Query 029090
Match_columns 199
No_of_seqs 71 out of 73
Neff 2.4
Searched_HMMs 46136
Date Fri Mar 29 07:20:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029090.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029090hhsearch_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 3.3E-76 7.2E-81 472.1 10.2 127 38-164 6-132 (132)
2 PF08821 CGGC: CGGC domain; I 89.9 0.39 8.4E-06 37.3 3.4 67 61-137 29-98 (107)
3 PF02899 Phage_int_SAM_1: Phag 86.3 0.51 1.1E-05 31.8 1.8 40 54-94 21-60 (84)
4 cd00798 INT_XerDC XerD and Xer 85.2 1.6 3.5E-05 33.6 4.3 69 54-149 21-91 (284)
5 cd00799 INT_Cre Cre recombinas 78.6 9.8 0.00021 30.7 6.7 77 54-162 6-82 (287)
6 PRK00283 xerD site-specific ty 78.6 2.9 6.3E-05 33.2 3.7 68 55-150 30-99 (299)
7 COG1080 PtsA Phosphoenolpyruva 78.3 2.1 4.6E-05 42.3 3.3 41 120-160 305-367 (574)
8 TIGR02225 recomb_XerD tyrosine 77.2 4.4 9.6E-05 31.6 4.3 70 53-150 19-90 (291)
9 TIGR02224 recomb_XerC tyrosine 69.5 9.8 0.00021 29.8 4.5 69 56-150 22-92 (295)
10 TIGR01418 PEP_synth phosphoeno 60.3 15 0.00033 36.8 4.9 42 127-168 547-618 (782)
11 PRK11061 fused phosphoenolpyru 55.4 18 0.00039 36.0 4.5 35 125-159 475-530 (748)
12 PF02896 PEP-utilizers_C: PEP- 51.6 22 0.00048 31.8 4.1 46 123-168 58-128 (293)
13 PF05528 Coronavirus_5: Corona 50.5 2.7 5.9E-05 32.4 -1.5 19 144-162 4-25 (82)
14 PF00539 Tat: Transactivating 50.3 7.5 0.00016 29.0 0.8 16 166-181 45-60 (68)
15 cd01185 INT_Tn4399 Tn4399 and 49.9 34 0.00075 27.6 4.6 68 58-150 44-115 (299)
16 PRK10529 DNA-binding transcrip 46.7 17 0.00036 27.7 2.2 17 125-141 191-207 (225)
17 smart00259 ZnF_A20 A20-like zi 44.7 11 0.00024 23.2 0.8 16 101-116 7-22 (26)
18 PRK09279 pyruvate phosphate di 41.0 27 0.00059 36.0 3.4 25 144-168 658-685 (879)
19 TIGR01417 PTS_I_fam phosphoeno 40.9 29 0.00063 33.5 3.4 44 125-168 308-375 (565)
20 PF13276 HTH_21: HTH-like doma 40.6 41 0.00088 22.4 3.1 29 127-160 4-32 (60)
21 PRK00236 xerC site-specific ty 40.3 61 0.0013 25.4 4.5 69 55-150 31-101 (297)
22 PF00486 Trans_reg_C: Transcri 38.9 31 0.00067 22.9 2.4 21 124-144 44-64 (77)
23 PRK10816 DNA-binding transcrip 37.6 25 0.00054 26.8 2.0 26 115-140 171-204 (223)
24 TIGR01828 pyru_phos_dikin pyru 36.9 21 0.00046 36.4 1.9 26 143-168 651-679 (856)
25 PF14768 RPA_interact_C: Repli 36.8 33 0.00071 25.1 2.4 35 114-148 18-56 (82)
26 cd08781 Death_UNC5-like Death 35.6 25 0.00054 25.8 1.6 23 121-143 51-76 (83)
27 cd00801 INT_P4 Bacteriophage P 35.5 35 0.00077 27.9 2.6 26 124-150 135-163 (357)
28 PF00140 Sigma70_r1_2: Sigma-7 34.3 27 0.00059 22.2 1.5 13 152-164 2-14 (37)
29 smart00243 GAS2 Growth-Arrest- 34.1 27 0.00057 26.6 1.6 15 58-72 55-69 (73)
30 smart00862 Trans_reg_C Transcr 33.4 42 0.00091 22.1 2.3 19 124-142 45-63 (78)
31 PF10865 DUF2703: Domain of un 32.4 24 0.00052 28.3 1.2 43 83-145 2-44 (120)
32 cd08793 Death_IRAK4 Death doma 31.9 24 0.00051 27.9 1.0 64 58-143 23-86 (100)
33 KOG4670 Uncharacterized conser 30.6 34 0.00074 34.3 2.1 59 54-112 468-544 (602)
34 COG4974 XerD Site-specific rec 30.2 27 0.00058 32.2 1.3 38 56-95 31-69 (300)
35 PLN02837 threonine-tRNA ligase 29.3 41 0.00088 32.6 2.3 15 120-134 489-503 (614)
36 PF01488 Shikimate_DH: Shikima 29.2 38 0.00082 25.9 1.7 17 2-18 18-34 (135)
37 KOG1452 Predicted Rho GTPase-a 27.4 34 0.00073 33.0 1.4 30 132-162 233-270 (442)
38 PRK11177 phosphoenolpyruvate-p 27.3 57 0.0012 31.9 2.9 44 125-168 309-376 (575)
39 PF02187 GAS2: Growth-Arrest-S 27.0 16 0.00034 27.6 -0.7 13 59-71 56-68 (73)
40 PRK12548 shikimate 5-dehydroge 26.4 35 0.00076 29.5 1.2 21 123-143 256-276 (289)
41 PF12067 Sox_C_TAD: Sox C-term 25.6 39 0.00084 29.3 1.3 13 57-69 141-153 (197)
42 cd04372 RhoGAP_chimaerin RhoGA 24.6 61 0.0013 26.4 2.2 36 128-163 45-87 (194)
43 PF13495 Phage_int_SAM_4: Phag 23.9 18 0.00039 24.5 -0.8 54 57-139 24-77 (85)
44 PF09958 DUF2192: Uncharacteri 23.0 71 0.0015 28.6 2.5 21 125-145 27-47 (231)
45 cd00383 trans_reg_C Effector d 22.9 73 0.0016 21.8 2.1 20 124-143 62-81 (95)
46 PF11709 Mit_ribos_Mrp51: Mito 22.9 66 0.0014 29.0 2.3 66 45-110 145-229 (312)
47 PF09674 DUF2400: Protein of u 22.7 77 0.0017 27.8 2.6 25 120-144 24-48 (232)
48 PTZ00398 phosphoenolpyruvate c 22.6 1.2E+02 0.0027 31.8 4.4 42 123-164 264-336 (974)
49 cd00778 ProRS_core_arch_euk Pr 22.2 63 0.0014 27.5 2.0 17 119-135 244-260 (261)
50 COG4865 Glutamate mutase epsil 21.7 63 0.0014 31.5 2.0 23 129-151 196-218 (485)
51 PRK06464 phosphoenolpyruvate s 21.7 56 0.0012 33.1 1.8 25 144-168 596-625 (795)
52 PF10520 Kua-UEV1_localn: Kua- 21.7 44 0.00095 28.4 0.9 24 122-145 17-41 (178)
53 PHA03019 hypothetical protein; 21.2 64 0.0014 24.7 1.6 21 56-76 45-65 (77)
54 PF04221 RelB: RelB antitoxin; 20.9 1.5E+02 0.0033 21.4 3.5 39 128-176 11-49 (83)
55 COG0745 OmpR Response regulato 20.7 79 0.0017 26.8 2.3 37 108-144 168-212 (229)
56 PF01754 zf-A20: A20-like zinc 20.7 39 0.00085 20.8 0.3 16 100-115 5-20 (25)
57 PF06480 FtsH_ext: FtsH Extrac 20.5 1.3E+02 0.0027 20.7 2.9 26 123-148 84-109 (110)
58 TIGR02384 RelB_DinJ addiction 20.5 1.8E+02 0.0038 21.5 3.8 39 128-176 12-50 (83)
59 PRK11235 bifunctional antitoxi 20.1 1.6E+02 0.0036 22.1 3.6 37 128-174 11-47 (80)
60 PRK06940 short chain dehydroge 20.1 61 0.0013 26.8 1.4 17 2-18 8-24 (275)
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=3.3e-76 Score=472.10 Aligned_cols=127 Identities=74% Similarity=1.335 Sum_probs=121.4
Q ss_pred CCCCCCCCCCCChhhhhhhhhhhHHHHHHHhcCCCcccCCCCccchhhhhheeccCCceeeecccccCcCCCCCCCCCCC
Q 029090 38 QPQPQPHPVPLSRYESQKRRDWNTFGQYLKNQRPPVSLSQCSCNHVLDFLRYLDQFGKTKVHLHGCVFFGQPDPPAPCTC 117 (199)
Q Consensus 38 ~~~~~~~~~~~SrYesQKrrdWntf~qyL~n~rPPlsLs~cs~~hVleFLrylDqfGkTkVH~~~C~ffg~p~ppapC~C 117 (199)
+....++++++||||+|||||||||+|||+||+||++|++|+++|||+||+|+|||||||||.++|+|||+|+||+||+|
T Consensus 6 ~~~~~~~~~~~SrYesQKrrdwntf~qyL~n~rPP~~L~~csg~hVl~FL~~~d~~GkTkVh~~~C~~~g~~~~p~~C~C 85 (132)
T PF04852_consen 6 ETSSRSPQPAPSRYESQKRRDWNTFGQYLRNHRPPLSLSRCSGNHVLEFLRYLDQFGKTKVHGQGCPFFGHPSPPAPCPC 85 (132)
T ss_pred cCCCCCCCCCCcccchhhhHHHHHHHHHHHccCCCcchhhcChHHHHHHHHHHhccCCeeecCCCCCCCCCCCCCCCCCC
Confidence 34444555688999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhhhcchhHHHHHHHHHHHHHhCCCCCCCCCCcchhHHHHHHHHHH
Q 029090 118 PLRQAWGSLDALIGRLRAAYEEHGGSPETNPFGNGAIRVYLREVREC 164 (199)
Q Consensus 118 PlRQAwGSLDALIGRLRAafeE~Gg~pE~NPF~araVRlYLReVRd~ 164 (199)
|||||||||||||||||||||||||+||+|||+++|||+|||||||+
T Consensus 86 PlrqAwGSlDalIGrLraafee~Gg~pe~NPf~~~~vr~yLr~vr~~ 132 (132)
T PF04852_consen 86 PLRQAWGSLDALIGRLRAAFEEHGGHPEANPFAARAVRLYLREVRDS 132 (132)
T ss_pred cHHHHhccHHHHHHHHHHHHHHhCCCCCCCchhhHHHHHHHHHHhcC
Confidence 99999999999999999999999999999999999999999999985
No 2
>PF08821 CGGC: CGGC domain; InterPro: IPR014925 Proteins in this entry are a quite highly conserved sequence of CGGC in its central region. The region has many conserved cysteines and histidines suggestive of a zinc binding function.
