Query 029917
Match_columns 185
No_of_seqs 82 out of 84
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 05:41:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029917.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029917hhsearch_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 1.7E-76 3.7E-81 470.0 10.3 122 32-153 11-132 (132)
2 PF08821 CGGC: CGGC domain; I 92.0 0.28 6E-06 37.8 4.3 67 50-126 29-98 (107)
3 PF02899 Phage_int_SAM_1: Phag 87.4 0.61 1.3E-05 31.2 2.7 40 43-83 21-60 (84)
4 cd00798 INT_XerDC XerD and Xer 84.2 2.5 5.5E-05 32.4 4.9 68 44-138 22-91 (284)
5 cd00799 INT_Cre Cre recombinas 82.2 9.2 0.0002 30.6 7.6 76 44-151 7-82 (287)
6 TIGR02225 recomb_XerD tyrosine 79.9 5 0.00011 31.1 5.2 69 43-139 20-90 (291)
7 PRK00283 xerD site-specific ty 77.4 4.6 0.0001 31.9 4.4 68 44-139 30-99 (299)
8 TIGR02224 recomb_XerC tyrosine 68.0 18 0.00038 28.2 5.7 69 45-139 22-92 (295)
9 COG1080 PtsA Phosphoenolpyruva 67.3 6.1 0.00013 38.8 3.6 41 109-149 305-367 (574)
10 PF00539 Tat: Transactivating 63.2 3.7 7.9E-05 30.4 1.0 20 155-174 45-64 (68)
11 cd01185 INT_Tn4399 Tn4399 and 55.9 34 0.00073 27.5 5.4 68 47-139 44-115 (299)
12 PRK10529 DNA-binding transcrip 51.3 13 0.00028 28.1 2.2 17 114-130 191-207 (225)
13 smart00259 ZnF_A20 A20-like zi 48.7 8.7 0.00019 23.4 0.8 16 90-105 7-22 (26)
14 PF05528 Coronavirus_5: Corona 46.0 3.4 7.3E-05 31.6 -1.6 20 133-152 4-26 (82)
15 PF00486 Trans_reg_C: Transcri 43.2 24 0.00053 23.2 2.4 21 113-133 44-64 (77)
16 PRK10816 DNA-binding transcrip 42.9 18 0.00038 27.4 1.8 24 106-129 173-204 (223)
17 cd00801 INT_P4 Bacteriophage P 42.8 33 0.00071 27.8 3.5 26 113-139 135-163 (357)
18 cd08800 Death_UNC5A Death doma 42.0 15 0.00032 28.0 1.3 17 116-132 60-76 (84)
19 PF14768 RPA_interact_C: Repli 41.6 25 0.00054 25.5 2.4 35 103-137 18-56 (82)
20 cd08781 Death_UNC5-like Death 40.6 26 0.00056 25.5 2.3 23 110-132 51-76 (83)
21 PF13495 Phage_int_SAM_4: Phag 39.5 26 0.00056 23.5 2.1 54 46-128 24-77 (85)
22 PF13276 HTH_21: HTH-like doma 37.6 52 0.0011 21.6 3.3 29 116-149 4-32 (60)
23 smart00862 Trans_reg_C Transcr 37.4 34 0.00074 22.4 2.4 20 112-131 44-63 (78)
24 PF00140 Sigma70_r1_2: Sigma-7 36.1 25 0.00055 22.2 1.5 13 141-153 2-14 (37)
25 PRK00236 xerC site-specific ty 34.7 1.2E+02 0.0026 23.6 5.3 36 45-81 32-67 (297)
26 COG4974 XerD Site-specific rec 34.0 29 0.00063 31.7 2.1 44 35-84 25-69 (300)
27 KOG4670 Uncharacterized conser 33.6 26 0.00056 34.9 1.8 59 43-101 468-544 (602)
28 PF10865 DUF2703: Domain of un 32.1 19 0.0004 28.6 0.5 43 72-134 2-44 (120)
29 cd04372 RhoGAP_chimaerin RhoGA 32.0 41 0.00088 27.2 2.4 36 117-152 45-87 (194)
