Query 025815
Match_columns 247
No_of_seqs 78 out of 80
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 09:52:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025815.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025815hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04852 DUF640: Protein of un 100.0 2E-74 4.4E-79 472.6 11.2 123 92-214 10-132 (132)
2 PF08821 CGGC: CGGC domain; I 89.6 0.54 1.2E-05 37.5 4.1 55 123-187 41-98 (107)
3 PF02899 Phage_int_SAM_1: Phag 88.0 0.74 1.6E-05 31.8 3.4 40 104-144 21-60 (84)
4 cd00798 INT_XerDC XerD and Xer 84.3 3.7 8E-05 32.5 6.0 69 104-199 21-91 (284)
5 cd00799 INT_Cre Cre recombinas 79.8 15 0.00033 30.4 8.3 77 104-212 6-82 (287)
6 TIGR02225 recomb_XerD tyrosine 78.9 7.2 0.00016 31.2 6.0 70 103-200 19-90 (291)
7 PRK00283 xerD site-specific ty 78.5 5.7 0.00012 32.4 5.4 68 105-200 30-99 (299)
8 COG1080 PtsA Phosphoenolpyruva 77.1 2.6 5.7E-05 42.7 3.7 41 170-210 305-367 (574)
9 TIGR02224 recomb_XerC tyrosine 66.3 20 0.00044 28.8 5.8 69 106-200 22-92 (295)
10 PF10865 DUF2703: Domain of un 56.1 4 8.6E-05 33.6 0.1 43 133-195 2-44 (120)
11 TIGR01418 PEP_synth phosphoeno 54.5 20 0.00043 36.9 4.7 42 177-218 547-618 (782)
12 PF02896 PEP-utilizers_C: PEP- 53.6 30 0.00064 31.9 5.3 40 173-212 58-120 (293)
13 cd01185 INT_Tn4399 Tn4399 and 52.9 55 0.0012 27.2 6.3 33 108-140 44-78 (299)
14 PRK10529 DNA-binding transcrip 52.2 12 0.00026 29.2 2.2 19 175-193 191-209 (225)
15 PHA03385 IX capsid protein IX, 49.6 19 0.00042 30.9 3.2 33 26-58 39-71 (135)
16 PRK11061 fused phosphoenolpyru 48.8 24 0.00051 36.1 4.3 36 175-210 475-531 (748)
17 PF00539 Tat: Transactivating 44.8 9.3 0.0002 29.3 0.6 19 216-235 45-63 (68)
18 PF05528 Coronavirus_5: Corona 42.7 4.4 9.6E-05 32.1 -1.5 20 194-213 4-26 (82)
19 PRK10816 DNA-binding transcrip 42.5 18 0.0004 28.2 1.9 17 175-191 189-205 (223)
20 PRK00236 xerC site-specific ty 42.4 1E+02 0.0023 24.7 6.2 37 105-142 31-67 (297)
21 smart00259 ZnF_A20 A20-like zi 42.3 13 0.00028 23.6 0.9 16 151-166 7-22 (26)
22 PF13276 HTH_21: HTH-like doma 40.3 46 0.001 22.7 3.5 29 177-210 4-32 (60)
23 PF00486 Trans_reg_C: Transcri 38.5 31 0.00067 23.5 2.4 21 174-194 44-64 (77)
24 cd08793 Death_IRAK4 Death doma 36.3 37 0.0008 27.6 2.8 64 108-193 23-86 (100)
25 PF13495 Phage_int_SAM_4: Phag 36.0 43 0.00092 23.3 2.8 53 107-189 24-77 (85)
26 PF14768 RPA_interact_C: Repli 35.7 33 0.00072 25.8 2.3 35 164-198 18-56 (82)
27 cd00801 INT_P4 Bacteriophage P 35.0 67 0.0014 26.9 4.2 52 121-200 109-163 (357)
28 PRK09279 pyruvate phosphate di 34.0 37 0.00081 35.9 3.1 25 194-218 658-685 (879)
29 smart00862 Trans_reg_C Transcr 33.8 42 0.00092 22.8 2.4 19 174-192 45-63 (78)
30 TIGR01417 PTS_I_fam phosphoeno 33.3 52 0.0011 32.7 3.9 36 175-210 308-365 (565)
31 COG4974 XerD Site-specific rec 33.0 39 0.00085 32.0 2.8 43 97-145 26-69 (300)
32 PF06252 DUF1018: Protein of u 31.2 2.2E+02 0.0049 22.2 6.4 86 108-208 2-88 (119)
33 PF00140 Sigma70_r1_2: Sigma-7 29.5 39 0.00084 22.2 1.6 12 202-213 2-13 (37)
34 TIGR01828 pyru_phos_dikin pyru 28.9 32 0.00069 36.1 1.7 26 193-218 651-679 (856)
35 cd04372 RhoGAP_chimaerin RhoGA 28.7 58 0.0013 27.2 2.9 36 178-213 45-87 (194)
36 PF08544 GHMP_kinases_C: GHMP 28.7 10 0.00022 26.3 -1.3 72 105-188 6-84 (85)
37 PRK11177 phosphoenolpyruvate-p 26.9 88 0.0019 31.4 4.2 36 175-210 309-366 (575)
38 smart00243 GAS2 Growth-Arrest- 26.7 43 0.00094 26.2 1.6 14 108-121 55-68 (73)
39 PRK10701 DNA-binding transcrip 25.6 54 0.0012 26.1 2.1 17 175-191 201-217 (240)
40 PTZ00398 phosphoenolpyruvate c 25.3 1.2E+02 0.0026 32.6 5.1 43 173-215 264-337 (974)
41 KOG1452 Predicted Rho GTPase-a 24.4 41 0.0009 33.2 1.4 31 182-213 233-271 (442)
42 cd00383 trans_reg_C Effector d 24.2 66 0.0014 22.6 2.1 20 174-193 62-81 (95)
43 COG1615 Uncharacterized conser 23.9 97 0.0021 33.4 4.0 102 1-119 772-876 (885)
44 PF09336 Vps4_C: Vps4 C termin 23.7 60 0.0013 23.6 1.8 31 109-144 32-62 (62)
45 cd04388 RhoGAP_p85 RhoGAP_p85: 23.5 74 0.0016 27.8 2.7 34 180-213 45-82 (200)
46 cd04379 RhoGAP_SYD1 RhoGAP_SYD 23.3 89 0.0019 27.0 3.1 40 173-213 43-89 (207)
47 cd04396 RhoGAP_fSAC7_BAG7 RhoG 23.3 2.9E+02 0.0063 23.9 6.3 37 177-213 60-103 (225)
48 PF11709 Mit_ribos_Mrp51: Mito 23.0 95 0.0021 28.7 3.4 67 94-160 144-229 (312)
49 PF09958 DUF2192: Uncharacteri 22.9 71 0.0015 29.4 2.5 21 175-195 27-47 (231)
50 KOG3248 Transcription factor T 22.8 48 0.001 32.8 1.5 21 37-57 117-137 (421)
51 PF06480 FtsH_ext: FtsH Extrac 22.5 1.1E+02 0.0023 21.7 2.9 26 173-198 84-109 (110)
52 COG0745 OmpR Response regulato 21.9 70 0.0015 27.8 2.2 26 169-194 179-212 (229)
53 PF07700 HNOB: Heme NO binding 21.7 37 0.00079 27.8 0.5 36 107-142 65-103 (171)
54 PRK11173 two-component respons 21.5 72 0.0016 25.4 2.1 20 174-193 199-218 (237)
55 PRK09468 ompR osmolarity respo 21.4 73 0.0016 25.2 2.1 18 174-191 200-217 (239)
56 PF01754 zf-A20: A20-like zinc 21.1 46 0.001 21.1 0.7 16 150-165 5-20 (25)
57 PF09674 DUF2400: Protein of u 21.1 82 0.0018 28.4 2.5 51 170-220 24-93 (232)
58 COG4865 Glutamate mutase epsil 20.9 64 0.0014 32.3 2.0 23 179-201 196-218 (485)
59 PF01663 Phosphodiest: Type I 20.6 80 0.0017 26.7 2.3 27 169-195 208-234 (365)
60 PF09107 SelB-wing_3: Elongati 20.6 46 0.001 23.5 0.7 21 127-147 21-41 (50)
61 PF10520 Kua-UEV1_localn: Kua- 20.1 49 0.0011 28.9 0.9 24 172-195 17-41 (178)
No 1
>PF04852 DUF640: Protein of unknown function (DUF640); InterPro: IPR006936 This conserved region is found in plant proteins including the resistance protein-like protein (O49468 from SWISSPROT).
Probab=100.00 E-value=2e-74 Score=472.62 Aligned_cols=123 Identities=75% Similarity=1.349 Sum_probs=119.3
Q ss_pred CCCCCCCchhHHhhhhhHhHHHHHHHhcCCCCccccCcchhhhHHhhhhccccccccccCCCccccCCCCCCCCCCchhh
Q 025815 92 QSPVVSFGRYEAQKRRDWDTFMQYLSQHRPPLALSRCSGAHVLEFLKYLDQFGKTKVHAQSCPLFGHAHAPAPCRCPMMQ 171 (247)
Q Consensus 92 ~~~~~~~SRYesQKRrDWntf~qyL~nhrPPlsLs~Csg~hVleFLrylDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQ 171 (247)
.++++++||||+|||||||||+|||+||+||++|++|+|+|||+||+|+|||||||||.++|+|||+|+||+||+|||||
T Consensus 10 ~~~~~~~SrYesQKrrdwntf~qyL~n~rPP~~L~~csg~hVl~FL~~~d~~GkTkVh~~~C~~~g~~~~p~~C~CPlrq 89 (132)
T PF04852_consen 10 RSPQPAPSRYESQKRRDWNTFGQYLRNHRPPLSLSRCSGNHVLEFLRYLDQFGKTKVHGQGCPFFGHPSPPAPCPCPLRQ 89 (132)
T ss_pred CCCCCCCcccchhhhHHHHHHHHHHHccCCCcchhhcChHHHHHHHHHHhccCCeeecCCCCCCCCCCCCCCCCCCcHHH
Confidence 34455789999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhchhHHHHHHHHHHHHHhCCCCCCCccchhhHHHHHHHhHHH
Q 025815 172 AWGSLDALVGRLRAAYEENGGQPEINPFSARAVRLYLRDVRDV 214 (247)
Q Consensus 172 AWGSLDALIGRLRAAfEE~GG~PE~NPF~araVRlYLReVRd~ 214 (247)
|||||||||||||||||||||+||+|||+++|||+|||||||+
T Consensus 90 AwGSlDalIGrLraafee~Gg~pe~NPf~~~~vr~yLr~vr~~ 132 (132)
T PF04852_consen 90 AWGSLDALIGRLRAAFEEHGGHPEANPFAARAVRLYLREVRDS 132 (132)
T ss_pred HhccHHHHHHHHHHHHHHhCCCCCCCchhhHHHHHHHHHHhcC
Confidence 9999999999999999999999999999999999999999985
No 2
>PF08821 CGGC: CGGC domain; InterPro: IPR014925 Proteins in this entry are a quite highly conserved sequence of CGGC in its central region. The region has many conserved cysteines and histidines suggestive of a zinc binding function.