Probab=89.89 E-value=0.39 Score=37.28 Aligned_cols=67 Identities=21% Similarity=0.510 Sum_probs=49.4
Q ss_pred HHHHHHHhcCCCcccCCCC---ccchhhhhheeccCCceeeecccccCcCCCCCCCCCCCchhhhcchhHHHHHHHHHHH
Q 029090 61 TFGQYLKNQRPPVSLSQCS---CNHVLDFLRYLDQFGKTKVHLHGCVFFGQPDPPAPCTCPLRQAWGSLDALIGRLRAAY 137 (199)
Q Consensus 61 tf~qyL~n~rPPlsLs~cs---~~hVleFLrylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQAwGSLDALIGRLRAaf 137 (199)
.|.+|=.+..--+.+.+|. +..|+..+..+-..|-..||..+|.+.+.+.+ +||. +|.|+-.|+++|
T Consensus 29 ~F~~y~~~~~elvgf~~CgGCpg~~~~~~~~~l~~~~~d~IHlssC~~~~~~~~----~CP~------~~~~~~~I~~~~ 98 (107)
T PF08821_consen 29 AFARYDDEDVELVGFFTCGGCPGRKLVRRIKKLKKNGADVIHLSSCMVKGNPHG----PCPH------IDEIKKIIEEKF 98 (107)
T ss_pred ccccCCCCCeEEEEEeeCCCCChhHHHHHHHHHHHCCCCEEEEcCCEecCCCCC----CCCC------HHHHHHHHHHHh
Confidence 3444443223334455655 57888888888899999999999999887654 6665 899999999887
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=86.30 E-value=0.51 Score=31.79 Aligned_cols=40 Identities=30% Similarity=0.483 Sum_probs=31.1
Q ss_pred hhhhhhhHHHHHHHhcCCCcccCCCCccchhhhhheeccCC
Q 029090 54 QKRRDWNTFGQYLKNQRPPVSLSQCSCNHVLDFLRYLDQFG 94 (199)
Q Consensus 54 QKrrdWntf~qyL~n~rPPlsLs~cs~~hVleFLrylDqfG 94 (199)
.-+++++.|.+||.+ ....++..++..||.+||.++-+.|
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 6677778899999999999977655
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=85.17 E-value=1.6 Score=33.65 Aligned_cols=69 Identities=22% Similarity=0.259 Sum_probs=48.1
Q ss_pred hhhhhhhHHHHHHHhcCCCcccCCCCccchhhhhheeccCCceeeecccccCcCCCCCCCCCCCchhhhcchhHHHHHHH
Q 029090 54 QKRRDWNTFGQYLKNQRPPVSLSQCSCNHVLDFLRYLDQFGKTKVHLHGCVFFGQPDPPAPCTCPLRQAWGSLDALIGRL 133 (199)
Q Consensus 54 QKrrdWntf~qyL~n~rPPlsLs~cs~~hVleFLrylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQAwGSLDALIGRL 133 (199)
+-+..|+.|.+|+.....+. +..-+..||.+|+.++...| ....++...++-|
T Consensus 21 ~~~~~~~~~~~~~~~~~~~~-~~~l~~~~i~~~~~~~~~~~--------------------------~~~~t~~~~~~~l 73 (284)
T cd00798 21 AYRRDLERFLEFLEERGILF-PADVTPDDIRRFLAELKDQG--------------------------LSARSIARKLSAL 73 (284)
T ss_pred HHHHHHHHHHHHHHHcCCCc-hhhCCHHHHHHHHHHhhhcC--------------------------CCHHHHHHHHHHH
Confidence 34567899999998754333 56677899999999876543 2335778888888
Q ss_pred HHHHHHhC--CCCCCCCC
Q 029090 134 RAAYEEHG--GSPETNPF 149 (199)
Q Consensus 134 RAafeE~G--g~pE~NPF 149 (199)
+++|.-.. +..+.||+
T Consensus 74 ~~~~~~~~~~~~~~~~p~ 91 (284)
T cd00798 74 RSFFKFLLREGLILANPA 91 (284)
T ss_pred HHHHHHHHHcCCccCChh
Confidence 88887432 34556887
No 5
>cd00799 INT_Cre Cre recombinase, C-terminal catalytic domain. Cre-like recombinases belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The bacteriophage P1 Cre recombinase maintains the circular phage replicon in a monomeric state by catalyzing a site-specific recombination between two loxP sites. The catalytic core domain of Cre recombinase is linked to a more divergent helical N-terminal domain, which interacts primarily with the DNA major groove proximal to the crossover region.
Probab=78.65 E-value=9.8 Score=30.70 Aligned_cols=77 Identities=19% Similarity=0.269 Sum_probs=52.5
Q ss_pred hhhhhhhHHHHHHHhcCCCcccCCCCccchhhhhheeccCCceeeecccccCcCCCCCCCCCCCchhhhcchhHHHHHHH
Q 029090 54 QKRRDWNTFGQYLKNQRPPVSLSQCSCNHVLDFLRYLDQFGKTKVHLHGCVFFGQPDPPAPCTCPLRQAWGSLDALIGRL 133 (199)
Q Consensus 54 QKrrdWntf~qyL~n~rPPlsLs~cs~~hVleFLrylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQAwGSLDALIGRL 133 (199)
.-..+++.|..|+..+. +....-+..+|.+||.||.+ ..+..++-..++.|
T Consensus 6 ~y~~~l~~f~~~~~~~~--~~~~~~~~~~i~~~~~~l~~---------------------------~~s~~ti~~~~~~l 56 (287)
T cd00799 6 AYLSDWRRFAAWCQAHG--RTPLPASPETVTLYLTDLAD---------------------------SLAPSTISRRLSAL 56 (287)
T ss_pred HHHHHHHHHHHHHHhcC--CCCCCCCHHHHHHHHHHHHh---------------------------ccChHHHHHHHHHH
Confidence 34568889999998752 12222357999999998742 12457888999999
Q ss_pred HHHHHHhCCCCCCCCCCcchhHHHHHHHH
Q 029090 134 RAAYEEHGGSPETNPFGNGAIRVYLREVR 162 (199)
Q Consensus 134 RAafeE~Gg~pE~NPF~araVRlYLReVR 162 (199)
+.+|+..+. .||+....+..-|+.++
T Consensus 57 ~~~~~~~~~---~~p~~~~~~~~~~~~~~ 82 (287)
T cd00799 57 SQLHRRSGL---PSPADSPLVRLVLRGIR 82 (287)
T ss_pred HHHHHHcCC---CCCccCHHHHHHHHHHH
Confidence 999985432 58877655665565554
No 6
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed
Probab=78.59 E-value=2.9 Score=33.21 Aligned_cols=68 Identities=25% Similarity=0.302 Sum_probs=47.9
Q ss_pred hhhhhhHHHHHHHhcCCCcccCCCCccchhhhhheeccCCceeeecccccCcCCCCCCCCCCCchhhhcchhHHHHHHHH
Q 029090 55 KRRDWNTFGQYLKNQRPPVSLSQCSCNHVLDFLRYLDQFGKTKVHLHGCVFFGQPDPPAPCTCPLRQAWGSLDALIGRLR 134 (199)
Q Consensus 55 KrrdWntf~qyL~n~rPPlsLs~cs~~hVleFLrylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQAwGSLDALIGRLR 134 (199)
-+.+|+.|..||..+.- .+...+..||.+|+.++.+.+ .+--++...+..|+
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 556678899999998864421 23457788899999
Q ss_pred HHHHHhC--CCCCCCCCC
Q 029090 135 AAYEEHG--GSPETNPFG 150 (199)
Q Consensus 135 AafeE~G--g~pE~NPF~ 150 (199)
++|+-.. +.-..|||.
