Query 047785
Match_columns 174
No_of_seqs 82 out of 84
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 03:09:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047785.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047785hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04852 DUF640: Protein of un 100.0 2E-77 4.4E-82 471.7 12.0 122 21-142 11-132 (132)
2 PF08821 CGGC: CGGC domain; I 93.1 0.22 4.8E-06 38.0 5.0 66 40-115 30-98 (107)
3 PF02899 Phage_int_SAM_1: Phag 90.3 0.47 1E-05 31.4 3.6 40 32-72 21-60 (84)
4 cd00798 INT_XerDC XerD and Xer 90.2 1 2.2E-05 34.2 5.8 68 33-127 22-91 (284)
5 PRK00283 xerD site-specific ty 87.1 1.9 4.1E-05 33.7 5.6 68 33-128 30-99 (299)
6 TIGR02225 recomb_XerD tyrosine 85.5 2.8 6.2E-05 32.1 5.8 70 31-128 19-90 (291)
7 cd00799 INT_Cre Cre recombinas 85.3 8.8 0.00019 30.4 8.6 76 33-140 7-82 (287)
8 TIGR02224 recomb_XerC tyrosine 79.9 6.8 0.00015 30.2 5.9 69 34-128 22-92 (295)
9 COG1080 PtsA Phosphoenolpyruva 77.0 2.5 5.5E-05 41.0 3.4 41 98-138 305-367 (574)
10 PF00539 Tat: Transactivating 63.2 5.3 0.00011 29.3 1.8 19 144-162 45-63 (68)
11 cd01185 INT_Tn4399 Tn4399 and 63.0 34 0.00074 27.2 6.5 67 36-128 44-115 (299)
12 TIGR01418 PEP_synth phosphoeno 59.9 16 0.00034 36.1 4.8 42 105-146 547-618 (782)
13 PRK00236 xerC site-specific ty 57.4 48 0.001 25.5 6.2 68 34-128 32-101 (297)
14 PF13495 Phage_int_SAM_4: Phag 54.5 18 0.00039 24.1 3.2 54 35-117 24-77 (85)
15 PRK10529 DNA-binding transcrip 54.1 11 0.00025 28.1 2.3 17 103-119 191-207 (225)
16 PF05528 Coronavirus_5: Corona 52.5 2.3 5E-05 32.2 -1.6 20 122-141 4-26 (82)
17 smart00259 ZnF_A20 A20-like zi 51.4 7.8 0.00017 23.4 0.9 16 79-94 7-22 (26)
18 PRK11061 fused phosphoenolpyru 50.9 23 0.00049 34.8 4.3 105 21-138 397-531 (748)
19 PF02896 PEP-utilizers_C: PEP- 50.7 26 0.00057 30.8 4.4 38 101-138 58-118 (293)
20 cd00801 INT_P4 Bacteriophage P 50.6 32 0.0007 27.6 4.5 26 102-128 135-163 (357)
21 PF10865 DUF2703: Domain of un 47.0 6.7 0.00015 30.8 0.1 26 98-123 19-44 (120)
22 PRK10816 DNA-binding transcrip 46.8 15 0.00033 27.5 2.0 23 96-118 174-204 (223)
23 PF00486 Trans_reg_C: Transcri 46.4 21 0.00046 23.3 2.4 21 102-122 44-64 (77)
24 cd08781 Death_UNC5-like Death 46.2 25 0.00055 25.3 3.0 25 97-121 49-76 (83)
25 COG4974 XerD Site-specific rec 43.9 24 0.00051 32.1 3.1 44 25-74 26-70 (300)
26 KOG4670 Uncharacterized conser 42.0 11 0.00024 37.0 0.8 59 32-90 468-544 (602)
27 PF14768 RPA_interact_C: Repli 40.1 26 0.00055 25.2 2.2 36 91-126 17-56 (82)
28 PRK09279 pyruvate phosphate di 39.7 29 0.00062 35.2 3.2 25 122-146 658-685 (879)
29 PF13276 HTH_21: HTH-like doma 39.3 48 0.0011 21.6 3.3 29 105-138 4-32 (60)
30 smart00862 Trans_reg_C Transcr 39.0 32 0.00069 22.4 2.4 19 102-120 45-63 (78)
31 TIGR01417 PTS_I_fam phosphoeno 38.5 35 0.00076 32.4 3.5 36 103-138 308-365 (565)
32 cd08793 Death_IRAK4 Death doma 38.3 43 0.00094 25.9 3.4 63 36-120 23-85 (100)
33 PF00140 Sigma70_r1_2: Sigma-7 37.5 24 0.00051 22.1 1.5 12 130-141 2-13 (37)
34 TIGR01828 pyru_phos_dikin pyru 35.4 23 0.00049 35.6 1.7 25 122-146 652-679 (856)
35 PRK12435 ferrochelatase; Provi 34.3 97 0.0021 27.2 5.3 16 106-121 37-52 (311)
36 PF08544 GHMP_kinases_C: GHMP 33.9 6.3 0.00014 26.2 -1.6 75 33-116 6-84 (85)
37 PF06252 DUF1018: Protein of u 32.6 1.8E+02 0.0039 21.7 5.8 86 36-136 2-88 (119)
38 cd04372 RhoGAP_chimaerin RhoGA 32.4 39 0.00084 27.1 2.4 36 106-141 45-87 (194)
39 PF09107 SelB-wing_3: Elongati 32.1 31 0.00067 23.2 1.5 21 55-75 21-41 (50)
40 PF00667 FAD_binding_1: FAD bi 31.1 53 0.0012 26.6 3.0 45 58-102 56-100 (219)
41 smart00243 GAS2 Growth-Arrest- 31.1 33 0.00072 25.6 1.6 15 36-50 55-69 (73)
42 PRK13197 pyrrolidone-carboxyla 30.8 1.7E+02 0.0037 24.5 6.0 83 25-117 108-199 (215)
43 PF04221 RelB: RelB antitoxin; 30.3 92 0.002 22.1 3.8 39 106-154 11-49 (83)
44 PRK11235 bifunctional antitoxi 30.2 1.1E+02 0.0023 22.7 4.1 38 106-153 11-48 (80)
45 TIGR02249 integrase_gron integ 29.9 1.1E+02 0.0024 24.8 4.6 33 34-70 23-55 (315)
46 PTZ00398 phosphoenolpyruvate c 29.9 83 0.0018 32.4 4.7 42 101-142 264-336 (974)
47 PRK05084 xerS site-specific ty 29.8 97 0.0021 25.8 4.3 68 35-118 43-120 (357)
48 PF12067 Sox_C_TAD: Sox C-term 29.7 30 0.00066 29.4 1.4 14 35-48 141-154 (197)
49 TIGR02384 RelB_DinJ addiction 29.5 1.1E+02 0.0025 22.1 4.2 39 106-154 12-50 (83)
50 cd04396 RhoGAP_fSAC7_BAG7 RhoG 29.2 1.4E+02 0.0031 24.7 5.2 37 105-141 60-103 (225)
51 cd01187 INT_SG4 INT_SG4, DNA b 29.2 1.8E+02 0.0039 23.2 5.6 59 36-127 25-86 (299)
52 cd00383 trans_reg_C Effector d 28.9 50 0.0011 22.2 2.1 19 102-120 62-80 (95)
53 PF09674 DUF2400: Protein of u 28.3 53 0.0011 28.3 2.6 25 98-122 24-48 (232)
54 cd01355 AcnX Putative Aconitas 28.1 71 0.0015 29.7 3.6 54 58-123 48-108 (389)
55 PF11709 Mit_ribos_Mrp51: Mito 27.0 65 0.0014 28.5 3.0 65 24-88 146-229 (312)
56 PF01754 zf-A20: A20-like zinc 26.8 26 0.00056 21.1 0.4 16 78-93 5-20 (25)
57 KOG1452 Predicted Rho GTPase-a 26.4 38 0.00081 32.1 1.5 31 110-141 233-271 (442)
58 COG0745 OmpR Response regulato 26.3 55 0.0012 27.2 2.3 29 94-122 176-212 (229)
59 PF09958 DUF2192: Uncharacteri 26.3 58 0.0013 28.7 2.6 21 103-123 27-47 (231)
60 PF07700 HNOB: Heme NO binding 26.0 24 0.00052 27.6 0.2 37 34-70 64-103 (171)
61 PLN02837 threonine-tRNA ligase 26.0 29 0.00063 33.0 0.7 16 97-112 488-503 (614)
62 PRK11173 two-component respons 26.0 55 0.0012 25.0 2.1 19 103-121 200-218 (237)
63 TIGR03190 benz_CoA_bzdN benzoy 25.9 4.7E+02 0.01 23.2 10.1 24 29-52 166-189 (377)
64 PF08135 EPV_E5: Major transfo 25.3 34 0.00074 23.5 0.8 12 61-72 25-36 (44)
65 PF07535 zf-DBF: DBF zinc fing 25.3 38 0.00081 23.1 1.0 12 101-112 37-48 (49)
66 PRK09468 ompR osmolarity respo 25.1 60 0.0013 24.6 2.2 16 103-118 201-216 (239)
67 PRK11177 phosphoenolpyruvate-p 24.4 69 0.0015 30.8 2.9 36 103-138 309-366 (575)
68 PF01663 Phosphodiest: Type I 24.3 65 0.0014 26.2 2.3 27 97-123 208-234 (365)
69 cd08782 Death_DAPK1 Death doma 24.3 41 0.00089 24.5 1.1 28 94-121 47-75 (82)
70 PF08290 Hep_core_N: Hepatitis 23.9 31 0.00067 21.6 0.3 11 91-101 10-20 (27)
71 PF13099 DUF3944: Domain of un 23.7 35 0.00076 22.2 0.6 22 54-75 11-34 (35)
72 cd03054 GST_N_Metaxin GST_N fa 23.7 57 0.0012 21.2 1.6 27 119-154 10-36 (72)
73 PF10780 MRP_L53: 39S ribosoma 23.6 38 0.00083 23.0 0.8 24 125-149 2-27 (51)
74 PF10520 Kua-UEV1_localn: Kua- 23.4 39 0.00084 28.2 0.9 24 100-123 17-41 (178)
75 PF06947 DUF1290: Protein of u 23.4 71 0.0015 24.6 2.3 17 102-118 16-32 (88)
76 cd04388 RhoGAP_p85 RhoGAP_p85: 23.3 68 0.0015 26.8 2.3 65 56-141 14-82 (200)
77 PF06540 GMAP: Galanin message 22.7 43 0.00094 24.4 0.9 10 59-68 27-36 (62)
78 PF06480 FtsH_ext: FtsH Extrac 22.2 1.1E+02 0.0025 20.5 2.9 26 101-126 84-109 (110)
79 cd08310 Death_NFkB-like Death 22.2 77 0.0017 22.5 2.1 23 99-121 43-65 (72)
80 cd04379 RhoGAP_SYD1 RhoGAP_SYD 22.1 78 0.0017 26.1 2.5 39 102-141 44-89 (207)
81 PF00618 RasGEF_N: RasGEF N-te 22.0 54 0.0012 23.0 1.3 12 101-112 4-15 (104)
82 cd04383 RhoGAP_srGAP RhoGAP_sr 21.9 83 0.0018 25.3 2.5 35 106-141 47-88 (188)
83 cd00778 ProRS_core_arch_euk Pr 21.5 42 0.00091 28.1 0.8 17 97-113 244-260 (261)
84 TIGR02284 conserved hypothetic 21.4 1.9E+02 0.0042 22.3 4.4 36 106-141 44-79 (139)
85 cd04384 RhoGAP_CdGAP RhoGAP_Cd 21.3 1.1E+02 0.0023 24.9 3.0 38 102-141 43-88 (195)
86 PF00179 UQ_con: Ubiquitin-con 21.2 2.1E+02 0.0045 21.4 4.4 45 100-147 90-137 (140)
87 PF02187 GAS2: Growth-Arrest-S 21.1 20 0.00043 26.5 -1.1 13 37-49 56-68 (73)
88 PRK06464 phosphoenolpyruvate s 21.0 57 0.0012 32.4 1.7 25 122-146 596-625 (795)
89 cd04399 RhoGAP_fRGD2 RhoGAP_fR 20.6 79 0.0017 26.1 2.2 35 106-141 51-94 (212)
90 TIGR00504 pyro_pdase pyrogluta 20.5 3.5E+02 0.0076 22.6 6.0 84 25-118 105-197 (212)
91 TIGR02258 2_5_ligase 2'-5' RNA 20.5 1.3E+02 0.0029 22.8 3.3 69 58-128 51-122 (179)
92 KOG2867 Phosphotyrosyl phospha 20.4 4.7E+02 0.01 24.7 7.3 96 21-145 83-189 (367)
93 PF12055 DUF3536: Domain of un 20.4 45 0.00097 29.9 0.8 42 96-142 8-49 (285)
94 COG4865 Glutamate mutase epsil 20.3 71 0.0015 30.7 2.1 22 107-128 196-217 (485)
95 COG3077 RelB DNA-damage-induci 20.3 1.7E+02 0.0038 22.3 3.8 37 106-152 14-50 (88)
96 cd04390 RhoGAP_ARHGAP22_24_25 20.2 1.3E+02 0.0028 24.0 3.3 36 105-141 50-90 (199)
97 PF09336 Vps4_C: Vps4 C termin 20.1 93 0.002 21.5 2.1 30 38-72 33-62 (62)
98 PRK10701 DNA-binding transcrip 20.1 77 0.0017 24.2 1.9 17 103-119 201-217 (240)
No 1
>PF04852 DUF640: Protein of unknown function (DUF640); InterPro: IPR006936 This conserved region is found in plant proteins including the resistance protein-like protein (O49468 from SWISSPROT).
