
Q ss_pred hhhccccccccccCCcccccc
Q psy1485 201 DRIELRQQNRWSKKGTKLHIF 221 (252)
Q Consensus 201 ~r~~ir~PHrf~~~~y~sptF 221 (252)
+|++++...+.+++...+..|
T Consensus 248 drmki~e~nkpevfq~ir~vf 268 (1283)
T KOG1011|consen 248 DRMKIQEQNKPEVFQMIRTVF 268 (1283)
T ss_pred HHHHHHhhcChHHHHHHHHHh
Confidence 777887777776666555433
No 12
>KOG4239|consensus
Probab=98.49 E-value=4.1e-08 Score=91.65 Aligned_cols=112 Identities=16% Similarity=0.255 Sum_probs=80.6
Q ss_pred ceeecCCCeEEEEecCCCCcCCCCCCcccccccccccccCCccccccccccccccccCCCCccccc--ccc-hhhhcccc
Q psy1485 131 KLHIFNDHTFIAKHLPGGTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRTETTCPHSTIQHL--ELN-KDRIELRQ 207 (252)
Q Consensus 131 klh~~~gH~F~a~~f~~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V~~~C~~~s~~~~--el~-~~r~~ir~ 207 (252)
.+...++|.|......-|++|+-|++++| |+.++|++|..|++.||.+|..++..+|.....++. +.. .--.+.+.
T Consensus 45 ~lv~~r~~~~~~~g~~~~~~~~~c~~~~~-~vl~egL~c~~c~~tch~rcr~lv~ldc~~p~~sS~~w~s~v~~~~~~~~ 123 (348)
T KOG4239|consen 45 LLVPLRGHNFYTAGLLLPTWCDKCGDFIW-GVLREGLLCIHCKFTCHIRCRMLVDLDCRSPPSSSTSWDSIVERYVNVDT 123 (348)
T ss_pred ceeeccccccccccccccccchhhhHHHH-HHHHHHHhhhhcCCccCHHHHhhhhhhhcCCCCCccCCCCccccccccCC
Confidence 34556899999999999999999999997 999999999999999999999999999987664432 211 11123333
Q ss_pred cccc------------ccCCccccccccccccccccCCcccccCCceeecc
Q psy1485 208 QNRW------------SKKGTKLHIFNDHTFIAKHLPGTLYTNSPFYFRRD 246 (252)
Q Consensus 208 PHrf------------~~~~y~sptFCdHCF~ak~L~g~~~~~~~~~~~~~ 246 (252)
|-.| ++++|....-++ +|-.+ ..|.|+-+.--.+.+
T Consensus 124 p~e~t~p~~~~~ei~~ki~syn~~~s~~--s~~L~-edg~~tg~i~v~~~l 171 (348)
T KOG4239|consen 124 PVEWTDPEPQEMEIEQKIHSYNSESSTL--SMGLH-EDGEYTGFIKVTLKL 171 (348)
T ss_pred CccccCCCchhhhhhcCcchhhchhccc--ccccC-cccccCCceEEEeec
Confidence 3333 456666554344 55454 778887766555443
No 13
>KOG0694|consensus
Probab=97.86 E-value=2.9e-06 Score=86.18 Aligned_cols=63 Identities=27% Similarity=0.519 Sum_probs=57.8
Q ss_pred eeecCCCeEEEEecCCCCcCCCCCCcccccccccccccCCccccccccccccccccCCCCcccc
Q psy1485 132 LHIFNDHTFIAKHLPGGTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRTETTCPHSTIQH 195 (252)
Q Consensus 132 lh~~~gH~F~a~~f~~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V~~~C~~~s~~~ 195 (252)
+...++|.|..+.+.+|+||.+|+.++| |..+||.+|..|+.+||.+|..++...|+.+....
T Consensus 225 ~~~~~Phrf~~~~~q~ptFc~hCGs~L~-r~~qqGlkCs~Cg~n~H~~c~~~va~~CG~s~t~~ 287 (694)
T KOG0694|consen 225 FTFRNPHRFVKLNRQRPTFCDHCGSVLY-RLRQQGLKCSTCGRNVHNRCVENLAPNCGGSRTFS 287 (694)
T ss_pred ccccCCCcchhhhccCccHHHhcchhhh-hhcccCeeehhhhccccHHHHHhcccCCCCchhhh
Confidence 5566789999999999999999999997 89999999999999999999999999999876654
No 14
>KOG2996|consensus
Probab=97.36 E-value=3.9e-05 Score=77.22 Aligned_cols=54 Identities=33% Similarity=0.658 Sum_probs=49.7
Q ss_pred ecCCCeEEEEecCCCCcCCCCCCcccccccccccccCCccccccccccccccccCC
Q psy1485 134 IFNDHTFIAKHLPGGTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRTETTCP 189 (252)
Q Consensus 134 ~~~gH~F~a~~f~~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V~~~C~ 189 (252)
..++|.|+.++|..+|.|.+|..++ +|...|||+|.-|+...||.|...||. |+
T Consensus 520 ~an~H~fqmhtF~~~tsCkvC~mll-rGtfYQGY~C~~c~~~ahkecl~~vp~-cg 573 (865)
T KOG2996|consen 520 RANNHDFQMHTFKNTTSCKVCQMLL-RGTFYQGYKCEKCGADAHKECLGRVPP-CG 573 (865)
T ss_pred cccCcceEEEeccCCcchHHHHHHh-hhhhhcceeeeeccccHHHHhccCCCC-cc
Confidence 4688999999999999999999988 699999999999999999999998874 53
No 15
>KOG3564|consensus
Probab=97.20 E-value=5.8e-05 Score=74.47 Aligned_cols=99 Identities=23% Similarity=0.407 Sum_probs=69.5
Q ss_pred cCCCeEEEEecCCCCcCCCCCCcccccccccccccCCccccccccccccccccCCCCcccccc-cchhhhcccccccccc
Q psy1485 135 FNDHTFIAKHLPGGTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRTETTCPHSTIQHLE-LNKDRIELRQQNRWSK 213 (252)
Q Consensus 135 ~~gH~F~a~~f~~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V~~~C~~~s~~~~e-l~~~r~~ir~PHrf~~ 213 (252)
...|.|+.+.|..+-.|..|++.| .|++-+++|++|...||..|..+++.+|.+......- .... +-.-|.+
T Consensus 284 mr~htfi~kt~~~~~~Cv~C~krI--kfg~~sLkCRdC~v~~H~~Cr~~l~lpCIP~l~g~~~k~geg-----~L~DF~~ 356 (604)
T KOG3564|consen 284 MRLHTFISKTVIKPENCVPCGKRI--KFGKLSLKCRDCPVVCHIECRDKLTLPCIPTLIGPPVKTGEG-----MLADFAP 356 (604)
T ss_pred cccchhhHhhccCcccchhhhhhh--hhhhcccccccCCeeechhHHhcCCCCCcCccCCCCCccCce-----ehhhhcc
Confidence 466999999999999999999999 5889999999999999999999999999875433210 0000 0111111
Q ss_pred CC-ccccccccccccccccCCcccccCCce
Q psy1485 214 KG-TKLHIFNDHTFIAKHLPGTLYTNSPFY 242 (252)
Q Consensus 214 ~~-y~sptFCdHCF~ak~L~g~~~~~~~~~ 242 (252)
.. -+.|..--||-..++.. +||+--.|
T Consensus 357 s~aPMIPalVVHCVneIEaR--GLteeGLY 384 (604)
T KOG3564|consen 357 STAPMIPALVVHCVNEIEAR--GLTEEGLY 384 (604)
T ss_pred cccccchHHHHHHHHHHHHc--ccccccee
Confidence 11 03455566888777744 35665555
No 16
>KOG0193|consensus
Probab=96.87 E-value=0.0005 Score=69.75 Aligned_cols=54 Identities=28% Similarity=0.736 Sum_probs=46.5
Q ss_pred cCCCeEEEEecCCCCcCCCCCCcccccccccccccCCccccccccccccccccCCCCc
Q psy1485 135 FNDHTFIAKHLPGGTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRTETTCPHST 192 (252)
Q Consensus 135 ~~gH~F~a~~f~~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V~~~C~~~s 192 (252)
...|.|.-+.|....||+.|+.-+| -.|++|+.|++.+|..|...|+..|....
