Query 023835
Match_columns 276
No_of_seqs 76 out of 78
Neff 2.0
Searched_HMMs 46136
Date Fri Mar 29 06:59:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023835.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023835hhsearch_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 4.4E-74 9.6E-79 475.2 12.0 126 35-160 7-132 (132)
2 PF08821 CGGC: CGGC domain; I 91.0 0.49 1.1E-05 38.1 5.0 66 58-133 30-98 (107)
3 PF02899 Phage_int_SAM_1: Phag 89.3 0.6 1.3E-05 32.5 3.7 40 50-90 21-60 (84)
4 cd00798 INT_XerDC XerD and Xer 88.8 1.7 3.6E-05 34.6 6.3 69 50-145 21-91 (284)
5 COG1080 PtsA Phosphoenolpyruva 87.1 0.76 1.7E-05 46.8 4.2 41 116-156 305-367 (574)
6 cd00799 INT_Cre Cre recombinas 83.1 9.7 0.00021 31.7 8.3 77 50-158 6-82 (287)
7 TIGR02225 recomb_XerD tyrosine 81.5 5.4 0.00012 32.1 6.1 70 49-146 19-90 (291)
8 PRK00283 xerD site-specific ty 80.6 4.2 9.1E-05 33.4 5.3 69 50-146 29-99 (299)
9 TIGR02224 recomb_XerC tyrosine 70.3 18 0.0004 29.3 6.4 69 52-146 22-92 (295)
10 PF00539 Tat: Transactivating 61.4 3.8 8.3E-05 31.8 0.8 19 162-180 45-63 (68)
11 PF10865 DUF2703: Domain of un 57.3 4.1 8.9E-05 33.8 0.4 43 79-141 2-44 (120)
12 cd01185 INT_Tn4399 Tn4399 and 56.3 46 0.001 27.8 6.5 33 54-86 44-78 (299)
13 PRK10529 DNA-binding transcrip 46.3 17 0.00037 28.5 2.3 17 121-137 191-207 (225)
14 PF13495 Phage_int_SAM_4: Phag 42.9 30 0.00066 24.3 2.9 54 53-135 24-77 (85)
15 TIGR01418 PEP_synth phosphoeno 42.6 39 0.00085 35.1 4.8 42 123-164 547-618 (782)
16 PRK11061 fused phosphoenolpyru 38.6 44 0.00095 34.6 4.4 35 121-155 475-530 (748)
17 COG4974 XerD Site-specific rec 38.5 29 0.00063 33.2 2.9 38 52-91 31-69 (300)
18 cd00801 INT_P4 Bacteriophage P 38.2 59 0.0013 27.5 4.4 26 120-146 135-163 (357)
19 PRK10816 DNA-binding transcrip 37.5 25 0.00054 27.6 2.0 16 121-136 189-204 (223)
20 PF13276 HTH_21: HTH-like doma 36.4 56 0.0012 22.5 3.4 29 123-156 4-32 (60)
21 PRK00236 xerC site-specific ty 36.2 1.3E+02 0.0028 24.3 5.9 37 51-88 31-67 (297)
22 PF05528 Coronavirus_5: Corona 35.1 6.8 0.00015 31.5 -1.5 17 141-157 5-24 (82)
23 PF08544 GHMP_kinases_C: GHMP 33.9 8.3 0.00018 27.0 -1.1 40 51-90 6-47 (85)
24 cd04383 RhoGAP_srGAP RhoGAP_sr 33.7 1.2E+02 0.0027 25.7 5.7 35 124-159 47-88 (188)
25 PF00486 Trans_reg_C: Transcri 33.6 42 0.0009 23.1 2.4 54 56-140 11-64 (77)
26 PF06252 DUF1018: Protein of u 32.9 2E+02 0.0043 22.7 6.4 87 54-155 2-89 (119)
27 smart00259 ZnF_A20 A20-like zi 32.6 23 0.00049 22.8 0.8 16 97-112 7-22 (26)
28 PF14768 RPA_interact_C: Repli 29.2 50 0.0011 25.1 2.4 35 110-144 18-56 (82)
29 smart00862 Trans_reg_C Transcr 28.4 60 0.0013 22.2 2.5 51 58-138 13-63 (78)
30 PF00140 Sigma70_r1_2: Sigma-7 27.5 43 0.00093 22.2 1.5 12 148-159 2-13 (37)
31 PF00667 FAD_binding_1: FAD bi 27.3 67 0.0014 27.4 3.1 45 76-120 56-100 (219)
32 smart00243 GAS2 Growth-Arrest- 26.9 42 0.00092 26.6 1.6 14 54-67 55-68 (73)
33 PF09336 Vps4_C: Vps4 C termin 26.9 55 0.0012 24.0 2.2 31 55-90 32-62 (62)
34 PRK05084 xerS site-specific ty 25.7 1.4E+02 0.003 26.2 4.7 68 52-135 42-119 (357)
35 PF11709 Mit_ribos_Mrp51: Mito 25.6 78 0.0017 29.6 3.4 64 43-106 147-229 (312)
36 TIGR01417 PTS_I_fam phosphoeno 25.0 71 0.0015 32.1 3.2 36 121-156 308-365 (565)
37 TIGR03190 benz_CoA_bzdN benzoy 25.0 5.8E+02 0.013 23.9 10.0 25 47-71 166-190 (377)
38 PF07700 HNOB: Heme NO binding 24.9 31 0.00068 28.5 0.6 37 52-88 64-103 (171)
39 KOG4670 Uncharacterized conser 24.5 30 0.00065 35.9 0.6 59 50-108 468-544 (602)
40 PRK09279 pyruvate phosphate di 23.6 74 0.0016 34.1 3.2 36 129-164 636-685 (879)
41 cd01187 INT_SG4 INT_SG4, DNA b 23.5 3.2E+02 0.0068 23.0 6.3 30 53-86 24-53 (299)
42 cd04372 RhoGAP_chimaerin RhoGA 23.3 82 0.0018 26.6 2.9 36 124-159 45-87 (194)
43 PF12067 Sox_C_TAD: Sox C-term 22.3 47 0.001 29.9 1.3 15 53-67 141-155 (197)
44 cd01355 AcnX Putative Aconitas 22.2 93 0.002 30.5 3.4 54 76-141 48-108 (389)
45 TIGR02384 RelB_DinJ addiction 21.9 2E+02 0.0043 22.1 4.5 39 124-172 12-50 (83)
46 PRK11235 bifunctional antitoxi 21.9 1.9E+02 0.0041 22.7 4.4 38 124-171 11-48 (80)
47 PRK10701 DNA-binding transcrip 21.9 73 0.0016 25.6 2.2 15 121-135 201-215 (240)
48 PF04221 RelB: RelB antitoxin; 21.4 1.9E+02 0.0041 21.7 4.2 39 124-172 11-49 (83)
49 KOG4405 GDP dissociation inhib 20.9 44 0.00095 34.4 0.9 79 57-139 224-331 (547)
50 PF09107 SelB-wing_3: Elongati 20.6 44 0.00095 23.9 0.6 20 74-93 22-41 (50)
51 COG0606 Predicted ATPase with 20.4 4.8E+02 0.01 26.9 7.9 45 97-143 336-380 (490)
52 PF09958 DUF2192: Uncharacteri 20.3 86 0.0019 29.2 2.6 21 121-141 27-47 (231)
53 COG0745 OmpR Response regulato 20.3 82 0.0018 27.7 2.3 30 111-140 175-212 (229)
54 TIGR01828 pyru_phos_dikin pyru 20.1 60 0.0013 34.5 1.7 26 139-164 651-679 (856)
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=4.4e-74 Score=475.22 Aligned_cols=126 Identities=78% Similarity=1.425 Sum_probs=121.0
Q ss_pred CCCCCCCCCCChhhhhhhhhHHHHHHHHHhCCCCcccccccchhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCc
Q 023835 35 TSPPAAAAPPSRYESQKRRDWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACP 114 (276)
Q Consensus 35 ~s~~~~~~~~SRYEsQKRRDWnTF~QyL~NhrPPlsLs~CSgaHVleFLryLDqfGKTKVH~~~C~ffG~p~ppapC~CP 114 (276)
.++..+++.+||||+|||||||||+|||+||+|||+|++|+++|||+||+|||||||||||.++|+|||+|+||+||+||
T Consensus 7 ~~~~~~~~~~SrYesQKrrdwntf~qyL~n~rPP~~L~~csg~hVl~FL~~~d~~GkTkVh~~~C~~~g~~~~p~~C~CP 86 (132)
T PF04852_consen 7 TSSRSPQPAPSRYESQKRRDWNTFGQYLRNHRPPLSLSRCSGNHVLEFLRYLDQFGKTKVHGQGCPFFGHPSPPAPCPCP 86 (132)
T ss_pred CCCCCCCCCCcccchhhhHHHHHHHHHHHccCCCcchhhcChHHHHHHHHHHhccCCeeecCCCCCCCCCCCCCCCCCCc
