Query 046561
Match_columns 204
No_of_seqs 81 out of 83
Neff 2.4
Searched_HMMs 46136
Date Fri Mar 29 13:21:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046561.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046561hhsearch_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 6.5E-76 1.4E-80 471.8 11.8 122 45-166 11-132 (132)
2 PF08821 CGGC: CGGC domain; I 91.7 0.33 7.2E-06 37.8 4.5 67 63-139 29-98 (107)
3 PF02899 Phage_int_SAM_1: Phag 90.1 0.54 1.2E-05 31.8 3.9 40 56-96 21-60 (84)
4 cd00798 INT_XerDC XerD and Xer 87.7 2.4 5.1E-05 32.9 6.4 69 56-151 21-91 (284)
5 cd00799 INT_Cre Cre recombinas 86.0 7.4 0.00016 31.5 8.6 77 56-164 6-82 (287)
6 TIGR02225 recomb_XerD tyrosine 83.8 4.5 9.7E-05 31.7 6.3 70 55-152 19-90 (291)
7 PRK00283 xerD site-specific ty 83.2 3.6 7.9E-05 32.8 5.7 68 57-152 30-99 (299)
8 COG1080 PtsA Phosphoenolpyruva 79.8 2.4 5.2E-05 42.0 4.2 42 122-163 305-368 (574)
9 TIGR02224 recomb_XerC tyrosine 74.0 13 0.00028 29.3 6.1 69 58-152 22-92 (295)
10 PF10865 DUF2703: Domain of un 63.3 2.2 4.8E-05 34.2 -0.2 43 85-147 2-44 (120)
11 TIGR01418 PEP_synth phosphoeno 62.6 12 0.00026 37.6 4.7 42 129-170 547-618 (782)
12 PF00539 Tat: Transactivating 61.5 3 6.6E-05 31.2 0.3 19 168-186 45-63 (68)
13 PF02896 PEP-utilizers_C: PEP- 60.0 14 0.0003 33.3 4.2 46 125-170 58-126 (293)
14 cd01185 INT_Tn4399 Tn4399 and 59.9 38 0.00083 27.5 6.4 34 59-92 43-78 (299)
15 PRK10529 DNA-binding transcrip 55.6 9.9 0.00022 29.0 2.2 18 127-144 191-208 (225)
16 PF05528 Coronavirus_5: Corona 54.4 2.2 4.8E-05 33.0 -1.4 18 147-164 5-25 (82)
17 PF13495 Phage_int_SAM_4: Phag 53.0 21 0.00046 24.3 3.3 53 59-141 24-77 (85)
18 PRK11061 fused phosphoenolpyru 51.8 13 0.00029 37.0 3.0 36 127-162 475-531 (748)
19 PRK00236 xerC site-specific ty 50.8 78 0.0017 24.9 6.6 37 57-94 31-67 (297)
20 TIGR01417 PTS_I_fam phosphoeno 49.4 19 0.00041 34.9 3.5 38 127-164 308-367 (565)
21 PRK10816 DNA-binding transcrip 47.5 14 0.00031 28.2 2.0 23 121-143 175-205 (223)
22 COG4974 XerD Site-specific rec 46.4 21 0.00046 33.0 3.2 38 58-97 31-69 (300)
23 PF06252 DUF1018: Protein of u 45.9 1.2E+02 0.0025 23.2 6.8 87 60-161 2-89 (119)
24 cd00801 INT_P4 Bacteriophage P 44.7 45 0.00098 27.3 4.6 26 126-152 135-163 (357)
25 smart00259 ZnF_A20 A20-like zi 43.9 12 0.00027 23.0 0.9 16 103-118 7-22 (26)
26 PF00486 Trans_reg_C: Transcri 43.4 25 0.00053 23.5 2.4 21 126-146 44-64 (77)
27 PF13276 HTH_21: HTH-like doma 42.0 44 0.00096 22.3 3.5 29 129-162 4-32 (60)
28 PF14768 RPA_interact_C: Repli 40.0 27 0.00059 25.7 2.4 36 115-150 17-56 (82)
29 PRK09279 pyruvate phosphate di 39.3 27 0.00058 36.1 3.0 36 135-170 636-685 (879)
30 smart00862 Trans_reg_C Transcr 38.7 33 0.00072 22.7 2.5 19 126-144 45-63 (78)
31 PRK06464 phosphoenolpyruvate s 37.2 42 0.00091 34.0 4.0 16 147-162 597-613 (795)
32 PF11709 Mit_ribos_Mrp51: Mito 35.0 52 0.0011 29.7 3.8 65 48-112 146-229 (312)
33 PRK11177 phosphoenolpyruvate-p 35.0 35 0.00076 33.4 2.9 37 127-163 309-367 (575)
34 TIGR01828 pyru_phos_dikin pyru 34.4 22 0.00048 36.4 1.5 25 146-170 652-679 (856)
35 PF09107 SelB-wing_3: Elongati 34.2 23 0.00049 24.4 1.1 21 79-99 21-41 (50)
36 PF03344 Daxx: Daxx Family; I 33.7 1.5E+02 0.0032 30.3 7.1 75 53-168 66-140 (713)
37 PF00140 Sigma70_r1_2: Sigma-7 33.6 32 0.00069 22.0 1.7 12 154-165 2-13 (37)
38 cd04372 RhoGAP_chimaerin RhoGA 33.4 47 0.001 27.2 3.1 36 130-165 45-87 (194)
39 PF08544 GHMP_kinases_C: GHMP 31.6 7.5 0.00016 26.4 -1.6 72 57-140 6-84 (85)
40 PF09336 Vps4_C: Vps4 C termin 31.4 44 0.00096 23.6 2.3 31 61-96 32-62 (62)
41 smart00243 GAS2 Growth-Arrest- 31.3 32 0.00069 26.3 1.6 14 60-73 55-68 (73)
42 PF03732 Retrotrans_gag: Retro 31.1 1.3E+02 0.0027 20.2 4.4 38 121-163 56-94 (96)
43 cd08793 Death_IRAK4 Death doma 30.5 58 0.0013 25.8 3.0 63 60-144 23-85 (100)
44 cd04396 RhoGAP_fSAC7_BAG7 RhoG 30.2 1.8E+02 0.0039 24.6 6.1 37 129-165 60-103 (225)
45 PRK05084 xerS site-specific ty 30.0 1.1E+02 0.0024 25.9 4.8 68 58-141 42-119 (357)
46 PRK10701 DNA-binding transcrip 29.1 44 0.00096 26.0 2.1 16 127-142 201-216 (240)
47 PF04221 RelB: RelB antitoxin; 28.7 1.2E+02 0.0027 21.9 4.3 39 130-178 11-49 (83)
48 cd04400 RhoGAP_fBEM3 RhoGAP_fB 27.8 1.2E+02 0.0026 24.6 4.5 39 126-165 49-94 (190)
49 PF07700 HNOB: Heme NO binding 27.6 25 0.00054 28.1 0.5 36 59-94 65-103 (171)
50 PTZ00398 phosphoenolpyruvate c 27.6 98 0.0021 32.6 4.8 42 125-166 264-336 (974)
51 cd00383 trans_reg_C Effector d 27.4 54 0.0012 22.5 2.1 20 126-145 62-81 (95)
52 PF09958 DUF2192: Uncharacteri 26.8 55 0.0012 29.4 2.6 21 127-147 27-47 (231)
53 cd01355 AcnX Putative Aconitas 26.7 68 0.0015 30.4 3.3 54 82-147 48-108 (389)
54 TIGR03190 benz_CoA_bzdN benzoy 26.7 4.9E+02 0.011 23.7 9.5 24 53-76 166-189 (377)
55 COG0745 OmpR Response regulato 26.6 52 0.0011 28.0 2.3 28 119-146 177-212 (229)
56 PRK11235 bifunctional antitoxi 26.1 1.3E+02 0.0029 22.7 4.2 38 130-177 11-48 (80)
57 TIGR02249 integrase_gron integ 26.0 1.8E+02 0.0039 24.0 5.3 33 58-94 23-55 (315)
58 KOG1452 Predicted Rho GTPase-a 26.0 37 0.00081 32.8 1.4 31 134-165 233-271 (442)
59 cd04436 DEP_fRgd2 DEP (Disheve 26.0 50 0.0011 25.5 1.9 40 62-101 33-76 (84)
60 cd01187 INT_SG4 INT_SG4, DNA b 25.6 2.9E+02 0.0063 22.5 6.4 29 60-92 25-53 (299)
61 cd04388 RhoGAP_p85 RhoGAP_p85: 25.2 74 0.0016 27.2 3.0 34 132-165 45-82 (200)
62 PF09674 DUF2400: Protein of u 25.1 63 0.0014 28.5 2.6 52 122-173 24-94 (232)
63 PF10780 MRP_L53: 39S ribosoma 25.0 37 0.0008 23.6 0.9 25 149-174 2-28 (51)
64 PF00179 UQ_con: Ubiquitin-con 25.0 1.7E+02 0.0036 22.4 4.6 45 124-171 90-137 (140)
65 PRK09468 ompR osmolarity respo 24.7 59 0.0013 25.2 2.1 17 127-143 201-217 (239)
66 PRK11173 two-component respons 24.1 62 0.0013 25.3 2.1 19 127-145 200-218 (237)
67 PF06947 DUF1290: Protein of u 23.7 67 0.0014 25.3 2.2 17 126-142 16-32 (88)
68 PF02187 GAS2: Growth-Arrest-S 23.6 18 0.0004 27.3 -0.9 13 61-73 56-68 (73)
69 PF00667 FAD_binding_1: FAD bi 23.5 71 0.0015 26.4 2.5 45 82-126 56-100 (219)
70 COG4865 Glutamate mutase epsil 23.4 54 0.0012 32.1 2.0 22 131-152 196-217 (485)
71 PF10520 Kua-UEV1_localn: Kua- 23.3 39 0.00085 28.8 1.0 24 124-147 17-41 (178)
72 PF07535 zf-DBF: DBF zinc fing 23.2 41 0.00088 23.4 0.9 12 125-136 37-48 (49)
73 TIGR02384 RelB_DinJ addiction 23.1 1.8E+02 0.004 21.5 4.4 39 130-178 12-50 (83)
74 PF06480 FtsH_ext: FtsH Extrac 22.9 1.1E+02 0.0023 21.2 2.9 26 125-150 84-109 (110)
75 cd04383 RhoGAP_srGAP RhoGAP_sr 22.9 97 0.0021 25.4 3.2 35 130-165 47-88 (188)
76 KOG3816 Cell differentiation r 22.8 1E+02 0.0022 30.6 3.7 83 63-160 274-369 (526)
77 cd04379 RhoGAP_SYD1 RhoGAP_SYD 22.7 97 0.0021 26.1 3.2 39 126-165 44-89 (207)
78 PF01663 Phosphodiest: Type I 22.6 65 0.0014 26.7 2.1 27 121-147 208-234 (365)
79 cd04399 RhoGAP_fRGD2 RhoGAP_fR 22.3 90 0.0019 26.3 2.9 35 130-165 51-94 (212)
80 PF12067 Sox_C_TAD: Sox C-term 21.8 49 0.0011 28.8 1.3 17 57-73 139-155 (197)
81 PRK13977 myosin-cross-reactive 21.8 1.1E+02 0.0023 30.6 3.7 101 59-177 160-270 (576)
82 cd04390 RhoGAP_ARHGAP22_24_25 21.5 1.4E+02 0.003 24.4 3.8 37 129-165 50-90 (199)
83 cd08802 Death_UNC5B Death doma 20.9 59 0.0013 24.9 1.4 17 129-145 60-76 (84)
84 cd08782 Death_DAPK1 Death doma 20.8 52 0.0011 24.5 1.1 28 118-145 47-75 (82)
85 PF01754 zf-A20: A20-like zinc 20.6 43 0.00092 20.7 0.5 16 102-117 5-20 (25)
86 PF13099 DUF3944: Domain of un 20.6 54 0.0012 21.9 1.0 22 78-99 11-34 (35)
87 cd04406 RhoGAP_myosin_IXA RhoG 20.5 1.1E+02 0.0023 25.2 2.9 36 130-165 44-83 (186)
88 PF12055 DUF3536: Domain of un 20.4 74 0.0016 29.2 2.1 42 120-166 8-49 (285)
89 cd08799 Death_UNC5C Death doma 20.4 54 0.0012 25.0 1.1 17 129-145 60-76 (84)
90 PF00618 RasGEF_N: RasGEF N-te 20.2 61 0.0013 23.2 1.3 12 125-136 4-15 (104)
91 PF10774 DUF4226: Domain of un 20.1 1.5E+02 0.0032 23.7 3.5 34 127-161 48-81 (112)
92 KOG4329 DNA-binding protein [G 20.1 57 0.0012 31.8 1.4 31 80-111 211-241 (445)
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=6.5e-76 Score=471.83 Aligned_cols=122 Identities=85% Similarity=1.501 Sum_probs=119.0
Q ss_pred CCCCCCchHHHhhhhhhhHHHHHHHhcCCCCccccCcchhHHHHHHhhcccCcccccCCCCCCCCCCCCCCCCCCchhhh
Q 046561 45 AATSSSSRYENQKRRDWNTFGQYLKNHRPPLSLSRCSGAHVLEFLRYLDQFGKTKVHTPICPFYGHPNPPAPCPCPLRQA 124 (204)
Q Consensus 45 ~~~~~~SrYesQKRrdwntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGkTkVH~~~C~ffG~p~ppapC~CPlRQA 124 (204)
.+++.+||||+|||||||||+|||+||+|||+|++|+|+|||+||+|+|||||||||.++|+|||+|+||+||+||||||
T Consensus 11 ~~~~~~SrYesQKrrdwntf~qyL~n~rPP~~L~~csg~hVl~FL~~~d~~GkTkVh~~~C~~~g~~~~p~~C~CPlrqA 90 (132)
T PF04852_consen 11 SPQPAPSRYESQKRRDWNTFGQYLRNHRPPLSLSRCSGNHVLEFLRYLDQFGKTKVHGQGCPFFGHPSPPAPCPCPLRQA 90 (132)
T ss_pred CCCCCCcccchhhhHHHHHHHHHHHccCCCcchhhcChHHHHHHHHHHhccCCeeecCCCCCCCCCCCCCCCCCCcHHHH