T Consensus 82 ~~~~~a~~~~~i~~np~~ 99 (299)
T PRK00283 82 RFFQFLLREGLREDDPSA 99 (299)
T ss_pred HHHHHHHHcCCcccCchh
Confidence 9988432 334578874
No 7
>COG1080 PtsA Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]
Probab=78.28 E-value=2.1 Score=42.26 Aligned_cols=41 Identities=39% Similarity=0.605 Sum_probs=33.5
Q ss_pred hhhcchhHHHHHHHHHHHHHhCCC--------------------C-CCCCC-CcchhHHHHHH
Q 029090 120 RQAWGSLDALIGRLRAAYEEHGGS--------------------P-ETNPF-GNGAIRVYLRE 160 (199)
Q Consensus 120 RQAwGSLDALIGRLRAafeE~Gg~--------------------p-E~NPF-~araVRlYLRe 160 (199)
|..|=+.|..----++..|.+||+ | |.||| +-|+||+||..
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 455667788777788888999888 3 79999 89999999964
No 8
>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=77.25 E-value=4.4 Score=31.60 Aligned_cols=70 Identities=26% Similarity=0.426 Sum_probs=47.8
Q ss_pred hhhhhhhhHHHHHHHhcCCCcccCCCCccchhhhhheeccCCceeeecccccCcCCCCCCCCCCCchhhhcchhHHHHHH
Q 029090 53 SQKRRDWNTFGQYLKNQRPPVSLSQCSCNHVLDFLRYLDQFGKTKVHLHGCVFFGQPDPPAPCTCPLRQAWGSLDALIGR 132 (199)
Q Consensus 53 sQKrrdWntf~qyL~n~rPPlsLs~cs~~hVleFLrylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQAwGSLDALIGR 132 (199)
.+-+..++.|..|+.... ..+..-+..||.+|+.++.+.| ...-++...+.-
T Consensus 19 ~~~~~~~~~~~~~~~~~~--~~~~~it~~~i~~~~~~~~~~~--------------------------~~~~t~~~~~~~ 70 (291)
T TIGR02225 19 EAYRRDLEKFLEFLEERG--IDLEEVDRGDIVDFLAELKEAG--------------------------LSARSIARALSA 70 (291)
T ss_pred HHHHHHHHHHHHHHHhcC--CChHHCCHHHHHHHHHHhhcCC--------------------------CCHhHHHHHHHH
Confidence 445567888999998542 2445567899999998876543 122467889999
Q ss_pred HHHHHHHh--CCCCCCCCCC
Q 029090 133 LRAAYEEH--GGSPETNPFG 150 (199)
Q Consensus 133 LRAafeE~--Gg~pE~NPF~ 150 (199)
|+++|+-. -+..+.|||.
T Consensus 71 l~~~~~~a~~~~~~~~np~~ 90 (291)
T TIGR02225 71 LRSFYRFLLREGIREDDPSA 90 (291)
T ss_pred HHHHHHHHHhcccccCCchh
Confidence 99999732 2345578874
No 9
>TIGR02224 recomb_XerC tyrosine recombinase XerC. The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerC, one of two closely related chromosomal proteins along with XerD (TIGR02225). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and homologs of XerC on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerC, as some apparent XerC examples score in the gray zone between trusted (450) and noise (410) cutoffs, along with some XerD examples. XerC and XerD interact with cell division protein FtsK.
Probab=69.46 E-value=9.8 Score=29.85 Aligned_cols=69 Identities=28% Similarity=0.370 Sum_probs=47.2
Q ss_pred hhhhhHHHHHHHhcCCCcccCCCCccchhhhhheeccCCceeeecccccCcCCCCCCCCCCCchhhhcchhHHHHHHHHH
Q 029090 56 RRDWNTFGQYLKNQRPPVSLSQCSCNHVLDFLRYLDQFGKTKVHLHGCVFFGQPDPPAPCTCPLRQAWGSLDALIGRLRA 135 (199)
Q Consensus 56 rrdWntf~qyL~n~rPPlsLs~cs~~hVleFLrylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQAwGSLDALIGRLRA 135 (199)
+.+++.|.+||........+..-+..||.+||.++.+.| .+..++...+..|++
T Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~l~~~~i~~~~~~~~~~~--------------------------~~~~T~~~~~~~l~~ 75 (295)
T TIGR02224 22 RRDLKAFLEFLEEEGGLASLAEVTAADLRSFLAELHARG--------------------------LSRRSLARKLSALRS 75 (295)
T ss_pred HHHHHHHHHHHHhcCCCCccccCcHHHHHHHHHHhcccC--------------------------CCHHHHHHHHHHHHH
Confidence 346677888888866567788888999999998865521 123567777888888
Q ss_pred HHHHhC--CCCCCCCCC
Q 029090 136 AYEEHG--GSPETNPFG 150 (199)
Q Consensus 136 afeE~G--g~pE~NPF~ 150 (199)
+|.-.. +.-+.|||.
T Consensus 76 ~~~~a~~~~~~~~np~~ 92 (295)
T TIGR02224 76 FYRFLVRRGLIKANPAA 92 (295)
T ss_pred HHHHHHHcCccccChHh
Confidence 877432 233468863
No 10
>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=60.26 E-value=15 Score=36.75 Aligned_cols=42 Identities=21% Similarity=0.240 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHhCCC-------------------------CCCCCC-CcchhHHHH----HHHHHHHHhh
Q 029090 127 DALIGRLRAAYEEHGGS-------------------------PETNPF-GNGAIRVYL----REVRECQAKA 168 (199)
Q Consensus 127 DALIGRLRAafeE~Gg~-------------------------pE~NPF-~araVRlYL----ReVRd~QAkA 168 (199)
|.+.-.+|.+++.++++ .|.||| +.|.||+|| .++=+.|.+|
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 55566777777776544 378999 899999999 5566677655
No 11
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=55.38 E-value=18 Score=36.03 Aligned_cols=35 Identities=23% Similarity=0.341 Sum_probs=29.3
Q ss_pred hhHHHHHHHHHHHHHhCCC--------------------CCCCCC-CcchhHHHHH
Q 029090 125 SLDALIGRLRAAYEEHGGS--------------------PETNPF-GNGAIRVYLR 159 (199)
Q Consensus 125 SLDALIGRLRAafeE~Gg~--------------------pE~NPF-~araVRlYLR 159 (199)
+-|......|.+.+.++++ +|.||| |.|+||+||.
T Consensus 475 ~e~eQ~~~y~~~~~~~~~~pv~iRtlDiGgDK~~~~~~~~E~NP~lG~RgiR~~l~ 530 (748)
T PRK11061 475 SEEEQVAQYQGMLQMFPDKPVTLRTLDIGADKQLPYMPISEENPCLGWRGIRITLD 530 (748)
T ss_pred CHHHHHHHHHHHHHHcCCCeEEEECCCCCcCCCCCCCCCCCCCcccccchhhcccc
Confidence 4677888889888888765 589999 7899999984
No 12
>PF02896 PEP-utilizers_C: PEP-utilising enzyme, TIM barrel domain; InterPro: IPR000121 A number of enzymes that catalyze the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) via a phospho-histidine intermediate have been shown to be structurally related [, , , ]. All these enzymes share the same catalytic mechanism: they bind PEP and transfer the phosphoryl group from it to a histidine residue. The sequence around that residue is highly conserved. This domain is often found associated with the pyruvate phosphate dikinase, PEP/pyruvate-binding domain (IPR002192 from INTERPRO) at its N terminus and the PEP-utilizing enzyme mobile domain.; GO: 0016772 transferase activity, transferring phosphorus-containing groups, 0016310 phosphorylation; PDB: 2HRO_A 2OLS_A 2DIK_A 2R82_A 1JDE_A 1DIK_A 1GGO_A 1KBL_A 1KC7_A 2BG5_B ....