T Consensus 176 l~~H~~~rktf~~~~fC~~~~~~~l----~~gfrC~~C~~KfHq~Cs~~vp~~C~~~~ 229 (678)
T KOG0193|consen 176 LTTHNFVRKTFFPLAFCDSCCNKFL----FTGFRCQTCGYKFHQSCSPRVPTSCVNPD 229 (678)
T ss_pred ccceeeeeccccchhhhhhhcchhh----hcccccCCCCCccccccCCCCCCCCCCcc
Confidence 5679999999999999996665443 58999999999999999999999999443
No 17
>cd06402 PB1_p62 The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover. The PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=96.56 E-value=0.00063 Score=53.14 Aligned_cols=39 Identities=18% Similarity=0.197 Sum_probs=31.7
Q ss_pred hHHHHHHHh-----HhhhhhhccCCCCCCCCCCCCCcccchhhhhcccc
Q psy1485 43 RVDLIRSAC-----QVYLMVFVLNDHCSSVGPLREGSARSSLSEASGVS 86 (252)
Q Consensus 43 ~~~~~~~~~-----~~~~~~~~~~d~~~~~~~~~~~s~~~~Lseas~~s 86 (252)
=.+.||++| |.|||+|.|+| |++.++|+++||++|...+
T Consensus 32 L~~~V~~~f~~l~~~~ftlky~Dee-----GDlvtIssdeEL~~A~~~~ 75 (87)
T cd06402 32 LVEKVAAVFPSLRGKNFQLFWKDEE-----GDLVAFSSDEELVMALGSL 75 (87)
T ss_pred HHHHHHHHccccCCCcEEEEEECCC-----CCEEeecCHHHHHHHHHcC
Confidence 357889999 58999999955 5555899999999999554
No 18
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
Probab=95.77 E-value=0.0018 Score=49.96 Aligned_cols=41 Identities=10% Similarity=0.094 Sum_probs=33.4
Q ss_pred HHHHHHHhH--hhhhhhcc--CCCCCCCCCCCCCcccchhhhhccccCCccc
Q psy1485 44 VDLIRSACQ--VYLMVFVL--NDHCSSVGPLREGSARSSLSEASGVSGASTR 91 (252)
Q Consensus 44 ~~~~~~~~~--~~~~~~~~--~d~~~~~~~~~~~s~~~~Lseas~~s~~~~~ 91 (252)
-.||+..|. .|++|||| +||| .++++.+|+|+++++.-+++
T Consensus 28 ~~ev~~rf~l~~f~lKYlDde~e~v-------~lssd~eLeE~~rl~~~~~~ 72 (81)
T cd06396 28 EAMVKVSFGLNDIQIKYVDEENEEV-------SVNSQGEYEEALKSAVRQGN 72 (81)
T ss_pred HHHHHHHhCCCcceeEEEcCCCCEE-------EEEchhhHHHHHHHHHhCCC
Confidence 357888884 69999998 6677 69999999999988874443
No 19
>cd06408 PB1_NoxR The PB1 domain is present in the Epichloe festucae NoxR protein (NADPH oxidase regulator), a key regulator of NADPH oxidase isoform, NoxA. NoxA is essential for growth control of the fungal endophyte in plant tissue in the process of symbiotic interaction between a fungi and its plant host. The Epichloe festucae p67(phox)-like regulator, NoxR, dispensable in culture but essential in plants for the symbiotic interaction. Plants infected with a noxR deletion mutant show severe stunting and premature senescence, whereas hyphae in the meristematic tissues show increased branching leading to increased fungal colonization of pseudostem and leaf blade tissue. The PB1 domain is a modular domain mediating specific protein-protein interactions which a play role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is
Probab=95.54 E-value=0.004 Score=48.63 Aligned_cols=37 Identities=16% Similarity=0.053 Sum_probs=31.0
Q ss_pred hHHHHHHHh---Hhhhhhhcc-CCCCCCCCCCCCCcccchhhhhcccc
Q psy1485 43 RVDLIRSAC---QVYLMVFVL-NDHCSSVGPLREGSARSSLSEASGVS 86 (252)
Q Consensus 43 ~~~~~~~~~---~~~~~~~~~-~d~~~~~~~~~~~s~~~~Lseas~~s 86 (252)
=.+.||+.| |.|+++|.| +|+| +++++.+|++|+..+
T Consensus 27 L~~kIrdkf~~~~~~~iKykDEGD~i-------ti~sq~DLd~Ai~~a 67 (86)
T cd06408 27 FEDKIRDKFGFKRRLKIKMKDDGDMI-------TMGDQDDLDMAIDTA 67 (86)
T ss_pred HHHHHHHHhCCCCceEEEEEcCCCCc-------cccCHHHHHHHHHHH
Confidence 468899999 789999999 5555 899999999999443
No 20
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=94.85 E-value=0.018 Score=36.06 Aligned_cols=29 Identities=24% Similarity=0.744 Sum_probs=25.0
Q ss_pred cCCCCCCcccccccccccccCCcccccccccc
Q psy1485 150 VCQMCCKPLARRLGKQGYECRDCHVKCHKQCH 181 (252)
Q Consensus 150 ~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~ 181 (252)
.|++|.+.+ .|+. +|.|..|.+..|.+|+
T Consensus 2 ~C~~C~~~~-~~~~--~Y~C~~c~f~lh~~Ca 30 (30)
T PF03107_consen 2 WCDVCRRKI-DGFY--FYHCSECCFTLHVRCA 30 (30)
T ss_pred CCCCCCCCc-CCCE--eEEeCCCCCeEcCccC
Confidence 599999987 3654 9999999999999985
No 21
>KOG1453|consensus
Probab=94.39 E-value=0.0082 Score=63.82 Aligned_cols=58 Identities=19% Similarity=0.416 Sum_probs=46.8
Q ss_pred eeecCCCeEEEEecCC--CCcCCCCCCcccccccccccccCCccccccccccccccccCCCCccc
Q psy1485 132 LHIFNDHTFIAKHLPG--GTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRTETTCPHSTIQ 194 (252)
Q Consensus 132 lh~~~gH~F~a~~f~~--pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V~~~C~~~s~~ 194 (252)
+-.++| .|..+.+.. |+.|..|...+| . +++.|..|.++||++|...+...|+.....