Confidence 34567899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchhHHHHHHHHHHHHHhCCCCCCCccchhhHHHHHHHHhhH
Q 046561 125 WGSLDALIGRLRAAFEENGGKPEANPFGARAVRLYLREVRDV 166 (204)
Q Consensus 125 wGSLDALIGRLRAafEE~Gg~pE~NPF~araVRlYLReVRd~ 166 (204)
||||||||||||||||||||+||+|||+++|||+|||||||+
T Consensus 91 wGSlDalIGrLraafee~Gg~pe~NPf~~~~vr~yLr~vr~~ 132 (132)
T PF04852_consen 91 WGSLDALIGRLRAAFEEHGGHPEANPFAARAVRLYLREVRDS 132 (132)
T ss_pred hccHHHHHHHHHHHHHHhCCCCCCCchhhHHHHHHHHHHhcC
Confidence 999999999999999999999999999999999999999985
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=91.70 E-value=0.33 Score=37.79 Aligned_cols=67 Identities=22% Similarity=0.545 Sum_probs=49.5
Q ss_pred HHHHHHHhcCCCCccccCc---chhHHHHHHhhcccCcccccCCCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHHHH
Q 046561 63 TFGQYLKNHRPPLSLSRCS---GAHVLEFLRYLDQFGKTKVHTPICPFYGHPNPPAPCPCPLRQAWGSLDALIGRLRAAF 139 (204)
Q Consensus 63 tf~qyL~n~rPPlsL~~cs---g~hVleFLrylDqfGkTkVH~~~C~ffG~p~ppapC~CPlRQAwGSLDALIGRLRAaf 139 (204)
.|.+|=.+..--+.+.+|. +..|+..++.+-..|-..||...|.+.+.+.+ +||. +|.|+-.|+++|
T Consensus 29 ~F~~y~~~~~elvgf~~CgGCpg~~~~~~~~~l~~~~~d~IHlssC~~~~~~~~----~CP~------~~~~~~~I~~~~ 98 (107)
T PF08821_consen 29 AFARYDDEDVELVGFFTCGGCPGRKLVRRIKKLKKNGADVIHLSSCMVKGNPHG----PCPH------IDEIKKIIEEKF 98 (107)
T ss_pred ccccCCCCCeEEEEEeeCCCCChhHHHHHHHHHHHCCCCEEEEcCCEecCCCCC----CCCC------HHHHHHHHHHHh
Confidence 3444433222233444554 68899999999999999999999999987653 6665 899999999888
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=90.10 E-value=0.54 Score=31.78 Aligned_cols=40 Identities=28% Similarity=0.465 Sum_probs=31.8
Q ss_pred hhhhhhhHHHHHHHhcCCCCccccCcchhHHHHHHhhcccC
Q 046561 56 QKRRDWNTFGQYLKNHRPPLSLSRCSGAHVLEFLRYLDQFG 96 (204)
Q Consensus 56 QKRrdwntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfG 96 (204)
.-+++++.|.+||.+ ....++..++..||.+|+.++-+.|
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 456789999999999 5667788899999999999998766
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=87.66 E-value=2.4 Score=32.86 Aligned_cols=69 Identities=25% Similarity=0.269 Sum_probs=48.3
Q ss_pred hhhhhhhHHHHHHHhcCCCCccccCcchhHHHHHHhhcccCcccccCCCCCCCCCCCCCCCCCCchhhhcchhHHHHHHH
Q 046561 56 QKRRDWNTFGQYLKNHRPPLSLSRCSGAHVLEFLRYLDQFGKTKVHTPICPFYGHPNPPAPCPCPLRQAWGSLDALIGRL 135 (204)
Q Consensus 56 QKRrdwntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGkTkVH~~~C~ffG~p~ppapC~CPlRQAwGSLDALIGRL 135 (204)
+-+..|+.|.+|+....... +..-+..||.+|+.++.+.| ....++...++-|
T Consensus 21 ~~~~~~~~~~~~~~~~~~~~-~~~l~~~~i~~~~~~~~~~~--------------------------~~~~t~~~~~~~l 73 (284)
T cd00798 21 AYRRDLERFLEFLEERGILF-PADVTPDDIRRFLAELKDQG--------------------------LSARSIARKLSAL 73 (284)
T ss_pred HHHHHHHHHHHHHHHcCCCc-hhhCCHHHHHHHHHHhhhcC--------------------------CCHHHHHHHHHHH
Confidence 44567899999998754433 56678899999999887644 1335777788888
Q ss_pred HHHHHHhC--CCCCCCcc
Q 046561 136 RAAFEENG--GKPEANPF 151 (204)
Q Consensus 136 RAafEE~G--g~pE~NPF 151 (204)
+++|.-.. +--+.||+
T Consensus 74 ~~~~~~~~~~~~~~~~p~ 91 (284)
T cd00798 74 RSFFKFLLREGLILANPA 91 (284)
T ss_pred HHHHHHHHHcCCccCChh
Confidence 88887322 33456777
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=85.98 E-value=7.4 Score=31.51 Aligned_cols=77 Identities=23% Similarity=0.312 Sum_probs=52.6
Q ss_pred hhhhhhhHHHHHHHhcCCCCccccCcchhHHHHHHhhcccCcccccCCCCCCCCCCCCCCCCCCchhhhcchhHHHHHHH
Q 046561 56 QKRRDWNTFGQYLKNHRPPLSLSRCSGAHVLEFLRYLDQFGKTKVHTPICPFYGHPNPPAPCPCPLRQAWGSLDALIGRL 135 (204)
Q Consensus 56 QKRrdwntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGkTkVH~~~C~ffG~p~ppapC~CPlRQAwGSLDALIGRL 135 (204)
.-..+++.|..|+..+. +....-+..+|.+|+.||.+. .+..++-..++.|
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 44568889999998752 222234589999999988531 1456888899999
Q ss_pred HHHHHHhCCCCCCCccchhhHHHHHHHHh
Q 046561 136 RAAFEENGGKPEANPFGARAVRLYLREVR 164 (204)
Q Consensus 136 RAafEE~Gg~pE~NPF~araVRlYLReVR 164 (204)
+.+|+..+. .||+....++.-|+.++
T Consensus 57 ~~~~~~~~~---~~p~~~~~~~~~~~~~~ 82 (287)
T cd00799 57 SQLHRRSGL---PSPADSPLVRLVLRGIR 82 (287)
T ss_pred HHHHHHcCC---CCCccCHHHHHHHHHHH
Confidence 999985433 58876555555555554
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=83.84 E-value=4.5 Score=31.70 Aligned_cols=70 Identities=23% Similarity=0.393 Sum_probs=47.7
Q ss_pred HhhhhhhhHHHHHHHhcCCCCccccCcchhHHHHHHhhcccCcccccCCCCCCCCCCCCCCCCCCchhhhcchhHHHHHH
Q 046561 55 NQKRRDWNTFGQYLKNHRPPLSLSRCSGAHVLEFLRYLDQFGKTKVHTPICPFYGHPNPPAPCPCPLRQAWGSLDALIGR 134 (204)
Q Consensus 55 sQKRrdwntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGkTkVH~~~C~ffG~p~ppapC~CPlRQAwGSLDALIGR 134 (204)
.+-+..++.|..|+.... ..+..-+..||.+|+.++.+.| .+.-++...+..
T Consensus 19 ~~~~~~~~~~~~~~~~~~--~~~~~it~~~i~~~~~~~~~~~--------------------------~~~~t~~~~~~~ 70 (291)
T TIGR02225 19 EAYRRDLEKFLEFLEERG--IDLEEVDRGDIVDFLAELKEAG--------------------------LSARSIARALSA 70 (291)
T ss_pred HHHHHHHHHHHHHHHhcC--CChHHCCHHHHHHHHHHhhcCC--------------------------CCHhHHHHHHHH
Confidence 445567888999998542 2455567899999999887644 122367888999
Q ss_pred HHHHHHHh--CCCCCCCccc
Q 046561 135 LRAAFEEN--GGKPEANPFG 152 (204)
Q Consensus 135 LRAafEE~--Gg~pE~NPF~ 152 (204)
|+++|+-. -+--+.|||.
T Consensus 71 l~~~~~~a~~~~~~~~np~~ 90 (291)
T TIGR02225 71 LRSFYRFLLREGIREDDPSA 90 (291)
T ss_pred HHHHHHHHHhcccccCCchh
Confidence 99988732 2334568863
No 7
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed
Probab=83.20 E-value=3.6 Score=32.79 Aligned_cols=68 Identities=26% Similarity=0.289 Sum_probs=47.6
Q ss_pred hhhhhhHHHHHHHhcCCCCccccCcchhHHHHHHhhcccCcccccCCCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHH
Q 046561 57 KRRDWNTFGQYLKNHRPPLSLSRCSGAHVLEFLRYLDQFGKTKVHTPICPFYGHPNPPAPCPCPLRQAWGSLDALIGRLR 136 (204)
Q Consensus 57 KRrdwntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGkTkVH~~~C~ffG~p~ppapC~CPlRQAwGSLDALIGRLR 136 (204)
-+.+|+.|..||..+.- .+...+..||.+|+.++.+.| .+-.++...+..|+
T Consensus 30 ~~~~~~~~~~~~~~~~~--~~~~l~~~~i~~~~~~~~~~~--------------------------~~~~t~~~~~~~l~ 81 (299)
T PRK00283 30 YRRDLELFAEWLAARGL--SLAEATRDDLQAFLAELAEGG--------------------------YKATSSARRLSALR 81 (299)
T ss_pred HHHHHHHHHHHHHhcCC--ChHHCCHHHHHHHHHHHHhCC--------------------------CCHHHHHHHHHHHH
Confidence 45688899999986532 566778999999999885432 23457778888888
Q ss_pred HHHHHhC--CCCCCCccc
Q 046561 137 AAFEENG--GKPEANPFG 152 (204)
Q Consensus 137 AafEE~G--g~pE~NPF~ 152 (204)
++|+-.. +--..|||.
T Consensus 82 ~~~~~a~~~~~i~~np~~ 99 (299)
T PRK00283 82 RFFQFLLREGLREDDPSA 99 (299)
T ss_pred HHHHHHHHcCCcccCchh
Confidence 8887331 234468863
No 8
>COG1080 PtsA Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]
Probab=79.76 E-value=2.4 Score=42.00 Aligned_cols=42 Identities=43% Similarity=0.660 Sum_probs=33.1
Q ss_pred hhhcchhHHHHHHHHHHHHHhCCC--------------------C-CCCcc-chhhHHHHHHHH
Q 046561 122 RQAWGSLDALIGRLRAAFEENGGK--------------------P-EANPF-GARAVRLYLREV 163 (204)
Q Consensus 122 RQAwGSLDALIGRLRAafEE~Gg~--------------------p-E~NPF-~araVRlYLReV 163 (204)
|..|=+.|..----++..|.+||+ | |.||| |-|+||+||...
T Consensus 305 r~~~P~EeEQ~~aY~~vlea~~g~pviiRTlDiGGDK~lpyl~lp~E~NPfLG~RaIRl~l~~~ 368 (574)
T COG1080 305 RDALPDEEEQFEAYKAVLEAMGGKPVIIRTLDIGGDKPLPYLNLPKEENPFLGYRAIRLSLERP 368 (574)
T ss_pred CCCCCChHHHHHHHHHHHHHcCCCceEEEecccCCCCcCCCCCCccccCchhhhHHHHHhhccH
Confidence 345556777777778888888887 3 79999 899999999643
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=73.96 E-value=13 Score=29.34 Aligned_cols=69 Identities=29% Similarity=0.351 Sum_probs=46.8
Q ss_pred hhhhhHHHHHHHhcCCCCccccCcchhHHHHHHhhcccCcccccCCCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHH
Q 046561 58 RRDWNTFGQYLKNHRPPLSLSRCSGAHVLEFLRYLDQFGKTKVHTPICPFYGHPNPPAPCPCPLRQAWGSLDALIGRLRA 137 (204)
Q Consensus 58 Rrdwntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGkTkVH~~~C~ffG~p~ppapC~CPlRQAwGSLDALIGRLRA 137 (204)
+.+++.|.+||......+.+..-+..||.+|+.++.+.|. +..++...++.||+
T Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~l~~~~i~~~~~~~~~~~~--------------------------~~~T~~~~~~~l~~ 75 (295)
T TIGR02224 22 RRDLKAFLEFLEEEGGLASLAEVTAADLRSFLAELHARGL--------------------------SRRSLARKLSALRS 75 (295)
T ss_pred HHHHHHHHHHHHhcCCCCccccCcHHHHHHHHHHhcccCC--------------------------CHHHHHHHHHHHHH
Confidence 4466678888888665677888889999999998765321 22456677777887
Q ss_pred HHHHhC--CCCCCCccc
Q 046561 138 AFEENG--GKPEANPFG 152 (204)
Q Consensus 138 afEE~G--g~pE~NPF~ 152 (204)
+|.-.. +.-+.|||.
T Consensus 76 ~~~~a~~~~~~~~np~~ 92 (295)
T TIGR02224 76 FYRFLVRRGLIKANPAA 92 (295)
T ss_pred HHHHHHHcCccccChHh
Confidence 776421 223467763
No 10
>PF10865 DUF2703: Domain of unknown function (DUF2703); InterPro: IPR021219 This family of protein has no known function.