Probab=51.58 E-value=22 Score=31.83 Aligned_cols=46 Identities=30% Similarity=0.260 Sum_probs=33.8
Q ss_pred cchhHHHHHHHHHHHHHhCCC----------------------CCCCCC-CcchhHHHHHH--HHHHHHhh
Q 029090 123 WGSLDALIGRLRAAYEEHGGS----------------------PETNPF-GNGAIRVYLRE--VRECQAKA 168 (199)
Q Consensus 123 wGSLDALIGRLRAafeE~Gg~----------------------pE~NPF-~araVRlYLRe--VRd~QAkA 168 (199)
+=+.|.+...++.+.+.++++ .|.||| |-|.||+||.. +=+.|.+|
T Consensus 58 ~p~e~eq~~~y~~i~~~~~~~pV~iRtlD~g~dK~l~~~~~~~~E~NP~LG~RGiR~~l~~p~~f~~QlrA 128 (293)
T PF02896_consen 58 PPSEEEQYEIYRKIAEAMGGKPVTIRTLDIGGDKPLPYLSREPKEENPALGLRGIRRSLAHPELFRTQLRA 128 (293)
T ss_dssp HHHHHHHHHHHHHHHHHTTTSEEEEE---SBCCCGSCSSHHCH--SSGGGSSBTHHHHHHSHHHHHHHHHH
T ss_pred CchHHHHHHHHHHHHHHhccCcEEEEecCCCCCccCCcccccccccccccccccccccccchhhHHHHHHH
Confidence 446788888999999988876 569998 88999999975 33444443
No 13
>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=50.52 E-value=2.7 Score=32.39 Aligned_cols=19 Identities=42% Similarity=0.621 Sum_probs=15.0
Q ss_pred CCCCCC---CcchhHHHHHHHH
Q 029090 144 PETNPF---GNGAIRVYLREVR 162 (199)
Q Consensus 144 pE~NPF---~araVRlYLReVR 162 (199)
..+||| .||-+|+||||=-
T Consensus 4 ~k~NPfr~aiARKaRiyLr~Gl 25 (82)
T PF05528_consen 4 SKDNPFRGAIARKARIYLREGL 25 (82)
T ss_pred cccCchhhhhhhheeeeeecCC
Confidence 358999 4788999999743
No 14
>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=50.25 E-value=7.5 Score=29.03 Aligned_cols=16 Identities=31% Similarity=0.706 Sum_probs=13.0
Q ss_pred HhhhCCchhhhhhhcc
Q 029090 166 AKARGIPYKKKKKKKY 181 (199)
Q Consensus 166 AkARgi~y~kkk~k~~ 181 (199)
-|+-||.|..|||||.
T Consensus 45 ~KgLGI~Y~r~rrRrr 60 (68)
T PF00539_consen 45 QKGLGISYGRKRRRRR 60 (68)
T ss_dssp CTSSSTSSSSSSCSCC
T ss_pred eCCCcccccccccCcC
Confidence 4788999999988663
No 15
>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=49.95 E-value=34 Score=27.65 Aligned_cols=68 Identities=12% Similarity=0.249 Sum_probs=44.4
Q ss_pred hhhHHHHHHHhcCC--CcccCCCCccchhhhhheeccCCceeeecccccCcCCCCCCCCCCCchhhhcchhHHHHHHHHH
Q 029090 58 DWNTFGQYLKNQRP--PVSLSQCSCNHVLDFLRYLDQFGKTKVHLHGCVFFGQPDPPAPCTCPLRQAWGSLDALIGRLRA 135 (199)
Q Consensus 58 dWntf~qyL~n~rP--PlsLs~cs~~hVleFLrylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQAwGSLDALIGRLRA 135 (199)
.++.|..||....+ .+.+..-+..||.+|+.|+-+.. ...-.++...+.-||+
T Consensus 44 ~~~~~~~~~~~~~~~~~~~l~~i~~~~i~~~~~~l~~~~-------------------------~~s~~t~~~~~~~l~~ 98 (299)
T cd01185 44 HLKNLREFIECTYKEIDIALLELTREFILEFKLFLRKEK-------------------------KLSRNTAVHYLSWLKK 98 (299)
T ss_pred HHHHHHHHHHHhcCccCCCHHHccHHHHHHHHHHHhhcc-------------------------CcCcccHHHHHHHHHH
Confidence 46678888876554 67788888999999999872110 1223456677777888
Q ss_pred HHHHh--CCCCCCCCCC
Q 029090 136 AYEEH--GGSPETNPFG 150 (199)
Q Consensus 136 afeE~--Gg~pE~NPF~ 150 (199)
+|.-. .+.-..|||.
T Consensus 99 ~~~~a~~~~~i~~np~~ 115 (299)
T cd01185 99 LLKIAYRDKGLRDNPFA 115 (299)
T ss_pred HHHHHHHCcCccCCCcc
Confidence 77743 2333456774
No 16
>PRK10529 DNA-binding transcriptional activator KdpE; Provisional
Probab=46.72 E-value=17 Score=27.67 Aligned_cols=17 Identities=29% Similarity=0.450 Sum_probs=13.6
Q ss_pred hhHHHHHHHHHHHHHhC
Q 029090 125 SLDALIGRLRAAYEEHG 141 (199)
Q Consensus 125 SLDALIGRLRAafeE~G 141 (199)
+||.+|.|||.-+++.+
T Consensus 191 ~~~~~i~rlR~kl~~~~ 207 (225)
T PRK10529 191 YLRIYMGHLRQKLEQDP 207 (225)
T ss_pred CHHHHHHHHHHHhccCC
Confidence 58999999999887544
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=44.67 E-value=11 Score=23.18 Aligned_cols=16 Identities=44% Similarity=1.105 Sum_probs=13.7
Q ss_pred ccccCcCCCCCCCCCC
Q 029090 101 HGCVFFGQPDPPAPCT 116 (199)
Q Consensus 101 ~~C~ffg~p~ppapC~ 116 (199)
.+|.|||.|..-..|.
T Consensus 7 ~~CgF~G~~~t~~~Cs 22 (26)
T smart00259 7 PGCGFFGNPATEGLCS 22 (26)
T ss_pred CCCCCcCChhhcccCH
Confidence 6999999998877775
No 18
>PRK09279 pyruvate phosphate dikinase; Provisional
Probab=41.04 E-value=27 Score=35.96 Aligned_cols=25 Identities=40% Similarity=0.557 Sum_probs=21.5
Q ss_pred CCCCCC-CcchhHHHH--HHHHHHHHhh
Q 029090 144 PETNPF-GNGAIRVYL--REVRECQAKA 168 (199)
Q Consensus 144 pE~NPF-~araVRlYL--ReVRd~QAkA 168 (199)
-|.||| +.|.+|+|| .|+=++|.+|
T Consensus 658 ~E~NPmLG~RG~Rl~l~~pei~~~QlrA 685 (879)
T PRK09279 658 HEFNPMLGHRGCRLGITYPEIYEMQARA 685 (879)
T ss_pred CCCCCccccchhhcccCChHHHHHHHHH
Confidence 489999 889999999 5777888877
No 19
>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=40.89 E-value=29 Score=33.55 Aligned_cols=44 Identities=27% Similarity=0.417 Sum_probs=32.0
Q ss_pred hhHHHHHHHHHHHHHhCCC---------------------CCCCCC-CcchhHHHHHH--HHHHHHhh
Q 029090 125 SLDALIGRLRAAYEEHGGS---------------------PETNPF-GNGAIRVYLRE--VRECQAKA 168 (199)
Q Consensus 125 SLDALIGRLRAafeE~Gg~---------------------pE~NPF-~araVRlYLRe--VRd~QAkA 168 (199)
+.|...-..|.+.+.++++ .|.||| |-|+||+||.. +=..|.+|
T Consensus 308 ~e~eq~~~y~~i~~~~~~~pv~iRtlDig~DK~~~~~~~~~E~NP~LG~RgiR~~l~~~~lf~~QlrA 375 (565)
T TIGR01417 308 TEEEQFAAYKTVLEAMESDAVIVRTLDIGGDKELPYLNFPKEENPFLGYRAIRLALEREEILRTQLRA 375 (565)
T ss_pred CHHHHHHHHHHHHHHhCCCceEEECCCCCCcccccccCCCCCCCccccchhhhhcccCHHHHHHHHHH
Confidence 4467777788888888766 379998 88999999964 33444433
No 20
>PF13276 HTH_21: HTH-like domain
Probab=40.62 E-value=41 Score=22.39 Aligned_cols=29 Identities=24% Similarity=0.382 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHhCCCCCCCCCCcchhHHHHHH
Q 029090 127 DALIGRLRAAYEEHGGSPETNPFGNGAIRVYLRE 160 (199)
Q Consensus 127 DALIGRLRAafeE~Gg~pE~NPF~araVRlYLRe 160 (199)
|+|+-.++++|+++.+ =||.+-|..+|+.
T Consensus 4 ~~l~~~I~~i~~~~~~-----~yG~rri~~~L~~ 32 (60)
T PF13276_consen 4 EALRELIKEIFKESKP-----TYGYRRIWAELRR 32 (60)
T ss_pred HHHHHHHHHHHHHcCC-----CeehhHHHHHHhc
Confidence 6789999999999976 3788888888876
No 21
>PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=40.33 E-value=61 Score=25.35 Aligned_cols=69 Identities=26% Similarity=0.296 Sum_probs=43.5
Q ss_pred hhhhhhHHHHHHHhcCCCcccCCCCccchhhhhheeccCCceeeecccccCcCCCCCCCCCCCchhhhcchhHHHHHHHH
Q 029090 55 KRRDWNTFGQYLKNQRPPVSLSQCSCNHVLDFLRYLDQFGKTKVHLHGCVFFGQPDPPAPCTCPLRQAWGSLDALIGRLR 134 (199)
Q Consensus 55 KrrdWntf~qyL~n~rPPlsLs~cs~~hVleFLrylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQAwGSLDALIGRLR 134 (199)
-+.+|+.|..|+..... ..+..-+..||.+||.++-+.|. +--++...+.-|+
T Consensus 31 ~~~~~~~~~~~~~~~~~-~~~~~i~~~~i~~~~~~~~~~~~--------------------------~~~t~~~~~~~l~ 83 (297)
T PRK00236 31 YRRDLRAFLAFLEEHGI-SSLQDLDAADLRSFLARRRRQGL--------------------------SARSLARRLSALR 83 (297)
T ss_pred HHHHHHHHHHHHHHcCC-CchhhCCHHHHHHHHHHHHhccc--------------------------ChhHHHHHHHHHH
Confidence 34678889899887543 45666778999999987543211 1125666666677
Q ss_pred HHHHHhC--CCCCCCCCC
Q 029090 135 AAYEEHG--GSPETNPFG 150 (199)
Q Consensus 135 AafeE~G--g~pE~NPF~ 150 (199)
+.|.-.. +.-+.|||.