Probab=89.63 E-value=0.54 Score=37.47 Aligned_cols=55 Identities=24% Similarity=0.572 Sum_probs=45.1
Q ss_pred CccccCc---chhhhHHhhhhccccccccccCCCccccCCCCCCCCCCchhhhhchhHHHHHHHHHHH
Q 025815 123 LALSRCS---GAHVLEFLKYLDQFGKTKVHAQSCPLFGHAHAPAPCRCPMMQAWGSLDALVGRLRAAY 187 (247)
Q Consensus 123 lsLs~Cs---g~hVleFLrylDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQAWGSLDALIGRLRAAf 187 (247)
+.+.+|. +..++..++.+-..|-..||.-+|...+.+.+ +||. +|.++-.|+++|
T Consensus 41 vgf~~CgGCpg~~~~~~~~~l~~~~~d~IHlssC~~~~~~~~----~CP~------~~~~~~~I~~~~ 98 (107)
T PF08821_consen 41 VGFFTCGGCPGRKLVRRIKKLKKNGADVIHLSSCMVKGNPHG----PCPH------IDEIKKIIEEKF 98 (107)
T ss_pred EEEeeCCCCChhHHHHHHHHHHHCCCCEEEEcCCEecCCCCC----CCCC------HHHHHHHHHHHh
Confidence 4444554 58899999999999999999999999987664 6666 899999998887
No 3
>PF02899 Phage_int_SAM_1: Phage integrase, N-terminal SAM-like domain; InterPro: IPR004107 Proteins containing this domain cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [, ]. The phage integrase N-terminal SAM-like domain is almost always found with the signature that defines the phage integrase family (see IPR002104 from INTERPRO).; GO: 0003677 DNA binding, 0015074 DNA integration; PDB: 1Z1G_B 1Z19_A 1Z1B_A 2OXO_A 1P7D_B 3NRW_A 1A0P_A.
Probab=88.01 E-value=0.74 Score=31.79 Aligned_cols=40 Identities=28% Similarity=0.517 Sum_probs=31.8
Q ss_pred hhhhhHhHHHHHHHhcCCCCccccCcchhhhHHhhhhcccc
Q 025815 104 QKRRDWDTFMQYLSQHRPPLALSRCSGAHVLEFLKYLDQFG 144 (247)
Q Consensus 104 QKRrDWntf~qyL~nhrPPlsLs~Csg~hVleFLrylDqfG 144 (247)
.-+++++.|.+|+.+ ....++..++..||.+|+.++-+.|
T Consensus 21 ~Y~~~l~~f~~~~~~-~~~~~~~~i~~~~v~~f~~~~~~~~ 60 (84)
T PF02899_consen 21 SYRRDLRRFIRWLEE-HGIIDWEDITEEDVRDFLEYLAKEG 60 (84)
T ss_dssp HHHHHHHHHHHHHHH-TTS-CGGG--HHHHHHHHHHHHCTT
T ss_pred HHHHHHHHHHHhhhh-hhhhhhhhhhhHHHHHHHHHHHccC
Confidence 446789999999999 6667788999999999999988766
No 4
>cd00798 INT_XerDC XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid inheritance. They share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism with the DNA breaking-rejoining enzyme superfamily. In Escherichia coli, the Xer site-specific recombination system acts to convert dimeric chromosomes, which are formed by homologous recombination to monomers. Two related recombinases, XerC and XerD, bind cooperatively to a recombination site present in the E. coli chromosome. Each recombinase catalyzes the exchange of one pair of DNA strand in a reaction that proceeds through a Holliday junction intermediate. These enzymes can bridge two different and well-separated DNA sequen
Probab=84.29 E-value=3.7 Score=32.47 Aligned_cols=69 Identities=22% Similarity=0.286 Sum_probs=48.5
Q ss_pred hhhhhHhHHHHHHHhcCCCCccccCcchhhhHHhhhhccccccccccCCCccccCCCCCCCCCCchhhhhchhHHHHHHH
Q 025815 104 QKRRDWDTFMQYLSQHRPPLALSRCSGAHVLEFLKYLDQFGKTKVHAQSCPLFGHAHAPAPCRCPMMQAWGSLDALVGRL 183 (247)
Q Consensus 104 QKRrDWntf~qyL~nhrPPlsLs~Csg~hVleFLrylDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQAWGSLDALIGRL 183 (247)
+-+..|+.|.+|+....... +..-+..||.+|+.++.+.| ....++...++-|
T Consensus 21 ~~~~~~~~~~~~~~~~~~~~-~~~l~~~~i~~~~~~~~~~~--------------------------~~~~t~~~~~~~l 73 (284)
T cd00798 21 AYRRDLERFLEFLEERGILF-PADVTPDDIRRFLAELKDQG--------------------------LSARSIARKLSAL 73 (284)
T ss_pred HHHHHHHHHHHHHHHcCCCc-hhhCCHHHHHHHHHHhhhcC--------------------------CCHHHHHHHHHHH
Confidence 44567899999998754432 56778999999999887644 1335777788888
Q ss_pred HHHHHHhC--CCCCCCcc
Q 025815 184 RAAYEENG--GQPEINPF 199 (247)
Q Consensus 184 RAAfEE~G--G~PE~NPF 199 (247)
+++|.-.. |.-+.||+
T Consensus 74 ~~~~~~~~~~~~~~~~p~ 91 (284)
T cd00798 74 RSFFKFLLREGLILANPA 91 (284)
T ss_pred HHHHHHHHHcCCccCChh
Confidence 88887322 34456887
No 5
>cd00799 INT_Cre Cre recombinase, C-terminal catalytic domain. Cre-like recombinases belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The bacteriophage P1 Cre recombinase maintains the circular phage replicon in a monomeric state by catalyzing a site-specific recombination between two loxP sites. The catalytic core domain of Cre recombinase is linked to a more divergent helical N-terminal domain, which interacts primarily with the DNA major groove proximal to the crossover region.
Probab=79.77 E-value=15 Score=30.36 Aligned_cols=77 Identities=23% Similarity=0.276 Sum_probs=52.4
Q ss_pred hhhhhHhHHHHHHHhcCCCCccccCcchhhhHHhhhhccccccccccCCCccccCCCCCCCCCCchhhhhchhHHHHHHH
Q 025815 104 QKRRDWDTFMQYLSQHRPPLALSRCSGAHVLEFLKYLDQFGKTKVHAQSCPLFGHAHAPAPCRCPMMQAWGSLDALVGRL 183 (247)
Q Consensus 104 QKRrDWntf~qyL~nhrPPlsLs~Csg~hVleFLrylDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQAWGSLDALIGRL 183 (247)
.-..+++.|.+|+.... +....-+..||.+|+.|+.+. .+..++-..++.|
T Consensus 6 ~y~~~l~~f~~~~~~~~--~~~~~~~~~~i~~~~~~l~~~---------------------------~s~~ti~~~~~~l 56 (287)
T cd00799 6 AYLSDWRRFAAWCQAHG--RTPLPASPETVTLYLTDLADS---------------------------LAPSTISRRLSAL 56 (287)
T ss_pred HHHHHHHHHHHHHHhcC--CCCCCCCHHHHHHHHHHHHhc---------------------------cChHHHHHHHHHH
Confidence 34568889999998752 222224589999999988531 1457888899999
Q ss_pred HHHHHHhCCCCCCCccchhhHHHHHHHhH
Q 025815 184 RAAYEENGGQPEINPFSARAVRLYLRDVR 212 (247)
Q Consensus 184 RAAfEE~GG~PE~NPF~araVRlYLReVR 212 (247)
+..|+..+. .||+....++.-++.++
T Consensus 57 ~~~~~~~~~---~~p~~~~~~~~~~~~~~ 82 (287)
T cd00799 57 SQLHRRSGL---PSPADSPLVRLVLRGIR 82 (287)
T ss_pred HHHHHHcCC---CCCccCHHHHHHHHHHH
Confidence 999985432 58876655555555554
No 6
>TIGR02225 recomb_XerD tyrosine recombinase XerD. The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerD, one of two closely related chromosomal proteins along with XerC (TIGR02224). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and with homologs of XerD on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerD, as some apparent XerD examples score below the trusted and noise cutoff scores. XerC and XerD interact with cell division protein FtsK.
Probab=78.93 E-value=7.2 Score=31.19 Aligned_cols=70 Identities=24% Similarity=0.423 Sum_probs=47.9
Q ss_pred HhhhhhHhHHHHHHHhcCCCCccccCcchhhhHHhhhhccccccccccCCCccccCCCCCCCCCCchhhhhchhHHHHHH
Q 025815 103 AQKRRDWDTFMQYLSQHRPPLALSRCSGAHVLEFLKYLDQFGKTKVHAQSCPLFGHAHAPAPCRCPMMQAWGSLDALVGR 182 (247)
Q Consensus 103 sQKRrDWntf~qyL~nhrPPlsLs~Csg~hVleFLrylDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQAWGSLDALIGR 182 (247)
++-++.++.|..|+.... ..+..-+..||.+|+.++.+.| -..-+++..++.
T Consensus 19 ~~~~~~~~~~~~~~~~~~--~~~~~it~~~i~~~~~~~~~~~--------------------------~~~~t~~~~~~~ 70 (291)
T TIGR02225 19 EAYRRDLEKFLEFLEERG--IDLEEVDRGDIVDFLAELKEAG--------------------------LSARSIARALSA 70 (291)
T ss_pred HHHHHHHHHHHHHHHhcC--CChHHCCHHHHHHHHHHhhcCC--------------------------CCHhHHHHHHHH
Confidence 445567788889988542 2455667899999999887643 122467888999
Q ss_pred HHHHHHHh--CCCCCCCccc
Q 025815 183 LRAAYEEN--GGQPEINPFS 200 (247)
Q Consensus 183 LRAAfEE~--GG~PE~NPF~ 200 (247)
|+++|+-. .|-.+.||+.
T Consensus 71 l~~~~~~a~~~~~~~~np~~ 90 (291)
T TIGR02225 71 LRSFYRFLLREGIREDDPSA 90 (291)
T ss_pred HHHHHHHHHhcccccCCchh
Confidence 99998732 2345578874
No 7
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed
Probab=78.52 E-value=5.7 Score=32.38 Aligned_cols=68 Identities=24% Similarity=0.270 Sum_probs=47.8
Q ss_pred hhhhHhHHHHHHHhcCCCCccccCcchhhhHHhhhhccccccccccCCCccccCCCCCCCCCCchhhhhchhHHHHHHHH
Q 025815 105 KRRDWDTFMQYLSQHRPPLALSRCSGAHVLEFLKYLDQFGKTKVHAQSCPLFGHAHAPAPCRCPMMQAWGSLDALVGRLR 184 (247)
Q Consensus 105 KRrDWntf~qyL~nhrPPlsLs~Csg~hVleFLrylDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQAWGSLDALIGRLR 184 (247)
-+++|+.|..|+....- .+...+..||.+|+.++.+.| .+-.++...+..|+
T Consensus 30 ~~~~~~~~~~~~~~~~~--~~~~l~~~~i~~~~~~~~~~~--------------------------~~~~t~~~~~~~l~ 81 (299)
T PRK00283 30 YRRDLELFAEWLAARGL--SLAEATRDDLQAFLAELAEGG--------------------------YKATSSARRLSALR 81 (299)
T ss_pred HHHHHHHHHHHHHhcCC--ChHHCCHHHHHHHHHHHHhCC--------------------------CCHHHHHHHHHHHH
Confidence 45688899999986533 566778999999999885432 23457788888899
Q ss_pred HHHHHhC--CCCCCCccc
Q 025815 185 AAYEENG--GQPEINPFS 200 (247)
Q Consensus 185 AAfEE~G--G~PE~NPF~ 200 (247)
++|+-.. |.-+.||+.
T Consensus 82 ~~~~~a~~~~~i~~np~~ 99 (299)
T PRK00283 82 RFFQFLLREGLREDDPSA 99 (299)
T ss_pred HHHHHHHHcCCcccCchh
Confidence 8887331 234568863
No 8
>COG1080 PtsA Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]
Probab=77.10 E-value=2.6 Score=42.67 Aligned_cols=41 Identities=37% Similarity=0.524 Sum_probs=32.9
Q ss_pred hhhhchhHHHHHHHHHHHHHhCCC--------------------C-CCCcc-chhhHHHHHHH
Q 025815 170 MQAWGSLDALVGRLRAAYEENGGQ--------------------P-EINPF-SARAVRLYLRD 210 (247)
Q Consensus 170 RQAWGSLDALIGRLRAAfEE~GG~--------------------P-E~NPF-~araVRlYLRe 210 (247)
|..|=+.|.-----++..|.+||+ | |.||| |-|+||+||..