30 KOG4405 GDP dissociation inhib 31.7 17 0.00037 35.6 0.3 79 50-132 224-331 (547)
31 smart00243 GAS2 Growth-Arrest- 30.2 34 0.00074 25.8 1.6 15 47-61 55-69 (73)
32 PF06252 DUF1018: Protein of u 29.4 1.7E+02 0.0036 22.1 5.2 74 47-134 2-75 (119)
33 cd04436 DEP_fRgd2 DEP (Disheve 29.1 28 0.00062 26.5 1.0 40 49-88 33-76 (84)
34 PF04221 RelB: RelB antitoxin; 28.6 1E+02 0.0023 22.0 3.8 39 117-165 11-49 (83)
35 TIGR01418 PEP_synth phosphoeno 28.2 96 0.0021 31.0 4.7 42 116-157 547-618 (782)
36 PLN02837 threonine-tRNA ligase 27.8 35 0.00076 32.8 1.6 15 109-123 489-503 (614)
37 PF09958 DUF2192: Uncharacteri 27.4 53 0.0012 29.2 2.5 21 114-134 27-47 (231)
38 TIGR02384 RelB_DinJ addiction 27.4 1.2E+02 0.0027 22.1 4.1 39 117-165 12-50 (83)
39 PF08544 GHMP_kinases_C: GHMP 27.4 8.3 0.00018 25.9 -1.9 72 44-127 6-84 (85)
40 PTZ00398 phosphoenolpyruvate c 27.2 98 0.0021 32.2 4.7 43 111-153 263-336 (974)
41 PRK11235 bifunctional antitoxi 26.9 1.2E+02 0.0025 22.7 3.9 37 117-163 11-47 (80)
42 cd00383 trans_reg_C Effector d 26.5 57 0.0012 22.1 2.1 20 113-132 62-81 (95)
43 PF09674 DUF2400: Protein of u 25.9 62 0.0013 28.2 2.6 25 109-133 24-48 (232)
44 KOG1452 Predicted Rho GTPase-a 25.8 40 0.00086 32.2 1.6 31 121-152 233-271 (442)
45 cd01355 AcnX Putative Aconitas 25.5 70 0.0015 30.0 3.1 53 70-134 49-108 (389)
46 PF12067 Sox_C_TAD: Sox C-term 25.4 39 0.00085 29.0 1.3 14 46-59 141-154 (197)
47 PF11709 Mit_ribos_Mrp51: Mito 24.6 61 0.0013 28.9 2.4 64 36-99 147-229 (312)
48 COG0745 OmpR Response regulato 24.3 61 0.0013 27.2 2.3 37 97-133 168-212 (229)
49 TIGR01417 PTS_I_fam phosphoeno 24.0 81 0.0017 30.4 3.3 36 114-149 308-365 (565)
50 PF09107 SelB-wing_3: Elongati 24.0 38 0.00083 23.0 0.8 20 67-86 22-41 (50)
51 TIGR03190 benz_CoA_bzdN benzoy 23.9 5.3E+02 0.012 23.1 9.5 24 40-63 166-189 (377)
52 PF01754 zf-A20: A20-like zinc 23.7 30 0.00066 21.0 0.3 16 89-104 5-20 (25)
53 TIGR01828 pyru_phos_dikin pyru 23.6 46 0.001 33.8 1.7 26 132-157 651-679 (856)
54 PRK12435 ferrochelatase; Provi 23.6 1.5E+02 0.0033 26.3 4.7 16 117-132 37-52 (311)
55 PF10520 Kua-UEV1_localn: Kua- 23.6 39 0.00084 28.5 0.9 24 111-134 17-41 (178)
56 PF02187 GAS2: Growth-Arrest-S 23.5 20 0.00043 26.7 -0.7 13 48-60 56-68 (73)
57 PF07700 HNOB: Heme NO binding 23.5 29 0.00062 27.4 0.2 37 45-81 64-103 (171)
58 COG4865 Glutamate mutase epsil 23.4 55 0.0012 31.6 2.0 23 118-140 196-218 (485)
59 PF00667 FAD_binding_1: FAD bi 23.2 72 0.0016 26.0 2.4 45 69-113 56-100 (219)
60 PF07535 zf-DBF: DBF zinc fing 23.2 42 0.0009 23.1 0.9 12 112-123 37-48 (49)
61 PRK13197 pyrrolidone-carboxyla 22.8 2.6E+02 0.0056 23.6 5.7 84 36-129 108-200 (215)