Confidence 33445566889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhcchhHHHHHHHHHHHHHhCCCCCCCCccchhHHHHHHHHhHH
Q 023835 115 LKQAWGSLDALIGRLRAAYEENGGRPESNPFGARAVRIYLREVRES 160 (276)
Q Consensus 115 LRQAWGSLDALIGRLRAAfEE~GG~PEsNPFaAraVRlYLReVRd~ 160 (276)
||||||||||||||||||||||||+||+|||++|+||+|||||||+
T Consensus 87 lrqAwGSlDalIGrLraafee~Gg~pe~NPf~~~~vr~yLr~vr~~ 132 (132)
T PF04852_consen 87 LRQAWGSLDALIGRLRAAFEEHGGHPEANPFAARAVRLYLREVRDS 132 (132)
T ss_pred HHHHhccHHHHHHHHHHHHHHhCCCCCCCchhhHHHHHHHHHHhcC
Confidence 9999999999999999999999999999999999999999999985
No 2
>PF08821 CGGC: CGGC domain; InterPro: IPR014925 Proteins in this entry are a quite highly conserved sequence of CGGC in its central region. The region has many conserved cysteines and histidines suggestive of a zinc binding function.
Probab=91.04 E-value=0.49 Score=38.09 Aligned_cols=66 Identities=23% Similarity=0.530 Sum_probs=49.2
Q ss_pred HHHHHHhCCCCccccc---ccchhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHHHH
Q 023835 58 FLQYLKNHKPPLTLAR---CSGAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWGSLDALIGRLRAAY 133 (276)
Q Consensus 58 F~QyL~NhrPPlsLs~---CSgaHVleFLryLDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQAWGSLDALIGRLRAAf 133 (276)
|.+|=.+..--+.+.+ |.+..++..++.+-..|-..||...|...+.+.+ +||. +|.|+-.|+++|
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 4444332223344445 4568999999999999999999999999987653 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=89.28 E-value=0.6 Score=32.52 Aligned_cols=40 Identities=28% Similarity=0.525 Sum_probs=31.5
Q ss_pred hhhhhHHHHHHHHHhCCCCcccccccchhHhHHhhhhcccC
Q 023835 50 QKRRDWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFG 90 (276)
Q Consensus 50 QKRRDWnTF~QyL~NhrPPlsLs~CSgaHVleFLryLDqfG 90 (276)
.-+++++.|.+||.+ .....+..++..||.+|+.++-+.|
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 456899999999999 5667778899999999999987765
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=88.82 E-value=1.7 Score=34.63 Aligned_cols=69 Identities=25% Similarity=0.300 Sum_probs=49.3
Q ss_pred hhhhhHHHHHHHHHhCCCCcccccccchhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcchhHHHHHHH
Q 023835 50 QKRRDWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWGSLDALIGRL 129 (276)
Q Consensus 50 QKRRDWnTF~QyL~NhrPPlsLs~CSgaHVleFLryLDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQAWGSLDALIGRL 129 (276)
+-+..|+.|.+|+.....+. +..-+..||.+|+.++.+.| ....++...++-|
T Consensus 21 ~~~~~~~~~~~~~~~~~~~~-~~~l~~~~i~~~~~~~~~~~--------------------------~~~~t~~~~~~~l 73 (284)
T cd00798 21 AYRRDLERFLEFLEERGILF-PADVTPDDIRRFLAELKDQG--------------------------LSARSIARKLSAL 73 (284)
T ss_pred HHHHHHHHHHHHHHHcCCCc-hhhCCHHHHHHHHHHhhhcC--------------------------CCHHHHHHHHHHH
Confidence 44567899999998764433 56678999999999876543 2345778888889
Q ss_pred HHHHHHhC--CCCCCCCc
Q 023835 130 RAAYEENG--GRPESNPF 145 (276)
Q Consensus 130 RAAfEE~G--G~PEsNPF 145 (276)
+++|.-.. +.-+.||+
T Consensus 74 ~~~~~~~~~~~~~~~~p~ 91 (284)
T cd00798 74 RSFFKFLLREGLILANPA 91 (284)
T ss_pred HHHHHHHHHcCCccCChh
Confidence 98887432 33456887
No 5
>COG1080 PtsA Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]
Probab=87.05 E-value=0.76 Score=46.78 Aligned_cols=41 Identities=37% Similarity=0.646 Sum_probs=31.3
Q ss_pred hhhcchhHHHHHHHHHHHHHhCCC--------------------C-CCCCc-cchhHHHHHHH
Q 023835 116 KQAWGSLDALIGRLRAAYEENGGR--------------------P-ESNPF-GARAVRIYLRE 156 (276)
Q Consensus 116 RQAWGSLDALIGRLRAAfEE~GG~--------------------P-EsNPF-aAraVRlYLRe 156 (276)
|..|=+.|..----++..|.+||+ | |.||| |-|+||+||..
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 445556777777777888888876 3 79999 68999999853
No 6
>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=83.13 E-value=9.7 Score=31.74 Aligned_cols=77 Identities=23% Similarity=0.303 Sum_probs=52.8
Q ss_pred hhhhhHHHHHHHHHhCCCCcccccccchhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcchhHHHHHHH
Q 023835 50 QKRRDWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWGSLDALIGRL 129 (276)
Q Consensus 50 QKRRDWnTF~QyL~NhrPPlsLs~CSgaHVleFLryLDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQAWGSLDALIGRL 129 (276)
.-..+++.|.+|+..+. +....-+..||.+|+.||.+. .+..++-..++.|
T Consensus 6 ~y~~~l~~f~~~~~~~~--~~~~~~~~~~i~~~~~~l~~~---------------------------~s~~ti~~~~~~l 56 (287)
T cd00799 6 AYLSDWRRFAAWCQAHG--RTPLPASPETVTLYLTDLADS---------------------------LAPSTISRRLSAL 56 (287)
T ss_pred HHHHHHHHHHHHHHhcC--CCCCCCCHHHHHHHHHHHHhc---------------------------cChHHHHHHHHHH
Confidence 44568899999998752 122224589999999987521 2456888999999
Q ss_pred HHHHHHhCCCCCCCCccchhHHHHHHHHh
Q 023835 130 RAAYEENGGRPESNPFGARAVRIYLREVR 158 (276)
Q Consensus 130 RAAfEE~GG~PEsNPFaAraVRlYLReVR 158 (276)
+..|+..+. .||+....++.-|+.++
T Consensus 57 ~~~~~~~~~---~~p~~~~~~~~~~~~~~ 82 (287)
T cd00799 57 SQLHRRSGL---PSPADSPLVRLVLRGIR 82 (287)
T ss_pred HHHHHHcCC---CCCccCHHHHHHHHHHH
Confidence 999985433 58876655555555554
No 7
>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=81.52 E-value=5.4 Score=32.13 Aligned_cols=70 Identities=26% Similarity=0.448 Sum_probs=48.2
Q ss_pred hhhhhhHHHHHHHHHhCCCCcccccccchhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcchhHHHHHH
Q 023835 49 SQKRRDWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWGSLDALIGR 128 (276)
Q Consensus 49 sQKRRDWnTF~QyL~NhrPPlsLs~CSgaHVleFLryLDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQAWGSLDALIGR 128 (276)
.+-++.++.|.+|+..+. ..+..-+..||.+|+.++.+.| ...-++...+..