T Consensus 539 ~~~~sg-~~~~~~r~~~~P~~c~~c~~~~~-~---~~~~c~~c~~~chkkc~~~~~~~~~~~~l~ 598 (918)
T KOG1453|consen 539 VNLHSG-ALKHYLRSLRKPAPCRTCETYSW-F---MELECELCRLVCHKKCLEALKSLCGHERLP 598 (918)
T ss_pred chhccC-cchhhhhcccCCcccccccccch-h---hhcccceeeeeccccchhhccccCcccccc
Confidence 334444 565565555 999999999998 3 449999999999999999999999987764
No 22
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=92.96 E-value=0.031 Score=34.82 Aligned_cols=29 Identities=31% Similarity=0.865 Sum_probs=13.1
Q ss_pred cCCCCCCcccccccccccccCCcccccccccc
Q psy1485 150 VCQMCCKPLARRLGKQGYECRDCHVKCHKQCH 181 (252)
Q Consensus 150 ~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~ 181 (252)
.|+.|+..+. | ...|.|..|.+..|..|+
T Consensus 2 ~C~~C~~~~~-~--~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPID-G--GWFYRCSECDFDLHEECA 30 (30)
T ss_dssp --TTTS-----S----EEE-TTT-----HHHH
T ss_pred cCCcCCCcCC-C--CceEECccCCCccChhcC
Confidence 5899999773 3 578999999999999985
No 23
>KOG1169|consensus
Probab=92.69 E-value=0.054 Score=55.52 Aligned_cols=60 Identities=28% Similarity=0.472 Sum_probs=48.6
Q ss_pred eeecCCCeEEEEecCCCCcCCCCCCccc-ccc-cccccccCCccccccccccccccccCCCC
Q psy1485 132 LHIFNDHTFIAKHLPGGTVCQMCCKPLA-RRL-GKQGYECRDCHVKCHKQCHVRTETTCPHS 191 (252)
Q Consensus 132 lh~~~gH~F~a~~f~~pt~C~vC~~~Iw-~Gl-~kQGyqC~~Ck~~cHKKC~~~V~~~C~~~ 191 (252)
.+....|.+....+..|++|.+|.+..- -|+ .+||+.|..|++.+|..|+..+...|...
T Consensus 93 ~k~~~~~~~~~~~~~~~~~c~~c~~~c~~~~~~~~~g~~C~~C~~~vh~~C~~~~~~~~~~~ 154 (634)
T KOG1169|consen 93 HKTDGDHVWRPKHLWKPAYCFVCPKSCGSCGVGIKQGLCCDWCGRTVHERCVRRADPECQCK 154 (634)
T ss_pred hhccCceeccCCCCCCCceEEeccccccchhhcccCceeeccccchHHHHHHhhcCcccccc
Confidence 3456788999999999999999998741 033 48999999999999999999888876543
No 24
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=89.89 E-value=0.086 Score=40.51 Aligned_cols=37 Identities=11% Similarity=0.091 Sum_probs=30.8
Q ss_pred HHHHHHHh-----Hhhhhhhcc--CCCCCCCCCCCCCcccchhhhhccccC
Q psy1485 44 VDLIRSAC-----QVYLMVFVL--NDHCSSVGPLREGSARSSLSEASGVSG 87 (252)
Q Consensus 44 ~~~~~~~~-----~~~~~~~~~--~d~~~~~~~~~~~s~~~~Lseas~~s~ 87 (252)
.++|++.| +.|+++|+| +|+| .++.+..|+||++++.
T Consensus 26 ~~~i~~r~~~~~~~~f~LkY~Ddegd~v-------~ltsd~DL~eai~i~~ 69 (82)
T cd06407 26 KQEIAKRFKLDDMSAFDLKYLDDDEEWV-------LLTCDADLEECIDVYR 69 (82)
T ss_pred HHHHHHHhCCCCCCeeEEEEECCCCCeE-------EeecHHHHHHHHHHHH
Confidence 56778888 469999999 6666 6999999999997766
No 25
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=86.25 E-value=0.38 Score=32.92 Aligned_cols=31 Identities=13% Similarity=-0.053 Sum_probs=22.0
Q ss_pred cccccCCccccccccccccccc-cCCcccccC
Q psy1485 209 NRWSKKGTKLHIFNDHTFIAKH-LPGTLYTNS 239 (252)
Q Consensus 209 Hrf~~~~y~sptFCdHCF~ak~-L~g~~~~~~ 239 (252)
|.|...++..|++|++|...++ +...+|+++
T Consensus 1 H~f~~~~~~~~~~C~~C~~~i~g~~~~g~~C~ 32 (53)
T PF00130_consen 1 HHFVPTTFSKPTYCDVCGKFIWGLGKQGYRCS 32 (53)
T ss_dssp -EEEEEESSSTEB-TTSSSBECSSSSCEEEET
T ss_pred CeEEEccCCCCCCCcccCcccCCCCCCeEEEC
Confidence 8899999999999999986663 244455554
No 26
>KOG3532|consensus
Probab=84.88 E-value=0.19 Score=52.37 Aligned_cols=48 Identities=4% Similarity=-0.149 Sum_probs=42.7
Q ss_pred cCCCeEEEEecCCCCcCCCCCCcccccccccccccCCcccccccccccccc
Q psy1485 135 FNDHTFIAKHLPGGTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRTE 185 (252)
Q Consensus 135 ~~gH~F~a~~f~~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V~ 185 (252)
-.+|.|...+|.+.+-|+.|+.-|| .+-..+|+.|.+.||+||.....