T Consensus 305 r~~~P~EeEQ~~aY~~vlea~~g~pviiRTlDiGGDK~lpyl~lp~E~NPfLG~RaIRl~l~~ 367 (574)
T COG1080 305 RDALPDEEEQFEAYKAVLEAMGGKPVIIRTLDIGGDKPLPYLNLPKEENPFLGYRAIRLSLER 367 (574)
T ss_pred CCCCCChHHHHHHHHHHHHHcCCCceEEEecccCCCCcCCCCCCccccCchhhhHHHHHhhcc
Confidence 345556777777778888998888 3 79999 89999999964
No 9
>TIGR02224 recomb_XerC tyrosine recombinase XerC. The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerC, one of two closely related chromosomal proteins along with XerD (TIGR02225). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and homologs of XerC on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerC, as some apparent XerC examples score in the gray zone between trusted (450) and noise (410) cutoffs, along with some XerD examples. XerC and XerD interact with cell division protein FtsK.
Probab=66.25 E-value=20 Score=28.80 Aligned_cols=69 Identities=28% Similarity=0.388 Sum_probs=47.0
Q ss_pred hhhHhHHHHHHHhcCCCCccccCcchhhhHHhhhhccccccccccCCCccccCCCCCCCCCCchhhhhchhHHHHHHHHH
Q 025815 106 RRDWDTFMQYLSQHRPPLALSRCSGAHVLEFLKYLDQFGKTKVHAQSCPLFGHAHAPAPCRCPMMQAWGSLDALVGRLRA 185 (247)
Q Consensus 106 RrDWntf~qyL~nhrPPlsLs~Csg~hVleFLrylDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQAWGSLDALIGRLRA 185 (247)
+.+++.|.+||........+..-+..||.+|+.++.+.|. +..++...++.||+
T Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~l~~~~i~~~~~~~~~~~~--------------------------~~~T~~~~~~~l~~ 75 (295)
T TIGR02224 22 RRDLKAFLEFLEEEGGLASLAEVTAADLRSFLAELHARGL--------------------------SRRSLARKLSALRS 75 (295)
T ss_pred HHHHHHHHHHHHhcCCCCccccCcHHHHHHHHHHhcccCC--------------------------CHHHHHHHHHHHHH
Confidence 4466678888888666677888889999999998765321 22456677778887
Q ss_pred HHHHh--CCCCCCCccc
Q 025815 186 AYEEN--GGQPEINPFS 200 (247)
Q Consensus 186 AfEE~--GG~PE~NPF~ 200 (247)
+|.-. -+.-+.|||.
T Consensus 76 ~~~~a~~~~~~~~np~~ 92 (295)
T TIGR02224 76 FYRFLVRRGLIKANPAA 92 (295)
T ss_pred HHHHHHHcCccccChHh
Confidence 77642 1223467763
No 10
>PF10865 DUF2703: Domain of unknown function (DUF2703); InterPro: IPR021219 This family of protein has no known function.
Probab=56.15 E-value=4 Score=33.55 Aligned_cols=43 Identities=28% Similarity=0.274 Sum_probs=32.9
Q ss_pred hhHHhhhhccccccccccCCCccccCCCCCCCCCCchhhhhchhHHHHHHHHHHHHHhCCCCC
Q 025815 133 VLEFLKYLDQFGKTKVHAQSCPLFGHAHAPAPCRCPMMQAWGSLDALVGRLRAAYEENGGQPE 195 (247)
Q Consensus 133 VleFLrylDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQAWGSLDALIGRLRAAfEE~GG~PE 195 (247)
+++|+ |+|..|+| |... ...+.+|+..+-+|+.+|+..|..++
T Consensus 2 ~I~w~-~l~~~g~t------C~RC-------------~~Tg~~L~~av~~l~~~L~~~Giev~ 44 (120)
T PF10865_consen 2 VIEWQ-HLDLDGKT------CERC-------------GDTGETLREAVKELAPVLAPLGIEVR 44 (120)
T ss_pred eEEEE-EeecCCCc------CCch-------------hhHHHHHHHHHHHHHHHHHhCCcEEE
Confidence 46788 55555776 4333 36778999999999999999998765
No 11
>TIGR01418 PEP_synth phosphoenolpyruvate synthase. Also called pyruvate,water dikinase and PEP synthase. The member from Methanococcus jannaschii contains a large intein. This enzyme generates phosphoenolpyruvate (PEP) from pyruvate, hydrolyzing ATP to AMP and releasing inorganic phosphate in the process. The enzyme shows extensive homology to other enzymes that use PEP as substrate or product. This enzyme may provide PEP for gluconeogenesis, for PTS-type carbohydrate transport systems, or for other processes.
Probab=54.51 E-value=20 Score=36.87 Aligned_cols=42 Identities=19% Similarity=0.211 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHHhCCC-------------------------CCCCcc-chhhHHHHH----HHhHHHHHhh
Q 025815 177 DALVGRLRAAYEENGGQ-------------------------PEINPF-SARAVRLYL----RDVRDVQAEA 218 (247)
Q Consensus 177 DALIGRLRAAfEE~GG~-------------------------PE~NPF-~araVRlYL----ReVRd~QAKA 218 (247)
|.+.-.+|.+++.++++ .|.||| |.|+||+|| .|+=+.|.+|
T Consensus 547 ~~~~~~y~~i~~~~~~~pV~iRtlD~~~dk~~~~~ggdk~~~~E~NP~LG~RGir~~l~~~~~~lf~~qlra 618 (782)
T TIGR01418 547 DKLAEGIAKVAAAFYPKPVIVRTSDFKSNEYRNLIGGEEYEPDEENPMLGWRGASRYYSESYEEAFRLECRA 618 (782)
T ss_pred HHHHHHHHHHHHHcCCCeEEEEcCCCCccchhhhhCCCccCCCCCCcccccchhhhhcccccHHHHHHHHHH
Confidence 55566777887776544 378999 899999999 4566666655
No 12
>PF02896 PEP-utilizers_C: PEP-utilising enzyme, TIM barrel domain; InterPro: IPR000121 A number of enzymes that catalyze the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) via a phospho-histidine intermediate have been shown to be structurally related [, , , ]. All these enzymes share the same catalytic mechanism: they bind PEP and transfer the phosphoryl group from it to a histidine residue. The sequence around that residue is highly conserved. This domain is often found associated with the pyruvate phosphate dikinase, PEP/pyruvate-binding domain (IPR002192 from INTERPRO) at its N terminus and the PEP-utilizing enzyme mobile domain.; GO: 0016772 transferase activity, transferring phosphorus-containing groups, 0016310 phosphorylation; PDB: 2HRO_A 2OLS_A 2DIK_A 2R82_A 1JDE_A 1DIK_A 1GGO_A 1KBL_A 1KC7_A 2BG5_B ....
Probab=53.63 E-value=30 Score=31.89 Aligned_cols=40 Identities=28% Similarity=0.226 Sum_probs=31.6
Q ss_pred hchhHHHHHHHHHHHHHhCCC----------------------CCCCcc-chhhHHHHHHHhH
Q 025815 173 WGSLDALVGRLRAAYEENGGQ----------------------PEINPF-SARAVRLYLRDVR 212 (247)
Q Consensus 173 WGSLDALIGRLRAAfEE~GG~----------------------PE~NPF-~araVRlYLReVR 212 (247)
+=+.|.+...++.+.+..+++ .|.||| |-|+||.||..-.
T Consensus 58 ~p~e~eq~~~y~~i~~~~~~~pV~iRtlD~g~dK~l~~~~~~~~E~NP~LG~RGiR~~l~~p~ 120 (293)
T PF02896_consen 58 PPSEEEQYEIYRKIAEAMGGKPVTIRTLDIGGDKPLPYLSREPKEENPALGLRGIRRSLAHPE 120 (293)
T ss_dssp HHHHHHHHHHHHHHHHHTTTSEEEEE---SBCCCGSCSSHHCH--SSGGGSSBTHHHHHHSHH
T ss_pred CchHHHHHHHHHHHHHHhccCcEEEEecCCCCCccCCcccccccccccccccccccccccchh
Confidence 446788899999999988876 569998 8899999997633
No 13
>cd01185 INT_Tn4399 Tn4399 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains. This CD includes various bacterial integrases, including cLV25, a Bacteroides fragilis chromosomal transfer factor integrase similar to the Bacteroides mobilizable transposon, Tn4399, integrase.
Probab=52.89 E-value=55 Score=27.17 Aligned_cols=33 Identities=18% Similarity=0.345 Sum_probs=26.2
Q ss_pred hHhHHHHHHHhcCC--CCccccCcchhhhHHhhhh
Q 025815 108 DWDTFMQYLSQHRP--PLALSRCSGAHVLEFLKYL 140 (247)
Q Consensus 108 DWntf~qyL~nhrP--PlsLs~Csg~hVleFLryl 140 (247)
..+.|..|+....+ .+.+..-+..||.+|+.|+
T Consensus 44 ~~~~~~~~~~~~~~~~~~~l~~i~~~~i~~~~~~l 78 (299)
T cd01185 44 HLKNLREFIECTYKEIDIALLELTREFILEFKLFL 78 (299)
T ss_pred HHHHHHHHHHHhcCccCCCHHHccHHHHHHHHHHH
Confidence 45668888876554 6778888899999999988
No 14
>PRK10529 DNA-binding transcriptional activator KdpE; Provisional
Probab=52.16 E-value=12 Score=29.21 Aligned_cols=19 Identities=26% Similarity=0.454 Sum_probs=15.4
Q ss_pred hhHHHHHHHHHHHHHhCCC
Q 025815 175 SLDALVGRLRAAYEENGGQ 193 (247)
Q Consensus 175 SLDALIGRLRAAfEE~GG~ 193 (247)
+||..|.|||.-+++.+..
T Consensus 191 ~~~~~i~rlR~kl~~~~~~ 209 (225)
T PRK10529 191 YLRIYMGHLRQKLEQDPAR 209 (225)
T ss_pred CHHHHHHHHHHHhccCCCC
Confidence 6999999999999765543
No 15
>PHA03385 IX capsid protein IX,hexon associated protein IX; Provisional
Probab=49.62 E-value=19 Score=30.87 Aligned_cols=33 Identities=39% Similarity=0.370 Sum_probs=18.9
Q ss_pred cCCCCCCcceeeeecchhhHHHHHHHHHHHHHh
Q 025815 26 PFPAPNLSHIKIVSFPFQSLMSAAVSAAAAAAC 58 (247)
Q Consensus 26 ~~~~~~~~~~~~~~~~~~~~msaavaaaaaaa~ 58 (247)
|.+.+|-+.+..-.+---+|=+||.|||++||+
T Consensus 39 pV~Pans~~l~yat~~~S~lDtAAAAAAsaaA~ 71 (135)
T PHA03385 39 PVLPANSSTLTYATVSSSSLDTAAAAAAAAAAS 71 (135)
T ss_pred ccCCCCcceeeeeecCCCchHHHHHHHHHHHHH
Confidence 445566666665555444565666666555553
No 16
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=48.83 E-value=24 Score=36.13 Aligned_cols=36 Identities=22% Similarity=0.289 Sum_probs=29.7
Q ss_pred hhHHHHHHHHHHHHHhCCC--------------------CCCCcc-chhhHHHHHHH
Q 025815 175 SLDALVGRLRAAYEENGGQ--------------------PEINPF-SARAVRLYLRD 210 (247)
Q Consensus 175 SLDALIGRLRAAfEE~GG~--------------------PE~NPF-~araVRlYLRe 210 (247)
+-|......|.+.+.++|+ +|.||| |.|+||+||+.