T Consensus 19 ~~~~~~~~~~~~~~~~~~--~~~~~it~~~i~~~~~~~~~~~--------------------------~~~~t~~~~~~~ 70 (291)
T TIGR02225 19 EAYRRDLEKFLEFLEERG--IDLEEVDRGDIVDFLAELKEAG--------------------------LSARSIARALSA 70 (291)
T ss_pred HHHHHHHHHHHHHHHhcC--CChHHCCHHHHHHHHHHhhcCC--------------------------CCHhHHHHHHHH
Confidence 445667888999998543 2455567899999999877543 122367889999
Q ss_pred HHHHHHHh--CCCCCCCCcc
Q 023835 129 LRAAYEEN--GGRPESNPFG 146 (276)
Q Consensus 129 LRAAfEE~--GG~PEsNPFa 146 (276)
|+++|+-. -+-.+.|||.
T Consensus 71 l~~~~~~a~~~~~~~~np~~ 90 (291)
T TIGR02225 71 LRSFYRFLLREGIREDDPSA 90 (291)
T ss_pred HHHHHHHHHhcccccCCchh
Confidence 99999732 2334578864
No 8
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed
Probab=80.64 E-value=4.2 Score=33.38 Aligned_cols=69 Identities=25% Similarity=0.274 Sum_probs=48.5
Q ss_pred hhhhhHHHHHHHHHhCCCCcccccccchhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcchhHHHHHHH
Q 023835 50 QKRRDWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWGSLDALIGRL 129 (276)
Q Consensus 50 QKRRDWnTF~QyL~NhrPPlsLs~CSgaHVleFLryLDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQAWGSLDALIGRL 129 (276)
.-+++|+.|..||..+.- .+...+..||.+|+.++.+.| .+..++...+..|
T Consensus 29 ~~~~~~~~~~~~~~~~~~--~~~~l~~~~i~~~~~~~~~~~--------------------------~~~~t~~~~~~~l 80 (299)
T PRK00283 29 SYRRDLELFAEWLAARGL--SLAEATRDDLQAFLAELAEGG--------------------------YKATSSARRLSAL 80 (299)
T ss_pred HHHHHHHHHHHHHHhcCC--ChHHCCHHHHHHHHHHHHhCC--------------------------CCHHHHHHHHHHH
Confidence 346788999999986533 566678999999999875431 2345778888999
Q ss_pred HHHHHHhC--CCCCCCCcc
Q 023835 130 RAAYEENG--GRPESNPFG 146 (276)
Q Consensus 130 RAAfEE~G--G~PEsNPFa 146 (276)
+++|+-.. +.-..|||.
T Consensus 81 ~~~~~~a~~~~~i~~np~~ 99 (299)
T PRK00283 81 RRFFQFLLREGLREDDPSA 99 (299)
T ss_pred HHHHHHHHHcCCcccCchh
Confidence 99987331 234568863
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=70.28 E-value=18 Score=29.26 Aligned_cols=69 Identities=30% Similarity=0.402 Sum_probs=47.6
Q ss_pred hhhHHHHHHHHHhCCCCcccccccchhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHH
Q 023835 52 RRDWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWGSLDALIGRLRA 131 (276)
Q Consensus 52 RRDWnTF~QyL~NhrPPlsLs~CSgaHVleFLryLDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQAWGSLDALIGRLRA 131 (276)
+.+++.|.+||......+.+..-+..||.+|+.++.+.| .+..++...+..||+
T Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~l~~~~i~~~~~~~~~~~--------------------------~~~~T~~~~~~~l~~ 75 (295)
T TIGR02224 22 RRDLKAFLEFLEEEGGLASLAEVTAADLRSFLAELHARG--------------------------LSRRSLARKLSALRS 75 (295)
T ss_pred HHHHHHHHHHHHhcCCCCccccCcHHHHHHHHHHhcccC--------------------------CCHHHHHHHHHHHHH
Confidence 456677889998866667888888999999999875522 122466777888888
Q ss_pred HHHHhC--CCCCCCCcc
Q 023835 132 AYEENG--GRPESNPFG 146 (276)
Q Consensus 132 AfEE~G--G~PEsNPFa 146 (276)
+|.-.. +.-+.|||.
T Consensus 76 ~~~~a~~~~~~~~np~~ 92 (295)
T TIGR02224 76 FYRFLVRRGLIKANPAA 92 (295)
T ss_pred HHHHHHHcCccccChHh
Confidence 876421 223467763
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=61.37 E-value=3.8 Score=31.80 Aligned_cols=19 Identities=37% Similarity=0.655 Sum_probs=14.6
Q ss_pred HhhhCCchhhhcccCCCcc
Q 023835 162 AKARGIPYEKKKRKRPVVT 180 (276)
Q Consensus 162 AKARGi~YeKKkrkr~~~~ 180 (276)
-|.-||.|..|||||...+
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 4788999999887666543
No 11
>PF10865 DUF2703: Domain of unknown function (DUF2703); InterPro: IPR021219 This family of protein has no known function.
Probab=57.29 E-value=4.1 Score=33.83 Aligned_cols=43 Identities=28% Similarity=0.292 Sum_probs=33.4
Q ss_pred HhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHHHHHHhCCCCC
Q 023835 79 VIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWGSLDALIGRLRAAYEENGGRPE 141 (276)
Q Consensus 79 VleFLryLDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQAWGSLDALIGRLRAAfEE~GG~PE 141 (276)
+|+|+ |||..|+| |... ...+.+|+..+-+|+.+|+..|..++
T Consensus 2 ~I~w~-~l~~~g~t------C~RC-------------~~Tg~~L~~av~~l~~~L~~~Giev~ 44 (120)
T PF10865_consen 2 VIEWQ-HLDLDGKT------CERC-------------GDTGETLREAVKELAPVLAPLGIEVR 44 (120)
T ss_pred eEEEE-EeecCCCc------CCch-------------hhHHHHHHHHHHHHHHHHHhCCcEEE
Confidence 46788 55555776 5444 57788999999999999999998754
No 12
>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=56.32 E-value=46 Score=27.83 Aligned_cols=33 Identities=12% Similarity=0.335 Sum_probs=26.5
Q ss_pred hHHHHHHHHHhCCC--CcccccccchhHhHHhhhh
Q 023835 54 DWNTFLQYLKNHKP--PLTLARCSGAHVIEFLKYL 86 (276)
Q Consensus 54 DWnTF~QyL~NhrP--PlsLs~CSgaHVleFLryL 86 (276)
.++.|..||....+ .+.|..-+..||.+|+.|+
T Consensus 44 ~~~~~~~~~~~~~~~~~~~l~~i~~~~i~~~~~~l 78 (299)
T cd01185 44 HLKNLREFIECTYKEIDIALLELTREFILEFKLFL 78 (299)
T ss_pred HHHHHHHHHHHhcCccCCCHHHccHHHHHHHHHHH
Confidence 46678888876554 6778888899999999997
No 13
>PRK10529 DNA-binding transcriptional activator KdpE; Provisional
Probab=46.30 E-value=17 Score=28.52 Aligned_cols=17 Identities=29% Similarity=0.485 Sum_probs=13.2
Q ss_pred hhHHHHHHHHHHHHHhC
Q 023835 121 SLDALIGRLRAAYEENG 137 (276)
Q Consensus 121 SLDALIGRLRAAfEE~G 137 (276)
+||.+|.|||.-+++.+
T Consensus 191 ~~~~~i~rlR~kl~~~~ 207 (225)
T PRK10529 191 YLRIYMGHLRQKLEQDP 207 (225)
T ss_pred CHHHHHHHHHHHhccCC
Confidence 58888888888887544
No 14
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=42.94 E-value=30 Score=24.25 Aligned_cols=54 Identities=17% Similarity=0.325 Sum_probs=32.7
Q ss_pred hhHHHHHHHHHhCCCCcccccccchhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHHH
Q 023835 53 RDWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWGSLDALIGRLRAA 132 (276)
Q Consensus 53 RDWnTF~QyL~NhrPPlsLs~CSgaHVleFLryLDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQAWGSLDALIGRLRAA 132 (276)
...+.|.+|+.+. .+...+..||.+||.||-..- +.+..++...+.-||..