Probab=100.00 E-value=2e-77 Score=471.74 Aligned_cols=122 Identities=77% Similarity=1.402 Sum_probs=119.1
Q ss_pred CCCCCCchhhhhhhhhHhHHHHHHHhCCCCCCCCCCCchhhhhHHHhhhccCCeeeeccCCCCCCCCCCCCCCCCchhhh
Q 047785 21 QQPATPSRYESQKRRDWNTFGQYLKNQRPPVPLSQCSCNHVLDFLRYLDQFGKTKVHLQGCMFYGQPEPPAPCTCPLRQA 100 (174)
Q Consensus 21 ~~~~~~srYesQKrrdwntf~qyL~n~rPPl~l~~cs~~hVleFL~ylDqfGkTkVH~~~C~~fg~p~ppapC~CPlRqA 100 (174)
++++++||||+|||||||||+|||+||+|||+|++|+++|||+||+|+|||||||||.++|+|||+|+||+||+||||||
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 44568899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hchhHHHHHHHHHHHHHhCCCCCCCCCccchHHHHHHHHHHH
Q 047785 101 WGSLDALIGRLRAAYEENGGSPETNPFASGAIRVYLREVREC 142 (174)
Q Consensus 101 wGSlDALIGRLRAafee~Gg~pe~NPf~araVr~YLreVRd~ 142 (174)
||||||||||||||||||||.||+|||+++|||+|||||||+
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=93.07 E-value=0.22 Score=37.95 Aligned_cols=66 Identities=23% Similarity=0.526 Sum_probs=49.5
Q ss_pred HHHHHHhCCCCCCCCCCC---chhhhhHHHhhhccCCeeeeccCCCCCCCCCCCCCCCCchhhhhchhHHHHHHHHHHH
Q 047785 40 FGQYLKNQRPPVPLSQCS---CNHVLDFLRYLDQFGKTKVHLQGCMFYGQPEPPAPCTCPLRQAWGSLDALIGRLRAAY 115 (174)
Q Consensus 40 f~qyL~n~rPPl~l~~cs---~~hVleFL~ylDqfGkTkVH~~~C~~fg~p~ppapC~CPlRqAwGSlDALIGRLRAaf 115 (174)
|.+|=.+..--+.+.+|. +..++..+..+-..|-..||..+|...+.+.+ +||. +|.|+-.|+++|
T Consensus 30 F~~y~~~~~elvgf~~CgGCpg~~~~~~~~~l~~~~~d~IHlssC~~~~~~~~----~CP~------~~~~~~~I~~~~ 98 (107)
T PF08821_consen 30 FARYDDEDVELVGFFTCGGCPGRKLVRRIKKLKKNGADVIHLSSCMVKGNPHG----PCPH------IDEIKKIIEEKF 98 (107)
T ss_pred cccCCCCCeEEEEEeeCCCCChhHHHHHHHHHHHCCCCEEEEcCCEecCCCCC----CCCC------HHHHHHHHHHHh
Confidence 444433222334454554 58899999999999999999999999887654 6666 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=90.26 E-value=0.47 Score=31.42 Aligned_cols=40 Identities=30% Similarity=0.473 Sum_probs=31.5
Q ss_pred hhhhhHhHHHHHHHhCCCCCCCCCCCchhhhhHHHhhhccC
Q 047785 32 QKRRDWNTFGQYLKNQRPPVPLSQCSCNHVLDFLRYLDQFG 72 (174)
Q Consensus 32 QKrrdwntf~qyL~n~rPPl~l~~cs~~hVleFL~ylDqfG 72 (174)
.-+++++.|.+||.+ ....++..++..||.+||.++-+.|
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 346789999999999 6667778899999999999998766
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=90.23 E-value=1 Score=34.18 Aligned_cols=68 Identities=22% Similarity=0.259 Sum_probs=48.8
Q ss_pred hhhhHhHHHHHHHhCCCCCCCCCCCchhhhhHHHhhhccCCeeeeccCCCCCCCCCCCCCCCCchhhhhchhHHHHHHHH
Q 047785 33 KRRDWNTFGQYLKNQRPPVPLSQCSCNHVLDFLRYLDQFGKTKVHLQGCMFYGQPEPPAPCTCPLRQAWGSLDALIGRLR 112 (174)
Q Consensus 33 Krrdwntf~qyL~n~rPPl~l~~cs~~hVleFL~ylDqfGkTkVH~~~C~~fg~p~ppapC~CPlRqAwGSlDALIGRLR 112 (174)
-+..|+.|.+|+.....+. +..-+..||.+|+.++...| ....++...++-|+
T Consensus 22 ~~~~~~~~~~~~~~~~~~~-~~~l~~~~i~~~~~~~~~~~--------------------------~~~~t~~~~~~~l~ 74 (284)
T cd00798 22 YRRDLERFLEFLEERGILF-PADVTPDDIRRFLAELKDQG--------------------------LSARSIARKLSALR 74 (284)
T ss_pred HHHHHHHHHHHHHHcCCCc-hhhCCHHHHHHHHHHhhhcC--------------------------CCHHHHHHHHHHHH
Confidence 3567899999998754433 56678999999999887654 23457788888888
Q ss_pred HHHHHhC--CCCCCCCC
Q 047785 113 AAYEENG--GSPETNPF 127 (174)
Q Consensus 113 Aafee~G--g~pe~NPf 127 (174)
++|.-.. |..+.||+
T Consensus 75 ~~~~~~~~~~~~~~~p~ 91 (284)
T cd00798 75 SFFKFLLREGLILANPA 91 (284)
T ss_pred HHHHHHHHcCCccCChh
Confidence 8887432 44556887
No 5
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed
Probab=87.08 E-value=1.9 Score=33.74 Aligned_cols=68 Identities=25% Similarity=0.298 Sum_probs=48.9
Q ss_pred hhhhHhHHHHHHHhCCCCCCCCCCCchhhhhHHHhhhccCCeeeeccCCCCCCCCCCCCCCCCchhhhhchhHHHHHHHH
Q 047785 33 KRRDWNTFGQYLKNQRPPVPLSQCSCNHVLDFLRYLDQFGKTKVHLQGCMFYGQPEPPAPCTCPLRQAWGSLDALIGRLR 112 (174)
Q Consensus 33 Krrdwntf~qyL~n~rPPl~l~~cs~~hVleFL~ylDqfGkTkVH~~~C~~fg~p~ppapC~CPlRqAwGSlDALIGRLR 112 (174)
-+.+|+.|..||....- .+...+..||.+|+.++.+.| .+-.++...+..|+
T Consensus 30 ~~~~~~~~~~~~~~~~~--~~~~l~~~~i~~~~~~~~~~~--------------------------~~~~t~~~~~~~l~ 81 (299)
T PRK00283 30 YRRDLELFAEWLAARGL--SLAEATRDDLQAFLAELAEGG--------------------------YKATSSARRLSALR 81 (299)
T ss_pred HHHHHHHHHHHHHhcCC--ChHHCCHHHHHHHHHHHHhCC--------------------------CCHHHHHHHHHHHH
Confidence 35688899999986432 566778999999999886531 23457788899999
Q ss_pred HHHHHhC--CCCCCCCCc
Q 047785 113 AAYEENG--GSPETNPFA 128 (174)
Q Consensus 113 Aafee~G--g~pe~NPf~ 128 (174)
++|+-.. |.-..|||.
T Consensus 82 ~~~~~a~~~~~i~~np~~ 99 (299)
T PRK00283 82 RFFQFLLREGLREDDPSA 99 (299)
T ss_pred HHHHHHHHcCCcccCchh
Confidence 9988432 345578863
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=85.53 E-value=2.8 Score=32.14 Aligned_cols=70 Identities=27% Similarity=0.424 Sum_probs=48.5
Q ss_pred hhhhhhHhHHHHHHHhCCCCCCCCCCCchhhhhHHHhhhccCCeeeeccCCCCCCCCCCCCCCCCchhhhhchhHHHHHH
Q 047785 31 SQKRRDWNTFGQYLKNQRPPVPLSQCSCNHVLDFLRYLDQFGKTKVHLQGCMFYGQPEPPAPCTCPLRQAWGSLDALIGR 110 (174)
Q Consensus 31 sQKrrdwntf~qyL~n~rPPl~l~~cs~~hVleFL~ylDqfGkTkVH~~~C~~fg~p~ppapC~CPlRqAwGSlDALIGR 110 (174)
.+-+..++.|..|+.... ..+..-+..||.+|+.++.+.| -+.-++...+.-
T Consensus 19 ~~~~~~~~~~~~~~~~~~--~~~~~it~~~i~~~~~~~~~~~--------------------------~~~~t~~~~~~~ 70 (291)
T TIGR02225 19 EAYRRDLEKFLEFLEERG--IDLEEVDRGDIVDFLAELKEAG--------------------------LSARSIARALSA 70 (291)
T ss_pred HHHHHHHHHHHHHHHhcC--CChHHCCHHHHHHHHHHhhcCC--------------------------CCHhHHHHHHHH
Confidence 334557788999998542 2455567899999999887644 122467889999
Q ss_pred HHHHHHHh--CCCCCCCCCc
Q 047785 111 LRAAYEEN--GGSPETNPFA 128 (174)
Q Consensus 111 LRAafee~--Gg~pe~NPf~ 128 (174)
|+++|+-. -|..+.||+.
T Consensus 71 l~~~~~~a~~~~~~~~np~~ 90 (291)
T TIGR02225 71 LRSFYRFLLREGIREDDPSA 90 (291)
T ss_pred HHHHHHHHHhcccccCCchh
Confidence 99999742 2445578874
No 7
>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=85.27 E-value=8.8 Score=30.44 Aligned_cols=76 Identities=21% Similarity=0.265 Sum_probs=52.6
Q ss_pred hhhhHhHHHHHHHhCCCCCCCCCCCchhhhhHHHhhhccCCeeeeccCCCCCCCCCCCCCCCCchhhhhchhHHHHHHHH
Q 047785 33 KRRDWNTFGQYLKNQRPPVPLSQCSCNHVLDFLRYLDQFGKTKVHLQGCMFYGQPEPPAPCTCPLRQAWGSLDALIGRLR 112 (174)
Q Consensus 33 Krrdwntf~qyL~n~rPPl~l~~cs~~hVleFL~ylDqfGkTkVH~~~C~~fg~p~ppapC~CPlRqAwGSlDALIGRLR 112 (174)
-..+++.|..|+...- +....-+..+|.+||.||.+. .+..++-..++.|+
T Consensus 7 y~~~l~~f~~~~~~~~--~~~~~~~~~~i~~~~~~l~~~---------------------------~s~~ti~~~~~~l~ 57 (287)
T cd00799 7 YLSDWRRFAAWCQAHG--RTPLPASPETVTLYLTDLADS---------------------------LAPSTISRRLSALS 57 (287)
T ss_pred HHHHHHHHHHHHHhcC--CCCCCCCHHHHHHHHHHHHhc---------------------------cChHHHHHHHHHHH
Confidence 3567889999998752 122223589999999988631 24578888999999
Q ss_pred HHHHHhCCCCCCCCCccchHHHHHHHHH
Q 047785 113 AAYEENGGSPETNPFASGAIRVYLREVR 140 (174)
Q Consensus 113 Aafee~Gg~pe~NPf~araVr~YLreVR 140 (174)
.+|+..+. .||+....+..-|+.++
T Consensus 58 ~~~~~~~~---~~p~~~~~~~~~~~~~~ 82 (287)
T cd00799 58 QLHRRSGL---PSPADSPLVRLVLRGIR 82 (287)
T ss_pred HHHHHcCC---CCCccCHHHHHHHHHHH
Confidence 99985432 58877655666665554
No 8
>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=79.85 E-value=6.8 Score=30.23 Aligned_cols=69 Identities=28% Similarity=0.365 Sum_probs=48.1
Q ss_pred hhhHhHHHHHHHhCCCCCCCCCCCchhhhhHHHhhhccCCeeeeccCCCCCCCCCCCCCCCCchhhhhchhHHHHHHHHH
Q 047785 34 RRDWNTFGQYLKNQRPPVPLSQCSCNHVLDFLRYLDQFGKTKVHLQGCMFYGQPEPPAPCTCPLRQAWGSLDALIGRLRA 113 (174)
Q Consensus 34 rrdwntf~qyL~n~rPPl~l~~cs~~hVleFL~ylDqfGkTkVH~~~C~~fg~p~ppapC~CPlRqAwGSlDALIGRLRA 113 (174)
+.+++.|.+||........+..-+..||.+||.++.+.| .+..++...+..|++
T Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~l~~~~i~~~~~~~~~~~--------------------------~~~~T~~~~~~~l~~ 75 (295)
T TIGR02224 22 RRDLKAFLEFLEEEGGLASLAEVTAADLRSFLAELHARG--------------------------LSRRSLARKLSALRS 75 (295)
T ss_pred HHHHHHHHHHHHhcCCCCccccCcHHHHHHHHHHhcccC--------------------------CCHHHHHHHHHHHHH
Confidence 346677888888866667788888999999999876622 123567777888888
Q ss_pred HHHHhC--CCCCCCCCc
Q 047785 114 AYEENG--GSPETNPFA 128 (174)
Q Consensus 114 afee~G--g~pe~NPf~ 128 (174)
+|.-.. +.-+.|||.
T Consensus 76 ~~~~a~~~~~~~~np~~ 92 (295)
T TIGR02224 76 FYRFLVRRGLIKANPAA 92 (295)
T ss_pred HHHHHHHcCccccChHh
Confidence 877432 334468863
No 9
>COG1080 PtsA Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]
Probab=77.03 E-value=2.5 Score=41.01 Aligned_cols=41 Identities=37% Similarity=0.545 Sum_probs=32.6
Q ss_pred hhhhchhHHHHHHHHHHHHHhCCC--------------------C-CCCCC-ccchHHHHHHH
Q 047785 98 RQAWGSLDALIGRLRAAYEENGGS--------------------P-ETNPF-ASGAIRVYLRE 138 (174)
Q Consensus 98 RqAwGSlDALIGRLRAafee~Gg~--------------------p-e~NPf-~araVr~YLre 138 (174)
|..|=+.|..----++..|.+||+ | |.||| |-||||+||..
T Consensus 305 r~~~P~EeEQ~~aY~~vlea~~g~pviiRTlDiGGDK~lpyl~lp~E~NPfLG~RaIRl~l~~ 367 (574)
T COG1080 305 RDALPDEEEQFEAYKAVLEAMGGKPVIIRTLDIGGDKPLPYLNLPKEENPFLGYRAIRLSLER 367 (574)
T ss_pred CCCCCChHHHHHHHHHHHHHcCCCceEEEecccCCCCcCCCCCCccccCchhhhHHHHHhhcc
Confidence 445556777777778888888886 3 79999 89999999964
No 10
>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=63.16 E-value=5.3 Score=29.30 Aligned_cols=19 Identities=26% Similarity=0.559 Sum_probs=14.4
Q ss_pred HhhhCCcccccccCCCCCC
Q 047785 144 AKARGIPYKKKKKKPSQGK 162 (174)
Q Consensus 144 AkArgi~y~kkk~~~~~~~ 162 (174)
-|+-||.|..|||||+...
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 4788999998887665544
No 11
>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=63.00 E-value=34 Score=27.22 Aligned_cols=67 Identities=13% Similarity=0.251 Sum_probs=43.8
Q ss_pred hHhHHHHHHHhCCC--CCCCCCCCchhhhhHHHhhh-ccCCeeeeccCCCCCCCCCCCCCCCCchhhhhchhHHHHHHHH
Q 047785 36 DWNTFGQYLKNQRP--PVPLSQCSCNHVLDFLRYLD-QFGKTKVHLQGCMFYGQPEPPAPCTCPLRQAWGSLDALIGRLR 112 (174)
Q Consensus 36 dwntf~qyL~n~rP--Pl~l~~cs~~hVleFL~ylD-qfGkTkVH~~~C~~fg~p~ppapC~CPlRqAwGSlDALIGRLR 112 (174)
..+.|..||....+ .+.+..-+..||.+|+.|+. .-| ..-.++...++-||
T Consensus 44 ~~~~~~~~~~~~~~~~~~~l~~i~~~~i~~~~~~l~~~~~--------------------------~s~~t~~~~~~~l~ 97 (299)
T cd01185 44 HLKNLREFIECTYKEIDIALLELTREFILEFKLFLRKEKK--------------------------LSRNTAVHYLSWLK 97 (299)
T ss_pred HHHHHHHHHHHhcCccCCCHHHccHHHHHHHHHHHhhccC--------------------------cCcccHHHHHHHHH
Confidence 45678888876554 67788888999999999983 211 22345566777777
Q ss_pred HHHHHh--CCCCCCCCCc
Q 047785 113 AAYEEN--GGSPETNPFA 128 (174)
Q Consensus 113 Aafee~--Gg~pe~NPf~ 128 (174)
++|.-. .+.-..|||.