62 PF06480 FtsH_ext: FtsH Extrac 22.8 1.1E+02 0.0023 20.9 2.9 26 112-137 84-109 (110)
63 PRK11173 two-component respons 22.7 67 0.0015 24.7 2.1 18 114-131 200-217 (237)
64 cd04383 RhoGAP_srGAP RhoGAP_sr 22.4 86 0.0019 25.4 2.7 35 117-152 47-88 (188)
65 PF01663 Phosphodiest: Type I 22.2 69 0.0015 26.3 2.1 27 108-134 208-234 (365)
66 PF06947 DUF1290: Protein of u 22.2 77 0.0017 24.6 2.3 17 113-129 16-32 (88)
67 cd04379 RhoGAP_SYD1 RhoGAP_SYD 22.0 80 0.0017 26.3 2.5 36 117-152 47-89 (207)
68 PRK09468 ompR osmolarity respo 22.0 73 0.0016 24.4 2.1 16 114-129 201-216 (239)
69 PF09336 Vps4_C: Vps4 C termin 21.8 48 0.001 23.2 1.0 31 48-83 32-62 (62)
70 PRK05084 xerS site-specific ty 21.5 1.2E+02 0.0026 25.4 3.5 67 46-128 43-119 (357)
71 PF02896 PEP-utilizers_C: PEP- 20.7 1.4E+02 0.0031 26.6 3.9 38 112-149 58-118 (293)
72 cd00778 ProRS_core_arch_euk Pr 20.5 56 0.0012 27.6 1.3 17 108-124 244-260 (261)
73 PHA03019 hypothetical protein; 20.3 69 0.0015 24.3 1.6 22 44-65 44-65 (77)
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=1.7e-76 Score=470.03 Aligned_cols=122 Identities=77% Similarity=1.392 Sum_probs=119.2
Q ss_pred CCCCCCchhhhhhhhhhhHHHHHHHhcCCCcccCCCCccchhhhhhhhccCCceeeecccccccCCCCCCCCCCCchhhh
Q 029917 32 QSPAPLSRYESQKRRDWNTFGQYLRNQRPPVALSQCNSNHVLDFLRYLDQFGKTKVHLQGCVFFGQPEPPGPCSCPLKQA 111 (185)
Q Consensus 32 ~~~~~~srYesQKrrdwntf~qyL~n~rPPlsl~~cs~~hVleFL~ylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQA 111 (185)
++++++||||+|||||||||+|||+||+||++|++|+++|||+||+|+|||||||||.++|+|||+|+||+||+||||||
T Consensus 11 ~~~~~~SrYesQKrrdwntf~qyL~n~rPP~~L~~csg~hVl~FL~~~d~~GkTkVh~~~C~~~g~~~~p~~C~CPlrqA 90 (132)
T PF04852_consen 11 SPQPAPSRYESQKRRDWNTFGQYLRNHRPPLSLSRCSGNHVLEFLRYLDQFGKTKVHGQGCPFFGHPSPPAPCPCPLRQA 90 (132)
T ss_pred CCCCCCcccchhhhHHHHHHHHHHHccCCCcchhhcChHHHHHHHHHHhccCCeeecCCCCCCCCCCCCCCCCCCcHHHH
Confidence 44568899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchhHHHHHHHHHHHHHhCCCCCCCCccchhHHHHHHHHhHH
Q 029917 112 WGSLDALIGRLRAAYEENGGLPETNPFASGAIRIYLREVRDS 153 (185)
Q Consensus 112 wGSLDALIGRLRAafeE~Gg~pE~NPF~araVR~YLReVRd~ 153 (185)
||||||||||||||||||||.||+|||+++|||+|||||||+
T Consensus 91 wGSlDalIGrLraafee~Gg~pe~NPf~~~~vr~yLr~vr~~ 132 (132)
T PF04852_consen 91 WGSLDALIGRLRAAFEEHGGHPEANPFAARAVRLYLREVRDS 132 (132)
T ss_pred hccHHHHHHHHHHHHHHhCCCCCCCchhhHHHHHHHHHHhcC
Confidence 999999999999999999999999999999999999999985
No 2
>PF08821 CGGC: CGGC domain; InterPro: IPR014925 Proteins in this entry are a quite highly conserved sequence of CGGC in its central region. The region has many conserved cysteines and histidines suggestive of a zinc binding function.