T Consensus 744 ~~~~d~~~~h~~r~~~~~~~~~ki~---~~~a~~~~~~~~~~~~k~~~~~~ 791 (1051)
T KOG3532|consen 744 EDGGDDEEAHLDRKRSASTRKAKIQ---ATFAAGKKKVLDLMPQKRKNTDA 791 (1051)
T ss_pred CCCCchHHhhhhhhcccchhcccee---ehhhhcccHHHHhcchhhhcchh
Confidence 4679999999999999999999998 57788999999999999976553
No 27
>KOG3532|consensus
Probab=81.58 E-value=0.22 Score=51.84 Aligned_cols=50 Identities=10% Similarity=-0.044 Sum_probs=44.0
Q ss_pred ecCCCeEEEEecCCCCcCCCCCCcccccccccccccCCccccccccccccccc
Q psy1485 134 IFNDHTFIAKHLPGGTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRTET 186 (252)
Q Consensus 134 ~~~gH~F~a~~f~~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V~~ 186 (252)
..+-|+|....+..+|||..|.+-.| .+..-+|.-|.|+||++|+++..+
T Consensus 69 ~~N~~r~~~t~~~~~t~~~~~~~~~~---~~~AS~c~s~~~V~h~lfqE~k~a 118 (1051)
T KOG3532|consen 69 PINQFRPAQIPEELRTFLKSGEDGQG---ISKASSCNSISLVLHMLFQEHKDT 118 (1051)
T ss_pred chhhcChhcCcccccccccccccchh---hHHHHHHHHHHHHHHHHHHHhhhh
Confidence 46779999999999999999999987 578889999999999999876543
No 28
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=77.53 E-value=1.6 Score=28.60 Aligned_cols=31 Identities=6% Similarity=-0.286 Sum_probs=22.2
Q ss_pred cccccCCccccccccccccccccCCcccccC
Q psy1485 209 NRWSKKGTKLHIFNDHTFIAKHLPGTLYTNS 239 (252)
Q Consensus 209 Hrf~~~~y~sptFCdHCF~ak~L~g~~~~~~ 239 (252)
|.|...++..+++|++|.-.++.....|.++
T Consensus 1 H~~~~~~~~~~~~C~~C~~~i~~~~~~~~C~ 31 (49)
T smart00109 1 HHFVERTFKKPTKCCVCRKSIWGSFQGLRCS 31 (49)
T ss_pred CceEEeccCCCCCccccccccCcCCCCcCCC
Confidence 7888899999999999986655321245544
No 29
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=75.95 E-value=0.81 Score=30.99 Aligned_cols=28 Identities=36% Similarity=0.985 Sum_probs=16.5
Q ss_pred CCCCCCcccccccccccccC--Ccccccccccccc
Q psy1485 151 CQMCCKPLARRLGKQGYECR--DCHVKCHKQCHVR 183 (252)
Q Consensus 151 C~vC~~~Iw~Gl~kQGyqC~--~Ck~~cHKKC~~~ 183 (252)
|..|.+++ -||.+|. +|....|..|...
T Consensus 1 C~~C~~iv-----~~G~~C~~~~C~~r~H~~C~~~ 30 (43)
T PF08746_consen 1 CEACKEIV-----TQGQRCSNRDCNVRLHDDCFKK 30 (43)
T ss_dssp -TTT-SB------SSSEE-SS--S--EE-HHHHHH
T ss_pred CcccchhH-----eeeccCCCCccCchHHHHHHHH
Confidence 78898865 3899998 7999999999753
No 30
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=75.47 E-value=2.5 Score=37.37 Aligned_cols=40 Identities=25% Similarity=0.750 Sum_probs=31.3
Q ss_pred CCcCCCCC--Ccccccccc-cccccCCccccccccccccccccCCC
Q psy1485 148 GTVCQMCC--KPLARRLGK-QGYECRDCHVKCHKQCHVRTETTCPH 190 (252)
Q Consensus 148 pt~C~vC~--~~Iw~Gl~k-QGyqC~~Ck~~cHKKC~~~V~~~C~~ 190 (252)
.-.|++|. +.|+ -+-. ...+|..|+-..|+.|... ..|+.
T Consensus 152 GfiCe~C~~~~~If-PF~~~~~~~C~~C~~v~H~~C~~~--~~Cpk 194 (202)
T PF13901_consen 152 GFICEICNSDDIIF-PFQIDTTVRCPKCKSVFHKSCFRK--KSCPK 194 (202)
T ss_pred CCCCccCCCCCCCC-CCCCCCeeeCCcCccccchhhcCC--CCCCC
Confidence 55899998 4665 4444 6689999999999999986 56764
No 31
>KOG0612|consensus
Probab=75.07 E-value=0.53 Score=51.51 Aligned_cols=55 Identities=38% Similarity=0.733 Sum_probs=49.0
Q ss_pred ecCCCeEEEEecCCCCcCCCCCCcccccccccccccCCccccccccccccccccCCC
Q psy1485 134 IFNDHTFIAKHLPGGTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRTETTCPH 190 (252)
Q Consensus 134 ~~~gH~F~a~~f~~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V~~~C~~ 190 (252)
...+|.|.+..+..|++|..|...+| +.++ .|.|..|.+.+|+.=..++..+|..
T Consensus 1206 v~~~~~~~~~l~~~~~~~~~~~k~l~-~~~~-~ye~~~~~~~~~~d~~~k~m~p~ky 1260 (1317)
T KOG0612|consen 1206 VHKGHEFIPFLYHFPTNCEACIKPLW-HMFK-AYECRRCHIKCHKDHMDKIMAPCKY 1260 (1317)
T ss_pred cCCCCcchHHHhhcchhHHHHhhhcc-cchh-HHHHHHhhccccccccccccCcccc
Confidence 35789999999999999999999997 7666 9999999999999888888888873
No 32
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=74.76 E-value=1.6 Score=28.99 Aligned_cols=22 Identities=18% Similarity=0.090 Sum_probs=18.9
Q ss_pred cccccCCccccccccccccccc
Q psy1485 209 NRWSKKGTKLHIFNDHTFIAKH 230 (252)
Q Consensus 209 Hrf~~~~y~sptFCdHCF~ak~ 230 (252)
|.|.+.++..|++|++|.-.++
T Consensus 1 H~f~~~~~~~~~~C~~C~~~i~ 22 (50)
T cd00029 1 HRFVRKSFFKPTFCDVCRKSIW 22 (50)
T ss_pred CccEEeeCCCCCChhhcchhhh
Confidence 7899999999999999976554
No 33
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=72.45 E-value=1.8 Score=31.10 Aligned_cols=35 Identities=26% Similarity=0.682 Sum_probs=29.0
Q ss_pred CCcCCCCCCcccccccccccccCCccccccccccccc
Q psy1485 148 GTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRT 184 (252)
Q Consensus 148 pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V 184 (252)
...|..|++.|- ..-....|..|+...|+.|....