T Consensus 98 ~~~~~a~~~~~i~~np~~ 115 (299)
T cd01185 98 KLLKIAYRDKGLRDNPFA 115 (299)
T ss_pred HHHHHHHHCcCccCCCcc
Confidence 777643 2333456764
No 12
>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=59.93 E-value=16 Score=36.06 Aligned_cols=42 Identities=19% Similarity=0.170 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHHhCCC-------------------------CCCCCC-ccchHHHHH----HHHHHHHHhh
Q 047785 105 DALIGRLRAAYEENGGS-------------------------PETNPF-ASGAIRVYL----REVRECQAKA 146 (174)
Q Consensus 105 DALIGRLRAafee~Gg~-------------------------pe~NPf-~araVr~YL----reVRd~QAkA 146 (174)
|.+.-.+|.+++.++++ .|.||| +.|+||+|| .++=+.|.+|
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 55566777887776543 378999 899999999 4566666655
No 13
>PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=57.36 E-value=48 Score=25.53 Aligned_cols=68 Identities=26% Similarity=0.305 Sum_probs=44.3
Q ss_pred hhhHhHHHHHHHhCCCCCCCCCCCchhhhhHHHhhhccCCeeeeccCCCCCCCCCCCCCCCCchhhhhchhHHHHHHHHH
Q 047785 34 RRDWNTFGQYLKNQRPPVPLSQCSCNHVLDFLRYLDQFGKTKVHLQGCMFYGQPEPPAPCTCPLRQAWGSLDALIGRLRA 113 (174)
Q Consensus 34 rrdwntf~qyL~n~rPPl~l~~cs~~hVleFL~ylDqfGkTkVH~~~C~~fg~p~ppapC~CPlRqAwGSlDALIGRLRA 113 (174)
+.+|+.|..|+..... ..+..-+..||.+||.++-+.|. +--++...+.-|++
T Consensus 32 ~~~~~~~~~~~~~~~~-~~~~~i~~~~i~~~~~~~~~~~~--------------------------~~~t~~~~~~~l~~ 84 (297)
T PRK00236 32 RRDLRAFLAFLEEHGI-SSLQDLDAADLRSFLARRRRQGL--------------------------SARSLARRLSALRS 84 (297)
T ss_pred HHHHHHHHHHHHHcCC-CchhhCCHHHHHHHHHHHHhccc--------------------------ChhHHHHHHHHHHH
Confidence 4678889999887543 55667788999999987754321 11255566666666
Q ss_pred HHHHhC--CCCCCCCCc
Q 047785 114 AYEENG--GSPETNPFA 128 (174)
Q Consensus 114 afee~G--g~pe~NPf~ 128 (174)
.|.-.. |.-+.|||.
T Consensus 85 ~~~~a~~~~~i~~np~~ 101 (297)
T PRK00236 85 FYRWLVRRGLLKANPAA 101 (297)
T ss_pred HHHHHHhcccccCCchh
Confidence 665332 445678874
No 14
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=54.51 E-value=18 Score=24.07 Aligned_cols=54 Identities=17% Similarity=0.326 Sum_probs=32.9
Q ss_pred hhHhHHHHHHHhCCCCCCCCCCCchhhhhHHHhhhccCCeeeeccCCCCCCCCCCCCCCCCchhhhhchhHHHHHHHHHH
Q 047785 35 RDWNTFGQYLKNQRPPVPLSQCSCNHVLDFLRYLDQFGKTKVHLQGCMFYGQPEPPAPCTCPLRQAWGSLDALIGRLRAA 114 (174)
Q Consensus 35 rdwntf~qyL~n~rPPl~l~~cs~~hVleFL~ylDqfGkTkVH~~~C~~fg~p~ppapC~CPlRqAwGSlDALIGRLRAa 114 (174)
...+.|.+|+.+. ++...+..||.+||.||-..-+ .+..++...+.-||+.
T Consensus 24 ~~l~~f~~~~~~~----~~~~it~~~i~~y~~~l~~~~~-------------------------~s~~T~~~~~~~l~~f 74 (85)
T PF13495_consen 24 YHLKRFLRFLGNK----PPDEITPEDIEQYLNYLQNERG-------------------------LSPSTINQYLSALRSF 74 (85)
T ss_dssp HHHHHHHTTSSS------GGG--HHHHHHHHHHHHTTT----------------------------HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcccC----ccchhHHHHHHHHHHHHHHhcC-------------------------CCHHHHHHHHHHHHHH
Confidence 3445677777633 4556679999999999873211 4556777777777777
Q ss_pred HHH
Q 047785 115 YEE 117 (174)
Q Consensus 115 fee 117 (174)
|+-
T Consensus 75 f~~ 77 (85)
T PF13495_consen 75 FRW 77 (85)
T ss_dssp HHC
T ss_pred HHH
Confidence 764
No 15
>PRK10529 DNA-binding transcriptional activator KdpE; Provisional
Probab=54.13 E-value=11 Score=28.11 Aligned_cols=17 Identities=29% Similarity=0.485 Sum_probs=13.2
Q ss_pred hhHHHHHHHHHHHHHhC
Q 047785 103 SLDALIGRLRAAYEENG 119 (174)
Q Consensus 103 SlDALIGRLRAafee~G 119 (174)
+||..|.|||.-+++.+
T Consensus 191 ~~~~~i~rlR~kl~~~~ 207 (225)
T PRK10529 191 YLRIYMGHLRQKLEQDP 207 (225)
T ss_pred CHHHHHHHHHHHhccCC
Confidence 58888888888887544
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=52.52 E-value=2.3 Score=32.20 Aligned_cols=20 Identities=40% Similarity=0.723 Sum_probs=15.5
Q ss_pred CCCCCCc---cchHHHHHHHHHH
Q 047785 122 PETNPFA---SGAIRVYLREVRE 141 (174)
Q Consensus 122 pe~NPf~---araVr~YLreVRd 141 (174)
..+|||+ ||-+|+||||=-|
T Consensus 4 ~k~NPfr~aiARKaRiyLr~Gld 26 (82)
T PF05528_consen 4 SKDNPFRGAIARKARIYLREGLD 26 (82)
T ss_pred cccCchhhhhhhheeeeeecCCc
Confidence 3589995 8899999997443
No 17
>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=51.43 E-value=7.8 Score=23.39 Aligned_cols=16 Identities=38% Similarity=1.086 Sum_probs=13.7
Q ss_pred cCCCCCCCCCCCCCCC
Q 047785 79 QGCMFYGQPEPPAPCT 94 (174)
Q Consensus 79 ~~C~~fg~p~ppapC~ 94 (174)
.+|.|||.|..-..|.
T Consensus 7 ~~CgF~G~~~t~~~Cs 22 (26)
T smart00259 7 PGCGFFGNPATEGLCS 22 (26)
T ss_pred CCCCCcCChhhcccCH
Confidence 6899999998877774
No 18
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=50.91 E-value=23 Score=34.77 Aligned_cols=105 Identities=15% Similarity=0.080 Sum_probs=57.6
Q ss_pred CCCCCCchhhhhhhhhHhHHHHHHHhC-CCCCCCC------CCCchhhhhHHHhhhccCCeeeeccCC--CCCCCCCCCC
Q 047785 21 QQPATPSRYESQKRRDWNTFGQYLKNQ-RPPVPLS------QCSCNHVLDFLRYLDQFGKTKVHLQGC--MFYGQPEPPA 91 (174)
Q Consensus 21 ~~~~~~srYesQKrrdwntf~qyL~n~-rPPl~l~------~cs~~hVleFL~ylDqfGkTkVH~~~C--~~fg~p~ppa 91 (174)
|.+.....|+..+........+..... .|..+.- .++-..+-|. .-..+.|-.=|..--= .|....+.|
T Consensus 397 P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~T~dg~~i~l~~Ni~~~~d~-~~~~~~ga~GvGL~RtEfl~~~~~~~P- 474 (748)
T PRK11061 397 PEPVLLQEYQRLISEEIELSRLAEDDVNLPAQLKSGERIKVMLNAGLSAEH-EEKLGSRVDGVGLYRTEIPFMLQSGFP- 474 (748)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhhcCCCCccCCCCeeeEEEecCCHHHH-HHHHhCCCCeEecccchhhhccCCCCC-
Confidence 344556778765555444444444432 3433322 2333334444 3344444333322111 222223322
Q ss_pred CCCCchhhhhchhHHHHHHHHHHHHHhCCC--------------------CCCCCC-ccchHHHHHHH
Q 047785 92 PCTCPLRQAWGSLDALIGRLRAAYEENGGS--------------------PETNPF-ASGAIRVYLRE 138 (174)
Q Consensus 92 pC~CPlRqAwGSlDALIGRLRAafee~Gg~--------------------pe~NPf-~araVr~YLre 138 (174)
+-|......|.+.+.++|+ +|.||| |.|+||+||..
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 4577888889888888764 589999 78999999853
No 19
>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=50.66 E-value=26 Score=30.83 Aligned_cols=38 Identities=29% Similarity=0.217 Sum_probs=30.4
Q ss_pred hchhHHHHHHHHHHHHHhCCC----------------------CCCCCC-ccchHHHHHHH
Q 047785 101 WGSLDALIGRLRAAYEENGGS----------------------PETNPF-ASGAIRVYLRE 138 (174)
Q Consensus 101 wGSlDALIGRLRAafee~Gg~----------------------pe~NPf-~araVr~YLre 138 (174)
+=+.+.+...++.+.+.++++ .|.||| |-|+||+||..
T Consensus 58 ~p~e~eq~~~y~~i~~~~~~~pV~iRtlD~g~dK~l~~~~~~~~E~NP~LG~RGiR~~l~~ 118 (293)
T PF02896_consen 58 PPSEEEQYEIYRKIAEAMGGKPVTIRTLDIGGDKPLPYLSREPKEENPALGLRGIRRSLAH 118 (293)
T ss_dssp HHHHHHHHHHHHHHHHHTTTSEEEEE---SBCCCGSCSSHHCH--SSGGGSSBTHHHHHHS
T ss_pred CchHHHHHHHHHHHHHHhccCcEEEEecCCCCCccCCcccccccccccccccccccccccc
Confidence 446788888999999988874 569998 78999999975
No 20
>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=50.60 E-value=32 Score=27.62 Aligned_cols=26 Identities=27% Similarity=0.344 Sum_probs=20.0
Q ss_pred chhHHHHHHHHHHHHH---hCCCCCCCCCc
Q 047785 102 GSLDALIGRLRAAYEE---NGGSPETNPFA 128 (174)
Q Consensus 102 GSlDALIGRLRAafee---~Gg~pe~NPf~ 128 (174)
.++...+..|+++|+- +|. -..|||.
T Consensus 135 ~t~~~~~~~l~~~~~~a~~~g~-i~~nP~~ 163 (357)
T cd00801 135 ETARRVRQRLKQVFRYAIARGL-IEANPAA 163 (357)
T ss_pred HHHHHHHHHHHHHHHHHHHcCC-cccCchH
Confidence 4788999999999984 444 4489985
No 21
>PF10865 DUF2703: Domain of unknown function (DUF2703); InterPro: IPR021219 This family of protein has no known function.
Probab=47.03 E-value=6.7 Score=30.83 Aligned_cols=26 Identities=12% Similarity=0.045 Sum_probs=22.7
Q ss_pred hhhhchhHHHHHHHHHHHHHhCCCCC
Q 047785 98 RQAWGSLDALIGRLRAAYEENGGSPE 123 (174)
Q Consensus 98 RqAwGSlDALIGRLRAafee~Gg~pe 123 (174)
...+.+|+..+-+|+.+|+..|..++
T Consensus 19 ~~Tg~~L~~av~~l~~~L~~~Giev~ 44 (120)
T PF10865_consen 19 GDTGETLREAVKELAPVLAPLGIEVR 44 (120)
T ss_pred hhHHHHHHHHHHHHHHHHHhCCcEEE
Confidence 46778999999999999999998654
No 22
>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional
Probab=46.83 E-value=15 Score=27.46 Aligned_cols=23 Identities=30% Similarity=0.563 Sum_probs=16.8
Q ss_pred chhhhhc--------hhHHHHHHHHHHHHHh
Q 047785 96 PLRQAWG--------SLDALIGRLRAAYEEN 118 (174)
Q Consensus 96 PlRqAwG--------SlDALIGRLRAafee~ 118 (174)
-+.+.|| +||..|.|||.-+++.
T Consensus 174 l~~~~w~~~~~~~~~~v~~~i~rLR~kl~~~ 204 (223)
T PRK10816 174 LMLQLYPDAELRESHTIDVLMGRLRKKIQAQ 204 (223)
T ss_pred HHHHhcCCCCCCCcCCHHHHHHHHHHHhccC
Confidence 3556676 6888888888888754
No 23
>PF00486 Trans_reg_C: Transcriptional regulatory protein, C terminal; InterPro: IPR001867 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain that is almost always found associated with the response regulator receiver domain (see IPR001789 from INTERPRO). It may play a role in DNA binding [].; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2K4J_A 2JPB_A 1ODD_A 1OPC_A 1KGS_A 2PMU_E 2JZY_A 1GXP_B 1QQI_A 2Z33_A ....
Probab=46.44 E-value=21 Score=23.33 Aligned_cols=21 Identities=52% Similarity=0.854 Sum_probs=18.1
Q ss_pred chhHHHHHHHHHHHHHhCCCC
Q 047785 102 GSLDALIGRLRAAYEENGGSP 122 (174)
Q Consensus 102 GSlDALIGRLRAafee~Gg~p 122 (174)
-+||.+|-|||..++..|+.+
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 24
>cd08781 Death_UNC5-like Death domain found in Uncoordinated-5 homolog family. Death Domain (DD) found in Uncoordinated-5 (UNC-5) homolog family, which includes Unc5A, B, C and D in vertebrates. UNC5 proteins are receptors for secreted netrins (netrin-1, -3 and -4) that are involved in diverse processes like axonal guidance, neuronal migration, blood vessel patterning, and apoptosis. They 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. They serve as adaptors in signaling pathways and can recruit
Probab=46.16 E-value=25 Score=25.32 Aligned_cols=25 Identities=24% Similarity=0.413 Sum_probs=19.8
Q ss_pred hhhhhc---hhHHHHHHHHHHHHHhCCC
Q 047785 97 LRQAWG---SLDALIGRLRAAYEENGGS 121 (174)
Q Consensus 97 lRqAwG---SlDALIGRLRAafee~Gg~ 121 (174)
+=.-|. +-|+-|+.|.++++++|..
T Consensus 49 LL~~We~~~~~~~tv~~L~~~L~~mgr~ 76 (83)
T cd08781 49 ILDLWEARHRDDGALNDLAQILEEMGRT 76 (83)
T ss_pred HHHHHHhcCCCcchHHHHHHHHHHcCcH
Confidence 335674 4589999999999999964
No 25
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair]
Probab=43.89 E-value=24 Score=32.05 Aligned_cols=44 Identities=27% Similarity=0.522 Sum_probs=37.3
Q ss_pred CCchhhhhhhhhHhHHHHHHHhCCCCC-CCCCCCchhhhhHHHhhhccCCe
Q 047785 25 TPSRYESQKRRDWNTFGQYLKNQRPPV-PLSQCSCNHVLDFLRYLDQFGKT 74 (174)
Q Consensus 25 ~~srYesQKrrdwntf~qyL~n~rPPl-~l~~cs~~hVleFL~ylDqfGkT 74 (174)
|.+.| |||-+.|.+||..+- + +|...+..||.+||.++-.+|..