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 4455677777633 455667999999999976221 13556777777777777
Q ss_pred HHH
Q 023835 133 YEE 135 (276)
Q Consensus 133 fEE 135 (276)
|+-
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
>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=42.62 E-value=39 Score=35.08 Aligned_cols=42 Identities=24% Similarity=0.283 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHHhCCC-------------------------CCCCCc-cchhHHHHH----HHHhHHHHhh
Q 023835 123 DALIGRLRAAYEENGGR-------------------------PESNPF-GARAVRIYL----REVRESQAKA 164 (276)
Q Consensus 123 DALIGRLRAAfEE~GG~-------------------------PEsNPF-aAraVRlYL----ReVRd~QAKA 164 (276)
|.+.-.+|.+++.++++ .|.||| |.|.||+|| .++=+.|.+|
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 55556777777776544 378997 679999999 5566666655
No 16
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=38.60 E-value=44 Score=34.55 Aligned_cols=35 Identities=26% Similarity=0.395 Sum_probs=28.7
Q ss_pred hhHHHHHHHHHHHHHhCCC--------------------CCCCCc-cchhHHHHHH
Q 023835 121 SLDALIGRLRAAYEENGGR--------------------PESNPF-GARAVRIYLR 155 (276)
Q Consensus 121 SLDALIGRLRAAfEE~GG~--------------------PEsNPF-aAraVRlYLR 155 (276)
+-|......|.+.+.++++ +|.||| |.|+||+||+
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 4677888888888888775 589998 5699999984
No 17
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair]
Probab=38.52 E-value=29 Score=33.20 Aligned_cols=38 Identities=32% Similarity=0.540 Sum_probs=33.7
Q ss_pred hhhHHHHHHHHHhCCCCc-ccccccchhHhHHhhhhcccCc
Q 023835 52 RRDWNTFLQYLKNHKPPL-TLARCSGAHVIEFLKYLDQFGK 91 (276)
Q Consensus 52 RRDWnTF~QyL~NhrPPl-sLs~CSgaHVleFLryLDqfGK 91 (276)
|||-+.|.+||..+. + +|...+..||.+||.++-.+|.
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 789999999999886 4 6788889999999999999983
No 18
>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=38.19 E-value=59 Score=27.47 Aligned_cols=26 Identities=19% Similarity=0.276 Sum_probs=19.9
Q ss_pred chhHHHHHHHHHHHHH---hCCCCCCCCcc
Q 023835 120 GSLDALIGRLRAAYEE---NGGRPESNPFG 146 (276)
Q Consensus 120 GSLDALIGRLRAAfEE---~GG~PEsNPFa 146 (276)
-++...+..||++|+- +|.-+ .|||.
T Consensus 135 ~t~~~~~~~l~~~~~~a~~~g~i~-~nP~~ 163 (357)
T cd00801 135 ETARRVRQRLKQVFRYAIARGLIE-ANPAA 163 (357)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCcc-cCchH
Confidence 4788999999999984 45433 89985
No 19
>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional
Probab=37.46 E-value=25 Score=27.65 Aligned_cols=16 Identities=38% Similarity=0.760 Sum_probs=12.4
Q ss_pred hhHHHHHHHHHHHHHh
Q 023835 121 SLDALIGRLRAAYEEN 136 (276)
Q Consensus 121 SLDALIGRLRAAfEE~ 136 (276)
+||.+|.|||.-+++.
T Consensus 189 ~v~~~i~rLR~kl~~~ 204 (223)
T PRK10816 189 TIDVLMGRLRKKIQAQ 204 (223)
T ss_pred CHHHHHHHHHHHhccC
Confidence 6888888888888654
No 20
>PF13276 HTH_21: HTH-like domain
Probab=36.40 E-value=56 Score=22.54 Aligned_cols=29 Identities=24% Similarity=0.430 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHhCCCCCCCCccchhHHHHHHH
Q 023835 123 DALIGRLRAAYEENGGRPESNPFGARAVRIYLRE 156 (276)
Q Consensus 123 DALIGRLRAAfEE~GG~PEsNPFaAraVRlYLRe 156 (276)
|+|+-.++++|+++++ =||.+-|..+|+.
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 3788888888875
No 21
>PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=36.23 E-value=1.3e+02 Score=24.33 Aligned_cols=37 Identities=30% Similarity=0.443 Sum_probs=27.9
Q ss_pred hhhhHHHHHHHHHhCCCCcccccccchhHhHHhhhhcc
Q 023835 51 KRRDWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQ 88 (276)
Q Consensus 51 KRRDWnTF~QyL~NhrPPlsLs~CSgaHVleFLryLDq 88 (276)
-+.+|+.|..|+..... ..+..-...||.+||.++-+
T Consensus 31 ~~~~~~~~~~~~~~~~~-~~~~~i~~~~i~~~~~~~~~ 67 (297)
T PRK00236 31 YRRDLRAFLAFLEEHGI-SSLQDLDAADLRSFLARRRR 67 (297)
T ss_pred HHHHHHHHHHHHHHcCC-CchhhCCHHHHHHHHHHHHh
Confidence 35678889999887543 55667788999999988654
No 22
>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=35.07 E-value=6.8 Score=31.50 Aligned_cols=17 Identities=65% Similarity=1.007 Sum_probs=13.8
Q ss_pred CCCCcc---chhHHHHHHHH
Q 023835 141 ESNPFG---ARAVRIYLREV 157 (276)
Q Consensus 141 EsNPFa---AraVRlYLReV 157 (276)
..|||+ ||-+|+||||=
T Consensus 5 k~NPfr~aiARKaRiyLr~G 24 (82)
T PF05528_consen 5 KDNPFRGAIARKARIYLREG 24 (82)
T ss_pred ccCchhhhhhhheeeeeecC
Confidence 479995 78899999863
No 23
>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=33.86 E-value=8.3 Score=27.02 Aligned_cols=40 Identities=10% Similarity=0.166 Sum_probs=31.5
Q ss_pred hhhhHHHHHHHHHhCCC--CcccccccchhHhHHhhhhcccC
Q 023835 51 KRRDWNTFLQYLKNHKP--PLTLARCSGAHVIEFLKYLDQFG 90 (276)
Q Consensus 51 KRRDWnTF~QyL~NhrP--PlsLs~CSgaHVleFLryLDqfG 90 (276)
++.||..|.+.+.+... |.....+...+|.+.+.++-+.|
T Consensus 6 ~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~G 47 (85)
T PF08544_consen 6 AEGDLELLGELMNENQENEPENYREVLTPEIDELKEAAEENG 47 (85)
T ss_dssp HTTCHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHTT
T ss_pred HCcCHHHHHHHHHHhhhhcchHHHHHcCHHHHHHHHHHHHCC
Confidence 56899999999995544 55566677888888888888888
No 24
>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=33.69 E-value=1.2e+02 Score=25.65 Aligned_cols=35 Identities=23% Similarity=0.558 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHhCCCC---CCCCc----cchhHHHHHHHHhH
Q 023835 124 ALIGRLRAAYEENGGRP---ESNPF----GARAVRIYLREVRE 159 (276)
Q Consensus 124 ALIGRLRAAfEE~GG~P---EsNPF----aAraVRlYLReVRd 159 (276)
.-|.+||..|+. |..+ +.+.+ .+..++.||||..+
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 11222 58899999999754
No 25
>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=33.63 E-value=42 Score=23.12 Aligned_cols=54 Identities=33% Similarity=0.398 Sum_probs=35.1
Q ss_pred HHHHHHHHhCCCCcccccccchhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHHHHHH
Q 023835 56 NTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWGSLDALIGRLRAAYEE 135 (276)
Q Consensus 56 nTF~QyL~NhrPPlsLs~CSgaHVleFLryLDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQAWGSLDALIGRLRAAfEE 135 (276)
..+.++|-.+.+ . -++-.++++.+ |-+.. .-.--+||.+|-|||..++.