T Consensus 84 ~~~~~a~~~~~i~~np~~ 101 (297)
T PRK00236 84 SFYRWLVRRGLLKANPAA 101 (297)
T ss_pred HHHHHHHhcccccCCchh
Confidence 7665322 445678874
No 22
>PF00486 Trans_reg_C: Transcriptional regulatory protein, C terminal; InterPro: IPR001867 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain that is almost always found associated with the response regulator receiver domain (see IPR001789 from INTERPRO). It may play a role in DNA binding [].; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2K4J_A 2JPB_A 1ODD_A 1OPC_A 1KGS_A 2PMU_E 2JZY_A 1GXP_B 1QQI_A 2Z33_A ....
Probab=38.86 E-value=31 Score=22.92 Aligned_cols=21 Identities=52% Similarity=0.846 Sum_probs=18.1
Q ss_pred chhHHHHHHHHHHHHHhCCCC
Q 029090 124 GSLDALIGRLRAAYEEHGGSP 144 (199)
Q Consensus 124 GSLDALIGRLRAafeE~Gg~p 144 (199)
-+||.+|-|||..++..|..+
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 489999999999999986543
No 23
>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional
Probab=37.59 E-value=25 Score=26.77 Aligned_cols=26 Identities=27% Similarity=0.470 Sum_probs=18.9
Q ss_pred CCCchhhhcc--------hhHHHHHHHHHHHHHh
Q 029090 115 CTCPLRQAWG--------SLDALIGRLRAAYEEH 140 (199)
Q Consensus 115 C~CPlRQAwG--------SLDALIGRLRAafeE~ 140 (199)
..--+++.|| +||.+|.|||.-+++.
T Consensus 171 ~~~l~~~~w~~~~~~~~~~v~~~i~rLR~kl~~~ 204 (223)
T PRK10816 171 KDSLMLQLYPDAELRESHTIDVLMGRLRKKIQAQ 204 (223)
T ss_pred HHHHHHHhcCCCCCCCcCCHHHHHHHHHHHhccC
Confidence 3334566776 7899999999988764
No 24
>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=36.89 E-value=21 Score=36.42 Aligned_cols=26 Identities=35% Similarity=0.507 Sum_probs=20.6
Q ss_pred CCCCCCC-CcchhHHHH--HHHHHHHHhh
Q 029090 143 SPETNPF-GNGAIRVYL--REVRECQAKA 168 (199)
Q Consensus 143 ~pE~NPF-~araVRlYL--ReVRd~QAkA 168 (199)
..|.||| +.|.||+|| .|+=+.|.+|
T Consensus 651 ~~E~NP~LG~RGiRl~l~~pei~~~QlrA 679 (856)
T TIGR01828 651 LHEVNPMLGHRGCRLGITYPEIYEMQVRA 679 (856)
T ss_pred CCCCCCccccchhhhccCChHHHHHHHHH
Confidence 3599999 889999999 5666667665
No 25
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=36.83 E-value=33 Score=25.13 Aligned_cols=35 Identities=31% Similarity=0.519 Sum_probs=30.2
Q ss_pred CCCCchhhhcc----hhHHHHHHHHHHHHHhCCCCCCCC
Q 029090 114 PCTCPLRQAWG----SLDALIGRLRAAYEEHGGSPETNP 148 (199)
Q Consensus 114 pC~CPlRQAwG----SLDALIGRLRAafeE~Gg~pE~NP 148 (199)
-|+|-|+..-+ ++|.|=-+|..+++||--....+|
T Consensus 18 ~C~Cgl~l~~~~~~~tl~~l~~~L~~~~~~H~~~C~~~p 56 (82)
T PF14768_consen 18 SCSCGLRLNTQQDELTLEELRQLLEEAVTEHSDRCSSTP 56 (82)
T ss_pred ECCCccEEecCCCCCCHHHHHHHHHHHHHHHHHhCCCCC
Confidence 47777888888 999999999999999987776666
No 26
>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=35.64 E-value=25 Score=25.82 Aligned_cols=23 Identities=26% Similarity=0.453 Sum_probs=19.0
Q ss_pred hhcc---hhHHHHHHHHHHHHHhCCC
Q 029090 121 QAWG---SLDALIGRLRAAYEEHGGS 143 (199)
Q Consensus 121 QAwG---SLDALIGRLRAafeE~Gg~ 143 (199)
.-|. +-|.-|+.|..+|+|+|..
T Consensus 51 ~~We~~~~~~~tv~~L~~~L~~mgr~ 76 (83)
T cd08781 51 DLWEARHRDDGALNDLAQILEEMGRT 76 (83)
T ss_pred HHHHhcCCCcchHHHHHHHHHHcCcH
Confidence 4574 4589999999999999975
No 27
>cd00801 INT_P4 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall reaction mechanism with the superfamily of DNA breaking-rejoining enzymes. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes.
Probab=35.46 E-value=35 Score=27.85 Aligned_cols=26 Identities=23% Similarity=0.333 Sum_probs=20.0
Q ss_pred chhHHHHHHHHHHHHH---hCCCCCCCCCC
Q 029090 124 GSLDALIGRLRAAYEE---HGGSPETNPFG 150 (199)
Q Consensus 124 GSLDALIGRLRAafeE---~Gg~pE~NPF~ 150 (199)
-++...+..|+++|+- +|.- +.|||.
T Consensus 135 ~t~~~~~~~l~~~~~~a~~~g~i-~~nP~~ 163 (357)
T cd00801 135 ETARRVRQRLKQVFRYAIARGLI-EANPAA 163 (357)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCc-ccCchH
Confidence 4788999999999984 4443 489985
No 28
>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=34.27 E-value=27 Score=22.22 Aligned_cols=13 Identities=31% Similarity=0.784 Sum_probs=10.4
Q ss_pred chhHHHHHHHHHH
Q 029090 152 GAIRVYLREVREC 164 (199)
Q Consensus 152 raVRlYLReVRd~ 164 (199)
-+|++||++|+..
T Consensus 2 D~l~~Yl~ei~~~ 14 (37)
T PF00140_consen 2 DSLRLYLKEIGRY 14 (37)
T ss_dssp HHHHHHHHHHHHS
T ss_pred cHHHHHHHHHcCC
Confidence 4789999999753
No 29
>smart00243 GAS2 Growth-Arrest-Specific Protein 2 Domain. GROWTH-ARREST-SPECIFIC PROTEIN 2 Domain
Probab=34.15 E-value=27 Score=26.58 Aligned_cols=15 Identities=33% Similarity=0.831 Sum_probs=13.3
Q ss_pred hhhHHHHHHHhcCCC
Q 029090 58 DWNTFGQYLKNQRPP 72 (199)
Q Consensus 58 dWntf~qyL~n~rPP 72 (199)
-|.||.+||..|.|=
T Consensus 55 GW~tL~~fL~khDPC 69 (73)
T smart00243 55 GWETLDEYLLKHDPC 69 (73)
T ss_pred cHHHHHHHHHhCCCc
Confidence 499999999999883
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=33.45 E-value=42 Score=22.15 Aligned_cols=19 Identities=42% Similarity=0.695 Sum_probs=17.1
Q ss_pred chhHHHHHHHHHHHHHhCC
Q 029090 124 GSLDALIGRLRAAYEEHGG 142 (199)
Q Consensus 124 GSLDALIGRLRAafeE~Gg 142 (199)
.+|+.+|-|||..+++.|+
T Consensus 45 ~~l~~~i~~LR~~l~~~~~ 63 (78)
T smart00862 45 NTLDVHISRLRKKLEDDGA 63 (78)
T ss_pred chHHHHHHHHHHHHhcCCC
Confidence 6799999999999998765
No 31
>PF10865 DUF2703: Domain of unknown function (DUF2703); InterPro: IPR021219 This family of protein has no known function.