T Consensus 475 ~e~eQ~~~y~~~~~~~~~~pv~iRtlDiGgDK~~~~~~~~E~NP~lG~RgiR~~l~~ 531 (748)
T PRK11061 475 SEEEQVAQYQGMLQMFPDKPVTLRTLDIGADKQLPYMPISEENPCLGWRGIRITLDQ 531 (748)
T ss_pred CHHHHHHHHHHHHHHcCCCeEEEECCCCCcCCCCCCCCCCCCCcccccchhhccccC
Confidence 4678888889888888765 589999 88999999853
No 17
>PF00539 Tat: Transactivating regulatory protein (Tat); InterPro: IPR001831 Like other lentiviruses, Human immunodeficiency virus 1 (HIV-1) encodes a trans-activating regulatory protein (Tat), which is essential for efficient transcription of the viral genome [, ]. Tat acts by binding to an RNA stem-loop structure, the trans-activating response element (TAR), found at the 5' ends of nascent HIV-1 transcripts. In binding to TAR, Tat alters the properties of the transcription complex, recruits a positive transcription elongation complex (P-TEFb) and hence increases the production of full-length viral RNA []. Tat protein also associates with RNA polymerase II complexes during early transcription elongation after the promoter clearance and before the synthesis of full-length TAR RNA transcript. This interaction of Tat with RNA polymerase II elongation complexes is P-TEFb-independent. There are two Tat binding sites on each transcription elongation complex; one is located on TAR RNA and the other one on RNA polymerase II near the exit site for nascent mRNA transcripts which suggests that two Tat molecules are involved in performing various functions during a single round of HIV-1 mRNA synthesis []. The minimum Tat sequence that can mediate specific TAR binding in vitro has been mapped to a basic domain of 10 amino acids, comprising mostly Arg and Lys residues. Regulatory activity, however, also requires the 47 N-terminal residues, which interact with components of the transcription complex and function as a transcriptional activation domain [, , ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 2W2H_D 1ZBN_B 1TVS_A 1TVT_A 3O6L_C 3O6M_C 3MI9_C 3MIA_C 1JFW_A 1TBC_A ....
Probab=44.79 E-value=9.3 Score=29.35 Aligned_cols=19 Identities=26% Similarity=0.518 Sum_probs=14.1
Q ss_pred HhhhcccchhhhhccCCCCC
Q 025815 216 AEARGMIGYDQKKTRKNNYM 235 (247)
Q Consensus 216 AKARg~i~y~kKkrkr~~~~ 235 (247)
.|.-| |.|..|||||...+
T Consensus 45 ~KgLG-I~Y~r~rrRrr~~~ 63 (68)
T PF00539_consen 45 QKGLG-ISYGRKRRRRRTPQ 63 (68)
T ss_dssp CTSSS-TSSSSSSCSCCCSS
T ss_pred eCCCc-ccccccccCcCCCC
Confidence 47789 99998887665544
No 18
>PF05528 Coronavirus_5: Coronavirus gene 5 protein; InterPro: IPR008458 Infectious bronchitis virus, a member of Coronaviridae family, has a single-stranded positive-sense RNA genome, which is 27 kb in length. Gene 5 contains two (5a and 5b) open reading frames. The function of the 5a and 5b proteins is unknown [].
Probab=42.71 E-value=4.4 Score=32.12 Aligned_cols=20 Identities=50% Similarity=0.785 Sum_probs=15.6
Q ss_pred CCCCcc---chhhHHHHHHHhHH
Q 025815 194 PEINPF---SARAVRLYLRDVRD 213 (247)
Q Consensus 194 PE~NPF---~araVRlYLReVRd 213 (247)
..+||| .||-+|+||||=-|
T Consensus 4 ~k~NPfr~aiARKaRiyLr~Gld 26 (82)
T PF05528_consen 4 SKDNPFRGAIARKARIYLREGLD 26 (82)
T ss_pred cccCchhhhhhhheeeeeecCCc
Confidence 358999 57889999997543
No 19
>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional
Probab=42.47 E-value=18 Score=28.20 Aligned_cols=17 Identities=35% Similarity=0.620 Sum_probs=14.5
Q ss_pred hhHHHHHHHHHHHHHhC
Q 025815 175 SLDALVGRLRAAYEENG 191 (247)
Q Consensus 175 SLDALIGRLRAAfEE~G 191 (247)
++|..|.|||.-+++.+
T Consensus 189 ~v~~~i~rLR~kl~~~~ 205 (223)
T PRK10816 189 TIDVLMGRLRKKIQAQY 205 (223)
T ss_pred CHHHHHHHHHHHhccCC
Confidence 79999999999997643
No 20
>PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=42.42 E-value=1e+02 Score=24.70 Aligned_cols=37 Identities=27% Similarity=0.428 Sum_probs=27.5
Q ss_pred hhhhHhHHHHHHHhcCCCCccccCcchhhhHHhhhhcc
Q 025815 105 KRRDWDTFMQYLSQHRPPLALSRCSGAHVLEFLKYLDQ 142 (247)
Q Consensus 105 KRrDWntf~qyL~nhrPPlsLs~Csg~hVleFLrylDq 142 (247)
-+.+|+.|..|+..... ..+..-+..||.+|+.++-+
T Consensus 31 ~~~~~~~~~~~~~~~~~-~~~~~i~~~~i~~~~~~~~~ 67 (297)
T PRK00236 31 YRRDLRAFLAFLEEHGI-SSLQDLDAADLRSFLARRRR 67 (297)
T ss_pred HHHHHHHHHHHHHHcCC-CchhhCCHHHHHHHHHHHHh
Confidence 34677888888887543 55667788999999987754
No 21
>smart00259 ZnF_A20 A20-like zinc fingers. A20- (an inhibitor of cell death)-like zinc fingers. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappaB activation.
Probab=42.31 E-value=13 Score=23.56 Aligned_cols=16 Identities=25% Similarity=0.750 Sum_probs=13.7
Q ss_pred CCCccccCCCCCCCCC
Q 025815 151 QSCPLFGHAHAPAPCR 166 (247)
Q Consensus 151 ~~C~ffG~p~ppapC~ 166 (247)
.+|.|||.|..-..|.
T Consensus 7 ~~CgF~G~~~t~~~Cs 22 (26)
T smart00259 7 PGCGFFGNPATEGLCS 22 (26)
T ss_pred CCCCCcCChhhcccCH
Confidence 7999999998877774
No 22
>PF13276 HTH_21: HTH-like domain
Probab=40.35 E-value=46 Score=22.74 Aligned_cols=29 Identities=21% Similarity=0.350 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHhCCCCCCCccchhhHHHHHHH
Q 025815 177 DALVGRLRAAYEENGGQPEINPFSARAVRLYLRD 210 (247)
Q Consensus 177 DALIGRLRAAfEE~GG~PE~NPF~araVRlYLRe 210 (247)
|+|+-.++++|+++++. ||.+-|..+|++
T Consensus 4 ~~l~~~I~~i~~~~~~~-----yG~rri~~~L~~ 32 (60)
T PF13276_consen 4 EALRELIKEIFKESKPT-----YGYRRIWAELRR 32 (60)
T ss_pred HHHHHHHHHHHHHcCCC-----eehhHHHHHHhc
Confidence 67899999999999773 788888888876
No 23
>PF00486 Trans_reg_C: Transcriptional regulatory protein, C terminal; InterPro: IPR001867 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain that is almost always found associated with the response regulator receiver domain (see IPR001789 from INTERPRO). It may play a role in DNA binding [].; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2K4J_A 2JPB_A 1ODD_A 1OPC_A 1KGS_A 2PMU_E 2JZY_A 1GXP_B 1QQI_A 2Z33_A ....
Probab=38.49 E-value=31 Score=23.55 Aligned_cols=21 Identities=48% Similarity=0.846 Sum_probs=18.3
Q ss_pred chhHHHHHHHHHHHHHhCCCC
Q 025815 174 GSLDALVGRLRAAYEENGGQP 194 (247)
Q Consensus 174 GSLDALIGRLRAAfEE~GG~P 194 (247)
-+||..|-|||..+++.|+.+
T Consensus 44 ~~l~~~I~rLR~kL~~~~~~~ 64 (77)
T PF00486_consen 44 NSLDVHISRLRKKLEDAGGDP 64 (77)
T ss_dssp HHHHHHHHHHHHHHHSSTTSS
T ss_pred hhHHHHHHHHHHHHhhcCCCC
Confidence 489999999999999987554
No 24
>cd08793 Death_IRAK4 Death domain of Interleukin-1 Receptor-Associated Kinase 4. Death Domain (DD) of Interleukin-1 Receptor-Associated Kinase 4 (IRAK4). IRAKs are essential components of innate immunity and inflammation in mammals and other vertebrates. They are involved in signal transduction pathways involving IL-1 and IL-18 receptors, Toll-like receptors, nuclear factor-kappaB, and mitogen-activated protein kinases. IRAKs contain an N-terminal DD domain and a C-terminal kinase domain. IRAK4 is an active kinase that is also involved in T-cell receptor signaling pathways, implying that it may function in acquired immunity and not just in innate immunity. It is known as the master IRAK member because its absence strongly impairs TLR- and IL-1-mediated signaling and innate immune defenses, while the absence of other IRAK proteins only shows slight effects. IRAK4-deficient patients have impaired inflammatory responses and recurrent life-threatening infections. DDs are protein-protein int
Probab=36.31 E-value=37 Score=27.57 Aligned_cols=64 Identities=23% Similarity=0.441 Sum_probs=44.4
Q ss_pred hHhHHHHHHHhcCCCCccccCcchhhhHHhhhhccccccccccCCCccccCCCCCCCCCCchhhhhchhHHHHHHHHHHH
Q 025815 108 DWDTFMQYLSQHRPPLALSRCSGAHVLEFLKYLDQFGKTKVHAQSCPLFGHAHAPAPCRCPMMQAWGSLDALVGRLRAAY 187 (247)
Q Consensus 108 DWntf~qyL~nhrPPlsLs~Csg~hVleFLrylDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQAWGSLDALIGRLRAAf 187 (247)
+|.++-..+.. |-.-.+.+--||-+|=++.++ | .+| +|-|=..||+-++-||.|-..+
T Consensus 23 ~W~~LA~~i~~---~~~~~~y~~~ei~~ie~~~~~--------------g-~SP----T~~LL~dWgt~N~TV~~L~~lL 80 (100)
T cd08793 23 GWKKIAVAIKK---PSGDPRYSQFHIRRFEALVQQ--------------G-KSP----TCELLFDWGTTNCTVGDLVDLL 80 (100)
T ss_pred cHHHHHHHHhc---ccCCCCCCHHHHHHHHHHHHc--------------C-CCh----HHHHHHHHccCCCcHHHHHHHH
Confidence 89998888765 333334544566666544333 3 222 5567789999999999999999
Q ss_pred HHhCCC
Q 025815 188 EENGGQ 193 (247)
Q Consensus 188 EE~GG~ 193 (247)
.++|-.
T Consensus 81 ~k~~l~ 86 (100)
T cd08793 81 IQNEFF 86 (100)
T ss_pred HHcccH
Confidence 998843
No 25
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=35.96 E-value=43 Score=23.28 Aligned_cols=53 Identities=15% Similarity=0.376 Sum_probs=31.4
Q ss_pred hhHhHHHHHHHhcCCCCccccCcchhhhHHhhhhc-cccccccccCCCccccCCCCCCCCCCchhhhhchhHHHHHHHHH
Q 025815 107 RDWDTFMQYLSQHRPPLALSRCSGAHVLEFLKYLD-QFGKTKVHAQSCPLFGHAHAPAPCRCPMMQAWGSLDALVGRLRA 185 (247)
Q Consensus 107 rDWntf~qyL~nhrPPlsLs~Csg~hVleFLrylD-qfGKTKVH~~~C~ffG~p~ppapC~CPLRQAWGSLDALIGRLRA 185 (247)
...+.|.+|+.+. ++...+..||.+|+.|+- .-| .+..++...+.-||.