T Consensus 5 ~~~C~~Cg~~~~--~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 5 GCKCPVCGKKFK--DGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred CccChhhCCccc--CCCCEEECCCCCCcccHHHHhhC
Confidence 568999999772 46788999999999999998553
No 34
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=65.10 E-value=5 Score=27.00 Aligned_cols=31 Identities=19% Similarity=0.530 Sum_probs=25.5
Q ss_pred cCCCCCCcccccccccccccCCcccccccccccc
Q psy1485 150 VCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVR 183 (252)
Q Consensus 150 ~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~ 183 (252)
+|.+|+.. +-....++|..|....|-.|...
T Consensus 1 ~C~vC~~~---~~~~~~i~C~~C~~~~H~~C~~~ 31 (51)
T PF00628_consen 1 YCPVCGQS---DDDGDMIQCDSCNRWYHQECVGP 31 (51)
T ss_dssp EBTTTTSS---CTTSSEEEBSTTSCEEETTTSTS
T ss_pred eCcCCCCc---CCCCCeEEcCCCChhhCcccCCC
Confidence 58889882 34678899999999999999864
No 35
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=56.51 E-value=3.2 Score=27.14 Aligned_cols=20 Identities=25% Similarity=0.564 Sum_probs=13.2
Q ss_pred cccccCCccccccccccccc
Q psy1485 165 QGYECRDCHVKCHKQCHVRT 184 (252)
Q Consensus 165 QGyqC~~Ck~~cHKKC~~~V 184 (252)
+-++|..|++.+|..|....
T Consensus 3 ~ll~C~~C~v~VH~~CYGv~ 22 (36)
T PF13831_consen 3 PLLFCDNCNVAVHQSCYGVS 22 (36)
T ss_dssp EEEE-SSS--EEEHHHHT-S
T ss_pred ceEEeCCCCCcCChhhCCcc
Confidence 44789999999999998643
No 36
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=45.95 E-value=15 Score=29.52 Aligned_cols=36 Identities=36% Similarity=0.717 Sum_probs=26.2
Q ss_pred CCCcCCCCCCcccccccccccccCCcccccccccccc
Q psy1485 147 GGTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVR 183 (252)
Q Consensus 147 ~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~ 183 (252)
....|..|...+ +-++..|-.|.+|+..+=++|...
T Consensus 53 ~~~~C~~C~~~f-g~l~~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPF-GFLFNRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BC-SCTSTTCEEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcc-cccCCCCCcCCcCCccccCccCCc
Confidence 456899998855 234568899999998888888765
No 37
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=43.04 E-value=17 Score=24.51 Aligned_cols=30 Identities=23% Similarity=0.744 Sum_probs=23.0
Q ss_pred cCCCCCCcccccccccccccCCc-ccccccccccc
Q psy1485 150 VCQMCCKPLARRLGKQGYECRDC-HVKCHKQCHVR 183 (252)
Q Consensus 150 ~C~vC~~~Iw~Gl~kQGyqC~~C-k~~cHKKC~~~ 183 (252)
.|+.|+..|+ | .-|+|..| .+..+..|...
T Consensus 2 ~Cd~C~~~i~-G---~ry~C~~C~d~dLC~~C~~~ 32 (43)
T cd02340 2 ICDGCQGPIV-G---VRYKCLVCPDYDLCESCEAK 32 (43)
T ss_pred CCCCCCCcCc-C---CeEECCCCCCccchHHhhCc
Confidence 6999999774 5 46899999 57777777653
No 38
>KOG3362|consensus
Probab=40.67 E-value=10 Score=32.67 Aligned_cols=37 Identities=32% Similarity=0.661 Sum_probs=23.7
Q ss_pred CeEEEEecC--CCCcCCCCCCcccccccccccccCCcccc-cccccc
Q psy1485 138 HTFIAKHLP--GGTVCQMCCKPLARRLGKQGYECRDCHVK-CHKQCH 181 (252)
Q Consensus 138 H~F~a~~f~--~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~-cHKKC~ 181 (252)
|+-.+..+. ..+||++|+ +| + -|.|..||-. |-.+|.
T Consensus 106 ~~~~a~p~~KP~r~fCaVCG--~~-S----~ysC~~CG~kyCsv~C~ 145 (156)
T KOG3362|consen 106 HTAYAKPSFKPLRKFCAVCG--YD-S----KYSCVNCGTKYCSVRCL 145 (156)
T ss_pred hhcccCCCCCCcchhhhhcC--CC-c----hhHHHhcCCceeechhh
Confidence 444444333 367999999 55 3 3899999854 444553
No 39
>KOG0955|consensus
Probab=39.41 E-value=23 Score=38.98 Aligned_cols=39 Identities=21% Similarity=0.445 Sum_probs=29.5
Q ss_pred cCCCCcCCCCCCcccccccccccccCCccccccccccccc
Q psy1485 145 LPGGTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRT 184 (252)
Q Consensus 145 f~~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V 184 (252)
+.-..+|.+|.+-=- --...-+.|.+|+..+|-.|....
T Consensus 216 ~~~D~~C~iC~~~~~-~n~n~ivfCD~Cnl~VHq~Cygi~ 254 (1051)
T KOG0955|consen 216 LEEDAVCCICLDGEC-QNSNVIVFCDGCNLAVHQECYGIP 254 (1051)
T ss_pred cCCCccceeeccccc-CCCceEEEcCCCcchhhhhccCCC
Confidence 345889999998221 113677899999999999999843
No 40
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=37.66 E-value=21 Score=35.36 Aligned_cols=40 Identities=18% Similarity=0.532 Sum_probs=28.9
Q ss_pred CCeEEEEecCCCCcCCCCCCcccccccccccccCCccccccc
Q psy1485 137 DHTFIAKHLPGGTVCQMCCKPLARRLGKQGYECRDCHVKCHK 178 (252)
Q Consensus 137 gH~F~a~~f~~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHK 178 (252)
-|.+.. .-..-+.|..|+..+ ...++.||+|..|+...-.
T Consensus 340 v~~l~~-~~~~~p~Cp~Cg~~m-~S~G~~g~rC~kCg~~~~~ 379 (421)
T COG1571 340 VLKLAR-YERVNPVCPRCGGRM-KSAGRNGFRCKKCGTRARE 379 (421)
T ss_pred EEEeee-eEEcCCCCCccCCch-hhcCCCCcccccccccCCc
Confidence 344444 334466999999988 4677779999999877543
No 41
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=37.42 E-value=25 Score=26.60 Aligned_cols=33 Identities=27% Similarity=0.490 Sum_probs=22.2
Q ss_pred CCCCcCCCCCCcccccccccccccCCccccccccccc
Q psy1485 146 PGGTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHV 182 (252)
Q Consensus 146 ~~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~ 182 (252)
..-+.|++|+..| |- ..+----|+-.+|..|..