Probab=32.41 E-value=24 Score=28.28 Aligned_cols=43 Identities=26% Similarity=0.375 Sum_probs=32.9
Q ss_pred hhhhhheeccCCceeeecccccCcCCCCCCCCCCCchhhhcchhHHHHHHHHHHHHHhCCCCC
Q 029090 83 VLDFLRYLDQFGKTKVHLHGCVFFGQPDPPAPCTCPLRQAWGSLDALIGRLRAAYEEHGGSPE 145 (199)
Q Consensus 83 VleFLrylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQAwGSLDALIGRLRAafeE~Gg~pE 145 (199)
+|+|+ |||..|+| |. +| ...+.+|+..+-+|+.+|+..|..++
T Consensus 2 ~I~w~-~l~~~g~t------C~---------RC----~~Tg~~L~~av~~l~~~L~~~Giev~ 44 (120)
T PF10865_consen 2 VIEWQ-HLDLDGKT------CE---------RC----GDTGETLREAVKELAPVLAPLGIEVR 44 (120)
T ss_pred eEEEE-EeecCCCc------CC---------ch----hhHHHHHHHHHHHHHHHHHhCCcEEE
Confidence 47887 55555876 43 22 57788999999999999999998754
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=31.88 E-value=24 Score=27.87 Aligned_cols=64 Identities=25% Similarity=0.413 Sum_probs=43.2
Q ss_pred hhhHHHHHHHhcCCCcccCCCCccchhhhhheeccCCceeeecccccCcCCCCCCCCCCCchhhhcchhHHHHHHHHHHH
Q 029090 58 DWNTFGQYLKNQRPPVSLSQCSCNHVLDFLRYLDQFGKTKVHLHGCVFFGQPDPPAPCTCPLRQAWGSLDALIGRLRAAY 137 (199)
Q Consensus 58 dWntf~qyL~n~rPPlsLs~cs~~hVleFLrylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQAwGSLDALIGRLRAaf 137 (199)
+|.++-.++.. |-.-.+.+--||-+|= .|...| .+| +|-|=..||+-++-||.|-..|
T Consensus 23 ~W~~LA~~i~~---~~~~~~y~~~ei~~ie--------------~~~~~g-~SP----T~~LL~dWgt~N~TV~~L~~lL 80 (100)
T cd08793 23 GWKKIAVAIKK---PSGDPRYSQFHIRRFE--------------ALVQQG-KSP----TCELLFDWGTTNCTVGDLVDLL 80 (100)
T ss_pred cHHHHHHHHhc---ccCCCCCCHHHHHHHH--------------HHHHcC-CCh----HHHHHHHHccCCCcHHHHHHHH
Confidence 88888887765 2222333334555553 344443 333 5777889999999999999999
Q ss_pred HHhCCC
Q 029090 138 EEHGGS 143 (199)
Q Consensus 138 eE~Gg~ 143 (199)
.+++-.
T Consensus 81 ~k~~l~ 86 (100)
T cd08793 81 IQNEFF 86 (100)
T ss_pred HHcccH
Confidence 998843
No 33
>KOG4670 consensus Uncharacterized conserved membrane protein [Function unknown]
Probab=30.62 E-value=34 Score=34.34 Aligned_cols=59 Identities=27% Similarity=0.404 Sum_probs=41.6
Q ss_pred hhhhhhhH------------HHHHHHhcCCCcccCCCCccchhhhhheeccCCce-----eee-cccccCcCCCCCC
Q 029090 54 QKRRDWNT------------FGQYLKNQRPPVSLSQCSCNHVLDFLRYLDQFGKT-----KVH-LHGCVFFGQPDPP 112 (199)
Q Consensus 54 QKrrdWnt------------f~qyL~n~rPPlsLs~cs~~hVleFLrylDqfGkT-----kVH-~~~C~ffg~p~pp 112 (199)
-|+|.|++ ||-||..|.+|..+--=.-.---.||+-+++.-++ .|| ...|.+-.-.+||
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 57777864 99999999999887632122225677888888666 345 4668877777774
No 34
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair]
Probab=30.25 E-value=27 Score=32.24 Aligned_cols=38 Identities=24% Similarity=0.514 Sum_probs=33.2
Q ss_pred hhhhhHHHHHHHhcCCCc-ccCCCCccchhhhhheeccCCc
Q 029090 56 RRDWNTFGQYLKNQRPPV-SLSQCSCNHVLDFLRYLDQFGK 95 (199)
Q Consensus 56 rrdWntf~qyL~n~rPPl-sLs~cs~~hVleFLrylDqfGk 95 (199)
|||-+.|.+||..+- + +|...+..||.+||.++-.+|.
T Consensus 31 rrDL~~f~~~L~~~~--~~~l~~~~~~di~~yl~~l~~~g~ 69 (300)
T COG4974 31 RRDLEDFREWLEERG--ITDLADATEADIREYLTELAEQGL 69 (300)
T ss_pred HHHHHHHHHHHHhcC--CCChhhcCHHHHHHHHHHHHhCCc
Confidence 689999999999885 5 6778888999999999999983
No 35
>PLN02837 threonine-tRNA ligase
Probab=29.30 E-value=41 Score=32.61 Aligned_cols=15 Identities=40% Similarity=0.603 Sum_probs=11.7
Q ss_pred hhhcchhHHHHHHHH
Q 029090 120 RQAWGSLDALIGRLR 134 (199)
Q Consensus 120 RQAwGSLDALIGRLR 134 (199)
|-.|||+|.|||-|-
T Consensus 489 ~~~~G~~eRlia~Li 503 (614)
T PLN02837 489 RAILGSLERFFGVLI 503 (614)
T ss_pred cCCccCHHHHHHHHH
Confidence 677999998887553
No 36
>PF01488 Shikimate_DH: Shikimate / quinate 5-dehydrogenase; InterPro: IPR006151 This entry represents a domain found in shikimate and quinate dehydrogenases, as well as glutamyl-tRNA reductases. Shikimate 5-dehydrogenase (1.1.1.25 from EC) catalyses the conversion of shikimate to 5-dehydroshikimate [, ]. This reaction is part of the shikimate pathway which is involved in the biosynthesis of aromatic amino acids []. Quinate 5-dehydrogenase catalyses the conversion of quinate to 5-dehydroquinate. This reaction is part of the quinate pathway where quinic acid is exploited as a source of carbon in prokaryotes and microbial eukaryotes. Both the shikimate and quinate pathways share two common pathway metabolites, 3-dehydroquinate and dehydroshikimate. Glutamyl-tRNA reductase (1.2.1.70 from EC) catalyzes the first step of tetrapyrrole biosynthesis in plants, archaea and most bacteria. The dimeric enzyme has an unusual V-shaped architecture where each monomer consists of three domains linked by a long 'spinal' alpha-helix. The central catalytic domain specifically recognises the glutamate moiety of the substrate []. ; PDB: 2EV9_B 2CY0_B 1WXD_A 2D5C_A 1NVT_B 2EGG_A 3PWZ_A 3DOO_A 3DON_A 3FBT_C ....
Probab=29.18 E-value=38 Score=25.91 Aligned_cols=17 Identities=59% Similarity=0.610 Sum_probs=14.8
Q ss_pred CCcchhHHHHHHHHhcc
Q 029090 2 SGAGGIAKACAAAAAEG 18 (199)
Q Consensus 2 ~~~~~~~~~~a~~~~~~ 18 (199)
-||||+|.+++..+.+-
T Consensus 18 iGaGg~ar~v~~~L~~~ 34 (135)
T PF01488_consen 18 IGAGGAARAVAAALAAL 34 (135)
T ss_dssp ESSSHHHHHHHHHHHHT
T ss_pred ECCHHHHHHHHHHHHHc
Confidence 49999999999998764
No 37
>KOG1452 consensus Predicted Rho GTPase-activating protein [Signal transduction mechanisms]
Probab=27.41 E-value=34 Score=32.99 Aligned_cols=30 Identities=33% Similarity=0.537 Sum_probs=22.8
Q ss_pred HHHHHHHHhCCC--------CCCCCCCcchhHHHHHHHH
Q 029090 132 RLRAAYEEHGGS--------PETNPFGNGAIRVYLREVR 162 (199)
Q Consensus 132 RLRAafeE~Gg~--------pE~NPF~araVRlYLReVR 162 (199)
-||++||-||.. |+.|=. ...++.||||+=
T Consensus 233 mLR~~fe~n~r~~el~~E~iPD~nvI-tg~~kD~lrElp 270 (442)
T KOG1452|consen 233 MLRRDFEPNGRDFELGAESIPDYNVI-TGDSKDELRELP 270 (442)
T ss_pred HHHHHhccCCcccccccccCCCccee-ecccHhHHHhCC
Confidence 589999999966 445543 458999999974
No 38
>PRK11177 phosphoenolpyruvate-protein phosphotransferase; Provisional
Probab=27.32 E-value=57 Score=31.86 Aligned_cols=44 Identities=30% Similarity=0.415 Sum_probs=32.6
Q ss_pred hhHHHHHHHHHHHHHhCCC---------------------CCCCCC-CcchhHHHHHH--HHHHHHhh
Q 029090 125 SLDALIGRLRAAYEEHGGS---------------------PETNPF-GNGAIRVYLRE--VRECQAKA 168 (199)
Q Consensus 125 SLDALIGRLRAafeE~Gg~---------------------pE~NPF-~araVRlYLRe--VRd~QAkA 168 (199)
+-|...--.|.+.+.++++ .|.||| |-|+||+||.. +=..|.+|
T Consensus 309 ~eeeq~~~y~~i~~~~~~~~v~iRtlDiGgDK~~~~~~~~~E~NP~LG~RgiR~~l~~~~~f~~QlrA 376 (575)
T PRK11177 309 TEEEQFQAYKAVAEAMGSQAVIVRTMDIGGDKELPYMNLPKEENPFLGWRAIRIAMDRKEILHDQLRA 376 (575)
T ss_pred CHHHHHHHHHHHHHHcCCCeEEEECcCCCcccccccCCCCCCCCcccccchhhhcCCCHHHHHHHHHH
Confidence 4677788888888888776 379999 77999999964 33344444
No 39
>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=27.03 E-value=16 Score=27.55 Aligned_cols=13 Identities=38% Similarity=1.112 Sum_probs=11.2
Q ss_pred hhHHHHHHHhcCC
Q 029090 59 WNTFGQYLKNQRP 71 (199)
Q Consensus 59 Wntf~qyL~n~rP 71 (199)
|.||.+||..|.|
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 40
>PRK12548 shikimate 5-dehydrogenase; Provisional
Probab=26.36 E-value=35 Score=29.50 Aligned_cols=21 Identities=29% Similarity=0.305 Sum_probs=16.9
Q ss_pred cchhHHHHHHHHHHHHHhCCC
Q 029090 123 WGSLDALIGRLRAAYEEHGGS 143 (199)
Q Consensus 123 wGSLDALIGRLRAafeE~Gg~ 143 (199)
...++-||..--.+||-.-|.