T Consensus 24 ~~l~~f~~~~~~~----~~~~it~~~i~~y~~~l~~~~~--------------------------~s~~T~~~~~~~l~~ 73 (85)
T PF13495_consen 24 YHLKRFLRFLGNK----PPDEITPEDIEQYLNYLQNERG--------------------------LSPSTINQYLSALRS 73 (85)
T ss_dssp HHHHHHHTTSSS------GGG--HHHHHHHHHHHHTTT-----------------------------HHHHHHHHHHHHH
T ss_pred HHHHHHHHHcccC----ccchhHHHHHHHHHHHHHHhcC--------------------------CCHHHHHHHHHHHHH
Confidence 3445566676532 556678999999999887 322 345566666666776
Q ss_pred HHHH
Q 025815 186 AYEE 189 (247)
Q Consensus 186 AfEE 189 (247)
-|+-
T Consensus 74 ff~~ 77 (85)
T PF13495_consen 74 FFRW 77 (85)
T ss_dssp HHHC
T ss_pred HHHH
Confidence 6653
No 26
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=35.65 E-value=33 Score=25.81 Aligned_cols=35 Identities=23% Similarity=0.374 Sum_probs=30.3
Q ss_pred CCCCchhhhhc----hhHHHHHHHHHHHHHhCCCCCCCc
Q 025815 164 PCRCPMMQAWG----SLDALVGRLRAAYEENGGQPEINP 198 (247)
Q Consensus 164 pC~CPLRQAWG----SLDALIGRLRAAfEE~GG~PE~NP 198 (247)
-|+|-+|..-+ ++|.|=.+|..+++||......+|
T Consensus 18 ~C~Cgl~l~~~~~~~tl~~l~~~L~~~~~~H~~~C~~~p 56 (82)
T PF14768_consen 18 SCSCGLRLNTQQDELTLEELRQLLEEAVTEHSDRCSSTP 56 (82)
T ss_pred ECCCccEEecCCCCCCHHHHHHHHHHHHHHHHHhCCCCC
Confidence 47777888888 999999999999999987777666
No 27
>cd00801 INT_P4 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall reaction mechanism with the superfamily of DNA breaking-rejoining enzymes. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes.
Probab=34.98 E-value=67 Score=26.94 Aligned_cols=52 Identities=19% Similarity=0.325 Sum_probs=35.9
Q ss_pred CCCccccCcchhhhHHhhhhccccccccccCCCccccCCCCCCCCCCchhhhhchhHHHHHHHHHHHHH---hCCCCCCC
Q 025815 121 PPLALSRCSGAHVLEFLKYLDQFGKTKVHAQSCPLFGHAHAPAPCRCPMMQAWGSLDALVGRLRAAYEE---NGGQPEIN 197 (247)
Q Consensus 121 PPlsLs~Csg~hVleFLrylDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQAWGSLDALIGRLRAAfEE---~GG~PE~N 197 (247)
.-+.|...+..||.+|+..+-+.| .-.++...++.||++|+- +|.- +.|
T Consensus 109 g~~~l~~i~~~~~~~~~~~~~~~~---------------------------~~~t~~~~~~~l~~~~~~a~~~g~i-~~n 160 (357)
T cd00801 109 GKKPITEITARDLLDVLRRIEARG---------------------------ALETARRVRQRLKQVFRYAIARGLI-EAN 160 (357)
T ss_pred cCCCHHHcCHHHHHHHHHHHHHcC---------------------------CHHHHHHHHHHHHHHHHHHHHcCCc-ccC
Confidence 345566778888888887553321 024788899999999984 4544 489
Q ss_pred ccc
Q 025815 198 PFS 200 (247)
Q Consensus 198 PF~ 200 (247)
|+.
T Consensus 161 P~~ 163 (357)
T cd00801 161 PAA 163 (357)
T ss_pred chH
Confidence 985
No 28
>PRK09279 pyruvate phosphate dikinase; Provisional
Probab=33.99 E-value=37 Score=35.90 Aligned_cols=25 Identities=36% Similarity=0.589 Sum_probs=21.0
Q ss_pred CCCCcc-chhhHHHHH--HHhHHHHHhh
Q 025815 194 PEINPF-SARAVRLYL--RDVRDVQAEA 218 (247)
Q Consensus 194 PE~NPF-~araVRlYL--ReVRd~QAKA 218 (247)
-|.||+ |.|.+|+|| .|+=++|.+|
T Consensus 658 ~E~NPmLG~RG~Rl~l~~pei~~~QlrA 685 (879)
T PRK09279 658 HEFNPMLGHRGCRLGITYPEIYEMQARA 685 (879)
T ss_pred CCCCCccccchhhcccCChHHHHHHHHH
Confidence 489999 889999999 5677788776
No 29
>smart00862 Trans_reg_C Transcriptional regulatory protein, C terminal. This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.
Probab=33.77 E-value=42 Score=22.75 Aligned_cols=19 Identities=37% Similarity=0.711 Sum_probs=17.2
Q ss_pred chhHHHHHHHHHHHHHhCC
Q 025815 174 GSLDALVGRLRAAYEENGG 192 (247)
Q Consensus 174 GSLDALIGRLRAAfEE~GG 192 (247)
.+++..|-|||..+++.|+
T Consensus 45 ~~l~~~i~~LR~~l~~~~~ 63 (78)
T smart00862 45 NTLDVHISRLRKKLEDDGA 63 (78)
T ss_pred chHHHHHHHHHHHHhcCCC
Confidence 6799999999999999865
No 30
>TIGR01417 PTS_I_fam phosphoenolpyruvate-protein phosphotransferase. This model recognizes a distinct clade of phophoenolpyruvate (PEP)-dependent enzymes. Most members are known or deduced to function as the phosphoenolpyruvate-protein phosphotransferase (or enzyme I) of PTS sugar transport systems. However, some species with both a member of this family and a homolog of the phosphocarrier protein HPr lack a IIC component able to serve as a permease. An HPr homolog designated NPr has been implicated in the regulation of nitrogen assimilation, which demonstrates that not all phosphotransferase system components are associated directly with PTS transport.
Probab=33.35 E-value=52 Score=32.67 Aligned_cols=36 Identities=28% Similarity=0.398 Sum_probs=28.8
Q ss_pred hhHHHHHHHHHHHHHhCCC---------------------CCCCcc-chhhHHHHHHH
Q 025815 175 SLDALVGRLRAAYEENGGQ---------------------PEINPF-SARAVRLYLRD 210 (247)
Q Consensus 175 SLDALIGRLRAAfEE~GG~---------------------PE~NPF-~araVRlYLRe 210 (247)
+.|...-..|.+.+..+++ .|.||| |-|++|+||+.
T Consensus 308 ~e~eq~~~y~~i~~~~~~~pv~iRtlDig~DK~~~~~~~~~E~NP~LG~RgiR~~l~~ 365 (565)
T TIGR01417 308 TEEEQFAAYKTVLEAMESDAVIVRTLDIGGDKELPYLNFPKEENPFLGYRAIRLALER 365 (565)
T ss_pred CHHHHHHHHHHHHHHhCCCceEEECCCCCCcccccccCCCCCCCccccchhhhhcccC
Confidence 4467777788888888766 379998 89999999974
No 31
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair]
Probab=33.01 E-value=39 Score=32.02 Aligned_cols=43 Identities=28% Similarity=0.573 Sum_probs=36.3
Q ss_pred CCchhHHhhhhhHhHHHHHHHhcCCCC-ccccCcchhhhHHhhhhccccc
Q 025815 97 SFGRYEAQKRRDWDTFMQYLSQHRPPL-ALSRCSGAHVLEFLKYLDQFGK 145 (247)
Q Consensus 97 ~~SRYesQKRrDWntf~qyL~nhrPPl-sLs~Csg~hVleFLrylDqfGK 145 (247)
+.+.| |||-+.|.+||..+. + ++...+-.||.+||.++-.+|.
T Consensus 26 Tl~sY----rrDL~~f~~~L~~~~--~~~l~~~~~~di~~yl~~l~~~g~ 69 (300)
T COG4974 26 TLSSY----RRDLEDFREWLEERG--ITDLADATEADIREYLTELAEQGL 69 (300)
T ss_pred hHHHH----HHHHHHHHHHHHhcC--CCChhhcCHHHHHHHHHHHHhCCc
Confidence 44555 689999999999876 4 6788889999999999999995
No 32
>PF06252 DUF1018: Protein of unknown function (DUF1018); InterPro: IPR009363 This family consists of several bacterial and phage proteins, related to Gp16 of phage Mu, of unknown function.
Probab=31.15 E-value=2.2e+02 Score=22.19 Aligned_cols=86 Identities=16% Similarity=0.168 Sum_probs=56.2
Q ss_pred hHhHHHHHHHhcCCCCccccCcchhhhHHhhhhccccccccccCCCccccCCCCCCCCCCchhhhhchhHHHHHHHHHHH
Q 025815 108 DWDTFMQYLSQHRPPLALSRCSGAHVLEFLKYLDQFGKTKVHAQSCPLFGHAHAPAPCRCPMMQAWGSLDALVGRLRAAY 187 (247)
Q Consensus 108 DWntf~qyL~nhrPPlsLs~Csg~hVleFLrylDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQAWGSLDALIGRLRAAf 187 (247)
|..+....|.+...=-+...||-.+..++|..+.+.|-. +....=..-+.|. . ...+.+.+++|..
T Consensus 2 ddd~YR~~L~~~~Gk~S~k~lt~~el~~vl~~l~~~G~k-~~~~~~~~~~~~~--~-----------~~~~q~~KI~aLw 67 (119)
T PF06252_consen 2 DDDTYRALLQRVTGKSSSKDLTEAELEKVLDELKRLGFK-PPKPARRPGRRPG--M-----------ATSAQLRKIRALW 67 (119)
T ss_pred CHHHHHHHHHHHhChhhHHHCCHHHHHHHHHHHHHccCc-CccccccCCCCCC--C-----------cchHHHHHHHHHH
Confidence 567788888888887788888999988899888888853 2111111111111 1 1778999999999
Q ss_pred HHhCCCCC-CCccchhhHHHHH
Q 025815 188 EENGGQPE-INPFSARAVRLYL 208 (247)
Q Consensus 188 EE~GG~PE-~NPF~araVRlYL 208 (247)
.++|.... .||- ..+..-|+
T Consensus 68 ~~~~~~~~v~~~s-~~aL~~fv 88 (119)
T PF06252_consen 68 KQLGKPGAVRDPS-EAALDAFV 88 (119)
T ss_pred HHhhccCCccchH-HHHHHHHH
Confidence 99997765 3332 33444443
No 33
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, 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 []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=29.45 E-value=39 Score=22.17 Aligned_cols=12 Identities=33% Similarity=0.841 Sum_probs=10.1
Q ss_pred hhHHHHHHHhHH
Q 025815 202 RAVRLYLRDVRD 213 (247)
Q Consensus 202 raVRlYLReVRd 213 (247)
.+|+.||++|+.
T Consensus 2 D~l~~Yl~ei~~ 13 (37)
T PF00140_consen 2 DSLRLYLKEIGR 13 (37)
T ss_dssp HHHHHHHHHHHH
T ss_pred cHHHHHHHHHcC
Confidence 479999999975
No 34
>TIGR01828 pyru_phos_dikin pyruvate, phosphate dikinase. This model represents pyruvate,phosphate dikinase, also called pyruvate,orthophosphate dikinase. It is similar in sequence to other PEP-utilizing enzymes.