Probab=63.29 E-value=2.2 Score=34.21 Aligned_cols=43 Identities=26% Similarity=0.297 Sum_probs=32.7
Q ss_pred HHHHHHhhcccCcccccCCCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHHHHHHhCCCCC
Q 046561 85 VLEFLRYLDQFGKTKVHTPICPFYGHPNPPAPCPCPLRQAWGSLDALIGRLRAAFEENGGKPE 147 (204)
Q Consensus 85 VleFLrylDqfGkTkVH~~~C~ffG~p~ppapC~CPlRQAwGSLDALIGRLRAafEE~Gg~pE 147 (204)
+|+|+ |||..|+| |... ...+.+|+..+-+|+.+|+..|..++
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 46777 55555776 5443 36678999999999999999998754
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=62.61 E-value=12 Score=37.60 Aligned_cols=42 Identities=26% Similarity=0.309 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHhCCC-------------------------CCCCcc-chhhHHHHH----HHHhhHHHhh
Q 046561 129 DALIGRLRAAFEENGGK-------------------------PEANPF-GARAVRLYL----REVRDVQSKA 170 (204)
Q Consensus 129 DALIGRLRAafEE~Gg~-------------------------pE~NPF-~araVRlYL----ReVRd~QAkA 170 (204)
|.+.-.+|.+++.++++ .|.||| |.|.||+|| .++=+.|.+|
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 55566777888776544 378999 889999999 4466666554
No 12
>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=61.49 E-value=3 Score=31.20 Aligned_cols=19 Identities=47% Similarity=0.770 Sum_probs=14.4
Q ss_pred HhhhccchhhhhcCCCCCc
Q 046561 168 SKARGISYEKKKRKRPPQQ 186 (204)
Q Consensus 168 AkARgi~y~kkkrkr~~~~ 186 (204)
.|+-||.|..|||||..++
T Consensus 45 ~KgLGI~Y~r~rrRrr~~~ 63 (68)
T PF00539_consen 45 QKGLGISYGRKRRRRRTPQ 63 (68)
T ss_dssp CTSSSTSSSSSSCSCCCSS
T ss_pred eCCCcccccccccCcCCCC
Confidence 4788999998777665544
No 13
>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=59.97 E-value=14 Score=33.28 Aligned_cols=46 Identities=28% Similarity=0.271 Sum_probs=33.7
Q ss_pred cchhHHHHHHHHHHHHHhCCC----------------------CCCCcc-chhhHHHHHHHHhhHHHhh
Q 046561 125 WGSLDALIGRLRAAFEENGGK----------------------PEANPF-GARAVRLYLREVRDVQSKA 170 (204)
Q Consensus 125 wGSLDALIGRLRAafEE~Gg~----------------------pE~NPF-~araVRlYLReVRd~QAkA 170 (204)
+=+.|.+...++.+.+.++++ .|.||| |-|+||+||..-.-...+-
T Consensus 58 ~p~e~eq~~~y~~i~~~~~~~pV~iRtlD~g~dK~l~~~~~~~~E~NP~LG~RGiR~~l~~p~~f~~Ql 126 (293)
T PF02896_consen 58 PPSEEEQYEIYRKIAEAMGGKPVTIRTLDIGGDKPLPYLSREPKEENPALGLRGIRRSLAHPELFRTQL 126 (293)
T ss_dssp HHHHHHHHHHHHHHHHHTTTSEEEEE---SBCCCGSCSSHHCH--SSGGGSSBTHHHHHHSHHHHHHHH
T ss_pred CchHHHHHHHHHHHHHHhccCcEEEEecCCCCCccCCcccccccccccccccccccccccchhhHHHHH
Confidence 346788889999999988876 569998 8899999997644333333
No 14
>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=59.94 E-value=38 Score=27.49 Aligned_cols=34 Identities=15% Similarity=0.344 Sum_probs=26.7
Q ss_pred hhhhHHHHHHHhcCC--CCccccCcchhHHHHHHhh
Q 046561 59 RDWNTFGQYLKNHRP--PLSLSRCSGAHVLEFLRYL 92 (204)
Q Consensus 59 rdwntf~qyL~n~rP--PlsL~~csg~hVleFLryl 92 (204)
..++.|..||....+ .+.+..-+..||.+|+.|+
T Consensus 43 ~~~~~~~~~~~~~~~~~~~~l~~i~~~~i~~~~~~l 78 (299)
T cd01185 43 THLKNLREFIECTYKEIDIALLELTREFILEFKLFL 78 (299)
T ss_pred HHHHHHHHHHHHhcCccCCCHHHccHHHHHHHHHHH
Confidence 346678888876554 6678888899999999998
No 15
>PRK10529 DNA-binding transcriptional activator KdpE; Provisional
Probab=55.59 E-value=9.9 Score=29.00 Aligned_cols=18 Identities=28% Similarity=0.504 Sum_probs=14.4
Q ss_pred hhHHHHHHHHHHHHHhCC
Q 046561 127 SLDALIGRLRAAFEENGG 144 (204)
Q Consensus 127 SLDALIGRLRAafEE~Gg 144 (204)
+||.+|.|||.-+++.+.
T Consensus 191 ~~~~~i~rlR~kl~~~~~ 208 (225)
T PRK10529 191 YLRIYMGHLRQKLEQDPA 208 (225)
T ss_pred CHHHHHHHHHHHhccCCC
Confidence 589999999999976443
No 16
>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=54.45 E-value=2.2 Score=32.97 Aligned_cols=18 Identities=56% Similarity=0.809 Sum_probs=14.7
Q ss_pred CCCcc---chhhHHHHHHHHh
Q 046561 147 EANPF---GARAVRLYLREVR 164 (204)
Q Consensus 147 E~NPF---~araVRlYLReVR 164 (204)
.+||| .||-+|+||||=-
T Consensus 5 k~NPfr~aiARKaRiyLr~Gl 25 (82)
T PF05528_consen 5 KDNPFRGAIARKARIYLREGL 25 (82)
T ss_pred ccCchhhhhhhheeeeeecCC
Confidence 48999 5789999999743
No 17
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=52.95 E-value=21 Score=24.26 Aligned_cols=53 Identities=19% Similarity=0.359 Sum_probs=32.5
Q ss_pred hhhhHHHHHHHhcCCCCccccCcchhHHHHHHhhc-ccCcccccCCCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHH
Q 046561 59 RDWNTFGQYLKNHRPPLSLSRCSGAHVLEFLRYLD-QFGKTKVHTPICPFYGHPNPPAPCPCPLRQAWGSLDALIGRLRA 137 (204)
Q Consensus 59 rdwntf~qyL~n~rPPlsL~~csg~hVleFLrylD-qfGkTkVH~~~C~ffG~p~ppapC~CPlRQAwGSLDALIGRLRA 137 (204)
...+.|.+|+.+. .+...+..||.+||.||- .-| .+..++...+.-||.
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 4456677777633 456678999999999887 322 345566777777777
Q ss_pred HHHH
Q 046561 138 AFEE 141 (204)
Q Consensus 138 afEE 141 (204)
.|+-
T Consensus 74 ff~~ 77 (85)
T PF13495_consen 74 FFRW 77 (85)
T ss_dssp HHHC
T ss_pred HHHH
Confidence 7663
No 18
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=51.79 E-value=13 Score=37.03 Aligned_cols=36 Identities=25% Similarity=0.410 Sum_probs=29.6
Q ss_pred hhHHHHHHHHHHHHHhCCC--------------------CCCCcc-chhhHHHHHHH
Q 046561 127 SLDALIGRLRAAFEENGGK--------------------PEANPF-GARAVRLYLRE 162 (204)
Q Consensus 127 SLDALIGRLRAafEE~Gg~--------------------pE~NPF-~araVRlYLRe 162 (204)
+-|......|.+.+.++++ +|.||| |.|+||+||+.
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 4677888888888888765 589999 78999999853
No 19
>PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=50.79 E-value=78 Score=24.85 Aligned_cols=37 Identities=30% Similarity=0.379 Sum_probs=27.5
Q ss_pred hhhhhhHHHHHHHhcCCCCccccCcchhHHHHHHhhcc
Q 046561 57 KRRDWNTFGQYLKNHRPPLSLSRCSGAHVLEFLRYLDQ 94 (204)
Q Consensus 57 KRrdwntf~qyL~n~rPPlsL~~csg~hVleFLrylDq 94 (204)
-+.+|+.|..|+..... ..+..-...||.+||.++-+
T Consensus 31 ~~~~~~~~~~~~~~~~~-~~~~~i~~~~i~~~~~~~~~ 67 (297)
T PRK00236 31 YRRDLRAFLAFLEEHGI-SSLQDLDAADLRSFLARRRR 67 (297)
T ss_pred HHHHHHHHHHHHHHcCC-CchhhCCHHHHHHHHHHHHh
Confidence 34677888888887543 55667778999999987754
No 20
>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=49.40 E-value=19 Score=34.94 Aligned_cols=38 Identities=29% Similarity=0.469 Sum_probs=29.6
Q ss_pred hhHHHHHHHHHHHHHhCCC---------------------CCCCcc-chhhHHHHHHHHh
Q 046561 127 SLDALIGRLRAAFEENGGK---------------------PEANPF-GARAVRLYLREVR 164 (204)
Q Consensus 127 SLDALIGRLRAafEE~Gg~---------------------pE~NPF-~araVRlYLReVR 164 (204)
+.|...-..|.+.+..+++ .|.||| |-|+||+||..-.
T Consensus 308 ~e~eq~~~y~~i~~~~~~~pv~iRtlDig~DK~~~~~~~~~E~NP~LG~RgiR~~l~~~~ 367 (565)
T TIGR01417 308 TEEEQFAAYKTVLEAMESDAVIVRTLDIGGDKELPYLNFPKEENPFLGYRAIRLALEREE 367 (565)
T ss_pred CHHHHHHHHHHHHHHhCCCceEEECCCCCCcccccccCCCCCCCccccchhhhhcccCHH
Confidence 4577777788888888766 379998 8899999997533
No 21
>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional
Probab=47.51 E-value=14 Score=28.23 Aligned_cols=23 Identities=30% Similarity=0.563 Sum_probs=17.5
Q ss_pred hhhhcc--------hhHHHHHHHHHHHHHhC
Q 046561 121 LRQAWG--------SLDALIGRLRAAFEENG 143 (204)
Q Consensus 121 lRQAwG--------SLDALIGRLRAafEE~G 143 (204)
+++.|| +||.+|.|||.-+++.+
T Consensus 175 ~~~~w~~~~~~~~~~v~~~i~rLR~kl~~~~ 205 (223)
T PRK10816 175 MLQLYPDAELRESHTIDVLMGRLRKKIQAQY 205 (223)
T ss_pred HHHhcCCCCCCCcCCHHHHHHHHHHHhccCC
Confidence 556676 78999999999887643
No 22
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair]
Probab=46.40 E-value=21 Score=33.00 Aligned_cols=38 Identities=29% Similarity=0.544 Sum_probs=34.0
Q ss_pred hhhhhHHHHHHHhcCCCC-ccccCcchhHHHHHHhhcccCc
Q 046561 58 RRDWNTFGQYLKNHRPPL-SLSRCSGAHVLEFLRYLDQFGK 97 (204)
Q Consensus 58 Rrdwntf~qyL~n~rPPl-sL~~csg~hVleFLrylDqfGk 97 (204)
|||-+.|.+||..+- + +|...+-.||.+||.++-.+|.
T Consensus 31 rrDL~~f~~~L~~~~--~~~l~~~~~~di~~yl~~l~~~g~ 69 (300)
T COG4974 31 RRDLEDFREWLEERG--ITDLADATEADIREYLTELAEQGL 69 (300)
T ss_pred HHHHHHHHHHHHhcC--CCChhhcCHHHHHHHHHHHHhCCc
Confidence 689999999999876 5 6888899999999999999995
No 23
>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=45.87 E-value=1.2e+02 Score=23.21 Aligned_cols=87 Identities=18% Similarity=0.242 Sum_probs=57.1
Q ss_pred hhhHHHHHHHhcCCCCccccCcchhHHHHHHhhcccCcccccCCCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHHHH
Q 046561 60 DWNTFGQYLKNHRPPLSLSRCSGAHVLEFLRYLDQFGKTKVHTPICPFYGHPNPPAPCPCPLRQAWGSLDALIGRLRAAF 139 (204)
Q Consensus 60 dwntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGkTkVH~~~C~ffG~p~ppapC~CPlRQAwGSLDALIGRLRAaf 139 (204)
|..++..+|.++..=-+...|+-....++|.++.+.|-. +....=.+-+.|.. ...+.+.+|+|..
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-PPKPARRPGRRPGM-------------ATSAQLRKIRALW 67 (119)
T ss_pred CHHHHHHHHHHHhChhhHHHCCHHHHHHHHHHHHHccCc-CccccccCCCCCCC-------------cchHHHHHHHHHH
Confidence 456788888888887788889999999999988888853 22111111111111 1788999999999
Q ss_pred HHhCCCCC-CCccchhhHHHHHH
Q 046561 140 EENGGKPE-ANPFGARAVRLYLR 161 (204)
Q Consensus 140 EE~Gg~pE-~NPF~araVRlYLR 161 (204)
.++|.... .|| ...++.-|++
T Consensus 68 ~~~~~~~~v~~~-s~~aL~~fvk 89 (119)
T PF06252_consen 68 KQLGKPGAVRDP-SEAALDAFVK 89 (119)
T ss_pred HHhhccCCccch-HHHHHHHHHH
Confidence 99997655 333 2334444443
No 24
>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=44.67 E-value=45 Score=27.35 Aligned_cols=26 Identities=31% Similarity=0.373 Sum_probs=19.8
Q ss_pred chhHHHHHHHHHHHHH---hCCCCCCCccc
Q 046561 126 GSLDALIGRLRAAFEE---NGGKPEANPFG 152 (204)
Q Consensus 126 GSLDALIGRLRAafEE---~Gg~pE~NPF~ 152 (204)
.++...++.|+++|+- +|.- +.|||.
T Consensus 135 ~t~~~~~~~l~~~~~~a~~~g~i-~~nP~~ 163 (357)
T cd00801 135 ETARRVRQRLKQVFRYAIARGLI-EANPAA 163 (357)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCc-ccCchH
Confidence 4788999999999984 4443 389985
No 25
>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=43.92 E-value=12 Score=23.04 Aligned_cols=16 Identities=38% Similarity=1.038 Sum_probs=13.5
Q ss_pred CCCCCCCCCCCCCCCC
Q 046561 103 PICPFYGHPNPPAPCP 118 (204)
Q Consensus 103 ~~C~ffG~p~ppapC~ 118 (204)
.+|.|||.+..-..|.
T Consensus 7 ~~CgF~G~~~t~~~Cs 22 (26)
T smart00259 7 PGCGFFGNPATEGLCS 22 (26)
T ss_pred CCCCCcCChhhcccCH
Confidence 7999999998877774
No 26
>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=43.38 E-value=25 Score=23.51 Aligned_cols=21 Identities=52% Similarity=0.885 Sum_probs=18.1
Q ss_pred chhHHHHHHHHHHHHHhCCCC
Q 046561 126 GSLDALIGRLRAAFEENGGKP 146 (204)
Q Consensus 126 GSLDALIGRLRAafEE~Gg~p 146 (204)
-+||.+|-|||..++..|+.+
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 489999999999999987543
No 27
>PF13276 HTH_21: HTH-like domain
Probab=42.01 E-value=44 Score=22.28 Aligned_cols=29 Identities=28% Similarity=0.447 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHhCCCCCCCccchhhHHHHHHH
Q 046561 129 DALIGRLRAAFEENGGKPEANPFGARAVRLYLRE 162 (204)
Q Consensus 129 DALIGRLRAafEE~Gg~pE~NPF~araVRlYLRe 162 (204)
|+|+-.++++|+++++ =||.+-|..+|+.