Probab=92.00 E-value=0.28 Score=37.78 Aligned_cols=67 Identities=21% Similarity=0.522 Sum_probs=50.4
Q ss_pred HHHHHHHhcCCCcccCCCC---ccchhhhhhhhccCCceeeecccccccCCCCCCCCCCCchhhhcchhHHHHHHHHHHH
Q 029917 50 TFGQYLRNQRPPVALSQCN---SNHVLDFLRYLDQFGKTKVHLQGCVFFGQPEPPGPCSCPLKQAWGSLDALIGRLRAAY 126 (185)
Q Consensus 50 tf~qyL~n~rPPlsl~~cs---~~hVleFL~ylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQAwGSLDALIGRLRAaf 126 (185)
.|.+|=.+..--+.+.+|. +..|+..+..+-..|-..||..+|...+.+.+ +||. +|.|+-.|+++|
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 3444443233345566664 58888888998899999999999999887654 5665 899999999888
No 3
>PF02899 Phage_int_SAM_1: Phage integrase, N-terminal SAM-like domain; InterPro: IPR004107 Proteins containing this domain cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [, ]. The phage integrase N-terminal SAM-like domain is almost always found with the signature that defines the phage integrase family (see IPR002104 from INTERPRO).; GO: 0003677 DNA binding, 0015074 DNA integration; PDB: 1Z1G_B 1Z19_A 1Z1B_A 2OXO_A 1P7D_B 3NRW_A 1A0P_A.
Probab=87.41 E-value=0.61 Score=31.18 Aligned_cols=40 Identities=30% Similarity=0.488 Sum_probs=31.1
Q ss_pred hhhhhhhHHHHHHHhcCCCcccCCCCccchhhhhhhhccCC
Q 029917 43 QKRRDWNTFGQYLRNQRPPVALSQCNSNHVLDFLRYLDQFG 83 (185)
Q Consensus 43 QKrrdwntf~qyL~n~rPPlsl~~cs~~hVleFL~ylDqfG 83 (185)
.-+++++.|.+||.+ ....++..++..||.+||.++-+.|
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 6677778899999999999987665
No 4
>cd00798 INT_XerDC XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid inheritance. They share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism with the DNA breaking-rejoining enzyme superfamily. In Escherichia coli, the Xer site-specific recombination system acts to convert dimeric chromosomes, which are formed by homologous recombination to monomers. Two related recombinases, XerC and XerD, bind cooperatively to a recombination site present in the E. coli chromosome. Each recombinase catalyzes the exchange of one pair of DNA strand in a reaction that proceeds through a Holliday junction intermediate. These enzymes can bridge two different and well-separated DNA sequen
Probab=84.19 E-value=2.5 Score=32.36 Aligned_cols=68 Identities=24% Similarity=0.314 Sum_probs=47.4
Q ss_pred hhhhhhHHHHHHHhcCCCcccCCCCccchhhhhhhhccCCceeeecccccccCCCCCCCCCCCchhhhcchhHHHHHHHH
Q 029917 44 KRRDWNTFGQYLRNQRPPVALSQCNSNHVLDFLRYLDQFGKTKVHLQGCVFFGQPEPPGPCSCPLKQAWGSLDALIGRLR 123 (185)