Probab=28.87 E-value=32 Score=36.09 Aligned_cols=26 Identities=31% Similarity=0.543 Sum_probs=20.2
Q ss_pred CCCCCcc-chhhHHHHH--HHhHHHHHhh
Q 025815 193 QPEINPF-SARAVRLYL--RDVRDVQAEA 218 (247)
Q Consensus 193 ~PE~NPF-~araVRlYL--ReVRd~QAKA 218 (247)
..|.||| |.|.||+|| .|+=++|.+|
T Consensus 651 ~~E~NP~LG~RGiRl~l~~pei~~~QlrA 679 (856)
T TIGR01828 651 LHEVNPMLGHRGCRLGITYPEIYEMQVRA 679 (856)
T ss_pred CCCCCCccccchhhhccCChHHHHHHHHH
Confidence 3599999 889999999 4555666655
No 35
>cd04372 RhoGAP_chimaerin RhoGAP_chimaerin: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of chimaerins. Chimaerins are a family of phorbolester- and diacylglycerol-responsive GAPs specific for the Rho-like GTPase Rac. Chimaerins exist in two alternative splice forms that each contain a C-terminal GAP domain, and a central C1 domain which binds phorbol esters, inducing a conformational change that activates the protein; one splice form is lacking the N-terminal Src homology-2 (SH2) domain. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GT
Probab=28.71 E-value=58 Score=27.25 Aligned_cols=36 Identities=19% Similarity=0.466 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHhCCCCC---C---Cc-cchhhHHHHHHHhHH
Q 025815 178 ALVGRLRAAYEENGGQPE---I---NP-FSARAVRLYLRDVRD 213 (247)
Q Consensus 178 ALIGRLRAAfEE~GG~PE---~---NP-F~araVRlYLReVRd 213 (247)
.-|.+|+..|++.|...+ . ++ -.+..+|.||||.-+
T Consensus 45 ~~i~~l~~~~d~~~~~~~~~~~~~~d~h~va~lLK~flReLP~ 87 (194)
T cd04372 45 EEIEDVKMAFDRDGEKADISATVYPDINVITGALKLYFRDLPI 87 (194)
T ss_pred HHHHHHHHHHcCCCCccCCcccccccHHHHHHHHHHHHHhCCC
Confidence 478889999998775432 1 22 267889999999864
No 36
>PF08544 GHMP_kinases_C: GHMP kinases C terminal ; InterPro: IPR013750 This domain is found in homoserine kinases (2.7.1.39 from EC), galactokinases (2.7.1.6 from EC) and mevalonate kinases (2.7.1.36 from EC). These kinases make up the GHMP kinase superfamily of ATP-dependent enzymes []. These enzymes are involved in the biosynthesis of isoprenes and amino acids as well as in carbohydrate metabolism. The C-terminal domain of homoserine kinase has a central alpha-beta plait fold and an insertion of four helices, which, together with the N-terminal fold, create a novel nucleotide binding fold [].; PDB: 2R3V_C 4EMD_A 4DXL_A 4ED4_A 2GS8_A 1K47_E 3GON_A 3K17_B 1PIE_A 2AJ4_A ....
Probab=28.70 E-value=10 Score=26.32 Aligned_cols=72 Identities=11% Similarity=0.190 Sum_probs=45.4
Q ss_pred hhhhHhHHHHHHHhcCC--CCccccCcchhhhHHhhhhcccc--cccc---ccCCCccccCCCCCCCCCCchhhhhchhH
Q 025815 105 KRRDWDTFMQYLSQHRP--PLALSRCSGAHVLEFLKYLDQFG--KTKV---HAQSCPLFGHAHAPAPCRCPMMQAWGSLD 177 (247)
Q Consensus 105 KRrDWntf~qyL~nhrP--PlsLs~Csg~hVleFLrylDqfG--KTKV---H~~~C~ffG~p~ppapC~CPLRQAWGSLD 177 (247)
++.||..|.+.+.+..- +.....+...+|.+.+.++.+.| -+++ +.-+|.|- +=.--...|
T Consensus 6 ~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~Ga~~~~~sGsG~G~~v~~------------l~~~~~~~~ 73 (85)
T PF08544_consen 6 AEGDLELLGELMNENQENEPENYREVLTPEIDELKEAAEENGALGAKMSGSGGGPTVFA------------LCKDEDDAE 73 (85)
T ss_dssp HTTCHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHTTESEEEEETTSSSSEEEE------------EESSHHHHH
T ss_pred HCcCHHHHHHHHHHhhhhcchHHHHHcCHHHHHHHHHHHHCCCCceecCCCCCCCeEEE------------EECCHHHHH
Confidence 56899999999995544 44455677788888888887887 3333 11333332 222234566
Q ss_pred HHHHHHHHHHH
Q 025815 178 ALVGRLRAAYE 188 (247)
Q Consensus 178 ALIGRLRAAfE 188 (247)
.++-+|++.|+
T Consensus 74 ~v~~~l~~~~~ 84 (85)
T PF08544_consen 74 RVAEALREHYK 84 (85)
T ss_dssp HHHHHHHHHTH
T ss_pred HHHHHHHHhCC
Confidence 67777776664
No 37
>PRK11177 phosphoenolpyruvate-protein phosphotransferase; Provisional
Probab=26.94 E-value=88 Score=31.36 Aligned_cols=36 Identities=31% Similarity=0.423 Sum_probs=29.5
Q ss_pred hhHHHHHHHHHHHHHhCCC---------------------CCCCcc-chhhHHHHHHH
Q 025815 175 SLDALVGRLRAAYEENGGQ---------------------PEINPF-SARAVRLYLRD 210 (247)
Q Consensus 175 SLDALIGRLRAAfEE~GG~---------------------PE~NPF-~araVRlYLRe 210 (247)
+-|...--.|.+.+.++++ .|.||| |-|++|++|+.
T Consensus 309 ~eeeq~~~y~~i~~~~~~~~v~iRtlDiGgDK~~~~~~~~~E~NP~LG~RgiR~~l~~ 366 (575)
T PRK11177 309 TEEEQFQAYKAVAEAMGSQAVIVRTMDIGGDKELPYMNLPKEENPFLGWRAIRIAMDR 366 (575)
T ss_pred CHHHHHHHHHHHHHHcCCCeEEEECcCCCcccccccCCCCCCCCcccccchhhhcCCC
Confidence 4677788888888888766 379999 78999999964
No 38
>smart00243 GAS2 Growth-Arrest-Specific Protein 2 Domain. GROWTH-ARREST-SPECIFIC PROTEIN 2 Domain
Probab=26.65 E-value=43 Score=26.19 Aligned_cols=14 Identities=43% Similarity=1.063 Sum_probs=13.1
Q ss_pred hHhHHHHHHHhcCC
Q 025815 108 DWDTFMQYLSQHRP 121 (247)
Q Consensus 108 DWntf~qyL~nhrP 121 (247)
-|.||.+||..|.|
T Consensus 55 GW~tL~~fL~khDP 68 (73)
T smart00243 55 GWETLDEYLLKHDP 68 (73)
T ss_pred cHHHHHHHHHhCCC
Confidence 49999999999999
No 39
>PRK10701 DNA-binding transcriptional regulator RstA; Provisional
Probab=25.64 E-value=54 Score=26.10 Aligned_cols=17 Identities=35% Similarity=0.548 Sum_probs=13.8
Q ss_pred hhHHHHHHHHHHHHHhC
Q 025815 175 SLDALVGRLRAAYEENG 191 (247)
Q Consensus 175 SLDALIGRLRAAfEE~G 191 (247)
+||..|.|||.-+++.+
T Consensus 201 ~i~~~i~rlR~kl~~~~ 217 (240)
T PRK10701 201 SVDVAISRLRKKLLDNA 217 (240)
T ss_pred CHHHHHHHHHHhcccCC
Confidence 68999999999987544
No 40
>PTZ00398 phosphoenolpyruvate carboxylase; Provisional
Probab=25.34 E-value=1.2e+02 Score=32.60 Aligned_cols=43 Identities=19% Similarity=0.357 Sum_probs=32.2
Q ss_pred hchhHHHHHHHHHHHHHhCC------------------CCCCCccch-------------hhHHHHHHHhHHHH
Q 025815 173 WGSLDALVGRLRAAYEENGG------------------QPEINPFSA-------------RAVRLYLRDVRDVQ 215 (247)
Q Consensus 173 WGSLDALIGRLRAAfEE~GG------------------~PE~NPF~a-------------raVRlYLReVRd~Q 215 (247)
|-.+=.+..+|+.+++++|+ .=++|||.. .|+++|+++|++.-
T Consensus 264 ~~aiP~~~~~l~~al~~~~~~~~~~~~~~i~fGSWiGGDRDGNP~VTaevT~~~l~~~r~~al~~Y~~~l~~L~ 337 (974)
T PTZ00398 264 FDALPNFIRYIDNVLYEYNLDPLPPTKKLFTFSSWVGGDRDGNPFVTAEVTRQVVYFNRIRACELFIHMIEKLM 337 (974)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCCCCceeccCCCCCCCCCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55667788899999988754 334999974 47789999988753
No 41
>KOG1452 consensus Predicted Rho GTPase-activating protein [Signal transduction mechanisms]
Probab=24.42 E-value=41 Score=33.21 Aligned_cols=31 Identities=29% Similarity=0.501 Sum_probs=23.3
Q ss_pred HHHHHHHHhCCC--------CCCCccchhhHHHHHHHhHH
Q 025815 182 RLRAAYEENGGQ--------PEINPFSARAVRLYLRDVRD 213 (247)
Q Consensus 182 RLRAAfEE~GG~--------PE~NPF~araVRlYLReVRd 213 (247)
-||++||-||+. |+.|=- +..++.||||+=|
T Consensus 233 mLR~~fe~n~r~~el~~E~iPD~nvI-tg~~kD~lrElpE 271 (442)
T KOG1452|consen 233 MLRRDFEPNGRDFELGAESIPDYNVI-TGDSKDELRELPE 271 (442)
T ss_pred HHHHHhccCCcccccccccCCCccee-ecccHhHHHhCCC
Confidence 589999999976 444543 4589999999743
No 42
>cd00383 trans_reg_C Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase.
Probab=24.23 E-value=66 Score=22.62 Aligned_cols=20 Identities=25% Similarity=0.489 Sum_probs=17.3
Q ss_pred chhHHHHHHHHHHHHHhCCC
Q 025815 174 GSLDALVGRLRAAYEENGGQ 193 (247)
Q Consensus 174 GSLDALIGRLRAAfEE~GG~ 193 (247)
.+|+.+|-|||..+.+.|+.
T Consensus 62 ~~l~~~I~rLRkkl~~~~~~ 81 (95)
T cd00383 62 RTVDVHISRLRKKLEDDPSN 81 (95)
T ss_pred ccHHHHHHHHHHHhccCCCC
Confidence 57999999999999987653
No 43
>COG1615 Uncharacterized conserved protein [Function unknown]
Probab=23.93 E-value=97 Score=33.37 Aligned_cols=102 Identities=25% Similarity=0.357 Sum_probs=58.2
Q ss_pred CCCCCCCCCCcc-ccchhhhhhh-hcccCCCCCCcceeeeecchhhHHHHHHHHHHHHHhhccCCCCCccCcccchhhhh
Q 025815 1 MGHLLSPPIPRS-IFFPSFIYLT-ALIPFPAPNLSHIKIVSFPFQSLMSAAVSAAAAAACCSSKSSGTTTSRTTTTAART 78 (247)
Q Consensus 1 ~~~~~~~~~~~~-~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~msaavaaaaaaa~~~~~~~~~~~s~~~~~~~~~ 78 (247)
||.||.-||-.| +..=.=+||- +--+---|.|..+ +|++==+..|.-.++-|.-+-.- ...++....+
T Consensus 772 ~GNLL~lPI~~s~lLYVEPvYl~~~~~~ss~P~L~RV-~v~y~~~i~~a~tl~eAL~~iF~--p~~~t~~pat------- 841 (885)
T COG1615 772 MGNLLVLPIAVSGLLYVEPVYLSQGDSASSSPQLQRV-LVGYGGKLGYAPTLSEALEQIFG--PGAGTPPPAT------- 841 (885)
T ss_pred cCceEEEEecCceEEEEeehhcccccccCCCccceEE-EEEECCEEeehhhHHHHHHHhhC--CCCCCCCCCc-------
Confidence 689999999999 7777778887 4444444555543 56666666666666554443311 1111111111
Q ss_pred hcccccCCCCCCCCCCC-CCCchhHHhhhhhHhHHHHHHHhc
Q 025815 79 HHSMLFSSPQASIQSPV-VSFGRYEAQKRRDWDTFMQYLSQH 119 (247)
Q Consensus 79 ~~~~~~~~p~~~~~~~~-~~~SRYesQKRrDWntf~qyL~nh 119 (247)
..|.+.....+ ...--| .||+-||.+++++|...