T Consensus 76 ~~~~~C~vC~k~l--~~--~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 76 TESTKCSVCGKPL--GN--SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCCccCcCCcC--CC--ceEEEeCCCeEEeccccc
Confidence 4567899999988 22 222223356889999975
No 42
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the smart00661 RPOL9 RNA polymerase subunit 9.
Probab=32.92 E-value=32 Score=23.08 Aligned_cols=27 Identities=30% Similarity=0.710 Sum_probs=18.3
Q ss_pred cCCCCCCcccccccc--cccccCCccccc
Q psy1485 150 VCQMCCKPLARRLGK--QGYECRDCHVKC 176 (252)
Q Consensus 150 ~C~vC~~~Iw~Gl~k--QGyqC~~Ck~~c 176 (252)
||..|+.++..--.. .-+.|..|++..
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 899999987521122 247899998654
No 44
>KOG1170|consensus
Probab=32.79 E-value=26 Score=37.82 Aligned_cols=60 Identities=25% Similarity=0.522 Sum_probs=48.2
Q ss_pred eecCCCeEEEEecCCCCcCCCCCCcccccccccccccCCccccccccccccccccCCCCc
Q psy1485 133 HIFNDHTFIAKHLPGGTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRTETTCPHST 192 (252)
Q Consensus 133 h~~~gH~F~a~~f~~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V~~~C~~~s 192 (252)
+...+|.|..--...+..|++|.+.--.-+.-|.|.|--|+..+|-.|.......|.-..
T Consensus 103 ~a~mphqw~Egnlpvsskc~vc~k~cgs~~rlqd~rclwc~~~vh~~c~~~~~~~cs~~~ 162 (1099)
T KOG1170|consen 103 NAIMPHQWMEGNLPVSSKCSVCEKPCGSVLRLQDYRCLWCGCCVHDTCIGNLARACSLGH 162 (1099)
T ss_pred cccCchhhhhcCCCccccccccccccccccccCCcceEeeccEeehhhhhhHHhhccccc
Confidence 457788888877778889999987542235678899999999999999999999887543
No 45
>KOG1170|consensus
Probab=31.58 E-value=20 Score=38.53 Aligned_cols=67 Identities=9% Similarity=0.103 Sum_probs=44.1
Q ss_pred ccccccccccccccccCCCCcccccccchhhh---ccccccccccCCccccccccccccccccCCcccccCCc
Q psy1485 172 CHVKCHKQCHVRTETTCPHSTIQHLELNKDRI---ELRQQNRWSKKGTKLHIFNDHTFIAKHLPGTLYTNSPF 241 (252)
Q Consensus 172 Ck~~cHKKC~~~V~~~C~~~s~~~~el~~~r~---~ir~PHrf~~~~y~sptFCdHCF~ak~L~g~~~~~~~~ 241 (252)
|...-|..|+..-...|.+..+...-...+.+ .-+|||.|.+++...+.-|..| ++.+|++++=-||
T Consensus 68 ~~~rk~r~~adn~ke~e~wi~~~kt~q~~e~~s~~~a~mphqw~Egnlpvsskc~vc---~k~cgs~~rlqd~ 137 (1099)
T KOG1170|consen 68 TPVRKHRLCADNRKEMEKWINQSKTPQHLEFISPENAIMPHQWMEGNLPVSSKCSVC---EKPCGSVLRLQDY 137 (1099)
T ss_pred cccHHhhhhccchhHHHHhhccccchhhccccCCCcccCchhhhhcCCCcccccccc---ccccccccccCCc
Confidence 44455677777666666665554432111111 2279999999999998777766 8889999874444
No 46
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=28.54 E-value=45 Score=23.80 Aligned_cols=32 Identities=16% Similarity=0.509 Sum_probs=24.3
Q ss_pred CCCcCCCCCCcccccccccccccCCccccccc
Q psy1485 147 GGTVCQMCCKPLARRLGKQGYECRDCHVKCHK 178 (252)
Q Consensus 147 ~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHK 178 (252)
....|..|+...-.......+.|..|++..|.
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCEECc
Confidence 56779999997631256778999999988764
No 47
>KOG0612|consensus
Probab=28.54 E-value=8.3 Score=42.72 Aligned_cols=54 Identities=15% Similarity=0.334 Sum_probs=41.1
Q ss_pred CCCeEEEEecCCCCcCCCCCCcccccccccccccCCccccccccccccccccCCCCccccc
Q psy1485 136 NDHTFIAKHLPGGTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRTETTCPHSTIQHL 196 (252)
Q Consensus 136 ~gH~F~a~~f~~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V~~~C~~~s~~~~ 196 (252)
..|.|....+..| ...+. |+.+||+.|.+|.+.||.-|...++..|+..+....
T Consensus 892 ~~~el~~e~~~~~------t~~~~-g~hRqe~~~k~~t~ac~~e~~~~l~q~~~i~~~E~e 945 (1317)
T KOG0612|consen 892 RIEELEQEKISKK------TKDVL-GLHRQELTCKDCTLACLEETNRTLTQKCKLLSEEKE 945 (1317)
T ss_pred HHHHHHHHHhhhh------HHHHH-HHHHHHHHHHHHhHHHHHHHHHHhhhhcCCchhhhh
Confidence 3455555555555 22333 899999999999999999999999999998766543
No 48
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=28.50 E-value=19 Score=25.24 Aligned_cols=21 Identities=48% Similarity=1.126 Sum_probs=14.4
Q ss_pred cCCCCCCccccccc-----ccccccCCc
Q psy1485 150 VCQMCCKPLARRLG-----KQGYECRDC 172 (252)
Q Consensus 150 ~C~vC~~~Iw~Gl~-----kQGyqC~~C 172 (252)
.|++|++-| |+. ..||-|.+|
T Consensus 1 ~C~iCg~ki--gl~~~~k~~DG~iC~~C 26 (51)
T PF14471_consen 1 KCAICGKKI--GLFKRFKIKDGYICKDC 26 (51)
T ss_pred CCCcccccc--ccccceeccCccchHHH
Confidence 489999987 553 356767654
No 49
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=27.78 E-value=43 Score=24.20 Aligned_cols=25 Identities=36% Similarity=0.929 Sum_probs=18.6
Q ss_pred cCCCCCCcccccccccccccCCcccccc
Q psy1485 150 VCQMCCKPLARRLGKQGYECRDCHVKCH 177 (252)
Q Consensus 150 ~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cH 177 (252)
+|.+|..-. -..+.|.|.+||+..|
T Consensus 1 ~Cpv~~~~~---~~~v~~~Cp~cGipth 25 (55)
T PF13824_consen 1 LCPVCKKDL---PAHVNFECPDCGIPTH 25 (55)
T ss_pred CCCCCcccc---ccccCCcCCCCCCcCc
Confidence 477777754 2467899999998777
No 50
>KOG4323|consensus
Probab=26.35 E-value=23 Score=35.51 Aligned_cols=35 Identities=23% Similarity=0.537 Sum_probs=29.8
Q ss_pred CCCCCCcccccccccccccCCccccccccccccccc
Q psy1485 151 CQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRTET 186 (252)
Q Consensus 151 C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V~~ 186 (252)
|.||.... .|.+.+.++|..|+--.|.-||.-...