Q Consensus 44 Krrdwntf~qyL~n~rPPlsl~~cs~~hVleFL~ylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQAwGSLDALIGRLR 123 (185)
-+..|+.|.+|+.....+. +..-+..||.+|+.++...| ....++...++-|+
T Consensus 22 ~~~~~~~~~~~~~~~~~~~-~~~l~~~~i~~~~~~~~~~~--------------------------~~~~t~~~~~~~l~ 74 (284)
T cd00798 22 YRRDLERFLEFLEERGILF-PADVTPDDIRRFLAELKDQG--------------------------LSARSIARKLSALR 74 (284)
T ss_pred HHHHHHHHHHHHHHcCCCc-hhhCCHHHHHHHHHHhhhcC--------------------------CCHHHHHHHHHHHH
Confidence 3557899999998754332 56667899999999876543 23457788888888
Q ss_pred HHHHHh--CCCCCCCCc
Q 029917 124 AAYEEN--GGLPETNPF 138 (185)
Q Consensus 124 AafeE~--Gg~pE~NPF 138 (185)
++|.-. -+..+.||+
T Consensus 75 ~~~~~~~~~~~~~~~p~ 91 (284)
T cd00798 75 SFFKFLLREGLILANPA 91 (284)
T ss_pred HHHHHHHHcCCccCChh
Confidence 888732 133456887
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=82.18 E-value=9.2 Score=30.62 Aligned_cols=76 Identities=20% Similarity=0.294 Sum_probs=52.3
Q ss_pred hhhhhhHHHHHHHhcCCCcccCCCCccchhhhhhhhccCCceeeecccccccCCCCCCCCCCCchhhhcchhHHHHHHHH
Q 029917 44 KRRDWNTFGQYLRNQRPPVALSQCNSNHVLDFLRYLDQFGKTKVHLQGCVFFGQPEPPGPCSCPLKQAWGSLDALIGRLR 123 (185)
Q Consensus 44 Krrdwntf~qyL~n~rPPlsl~~cs~~hVleFL~ylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQAwGSLDALIGRLR 123 (185)
-..+++.|..|+...- +....-+..+|.+||.||.+ ..+..++-..++.|+
T Consensus 7 y~~~l~~f~~~~~~~~--~~~~~~~~~~i~~~~~~l~~---------------------------~~s~~ti~~~~~~l~ 57 (287)
T cd00799 7 YLSDWRRFAAWCQAHG--RTPLPASPETVTLYLTDLAD---------------------------SLAPSTISRRLSALS 57 (287)
T ss_pred HHHHHHHHHHHHHhcC--CCCCCCCHHHHHHHHHHHHh---------------------------ccChHHHHHHHHHHH
Confidence 3567889999998752 12222357899999998752 124578889999999
Q ss_pred HHHHHhCCCCCCCCccchhHHHHHHHHh
Q 029917 124 AAYEENGGLPETNPFASGAIRIYLREVR 151 (185)
Q Consensus 124 AafeE~Gg~pE~NPF~araVR~YLReVR 151 (185)
.+|+..+. .||+....+..-|+.++
T Consensus 58 ~~~~~~~~---~~p~~~~~~~~~~~~~~ 82 (287)
T cd00799 58 QLHRRSGL---PSPADSPLVRLVLRGIR 82 (287)
T ss_pred HHHHHcCC---CCCccCHHHHHHHHHHH
Confidence 99985432 58877655666665554
No 6
>TIGR02225 recomb_XerD tyrosine recombinase XerD. The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerD, one of two closely related chromosomal proteins along with XerC (TIGR02224). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and with homologs of XerD on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerD, as some apparent XerD examples score below the trusted and noise cutoff scores. XerC and XerD interact with cell division protein FtsK.