T Consensus 842 ------~~p~a~~~~~~~~~~~~~-A~k~gd~~~yg~~l~~l 876 (885)
T COG1615 842 ------VTPPAPVGEVPLSAAKTY-AQKNGDFAAYGSALDRL 876 (885)
T ss_pred ------cCCCCCCcccccchhHHH-HHhcCCHHHHHHHHHHH
Confidence 11111111111 122334 99999999999999853
No 44
>PF09336 Vps4_C: Vps4 C terminal oligomerisation domain; InterPro: IPR015415 This domain is found at the C-terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerisation []. ; PDB: 1XWI_A 3EIH_C 2QPA_C 3EIE_A 2RKO_A 2QP9_X 3MHV_C 3CF3_C 3CF1_A 3CF2_A ....
Probab=23.69 E-value=60 Score=23.56 Aligned_cols=31 Identities=19% Similarity=0.479 Sum_probs=25.0
Q ss_pred HhHHHHHHHhcCCCCccccCcchhhhHHhhhhcccc
Q 025815 109 WDTFMQYLSQHRPPLALSRCSGAHVLEFLKYLDQFG 144 (247)
Q Consensus 109 Wntf~qyL~nhrPPlsLs~Csg~hVleFLrylDqfG 144 (247)
-+.|.+=|++-+| +.|.+||..|..|-.+||
T Consensus 32 ~~DF~~Al~~~kp-----SVs~~dl~~ye~w~~~FG 62 (62)
T PF09336_consen 32 MEDFEEALKKVKP-----SVSQEDLKKYEEWTKEFG 62 (62)
T ss_dssp HHHHHHHHHTCGG-----SS-HHHHHHHHHHHHHTS
T ss_pred HHHHHHHHHHcCC-----CCCHHHHHHHHHHHHHcC
Confidence 3567778888887 456899999999999998
No 45
>cd04388 RhoGAP_p85 RhoGAP_p85: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in the p85 isoforms of the regulatory subunit of the class IA PI3K (phosphatidylinositol 3'-kinase). This domain is also called Bcr (breakpoint cluster region protein) homology (BH) domain. Class IA PI3Ks are heterodimers, containing a regulatory subunit (p85) and a catalytic subunit (p110) and are activated by growth factor receptor tyrosine kinases (RTKs); this activation is mediated by the p85 subunit. p85 isoforms, alpha and beta, contain a C-terminal p110-binding domain flanked by two SH2 domains, an N-terminal SH3 domain, and a RhoGAP domain flanked by two proline-rich regions. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell p
Probab=23.52 E-value=74 Score=27.81 Aligned_cols=34 Identities=21% Similarity=0.352 Sum_probs=24.5
Q ss_pred HHHHHHHHHHhCCCCCC---Ccc-chhhHHHHHHHhHH
Q 025815 180 VGRLRAAYEENGGQPEI---NPF-SARAVRLYLRDVRD 213 (247)
Q Consensus 180 IGRLRAAfEE~GG~PE~---NPF-~araVRlYLReVRd 213 (247)
+-.||.+||+.+...+- ++. .+.++|.||||.-|
T Consensus 45 ~~~lk~~~d~~~~~~d~~~~dv~~va~~LK~ylReLPe 82 (200)
T cd04388 45 LTELRQILDCDAASVDLEQFDVAALADALKRYLLDLPN 82 (200)
T ss_pred HHHHHHHHhcCCCCCCcccccHHHHHHHHHHHHHhCCC
Confidence 45689999986554432 222 78999999999765
No 46
>cd04379 RhoGAP_SYD1 RhoGAP_SYD1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in SYD-1_like proteins. Syd-1, first identified and best studied in C.elegans, has been shown to play an important role in neuronal development by specifying axonal properties. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=23.32 E-value=89 Score=26.95 Aligned_cols=40 Identities=28% Similarity=0.405 Sum_probs=27.3
Q ss_pred hchhHHHHHHHHHHHHHhCCCCCC------Ccc-chhhHHHHHHHhHH
Q 025815 173 WGSLDALVGRLRAAYEENGGQPEI------NPF-SARAVRLYLRDVRD 213 (247)
Q Consensus 173 WGSLDALIGRLRAAfEE~GG~PE~------NPF-~araVRlYLReVRd 213 (247)
.|+.+ .|..||..|+..+...+- ++. .|..+|.||||.-|
T Consensus 43 sGs~~-~i~~L~~~~d~~~~~~~l~~~~~~dvh~vA~lLK~fLReLPe 89 (207)
T cd04379 43 CGSAA-KKKELRDAFERNSAAVELSEELYPDINVITGVLKDYLRELPE 89 (207)
T ss_pred CCcHH-HHHHHHHHHcCCCCcCCCChhhcccHHHHHHHHHHHHHhCCC
Confidence 34443 499999999986543322 222 58899999999654
No 47
>cd04396 RhoGAP_fSAC7_BAG7 RhoGAP_fSAC7_BAG7: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of fungal SAC7 and BAG7-like proteins. Both proteins are GTPase activating proteins of Rho1, but differ functionally in vivo: SAC7, but not BAG7, is involved in the control of Rho1-mediated activation of the PKC-MPK1 pathway. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=23.28 E-value=2.9e+02 Score=23.90 Aligned_cols=37 Identities=14% Similarity=0.309 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHhC---CCCCCCcc----chhhHHHHHHHhHH
Q 025815 177 DALVGRLRAAYEENG---GQPEINPF----SARAVRLYLRDVRD 213 (247)
Q Consensus 177 DALIGRLRAAfEE~G---G~PE~NPF----~araVRlYLReVRd 213 (247)
-+-|.+|+..|++.+ ...+-+.+ .+..++.||||.-+
T Consensus 60 ~~~i~~L~~~~d~~~~~~~~~~~~~~~vh~va~lLK~fLReLPe 103 (225)
T cd04396 60 SKRIRELQLIFSTPPDYGKSFDWDGYTVHDAASVLRRYLNNLPE 103 (225)
T ss_pred HHHHHHHHHHHccCcccCCcCCccCCCHHHHHHHHHHHHHhCCC
Confidence 357889999998753 22222333 68899999999754
No 48
>PF11709 Mit_ribos_Mrp51: Mitochondrial ribosomal protein subunit ; InterPro: IPR016712 The function of mitochondrial ribosomal small-subunit protein MRP51 is not entirely clear, but deletion of the MRP51 gene completely blocks mitochondrial gene expression [].
Probab=23.01 E-value=95 Score=28.73 Aligned_cols=67 Identities=21% Similarity=0.238 Sum_probs=48.2
Q ss_pred CCCCCchhHHhhhhhHhHHHHHHHhcCCCCcc--ccCcchhhhHHhhh-----------------hccccccccccCCCc
Q 025815 94 PVVSFGRYEAQKRRDWDTFMQYLSQHRPPLAL--SRCSGAHVLEFLKY-----------------LDQFGKTKVHAQSCP 154 (247)
Q Consensus 94 ~~~~~SRYesQKRrDWntf~qyL~nhrPPlsL--s~Csg~hVleFLry-----------------lDqfGKTKVH~~~C~ 154 (247)
......+|-++=|..-.+|.+||+.+.|-... ..--...|.|||.. ....|..++|.-+=-
T Consensus 144 t~~ef~~yL~kvr~~R~eF~~~L~~~~~e~~~~~~~~l~~~v~eFL~~~~~~~~~~~~~~~~~~~~~~~~~~~~hpsgGL 223 (312)
T PF11709_consen 144 TEGEFERYLKKVRPLRPEFKKWLREKHPESLTFDPSDLYDLVKEFLDLAPLKPPDVPDSKKSSSPYAEAGPPKTHPSGGL 223 (312)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHHHhChhhhccCHHHHHHHHHHHHhcccccCcccccchhccCcccccCCCccccCcCc
Confidence 33456788888899999999999999886621 23345678899975 334677778877776
Q ss_pred cccCCC
Q 025815 155 LFGHAH 160 (247)
Q Consensus 155 ffG~p~ 160 (247)
-|.+++
T Consensus 224 SY~~~g 229 (312)
T PF11709_consen 224 SYNRTG 229 (312)
T ss_pred CcCCCc
Confidence 676554
No 49
>PF09958 DUF2192: Uncharacterized protein conserved in archaea (DUF2192); InterPro: IPR018693 This family of various hypothetical archaeal proteins has no known function.
Probab=22.89 E-value=71 Score=29.43 Aligned_cols=21 Identities=48% Similarity=0.643 Sum_probs=18.4
Q ss_pred hhHHHHHHHHHHHHHhCCCCC
Q 025815 175 SLDALVGRLRAAYEENGGQPE 195 (247)
Q Consensus 175 SLDALIGRLRAAfEE~GG~PE 195 (247)
+=|.||.-||..||++|..|=
T Consensus 27 ~R~~lv~~L~~~Y~~~gIeP~ 47 (231)
T PF09958_consen 27 DREELVELLREVYEENGIEPF 47 (231)
T ss_pred CHHHHHHHHHHHHHHcCCCcC
Confidence 558999999999999998863
No 50
>KOG3248 consensus Transcription factor TCF-4 [Transcription]
Probab=22.79 E-value=48 Score=32.78 Aligned_cols=21 Identities=24% Similarity=0.338 Sum_probs=12.3
Q ss_pred eeecchhhHHHHHHHHHHHHH
Q 025815 37 IVSFPFQSLMSAAVSAAAAAA 57 (247)
Q Consensus 37 ~~~~~~~~~msaavaaaaaaa 57 (247)
|-.|+|-..+-++|-|+-+++
T Consensus 117 ~pt~~~~~p~p~~~~asmsrf 137 (421)
T KOG3248|consen 117 IPTFGFRHPYPGVVNASMSRF 137 (421)
T ss_pred CCCCCCCCCCchhhhhhhhhc
Confidence 344677766666665555543
No 51
>PF06480 FtsH_ext: FtsH Extracellular; InterPro: IPR011546 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This domain is found in the FtsH family of proteins that include FtsH a membrane-bound ATP-dependent protease universally conserved in prokaryotes []. The FtsH peptidases, which belong to MEROPS peptidase family M41 (clan MA(E)), efficiently degrade proteins that have a low thermodynamic stability - e.g. they lack robust unfoldase activity. This feature may be key and implies that this could be a criterion for degrading a protein. In Oenococcus oeni (Leuconostoc oenos) FtsH is involved in protection against environmental stress [], and shows increased expression under heat or osmotic stress. These two lines of evidence suggest that it is a fundamental prokaryotic self-protection mechanism that checks if proteins are correctly folded. The precise function of this N-terminal region is unclear. ; GO: 0004222 metalloendopeptidase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0016021 integral to membrane; PDB: 2LNA_A.