T Consensus 4 ~~l~~~I~~i~~~~~~-----~yG~rri~~~L~~ 32 (60)
T PF13276_consen 4 EALRELIKEIFKESKP-----TYGYRRIWAELRR 32 (60)
T ss_pred HHHHHHHHHHHHHcCC-----CeehhHHHHHHhc
Confidence 6789999999999977 3788888888886
No 28
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=39.98 E-value=27 Score=25.67 Aligned_cols=36 Identities=28% Similarity=0.477 Sum_probs=30.6
Q ss_pred CCCCCchhhhcc----hhHHHHHHHHHHHHHhCCCCCCCc
Q 046561 115 APCPCPLRQAWG----SLDALIGRLRAAFEENGGKPEANP 150 (204)
Q Consensus 115 apC~CPlRQAwG----SLDALIGRLRAafEE~Gg~pE~NP 150 (204)
--|+|-||..-+ ++|.|=-+|..+++||..+...+|
T Consensus 17 i~C~Cgl~l~~~~~~~tl~~l~~~L~~~~~~H~~~C~~~p 56 (82)
T PF14768_consen 17 ISCSCGLRLNTQQDELTLEELRQLLEEAVTEHSDRCSSTP 56 (82)
T ss_pred EECCCccEEecCCCCCCHHHHHHHHHHHHHHHHHhCCCCC
Confidence 347777988888 999999999999999987766666
No 29
>PRK09279 pyruvate phosphate dikinase; Provisional
Probab=39.33 E-value=27 Score=36.13 Aligned_cols=36 Identities=33% Similarity=0.478 Sum_probs=0.0
Q ss_pred HHHHHHHhCCC-----------CCCCcc-chhhHHHHH--HHHhhHHHhh
Q 046561 135 LRAAFEENGGK-----------PEANPF-GARAVRLYL--REVRDVQSKA 170 (204)
Q Consensus 135 LRAafEE~Gg~-----------pE~NPF-~araVRlYL--ReVRd~QAkA 170 (204)
++..-++.|+. -|.||| |.|.+|+|| .|+=++|.+|
T Consensus 636 ~~~~a~~~g~~~~k~~~~~~~~~E~NPmLG~RG~Rl~l~~pei~~~QlrA 685 (879)
T PRK09279 636 IEELAEALGLSLEELKARVEALHEFNPMLGHRGCRLGITYPEIYEMQARA 685 (879)
T ss_pred HHHHHHHcCCCHHHHHHHhcCCCCCCCccccchhhcccCChHHHHHHHHH
No 30
>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=38.74 E-value=33 Score=22.74 Aligned_cols=19 Identities=42% Similarity=0.761 Sum_probs=17.1
Q ss_pred chhHHHHHHHHHHHHHhCC
Q 046561 126 GSLDALIGRLRAAFEENGG 144 (204)
Q Consensus 126 GSLDALIGRLRAafEE~Gg 144 (204)
.+|+.+|-|||..+++.|+
T Consensus 45 ~~l~~~i~~LR~~l~~~~~ 63 (78)
T smart00862 45 NTLDVHISRLRKKLEDDGA 63 (78)
T ss_pred chHHHHHHHHHHHHhcCCC
Confidence 5799999999999999865
No 31
>PRK06464 phosphoenolpyruvate synthase; Validated
Probab=37.20 E-value=42 Score=34.01 Aligned_cols=16 Identities=50% Similarity=0.812 Sum_probs=14.1
Q ss_pred CCCcc-chhhHHHHHHH
Q 046561 147 EANPF-GARAVRLYLRE 162 (204)
Q Consensus 147 E~NPF-~araVRlYLRe 162 (204)
|.||| |.|.||+||..
T Consensus 597 E~NP~LG~RGiR~~l~~ 613 (795)
T PRK06464 597 EENPMLGFRGASRYLSE 613 (795)
T ss_pred CCCCccccchhhhcccC
Confidence 78999 88999999963
No 32
>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=35.05 E-value=52 Score=29.75 Aligned_cols=65 Identities=22% Similarity=0.229 Sum_probs=47.0
Q ss_pred CCCchHHHhhhhhhhHHHHHHHhcCCCCcc--ccCcchhHHHHHHh-----------------hcccCcccccCCCCCCC
Q 046561 48 SSSSRYENQKRRDWNTFGQYLKNHRPPLSL--SRCSGAHVLEFLRY-----------------LDQFGKTKVHTPICPFY 108 (204)
Q Consensus 48 ~~~SrYesQKRrdwntf~qyL~n~rPPlsL--~~csg~hVleFLry-----------------lDqfGkTkVH~~~C~ff 108 (204)
..-.+|-++=|..-.+|.+||+.+.|-... ..--...|.|||.. ....|..++|..+=--|
T Consensus 146 ~ef~~yL~kvr~~R~eF~~~L~~~~~e~~~~~~~~l~~~v~eFL~~~~~~~~~~~~~~~~~~~~~~~~~~~~hpsgGLSY 225 (312)
T PF11709_consen 146 GEFERYLKKVRPLRPEFKKWLREKHPESLTFDPSDLYDLVKEFLDLAPLKPPDVPDSKKSSSPYAEAGPPKTHPSGGLSY 225 (312)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHhChhhhccCHHHHHHHHHHHHhcccccCcccccchhccCcccccCCCccccCcCcCc
Confidence 345688888899999999999999986621 23345678899975 33567778887776666
Q ss_pred CCCC
Q 046561 109 GHPN 112 (204)
Q Consensus 109 G~p~ 112 (204)
.+++
T Consensus 226 ~~~g 229 (312)
T PF11709_consen 226 NRTG 229 (312)
T ss_pred CCCc
Confidence 6554
No 33
>PRK11177 phosphoenolpyruvate-protein phosphotransferase; Provisional
Probab=35.04 E-value=35 Score=33.38 Aligned_cols=37 Identities=30% Similarity=0.479 Sum_probs=29.7
Q ss_pred hhHHHHHHHHHHHHHhCCC---------------------CCCCcc-chhhHHHHHHHH
Q 046561 127 SLDALIGRLRAAFEENGGK---------------------PEANPF-GARAVRLYLREV 163 (204)
Q Consensus 127 SLDALIGRLRAafEE~Gg~---------------------pE~NPF-~araVRlYLReV 163 (204)
+-|...--.|.+.+.++++ .|.||| |-|+||+||+.-
T Consensus 309 ~eeeq~~~y~~i~~~~~~~~v~iRtlDiGgDK~~~~~~~~~E~NP~LG~RgiR~~l~~~ 367 (575)
T PRK11177 309 TEEEQFQAYKAVAEAMGSQAVIVRTMDIGGDKELPYMNLPKEENPFLGWRAIRIAMDRK 367 (575)
T ss_pred CHHHHHHHHHHHHHHcCCCeEEEECcCCCcccccccCCCCCCCCcccccchhhhcCCCH
Confidence 4677778888888888765 379999 779999999653
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=34.37 E-value=22 Score=36.44 Aligned_cols=25 Identities=40% Similarity=0.656 Sum_probs=19.3
Q ss_pred CCCCcc-chhhHHHHH--HHHhhHHHhh
Q 046561 146 PEANPF-GARAVRLYL--REVRDVQSKA 170 (204)
Q Consensus 146 pE~NPF-~araVRlYL--ReVRd~QAkA 170 (204)
.|.||| |.|.||+|| .++=+.|.+|
T Consensus 652 ~E~NP~LG~RGiRl~l~~pei~~~QlrA 679 (856)
T TIGR01828 652 HEVNPMLGHRGCRLGITYPEIYEMQVRA 679 (856)
T ss_pred CCCCCccccchhhhccCChHHHHHHHHH
Confidence 599999 889999999 4555566544
No 35
>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=34.16 E-value=23 Score=24.43 Aligned_cols=21 Identities=33% Similarity=0.456 Sum_probs=17.3
Q ss_pred cCcchhHHHHHHhhcccCccc
Q 046561 79 RCSGAHVLEFLRYLDQFGKTK 99 (204)
Q Consensus 79 ~csg~hVleFLrylDqfGkTk 99 (204)
..|=+-++-+|.|+|+.|.|+
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 36
>PF03344 Daxx: Daxx Family; InterPro: IPR005012 Daxx is a ubiquitously expressed protein that functions, in part, as a transcriptional co-repressor through its interaction with a growing number of nuclear, DNA-associated proteins. Human Daxx contains four structural domains commonly found in transcriptional regulatory proteins: two predicted paired amphipathic helices, an acid-rich domain and a Ser/Pro/Thr (SPT)-rich domain. The post-translational modification status of the SPT-domain of hDaxx regulates its association with transcription factors such as Pax3 and ETS-1, effectively bringing hDaxx to sites of active transcription. Through its presence at the site of active transcription, hDaxx could then be able to associate with acetylated histones present in the nucleosomes and Dek that is associated with chromatin. Through its association with the SPT-domain of hDaxx, histone deacetylases may also be brought to the site of active transcription. As a consequence, nucleosomes in the vicinity of the site of active transcription will have the histone tails deacetylated, allowing the deactylated tail to bind to DNA, thereby leading to an inactive chromatin structure and transcriptional repression []. The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis as a component of nuclear promyelocytic leukemia protein (PML) oncogenic domains (PODS). Daxx associates with PODs through a direct interaction with PML, a critical component of PODs. The interaction is a dynamic, cell cycle regulated event and is dependent on the post-translational modification of PML by the small ubiquitin-related modifier SUMO-1. ; PDB: 2KZS_A 2KZU_A.
Probab=33.66 E-value=1.5e+02 Score=30.31 Aligned_cols=75 Identities=23% Similarity=0.254 Sum_probs=44.5
Q ss_pred HHHhhhhhhhHHHHHHHhcCCCCccccCcchhHHHHHHhhcccCcccccCCCCCCCCCCCCCCCCCCchhhhcchhHHHH
Q 046561 53 YENQKRRDWNTFGQYLKNHRPPLSLSRCSGAHVLEFLRYLDQFGKTKVHTPICPFYGHPNPPAPCPCPLRQAWGSLDALI 132 (204)
Q Consensus 53 YesQKRrdwntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGkTkVH~~~C~ffG~p~ppapC~CPlRQAwGSLDALI 132 (204)
||+|| ++..|..+-..+.- ....|+.||+ +.|...++ .-++.-..=-+|
T Consensus 66 ~~~~~--lf~eFi~~C~~~~~-------d~~evv~~L~--------~~~~~~~~--------------~f~~S~~F~~~l 114 (713)
T PF03344_consen 66 YENQK--LFEEFIELCLAQTS-------DMPEVVKFLK--------RRYEKAHP--------------EFLSSEEFRNFL 114 (713)
T ss_dssp -HHHH--HHHHHHHHHHHHTT-------T-TTHHHHHH--------HHHHTC-C--------------CHHCSHHHHHHH
T ss_pred ChHHH--HHHHHHHHhccccc-------CCHHHHHHHH--------HHHHhCCH--------------HHHhHHHHHHHH
Confidence 45553 56666666554321 2346999997 33333333 334444555677
Q ss_pred HHHHHHHHHhCCCCCCCccchhhHHHHHHHHhhHHH
Q 046561 133 GRLRAAFEENGGKPEANPFGARAVRLYLREVRDVQS 168 (204)
Q Consensus 133 GRLRAafEE~Gg~pE~NPF~araVRlYLReVRd~QA 168 (204)
++-++....+..+ |=+||.+|-+.=.
T Consensus 115 ~~~~~~~~~~~~k----------~yv~i~~v~~~lk 140 (713)
T PF03344_consen 115 SRCLARIQNNPKK----------VYVHINEVCTELK 140 (713)
T ss_dssp HHHHHHHHH-CCC----------HHHHHHHHHHHHH
T ss_pred HHHHHHHHCCCCe----------EEEEHHHHHHHHH
Confidence 8887777777655 8899999987643
No 37
>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=33.58 E-value=32 Score=21.99 Aligned_cols=12 Identities=42% Similarity=0.866 Sum_probs=10.1
Q ss_pred hhHHHHHHHHhh
Q 046561 154 RAVRLYLREVRD 165 (204)
Q Consensus 154 raVRlYLReVRd 165 (204)
-+|++||++|+.
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 478999999975
No 38
>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=33.44 E-value=47 Score=27.16 Aligned_cols=36 Identities=25% Similarity=0.475 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHhCCCCC---C---Cc-cchhhHHHHHHHHhh
Q 046561 130 ALIGRLRAAFEENGGKPE---A---NP-FGARAVRLYLREVRD 165 (204)
Q Consensus 130 ALIGRLRAafEE~Gg~pE---~---NP-F~araVRlYLReVRd 165 (204)
.-|.+|+..|++.|...+ . ++ -.|..++.||||.-+
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 268889999999755
No 39
>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=31.63 E-value=7.5 Score=26.40 Aligned_cols=72 Identities=14% Similarity=0.214 Sum_probs=45.3
Q ss_pred hhhhhhHHHHHHHhcCC--CCccccCcchhHHHHHHhhcccC--cccccC---CCCCCCCCCCCCCCCCCchhhhcchhH
Q 046561 57 KRRDWNTFGQYLKNHRP--PLSLSRCSGAHVLEFLRYLDQFG--KTKVHT---PICPFYGHPNPPAPCPCPLRQAWGSLD 129 (204)
Q Consensus 57 KRrdwntf~qyL~n~rP--PlsL~~csg~hVleFLrylDqfG--kTkVH~---~~C~ffG~p~ppapC~CPlRQAwGSLD 129 (204)
++.||..|.+.+.+..- +.....+...+|.+.+.++-+.| -+++-. -+|.|- |=.--...|
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 46899999999995544 44456677788888888888888 333311 333221 212223566
Q ss_pred HHHHHHHHHHH
Q 046561 130 ALIGRLRAAFE 140 (204)
Q Consensus 130 ALIGRLRAafE 140 (204)
.++-+|++.|+
T Consensus 74 ~v~~~l~~~~~ 84 (85)
T PF08544_consen 74 RVAEALREHYK 84 (85)
T ss_dssp HHHHHHHHHTH
T ss_pred HHHHHHHHhCC
Confidence 77777777664
No 40
>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=31.39 E-value=44 Score=23.65 Aligned_cols=31 Identities=23% Similarity=0.490 Sum_probs=24.4
Q ss_pred hhHHHHHHHhcCCCCccccCcchhHHHHHHhhcccC
Q 046561 61 WNTFGQYLKNHRPPLSLSRCSGAHVLEFLRYLDQFG 96 (204)
Q Consensus 61 wntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfG 96 (204)
-+.|.+=|++-+| +.+.+||..|..|-.+||
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 3557777777777 456899999999999998
No 41
>smart00243 GAS2 Growth-Arrest-Specific Protein 2 Domain. GROWTH-ARREST-SPECIFIC PROTEIN 2 Domain
Probab=31.28 E-value=32 Score=26.26 Aligned_cols=14 Identities=43% Similarity=1.077 Sum_probs=13.1
Q ss_pred hhhHHHHHHHhcCC
Q 046561 60 DWNTFGQYLKNHRP 73 (204)
Q Consensus 60 dwntf~qyL~n~rP 73 (204)
-|.||.+||..|.|
T Consensus 55 GW~tL~~fL~khDP 68 (73)
T smart00243 55 GWETLDEYLLKHDP 68 (73)
T ss_pred cHHHHHHHHHhCCC
Confidence 39999999999998
No 42
>PF03732 Retrotrans_gag: Retrotransposon gag protein ; InterPro: IPR005162 Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more specifically, than other cellular processes. Retrotransposons are structurally similar to retroviruses and are bounded by long terminal repeats. This entry represents eukaryotic Gag or capsid-related retrotranspon-related proteins. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.