T Consensus 11 ~~lL~~L~~~~~-~---~vs~~~l~~~~-w~~~~--------------------------~~~~~~l~~~I~rLR~kL~~ 59 (77)
T PF00486_consen 11 FRLLELLLRNPG-R---VVSREELIEAL-WGDEE--------------------------DVSDNSLDVHISRLRKKLED 59 (77)
T ss_dssp HHHHHHHHHTTT-S---EEEHHHHHHHH-TSSSS--------------------------TTCTHHHHHHHHHHHHHHHS
T ss_pred HHHHHHHHhCCC-C---CCCHHHhCChh-hhccc--------------------------ccchhhHHHHHHHHHHHHhh
Confidence 345666666643 2 25567788877 63322 11234899999999999999
Q ss_pred hCCCC
Q 023835 136 NGGRP 140 (276)
Q Consensus 136 ~GG~P 140 (276)
.|..+
T Consensus 60 ~~~~~ 64 (77)
T PF00486_consen 60 AGGDP 64 (77)
T ss_dssp STTSS
T ss_pred cCCCC
Confidence 87543
No 26
>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=32.91 E-value=2e+02 Score=22.74 Aligned_cols=87 Identities=16% Similarity=0.206 Sum_probs=56.4
Q ss_pred hHHHHHHHHHhCCCCcccccccchhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHHHH
Q 023835 54 DWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWGSLDALIGRLRAAY 133 (276)
Q Consensus 54 DWnTF~QyL~NhrPPlsLs~CSgaHVleFLryLDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQAWGSLDALIGRLRAAf 133 (276)
|..++.++|.++..=-+...++-.+..++|.++.+.|-. .....=.+-. .|.. ...+.+.+|+|..
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-PPKPARRPGR--RPGM-----------ATSAQLRKIRALW 67 (119)
T ss_pred CHHHHHHHHHHHhChhhHHHCCHHHHHHHHHHHHHccCc-CccccccCCC--CCCC-----------cchHHHHHHHHHH
Confidence 456788888888887788889999999999988888852 1111111111 1111 1778999999999
Q ss_pred HHhCCCCC-CCCccchhHHHHHH
Q 023835 134 EENGGRPE-SNPFGARAVRIYLR 155 (276)
Q Consensus 134 EE~GG~PE-sNPFaAraVRlYLR 155 (276)
.++|.... .|| ...++.-|++
T Consensus 68 ~~~~~~~~v~~~-s~~aL~~fvk 89 (119)
T PF06252_consen 68 KQLGKPGAVRDP-SEAALDAFVK 89 (119)
T ss_pred HHhhccCCccch-HHHHHHHHHH
Confidence 99997655 333 2334444443
No 27
>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=32.58 E-value=23 Score=22.78 Aligned_cols=16 Identities=38% Similarity=1.134 Sum_probs=13.5
Q ss_pred cCCCCCCCCCCCCCCC
Q 023835 97 SGCPYFGHPNPPAPCA 112 (276)
Q Consensus 97 ~~C~ffG~p~ppapC~ 112 (276)
.+|.|||.|..-..|.
T Consensus 7 ~~CgF~G~~~t~~~Cs 22 (26)
T smart00259 7 PGCGFFGNPATEGLCS 22 (26)
T ss_pred CCCCCcCChhhcccCH
Confidence 6999999998777774
No 28
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=29.18 E-value=50 Score=25.11 Aligned_cols=35 Identities=31% Similarity=0.504 Sum_probs=30.1
Q ss_pred CCCCchhhhcc----hhHHHHHHHHHHHHHhCCCCCCCC
Q 023835 110 PCACPLKQAWG----SLDALIGRLRAAYEENGGRPESNP 144 (276)
Q Consensus 110 pC~CPLRQAWG----SLDALIGRLRAAfEE~GG~PEsNP 144 (276)
-|+|-||..-+ ++|.|=-+|..+++||..+...+|
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 29
>smart00862 Trans_reg_C Transcriptional regulatory protein, C terminal. This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.
Probab=28.36 E-value=60 Score=22.21 Aligned_cols=51 Identities=25% Similarity=0.309 Sum_probs=33.9
Q ss_pred HHHHHHhCCCCcccccccchhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHHHHHHhC
Q 023835 58 FLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWGSLDALIGRLRAAYEENG 137 (276)
Q Consensus 58 F~QyL~NhrPPlsLs~CSgaHVleFLryLDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQAWGSLDALIGRLRAAfEE~G 137 (276)
+..||-.+..- .++-.++++.| |-+.+ -..+-.+|+.+|-|||..+++.|
T Consensus 13 lL~~L~~~~~~----~vs~~~l~~~l-w~~~~-------------------------~~~~~~~l~~~i~~LR~~l~~~~ 62 (78)
T smart00862 13 LLELLLRNPGR----VVSREELLEAV-WGDDD-------------------------DDVDDNTLDVHISRLRKKLEDDG 62 (78)
T ss_pred HHHHHHhCCCC----ccCHHHHHHHH-cCCCC-------------------------CCCccchHHHHHHHHHHHHhcCC
Confidence 66777777542 25677888866 62211 01123679999999999999976
Q ss_pred C
Q 023835 138 G 138 (276)
Q Consensus 138 G 138 (276)
+
T Consensus 63 ~ 63 (78)
T smart00862 63 A 63 (78)
T ss_pred C
Confidence 5
No 30
>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=27.51 E-value=43 Score=22.23 Aligned_cols=12 Identities=33% Similarity=0.852 Sum_probs=10.0
Q ss_pred hhHHHHHHHHhH
Q 023835 148 RAVRIYLREVRE 159 (276)
Q Consensus 148 raVRlYLReVRd 159 (276)
-+|++||++|+.