T Consensus 26 Tl~sY----rrDL~~f~~~L~~~~--~~~l~~~~~~di~~yl~~l~~~g~s 70 (300)
T COG4974 26 TLSSY----RRDLEDFREWLEERG--ITDLADATEADIREYLTELAEQGLS 70 (300)
T ss_pred hHHHH----HHHHHHHHHHHHhcC--CCChhhcCHHHHHHHHHHHHhCCcC
Confidence 66666 689999999999876 4 67788899999999999999843
No 26
>KOG4670 consensus Uncharacterized conserved membrane protein [Function unknown]
Probab=41.95 E-value=11 Score=36.96 Aligned_cols=59 Identities=27% Similarity=0.430 Sum_probs=41.6
Q ss_pred hhhhhHhH------------HHHHHHhCCCCCCCCCCCchhhhhHHHhhhccCCee-----eec-cCCCCCCCCCCC
Q 047785 32 QKRRDWNT------------FGQYLKNQRPPVPLSQCSCNHVLDFLRYLDQFGKTK-----VHL-QGCMFYGQPEPP 90 (174)
Q Consensus 32 QKrrdwnt------------f~qyL~n~rPPl~l~~cs~~hVleFL~ylDqfGkTk-----VH~-~~C~~fg~p~pp 90 (174)
-|+|.|++ ||-||..|.+|..+--=...---.|++-+++.-+|. ||. ..|.+-.-.+||
T Consensus 468 ~kgrkwd~~lPTDsalifhlFcaYLDsqL~p~p~~gdg~pftsrf~v~~p~K~~~pdv~nav~~~~fc~~~vtknp~ 544 (602)
T KOG4670|consen 468 EKGRKWDLELPTDSALIFHLFCAYLDSQLDPSPYTGDGAPFTSRFLVVLPPKERFPDVYNAVVSPGFCVLAVTKNPP 544 (602)
T ss_pred ccccccccCCCchhHHHHHHHHHHHHhcCCCCCCCCCCCccceeeEEecCccccCchhhhhccCcceEEEEecCCCC
Confidence 57777764 999999999998876311122235678888887665 564 448888877774
No 27
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=40.10 E-value=26 Score=25.24 Aligned_cols=36 Identities=28% Similarity=0.453 Sum_probs=30.5
Q ss_pred CCCCCchhhhhc----hhHHHHHHHHHHHHHhCCCCCCCC
Q 047785 91 APCTCPLRQAWG----SLDALIGRLRAAYEENGGSPETNP 126 (174)
Q Consensus 91 apC~CPlRqAwG----SlDALIGRLRAafee~Gg~pe~NP 126 (174)
--|+|-|+..-+ ++|.|=-+|..+++||......+|
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 347777888888 999999999999999987776666
No 28
>PRK09279 pyruvate phosphate dikinase; Provisional
Probab=39.75 E-value=29 Score=35.21 Aligned_cols=25 Identities=36% Similarity=0.457 Sum_probs=21.2
Q ss_pred CCCCCC-ccchHHHHH--HHHHHHHHhh
Q 047785 122 PETNPF-ASGAIRVYL--REVRECQAKA 146 (174)
Q Consensus 122 pe~NPf-~araVr~YL--reVRd~QAkA 146 (174)
-|.||| +.|.+|+|| .|+=++|.+|
T Consensus 658 ~E~NPmLG~RG~Rl~l~~pei~~~QlrA 685 (879)
T PRK09279 658 HEFNPMLGHRGCRLGITYPEIYEMQARA 685 (879)
T ss_pred CCCCCccccchhhcccCChHHHHHHHHH
Confidence 489999 789999999 5777888777
No 29
>PF13276 HTH_21: HTH-like domain
Probab=39.31 E-value=48 Score=21.61 Aligned_cols=29 Identities=21% Similarity=0.335 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHhCCCCCCCCCccchHHHHHHH
Q 047785 105 DALIGRLRAAYEENGGSPETNPFASGAIRVYLRE 138 (174)
Q Consensus 105 DALIGRLRAafee~Gg~pe~NPf~araVr~YLre 138 (174)
|+|+-.++++|+++++. ||++-|..+|+.
T Consensus 4 ~~l~~~I~~i~~~~~~~-----yG~rri~~~L~~ 32 (60)
T PF13276_consen 4 EALRELIKEIFKESKPT-----YGYRRIWAELRR 32 (60)
T ss_pred HHHHHHHHHHHHHcCCC-----eehhHHHHHHhc
Confidence 67899999999999763 788888888875
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=39.01 E-value=32 Score=22.35 Aligned_cols=19 Identities=42% Similarity=0.726 Sum_probs=17.1
Q ss_pred chhHHHHHHHHHHHHHhCC
Q 047785 102 GSLDALIGRLRAAYEENGG 120 (174)
Q Consensus 102 GSlDALIGRLRAafee~Gg 120 (174)
.+|+.+|-|||..+.+.|+
T Consensus 45 ~~l~~~i~~LR~~l~~~~~ 63 (78)
T smart00862 45 NTLDVHISRLRKKLEDDGA 63 (78)
T ss_pred chHHHHHHHHHHHHhcCCC
Confidence 6799999999999998765
No 31
>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=38.46 E-value=35 Score=32.44 Aligned_cols=36 Identities=25% Similarity=0.372 Sum_probs=28.4
Q ss_pred hhHHHHHHHHHHHHHhCCC---------------------CCCCCC-ccchHHHHHHH
Q 047785 103 SLDALIGRLRAAYEENGGS---------------------PETNPF-ASGAIRVYLRE 138 (174)
Q Consensus 103 SlDALIGRLRAafee~Gg~---------------------pe~NPf-~araVr~YLre 138 (174)
+.|...-..|.+.+.++++ .|.||| |-|+||+||..
T Consensus 308 ~e~eq~~~y~~i~~~~~~~pv~iRtlDig~DK~~~~~~~~~E~NP~LG~RgiR~~l~~ 365 (565)
T TIGR01417 308 TEEEQFAAYKTVLEAMESDAVIVRTLDIGGDKELPYLNFPKEENPFLGYRAIRLALER 365 (565)
T ss_pred CHHHHHHHHHHHHHHhCCCceEEECCCCCCcccccccCCCCCCCccccchhhhhcccC
Confidence 4467777788888888764 379998 88999999964
No 32
>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=38.33 E-value=43 Score=25.94 Aligned_cols=63 Identities=27% Similarity=0.476 Sum_probs=45.3
Q ss_pred hHhHHHHHHHhCCCCCCCCCCCchhhhhHHHhhhccCCeeeeccCCCCCCCCCCCCCCCCchhhhhchhHHHHHHHHHHH
Q 047785 36 DWNTFGQYLKNQRPPVPLSQCSCNHVLDFLRYLDQFGKTKVHLQGCMFYGQPEPPAPCTCPLRQAWGSLDALIGRLRAAY 115 (174)
Q Consensus 36 dwntf~qyL~n~rPPl~l~~cs~~hVleFL~ylDqfGkTkVH~~~C~~fg~p~ppapC~CPlRqAwGSlDALIGRLRAaf 115 (174)
+|.++-..+.. |-.-.+.+--||-+|=.+.++ | .+| +|-|=..||+-++-||.|-+.+
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 88888887765 333445555577777444333 2 333 6667889999999999999999
Q ss_pred HHhCC
Q 047785 116 EENGG 120 (174)
Q Consensus 116 ee~Gg 120 (174)
.+++-
T Consensus 81 ~k~~l 85 (100)
T cd08793 81 IQNEF 85 (100)
T ss_pred HHccc
Confidence 99984
No 33
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=37.51 E-value=24 Score=22.10 Aligned_cols=12 Identities=33% Similarity=0.863 Sum_probs=10.1
Q ss_pred chHHHHHHHHHH
Q 047785 130 GAIRVYLREVRE 141 (174)
Q Consensus 130 raVr~YLreVRd 141 (174)
-+|++||++|+.
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 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=35.39 E-value=23 Score=35.65 Aligned_cols=25 Identities=32% Similarity=0.456 Sum_probs=19.8
Q ss_pred CCCCCC-ccchHHHHH--HHHHHHHHhh
Q 047785 122 PETNPF-ASGAIRVYL--REVRECQAKA 146 (174)
Q Consensus 122 pe~NPf-~araVr~YL--reVRd~QAkA 146 (174)
.|.||| +.|.||+|| .++=+.|.+|
T Consensus 652 ~E~NP~LG~RGiRl~l~~pei~~~QlrA 679 (856)
T TIGR01828 652 HEVNPMLGHRGCRLGITYPEIYEMQVRA 679 (856)
T ss_pred CCCCCccccchhhhccCChHHHHHHHHH
Confidence 599999 789999999 4566666655
No 35
>PRK12435 ferrochelatase; Provisional
Probab=34.33 E-value=97 Score=27.25 Aligned_cols=16 Identities=31% Similarity=0.628 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHhCCC
Q 047785 106 ALIGRLRAAYEENGGS 121 (174)
Q Consensus 106 ALIGRLRAafee~Gg~ 121 (174)
.+|.+++..|+..||.
T Consensus 37 ~~l~~~~~~Y~~iGG~ 52 (311)
T PRK12435 37 EMLQDLKDRYEAIGGI 52 (311)
T ss_pred HHHHHHHHHHHHhCCc
Confidence 6778899999999974
No 36
>PF08544 GHMP_kinases_C: GHMP kinases C terminal ; InterPro: IPR013750 This domain is found in homoserine kinases (2.7.1.39 from EC), galactokinases (2.7.1.6 from EC) and mevalonate kinases (2.7.1.36 from EC). These kinases make up the GHMP kinase superfamily of ATP-dependent enzymes []. These enzymes are involved in the biosynthesis of isoprenes and amino acids as well as in carbohydrate metabolism. The C-terminal domain of homoserine kinase has a central alpha-beta plait fold and an insertion of four helices, which, together with the N-terminal fold, create a novel nucleotide binding fold [].; PDB: 2R3V_C 4EMD_A 4DXL_A 4ED4_A 2GS8_A 1K47_E 3GON_A 3K17_B 1PIE_A 2AJ4_A ....
Probab=33.88 E-value=6.3 Score=26.23 Aligned_cols=75 Identities=13% Similarity=0.221 Sum_probs=46.2
Q ss_pred hhhhHhHHHHHHHhCCC--CCCCCCCCchhhhhHHHhhhccC--CeeeeccCCCCCCCCCCCCCCCCchhhhhchhHHHH
Q 047785 33 KRRDWNTFGQYLKNQRP--PVPLSQCSCNHVLDFLRYLDQFG--KTKVHLQGCMFYGQPEPPAPCTCPLRQAWGSLDALI 108 (174)
Q Consensus 33 Krrdwntf~qyL~n~rP--Pl~l~~cs~~hVleFL~ylDqfG--kTkVH~~~C~~fg~p~ppapC~CPlRqAwGSlDALI 108 (174)
++.||..|.+.+.+..- |.....+...+|.+.+.++-+.| -+++-.- - .+||-.-+=.--...|.++
T Consensus 6 ~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~Ga~~~~~sGs-------G--~G~~v~~l~~~~~~~~~v~ 76 (85)
T PF08544_consen 6 AEGDLELLGELMNENQENEPENYREVLTPEIDELKEAAEENGALGAKMSGS-------G--GGPTVFALCKDEDDAERVA 76 (85)
T ss_dssp HTTCHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHTTESEEEEETT-------S--SSSEEEEEESSHHHHHHHH
T ss_pred HCcCHHHHHHHHHHhhhhcchHHHHHcCHHHHHHHHHHHHCCCCceecCCC-------C--CCCeEEEEECCHHHHHHHH
Confidence 46899999999995443 54455667888888888888888 3443221 0 0222222222234567777
Q ss_pred HHHHHHHH
Q 047785 109 GRLRAAYE 116 (174)
Q Consensus 109 GRLRAafe 116 (174)
-+|++.|+
T Consensus 77 ~~l~~~~~ 84 (85)
T PF08544_consen 77 EALREHYK 84 (85)
T ss_dssp HHHHHHTH
T ss_pred HHHHHhCC
Confidence 77777664
No 37
>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=32.61 E-value=1.8e+02 Score=21.74 Aligned_cols=86 Identities=15% Similarity=0.194 Sum_probs=55.4
Q ss_pred hHhHHHHHHHhCCCCCCCCCCCchhhhhHHHhhhccCCeeeeccCCCCCCCCCCCCCCCCchhhhhchhHHHHHHHHHHH
Q 047785 36 DWNTFGQYLKNQRPPVPLSQCSCNHVLDFLRYLDQFGKTKVHLQGCMFYGQPEPPAPCTCPLRQAWGSLDALIGRLRAAY 115 (174)
Q Consensus 36 dwntf~qyL~n~rPPl~l~~cs~~hVleFL~ylDqfGkTkVH~~~C~~fg~p~ppapC~CPlRqAwGSlDALIGRLRAaf 115 (174)
|..++.++|.+...=-|...++-....++|..+.+.|-. +..+.=.+-+.|. . ...+.+.+++|..