Probab=31.13 E-value=1.3e+02 Score=20.24 Aligned_cols=38 Identities=24% Similarity=0.297 Sum_probs=27.7
Q ss_pred hhhhcchhHHHHHHHHHHHHHhCC-CCCCCccchhhHHHHHHHH
Q 046561 121 LRQAWGSLDALIGRLRAAFEENGG-KPEANPFGARAVRLYLREV 163 (204)
Q Consensus 121 lRQAwGSLDALIGRLRAafEE~Gg-~pE~NPF~araVRlYLReV 163 (204)
++|.-+||+..+-|++......+. -+| .-.|..|++-+
T Consensus 56 l~Q~~esv~~y~~rf~~l~~~~~~~~~e-----~~~v~~f~~GL 94 (96)
T PF03732_consen 56 LRQGNESVREYVNRFRELARRAPPPMDE-----EMLVERFIRGL 94 (96)
T ss_pred hhccCCcHHHHHHHHHHHHHHCCCCcCH-----HHHHHHHHHCC
Confidence 778777999999999999999885 222 44555555433
No 43
>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=30.45 E-value=58 Score=25.80 Aligned_cols=63 Identities=27% Similarity=0.515 Sum_probs=43.4
Q ss_pred hhhHHHHHHHhcCCCCccccCcchhHHHHHHhhcccCcccccCCCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHHHH
Q 046561 60 DWNTFGQYLKNHRPPLSLSRCSGAHVLEFLRYLDQFGKTKVHTPICPFYGHPNPPAPCPCPLRQAWGSLDALIGRLRAAF 139 (204)
Q Consensus 60 dwntf~qyL~n~rPPlsL~~csg~hVleFLrylDqfGkTkVH~~~C~ffG~p~ppapC~CPlRQAwGSLDALIGRLRAaf 139 (204)
+|.++-.++.. |-.-.+.+-.||-+|=++.++ | .+| +|-|=..||+-++-||.|-..|
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 78888877754 223334544566666554443 2 222 4557789999999999999999
Q ss_pred HHhCC
Q 046561 140 EENGG 144 (204)
Q Consensus 140 EE~Gg 144 (204)
.++|-
T Consensus 81 ~k~~l 85 (100)
T cd08793 81 IQNEF 85 (100)
T ss_pred HHccc
Confidence 99884
No 44
>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=30.21 E-value=1.8e+02 Score=24.58 Aligned_cols=37 Identities=19% Similarity=0.300 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHhC---CCCCCCcc----chhhHHHHHHHHhh
Q 046561 129 DALIGRLRAAFEENG---GKPEANPF----GARAVRLYLREVRD 165 (204)
Q Consensus 129 DALIGRLRAafEE~G---g~pE~NPF----~araVRlYLReVRd 165 (204)
-+-|.+|+.+|++.. ...+-+.+ .+..++.|||+.-+
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 45
>PRK05084 xerS site-specific tyrosine recombinase XerS; Reviewed
Probab=30.05 E-value=1.1e+02 Score=25.94 Aligned_cols=68 Identities=16% Similarity=0.245 Sum_probs=43.6
Q ss_pred hhhhhHHHHHHHhcCC-----CC-----ccccCcchhHHHHHHhhcccCcccccCCCCCCCCCCCCCCCCCCchhhhcch
Q 046561 58 RRDWNTFGQYLKNHRP-----PL-----SLSRCSGAHVLEFLRYLDQFGKTKVHTPICPFYGHPNPPAPCPCPLRQAWGS 127 (204)
Q Consensus 58 Rrdwntf~qyL~n~rP-----Pl-----sL~~csg~hVleFLrylDqfGkTkVH~~~C~ffG~p~ppapC~CPlRQAwGS 127 (204)
+++...|.+||..+.. .. .|...+..||.+|+.|+.+.-.. + ++.+ +...+..+
T Consensus 42 ~~~l~~f~~~l~~~~~~~~~~~~~~~~~~l~~lt~~~i~~f~~~l~~~~~~------~---~~~~-------~~~~s~~T 105 (357)
T PRK05084 42 LTEYRRFFNWLISEGLSDASKIKDIPLSTLENLTKKDVEAFILYLRERPLL------N---GHST-------KKGNSQTT 105 (357)
T ss_pred HHHHHHHHHHHHHcCCCCcCCcccCCHHHHHhhhHHHHHHHHHHHHhcccc------c---cccc-------ccchhHHH
Confidence 4566778888876532 11 24567899999999998642110 0 0100 01246688
Q ss_pred hHHHHHHHHHHHHH
Q 046561 128 LDALIGRLRAAFEE 141 (204)
Q Consensus 128 LDALIGRLRAafEE 141 (204)
+...++-||++|.-
T Consensus 106 i~~~l~~l~~~~~~ 119 (357)
T PRK05084 106 INRTLSALKSLFKY 119 (357)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999999984
No 46
>PRK10701 DNA-binding transcriptional regulator RstA; Provisional
Probab=29.13 E-value=44 Score=26.02 Aligned_cols=16 Identities=44% Similarity=0.632 Sum_probs=11.3
Q ss_pred hhHHHHHHHHHHHHHh
Q 046561 127 SLDALIGRLRAAFEEN 142 (204)
Q Consensus 127 SLDALIGRLRAafEE~ 142 (204)
+||..|.|||.-+++.
T Consensus 201 ~i~~~i~rlR~kl~~~ 216 (240)
T PRK10701 201 SVDVAISRLRKKLLDN 216 (240)
T ss_pred CHHHHHHHHHHhcccC
Confidence 5777777777777643
No 47
>PF04221 RelB: RelB antitoxin; InterPro: IPR007337 Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. Several toxin/antitoxin pairs may occur in a single species. RelE and RelB form a toxin-antitoxin system; RelE represses translation, probably through binding ribosomes [, ]. RelB stably binds RelE, presumably deactivating it.; PDB: 2KC8_B 2K29_A.
Probab=28.75 E-value=1.2e+02 Score=21.92 Aligned_cols=39 Identities=26% Similarity=0.445 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHhCCCCCCCccchhhHHHHHHHHhhHHHhhhccchhhh
Q 046561 130 ALIGRLRAAFEENGGKPEANPFGARAVRLYLREVRDVQSKARGISYEKK 178 (204)
Q Consensus 130 ALIGRLRAafEE~Gg~pE~NPF~araVRlYLReVRd~QAkARgi~y~kk 178 (204)
.|--+..++|+++|-.+ .-||++||+.|= +.+|||++-+
T Consensus 11 ~lK~~a~~il~~~Glt~------s~ai~~fl~qiv----~~~~iPF~~~ 49 (83)
T PF04221_consen 11 ELKEEAEAILEELGLTL------SDAINMFLKQIV----REGGIPFELS 49 (83)
T ss_dssp HHHHHHHHHHHHTT--H------HHHHHHHHHHHH----HHSS-S----
T ss_pred HHHHHHHHHHHHcCCCH------HHHHHHHHHHHH----HhCCCCcccc
Confidence 45667788999999874 579999999874 4578998753
No 48
>cd04400 RhoGAP_fBEM3 RhoGAP_fBEM3: RhoGAP (GTPase-activator [GAP] protein for Rho-like small GTPases) domain of fungal BEM3-like proteins. Bem3 is a GAP protein of Cdc42, and is specifically involved in the control of the initial assembly of the septin ring in yeast bud formation. 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=27.80 E-value=1.2e+02 Score=24.64 Aligned_cols=39 Identities=28% Similarity=0.393 Sum_probs=26.6
Q ss_pred chhHHHHHHHHHHHHHhCC---C--C-CCC-ccchhhHHHHHHHHhh
Q 046561 126 GSLDALIGRLRAAFEENGG---K--P-EAN-PFGARAVRLYLREVRD 165 (204)
Q Consensus 126 GSLDALIGRLRAafEE~Gg---~--p-E~N-PF~araVRlYLReVRd 165 (204)
|+. ..|-+|+..|+..+. . + +.| .-.|..+|.||||.-+
T Consensus 49 G~~-~~i~~l~~~~~~~~~~~~~~~~~~~d~h~va~lLK~flreLP~ 94 (190)
T cd04400 49 GSA-SVIKQLKERFNTEYDVDLFSSSLYPDVHTVAGLLKLYLRELPT 94 (190)
T ss_pred CcH-HHHHHHHHHHcCCCCCCccccccccCHHHHHHHHHHHHHhCCc
Confidence 444 367999999987542 1 1 123 3468999999999854
No 49
>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=27.64 E-value=25 Score=28.14 Aligned_cols=36 Identities=28% Similarity=0.454 Sum_probs=29.3
Q ss_pred hhhhHHHHHHHh---cCCCCccccCcchhHHHHHHhhcc
Q 046561 59 RDWNTFGQYLKN---HRPPLSLSRCSGAHVLEFLRYLDQ 94 (204)
Q Consensus 59 rdwntf~qyL~n---~rPPlsL~~csg~hVleFLrylDq 94 (204)
..|..|++|+-. ..-|-.+.++.+.++.+||.-+|.
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 468889988876 445777789999999999998875
No 50
>PTZ00398 phosphoenolpyruvate carboxylase; Provisional
Probab=27.60 E-value=98 Score=32.57 Aligned_cols=42 Identities=21% Similarity=0.411 Sum_probs=31.6
Q ss_pred cchhHHHHHHHHHHHHHhCC------------------CCCCCccc-------------hhhHHHHHHHHhhH
Q 046561 125 WGSLDALIGRLRAAFEENGG------------------KPEANPFG-------------ARAVRLYLREVRDV 166 (204)
Q Consensus 125 wGSLDALIGRLRAafEE~Gg------------------~pE~NPF~-------------araVRlYLReVRd~ 166 (204)
|-.+=.|..+|+.+++++|+ .=++|||. ..|+++|+++|++.
T Consensus 264 ~~aiP~~~~~l~~al~~~~~~~~~~~~~~i~fGSWiGGDRDGNP~VTaevT~~~l~~~r~~al~~Y~~~l~~L 336 (974)
T PTZ00398 264 FDALPNFIRYIDNVLYEYNLDPLPPTKKLFTFSSWVGGDRDGNPFVTAEVTRQVVYFNRIRACELFIHMIEKL 336 (974)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCCCCceeccCCCCCCCCCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45566788899999988754 23499996 35778999998865
No 51
>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=27.43 E-value=54 Score=22.53 Aligned_cols=20 Identities=30% Similarity=0.539 Sum_probs=17.2
Q ss_pred chhHHHHHHHHHHHHHhCCC
Q 046561 126 GSLDALIGRLRAAFEENGGK 145 (204)
Q Consensus 126 GSLDALIGRLRAafEE~Gg~ 145 (204)
.+|+.+|=|||..+.+.|+.
T Consensus 62 ~~l~~~I~rLRkkl~~~~~~ 81 (95)
T cd00383 62 RTVDVHISRLRKKLEDDPSN 81 (95)
T ss_pred ccHHHHHHHHHHHhccCCCC
Confidence 57999999999999987653
No 52
>PF09958 DUF2192: Uncharacterized protein conserved in archaea (DUF2192); InterPro: IPR018693 This family of various hypothetical archaeal proteins has no known function.
Probab=26.84 E-value=55 Score=29.41 Aligned_cols=21 Identities=38% Similarity=0.588 Sum_probs=18.3
Q ss_pred hhHHHHHHHHHHHHHhCCCCC
Q 046561 127 SLDALIGRLRAAFEENGGKPE 147 (204)
Q Consensus 127 SLDALIGRLRAafEE~Gg~pE 147 (204)
+=+.||.-||..|+++|..|=
T Consensus 27 ~R~~lv~~L~~~Y~~~gIeP~ 47 (231)
T PF09958_consen 27 DREELVELLREVYEENGIEPF 47 (231)
T ss_pred CHHHHHHHHHHHHHHcCCCcC
Confidence 558999999999999998753
No 53
>cd01355 AcnX Putative Aconitase X catalytic domain. Putative Aconitase X catalytic domain. It is predicted by comparative genomic analysis. The proteins are mainly found in archaea and proteobacteria. They are distantly related to Aconitase family of proteins by sequence similarity and seconary structure prediction. The functions have not yet been experimentally characterized. Thus, the prediction should be treated with caution.
Probab=26.74 E-value=68 Score=30.43 Aligned_cols=54 Identities=37% Similarity=0.530 Sum_probs=35.1
Q ss_pred chhHHHHHHhhcccC-cccccCCCCCCCCCCCCCCCCCCchhhhcchh--HH----HHHHHHHHHHHhCCCCC
Q 046561 82 GAHVLEFLRYLDQFG-KTKVHTPICPFYGHPNPPAPCPCPLRQAWGSL--DA----LIGRLRAAFEENGGKPE 147 (204)
Q Consensus 82 g~hVleFLrylDqfG-kTkVH~~~C~ffG~p~ppapC~CPlRQAwGSL--DA----LIGRLRAafEE~Gg~pE 147 (204)
|.-=++||..|.+.| |-+|++ .-.|-.+.++ |..+ |. .--||..||+++|..|.
T Consensus 48 G~agl~f~e~l~~~gakv~VpT----------TlNp~~~D~~--w~~~gvd~~f~~~q~~i~~ay~~mG~~~t 108 (389)
T cd01355 48 GDAGLEFLERLADQGAKVAVPT----------TLNPISMDLH--WRELGVDEEFAEKQARLVKAYKAMGVDPT 108 (389)
T ss_pred chhhHHHHHHHHhCCCeEeecC----------ccCCcccCcc--hhhcCCCHHHHHHHHHHHHHHHHcCCccc
Confidence 344579999886666 344432 3455666676 8755 32 34477899999998765
No 54
>TIGR03190 benz_CoA_bzdN benzoyl-CoA reductase, bzd-type, N subunit. Members of this family are the N subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene.