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 31
>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=27.31 E-value=67 Score=27.41 Aligned_cols=45 Identities=20% Similarity=0.176 Sum_probs=34.7
Q ss_pred chhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcc
Q 023835 76 GAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWG 120 (276)
Q Consensus 76 gaHVleFLryLDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQAWG 120 (276)
.++|.+||..+.-.+.+.|......-.....+|.|.+|.++++--
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 567888999988888888877666544556678889999988753
No 32
>smart00243 GAS2 Growth-Arrest-Specific Protein 2 Domain. GROWTH-ARREST-SPECIFIC PROTEIN 2 Domain
Probab=26.87 E-value=42 Score=26.57 Aligned_cols=14 Identities=43% Similarity=0.999 Sum_probs=13.1
Q ss_pred hHHHHHHHHHhCCC
Q 023835 54 DWNTFLQYLKNHKP 67 (276)
Q Consensus 54 DWnTF~QyL~NhrP 67 (276)
-|.||.+||..|.|
T Consensus 55 GW~tL~~fL~khDP 68 (73)
T smart00243 55 GWETLDEYLLKHDP 68 (73)
T ss_pred cHHHHHHHHHhCCC
Confidence 49999999999999
No 33
>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=26.86 E-value=55 Score=24.01 Aligned_cols=31 Identities=26% Similarity=0.489 Sum_probs=24.9
Q ss_pred HHHHHHHHHhCCCCcccccccchhHhHHhhhhcccC
Q 023835 55 WNTFLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFG 90 (276)
Q Consensus 55 WnTF~QyL~NhrPPlsLs~CSgaHVleFLryLDqfG 90 (276)
-+.|.+=|++.+|- .+.+||..|..|-.+||
T Consensus 32 ~~DF~~Al~~~kpS-----Vs~~dl~~ye~w~~~FG 62 (62)
T PF09336_consen 32 MEDFEEALKKVKPS-----VSQEDLKKYEEWTKEFG 62 (62)
T ss_dssp HHHHHHHHHTCGGS-----S-HHHHHHHHHHHHHTS
T ss_pred HHHHHHHHHHcCCC-----CCHHHHHHHHHHHHHcC
Confidence 45677778888874 56889999999999998
No 34
>PRK05084 xerS site-specific tyrosine recombinase XerS; Reviewed
Probab=25.66 E-value=1.4e+02 Score=26.17 Aligned_cols=68 Identities=16% Similarity=0.275 Sum_probs=43.7
Q ss_pred hhhHHHHHHHHHhCCC-----Cc-----ccccccchhHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhcch
Q 023835 52 RRDWNTFLQYLKNHKP-----PL-----TLARCSGAHVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAWGS 121 (276)
Q Consensus 52 RRDWnTF~QyL~NhrP-----Pl-----sLs~CSgaHVleFLryLDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQAWGS 121 (276)
+++...|.+||..+.. +. .|...+..||.+|+.|+.+.-.. + ++.. +...+..+
T Consensus 42 ~~~l~~f~~~l~~~~~~~~~~~~~~~~~~l~~lt~~~i~~f~~~l~~~~~~------~---~~~~-------~~~~s~~T 105 (357)
T PRK05084 42 LTEYRRFFNWLISEGLSDASKIKDIPLSTLENLTKKDVEAFILYLRERPLL------N---GHST-------KKGNSQTT 105 (357)
T ss_pred HHHHHHHHHHHHHcCCCCcCCcccCCHHHHHhhhHHHHHHHHHHHHhcccc------c---cccc-------ccchhHHH
Confidence 3566778888876532 11 24567899999999998542100 0 0000 01246688
Q ss_pred hHHHHHHHHHHHHH
Q 023835 122 LDALIGRLRAAYEE 135 (276)
Q Consensus 122 LDALIGRLRAAfEE 135 (276)
+...++.||+.|.-
T Consensus 106 i~~~l~~l~~~~~~ 119 (357)
T PRK05084 106 INRTLSALKSLFKY 119 (357)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999999984
No 35
>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=25.64 E-value=78 Score=29.57 Aligned_cols=64 Identities=23% Similarity=0.264 Sum_probs=44.8
Q ss_pred CCChhhhhhhhhHHHHHHHHHhCCCCccc--ccccchhHhHHhhh-----------------hcccCceeeeecCCCCCC
Q 023835 43 PPSRYESQKRRDWNTFLQYLKNHKPPLTL--ARCSGAHVIEFLKY-----------------LDQFGKTKVHISGCPYFG 103 (276)
Q Consensus 43 ~~SRYEsQKRRDWnTF~QyL~NhrPPlsL--s~CSgaHVleFLry-----------------LDqfGKTKVH~~~C~ffG 103 (276)
.-.+|-++=|..-.+|.+||+.+.|-... ..--...|.|||.. ....|..++|-.+=--|.
T Consensus 147 ef~~yL~kvr~~R~eF~~~L~~~~~e~~~~~~~~l~~~v~eFL~~~~~~~~~~~~~~~~~~~~~~~~~~~~hpsgGLSY~ 226 (312)
T PF11709_consen 147 EFERYLKKVRPLRPEFKKWLREKHPESLTFDPSDLYDLVKEFLDLAPLKPPDVPDSKKSSSPYAEAGPPKTHPSGGLSYN 226 (312)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHhChhhhccCHHHHHHHHHHHHhcccccCcccccchhccCcccccCCCccccCcCcCcC
Confidence 34578888899999999999999986621 22345678899975 334667777776665665
Q ss_pred CCC
Q 023835 104 HPN 106 (276)
Q Consensus 104 ~p~ 106 (276)
+++
T Consensus 227 ~~g 229 (312)
T PF11709_consen 227 RTG 229 (312)
T ss_pred CCc
Confidence 544
No 36
>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=24.98 E-value=71 Score=32.06 Aligned_cols=36 Identities=28% Similarity=0.474 Sum_probs=28.2
Q ss_pred hhHHHHHHHHHHHHHhCCC---------------------CCCCCc-cchhHHHHHHH
Q 023835 121 SLDALIGRLRAAYEENGGR---------------------PESNPF-GARAVRIYLRE 156 (276)
Q Consensus 121 SLDALIGRLRAAfEE~GG~---------------------PEsNPF-aAraVRlYLRe 156 (276)
+.|...-..|.+.+.++++ .|.||| |-|++|+||..
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 4467777788888888776 379997 77999999964
No 37
>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=24.98 E-value=5.8e+02 Score=23.93 Aligned_cols=25 Identities=24% Similarity=0.335 Sum_probs=21.0
Q ss_pred hhhhhhhhHHHHHHHHHhCCCCccc
Q 023835 47 YESQKRRDWNTFLQYLKNHKPPLTL 71 (276)
Q Consensus 47 YEsQKRRDWnTF~QyL~NhrPPlsL 71 (276)
-.++.|+.|+.|.++.+.+.+|++.
T Consensus 166 ~~n~~r~~~~~~~~l~~~~p~pitg 190 (377)
T TIGR03190 166 VCDENRRLLRELFDYRKEADPKVTG 190 (377)
T ss_pred HHHHHHHHHHHHHHHHccCCCCcCH
Confidence 3567899999999999888888873
No 38
>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=24.90 E-value=31 Score=28.46 Aligned_cols=37 Identities=24% Similarity=0.353 Sum_probs=30.1
Q ss_pred hhhHHHHHHHHHh---CCCCcccccccchhHhHHhhhhcc
Q 023835 52 RRDWNTFLQYLKN---HKPPLTLARCSGAHVIEFLKYLDQ 88 (276)
Q Consensus 52 RRDWnTF~QyL~N---hrPPlsLs~CSgaHVleFLryLDq 88 (276)
...|..|++|+-. ..-|-.+.++.+.++.+||.-+|.