T Consensus 171 c~vC~~g~-~~~~NrmlqC~~C~~~fHq~Chqp~i~ 205 (464)
T KOG4323|consen 171 CSVCYCGG-PGAGNRMLQCDKCRQWYHQACHQPLIK 205 (464)
T ss_pred eeeeecCC-cCccceeeeecccccHHHHHhccCCCC
Confidence 99999766 478889999999999999999975543
No 51
>KOG2807|consensus
Probab=25.36 E-value=56 Score=31.73 Aligned_cols=78 Identities=17% Similarity=0.329 Sum_probs=0.0
Q ss_pred CCcCCCCCCcccccccccccccCCccccccccccccccccCCCCcccccccchhhhcccccccc--------ccCCcccc
Q psy1485 148 GTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRTETTCPHSTIQHLELNKDRIELRQQNRW--------SKKGTKLH 219 (252)
Q Consensus 148 pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V~~~C~~~s~~~~el~~~r~~ir~PHrf--------~~~~y~sp 219 (252)
|++|+ |...+ ..-||.|..|+..+- .+|..|+.-+. +-.......-.-.|-| ...+|...
T Consensus 263 ps~C~-CH~~~----~~~Gy~CP~CkakvC-----sLP~eCpiC~l--tLVss~hLARSyhhL~PL~~F~Eip~~~~~~~ 330 (378)
T KOG2807|consen 263 PSFCA-CHSEL----SGGGYFCPQCKAKVC-----SLPIECPICSL--TLVSSPHLARSYHHLFPLKPFVEIPETEYNGS 330 (378)
T ss_pred cchhe-ecccc----ccCceeCCcccCeee-----cCCccCCccce--eEecchHHHHHHHhhcCCcchhhccccccCCC
Q ss_pred ccccccccccccCCccccc
Q psy1485 220 IFNDHTFIAKHLPGTLYTN 238 (252)
Q Consensus 220 tFCdHCF~ak~L~g~~~~~ 238 (252)
+||--| ....+.++.|+|
T Consensus 331 ~~Cf~C-~~~~~~~~~y~C 348 (378)
T KOG2807|consen 331 RFCFAC-QGELLSSGRYRC 348 (378)
T ss_pred cceeee-ccccCCCCcEEc
No 52
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=24.99 E-value=42 Score=20.87 Aligned_cols=27 Identities=22% Similarity=0.490 Sum_probs=13.4
Q ss_pred CCcCCCCCCcccccccccccccCCccc
Q psy1485 148 GTVCQMCCKPLARRLGKQGYECRDCHV 174 (252)
Q Consensus 148 pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~ 174 (252)
-.||..|+...-.--.-...+|..|+.
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-
T ss_pred CcccCcCCccccCCCCcCEeECCCCcC
Confidence 358999998653222334567888874
No 53
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=24.18 E-value=31 Score=26.77 Aligned_cols=35 Identities=26% Similarity=0.752 Sum_probs=16.6
Q ss_pred CCCcCCCCCCcccccccccc---cccCCcccccccccccc
Q psy1485 147 GGTVCQMCCKPLARRLGKQG---YECRDCHVKCHKQCHVR 183 (252)
Q Consensus 147 ~pt~C~vC~~~Iw~Gl~kQG---yqC~~Ck~~cHKKC~~~ 183 (252)
....|..|++-| |+...| .-|..|.|.+-+-|...
T Consensus 8 ~~qiCqiCGD~V--Gl~~~Ge~FVAC~eC~fPvCr~CyEY 45 (80)
T PF14569_consen 8 NGQICQICGDDV--GLTENGEVFVACHECAFPVCRPCYEY 45 (80)
T ss_dssp SS-B-SSS--B----B-SSSSB--S-SSS-----HHHHHH
T ss_pred CCcccccccCcc--ccCCCCCEEEEEcccCCccchhHHHH
Confidence 356899999988 787777 46999999999999754
No 54
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=24.09 E-value=49 Score=25.60 Aligned_cols=27 Identities=22% Similarity=0.517 Sum_probs=21.0
Q ss_pred cCCCCCCcccccccccccccCCccccccc
Q psy1485 150 VCQMCCKPLARRLGKQGYECRDCHVKCHK 178 (252)
Q Consensus 150 ~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHK 178 (252)
||..|+.+|. .....+.|..|++....
T Consensus 2 fC~~Cg~~l~--~~~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLMT--PKNGVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCcccc--cCCCeEECcCCCCcccc
Confidence 8999999884 33456899999987654
No 55
>PF04571 Lipin_N: lipin, N-terminal conserved region; InterPro: IPR007651 Mutations in the lipin gene lead to fatty liver dystrophy in mice. The protein has been shown to be phosphorylated by the TOR Ser/Thr protein kinases in response to insulin stimulation. This entry represents a conserved domain found at the N terminus of the member proteins [, ].
Probab=23.69 E-value=42 Score=27.48 Aligned_cols=21 Identities=29% Similarity=0.368 Sum_probs=16.3
Q ss_pred ccccccCCcccccCCceeecc
Q psy1485 226 FIAKHLPGTLYTNSPFYFRRD 246 (252)
Q Consensus 226 F~ak~L~g~~~~~~~~~~~~~ 246 (252)
.++.+-++|.|++||||-|=-
T Consensus 30 VIVV~q~DGs~~sSPFhVRFG 50 (110)
T PF04571_consen 30 VIVVEQPDGSLKSSPFHVRFG 50 (110)
T ss_pred EEEEecCCCCEecCccEEEEc
Confidence 344555899999999998843
No 56
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=23.57 E-value=48 Score=22.24 Aligned_cols=29 Identities=28% Similarity=0.714 Sum_probs=21.9
Q ss_pred cCCCCCCcccccccccccccCCcc-ccccccccc
Q psy1485 150 VCQMCCKPLARRLGKQGYECRDCH-VKCHKQCHV 182 (252)
Q Consensus 150 ~C~vC~~~Iw~Gl~kQGyqC~~Ck-~~cHKKC~~ 182 (252)
.|+.|...|+ | .-|+|..|. +.....|..