T Consensus 2 ddd~YR~~L~~~~Gk~S~k~lt~~el~~vl~~l~~~G~k-~~~~~~~~~~~~~--~-----------~~~~q~~KI~aLw 67 (119)
T PF06252_consen 2 DDDTYRALLQRVTGKSSSKDLTEAELEKVLDELKRLGFK-PPKPARRPGRRPG--M-----------ATSAQLRKIRALW 67 (119)
T ss_pred CHHHHHHHHHHHhChhhHHHCCHHHHHHHHHHHHHccCc-CccccccCCCCCC--C-----------cchHHHHHHHHHH
Confidence 456778888888887788889999988999988888853 2111111111111 1 1778999999999
Q ss_pred HHhCCCCC-CCCCccchHHHHH
Q 047785 116 EENGGSPE-TNPFASGAIRVYL 136 (174)
Q Consensus 116 ee~Gg~pe-~NPf~araVr~YL 136 (174)
.++|.... .||- ..++.-|+
T Consensus 68 ~~~~~~~~v~~~s-~~aL~~fv 88 (119)
T PF06252_consen 68 KQLGKPGAVRDPS-EAALDAFV 88 (119)
T ss_pred HHhhccCCccchH-HHHHHHHH
Confidence 99996554 3433 33444443
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=32.42 E-value=39 Score=27.06 Aligned_cols=36 Identities=22% Similarity=0.558 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHhCCCCC---C---CC-CccchHHHHHHHHHH
Q 047785 106 ALIGRLRAAYEENGGSPE---T---NP-FASGAIRVYLREVRE 141 (174)
Q Consensus 106 ALIGRLRAafee~Gg~pe---~---NP-f~araVr~YLreVRd 141 (174)
.-|-+|+..|++.|...+ . ++ -.|..++.||||.-+
T Consensus 45 ~~i~~l~~~~d~~~~~~~~~~~~~~d~h~va~lLK~flReLP~ 87 (194)
T cd04372 45 EEIEDVKMAFDRDGEKADISATVYPDINVITGALKLYFRDLPI 87 (194)
T ss_pred HHHHHHHHHHcCCCCccCCcccccccHHHHHHHHHHHHHhCCC
Confidence 478889999998775332 1 22 268889999999754
No 39
>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=32.12 E-value=31 Score=23.23 Aligned_cols=21 Identities=33% Similarity=0.453 Sum_probs=17.6
Q ss_pred CCCchhhhhHHHhhhccCCee
Q 047785 55 QCSCNHVLDFLRYLDQFGKTK 75 (174)
Q Consensus 55 ~cs~~hVleFL~ylDqfGkTk 75 (174)
..|=+-++-+|.|+|+.|-|+
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 456678899999999999997
No 40
>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=31.07 E-value=53 Score=26.56 Aligned_cols=45 Identities=22% Similarity=0.195 Sum_probs=34.2
Q ss_pred chhhhhHHHhhhccCCeeeeccCCCCCCCCCCCCCCCCchhhhhc
Q 047785 58 CNHVLDFLRYLDQFGKTKVHLQGCMFYGQPEPPAPCTCPLRQAWG 102 (174)
Q Consensus 58 ~~hVleFL~ylDqfGkTkVH~~~C~~fg~p~ppapC~CPlRqAwG 102 (174)
.++|-+||..|.-.+.+.|......-.....+|.|.+|.++++--
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 567889999999988888766655543556677888999998753
No 41
>smart00243 GAS2 Growth-Arrest-Specific Protein 2 Domain. GROWTH-ARREST-SPECIFIC PROTEIN 2 Domain
Probab=31.05 E-value=33 Score=25.59 Aligned_cols=15 Identities=33% Similarity=0.831 Sum_probs=13.3
Q ss_pred hHhHHHHHHHhCCCC
Q 047785 36 DWNTFGQYLKNQRPP 50 (174)
Q Consensus 36 dwntf~qyL~n~rPP 50 (174)
-|.||.+||..|.|=
T Consensus 55 GW~tL~~fL~khDPC 69 (73)
T smart00243 55 GWETLDEYLLKHDPC 69 (73)
T ss_pred cHHHHHHHHHhCCCc
Confidence 499999999999883
No 42
>PRK13197 pyrrolidone-carboxylate peptidase; Provisional
Probab=30.81 E-value=1.7e+02 Score=24.47 Aligned_cols=83 Identities=19% Similarity=0.280 Sum_probs=50.7
Q ss_pred CCchhhhhhhhhHhHHHHHHHhCCCCCCCCCCCchhhhhHHHh-----hhccCC-ee---eeccCCCCCCCCCCCCCCCC
Q 047785 25 TPSRYESQKRRDWNTFGQYLKNQRPPVPLSQCSCNHVLDFLRY-----LDQFGK-TK---VHLQGCMFYGQPEPPAPCTC 95 (174)
Q Consensus 25 ~~srYesQKrrdwntf~qyL~n~rPPl~l~~cs~~hVleFL~y-----lDqfGk-Tk---VH~~~C~~fg~p~ppapC~C 95 (174)
.|..|.+ .-+...+.+.|++.--|..+|.=-|.-|++|+=| +.+.+. ++ ||.|..+--....+..| .+
T Consensus 108 gp~~~~t--~Lp~~~l~~~l~~~gip~~~S~dAG~YlCN~i~Y~sl~~~~~~~~~~~a~FIHvP~~~~~~~~~~~~p-~~ 184 (215)
T PRK13197 108 GPAAYFS--TLPIKAMVKAIREAGIPASVSNTAGTFVCNHVMYGLLHLLDKKYPNIRAGFIHIPYLPEQAVNKPGTP-SM 184 (215)
T ss_pred CCceeEc--CCCHHHHHHHHHHcCCCceeccCCCceeehHHHHHHHHHHHhcCCCceeEEEEcCCchhhhhcCCCCC-Cc
Confidence 4555654 3356777888888888999998889999999544 454443 33 79886544321111111 22
Q ss_pred chhhhhchhHHHHHHHHHHHHH
Q 047785 96 PLRQAWGSLDALIGRLRAAYEE 117 (174)
Q Consensus 96 PlRqAwGSlDALIGRLRAafee 117 (174)
+ ++.++.-+|++-++
T Consensus 185 ~-------~~~~~~av~~~i~~ 199 (215)
T PRK13197 185 S-------LEDIVRGLELAIEA 199 (215)
T ss_pred c-------HHHHHHHHHHHHHH
Confidence 3 56666666655544
No 43
>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=30.33 E-value=92 Score=22.09 Aligned_cols=39 Identities=31% Similarity=0.508 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHhCCCCCCCCCccchHHHHHHHHHHHHHhhhCCccccc
Q 047785 106 ALIGRLRAAYEENGGSPETNPFASGAIRVYLREVRECQAKARGIPYKKK 154 (174)
Q Consensus 106 ALIGRLRAafee~Gg~pe~NPf~araVr~YLreVRd~QAkArgi~y~kk 154 (174)
.|--+..++|+++|-.+ +.||++||+.| +..+|||++-+
T Consensus 11 ~lK~~a~~il~~~Glt~------s~ai~~fl~qi----v~~~~iPF~~~ 49 (83)
T PF04221_consen 11 ELKEEAEAILEELGLTL------SDAINMFLKQI----VREGGIPFELS 49 (83)
T ss_dssp HHHHHHHHHHHHTT--H------HHHHHHHHHHH----HHHSS-S----
T ss_pred HHHHHHHHHHHHcCCCH------HHHHHHHHHHH----HHhCCCCcccc
Confidence 45567788999999875 57999999987 44578998754
No 44
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=30.17 E-value=1.1e+02 Score=22.71 Aligned_cols=38 Identities=37% Similarity=0.529 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHhCCCCCCCCCccchHHHHHHHHHHHHHhhhCCcccc
Q 047785 106 ALIGRLRAAYEENGGSPETNPFASGAIRVYLREVRECQAKARGIPYKK 153 (174)
Q Consensus 106 ALIGRLRAafee~Gg~pe~NPf~araVr~YLreVRd~QAkArgi~y~k 153 (174)
.|--..-++|++.|-.+ +.||++||+.| ++-+|||++.
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 44456678899999875 56899999887 4557888873
No 45
>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=29.89 E-value=1.1e+02 Score=24.81 Aligned_cols=33 Identities=18% Similarity=0.056 Sum_probs=24.4
Q ss_pred hhhHhHHHHHHHhCCCCCCCCCCCchhhhhHHHhhhc
Q 047785 34 RRDWNTFGQYLKNQRPPVPLSQCSCNHVLDFLRYLDQ 70 (174)
Q Consensus 34 rrdwntf~qyL~n~rPPl~l~~cs~~hVleFL~ylDq 70 (174)
...++.|.+|+.+ +.+..-+..||.+||.++-+
T Consensus 23 ~~~~~~~~~~~g~----~~~~~it~~~i~~~l~~l~~ 55 (315)
T TIGR02249 23 LHWIKRFIRFHNK----RHPSTMGDTEVEAFLSDLAV 55 (315)
T ss_pred HHHHHHHHHHhCC----CChHhcCHHHHHHHHHHHHh
Confidence 3578888888653 34455689999999999854
No 46
>PTZ00398 phosphoenolpyruvate carboxylase; Provisional
Probab=29.89 E-value=83 Score=32.41 Aligned_cols=42 Identities=17% Similarity=0.336 Sum_probs=31.5
Q ss_pred hchhHHHHHHHHHHHHHhCC------------------CCCCCCCcc-------------chHHHHHHHHHHH
Q 047785 101 WGSLDALIGRLRAAYEENGG------------------SPETNPFAS-------------GAIRVYLREVREC 142 (174)
Q Consensus 101 wGSlDALIGRLRAafee~Gg------------------~pe~NPf~a-------------raVr~YLreVRd~ 142 (174)
|-.+=.+..+|..|++++|+ .=.+|||.. .|+++|+++|++.
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 44566788899999988754 234899973 4778999998764
No 47
>PRK05084 xerS site-specific tyrosine recombinase XerS; Reviewed
Probab=29.80 E-value=97 Score=25.75 Aligned_cols=68 Identities=13% Similarity=0.205 Sum_probs=43.4
Q ss_pred hhHhHHHHHHHhCCC-----CC-----CCCCCCchhhhhHHHhhhccCCeeeeccCCCCCCCCCCCCCCCCchhhhhchh
Q 047785 35 RDWNTFGQYLKNQRP-----PV-----PLSQCSCNHVLDFLRYLDQFGKTKVHLQGCMFYGQPEPPAPCTCPLRQAWGSL 104 (174)
Q Consensus 35 rdwntf~qyL~n~rP-----Pl-----~l~~cs~~hVleFL~ylDqfGkTkVH~~~C~~fg~p~ppapC~CPlRqAwGSl 104 (174)
.+...|.+||..+.. +. .|...+..||.+|+.|+.+.-.. + ++.+ +...+..|+
T Consensus 43 ~~l~~f~~~l~~~~~~~~~~~~~~~~~~l~~lt~~~i~~f~~~l~~~~~~------~---~~~~-------~~~~s~~Ti 106 (357)
T PRK05084 43 TEYRRFFNWLISEGLSDASKIKDIPLSTLENLTKKDVEAFILYLRERPLL------N---GHST-------KKGNSQTTI 106 (357)
T ss_pred HHHHHHHHHHHHcCCCCcCCcccCCHHHHHhhhHHHHHHHHHHHHhcccc------c---cccc-------ccchhHHHH
Confidence 456678888876532 11 24467899999999999642110 0 0000 022467889
Q ss_pred HHHHHHHHHHHHHh
Q 047785 105 DALIGRLRAAYEEN 118 (174)
Q Consensus 105 DALIGRLRAafee~ 118 (174)
...++-||++|.-.
T Consensus 107 ~~~l~~l~~~~~~~ 120 (357)
T PRK05084 107 NRTLSALKSLFKYL 120 (357)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999999843
No 48
>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=29.74 E-value=30 Score=29.42 Aligned_cols=14 Identities=43% Similarity=0.707 Sum_probs=11.1
Q ss_pred hhHhHHHHHHHhCC
Q 047785 35 RDWNTFGQYLKNQR 48 (174)
Q Consensus 35 rdwntf~qyL~n~r 48 (174)
-|.|+|+|||...+
T Consensus 141 VDR~EFdQYLn~~~ 154 (197)
T PF12067_consen 141 VDRTEFDQYLNSSR 154 (197)
T ss_pred hhHHHHHHHhcccc
Confidence 47899999999543
No 49
>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=29.55 E-value=1.1e+02 Score=22.12 Aligned_cols=39 Identities=36% Similarity=0.672 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHhCCCCCCCCCccchHHHHHHHHHHHHHhhhCCccccc
Q 047785 106 ALIGRLRAAYEENGGSPETNPFASGAIRVYLREVRECQAKARGIPYKKK 154 (174)
Q Consensus 106 ALIGRLRAafee~Gg~pe~NPf~araVr~YLreVRd~QAkArgi~y~kk 154 (174)
.|--..-++|+++|-.+ +.|||++|+.| ++-+|||++-+
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 34455667889999775 46999999876 45578888765
No 50
>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=29.20 E-value=1.4e+02 Score=24.68 Aligned_cols=37 Identities=22% Similarity=0.332 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHhC---CCCCCCCC----ccchHHHHHHHHHH
Q 047785 105 DALIGRLRAAYEENG---GSPETNPF----ASGAIRVYLREVRE 141 (174)
Q Consensus 105 DALIGRLRAafee~G---g~pe~NPf----~araVr~YLreVRd 141 (174)
-+-|..|+.+|++.. -..+-+.+ .+..++.|||+.-+
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 58899999999754
No 51
>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=29.18 E-value=1.8e+02 Score=23.23 Aligned_cols=59 Identities=10% Similarity=0.065 Sum_probs=37.9
Q ss_pred hHhHHHHHHHhCCCCCCCCCCCchhhhhHHHhhhccCCeeeeccCCCCCCCCCCCCCCCCchhhhhchhHHHHHHHHHHH
Q 047785 36 DWNTFGQYLKNQRPPVPLSQCSCNHVLDFLRYLDQFGKTKVHLQGCMFYGQPEPPAPCTCPLRQAWGSLDALIGRLRAAY 115 (174)
Q Consensus 36 dwntf~qyL~n~rPPl~l~~cs~~hVleFL~ylDqfGkTkVH~~~C~~fg~p~ppapC~CPlRqAwGSlDALIGRLRAaf 115 (174)
.=+.|.+|+.++. +...+..+|.+|+.++. ..+-.++...+.-|++.|
T Consensus 25 ~~~~f~~~~~~~~----~~~it~~~~~~~~~~~~----------------------------~~~~~t~~~~l~~l~~~~ 72 (299)
T cd01187 25 LLRDFVRFLERHG----AGFITTDLALRWAASPP----------------------------SAQPATWAGRLGVVRRFA 72 (299)
T ss_pred HHHHHHHHHHhCC----CCCCCHHHHHHHHhcCC----------------------------CCChHHHHHHHHHHHHHH
Confidence 3456888888653 56778889888877531 012246667777788887
Q ss_pred HH---hCCCCCCCCC
Q 047785 116 EE---NGGSPETNPF 127 (174)
Q Consensus 116 ee---~Gg~pe~NPf 127 (174)
.- .|. .+.||+
T Consensus 73 ~~~~~~~~-~~~~p~ 86 (299)
T cd01187 73 RHRRRADP-RTEVPP 86 (299)
T ss_pred HHHHhCCC-CccCCC
Confidence 72 333 346776
No 52
>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=28.86 E-value=50 Score=22.21 Aligned_cols=19 Identities=32% Similarity=0.518 Sum_probs=16.8
Q ss_pred chhHHHHHHHHHHHHHhCC
Q 047785 102 GSLDALIGRLRAAYEENGG 120 (174)
Q Consensus 102 GSlDALIGRLRAafee~Gg 120 (174)
.+|+.+|-|||..+.+.|+
T Consensus 62 ~~l~~~I~rLRkkl~~~~~ 80 (95)
T cd00383 62 RTVDVHISRLRKKLEDDPS 80 (95)
T ss_pred ccHHHHHHHHHHHhccCCC
Confidence 5799999999999998764
No 53
>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=28.25 E-value=53 Score=28.34 Aligned_cols=25 Identities=28% Similarity=0.425 Sum_probs=23.4
Q ss_pred hhhhchhHHHHHHHHHHHHHhCCCC
Q 047785 98 RQAWGSLDALIGRLRAAYEENGGSP 122 (174)
Q Consensus 98 RqAwGSlDALIGRLRAafee~Gg~p 122 (174)
-.|||.+.++|-.|..+++.+|..|
T Consensus 24 ~lAyG~~~~I~~~~~~ll~~~~~~P 48 (232)
T PF09674_consen 24 LLAYGNRKQIIKKLERLLDLMGPSP 48 (232)
T ss_pred HHHccCHHHHHHHHHHHHHHhCCCH
Confidence 4799999999999999999999986
No 54
>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=28.08 E-value=71 Score=29.68 Aligned_cols=54 Identities=33% Similarity=0.494 Sum_probs=35.0
Q ss_pred chhhhhHHHhhhccC-CeeeeccCCCCCCCCCCCCCCCCchhhhhchh--HH----HHHHHHHHHHHhCCCCC
Q 047785 58 CNHVLDFLRYLDQFG-KTKVHLQGCMFYGQPEPPAPCTCPLRQAWGSL--DA----LIGRLRAAYEENGGSPE 123 (174)
Q Consensus 58 ~~hVleFL~ylDqfG-kTkVH~~~C~~fg~p~ppapC~CPlRqAwGSl--DA----LIGRLRAafee~Gg~pe 123 (174)
|.--++||..|.+.| |.+|+ ..-.|-.+.+. |..+ |. .--||..||+++|-.|.