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 3468889988876 455777889999999999998875
No 39
>KOG4670 consensus Uncharacterized conserved membrane protein [Function unknown]
Probab=24.47 E-value=30 Score=35.92 Aligned_cols=59 Identities=25% Similarity=0.375 Sum_probs=42.2
Q ss_pred hhhhhHHH------------HHHHHHhCCCCcccccccchhHhHHhhhhcccCcee-----ee-ecCCCCCCCCCCC
Q 023835 50 QKRRDWNT------------FLQYLKNHKPPLTLARCSGAHVIEFLKYLDQFGKTK-----VH-ISGCPYFGHPNPP 108 (276)
Q Consensus 50 QKRRDWnT------------F~QyL~NhrPPlsLs~CSgaHVleFLryLDqfGKTK-----VH-~~~C~ffG~p~pp 108 (276)
-|+|.|++ ||-||..|.+|..+--=.-.---.|++-+++.-++. || ...|.+-...+||
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 67888875 999999999998776422222345677888886664 55 4668888877874
No 40
>PRK09279 pyruvate phosphate dikinase; Provisional
Probab=23.61 E-value=74 Score=34.09 Aligned_cols=36 Identities=36% Similarity=0.453 Sum_probs=0.0
Q ss_pred HHHHHHHhCCC-----------CCCCCc-cchhHHHHH--HHHhHHHHhh
Q 023835 129 LRAAYEENGGR-----------PESNPF-GARAVRIYL--REVRESQAKA 164 (276)
Q Consensus 129 LRAAfEE~GG~-----------PEsNPF-aAraVRlYL--ReVRd~QAKA 164 (276)
++..-++.|+. -|.||| |.|.+|+|| .|+=++|.+|
T Consensus 636 ~~~~a~~~g~~~~k~~~~~~~~~E~NPmLG~RG~Rl~l~~pei~~~QlrA 685 (879)
T PRK09279 636 IEELAEALGLSLEELKARVEALHEFNPMLGHRGCRLGITYPEIYEMQARA 685 (879)
T ss_pred HHHHHHHcCCCHHHHHHHhcCCCCCCCccccchhhcccCChHHHHHHHHH
No 41
>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=23.46 E-value=3.2e+02 Score=22.98 Aligned_cols=30 Identities=13% Similarity=0.228 Sum_probs=22.3
Q ss_pred hhHHHHHHHHHhCCCCcccccccchhHhHHhhhh
Q 023835 53 RDWNTFLQYLKNHKPPLTLARCSGAHVIEFLKYL 86 (276)
Q Consensus 53 RDWnTF~QyL~NhrPPlsLs~CSgaHVleFLryL 86 (276)
+.-+.|.+|+.++. +...+..||.+|+.++
T Consensus 24 ~~~~~f~~~~~~~~----~~~it~~~~~~~~~~~ 53 (299)
T cd01187 24 RLLRDFVRFLERHG----AGFITTDLALRWAASP 53 (299)
T ss_pred HHHHHHHHHHHhCC----CCCCCHHHHHHHHhcC
Confidence 34557888988754 5677899999988764
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=23.33 E-value=82 Score=26.60 Aligned_cols=36 Identities=17% Similarity=0.460 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHhCCCCC---C---CC-ccchhHHHHHHHHhH
Q 023835 124 ALIGRLRAAYEENGGRPE---S---NP-FGARAVRIYLREVRE 159 (276)
Q Consensus 124 ALIGRLRAAfEE~GG~PE---s---NP-FaAraVRlYLReVRd 159 (276)
.-|-+|+..|++.|...+ . ++ -.+..++.||||.-+
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 267888999999755
No 43
>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=22.34 E-value=47 Score=29.89 Aligned_cols=15 Identities=33% Similarity=0.448 Sum_probs=11.6
Q ss_pred hhHHHHHHHHHhCCC
Q 023835 53 RDWNTFLQYLKNHKP 67 (276)
Q Consensus 53 RDWnTF~QyL~NhrP 67 (276)
=|.|+|.|||...+.
T Consensus 141 VDR~EFdQYLn~~~~ 155 (197)
T PF12067_consen 141 VDRTEFDQYLNSSRC 155 (197)
T ss_pred hhHHHHHHHhccccC
Confidence 468999999996444
No 44
>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=22.24 E-value=93 Score=30.51 Aligned_cols=54 Identities=35% Similarity=0.524 Sum_probs=35.4
Q ss_pred chhHhHHhhhhcccC-ceeeeecCCCCCCCCCCCCCCCCchhhhcchh--HH----HHHHHHHHHHHhCCCCC
Q 023835 76 GAHVIEFLKYLDQFG-KTKVHISGCPYFGHPNPPAPCACPLKQAWGSL--DA----LIGRLRAAYEENGGRPE 141 (276)
Q Consensus 76 gaHVleFLryLDqfG-KTKVH~~~C~ffG~p~ppapC~CPLRQAWGSL--DA----LIGRLRAAfEE~GG~PE 141 (276)
|..=++||..|.+.| |-+|+. .-.|-.+.++ |..+ |. .--||..||+++|-.|.
T Consensus 48 G~agl~f~e~l~~~gakv~VpT----------TlNp~~~D~~--w~~~gvd~~f~~~q~~i~~ay~~mG~~~t 108 (389)
T cd01355 48 GDAGLEFLERLADQGAKVAVPT----------TLNPISMDLH--WRELGVDEEFAEKQARLVKAYKAMGVDPT 108 (389)
T ss_pred chhhHHHHHHHHhCCCeEeecC----------ccCCcccCcc--hhhcCCCHHHHHHHHHHHHHHHHcCCccc
Confidence 344479999887666 344433 3456666766 8755 32 34477899999999755
No 45
>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=21.90 E-value=2e+02 Score=22.12 Aligned_cols=39 Identities=31% Similarity=0.675 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHhCCCCCCCCccchhHHHHHHHHhHHHHhhhCCchhhh
Q 023835 124 ALIGRLRAAYEENGGRPESNPFGARAVRIYLREVRESQAKARGIPYEKK 172 (276)
Q Consensus 124 ALIGRLRAAfEE~GG~PEsNPFaAraVRlYLReVRd~QAKARGi~YeKK 172 (276)
.|--+.-++|+++|..+ ..|||++|+.| ++-+|||++-+
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 34456677889999875 56999999876 45589999875
No 46
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=21.89 E-value=1.9e+02 Score=22.69 Aligned_cols=38 Identities=32% Similarity=0.497 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHhCCCCCCCCccchhHHHHHHHHhHHHHhhhCCchhh
Q 023835 124 ALIGRLRAAYEENGGRPESNPFGARAVRIYLREVRESQAKARGIPYEK 171 (276)
Q Consensus 124 ALIGRLRAAfEE~GG~PEsNPFaAraVRlYLReVRd~QAKARGi~YeK 171 (276)
.|--+.-++|+++|-.+ ..|||+||+.+ ++-+|||++.