T Consensus 2 ~C~~C~~~i~-g---~r~~C~~C~d~dLC~~Cf~ 31 (46)
T cd02249 2 SCDGCLKPIV-G---VRYHCLVCEDFDLCSSCYA 31 (46)
T ss_pred CCcCCCCCCc-C---CEEECCCCCCCcCHHHHHC
Confidence 5999999885 5 568899887 666666665
No 57
>KOG1169|consensus
Probab=22.75 E-value=18 Score=37.62 Aligned_cols=84 Identities=15% Similarity=0.205 Sum_probs=58.8
Q ss_pred CCCeEEEEecCCCCcCCCCCCcccccccccccccCCccccccccccccccccCCCCcccccccchhhhccccccccccCC
Q psy1485 136 NDHTFIAKHLPGGTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHVRTETTCPHSTIQHLELNKDRIELRQQNRWSKKG 215 (252)
Q Consensus 136 ~gH~F~a~~f~~pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~~V~~~C~~~s~~~~el~~~r~~ir~PHrf~~~~ 215 (252)
..|.+.+--..+..+|.+|. | -.......|..|+...|-.|.......|+.......+ ..+.+.+.-|-|+...
T Consensus 32 ~~~~~~~~~~~~~~~~~~~~---~-~~~~~~~~~~~~g~~~~~~~~~~~~s~~~~~~~~~~~--~~~~k~~~~~~~~~~~ 105 (634)
T KOG1169|consen 32 ILHSSEPDCIIRQMVCCVCL---W-SEMAPSVDCDVDGGVSHEECVSGAASDCPLLVLLGFE--NQRHKTDGDHVWRPKH 105 (634)
T ss_pred cCcccCCchhHhhhhhhhhh---h-cccccccceeccccchhhhhhcccccchHHHHHHHhh--hhhhhccCceeccCCC
Confidence 45555555545555788874 4 4567889999999999999998888888764433221 2223445678889999
Q ss_pred cccccccccc
Q psy1485 216 TKLHIFNDHT 225 (252)
Q Consensus 216 y~sptFCdHC 225 (252)
+..|++|--|
T Consensus 106 ~~~~~~c~~c 115 (634)
T KOG1169|consen 106 LWKPAYCFVC 115 (634)
T ss_pred CCCCceEEec
Confidence 9999888765
No 58
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=22.65 E-value=40 Score=21.76 Aligned_cols=28 Identities=25% Similarity=0.519 Sum_probs=15.5
Q ss_pred CcCCCCCCccccccccccc-ccCCccccc
Q psy1485 149 TVCQMCCKPLARRLGKQGY-ECRDCHVKC 176 (252)
Q Consensus 149 t~C~vC~~~Iw~Gl~kQGy-qC~~Ck~~c 176 (252)
.||..|+.+|..--.+.+. .|+.|++..
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~~C~~C~Y~~ 30 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRVACRTCGYEE 30 (35)
T ss_dssp -BETTTTSBEEEEEETTTTEEESSSS-EE
T ss_pred eeCCCCCccceEcCCCccCcCCCCCCCcc
Confidence 4899999987521111111 488887653
No 59
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=22.39 E-value=55 Score=22.83 Aligned_cols=27 Identities=19% Similarity=0.450 Sum_probs=20.6
Q ss_pred CCcCCCCCC-cccccccccccccCCccccc
Q psy1485 148 GTVCQMCCK-PLARRLGKQGYECRDCHVKC 176 (252)
Q Consensus 148 pt~C~vC~~-~Iw~Gl~kQGyqC~~Ck~~c 176 (252)
..+|..|+. ++. .....+.|..|++..
T Consensus 20 ~~fCP~Cg~~~m~--~~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 20 NKFCPRCGSGFMA--EHLDRWHCGKCGYTE 47 (50)
T ss_pred cCcCcCCCcchhe--ccCCcEECCCcCCEE
Confidence 459999998 774 455678999998864
No 60
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=21.70 E-value=57 Score=23.19 Aligned_cols=33 Identities=24% Similarity=0.616 Sum_probs=18.6
Q ss_pred CCcCCCCCCcccccccccccccCCccccccccccc
Q psy1485 148 GTVCQMCCKPLARRLGKQGYECRDCHVKCHKQCHV 182 (252)
Q Consensus 148 pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cHKKC~~ 182 (252)
...|..|...+ ++.+.-..|..||.++=..|..
T Consensus 9 ~~~C~~C~~~F--~~~~rrhhCr~CG~~vC~~Cs~ 41 (69)
T PF01363_consen 9 ASNCMICGKKF--SLFRRRHHCRNCGRVVCSSCSS 41 (69)
T ss_dssp -SB-TTT--B---BSSS-EEE-TTT--EEECCCS-
T ss_pred CCcCcCcCCcC--CCceeeEccCCCCCEECCchhC
Confidence 56899999976 6778889999999887666653
No 61
>KOG1829|consensus
Probab=20.56 E-value=47 Score=34.34 Aligned_cols=64 Identities=16% Similarity=0.278 Sum_probs=37.5
Q ss_pred CCcCCCCCCcccccccccccccCCcccccc-------ccccccccccCCCCcccccccchhhhccccccccccCCccc
Q psy1485 148 GTVCQMCCKPLARRLGKQGYECRDCHVKCH-------KQCHVRTETTCPHSTIQHLELNKDRIELRQQNRWSKKGTKL 218 (252)
Q Consensus 148 pt~C~vC~~~Iw~Gl~kQGyqC~~Ck~~cH-------KKC~~~V~~~C~~~s~~~~el~~~r~~ir~PHrf~~~~y~s 218 (252)
-.+|..+.+ .||-+|||.|..|+...+ +.|...-...|..-.... +.-+-.|+-|.|.-..|.+
T Consensus 325 ~~~~~~~re---~gL~aQ~~~CAgC~~~i~~~~~~~~R~C~y~G~y~C~~Ch~~~----~svIPARVl~~WDf~~y~V 395 (580)
T KOG1829|consen 325 HIHPAIPRE---KGLDAQNFRCAGCGHTIGPDLEQRPRLCRYLGKYFCDCCHQND----KSVIPARVLHNWDFTKYPV 395 (580)
T ss_pred hcccCcchh---hhhhccCceecccCCCcccccccchhHhhhhhhhhCchhcccC----cccccccceecccCccccc
Confidence 445666666 378889999999988887 345554444444322211 1112345667776666655
No 62
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=20.49 E-value=75 Score=19.25 Aligned_cols=23 Identities=26% Similarity=0.801 Sum_probs=14.4
Q ss_pred CCCCCCccccccc-ccccccCCccc
Q psy1485 151 CQMCCKPLARRLG-KQGYECRDCHV 174 (252)
Q Consensus 151 C~vC~~~Iw~Gl~-kQGyqC~~Ck~ 174 (252)
|..|+..|- +.. .--|.|.+|++
T Consensus 1 C~sC~~~i~-~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIA-PREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCccc-CcccCceEeCCCCCC
Confidence 566776664 332 34588988874
Done!