T Consensus 48 G~agl~f~e~l~~~gakv~Vp----------TTlNp~~~D~~--w~~~gvd~~f~~~q~~i~~ay~~mG~~~t 108 (389)
T cd01355 48 GDAGLEFLERLADQGAKVAVP----------TTLNPISMDLH--WRELGVDEEFAEKQARLVKAYKAMGVDPT 108 (389)
T ss_pred chhhHHHHHHHHhCCCeEeec----------CccCCcccCcc--hhhcCCCHHHHHHHHHHHHHHHHcCCccc
Confidence 344589999987666 34443 23455566666 8755 32 33467899999998754
No 55
>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=26.99 E-value=65 Score=28.50 Aligned_cols=65 Identities=22% Similarity=0.325 Sum_probs=47.3
Q ss_pred CCCchhhhhhhhhHhHHHHHHHhCCCCCCC--CCCCchhhhhHHHh-----------------hhccCCeeeeccCCCCC
Q 047785 24 ATPSRYESQKRRDWNTFGQYLKNQRPPVPL--SQCSCNHVLDFLRY-----------------LDQFGKTKVHLQGCMFY 84 (174)
Q Consensus 24 ~~~srYesQKrrdwntf~qyL~n~rPPl~l--~~cs~~hVleFL~y-----------------lDqfGkTkVH~~~C~~f 84 (174)
..-.+|-++=|..-.+|.+||..+.|-... ..--...|.+||.. ....|..++|.-+=..|
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 344578888899999999999999987721 23345678899886 34577778888777777
Q ss_pred CCCC
Q 047785 85 GQPE 88 (174)
Q Consensus 85 g~p~ 88 (174)
.+++
T Consensus 226 ~~~g 229 (312)
T PF11709_consen 226 NRTG 229 (312)
T ss_pred CCCc
Confidence 6655
No 56
>PF01754 zf-A20: A20-like zinc finger; InterPro: IPR002653 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in A20. A20 is an inhibitor of cell death that inhibits NF-kappaB activation via the tumour necrosis factor receptor associated factor pathway []. The zinc finger domains appear to mediate self-association in A20. These fingers also mediate IL-1-induced NF-kappa B activation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 2FIF_F 2FID_B 2C7N_C 2C7M_A 2L00_A 2KZY_A 2EQG_A 2EQE_A 3OJ3_J 3OJ4_C ....
Probab=26.75 E-value=26 Score=21.13 Aligned_cols=16 Identities=44% Similarity=1.086 Sum_probs=10.8
Q ss_pred ccCCCCCCCCCCCCCC
Q 047785 78 LQGCMFYGQPEPPAPC 93 (174)
Q Consensus 78 ~~~C~~fg~p~ppapC 93 (174)
..+|.|||.+..-.-|
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 5789999988765544
No 57
>KOG1452 consensus Predicted Rho GTPase-activating protein [Signal transduction mechanisms]
Probab=26.41 E-value=38 Score=32.13 Aligned_cols=31 Identities=39% Similarity=0.597 Sum_probs=23.0
Q ss_pred HHHHHHHHhCCC--------CCCCCCccchHHHHHHHHHH
Q 047785 110 RLRAAYEENGGS--------PETNPFASGAIRVYLREVRE 141 (174)
Q Consensus 110 RLRAafee~Gg~--------pe~NPf~araVr~YLreVRd 141 (174)
-||++||-||.. |+.|=. +..++.||||+=|
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 589999999964 444543 4589999999743
No 58
>COG0745 OmpR Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=26.34 E-value=55 Score=27.23 Aligned_cols=29 Identities=34% Similarity=0.633 Sum_probs=22.8
Q ss_pred CCchhhhhc--------hhHHHHHHHHHHHHHhCCCC
Q 047785 94 TCPLRQAWG--------SLDALIGRLRAAYEENGGSP 122 (174)
Q Consensus 94 ~CPlRqAwG--------SlDALIGRLRAafee~Gg~p 122 (174)
.--+.+.|| +||..|+|||.-.+..++.+
T Consensus 176 ~~L~~~vw~~~~~~~~rtvdvhI~rLR~Kl~~~~~~~ 212 (229)
T COG0745 176 EQLLEAVWGYDFEVDSRTVDVHISRLRKKLEKDPGAG 212 (229)
T ss_pred HHHHHHhcCCCCCCCccCHHHHHHHHHHHhccCCCCC
Confidence 344678888 49999999999998876543
No 59
>PF09958 DUF2192: Uncharacterized protein conserved in archaea (DUF2192); InterPro: IPR018693 This family of various hypothetical archaeal proteins has no known function.
Probab=26.31 E-value=58 Score=28.66 Aligned_cols=21 Identities=43% Similarity=0.615 Sum_probs=18.2
Q ss_pred hhHHHHHHHHHHHHHhCCCCC
Q 047785 103 SLDALIGRLRAAYEENGGSPE 123 (174)
Q Consensus 103 SlDALIGRLRAafee~Gg~pe 123 (174)
+=+.||.-||..|+++|..|=
T Consensus 27 ~R~~lv~~L~~~Y~~~gIeP~ 47 (231)
T PF09958_consen 27 DREELVELLREVYEENGIEPF 47 (231)
T ss_pred CHHHHHHHHHHHHHHcCCCcC
Confidence 558999999999999998753
No 60
>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=26.04 E-value=24 Score=27.63 Aligned_cols=37 Identities=24% Similarity=0.379 Sum_probs=29.7
Q ss_pred hhhHhHHHHHHHh---CCCCCCCCCCCchhhhhHHHhhhc
Q 047785 34 RRDWNTFGQYLKN---QRPPVPLSQCSCNHVLDFLRYLDQ 70 (174)
Q Consensus 34 rrdwntf~qyL~n---~rPPl~l~~cs~~hVleFL~ylDq 70 (174)
...|..||+|+-. ..-|-.+..+.+.++.+||.-+|.
T Consensus 64 ~~~l~~fG~~~~~~~~~~~~~~~l~~~g~~~~~FL~~ld~ 103 (171)
T PF07700_consen 64 EELLEEFGEYFFDFLSESGYERLLRFLGRDLFDFLNNLDN 103 (171)
T ss_dssp HHHHHHHHHHHHHHHHHHCCHHHHHCTCSSHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhCcHHHHHhcCCCHHHHHHhHHH
Confidence 3468889988865 445777778999999999998885
No 61
>PLN02837 threonine-tRNA ligase
Probab=25.97 E-value=29 Score=33.01 Aligned_cols=16 Identities=38% Similarity=0.526 Sum_probs=12.0
Q ss_pred hhhhhchhHHHHHHHH
Q 047785 97 LRQAWGSLDALIGRLR 112 (174)
Q Consensus 97 lRqAwGSlDALIGRLR 112 (174)
-|-.|||+|.|||-|-
T Consensus 488 h~~~~G~~eRlia~Li 503 (614)
T PLN02837 488 HRAILGSLERFFGVLI 503 (614)
T ss_pred EcCCccCHHHHHHHHH
Confidence 3567999999887553
No 62
>PRK11173 two-component response regulator; Provisional
Probab=25.95 E-value=55 Score=25.00 Aligned_cols=19 Identities=26% Similarity=0.531 Sum_probs=15.9
Q ss_pred hhHHHHHHHHHHHHHhCCC
Q 047785 103 SLDALIGRLRAAYEENGGS 121 (174)
Q Consensus 103 SlDALIGRLRAafee~Gg~ 121 (174)
+||..|.|||.-+++.++.
T Consensus 200 ~~~~~i~rlR~kl~~~~~~ 218 (237)
T PRK11173 200 TVDVTIRRIRKHFESTPDT 218 (237)
T ss_pred cHHHHHHHHHHHhccCCCC
Confidence 8999999999999865533
No 63
>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=25.91 E-value=4.7e+02 Score=23.23 Aligned_cols=24 Identities=25% Similarity=0.296 Sum_probs=20.0
Q ss_pred hhhhhhhhHhHHHHHHHhCCCCCC
Q 047785 29 YESQKRRDWNTFGQYLKNQRPPVP 52 (174)
Q Consensus 29 YesQKrrdwntf~qyL~n~rPPl~ 52 (174)
-.++.|+.|+.|.++.+.+.+|++
T Consensus 166 ~~n~~r~~~~~~~~l~~~~p~pit 189 (377)
T TIGR03190 166 VCDENRRLLRELFDYRKEADPKVT 189 (377)
T ss_pred HHHHHHHHHHHHHHHHccCCCCcC
Confidence 346788999999999888888887
No 64
>PF08135 EPV_E5: Major transforming protein E5 family; InterPro: IPR012555 This family consists of the major transforming proteins (E5) of the bovine papilloma virus (BPV). The equine sarcoid is one of the most common dermatological lesion in equids. It is a benign, locally invasive dermal fibroblastic lesion and studies have shown an association of the lesions with BPV. E5 is a short hydrophobic membrane protein localising to the Golgi apparatus and other intracellular membranes. It binds to and constitutively activates the platelet-derived growth factor-beta in transformed cells. This stimulation activates a receptor signalling cascade which results in an intracellular growth stimulatory signal [].
Probab=25.35 E-value=34 Score=23.50 Aligned_cols=12 Identities=58% Similarity=1.010 Sum_probs=10.2
Q ss_pred hhhHHHhhhccC
Q 047785 61 VLDFLRYLDQFG 72 (174)
Q Consensus 61 VleFL~ylDqfG 72 (174)
++=||+|-||||
T Consensus 25 L~fFLV~Wd~fg 36 (44)
T PF08135_consen 25 LFFFLVYWDQFG 36 (44)
T ss_pred HHHHHHHHHhcC
Confidence 356999999998
No 65
>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=25.31 E-value=38 Score=23.09 Aligned_cols=12 Identities=42% Similarity=0.775 Sum_probs=10.4
Q ss_pred hchhHHHHHHHH
Q 047785 101 WGSLDALIGRLR 112 (174)
Q Consensus 101 wGSlDALIGRLR 112 (174)
|-.||.||.+|.
T Consensus 37 f~~lD~li~~l~ 48 (49)
T PF07535_consen 37 FKELDSLISQLQ 48 (49)
T ss_pred HHHHHHHHHHhc
Confidence 779999999884
No 66
>PRK09468 ompR osmolarity response regulator; Provisional
Probab=25.11 E-value=60 Score=24.65 Aligned_cols=16 Identities=50% Similarity=0.686 Sum_probs=11.8
Q ss_pred hhHHHHHHHHHHHHHh
Q 047785 103 SLDALIGRLRAAYEEN 118 (174)
Q Consensus 103 SlDALIGRLRAafee~ 118 (174)
+||..|.|||.-++..
T Consensus 201 ~l~~~i~~LR~kl~~~ 216 (239)
T PRK09468 201 SIDVQISRLRRLIEED 216 (239)
T ss_pred CHHHHHHHHHHHhccC
Confidence 5788888888877643
No 67
>PRK11177 phosphoenolpyruvate-protein phosphotransferase; Provisional
Probab=24.38 E-value=69 Score=30.75 Aligned_cols=36 Identities=28% Similarity=0.401 Sum_probs=29.2
Q ss_pred hhHHHHHHHHHHHHHhCCC---------------------CCCCCC-ccchHHHHHHH
Q 047785 103 SLDALIGRLRAAYEENGGS---------------------PETNPF-ASGAIRVYLRE 138 (174)
Q Consensus 103 SlDALIGRLRAafee~Gg~---------------------pe~NPf-~araVr~YLre 138 (174)
+-|...--.|.+.+.++++ .|.||| |-|+||+||..
T Consensus 309 ~eeeq~~~y~~i~~~~~~~~v~iRtlDiGgDK~~~~~~~~~E~NP~LG~RgiR~~l~~ 366 (575)
T PRK11177 309 TEEEQFQAYKAVAEAMGSQAVIVRTMDIGGDKELPYMNLPKEENPFLGWRAIRIAMDR 366 (575)
T ss_pred CHHHHHHHHHHHHHHcCCCeEEEECcCCCcccccccCCCCCCCCcccccchhhhcCCC
Confidence 4677778888888888774 379999 77999999964
No 68
>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=24.31 E-value=65 Score=26.18 Aligned_cols=27 Identities=37% Similarity=0.586 Sum_probs=23.1
Q ss_pred hhhhhchhHHHHHHHHHHHHHhCCCCC
Q 047785 97 LRQAWGSLDALIGRLRAAYEENGGSPE 123 (174)
Q Consensus 97 lRqAwGSlDALIGRLRAafee~Gg~pe 123 (174)
.+.+.-.+|..||+|.+++++.|...+
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 688999999999999999999976544
No 69
>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=24.29 E-value=41 Score=24.48 Aligned_cols=28 Identities=32% Similarity=0.433 Sum_probs=24.4
Q ss_pred CCchhhhhchhH-HHHHHHHHHHHHhCCC
Q 047785 94 TCPLRQAWGSLD-ALIGRLRAAYEENGGS 121 (174)
Q Consensus 94 ~CPlRqAwGSlD-ALIGRLRAafee~Gg~ 121 (174)
+|-+=+-|++-+ +-||.|-.+.+|+|..
T Consensus 47 T~~LL~~W~~~~~~tvg~L~~~L~~~gR~ 75 (82)
T cd08782 47 TDALLQEWATAPPSTIGTLIDKLRELGRE 75 (82)
T ss_pred HHHHHHHHhcCCcccHHHHHHHHHHcCcH
Confidence 666778899888 9999999999999964
No 70
>PF08290 Hep_core_N: Hepatitis core protein, putative zinc finger; InterPro: IPR013195 This entry represent a short region found at the N terminus of some viral capsid (HBcAg) proteins from various Hepatitis B virus (HBV), which is a major human pathogen. The conservation of four Cys residues suggests that this region acts as a zinc binding domain. Hepatitis virus is composed of an outer envelope of host-derived lipid containing the surface proteins, and an inner protein capsid that contains genomic DNA. The capsid is composed of a single polypeptide, HBcAg, also known as the core antigen. The capsid has a 5-helical fold, where two long helices form a hairpin that dimerises into a 4-helical bundle []; this fold is unusual for icosahedral viruses. The monomer fold is stabilised by a hydrophobic core that is highly conserved among human viral variants. The capsid is assembled from dimers via interactions involving a highly conserved arginine-rich region near the C terminus. This viral capsid acts as a core antigen, the major immunodominant region lying at the tips of the alpha-helical hairpins that form spikes on the capsid surface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005198 structural molecule activity, 0009405 pathogenesis
Probab=23.95 E-value=31 Score=21.61 Aligned_cols=11 Identities=45% Similarity=0.914 Sum_probs=9.0
Q ss_pred CCCCCchhhhh
Q 047785 91 APCTCPLRQAW 101 (174)
Q Consensus 91 apC~CPlRqAw 101 (174)
--|.||.-||.