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 44556678899999875 57999999876 4557888874
No 47
>PRK10701 DNA-binding transcriptional regulator RstA; Provisional
Probab=21.86 E-value=73 Score=25.56 Aligned_cols=15 Identities=40% Similarity=0.545 Sum_probs=8.9
Q ss_pred hhHHHHHHHHHHHHH
Q 023835 121 SLDALIGRLRAAYEE 135 (276)
Q Consensus 121 SLDALIGRLRAAfEE 135 (276)
+||..|.|||.-+++
T Consensus 201 ~i~~~i~rlR~kl~~ 215 (240)
T PRK10701 201 SVDVAISRLRKKLLD 215 (240)
T ss_pred CHHHHHHHHHHhccc
Confidence 456666666666653
No 48
>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=21.41 E-value=1.9e+02 Score=21.71 Aligned_cols=39 Identities=28% Similarity=0.502 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHhCCCCCCCCccchhHHHHHHHHhHHHHhhhCCchhhh
Q 023835 124 ALIGRLRAAYEENGGRPESNPFGARAVRIYLREVRESQAKARGIPYEKK 172 (276)
Q Consensus 124 ALIGRLRAAfEE~GG~PEsNPFaAraVRlYLReVRd~QAKARGi~YeKK 172 (276)
.|--+..++|+++|-.+ .-||++||+.| ++.+|||++-+
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 45589998764
No 49
>KOG4405 consensus GDP dissociation inhibitor [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=20.92 E-value=44 Score=34.36 Aligned_cols=79 Identities=30% Similarity=0.492 Sum_probs=60.3
Q ss_pred HHHHHHHhCCCCcccccc--------cch---------hHhHHhhhhcccCceeeeecCCCCCCCCCCCCCCCCchhhhc
Q 023835 57 TFLQYLKNHKPPLTLARC--------SGA---------HVIEFLKYLDQFGKTKVHISGCPYFGHPNPPAPCACPLKQAW 119 (276)
Q Consensus 57 TF~QyL~NhrPPlsLs~C--------Sga---------HVleFLryLDqfGKTKVH~~~C~ffG~p~ppapC~CPLRQAW 119 (276)
+|.+||+.++=+..|..| +.. -...||..+.+||.|-. -=|.||+-..| .|-|-+--..
T Consensus 224 ~F~EyL~~~rltp~lqs~vl~aIaM~~~~~~tt~eGm~at~~fl~slGrfgntpf---LfPlYGqGELp-QcFCRlcAVf 299 (547)
T KOG4405|consen 224 PFSEYLKTMRLTPKLQSIVLHAIAMLSESQLTTIEGMDATKNFLTSLGRFGNTPF---LFPLYGQGELP-QCFCRLCAVF 299 (547)
T ss_pred cHHHHHHhcCCChhhHHHHHHHHHhcCcccccHHHHHHHHHHHHHHhhccCCCcc---eeeccCCCcch-HHHHHHHHHh
Confidence 999999999988877654 222 24579999999999983 34678887755 6888777777
Q ss_pred ch------------hHHHHHHHHHHHHHhCCC
Q 023835 120 GS------------LDALIGRLRAAYEENGGR 139 (276)
Q Consensus 120 GS------------LDALIGRLRAAfEE~GG~ 139 (276)
|. ||..+++..++.+.+|-+
T Consensus 300 GgIYcLr~~Vq~ivldk~s~~~~~~l~s~g~r 331 (547)
T KOG4405|consen 300 GGIYCLRRPVQAIVLDKESLDCKAILDSFGQR 331 (547)
T ss_pred cceEEeccchhheeecccccchhhhHhhhcch
Confidence 75 577788888999999965
No 50
>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 3". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2PJP_A 2UWM_A 1WSU_B 1LVA_A 2PLY_A.
Probab=20.56 E-value=44 Score=23.89 Aligned_cols=20 Identities=40% Similarity=0.529 Sum_probs=17.0
Q ss_pred ccchhHhHHhhhhcccCcee
Q 023835 74 CSGAHVIEFLKYLDQFGKTK 93 (276)
Q Consensus 74 CSgaHVleFLryLDqfGKTK 93 (276)
.|=+-++-+|.|+|+.|-|+
T Consensus 22 ~sRK~ai~lLE~lD~~g~T~ 41 (50)
T PF09107_consen 22 LSRKYAIPLLEYLDREGITR 41 (50)
T ss_dssp S-HHHHHHHHHHHHHTTSEE
T ss_pred ccHHHHHHHHHHHhccCCEE
Confidence 56677899999999999987
No 51
>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]
Probab=20.41 E-value=4.8e+02 Score=26.88 Aligned_cols=45 Identities=22% Similarity=0.355 Sum_probs=36.2
Q ss_pred cCCCCCCCCCCCCCCCCchhhhcchhHHHHHHHHHHHHHhCCCCCCC
Q 023835 97 SGCPYFGHPNPPAPCACPLKQAWGSLDALIGRLRAAYEENGGRPESN 143 (276)
Q Consensus 97 ~~C~ffG~p~ppapC~CPLRQAWGSLDALIGRLRAAfEE~GG~PEsN 143 (276)
-.|.+++.+. ..|+|--+|--=-++-|.|=|+--++..+--|.-+
T Consensus 336 cpcG~~~~~~--~~C~c~~~~~~~Y~~klSgp~lDRiDl~vev~~~~ 380 (490)
T COG0606 336 CPCGNLGAPL--RRCPCSPRQIKRYLNKLSGPFLDRIDLMVEVPRLS 380 (490)
T ss_pred CCccCCCCCC--CCcCCCHHHHHHHHHHhhHHHHhhhhheecccCCC
Confidence 4688887654 67999999998889999999999888888765544
No 52
>PF09958 DUF2192: Uncharacterized protein conserved in archaea (DUF2192); InterPro: IPR018693 This family of various hypothetical archaeal proteins has no known function.
Probab=20.32 E-value=86 Score=29.20 Aligned_cols=21 Identities=43% Similarity=0.618 Sum_probs=18.4
Q ss_pred hhHHHHHHHHHHHHHhCCCCC
Q 023835 121 SLDALIGRLRAAYEENGGRPE 141 (276)
Q Consensus 121 SLDALIGRLRAAfEE~GG~PE 141 (276)
+=+.||.-||..|+++|..|=
T Consensus 27 ~R~~lv~~L~~~Y~~~gIeP~ 47 (231)
T PF09958_consen 27 DREELVELLREVYEENGIEPF 47 (231)
T ss_pred CHHHHHHHHHHHHHHcCCCcC
Confidence 458899999999999999864
No 53
>COG0745 OmpR Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=20.28 E-value=82 Score=27.66 Aligned_cols=30 Identities=33% Similarity=0.578 Sum_probs=22.9
Q ss_pred CCCchhhhcc--------hhHHHHHHHHHHHHHhCCCC
Q 023835 111 CACPLKQAWG--------SLDALIGRLRAAYEENGGRP 140 (276)
Q Consensus 111 C~CPLRQAWG--------SLDALIGRLRAAfEE~GG~P 140 (276)
-.--+.+.|| +||..|+|||.-.++.+..+
T Consensus 175 R~~L~~~vw~~~~~~~~rtvdvhI~rLR~Kl~~~~~~~ 212 (229)
T COG0745 175 REQLLEAVWGYDFEVDSRTVDVHISRLRKKLEKDPGAG 212 (229)
T ss_pred HHHHHHHhcCCCCCCCccCHHHHHHHHHHHhccCCCCC
Confidence 3344677887 49999999999998886543
No 54
>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=20.06 E-value=60 Score=34.47 Aligned_cols=26 Identities=38% Similarity=0.561 Sum_probs=19.9
Q ss_pred CCCCCCc-cchhHHHHH--HHHhHHHHhh
Q 023835 139 RPESNPF-GARAVRIYL--REVRESQAKA 164 (276)
Q Consensus 139 ~PEsNPF-aAraVRlYL--ReVRd~QAKA 164 (276)
..|.||| |.|.||+|| .++=+.|.+|
T Consensus 651 ~~E~NP~LG~RGiRl~l~~pei~~~QlrA 679 (856)
T TIGR01828 651 LHEVNPMLGHRGCRLGITYPEIYEMQVRA 679 (856)
T ss_pred CCCCCCccccchhhhccCChHHHHHHHHH
Confidence 3599998 679999999 4566666655
Done!