Probab=26.71 E-value=4.9e+02 Score=23.65 Aligned_cols=24 Identities=21% Similarity=0.308 Sum_probs=20.6
Q ss_pred HHHhhhhhhhHHHHHHHhcCCCCc
Q 046561 53 YENQKRRDWNTFGQYLKNHRPPLS 76 (204)
Q Consensus 53 YesQKRrdwntf~qyL~n~rPPls 76 (204)
..++.|+.|+.|.++.+.+.+|++
T Consensus 166 ~~n~~r~~~~~~~~l~~~~p~pit 189 (377)
T TIGR03190 166 VCDENRRLLRELFDYRKEADPKVT 189 (377)
T ss_pred HHHHHHHHHHHHHHHHccCCCCcC
Confidence 456789999999999988888887
No 55
>COG0745 OmpR Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=26.65 E-value=52 Score=27.97 Aligned_cols=28 Identities=36% Similarity=0.662 Sum_probs=22.2
Q ss_pred Cchhhhcc--------hhHHHHHHHHHHHHHhCCCC
Q 046561 119 CPLRQAWG--------SLDALIGRLRAAFEENGGKP 146 (204)
Q Consensus 119 CPlRQAwG--------SLDALIGRLRAafEE~Gg~p 146 (204)
--+.+.|| +||..|+|||.-+++.++.+
T Consensus 177 ~L~~~vw~~~~~~~~rtvdvhI~rLR~Kl~~~~~~~ 212 (229)
T COG0745 177 QLLEAVWGYDFEVDSRTVDVHISRLRKKLEKDPGAG 212 (229)
T ss_pred HHHHHhcCCCCCCCccCHHHHHHHHHHHhccCCCCC
Confidence 34677787 49999999999999886543
No 56
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=26.09 E-value=1.3e+02 Score=22.65 Aligned_cols=38 Identities=29% Similarity=0.454 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHhCCCCCCCccchhhHHHHHHHHhhHHHhhhccchhh
Q 046561 130 ALIGRLRAAFEENGGKPEANPFGARAVRLYLREVRDVQSKARGISYEK 177 (204)
Q Consensus 130 ALIGRLRAafEE~Gg~pE~NPF~araVRlYLReVRd~QAkARgi~y~k 177 (204)
.|--+.-++|++.|-.+ ..|||+||+.| ++.+|||++.
T Consensus 11 ~lK~~A~~vl~~lGls~------S~Ai~~fl~qi----~~~~~iPF~~ 48 (80)
T PRK11235 11 ELKARAYAVLEKLGVTP------SEALRLLLQYV----AENGRLPFKT 48 (80)
T ss_pred HHHHHHHHHHHHhCCCH------HHHHHHHHHHH----HHhCCCCCCC
Confidence 44556678899999874 57999999887 4457787763
No 57
>TIGR02249 integrase_gron integron integrase. Members of this family are integrases associated with integrons (and super-integrons), which are systems for incorporating and expressing cassettes of laterally transferred DNA. Incorporation occurs at an attI site. A super-integron, as in Vibrio sp., may include over 100 cassettes. This family belongs to the phage integrase family (pfam00589) that also includes recombinases XerC (TIGR02224) and XerD (TIGR02225), which are bacterial housekeeping proteins. Within this family of integron integrases, some are designated by class, e.g. IntI4, a class 4 integron integrase from Vibrio cholerae N16961.
Probab=26.03 E-value=1.8e+02 Score=24.04 Aligned_cols=33 Identities=18% Similarity=0.098 Sum_probs=24.4
Q ss_pred hhhhhHHHHHHHhcCCCCccccCcchhHHHHHHhhcc
Q 046561 58 RRDWNTFGQYLKNHRPPLSLSRCSGAHVLEFLRYLDQ 94 (204)
Q Consensus 58 Rrdwntf~qyL~n~rPPlsL~~csg~hVleFLrylDq 94 (204)
...++.|.+|+.+ +.+..-+..||.+||.++-+
T Consensus 23 ~~~~~~~~~~~g~----~~~~~it~~~i~~~l~~l~~ 55 (315)
T TIGR02249 23 LHWIKRFIRFHNK----RHPSTMGDTEVEAFLSDLAV 55 (315)
T ss_pred HHHHHHHHHHhCC----CChHhcCHHHHHHHHHHHHh
Confidence 4578888888642 34556689999999999854
No 58
>KOG1452 consensus Predicted Rho GTPase-activating protein [Signal transduction mechanisms]
Probab=26.02 E-value=37 Score=32.78 Aligned_cols=31 Identities=35% Similarity=0.511 Sum_probs=23.0
Q ss_pred HHHHHHHHhCCC--------CCCCccchhhHHHHHHHHhh
Q 046561 134 RLRAAFEENGGK--------PEANPFGARAVRLYLREVRD 165 (204)
Q Consensus 134 RLRAafEE~Gg~--------pE~NPF~araVRlYLReVRd 165 (204)
-||++||-||+. |+.|=. +..++.||||+=|
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 589999999975 334433 4589999999743
No 59
>cd04436 DEP_fRgd2 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGAP (GTPase-activator protein) Rgd2-like proteins. Rgd2-like proteins share a common domain architecture, containing, beside the RhoGAP domain, a DEP and a FCH (Fes/CIP4 homology) domain. Yeast Rgd2 is a GAP protein for Cdc42 and Rho5.
Probab=25.98 E-value=50 Score=25.54 Aligned_cols=40 Identities=28% Similarity=0.458 Sum_probs=30.0
Q ss_pred hHHHHHHHhcCCCCccccC--cchhHH--HHHHhhcccCccccc
Q 046561 62 NTFGQYLKNHRPPLSLSRC--SGAHVL--EFLRYLDQFGKTKVH 101 (204)
Q Consensus 62 ntf~qyL~n~rPPlsL~~c--sg~hVl--eFLrylDqfGkTkVH 101 (204)
.++++||..++|=.++..| -|.|++ .|||+.+..|.|-++
T Consensus 33 ~~Iv~~L~~n~~~~s~~~aE~fGQdLv~~gfir~~g~vG~~F~n 76 (84)
T cd04436 33 SEIVSWLQENMPEKDLDAAEAFGQDLLNQGFLRLVGGVGSTFVN 76 (84)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHHHHhCchHHHhcccCcceec
Confidence 4688899888887666644 366775 499999999987665
No 60
>cd01187 INT_SG4 INT_SG4, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 4, N- and C-terminal domains. The CD contains mainly predicted bacterial integrase/recombinases for which not much biochemical characterization is available.
Probab=25.62 E-value=2.9e+02 Score=22.49 Aligned_cols=29 Identities=14% Similarity=0.135 Sum_probs=20.7
Q ss_pred hhhHHHHHHHhcCCCCccccCcchhHHHHHHhh
Q 046561 60 DWNTFGQYLKNHRPPLSLSRCSGAHVLEFLRYL 92 (204)
Q Consensus 60 dwntf~qyL~n~rPPlsL~~csg~hVleFLryl 92 (204)
.-+.|.+|+.++. +...+..||.+|+.++
T Consensus 25 ~~~~f~~~~~~~~----~~~it~~~~~~~~~~~ 53 (299)
T cd01187 25 LLRDFVRFLERHG----AGFITTDLALRWAASP 53 (299)
T ss_pred HHHHHHHHHHhCC----CCCCCHHHHHHHHhcC
Confidence 3456888887654 5677888888888653
No 61
>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=25.17 E-value=74 Score=27.17 Aligned_cols=34 Identities=18% Similarity=0.289 Sum_probs=24.3
Q ss_pred HHHHHHHHHHhCCCCC---CCcc-chhhHHHHHHHHhh
Q 046561 132 IGRLRAAFEENGGKPE---ANPF-GARAVRLYLREVRD 165 (204)
Q Consensus 132 IGRLRAafEE~Gg~pE---~NPF-~araVRlYLReVRd 165 (204)
+-.||.+||+.+...+ .++. .+.+++.|||+.-|
T Consensus 45 ~~~lk~~~d~~~~~~d~~~~dv~~va~~LK~ylReLPe 82 (200)
T cd04388 45 LTELRQILDCDAASVDLEQFDVAALADALKRYLLDLPN 82 (200)
T ss_pred HHHHHHHHhcCCCCCCcccccHHHHHHHHHHHHHhCCC
Confidence 4568999998655443 2232 78999999999765
No 62
>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=25.13 E-value=63 Score=28.46 Aligned_cols=52 Identities=13% Similarity=0.257 Sum_probs=36.4
Q ss_pred hhhcchhHHHHHHHHHHHHHhCCCCC--------------CCccc-----hhhHHHHHHHHhhHHHhhhcc
Q 046561 122 RQAWGSLDALIGRLRAAFEENGGKPE--------------ANPFG-----ARAVRLYLREVRDVQSKARGI 173 (204)
Q Consensus 122 RQAwGSLDALIGRLRAafEE~Gg~pE--------------~NPF~-----araVRlYLReVRd~QAkARgi 173 (204)
-.|||.+..+|-.|..+|+.+|..|- -+-|- ..-+..+|..++..-.+.-++
T Consensus 24 ~lAyG~~~~I~~~~~~ll~~~~~~P~~~v~~~~~~~~~~~~~~~~yRf~~~~D~~~~~~~l~~i~~~~gsL 94 (232)
T PF09674_consen 24 LLAYGNRKQIIKKLERLLDLMGPSPYDFVLSGDEKDDRKDLEGFFYRFQNGEDMYAFFIALKRIYQEYGSL 94 (232)
T ss_pred HHHccCHHHHHHHHHHHHHHhCCCHHHHHHcCCHhhhHHHccCCCcCCCCHHHHHHHHHHHHHHHHccCCH
Confidence 36999999999999999999999862 23332 334556666666655544444
No 63
>PF10780 MRP_L53: 39S ribosomal protein L53/MRP-L53; InterPro: IPR019716 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Mitochondrial ribosomal protein L53 (also known as L44) is part of the 39S ribosome [].
Probab=24.97 E-value=37 Score=23.58 Aligned_cols=25 Identities=44% Similarity=0.786 Sum_probs=17.7
Q ss_pred Cccc--hhhHHHHHHHHhhHHHhhhccc
Q 046561 149 NPFG--ARAVRLYLREVRDVQSKARGIS 174 (204)
Q Consensus 149 NPF~--araVRlYLReVRd~QAkARgi~ 174 (204)
|||. ++..|++|.-+ ..-+|++|+.
T Consensus 2 nPF~~~aksaR~FL~~i-p~s~k~~~tn 28 (51)
T PF10780_consen 2 NPFSPNAKSARLFLSLI-PPSAKARGTN 28 (51)
T ss_pred CCCCcccHHHHHHHHhc-CCccccccCC
Confidence 7884 67799999988 4445555543
No 64
>PF00179 UQ_con: Ubiquitin-conjugating enzyme; InterPro: IPR000608 The post-translational attachment of ubiquitin (IPR000626 from INTERPRO) to proteins (ubiquitinylation) alters the function, location or trafficking of a protein, or targets it to the 26S proteasome for degradation [, , ]. Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade []. The E1 enzyme mediates an ATP-dependent transfer of a thioester-linked ubiquitin molecule to a cysteine residue on the E2 enzyme. The E2 enzyme (6.3.2.19 from EC) then either transfers the ubiquitin moiety directly to a substrate, or to an E3 ligase, which can also ubiquitinylate a substrate. There are several different E2 enzymes (over 30 in humans), which are broadly grouped into four classes, all of which have a core catalytic domain (containing the active site cysteine), and some of which have short N- and C-terminal amino acid extensions: class I enzymes consist of just the catalytic core domain (UBC), class II possess a UBC and a C-terminal extension, class III possess a UBC and an N-terminal extension, and class IV possess a UBC and both N- and C-terminal extensions. These extensions appear to be important for some subfamily function, including E2 localisation and protein-protein interactions []. In addition, there are proteins with an E2-like fold that are devoid of catalytic activity, but which appear to assist in poly-ubiquitin chain formation.; GO: 0016881 acid-amino acid ligase activity; PDB: 2AAK_A 3SY2_C 1FBV_C 3SQV_C 1C4Z_D 1JAT_B 2GMI_B 2H2Y_D 2R0J_A 3E95_B ....
Probab=24.96 E-value=1.7e+02 Score=22.37 Aligned_cols=45 Identities=20% Similarity=0.549 Sum_probs=36.1
Q ss_pred hcc---hhHHHHHHHHHHHHHhCCCCCCCccchhhHHHHHHHHhhHHHhhh
Q 046561 124 AWG---SLDALIGRLRAAFEENGGKPEANPFGARAVRLYLREVRDVQSKAR 171 (204)
Q Consensus 124 AwG---SLDALIGRLRAafEE~Gg~pE~NPF~araVRlYLReVRd~QAkAR 171 (204)
-|- ++..+|--|++.+.+- -..+|+-..|.++|..+-.+.+.+||
T Consensus 90 ~W~p~~~i~~il~~i~~ll~~p---~~~~~~n~~a~~~~~~~~~~f~~~~~ 137 (140)
T PF00179_consen 90 SWSPSYTIESILLSIQSLLSEP---NPEDPLNEEAAELYKNDREEFEKKAR 137 (140)
T ss_dssp TC-TTSHHHHHHHHHHHHHHST---CTTSTSSHHHHHHHHHCHHHHHHHHH
T ss_pred cCCcccccccHHHHHHHHHhCC---CCCCcchHHHHHHHHHCHHHHHHHHH
Confidence 377 8888888999999554 45789999999999999777777775
No 65
>PRK09468 ompR osmolarity response regulator; Provisional
Probab=24.65 E-value=59 Score=25.20 Aligned_cols=17 Identities=47% Similarity=0.647 Sum_probs=13.3
Q ss_pred hhHHHHHHHHHHHHHhC
Q 046561 127 SLDALIGRLRAAFEENG 143 (204)
Q Consensus 127 SLDALIGRLRAafEE~G 143 (204)
+||..|.|||.-++..+
T Consensus 201 ~l~~~i~~LR~kl~~~~ 217 (239)
T PRK09468 201 SIDVQISRLRRLIEEDP 217 (239)
T ss_pred CHHHHHHHHHHHhccCC
Confidence 68888999998886543
No 66
>PRK11173 two-component response regulator; Provisional
Probab=24.09 E-value=62 Score=25.26 Aligned_cols=19 Identities=32% Similarity=0.539 Sum_probs=15.9
Q ss_pred hhHHHHHHHHHHHHHhCCC
Q 046561 127 SLDALIGRLRAAFEENGGK 145 (204)
Q Consensus 127 SLDALIGRLRAafEE~Gg~ 145 (204)
+||..|.|||.-+++.+..
T Consensus 200 ~~~~~i~rlR~kl~~~~~~ 218 (237)
T PRK11173 200 TVDVTIRRIRKHFESTPDT 218 (237)
T ss_pred cHHHHHHHHHHHhccCCCC
Confidence 8999999999999865433
No 67
>PF06947 DUF1290: Protein of unknown function (DUF1290); InterPro: IPR009709 This family consists of several bacterial small basic proteins of around 100 residues in length. The function of this family is unknown.
Probab=23.74 E-value=67 Score=25.31 Aligned_cols=17 Identities=35% Similarity=0.782 Sum_probs=15.1
Q ss_pred chhHHHHHHHHHHHHHh
Q 046561 126 GSLDALIGRLRAAFEEN 142 (204)
Q Consensus 126 GSLDALIGRLRAafEE~ 142 (204)
..||++.|-+||..|++
T Consensus 16 AaLDsvfGgiRA~le~~ 32 (88)
T PF06947_consen 16 AALDSVFGGIRASLEDK 32 (88)
T ss_pred HHHHHHHHHHHHHHHhh
Confidence 46999999999999975
No 68
>PF02187 GAS2: Growth-Arrest-Specific Protein 2 Domain; InterPro: IPR003108 The growth-arrest-specific protein 2 domain is found associated with the spectrin repeat, calponin homology domain and EF hand in many proteins. It is found among others in the growth arrest-specific protein 2 [].; GO: 0007050 cell cycle arrest; PDB: 1V5R_A.