T Consensus 256 ~~G~~ML~~Qa~~~f~lwtg~ 276 (289)
T PRK12548 256 VGGLGMLLWQGAEAYKLYTGK 276 (289)
T ss_pred eCcHHHHHHHHHHHHHHhcCC
Confidence 457889999999999987664
No 41
>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=25.61 E-value=39 Score=29.33 Aligned_cols=13 Identities=38% Similarity=0.642 Sum_probs=10.7
Q ss_pred hhhhHHHHHHHhc
Q 029090 57 RDWNTFGQYLKNQ 69 (199)
Q Consensus 57 rdWntf~qyL~n~ 69 (199)
=|.|+|+|||...
T Consensus 141 VDR~EFdQYLn~~ 153 (197)
T PF12067_consen 141 VDRTEFDQYLNSS 153 (197)
T ss_pred hhHHHHHHHhccc
Confidence 3679999999954
No 42
>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=24.57 E-value=61 Score=26.43 Aligned_cols=36 Identities=22% Similarity=0.498 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHhCCCCC---C---CC-CCcchhHHHHHHHHH
Q 029090 128 ALIGRLRAAYEEHGGSPE---T---NP-FGNGAIRVYLREVRE 163 (199)
Q Consensus 128 ALIGRLRAafeE~Gg~pE---~---NP-F~araVRlYLReVRd 163 (199)
.-|-+|+..|++.|...+ . ++ -.+..++.||||.-+
T Consensus 45 ~~i~~l~~~~d~~~~~~~~~~~~~~d~h~va~lLK~flReLP~ 87 (194)
T cd04372 45 EEIEDVKMAFDRDGEKADISATVYPDINVITGALKLYFRDLPI 87 (194)
T ss_pred HHHHHHHHHHcCCCCccCCcccccccHHHHHHHHHHHHHhCCC
Confidence 478889999998775432 1 22 267888999999754
No 43
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=23.88 E-value=18 Score=24.52 Aligned_cols=54 Identities=15% Similarity=0.282 Sum_probs=31.7
Q ss_pred hhhhHHHHHHHhcCCCcccCCCCccchhhhhheeccCCceeeecccccCcCCCCCCCCCCCchhhhcchhHHHHHHHHHH
Q 029090 57 RDWNTFGQYLKNQRPPVSLSQCSCNHVLDFLRYLDQFGKTKVHLHGCVFFGQPDPPAPCTCPLRQAWGSLDALIGRLRAA 136 (199)
Q Consensus 57 rdWntf~qyL~n~rPPlsLs~cs~~hVleFLrylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQAwGSLDALIGRLRAa 136 (199)
...+.|.+|+.+. ++...+..||.+||.|+-..- ..+..++...+.-||..
T Consensus 24 ~~l~~f~~~~~~~----~~~~it~~~i~~y~~~l~~~~-------------------------~~s~~T~~~~~~~l~~f 74 (85)
T PF13495_consen 24 YHLKRFLRFLGNK----PPDEITPEDIEQYLNYLQNER-------------------------GLSPSTINQYLSALRSF 74 (85)
T ss_dssp HHHHHHHTTSSS------GGG--HHHHHHHHHHHHTTT----------------------------HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcccC----ccchhHHHHHHHHHHHHHHhc-------------------------CCCHHHHHHHHHHHHHH
Confidence 3455677777633 455667899999999875211 13556777777777777
Q ss_pred HHH
Q 029090 137 YEE 139 (199)
Q Consensus 137 feE 139 (199)
|+-
T Consensus 75 f~~ 77 (85)
T PF13495_consen 75 FRW 77 (85)
T ss_dssp HHC
T ss_pred HHH
Confidence 763
No 44
>PF09958 DUF2192: Uncharacterized protein conserved in archaea (DUF2192); InterPro: IPR018693 This family of various hypothetical archaeal proteins has no known function.
Probab=23.03 E-value=71 Score=28.64 Aligned_cols=21 Identities=38% Similarity=0.574 Sum_probs=18.2
Q ss_pred hhHHHHHHHHHHHHHhCCCCC
Q 029090 125 SLDALIGRLRAAYEEHGGSPE 145 (199)
Q Consensus 125 SLDALIGRLRAafeE~Gg~pE 145 (199)
+=+.||.-||..|+++|..|=
T Consensus 27 ~R~~lv~~L~~~Y~~~gIeP~ 47 (231)
T PF09958_consen 27 DREELVELLREVYEENGIEPF 47 (231)
T ss_pred CHHHHHHHHHHHHHHcCCCcC
Confidence 458899999999999998753
No 45
>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=22.90 E-value=73 Score=21.80 Aligned_cols=20 Identities=30% Similarity=0.478 Sum_probs=17.1
Q ss_pred chhHHHHHHHHHHHHHhCCC
Q 029090 124 GSLDALIGRLRAAYEEHGGS 143 (199)
Q Consensus 124 GSLDALIGRLRAafeE~Gg~ 143 (199)
.+|+.+|=|||..+.+.|+.
T Consensus 62 ~~l~~~I~rLRkkl~~~~~~ 81 (95)
T cd00383 62 RTVDVHISRLRKKLEDDPSN 81 (95)
T ss_pred ccHHHHHHHHHHHhccCCCC
Confidence 57999999999999987643
No 46
>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=22.87 E-value=66 Score=28.99 Aligned_cols=66 Identities=20% Similarity=0.310 Sum_probs=47.0
Q ss_pred CCCCChhhhhhhhhhhHHHHHHHhcCCCccc--CCCCccchhhhhhe-----------------eccCCceeeecccccC
Q 029090 45 PVPLSRYESQKRRDWNTFGQYLKNQRPPVSL--SQCSCNHVLDFLRY-----------------LDQFGKTKVHLHGCVF 105 (199)
Q Consensus 45 ~~~~SrYesQKrrdWntf~qyL~n~rPPlsL--s~cs~~hVleFLry-----------------lDqfGkTkVH~~~C~f 105 (199)
+..-.+|-++=|..-.+|.+||..+.|-... ..--...|.+||.. ....|..++|--+=..
T Consensus 145 ~~ef~~yL~kvr~~R~eF~~~L~~~~~e~~~~~~~~l~~~v~eFL~~~~~~~~~~~~~~~~~~~~~~~~~~~~hpsgGLS 224 (312)
T PF11709_consen 145 EGEFERYLKKVRPLRPEFKKWLREKHPESLTFDPSDLYDLVKEFLDLAPLKPPDVPDSKKSSSPYAEAGPPKTHPSGGLS 224 (312)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHHhChhhhccCHHHHHHHHHHHHhcccccCcccccchhccCcccccCCCccccCcCcC
Confidence 3345688888899999999999999887621 12334678899976 3346677888777766
Q ss_pred cCCCC
Q 029090 106 FGQPD 110 (199)
Q Consensus 106 fg~p~ 110 (199)
|.+++
T Consensus 225 Y~~~g 229 (312)
T PF11709_consen 225 YNRTG 229 (312)
T ss_pred cCCCc
Confidence 76655
No 47
>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=22.65 E-value=77 Score=27.84 Aligned_cols=25 Identities=28% Similarity=0.437 Sum_probs=23.5
Q ss_pred hhhcchhHHHHHHHHHHHHHhCCCC
Q 029090 120 RQAWGSLDALIGRLRAAYEEHGGSP 144 (199)
Q Consensus 120 RQAwGSLDALIGRLRAafeE~Gg~p 144 (199)
-.|||.+..+|-.|..+|+.+|..|
T Consensus 24 ~lAyG~~~~I~~~~~~ll~~~~~~P 48 (232)
T PF09674_consen 24 LLAYGNRKQIIKKLERLLDLMGPSP 48 (232)
T ss_pred HHHccCHHHHHHHHHHHHHHhCCCH
Confidence 4799999999999999999999986
No 48
>PTZ00398 phosphoenolpyruvate carboxylase; Provisional
Probab=22.62 E-value=1.2e+02 Score=31.77 Aligned_cols=42 Identities=17% Similarity=0.295 Sum_probs=31.5
Q ss_pred cchhHHHHHHHHHHHHHhCC------------------CCCCCCCCc-------------chhHHHHHHHHHH
Q 029090 123 WGSLDALIGRLRAAYEEHGG------------------SPETNPFGN-------------GAIRVYLREVREC 164 (199)
Q Consensus 123 wGSLDALIGRLRAafeE~Gg------------------~pE~NPF~a-------------raVRlYLReVRd~ 164 (199)
|-.+=.+..+|..+++++|+ .=++|||.. .|+++|+++|++.