T Consensus 10 iscscpt~qas 20 (27)
T PF08290_consen 10 ISCSCPTVQAS 20 (27)
T ss_pred eeccCCcchhh
Confidence 35999999986
No 71
>PF13099 DUF3944: Domain of unknown function (DUF3944)
Probab=23.72 E-value=35 Score=22.23 Aligned_cols=22 Identities=32% Similarity=0.629 Sum_probs=16.3
Q ss_pred CCCCchhhhhHHHhh--hccCCee
Q 047785 54 SQCSCNHVLDFLRYL--DQFGKTK 75 (174)
Q Consensus 54 ~~cs~~hVleFL~yl--DqfGkTk 75 (174)
..|+..|+-++...| |..|+++
T Consensus 11 ~~cs~edL~~L~~~Lt~dkdG~~R 34 (35)
T PF13099_consen 11 AECSNEDLKDLVDILTHDKDGKKR 34 (35)
T ss_pred HHCCHHHHHHHHHHHhcCCCCCcC
Confidence 469998887776655 7888765
No 72
>cd03054 GST_N_Metaxin GST_N family, Metaxin subfamily; composed of metaxins and related proteins. Metaxin 1 is a component of a preprotein import complex of the mitochondrial outer membrane. It extends to the cytosol and is anchored to the mitochondrial membrane through its C-terminal domain. In mice, metaxin is required for embryonic development. In humans, alterations in the metaxin gene may be associated with Gaucher disease. Metaxin 2 binds to metaxin 1 and may also play a role in protein translocation into the mitochondria. Genome sequencing shows that a third metaxin gene also exists in zebrafish, Xenopus, chicken and mammals. Sequence analysis suggests that all three metaxins share a common ancestry and that they possess similarity to GSTs. Also included in the subfamily are uncharacterized proteins with similarity to metaxins, including a novel GST from Rhodococcus with toluene o-monooxygenase and glutamylcysteine synthetase activities.
Probab=23.71 E-value=57 Score=21.19 Aligned_cols=27 Identities=37% Similarity=0.579 Sum_probs=18.8
Q ss_pred CCCCCCCCCccchHHHHHHHHHHHHHhhhCCccccc
Q 047785 119 GGSPETNPFASGAIRVYLREVRECQAKARGIPYKKK 154 (174)
Q Consensus 119 Gg~pe~NPf~araVr~YLreVRd~QAkArgi~y~kk 154 (174)
++.|...|| .+.|++||++ .||+|+-.
T Consensus 10 ~~~~s~sp~-~~~v~~~L~~--------~~i~~~~~ 36 (72)
T cd03054 10 FGLPSLSPE-CLKVETYLRM--------AGIPYEVV 36 (72)
T ss_pred CCCCCCCHH-HHHHHHHHHh--------CCCceEEE
Confidence 455666665 4567888887 68888854
No 73
>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=23.59 E-value=38 Score=22.98 Aligned_cols=24 Identities=42% Similarity=0.706 Sum_probs=16.8
Q ss_pred CCCc--cchHHHHHHHHHHHHHhhhCC
Q 047785 125 NPFA--SGAIRVYLREVRECQAKARGI 149 (174)
Q Consensus 125 NPf~--araVr~YLreVRd~QAkArgi 149 (174)
|||. +++.|++|--| ..-+|++|+
T Consensus 2 nPF~~~aksaR~FL~~i-p~s~k~~~t 27 (51)
T PF10780_consen 2 NPFSPNAKSARLFLSLI-PPSAKARGT 27 (51)
T ss_pred CCCCcccHHHHHHHHhc-CCccccccC
Confidence 8995 67899999988 344444443
No 74
>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=23.45 E-value=39 Score=28.24 Aligned_cols=24 Identities=33% Similarity=0.760 Sum_probs=21.6
Q ss_pred hhchhHH-HHHHHHHHHHHhCCCCC
Q 047785 100 AWGSLDA-LIGRLRAAYEENGGSPE 123 (174)
Q Consensus 100 AwGSlDA-LIGRLRAafee~Gg~pe 123 (174)
-|||+|- +||+.-++|.||-..|-
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 89999999999998875
No 75
>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=23.41 E-value=71 Score=24.61 Aligned_cols=17 Identities=35% Similarity=0.743 Sum_probs=15.1
Q ss_pred chhHHHHHHHHHHHHHh
Q 047785 102 GSLDALIGRLRAAYEEN 118 (174)
Q Consensus 102 GSlDALIGRLRAafee~ 118 (174)
..||++.|-+||..|+.
T Consensus 16 AaLDsvfGgiRA~le~~ 32 (88)
T PF06947_consen 16 AALDSVFGGIRASLEDK 32 (88)
T ss_pred HHHHHHHHHHHHHHHhh
Confidence 47999999999999975
No 76
>cd04388 RhoGAP_p85 RhoGAP_p85: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in the p85 isoforms of the regulatory subunit of the class IA PI3K (phosphatidylinositol 3'-kinase). This domain is also called Bcr (breakpoint cluster region protein) homology (BH) domain. Class IA PI3Ks are heterodimers, containing a regulatory subunit (p85) and a catalytic subunit (p110) and are activated by growth factor receptor tyrosine kinases (RTKs); this activation is mediated by the p85 subunit. p85 isoforms, alpha and beta, contain a C-terminal p110-binding domain flanked by two SH2 domains, an N-terminal SH3 domain, and a RhoGAP domain flanked by two proline-rich regions. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell p
Probab=23.27 E-value=68 Score=26.83 Aligned_cols=65 Identities=15% Similarity=0.252 Sum_probs=38.9
Q ss_pred CCchhhhhHHHhhhccCCeeeeccCCCCCCCCCCCCCCCCchhhhhchhHHHHHHHHHHHHHhCCCCCC---CCC-ccch
Q 047785 56 CSCNHVLDFLRYLDQFGKTKVHLQGCMFYGQPEPPAPCTCPLRQAWGSLDALIGRLRAAYEENGGSPET---NPF-ASGA 131 (174)
Q Consensus 56 cs~~hVleFL~ylDqfGkTkVH~~~C~~fg~p~ppapC~CPlRqAwGSlDALIGRLRAafee~Gg~pe~---NPf-~ara 131 (174)
+-+.-|...+.++.+.|-+.+.. .|. .|+-+ +-.||.+|++.+...+- ++. .+.+
T Consensus 14 ~~P~iv~~ci~~IE~~GL~~eGI------------------YRv-sgs~~--~~~lk~~~d~~~~~~d~~~~dv~~va~~ 72 (200)
T cd04388 14 VAPPLLIKLVEAIEKKGLESSTL------------------YRT-QSSSS--LTELRQILDCDAASVDLEQFDVAALADA 72 (200)
T ss_pred CCCHHHHHHHHHHHHhCCCCCce------------------eeC-CCccH--HHHHHHHHhcCCCCCCcccccHHHHHHH
Confidence 44556666677777776443221 222 12222 45689999986554432 222 6899
Q ss_pred HHHHHHHHHH
Q 047785 132 IRVYLREVRE 141 (174)
Q Consensus 132 Vr~YLreVRd 141 (174)
++.|||+.-|
T Consensus 73 LK~ylReLPe 82 (200)
T cd04388 73 LKRYLLDLPN 82 (200)
T ss_pred HHHHHHhCCC
Confidence 9999998765
No 77
>PF06540 GMAP: Galanin message associated peptide (GMAP); InterPro: IPR013068 Galanin is a peptide hormone that controls various biological activities []. Galanin-like immuno-reactivity has been found in the central and peripheral nervous systems of mammals, with high concentrations demonstrated in discrete regions of the central nervous system, including the median eminence, hypothalamus, arcuate nucleus, septum, neuro-intermediate lobe of the pituitary, and the spinal cord. Its localisation within neurosecretory granules suggests that galanin may function as a neurotransmitter, and it has been shown to coexist with a variety of other peptide and amine neurotransmitters within individual neurons []. Although the precise physiological role of galanin is uncertain, it has a number of pharmacological properties: it stimulates food intake, when injected into the third ventricle of rats; it increases levels of plasma growth hormone and prolactin, and decreases dopamine levels in the median eminence []; and infusion into humans results in hyperglycemia and glucose intolerance, and inhibits pancreatic release of insulin, somatostatin and pancreatic peptide. Galanin also modulates smooth muscle contractility within the gastro-intestinal and genito-urinary tracts, all such activities suggesting that the hormone may play an important role in the nervous modulation of endocrine and smooth muscle function []. This domain represents the galanin message-associated peptide (GMAP) domain which is found C-terminal to the galanin domain in the preprogalanin precursor protein. GMAP sequences in different species show a high degree of homology, but the biological function of the GMAP peptide is not known [].
Probab=22.74 E-value=43 Score=24.40 Aligned_cols=10 Identities=30% Similarity=0.949 Sum_probs=7.8
Q ss_pred hhhhhHHHhh
Q 047785 59 NHVLDFLRYL 68 (174)
Q Consensus 59 ~hVleFL~yl 68 (174)
.-|+|||.||
T Consensus 27 rTiiEFLtfL 36 (62)
T PF06540_consen 27 RTIIEFLTFL 36 (62)
T ss_pred HHHHHHHHHH
Confidence 3488999987
No 78
>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=22.19 E-value=1.1e+02 Score=20.53 Aligned_cols=26 Identities=31% Similarity=0.231 Sum_probs=18.7
Q ss_pred hchhHHHHHHHHHHHHHhCCCCCCCC
Q 047785 101 WGSLDALIGRLRAAYEENGGSPETNP 126 (174)
Q Consensus 101 wGSlDALIGRLRAafee~Gg~pe~NP 126 (174)
++++|.+.-+|..+-+|+|..+++.|
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 79
>cd08310 Death_NFkB-like Death domain of Nuclear Factor-KappaB precursor proteins. Death Domain (DD) of Nuclear Factor-KappaB (NF-kB) precursor proteins. The NF-kB family of transcription factors play a central role in cardiovascular growth, stress response, and inflammation by controlling the expression of a network of different genes. There are five NF-kB proteins, all containing an N-terminal REL Homology Domain (RHD). Two of these, NF-kB1 and NF-kB2 are produced from the processing of the precursor proteins p105 and p100, respectively. In addition to RHD, p105 and p100 contain ANK repeats and a C-terminal DD. NF-kBs are regulated by the Inhibitor of NF-kB (IkB) Kinase (IKK) complex through classical and non-canonical pathways, which differ in the IKK subunits involved and downstream targets. IKKs facilitate the release of NF-kB dimers from an inactive state, allowing them to migrate to the nucleus where they regulate gene transcription. The precursor proteins p105 and p100 function
Probab=22.16 E-value=77 Score=22.46 Aligned_cols=23 Identities=26% Similarity=0.310 Sum_probs=17.6
Q ss_pred hhhchhHHHHHHHHHHHHHhCCC
Q 047785 99 QAWGSLDALIGRLRAAYEENGGS 121 (174)
Q Consensus 99 qAwGSlDALIGRLRAafee~Gg~ 121 (174)
.-|-.-++-||.|..+.+++|..
T Consensus 43 ~~we~~~~tv~~L~~~L~~mgr~ 65 (72)
T cd08310 43 DYFEMQGGTLERLRDALEVLGET 65 (72)
T ss_pred HHHHhCCCCHHHHHHHHHHcCcH
Confidence 34555557899999999999864
No 80
>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=22.12 E-value=78 Score=26.12 Aligned_cols=39 Identities=38% Similarity=0.534 Sum_probs=26.4
Q ss_pred chhHHHHHHHHHHHHHhCCCCCC------CCC-ccchHHHHHHHHHH
Q 047785 102 GSLDALIGRLRAAYEENGGSPET------NPF-ASGAIRVYLREVRE 141 (174)
Q Consensus 102 GSlDALIGRLRAafee~Gg~pe~------NPf-~araVr~YLreVRd 141 (174)
|+. +.|..|+..|+..+...+- ++. .|..++.||||.-|
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 3599999999986532221 222 48899999999644
No 81
>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=21.98 E-value=54 Score=22.99 Aligned_cols=12 Identities=50% Similarity=0.736 Sum_probs=6.9
Q ss_pred hchhHHHHHHHH
Q 047785 101 WGSLDALIGRLR 112 (174)
Q Consensus 101 wGSlDALIGRLR 112 (174)
.||||+||.+|=
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 82
>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=21.89 E-value=83 Score=25.27 Aligned_cols=35 Identities=23% Similarity=0.656 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHhCCCC---CCCCC----ccchHHHHHHHHHH
Q 047785 106 ALIGRLRAAYEENGGSP---ETNPF----ASGAIRVYLREVRE 141 (174)
Q Consensus 106 ALIGRLRAafee~Gg~p---e~NPf----~araVr~YLreVRd 141 (174)
+-|..||..|+. |..+ +.+.+ .|..++.||||..|
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 578999999986 4333 12222 58899999999754
No 83
>cd00778 ProRS_core_arch_euk Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. This subfamily contains the core domain of ProRS from archaea, the cytoplasm of eukaryotes and some bacteria.
Probab=21.47 E-value=42 Score=28.11 Aligned_cols=17 Identities=29% Similarity=0.603 Sum_probs=12.2
Q ss_pred hhhhhchhHHHHHHHHH
Q 047785 97 LRQAWGSLDALIGRLRA 113 (174)
Q Consensus 97 lRqAwGSlDALIGRLRA 113 (174)
-+-.||+++.+||=|-+
T Consensus 244 h~~~~g~~~R~i~ali~ 260 (261)
T cd00778 244 HQTSWGISTRLIGAIIM 260 (261)
T ss_pred EEecccHHHHHHHHHHh
Confidence 45668988888876644
No 84
>TIGR02284 conserved hypothetical protein. Members of this protein family are found mostly in the Proteobacteria, although one member is found in the the marine planctomycete Pirellula sp. strain 1. The function is unknown.
Probab=21.39 E-value=1.9e+02 Score=22.34 Aligned_cols=36 Identities=22% Similarity=0.484 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHhCCCCCCCCCccchHHHHHHHHHH
Q 047785 106 ALIGRLRAAYEENGGSPETNPFASGAIRVYLREVRE 141 (174)
Q Consensus 106 ALIGRLRAafee~Gg~pe~NPf~araVr~YLreVRd 141 (174)
..|..|.+...++||.|+..+-..+++.-..-.||.