Probab=22.47 E-value=1.1e+02 Score=21.67 Aligned_cols=26 Identities=31% Similarity=0.218 Sum_probs=18.8
Q ss_pred hchhHHHHHHHHHHHHHhCCCCCCCc
Q 025815 173 WGSLDALVGRLRAAYEENGGQPEINP 198 (247)
Q Consensus 173 WGSLDALIGRLRAAfEE~GG~PE~NP 198 (247)
++++|.+.-+|..+-+|+|..+++.|
T Consensus 84 ~~~~~~~~~~L~~~~~~~~v~~~~~~ 109 (110)
T PF06480_consen 84 IPSVDSFDEFLIEALVEKGVKYESVP 109 (110)
T ss_dssp -S-HHHHHHHHHHHHHHTT--TTT--
T ss_pred CCCCHHHHHHHHHHHHHCCCccceec
Confidence 45699999999999999999998765
No 52
>COG0745 OmpR Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=21.93 E-value=70 Score=27.81 Aligned_cols=26 Identities=31% Similarity=0.693 Sum_probs=20.7
Q ss_pred hhhhhc--------hhHHHHHHHHHHHHHhCCCC
Q 025815 169 MMQAWG--------SLDALVGRLRAAYEENGGQP 194 (247)
Q Consensus 169 LRQAWG--------SLDALIGRLRAAfEE~GG~P 194 (247)
+.+.|| ++|..|+|||.-.++.++.+
T Consensus 179 ~~~vw~~~~~~~~rtvdvhI~rLR~Kl~~~~~~~ 212 (229)
T COG0745 179 LEAVWGYDFEVDSRTVDVHISRLRKKLEKDPGAG 212 (229)
T ss_pred HHHhcCCCCCCCccCHHHHHHHHHHHhccCCCCC
Confidence 556666 59999999999999887644
No 53
>PF07700 HNOB: Heme NO binding; InterPro: IPR011644 This ligand-binding domain is found in soluble guanylate cyclases. In soluble guanylate cyclases this domain binds heme via a covalent linkage to histidine []. Soluble guanylate cyclases are nitric oxide-responsive signaling proteins.; GO: 0020037 heme binding; PDB: 3TFE_A 2O0C_B 3TFA_A 2O09_B 2O0G_B 3L6J_A 3TFG_B 3TF8_A 3TFF_A 3TF9_B ....
Probab=21.71 E-value=37 Score=27.80 Aligned_cols=36 Identities=25% Similarity=0.371 Sum_probs=29.5
Q ss_pred hhHhHHHHHHHh---cCCCCccccCcchhhhHHhhhhcc
Q 025815 107 RDWDTFMQYLSQ---HRPPLALSRCSGAHVLEFLKYLDQ 142 (247)
Q Consensus 107 rDWntf~qyL~n---hrPPlsLs~Csg~hVleFLrylDq 142 (247)
..|..|++|+-. ..-|-.+.++.+.++.|||.-+|.
T Consensus 65 ~~l~~fG~~~~~~~~~~~~~~~l~~~g~~~~~FL~~ld~ 103 (171)
T PF07700_consen 65 ELLEEFGEYFFDFLSESGYERLLRFLGRDLFDFLNNLDN 103 (171)
T ss_dssp HHHHHHHHHHHHHHHHHCCHHHHHCTCSSHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhCcHHHHHhcCCCHHHHHHhHHH
Confidence 468899998876 455777889999999999998775
No 54
>PRK11173 two-component response regulator; Provisional
Probab=21.54 E-value=72 Score=25.43 Aligned_cols=20 Identities=20% Similarity=0.448 Sum_probs=16.5
Q ss_pred chhHHHHHHHHHHHHHhCCC
Q 025815 174 GSLDALVGRLRAAYEENGGQ 193 (247)
Q Consensus 174 GSLDALIGRLRAAfEE~GG~ 193 (247)
-+||..|.|||.-+++.+..
T Consensus 199 ~~~~~~i~rlR~kl~~~~~~ 218 (237)
T PRK11173 199 RTVDVTIRRIRKHFESTPDT 218 (237)
T ss_pred ccHHHHHHHHHHHhccCCCC
Confidence 47999999999999865543
No 55
>PRK09468 ompR osmolarity response regulator; Provisional
Probab=21.37 E-value=73 Score=25.24 Aligned_cols=18 Identities=39% Similarity=0.545 Sum_probs=14.9
Q ss_pred chhHHHHHHHHHHHHHhC
Q 025815 174 GSLDALVGRLRAAYEENG 191 (247)
Q Consensus 174 GSLDALIGRLRAAfEE~G 191 (247)
-+||..|.|||.-++..+
T Consensus 200 ~~l~~~i~~LR~kl~~~~ 217 (239)
T PRK09468 200 RSIDVQISRLRRLIEEDP 217 (239)
T ss_pred CCHHHHHHHHHHHhccCC
Confidence 479999999999997544
No 56
>PF01754 zf-A20: A20-like zinc finger; InterPro: IPR002653 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 zinc finger domain found in A20. A20 is an inhibitor of cell death that inhibits NF-kappaB activation via the tumour necrosis factor receptor associated factor pathway []. The zinc finger domains appear to mediate self-association in A20. These fingers also mediate IL-1-induced NF-kappa B activation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 2FIF_F 2FID_B 2C7N_C 2C7M_A 2L00_A 2KZY_A 2EQG_A 2EQE_A 3OJ3_J 3OJ4_C ....
Probab=21.08 E-value=46 Score=21.07 Aligned_cols=16 Identities=25% Similarity=0.746 Sum_probs=10.8
Q ss_pred cCCCccccCCCCCCCC
Q 025815 150 AQSCPLFGHAHAPAPC 165 (247)
Q Consensus 150 ~~~C~ffG~p~ppapC 165 (247)
+.+|.|||.+..-.-|
T Consensus 5 ~~gCgf~Gs~~~~~~C 20 (25)
T PF01754_consen 5 ANGCGFYGSPATNGLC 20 (25)
T ss_dssp TTTSSSB-BGGGTTS-
T ss_pred cCCCCCcccccccCcc
Confidence 5799999988755544
No 57
>PF09674 DUF2400: Protein of unknown function (DUF2400); InterPro: IPR014127 Members of this uncharacterised protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighbourhoods show little conservation.
Probab=21.06 E-value=82 Score=28.42 Aligned_cols=51 Identities=14% Similarity=0.335 Sum_probs=35.9
Q ss_pred hhhhchhHHHHHHHHHHHHHhCCCCC--------------CCcc-----chhhHHHHHHHhHHHHHhhhc
Q 025815 170 MQAWGSLDALVGRLRAAYEENGGQPE--------------INPF-----SARAVRLYLRDVRDVQAEARG 220 (247)
Q Consensus 170 RQAWGSLDALIGRLRAAfEE~GG~PE--------------~NPF-----~araVRlYLReVRd~QAKARg 220 (247)
-.|||.+..+|-+|...++.+|..|- .+-| ...-+..++..++..-.+-.+
T Consensus 24 ~lAyG~~~~I~~~~~~ll~~~~~~P~~~v~~~~~~~~~~~~~~~~yRf~~~~D~~~~~~~l~~i~~~~gs 93 (232)
T PF09674_consen 24 LLAYGNRKQIIKKLERLLDLMGPSPYDFVLSGDEKDDRKDLEGFFYRFQNGEDMYAFFIALKRIYQEYGS 93 (232)
T ss_pred HHHccCHHHHHHHHHHHHHHhCCCHHHHHHcCCHhhhHHHccCCCcCCCCHHHHHHHHHHHHHHHHccCC
Confidence 46999999999999999999999862 2333 233455566666665554434
No 58
>COG4865 Glutamate mutase epsilon subunit [Amino acid transport and metabolism]
Probab=20.87 E-value=64 Score=32.25 Aligned_cols=23 Identities=39% Similarity=0.612 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHhCCCCCCCccch
Q 025815 179 LVGRLRAAYEENGGQPEINPFSA 201 (247)
Q Consensus 179 LIGRLRAAfEE~GG~PE~NPF~a 201 (247)
.|.||.-+|||||.+=...||+-
T Consensus 196 YVDRL~G~YeE~Gi~INREpFgP 218 (485)
T COG4865 196 YVDRLMGMYEEHGIRINREPFGP 218 (485)
T ss_pred HHHHHHhHHHhcCeeeccccCCC
Confidence 35566669999999877777764
No 59
>PF01663 Phosphodiest: Type I phosphodiesterase / nucleotide pyrophosphatase; InterPro: IPR002591 This family consists of phosphodiesterases, including human plasma-cell membrane glycoprotein PC-1 / alkaline phosphodiesterase I / nucleotide pyrophosphatase (nppase). These enzymes catalyse the cleavage of phosphodiester and phosphosulphate bonds in NAD, deoxynucleotides and nucleotide sugars []. Another member of this family is ATX an autotaxin, tumor cell motility-stimulating protein which exhibits type I phosphodiesterases activity []. The alignment encompasses the active site [, ]. Also present within this family is 60 kDa Ca2+-ATPase from Myroides odoratus []. This signature also hits a number of ethanolamine phosphate transferase involved in glycosylphosphatidylinositol-anchor biosynthesis.; GO: 0003824 catalytic activity; PDB: 2XRG_A 2XR9_A 3T02_A 3T01_A 3SZZ_A 3SZY_A 3T00_A 3NKM_A 3NKN_A 3NKR_A ....
Probab=20.64 E-value=80 Score=26.75 Aligned_cols=27 Identities=33% Similarity=0.548 Sum_probs=23.4
Q ss_pred hhhhhchhHHHHHHHHHHHHHhCCCCC
Q 025815 169 MMQAWGSLDALVGRLRAAYEENGGQPE 195 (247)
Q Consensus 169 LRQAWGSLDALIGRLRAAfEE~GG~PE 195 (247)
.+++.-.+|..||+|.+++++.|...+
T Consensus 208 ~~~~~~~~D~~ig~l~~~l~~~~~~~~ 234 (365)
T PF01663_consen 208 IEDAYRRIDQAIGRLLEALDENGLLED 234 (365)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTT-TTT
T ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCc
Confidence 688999999999999999999977655
No 60
>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 3". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2PJP_A 2UWM_A 1WSU_B 1LVA_A 2PLY_A.
Probab=20.56 E-value=46 Score=23.50 Aligned_cols=21 Identities=33% Similarity=0.469 Sum_probs=17.3
Q ss_pred cCcchhhhHHhhhhccccccc
Q 025815 127 RCSGAHVLEFLKYLDQFGKTK 147 (247)
Q Consensus 127 ~Csg~hVleFLrylDqfGKTK 147 (247)
..|=+-++-+|.|+|+.|-|+
T Consensus 21 g~sRK~ai~lLE~lD~~g~T~ 41 (50)
T PF09107_consen 21 GLSRKYAIPLLEYLDREGITR 41 (50)
T ss_dssp TS-HHHHHHHHHHHHHTTSEE
T ss_pred CccHHHHHHHHHHHhccCCEE
Confidence 356677899999999999997
No 61
>PF10520 Kua-UEV1_localn: Kua-ubiquitin conjugating enzyme hybrid localisation domain; InterPro: IPR019547 This entry represents part of the transcript of the fusion of two genes, the UEV1. UEV1 is an enzymatically inactive variant of the E2 ubiquitin-conjugating enzymes that regulate non-canonical elongation of ubiquitin chains, and Kua, an otherwise unknown gene. UEV1A is a nuclear protein, whereas both Kua and Kua-UEV localise to cytoplasmic structures, indicating that the addition of a Kua domain to UEV confers new biological properties. UEV1-Kua carries the B domain with its characteristic double histidine motif, and it is probably this domain which determines the cytoplasmic localisation. It is postulated that this hybrid transcript could preferentially direct the variant polyubiquitination of substrates closely associated with the cytoplasmic face of the endoplasmic reticulum, possibly, although not necessarily, in conjunction with membrane-bound ubiquitin-conjugating enzymes [].
Probab=20.13 E-value=49 Score=28.94 Aligned_cols=24 Identities=29% Similarity=0.753 Sum_probs=21.9
Q ss_pred hhchhHH-HHHHHHHHHHHhCCCCC
Q 025815 172 AWGSLDA-LVGRLRAAYEENGGQPE 195 (247)
Q Consensus 172 AWGSLDA-LIGRLRAAfEE~GG~PE 195 (247)
-|||+|- +||+.-++|.||-..|-
T Consensus 17 ~~Gs~~tpi~G~~I~~Fr~HH~~P~ 41 (178)
T PF10520_consen 17 NWGSPDTPIIGKFIRPFREHHVDPT 41 (178)
T ss_pred cCCCCccchhhHHhHHHHHcccCHH
Confidence 5899998 89999999999999875
Done!