Probab=79.89 E-value=5 Score=31.09 Aligned_cols=69 Identities=28% Similarity=0.467 Sum_probs=46.7
Q ss_pred hhhhhhhHHHHHHHhcCCCcccCCCCccchhhhhhhhccCCceeeecccccccCCCCCCCCCCCchhhhcchhHHHHHHH
Q 029917 43 QKRRDWNTFGQYLRNQRPPVALSQCNSNHVLDFLRYLDQFGKTKVHLQGCVFFGQPEPPGPCSCPLKQAWGSLDALIGRL 122 (185)
Q Consensus 43 QKrrdwntf~qyL~n~rPPlsl~~cs~~hVleFL~ylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQAwGSLDALIGRL 122 (185)
+-+..++.|..|+.... ..+..-+..||.+|+.++.+.| .+.-++...+.-|
T Consensus 20 ~~~~~~~~~~~~~~~~~--~~~~~it~~~i~~~~~~~~~~~--------------------------~~~~t~~~~~~~l 71 (291)
T TIGR02225 20 AYRRDLEKFLEFLEERG--IDLEEVDRGDIVDFLAELKEAG--------------------------LSARSIARALSAL 71 (291)
T ss_pred HHHHHHHHHHHHHHhcC--CChHHCCHHHHHHHHHHhhcCC--------------------------CCHhHHHHHHHHH
Confidence 34456788889988542 2444556889999999877543 1224678899999
Q ss_pred HHHHHHh--CCCCCCCCcc
Q 029917 123 RAAYEEN--GGLPETNPFA 139 (185)
Q Consensus 123 RAafeE~--Gg~pE~NPF~ 139 (185)
+++|+-. -+..+.|||.
T Consensus 72 ~~~~~~a~~~~~~~~np~~ 90 (291)
T TIGR02225 72 RSFYRFLLREGIREDDPSA 90 (291)
T ss_pred HHHHHHHHhcccccCCchh
Confidence 9999732 2344578874
No 7
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed
Probab=77.41 E-value=4.6 Score=31.87 Aligned_cols=68 Identities=26% Similarity=0.352 Sum_probs=47.7
Q ss_pred hhhhhhHHHHHHHhcCCCcccCCCCccchhhhhhhhccCCceeeecccccccCCCCCCCCCCCchhhhcchhHHHHHHHH
Q 029917 44 KRRDWNTFGQYLRNQRPPVALSQCNSNHVLDFLRYLDQFGKTKVHLQGCVFFGQPEPPGPCSCPLKQAWGSLDALIGRLR 123 (185)
Q Consensus 44 Krrdwntf~qyL~n~rPPlsl~~cs~~hVleFL~ylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQAwGSLDALIGRLR 123 (185)
-+.+|+.|..||....- .+...+..||.+|+.++.+.| .+-.++...+..|+
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 556678899999999875421 23457788899999
Q ss_pred HHHHHh--CCCCCCCCcc
Q 029917 124 AAYEEN--GGLPETNPFA 139 (185)
Q Consensus 124 AafeE~--Gg~pE~NPF~ 139 (185)
++|+-. -+.-..|||.
T Consensus 82 ~~~~~a~~~~~i~~np~~ 99 (299)
T PRK00283 82 RFFQFLLREGLREDDPSA 99 (299)
T ss_pred HHHHHHHHcCCcccCchh
Confidence 998733 1234578864
No 8
>TIGR02224 recomb_XerC tyrosine recombinase XerC. The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerC, one of two closely related chromosomal proteins along with XerD (TIGR02225). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and homologs of XerC on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerC, as some apparent XerC examples score in the gray zone between trusted (450) and noise (410) cutoffs, along with some XerD examples. XerC and XerD interact with cell division protein FtsK.