Probab=23.57 E-value=18 Score=27.27 Aligned_cols=13 Identities=46% Similarity=1.234 Sum_probs=11.4
Q ss_pred hhHHHHHHHhcCC
Q 046561 61 WNTFGQYLKNHRP 73 (204)
Q Consensus 61 wntf~qyL~n~rP 73 (204)
|.||.+||..|.|
T Consensus 56 W~tL~~~L~khDP 68 (73)
T PF02187_consen 56 WDTLEEYLDKHDP 68 (73)
T ss_dssp EEEHHHHHHHH-H
T ss_pred HHHHHHHhhccCC
Confidence 9999999999887
No 69
>PF00667 FAD_binding_1: FAD binding domain; InterPro: IPR003097 This domain is found in sulphite reductase, NADPH cytochrome P450 reductase, nitric oxide synthase and methionine synthase reductase. Flavoprotein pyridine nucleotide cytochrome reductases [] (FPNCR) catalyse the interchange of reducing equivalents between one-electron carriers and the two-electron-carrying nicotinamide dinucleotides. The enzymes include ferredoxin:NADP+reductases (FNR) [], plant and fungal NAD(P)H:nitrate reductases [, ], NADH:cytochrome b5 reductases [], NADPH:P450 reductases [], NADPH:sulphite reductases [], nitric oxide synthases [], phthalate dioxygenase reductase [], and various other flavoproteins.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3QFR_B 3FJO_A 3QFC_B 3QE2_B 3QFS_A 3QFT_A 2B5O_B 2QTZ_A 2QTL_A 2BPO_B ....
Probab=23.51 E-value=71 Score=26.41 Aligned_cols=45 Identities=22% Similarity=0.203 Sum_probs=32.8
Q ss_pred chhHHHHHHhhcccCcccccCCCCCCCCCCCCCCCCCCchhhhcc
Q 046561 82 GAHVLEFLRYLDQFGKTKVHTPICPFYGHPNPPAPCPCPLRQAWG 126 (204)
Q Consensus 82 g~hVleFLrylDqfGkTkVH~~~C~ffG~p~ppapC~CPlRQAwG 126 (204)
.++|-+||..+.-.+.+.|......-.....++.|++|.++++--
T Consensus 56 ~~~V~~~l~~lgl~~d~~v~~~~~~~~~~~~~~~~~~~tl~~~l~ 100 (219)
T PF00667_consen 56 PEEVERLLKRLGLDPDEPVTLKPKEQNNSVKPPFPSPITLRDLLT 100 (219)
T ss_dssp HHHHHHHHHHHTSGTTSEEEEEESSTTSSCCSSSSSSEEHHHHHH
T ss_pred HHHHHHHHHHhCCCcceEEEEEecccccccccccccceeeeeeee
Confidence 567888999888888777765555433555667888999988753
No 70
>COG4865 Glutamate mutase epsilon subunit [Amino acid transport and metabolism]
Probab=23.37 E-value=54 Score=32.08 Aligned_cols=22 Identities=36% Similarity=0.729 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHhCCCCCCCccc
Q 046561 131 LIGRLRAAFEENGGKPEANPFG 152 (204)
Q Consensus 131 LIGRLRAafEE~Gg~pE~NPF~ 152 (204)
+|.||--+|||||.+=...||+
T Consensus 196 YVDRL~G~YeE~Gi~INREpFg 217 (485)
T COG4865 196 YVDRLMGMYEEHGIRINREPFG 217 (485)
T ss_pred HHHHHHhHHHhcCeeeccccCC
Confidence 4566667999999887766775
No 71
>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=23.34 E-value=39 Score=28.82 Aligned_cols=24 Identities=38% Similarity=0.786 Sum_probs=21.7
Q ss_pred hcchhHH-HHHHHHHHHHHhCCCCC
Q 046561 124 AWGSLDA-LIGRLRAAFEENGGKPE 147 (204)
Q Consensus 124 AwGSLDA-LIGRLRAafEE~Gg~pE 147 (204)
-|||+|- +||+.-++|.||-..|-
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
No 72
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=23.20 E-value=41 Score=23.45 Aligned_cols=12 Identities=42% Similarity=0.775 Sum_probs=10.4
Q ss_pred cchhHHHHHHHH
Q 046561 125 WGSLDALIGRLR 136 (204)
Q Consensus 125 wGSLDALIGRLR 136 (204)
|-.||.||.+|.
T Consensus 37 f~~lD~li~~l~ 48 (49)
T PF07535_consen 37 FKELDSLISQLQ 48 (49)
T ss_pred HHHHHHHHHHhc
Confidence 778999999885
No 73
>TIGR02384 RelB_DinJ addiction module antitoxin, RelB/DinJ family. Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. The resulting model appears to describe a narrower set of proteins than Pfam model pfam04221, although many in the scope of this model are not obviously paired with toxin proteins. Several toxin/antitoxin pairs may occur in a single species.
Probab=23.09 E-value=1.8e+02 Score=21.49 Aligned_cols=39 Identities=31% Similarity=0.626 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHhCCCCCCCccchhhHHHHHHHHhhHHHhhhccchhhh
Q 046561 130 ALIGRLRAAFEENGGKPEANPFGARAVRLYLREVRDVQSKARGISYEKK 178 (204)
Q Consensus 130 ALIGRLRAafEE~Gg~pE~NPF~araVRlYLReVRd~QAkARgi~y~kk 178 (204)
.|--..-++|+++|..+ ..|||++|+.| ++-+|||++-+
T Consensus 12 ~lK~~a~~i~~~lGl~~------s~ai~~fl~qv----v~~~~lPF~~~ 50 (83)
T TIGR02384 12 ELKKEAYAVFEELGLTP------STAIRMFLKQV----IREQGLPFDLR 50 (83)
T ss_pred HHHHHHHHHHHHhCCCH------HHHHHHHHHHH----HHhCCCCCCcC
Confidence 34456677889999874 56999999976 34578887753
No 74
>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=22.93 E-value=1.1e+02 Score=21.15 Aligned_cols=26 Identities=35% Similarity=0.291 Sum_probs=18.7
Q ss_pred cchhHHHHHHHHHHHHHhCCCCCCCc
Q 046561 125 WGSLDALIGRLRAAFEENGGKPEANP 150 (204)
Q Consensus 125 wGSLDALIGRLRAafEE~Gg~pE~NP 150 (204)
++++|.+.-+|..+.+|+|..+++.|
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 45699999999999999999988765
No 75
>cd04383 RhoGAP_srGAP RhoGAP_srGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in srGAPs. srGAPs are components of the intracellular part of Slit-Robo signalling pathway that is important for axon guidance and cell migration. srGAPs contain an N-terminal FCH domain, a central RhoGAP domain and a C-terminal SH3 domain; this SH3 domain interacts with the intracellular proline-rich-tail of the Roundabout receptor (Robo). This interaction with Robo then activates the rhoGAP domain which in turn inhibits Cdc42 activity. 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 group
Probab=22.90 E-value=97 Score=25.41 Aligned_cols=35 Identities=29% Similarity=0.603 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHhCCCC---CCCcc----chhhHHHHHHHHhh
Q 046561 130 ALIGRLRAAFEENGGKP---EANPF----GARAVRLYLREVRD 165 (204)
Q Consensus 130 ALIGRLRAafEE~Gg~p---E~NPF----~araVRlYLReVRd 165 (204)
.-|.+||..|+. |..+ +.+.+ .|..++.||||..+
T Consensus 47 ~~i~~l~~~~d~-g~~~~~~~~~~~d~~~va~lLK~fLReLPe 88 (188)
T cd04383 47 VEVNDIKNAFER-GEDPLADDQNDHDINSVAGVLKLYFRGLEN 88 (188)
T ss_pred HHHHHHHHHHhc-CCCccccccccccHHHHHHHHHHHHHhCCC
Confidence 478999999986 4333 11222 68899999999754
No 76
>KOG3816 consensus Cell differentiation regulator of the Headcase family [Signal transduction mechanisms]
Probab=22.82 E-value=1e+02 Score=30.56 Aligned_cols=83 Identities=25% Similarity=0.338 Sum_probs=41.2
Q ss_pred HHHHHHHhc---CCCC-------ccccCcchhHHHHHHhhcccC--cccccCCCCCCCCCCCCCCCCCCchhhhcchhHH
Q 046561 63 TFGQYLKNH---RPPL-------SLSRCSGAHVLEFLRYLDQFG--KTKVHTPICPFYGHPNPPAPCPCPLRQAWGSLDA 130 (204)
Q Consensus 63 tf~qyL~n~---rPPl-------sL~~csg~hVleFLrylDqfG--kTkVH~~~C~ffG~p~ppapC~CPlRQAwGSLDA 130 (204)
-+++||.|. ++|+ .+..|--..+..-+. .-||+ -|.|..++-.|- -|+-+-+|-.
T Consensus 274 ~~~~~l~N~~~l~~pk~~m~~q~~~r~~~~~~~pa~~~-~~~~~~~d~~vq~~~~vF~------------rRlD~s~lls 340 (526)
T KOG3816|consen 274 YLGEFLSNRSDLRWPKRDMGPQFELRCCIDPEIPAINV-DRQYYFEDETVQVNGSVFH------------RRLDYSNLLS 340 (526)
T ss_pred HHHHHHhccccCCcchhhhcchhhhhhhcCcccchhhh-hccccccccceeeccceee------------ecccHHHHHh
Confidence 356788774 3343 344455555544442 22333 244555544443 4555666666
Q ss_pred HHHHHHHHHHHhCCCCC-CCccchhhHHHHH
Q 046561 131 LIGRLRAAFEENGGKPE-ANPFGARAVRLYL 160 (204)
Q Consensus 131 LIGRLRAafEE~Gg~pE-~NPF~araVRlYL 160 (204)
+|=|-| |+-.-.+=| .-|-+..-||++|
T Consensus 341 ~iPr~k--lN~~hVkmEDd~~~G~de~Rlfi 369 (526)
T KOG3816|consen 341 VIPRSK--LNGIHVKMEDDCPQGGDEVRLFI 369 (526)
T ss_pred hccccc--ccceEEEecccCcCCccHHHHHH
Confidence 776543 222222322 3455556688875
No 77
>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=22.73 E-value=97 Score=26.13 Aligned_cols=39 Identities=36% Similarity=0.409 Sum_probs=26.6
Q ss_pred chhHHHHHHHHHHHHHhCCCCCC------Ccc-chhhHHHHHHHHhh
Q 046561 126 GSLDALIGRLRAAFEENGGKPEA------NPF-GARAVRLYLREVRD 165 (204)
Q Consensus 126 GSLDALIGRLRAafEE~Gg~pE~------NPF-~araVRlYLReVRd 165 (204)
|+. +.|..||..|+..+...+- ++. .|..++.||||.-+
T Consensus 44 Gs~-~~i~~L~~~~d~~~~~~~l~~~~~~dvh~vA~lLK~fLReLPe 89 (207)
T cd04379 44 GSA-AKKKELRDAFERNSAAVELSEELYPDINVITGVLKDYLRELPE 89 (207)
T ss_pred CcH-HHHHHHHHHHcCCCCcCCCChhhcccHHHHHHHHHHHHHhCCC
Confidence 444 3599999999986542221 222 58899999999654
No 78
>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=22.57 E-value=65 Score=26.70 Aligned_cols=27 Identities=37% Similarity=0.610 Sum_probs=23.2
Q ss_pred hhhhcchhHHHHHHHHHHHHHhCCCCC
Q 046561 121 LRQAWGSLDALIGRLRAAFEENGGKPE 147 (204)
Q Consensus 121 lRQAwGSLDALIGRLRAafEE~Gg~pE 147 (204)
.+++.-.+|..||+|.+++++.|...+
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 688999999999999999999976644
No 79
>cd04399 RhoGAP_fRGD2 RhoGAP_fRGD2: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of fungal RGD2-like proteins. Yeast Rgd2 is a GAP protein for Cdc42 and Rho5. 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=22.34 E-value=90 Score=26.29 Aligned_cols=35 Identities=31% Similarity=0.465 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHhCCCCC--------CCc-cchhhHHHHHHHHhh
Q 046561 130 ALIGRLRAAFEENGGKPE--------ANP-FGARAVRLYLREVRD 165 (204)
Q Consensus 130 ALIGRLRAafEE~Gg~pE--------~NP-F~araVRlYLReVRd 165 (204)
+-|-.||.+|++ |..+. .++ -.|.++|+||||.-|
T Consensus 51 ~~i~~Lr~~~d~-~~~~~~~~~~~~~~dv~~va~~LK~ylReLPe 94 (212)
T cd04399 51 KETHQLRNLLNK-PKKPDKEVIILKKFEPSTVASVLKLYLLELPD 94 (212)
T ss_pred HHHHHHHHHHcC-CCCcchhhhccccCCHHHHHHHHHHHHHHCCC
Confidence 568899999997 43331 223 378899999999765
No 80
>PF12067 Sox_C_TAD: Sox C-terminal transactivation domain; InterPro: IPR021934 The Sox family of high mobility group (HMG) box transcription factors that are homologous to the Y-chromosome encoded sex- determining factor SRY plays important roles in embryonic development. Sox18, together with Sox7 and -17, constitutes the subgroup F within this family. Bioinformatic analysis of the C-termini of subgroup F Sox family members from different species including humans, mice, rat, chicken and Xenopus revealed three conserved blocks including highly conserved residues. They were termed proline, charged, and serine according to the predominance of the respective amino acids. The charged block comprises a strong transactivating domain []. This entry covers the entire Sox C-terminal domain, and was previously annotated as DUF3547.
Probab=21.82 E-value=49 Score=28.81 Aligned_cols=17 Identities=35% Similarity=0.501 Sum_probs=12.3
Q ss_pred hhhhhhHHHHHHHhcCC
Q 046561 57 KRRDWNTFGQYLKNHRP 73 (204)
Q Consensus 57 KRrdwntf~qyL~n~rP 73 (204)
---|.++|.|||...+.