T Consensus 44 ~~~~eL~~~v~~lGg~p~~~gs~~g~lhr~w~~lks 79 (139)
T TIGR02284 44 AIVSELQQVVASLGGKPEDHGSMVGSLHQFWGKIRA 79 (139)
T ss_pred HHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHH
Confidence 567889999999999999888776665544444443
No 85
>cd04384 RhoGAP_CdGAP RhoGAP_CdGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of CdGAP-like proteins; CdGAP contains an N-terminal RhoGAP domain and a C-terminal proline-rich region, and it is active on both Cdc42 and Rac1 but not RhoA. CdGAP is recruited to focal adhesions via the interaction with the scaffold protein actopaxin (alpha-parvin). 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=21.33 E-value=1.1e+02 Score=24.85 Aligned_cols=38 Identities=26% Similarity=0.510 Sum_probs=26.4
Q ss_pred chhHHHHHHHHHHHHHhCCCCC-------CCCC-ccchHHHHHHHHHH
Q 047785 102 GSLDALIGRLRAAYEENGGSPE-------TNPF-ASGAIRVYLREVRE 141 (174)
Q Consensus 102 GSlDALIGRLRAafee~Gg~pe-------~NPf-~araVr~YLreVRd 141 (174)
|+. +-|.+||..|++.+ .++ .+|. .|..++.||||.-|
T Consensus 43 G~~-~~i~~l~~~~d~~~-~~~~~~~~~~~d~h~va~lLK~flReLPe 88 (195)
T cd04384 43 GIA-SNIQRLRHEFDSEQ-IPDLTKDVYIQDIHSVSSLCKLYFRELPN 88 (195)
T ss_pred CCH-HHHHHHHHHHcCCC-CCCcccccccccHHHHHHHHHHHHHhCCC
Confidence 554 56899999998643 332 2332 67889999999754
No 86
>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=21.18 E-value=2.1e+02 Score=21.39 Aligned_cols=45 Identities=20% Similarity=0.494 Sum_probs=35.8
Q ss_pred hhc---hhHHHHHHHHHHHHHhCCCCCCCCCccchHHHHHHHHHHHHHhhh
Q 047785 100 AWG---SLDALIGRLRAAYEENGGSPETNPFASGAIRVYLREVRECQAKAR 147 (174)
Q Consensus 100 AwG---SlDALIGRLRAafee~Gg~pe~NPf~araVr~YLreVRd~QAkAr 147 (174)
.|- ++..+|--|++.+.+- -..+|+-..|.++|..+-.+.+.+||
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 376 7888888999988554 45788999999999998777777775
No 87
>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=21.14 E-value=20 Score=26.53 Aligned_cols=13 Identities=38% Similarity=1.112 Sum_probs=11.1
Q ss_pred HhHHHHHHHhCCC
Q 047785 37 WNTFGQYLKNQRP 49 (174)
Q Consensus 37 wntf~qyL~n~rP 49 (174)
|.||..||..|.|
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 9999999998876
No 88
>PRK06464 phosphoenolpyruvate synthase; Validated
Probab=20.99 E-value=57 Score=32.43 Aligned_cols=25 Identities=28% Similarity=0.356 Sum_probs=18.4
Q ss_pred CCCCCC-ccchHHHHHH----HHHHHHHhh
Q 047785 122 PETNPF-ASGAIRVYLR----EVRECQAKA 146 (174)
Q Consensus 122 pe~NPf-~araVr~YLr----eVRd~QAkA 146 (174)
.|.||| |.|.||+||. ++=+.|.+|
T Consensus 596 ~E~NP~LG~RGiR~~l~~p~~~lf~~qlra 625 (795)
T PRK06464 596 EEENPMLGFRGASRYLSESFREAFALECEA 625 (795)
T ss_pred CCCCCccccchhhhcccCchHHHHHHHHHH
Confidence 488999 8899999996 344455443
No 89
>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=20.55 E-value=79 Score=26.07 Aligned_cols=35 Identities=20% Similarity=0.407 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHhCCCCC--------CCCC-ccchHHHHHHHHHH
Q 047785 106 ALIGRLRAAYEENGGSPE--------TNPF-ASGAIRVYLREVRE 141 (174)
Q Consensus 106 ALIGRLRAafee~Gg~pe--------~NPf-~araVr~YLreVRd 141 (174)
+-|-.||.+|++ |..+. .++. .+.++++||||.-|
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 2233 58899999999765
No 90
>TIGR00504 pyro_pdase pyroglutamyl-peptidase I. Alternate names include pyroglutamate aminopeptidase, pyrrolidone-carboxylate peptidase, and 5-oxoprolyl-peptidase. It removes pyroglutamate (pyrrolidone-carboxylate, a modified glutamine) that can otherwise block hydrolysis of a polypeptide at the amino end, and so can be extremely useful in the biochemical studies of proteins. The biological role in the various species in which it is found is not fully understood. The enzyme appears to be a homodimer. It does not closely resemble any other peptidases.
Probab=20.48 E-value=3.5e+02 Score=22.61 Aligned_cols=84 Identities=20% Similarity=0.163 Sum_probs=56.8
Q ss_pred CCchhhhhhhhhHhHHHHHHHhCCCCCCCCCCCchhhhhHHHh-----hhccCC-ee---eeccCCCCCCCCCCCCCCCC
Q 047785 25 TPSRYESQKRRDWNTFGQYLKNQRPPVPLSQCSCNHVLDFLRY-----LDQFGK-TK---VHLQGCMFYGQPEPPAPCTC 95 (174)
Q Consensus 25 ~~srYesQKrrdwntf~qyL~n~rPPl~l~~cs~~hVleFL~y-----lDqfGk-Tk---VH~~~C~~fg~p~ppapC~C 95 (174)
.|..|.+ .-+...+.+.|++.--|+.+|.=-|.-|++|+=| ..+.+. ++ ||.|..+--....+..
T Consensus 105 gp~~~~t--tLpv~~l~~~l~~~gip~~~S~dAG~ylCN~i~Y~sL~~~~~~~~~~~agFIHVP~~~~~~~~~~~~---- 178 (212)
T TIGR00504 105 GPAAYFA--TLPVRAMVLAMKKAGIPADVSYTAGTFVCNHLMYGLLHHLAQKGLPVRAGFIHVPYLPSQVALKHGV---- 178 (212)
T ss_pred CCceeec--CCCHHHHHHHHHHcCCCeeEeCCCCceeeHHHHHHHHHHHHhcCCCceeEEEEcCCchhhhhcCCCC----
Confidence 4555654 3346677888888888999998889999998776 345454 33 8998776554322111
Q ss_pred chhhhhchhHHHHHHHHHHHHHh
Q 047785 96 PLRQAWGSLDALIGRLRAAYEEN 118 (174)
Q Consensus 96 PlRqAwGSlDALIGRLRAafee~ 118 (174)
..-+|+.++.-++++.++.
T Consensus 179 ----~~~~~~~~~~a~~~~i~~~ 197 (212)
T TIGR00504 179 ----PSMSLDTAVAGVTIAIETA 197 (212)
T ss_pred ----CCccHHHHHHHHHHHHHHH
Confidence 2235889999888888764
No 91
>TIGR02258 2_5_ligase 2'-5' RNA ligase. This protein family consists of bacterial and archaeal proteins with two tandem copies of Pfam domain pfam02834. Members for which activity has been measured perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA. The physiological substrate(s) in prokaryotes may include small 2'-5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles.
Probab=20.46 E-value=1.3e+02 Score=22.85 Aligned_cols=69 Identities=22% Similarity=0.325 Sum_probs=42.3
Q ss_pred chhhhhHHHhhhccCCe--eeeccCCCCCCCCCCC-CCCCCchhhhhchhHHHHHHHHHHHHHhCCCCCCCCCc
Q 047785 58 CNHVLDFLRYLDQFGKT--KVHLQGCMFYGQPEPP-APCTCPLRQAWGSLDALIGRLRAAYEENGGSPETNPFA 128 (174)
Q Consensus 58 ~~hVleFL~ylDqfGkT--kVH~~~C~~fg~p~pp-apC~CPlRqAwGSlDALIGRLRAafee~Gg~pe~NPf~ 128 (174)
..++-+...-+++-... .|+..++..|+++..+ .-.-.+-.. ..|..|...|+.++..+|...+.-+|.
T Consensus 51 ~~~~~~l~~~l~~~~~~~f~l~l~~~~~F~~~~~~~vl~l~~~~~--~~L~~L~~~l~~~~~~~g~~~~~~~f~ 122 (179)
T TIGR02258 51 EEQVEELEDALAKIAEPPFTLKLEGIGVFGNPKRPRVLWAGVEQS--EELTQLHADLERELAKLGFSKEERPFT 122 (179)
T ss_pred HHHHHHHHHHHHHhcCCCeEEEEeeeeeCCCCCCCeEEEEeeCCC--HHHHHHHHHHHHHHHHcCCCCCCCCcC
Confidence 33443443344443332 4788888888874322 222222222 278999999999999999887777774
No 92
>KOG2867 consensus Phosphotyrosyl phosphatase activator [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=20.42 E-value=4.7e+02 Score=24.72 Aligned_cols=96 Identities=24% Similarity=0.387 Sum_probs=60.8
Q ss_pred CCCCCCchhhhhhhhhHh-----HHHHHHHhCCCCCCCCCCCchhhhhHHHhhhc-cCCeeeeccCCCCCCCCCCCCCCC
Q 047785 21 QQPATPSRYESQKRRDWN-----TFGQYLKNQRPPVPLSQCSCNHVLDFLRYLDQ-FGKTKVHLQGCMFYGQPEPPAPCT 94 (174)
Q Consensus 21 ~~~~~~srYesQKrrdwn-----tf~qyL~n~rPPl~l~~cs~~hVleFL~ylDq-fGkTkVH~~~C~~fg~p~ppapC~ 94 (174)
|+-..+.||.+.-=|+|- +.-+-|....| .-..++|.|-..||+. ||..
T Consensus 83 P~~~~~~Rfgn~AyR~w~~kl~~~~~~ll~~~~p-----~~~~~~v~El~~Yl~~SFGNs-------------------- 137 (367)
T KOG2867|consen 83 PPIDGPQRFGNKAYRTWYEKLYEELPKLLDEALP-----SLKHEAVNELGQYLTESFGNS-------------------- 137 (367)
T ss_pred CCCCChhhhcCHHHHHHHHHHHHHHHHHHHHHcc-----hHHHHHHHHHHHHHHhccCCc--------------------
Confidence 344566799999999994 34455555444 2335889999999874 5522
Q ss_pred CchhhhhchhHH--HHHHHHHHHHHhCCCCCCCCCccchHHH---HHHHHHHHHHh
Q 047785 95 CPLRQAWGSLDA--LIGRLRAAYEENGGSPETNPFASGAIRV---YLREVRECQAK 145 (174)
Q Consensus 95 CPlRqAwGSlDA--LIGRLRAafee~Gg~pe~NPf~araVr~---YLreVRd~QAk 145 (174)
.|.-+||=-. ...-|.+- --.|.-.+ |=..|-|+|+ ||+-+|..|-+
T Consensus 138 --~RIDYGtGHEL~Fl~~L~~L-~~~Gil~~-~D~~a~vl~lF~kYlev~R~Lq~t 189 (367)
T KOG2867|consen 138 --TRIDYGTGHELNFLFFLCAL-FKLGILDE-NDYVALVLRLFNKYLEVMRRLQTT 189 (367)
T ss_pred --ccccccchHHHHHHHHHHHH-HHccCccc-chhhHHHHHHHHHHHHHHHHHHHH
Confidence 2344443222 23333333 34677777 7777888887 88999998854
No 93
>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=20.36 E-value=45 Score=29.90 Aligned_cols=42 Identities=38% Similarity=0.628 Sum_probs=32.3
Q ss_pred chhhhhchhHHHHHHHHHHHHHhCCCCCCCCCccchHHHHHHHHHHH
Q 047785 96 PLRQAWGSLDALIGRLRAAYEENGGSPETNPFASGAIRVYLREVREC 142 (174)
Q Consensus 96 PlRqAwGSlDALIGRLRAafee~Gg~pe~NPf~araVr~YLreVRd~ 142 (174)
|||.| ||.|-.+|..+||+.|+.=-.+|..+| .-|.+-|-+.
T Consensus 8 PLR~A---ld~Lrd~l~~~fe~~~~~l~~Dpw~ar--~~Yi~Vil~~ 49 (285)
T PF12055_consen 8 PLREA---LDWLRDRLDELFEEEGGELFKDPWAAR--DEYIEVILDR 49 (285)
T ss_pred HHHHH---HHHHHHHHHHHHHHHHHHhcCCHHHHH--HHHHHHHcCC
Confidence 56664 899999999999999987667888765 3666655443
No 94
>COG4865 Glutamate mutase epsilon subunit [Amino acid transport and metabolism]
Probab=20.27 E-value=71 Score=30.66 Aligned_cols=22 Identities=36% Similarity=0.640 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHhCCCCCCCCCc
Q 047785 107 LIGRLRAAYEENGGSPETNPFA 128 (174)
Q Consensus 107 LIGRLRAafee~Gg~pe~NPf~ 128 (174)
+|.||--+|||+|.+=...||+
T Consensus 196 YVDRL~G~YeE~Gi~INREpFg 217 (485)
T COG4865 196 YVDRLMGMYEEHGIRINREPFG 217 (485)
T ss_pred HHHHHHhHHHhcCeeeccccCC
Confidence 4556667999999887777775
No 95
>COG3077 RelB DNA-damage-inducible protein J [DNA replication, recombination, and repair]
Probab=20.26 E-value=1.7e+02 Score=22.26 Aligned_cols=37 Identities=32% Similarity=0.502 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHhCCCCCCCCCccchHHHHHHHHHHHHHhhhCCccc
Q 047785 106 ALIGRLRAAYEENGGSPETNPFASGAIRVYLREVRECQAKARGIPYK 152 (174)
Q Consensus 106 ALIGRLRAafee~Gg~pe~NPf~araVr~YLreVRd~QAkArgi~y~ 152 (174)
.+--+--+.++++|-.+ +.|||++|.-| |+-.|||++
T Consensus 14 ~vK~eA~~Vl~~mGlt~------S~airm~L~~v----a~~~~lPfd 50 (88)
T COG3077 14 EVKEEATAVLEEMGLTI------SDAIRMFLTKV----AREGALPFD 50 (88)
T ss_pred HHHHHHHHHHHHhCCCH------HHHHHHHHHHH----HHcCCCCcc
Confidence 34444557899999886 57999999887 555778875
No 96
>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=20.17 E-value=1.3e+02 Score=24.02 Aligned_cols=36 Identities=31% Similarity=0.679 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHHhCCCC----CCCCC-ccchHHHHHHHHHH
Q 047785 105 DALIGRLRAAYEENGGSP----ETNPF-ASGAIRVYLREVRE 141 (174)
Q Consensus 105 DALIGRLRAafee~Gg~p----e~NPf-~araVr~YLreVRd 141 (174)
.+.|.+|+.+|+. |..+ +.+|. .|..++.||||.-+
T Consensus 50 ~~~i~~l~~~~d~-~~~~~~~~~~d~h~va~lLK~fLReLPe 90 (199)
T cd04390 50 ANLVKQLQDAFDA-GERPSFDSDTDVHTVASLLKLYLRELPE 90 (199)
T ss_pred HHHHHHHHHHHhC-CCCCCccccCCHHHHHHHHHHHHHhCCC
Confidence 4578999999975 4332 34553 68899999998754
No 97
>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=20.15 E-value=93 Score=21.52 Aligned_cols=30 Identities=27% Similarity=0.554 Sum_probs=23.4
Q ss_pred hHHHHHHHhCCCCCCCCCCCchhhhhHHHhhhccC
Q 047785 38 NTFGQYLKNQRPPVPLSQCSCNHVLDFLRYLDQFG 72 (174)
Q Consensus 38 ntf~qyL~n~rPPl~l~~cs~~hVleFL~ylDqfG 72 (174)
+.|.+=|++.+|-| |.+||..|..|-.+||
T Consensus 33 ~DF~~Al~~~kpSV-----s~~dl~~ye~w~~~FG 62 (62)
T PF09336_consen 33 EDFEEALKKVKPSV-----SQEDLKKYEEWTKEFG 62 (62)
T ss_dssp HHHHHHHHTCGGSS------HHHHHHHHHHHHHTS
T ss_pred HHHHHHHHHcCCCC-----CHHHHHHHHHHHHHcC
Confidence 45666777777654 5889999999999998
No 98
>PRK10701 DNA-binding transcriptional regulator RstA; Provisional
Probab=20.08 E-value=77 Score=24.18 Aligned_cols=17 Identities=41% Similarity=0.565 Sum_probs=14.6
Q ss_pred hhHHHHHHHHHHHHHhC
Q 047785 103 SLDALIGRLRAAYEENG 119 (174)
Q Consensus 103 SlDALIGRLRAafee~G 119 (174)
+||..|.|||.-+++.+
T Consensus 201 ~i~~~i~rlR~kl~~~~ 217 (240)
T PRK10701 201 SVDVAISRLRKKLLDNA 217 (240)
T ss_pred CHHHHHHHHHHhcccCC
Confidence 68999999999997544
Done!