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 55666788899999988754 234999974 4678899998764
No 49
>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=22.19 E-value=63 Score=27.53 Aligned_cols=17 Identities=29% Similarity=0.603 Sum_probs=12.4
Q ss_pred hhhhcchhHHHHHHHHH
Q 029090 119 LRQAWGSLDALIGRLRA 135 (199)
Q Consensus 119 lRQAwGSLDALIGRLRA 135 (199)
-+-.||+++.+||=|-+
T Consensus 244 h~~~~g~~~R~i~ali~ 260 (261)
T cd00778 244 HQTSWGISTRLIGAIIM 260 (261)
T ss_pred EEecccHHHHHHHHHHh
Confidence 45679988888876643
No 50
>COG4865 Glutamate mutase epsilon subunit [Amino acid transport and metabolism]
Probab=21.71 E-value=63 Score=31.53 Aligned_cols=23 Identities=43% Similarity=0.756 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHhCCCCCCCCCCc
Q 029090 129 LIGRLRAAYEEHGGSPETNPFGN 151 (199)
Q Consensus 129 LIGRLRAafeE~Gg~pE~NPF~a 151 (199)
+|.||.-+|||||.+=...||+-
T Consensus 196 YVDRL~G~YeE~Gi~INREpFgP 218 (485)
T COG4865 196 YVDRLMGMYEEHGIRINREPFGP 218 (485)
T ss_pred HHHHHHhHHHhcCeeeccccCCC
Confidence 45667779999998877777763
No 51
>PRK06464 phosphoenolpyruvate synthase; Validated
Probab=21.70 E-value=56 Score=33.05 Aligned_cols=25 Identities=32% Similarity=0.433 Sum_probs=18.7
Q ss_pred CCCCCC-CcchhHHHHH----HHHHHHHhh
Q 029090 144 PETNPF-GNGAIRVYLR----EVRECQAKA 168 (199)
Q Consensus 144 pE~NPF-~araVRlYLR----eVRd~QAkA 168 (199)
.|.||| +.|.||+||. ++=+.|.+|
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 444555443
No 52
>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=21.69 E-value=44 Score=28.44 Aligned_cols=24 Identities=38% Similarity=0.826 Sum_probs=21.6
Q ss_pred hcchhHH-HHHHHHHHHHHhCCCCC
Q 029090 122 AWGSLDA-LIGRLRAAYEEHGGSPE 145 (199)
Q Consensus 122 AwGSLDA-LIGRLRAafeE~Gg~pE 145 (199)
-|||+|- +||+.-++|.||-..|-
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 53
>PHA03019 hypothetical protein; Provisional
Probab=21.22 E-value=64 Score=24.71 Aligned_cols=21 Identities=29% Similarity=0.426 Sum_probs=17.7
Q ss_pred hhhhhHHHHHHHhcCCCcccC
Q 029090 56 RRDWNTFGQYLKNQRPPVSLS 76 (199)
Q Consensus 56 rrdWntf~qyL~n~rPPlsLs 76 (199)
-+--|+|.+|++||.|-+.|.
T Consensus 45 d~~in~~ld~~knh~~nidli 65 (77)
T PHA03019 45 DHCINKFLDFKKNHEPNIDLI 65 (77)
T ss_pred HHHHHHHHHHHHccCCCccee
Confidence 345689999999999988875
No 54
>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=20.91 E-value=1.5e+02 Score=21.40 Aligned_cols=39 Identities=28% Similarity=0.489 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHhCCCCCCCCCCcchhHHHHHHHHHHHHhhhCCchhhh
Q 029090 128 ALIGRLRAAYEEHGGSPETNPFGNGAIRVYLREVRECQAKARGIPYKKK 176 (199)
Q Consensus 128 ALIGRLRAafeE~Gg~pE~NPF~araVRlYLReVRd~QAkARgi~y~kk 176 (199)
.|--+..++|+++|-.+ +-||++||+.|= ..+|||++-+
T Consensus 11 ~lK~~a~~il~~~Glt~------s~ai~~fl~qiv----~~~~iPF~~~ 49 (83)
T PF04221_consen 11 ELKEEAEAILEELGLTL------SDAINMFLKQIV----REGGIPFELS 49 (83)
T ss_dssp HHHHHHHHHHHHTT--H------HHHHHHHHHHHH----HHSS-S----
T ss_pred HHHHHHHHHHHHcCCCH------HHHHHHHHHHHH----HhCCCCcccc
Confidence 45567788999999875 569999999874 4578887654
No 55
>COG0745 OmpR Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=20.74 E-value=79 Score=26.77 Aligned_cols=37 Identities=30% Similarity=0.509 Sum_probs=26.4
Q ss_pred CCCCCCCCCCchhhhcc--------hhHHHHHHHHHHHHHhCCCC
Q 029090 108 QPDPPAPCTCPLRQAWG--------SLDALIGRLRAAYEEHGGSP 144 (199)
Q Consensus 108 ~p~ppapC~CPlRQAwG--------SLDALIGRLRAafeE~Gg~p 144 (199)
+|+....-.--+.+.|| +||..|.|||.-+++.+..+
T Consensus 168 ~~g~v~sR~~L~~~vw~~~~~~~~rtvdvhI~rLR~Kl~~~~~~~ 212 (229)
T COG0745 168 HPGRVLSREQLLEAVWGYDFEVDSRTVDVHISRLRKKLEKDPGAG 212 (229)
T ss_pred CCCccCCHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhccCCCCC
Confidence 34444444455678888 49999999999999876543
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=20.66 E-value=39 Score=20.77 Aligned_cols=16 Identities=38% Similarity=1.038 Sum_probs=10.7
Q ss_pred cccccCcCCCCCCCCC
Q 029090 100 LHGCVFFGQPDPPAPC 115 (199)
Q Consensus 100 ~~~C~ffg~p~ppapC 115 (199)
..+|.|||.+..-.-|
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
>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=20.50 E-value=1.3e+02 Score=20.69 Aligned_cols=26 Identities=31% Similarity=0.229 Sum_probs=18.7
Q ss_pred cchhHHHHHHHHHHHHHhCCCCCCCC
Q 029090 123 WGSLDALIGRLRAAYEEHGGSPETNP 148 (199)
Q Consensus 123 wGSLDALIGRLRAafeE~Gg~pE~NP 148 (199)
++++|.+.=+|..+-+|+|..+++.|
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 45699999999999999999988766
No 58
>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=20.46 E-value=1.8e+02 Score=21.53 Aligned_cols=39 Identities=33% Similarity=0.670 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHhCCCCCCCCCCcchhHHHHHHHHHHHHhhhCCchhhh
Q 029090 128 ALIGRLRAAYEEHGGSPETNPFGNGAIRVYLREVRECQAKARGIPYKKK 176 (199)
Q Consensus 128 ALIGRLRAafeE~Gg~pE~NPF~araVRlYLReVRd~QAkARgi~y~kk 176 (199)
.|--..-++|+++|..+ ..|||++|+.| ++-+|||++-+
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 44578888765
No 59
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=20.10 E-value=1.6e+02 Score=22.11 Aligned_cols=37 Identities=35% Similarity=0.540 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHhCCCCCCCCCCcchhHHHHHHHHHHHHhhhCCchh
Q 029090 128 ALIGRLRAAYEEHGGSPETNPFGNGAIRVYLREVRECQAKARGIPYK 174 (199)
Q Consensus 128 ALIGRLRAafeE~Gg~pE~NPF~araVRlYLReVRd~QAkARgi~y~ 174 (199)
.|--..-++|+++|-.+ +.||++||+.| ++-++||++
T Consensus 11 ~lK~~A~~vl~~lGls~------S~Ai~~fl~qi----~~~~~iPF~ 47 (80)
T PRK11235 11 ELKARAYAVLEKLGVTP------SEALRLLLQYV----AENGRLPFK 47 (80)
T ss_pred HHHHHHHHHHHHhCCCH------HHHHHHHHHHH----HHhCCCCCC
Confidence 34456678899999875 56899999887 445788877
No 60
>PRK06940 short chain dehydrogenase; Provisional
Probab=20.09 E-value=61 Score=26.76 Aligned_cols=17 Identities=47% Similarity=0.708 Sum_probs=14.3
Q ss_pred CCcchhHHHHHHHHhcc
Q 029090 2 SGAGGIAKACAAAAAEG 18 (199)
Q Consensus 2 ~~~~~~~~~~a~~~~~~ 18 (199)
.|+||||.++|..+++|
T Consensus 8 tGa~gIG~~la~~l~~G 24 (275)
T PRK06940 8 IGAGGIGQAIARRVGAG 24 (275)
T ss_pred ECCChHHHHHHHHHhCC
Confidence 58899999999988654
Done!