T Consensus 139 geVDR~EFdQYLn~~~~ 155 (197)
T PF12067_consen 139 GEVDRTEFDQYLNSSRC 155 (197)
T ss_pred hhhhHHHHHHHhccccC
Confidence 33478999999996443
No 81
>PRK13977 myosin-cross-reactive antigen; Provisional
Probab=21.75 E-value=1.1e+02 Score=30.57 Aligned_cols=101 Identities=15% Similarity=0.147 Sum_probs=60.2
Q ss_pred hhhhHHHHHHHhcCCCCcccc-------Ccchh-HHHHHHhhccc--CcccccCCCCCCCCCCCCCCCCCCchhhhcchh
Q 046561 59 RDWNTFGQYLKNHRPPLSLSR-------CSGAH-VLEFLRYLDQF--GKTKVHTPICPFYGHPNPPAPCPCPLRQAWGSL 128 (204)
Q Consensus 59 rdwntf~qyL~n~rPPlsL~~-------csg~h-VleFLrylDqf--GkTkVH~~~C~ffG~p~ppapC~CPlRQAwGSL 128 (204)
.|-.++.+|+..+....++.. .-..| ..||+||+-+| ---..+...|-.|...++ -
T Consensus 160 Ld~~tI~d~f~~~Ff~t~Fw~~w~t~FaF~~whSA~E~rry~~rf~~~~~~l~~~s~l~ft~ynq--------------y 225 (576)
T PRK13977 160 LDDKTIEDWFSPEFFETNFWYYWRTMFAFEKWHSALEMRRYMHRFIHHIGGLPDLSGLKFTKYNQ--------------Y 225 (576)
T ss_pred hCCcCHHHHHhhcCchhHHHHHHHHHHCCchhhHHHHHHHHHHHHHHhhccCCccccccCCCCCc--------------h
Confidence 344567777777666443221 11111 56788888776 223355556666655553 4
Q ss_pred HHHHHHHHHHHHHhCCCCCCCccchhhHHHHHHHHhhHHHhhhccchhh
Q 046561 129 DALIGRLRAAFEENGGKPEANPFGARAVRLYLREVRDVQSKARGISYEK 177 (204)
Q Consensus 129 DALIGRLRAafEE~Gg~pE~NPF~araVRlYLReVRd~QAkARgi~y~k 177 (204)
|+||.-|+...+++|++=..| .++.+|. .+..+.+-++.||-+++
T Consensus 226 eSLV~PL~~~Le~~GV~f~~~---t~VtdL~-~~~d~~~~~VtgI~~~~ 270 (576)
T PRK13977 226 ESLVLPLIKYLEDHGVDFQYG---TKVTDID-FDITGGKKTATAIHLTR 270 (576)
T ss_pred hHHHHHHHHHHHhCCCEEEeC---CEEEEEE-EcCCCCceEEEEEEEEe
Confidence 999999999999999864432 3333332 12223456788888864
No 82
>cd04390 RhoGAP_ARHGAP22_24_25 RhoGAP_ARHGAP22_24_25: GTPase-activator protein (GAP) domain for Rho-like GTPases found in ARHGAP22, 24 and 25-like proteins; longer isoforms of these proteins contain an additional N-terminal pleckstrin homology (PH) domain. ARHGAP25 (KIA0053) has been identified as a GAP for Rac1 and Cdc42. Short isoforms (without the PH domain) of ARHGAP24, called RC-GAP72 and p73RhoGAP, and of ARHGAP22, called p68RacGAP, has been shown to be involved in angiogenesis and endothelial cell capillary formation. 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 r
Probab=21.51 E-value=1.4e+02 Score=24.37 Aligned_cols=37 Identities=27% Similarity=0.506 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHHhCCC---CCCCcc-chhhHHHHHHHHhh
Q 046561 129 DALIGRLRAAFEENGGK---PEANPF-GARAVRLYLREVRD 165 (204)
Q Consensus 129 DALIGRLRAafEE~Gg~---pE~NPF-~araVRlYLReVRd 165 (204)
.+.|.+||.+|+..... .+.+|. .|..++.||||.-+
T Consensus 50 ~~~i~~l~~~~d~~~~~~~~~~~d~h~va~lLK~fLReLPe 90 (199)
T cd04390 50 ANLVKQLQDAFDAGERPSFDSDTDVHTVASLLKLYLRELPE 90 (199)
T ss_pred HHHHHHHHHHHhCCCCCCccccCCHHHHHHHHHHHHHhCCC
Confidence 45789999999753321 234553 78899999998754
No 83
>cd08802 Death_UNC5B Death domain found in Uncoordinated-5B. Death Domain (DD) found in Uncoordinated-5B (UNC5B). UNC5B is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5B signaling is involved in the netrin-1-induced proliferation and migration of renal proximal tubular cells. It is also required for vascular patterning during embryonic development, and its activation inhibits sprouting angiogenesis. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activatio
Probab=20.90 E-value=59 Score=24.88 Aligned_cols=17 Identities=35% Similarity=0.466 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHhCCC
Q 046561 129 DALIGRLRAAFEENGGK 145 (204)
Q Consensus 129 DALIGRLRAafEE~Gg~ 145 (204)
|+-||+|.++++|+|+.
T Consensus 60 ~~~v~~L~~~L~~mgR~ 76 (84)
T cd08802 60 DGDLNSLASALEEMGKS 76 (84)
T ss_pred cccHHHHHHHHHHcCcc
Confidence 45689999999999975
No 84
>cd08782 Death_DAPK1 Death domain found in death-associated protein kinase 1. Death domain (DD) found in death-associated protein kinase 1 (DAPK1). DAPK1 is composed of several functional domains, including a kinase domain, a CaM regulatory domain, ankyrin repeats, a cytoskeletal binding domain and a C-terminal DD. It plays important roles in a diverse range of signal transduction pathways including apoptosis, growth factor signalling, and autophagy. Loss of DAPK1 expression, usually because of DNA methylation, is implicated in many tumor types. DAPK1 is highly abundant in the brain and has also been associated with neurodegeneration. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as ad
Probab=20.81 E-value=52 Score=24.49 Aligned_cols=28 Identities=29% Similarity=0.440 Sum_probs=23.7
Q ss_pred CCchhhhcchhH-HHHHHHHHHHHHhCCC
Q 046561 118 PCPLRQAWGSLD-ALIGRLRAAFEENGGK 145 (204)
Q Consensus 118 ~CPlRQAwGSLD-ALIGRLRAafEE~Gg~ 145 (204)
+|-+=+-|+.-+ +-||.|-.+.+|+|+.
T Consensus 47 T~~LL~~W~~~~~~tvg~L~~~L~~~gR~ 75 (82)
T cd08782 47 TDALLQEWATAPPSTIGTLIDKLRELGRE 75 (82)
T ss_pred HHHHHHHHhcCCcccHHHHHHHHHHcCcH
Confidence 455777899877 9999999999999974
No 85
>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=20.64 E-value=43 Score=20.68 Aligned_cols=16 Identities=38% Similarity=0.885 Sum_probs=10.4
Q ss_pred CCCCCCCCCCCCCCCC
Q 046561 102 TPICPFYGHPNPPAPC 117 (204)
Q Consensus 102 ~~~C~ffG~p~ppapC 117 (204)
..+|.|||.+..-.-|
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 5789999988754444
No 86
>PF13099 DUF3944: Domain of unknown function (DUF3944)
Probab=20.56 E-value=54 Score=21.87 Aligned_cols=22 Identities=27% Similarity=0.599 Sum_probs=15.5
Q ss_pred ccCcchhHHHHHHhh--cccCccc
Q 046561 78 SRCSGAHVLEFLRYL--DQFGKTK 99 (204)
Q Consensus 78 ~~csg~hVleFLryl--DqfGkTk 99 (204)
..|+..|+-++..+| |..|+++
T Consensus 11 ~~cs~edL~~L~~~Lt~dkdG~~R 34 (35)
T PF13099_consen 11 AECSNEDLKDLVDILTHDKDGKKR 34 (35)
T ss_pred HHCCHHHHHHHHHHHhcCCCCCcC
Confidence 368888877665554 7888764
No 87
>cd04406 RhoGAP_myosin_IXA RhoGAP_myosin_IXA: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in myosins IXA. Class IX myosins contain a characteristic head domain, a neck domain and a tail domain which contains a C6H2-zinc binding motif and a Rho-GAP domain. Class IX myosins are single-headed, processive myosins that are partly cytoplasmic, and partly associated with membranes and the actin cytoskeleton. Class IX myosins are implicated in the regulation of neuronal morphogenesis and function of sensory systems, like the inner ear. There are two major isoforms, myosin IXA and IXB with several splice variants, which are both expressed in developing neurons. 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 prolife
Probab=20.46 E-value=1.1e+02 Score=25.20 Aligned_cols=36 Identities=19% Similarity=0.310 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHhCCCCC---CCcc-chhhHHHHHHHHhh
Q 046561 130 ALIGRLRAAFEENGGKPE---ANPF-GARAVRLYLREVRD 165 (204)
Q Consensus 130 ALIGRLRAafEE~Gg~pE---~NPF-~araVRlYLReVRd 165 (204)
..|..|+..|+..+.... .++. .+..++.||||.-+
T Consensus 44 ~~i~~l~~~~d~~~~~~~~~~~d~h~va~lLK~fLReLPe 83 (186)
T cd04406 44 NKIKELRQGLDTDANSVNLDDYNIHVIASVFKQWLRDLPN 83 (186)
T ss_pred HHHHHHHHHHccCCCCCCcccCCHHHHHHHHHHHHHhCCC
Confidence 458899999987543322 2333 78899999999854
No 88
>PF12055 DUF3536: Domain of unknown function (DUF3536); InterPro: IPR021923 This presumed domain is functionally uncharacterised. This domain is found in bacteria and archaea. This domain is typically between 274 to 285 amino acids in length. This domain is found associated with PF03065 from PFAM.
Probab=20.37 E-value=74 Score=29.15 Aligned_cols=42 Identities=45% Similarity=0.698 Sum_probs=33.6
Q ss_pred chhhhcchhHHHHHHHHHHHHHhCCCCCCCccchhhHHHHHHHHhhH
Q 046561 120 PLRQAWGSLDALIGRLRAAFEENGGKPEANPFGARAVRLYLREVRDV 166 (204)
Q Consensus 120 PlRQAwGSLDALIGRLRAafEE~Gg~pE~NPF~araVRlYLReVRd~ 166 (204)
|||.| ||.|-.+|..+||+.|+.=-.+|..+|- -|.+-|-+.
T Consensus 8 PLR~A---ld~Lrd~l~~~fe~~~~~l~~Dpw~ar~--~Yi~Vil~~ 49 (285)
T PF12055_consen 8 PLREA---LDWLRDRLDELFEEEGGELFKDPWAARD--EYIEVILDR 49 (285)
T ss_pred HHHHH---HHHHHHHHHHHHHHHHHHhcCCHHHHHH--HHHHHHcCC
Confidence 56654 8999999999999999876678987764 677777655
No 89
>cd08799 Death_UNC5C Death domain found in Uncoordinated-5C. Death Domain (DD) found in Uncoordinated-5C (UNC5C). UNC5C is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5C plays a critical role in the development of spinal accesory motor neurons. Methylation of the UNC5C gene is associated with early stages of colorectal carcinogenesis. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN.
Probab=20.36 E-value=54 Score=24.97 Aligned_cols=17 Identities=41% Similarity=0.573 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHhCCC
Q 046561 129 DALIGRLRAAFEENGGK 145 (204)
Q Consensus 129 DALIGRLRAafEE~Gg~ 145 (204)
|+-||+|..+++|+|+.
T Consensus 60 ~~tv~~L~~~L~emgR~ 76 (84)
T cd08799 60 DGNLSRLAAVLEEMGRH 76 (84)
T ss_pred CCcHHHHHHHHHHcCCc
Confidence 56699999999999975
No 90
>PF00618 RasGEF_N: RasGEF N-terminal motif; InterPro: IPR000651 The crystal structure of the guanine nucleotide exchange factor (GEF) region of human Sos1 complexes with Ras has been solved []. The structure consists of two distinct alpha helical structural domains: the N-terminal domain which seems to have a purely structural role and the C-terminal domain which is sufficient for catalytic activity and contains all residues that interact with Ras. A main feature of the catalytic domain is the protrusion of a helical hairpin important for the nucleotide-exchange mechanism. The N-terminal domain is likely to be important for the stability and correct placement of the hairpin structure. This entry represents a domain found in several GEF for Ras-like small GTPases which lies N-terminal to the RasGef (Cdc25-like) domain. ; GO: 0005085 guanyl-nucleotide exchange factor activity, 0051056 regulation of small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3CF6_E 2BYV_E 1NVW_S 1BKD_S 1XDV_A 2II0_A 1NVU_S 1NVX_S 1NVV_S 1XD4_B ....
Probab=20.19 E-value=61 Score=23.21 Aligned_cols=12 Identities=50% Similarity=0.736 Sum_probs=6.7
Q ss_pred cchhHHHHHHHH
Q 046561 125 WGSLDALIGRLR 136 (204)
Q Consensus 125 wGSLDALIGRLR 136 (204)
.||||+||.+|=
T Consensus 4 ~gtl~~Li~~L~ 15 (104)
T PF00618_consen 4 AGTLEKLIERLT 15 (104)
T ss_dssp EE-HHHHHHHHC
T ss_pred eeCHHHHHHHHh
Confidence 366666666664
No 91
>PF10774 DUF4226: Domain of unknown function (DUF4226); InterPro: IPR019710 This entry represents an uncharacterised family of proteins belonging to Mycobacteria. It was previously incorrectly annotated as Biofilm regulator BssS (also known as YliH).
Probab=20.11 E-value=1.5e+02 Score=23.69 Aligned_cols=34 Identities=32% Similarity=0.494 Sum_probs=29.5
Q ss_pred hhHHHHHHHHHHHHHhCCCCCCCccchhhHHHHHH
Q 046561 127 SLDALIGRLRAAFEENGGKPEANPFGARAVRLYLR 161 (204)
Q Consensus 127 SLDALIGRLRAafEE~Gg~pE~NPF~araVRlYLR 161 (204)
.||+||..++++....+. --.-|.|+|.+--||+
T Consensus 48 ~Ld~i~aeI~~Av~~~~~-aldTPaG~r~f~~fL~ 81 (112)
T PF10774_consen 48 RLDAIQAEIEAAVAAQAP-ALDTPAGAREFQRFLR 81 (112)
T ss_pred HHHHHHHHHHHHHHhccc-ccCCHHHHHHHHHHHH
Confidence 799999999999988876 4578999999888875
No 92
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=20.07 E-value=57 Score=31.85 Aligned_cols=31 Identities=29% Similarity=0.375 Sum_probs=26.7
Q ss_pred CcchhHHHHHHhhcccCcccccCCCCCCCCCC
Q 046561 80 CSGAHVLEFLRYLDQFGKTKVHTPICPFYGHP 111 (204)
Q Consensus 80 csg~hVleFLrylDqfGkTkVH~~~C~ffG~p 111 (204)
-....|++|| ++++-|.++-|.+.|+--|.-
T Consensus 211 lpedEVie~l-~k~v~~~~~~~~~p~~P~gt~ 241 (445)
T KOG4329|consen 211 LPEDEVIEFL-LKAVVRLRKEHDQPCPPEGTE 241 (445)
T ss_pred CchHHHHHHH-HHHHHhhhcccCCCCCCcccc
Confidence 3467899999 999999999999999877754
Done!