Probab=68.05 E-value=18 Score=28.22 Aligned_cols=69 Identities=29% Similarity=0.403 Sum_probs=46.8
Q ss_pred hhhhhHHHHHHHhcCCCcccCCCCccchhhhhhhhccCCceeeecccccccCCCCCCCCCCCchhhhcchhHHHHHHHHH
Q 029917 45 RRDWNTFGQYLRNQRPPVALSQCNSNHVLDFLRYLDQFGKTKVHLQGCVFFGQPEPPGPCSCPLKQAWGSLDALIGRLRA 124 (185)
Q Consensus 45 rrdwntf~qyL~n~rPPlsl~~cs~~hVleFL~ylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQAwGSLDALIGRLRA 124 (185)
+.+++.|.+||........+..-+..||.+||.++.+.| .+..++...+..|++
T Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~l~~~~i~~~~~~~~~~~--------------------------~~~~T~~~~~~~l~~ 75 (295)
T TIGR02224 22 RRDLKAFLEFLEEEGGLASLAEVTAADLRSFLAELHARG--------------------------LSRRSLARKLSALRS 75 (295)
T ss_pred HHHHHHHHHHHHhcCCCCccccCcHHHHHHHHHHhcccC--------------------------CCHHHHHHHHHHHHH
Confidence 345667888888766567777888999999999865522 123567777888888
Q ss_pred HHHHh--CCCCCCCCcc
Q 029917 125 AYEEN--GGLPETNPFA 139 (185)
Q Consensus 125 afeE~--Gg~pE~NPF~ 139 (185)
+|.-. -+.-+.|||.
T Consensus 76 ~~~~a~~~~~~~~np~~ 92 (295)
T TIGR02224 76 FYRFLVRRGLIKANPAA 92 (295)
T ss_pred HHHHHHHcCccccChHh
Confidence 87642 1223468863
No 9
>COG1080 PtsA Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]
Probab=67.30 E-value=6.1 Score=38.84 Aligned_cols=41 Identities=34% Similarity=0.519 Sum_probs=32.9
Q ss_pred hhhcchhHHHHHHHHHHHHHhCCC--------------------C-CCCCc-cchhHHHHHHH
Q 029917 109 KQAWGSLDALIGRLRAAYEENGGL--------------------P-ETNPF-ASGAIRIYLRE 149 (185)
Q Consensus 109 RQAwGSLDALIGRLRAafeE~Gg~--------------------p-E~NPF-~araVR~YLRe 149 (185)
|..|=+.|..----++..|.+||+ | |.||| |-|+||+||..
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 556667788877788888998886 3 79998 68999999964
No 10
>PF00539 Tat: Transactivating regulatory protein (Tat); InterPro: IPR001831 Like other lentiviruses, Human immunodeficiency virus 1 (HIV-1) encodes a trans-activating regulatory protein (Tat), which is essential for efficient transcription of the viral genome [, ]. Tat acts by binding to an RNA stem-loop structure, the trans-activating response element (TAR), found at the 5' ends of nascent HIV-1 transcripts. In binding to TAR, Tat alters the properties of the transcription complex, recruits a positive transcription elongation complex (P-TEFb) and hence increases the production of full-length viral RNA []. Tat protein also associates with RNA polymerase II complexes during early transcription elongation after the promoter clearance and before the synthesis of full-length TAR RNA transcript. This interaction of Tat with RNA polymerase II elongation complexes is P-TEFb-independent. There are two Tat binding sites on each transcription elongation complex; one is located on TAR RNA and the other one on RNA polymerase II near the exit site for nascent mRNA transcripts which suggests that two Tat molecules are involved in performing various functions during a single round of HIV-1 mRNA synthesis []. The minimum Tat sequence that can mediate specific TAR binding in vitro has been mapped to a basic domain of 10 amino acids, comprising mostly Arg and Lys residues. Regulatory activity, however, also requires the 47 N-terminal residues, which interact with components of the transcription complex and function as a transcriptional activation domain [, , ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 2W2H_D 1ZBN_B 1TVS_A 1TVT_A 3O6L_C 3O6M_C 3MI9_C 3MIA_C 1JFW_A 1TBC_A ....
Probab=63.19 E-value=3.7 Score=30.38 Aligned_cols=20 Identities=35% Similarity=0.655 Sum_probs=15.3
Q ss_pred hhhhCCchhhhhhccCCccc
Q 029917 155 AKARGIPYKKKKKKRMTVKA 174 (185)
Q Consensus 155 AkArgi~y~kkk~k~~~~~~ 174 (185)
-|+-||.|..|||||+..+.
T Consensus 45 ~KgLGI~Y~r~rrRrr~~~~ 64 (68)
T PF00539_consen 45 QKGLGISYGRKRRRRRTPQS 64 (68)
T ss_dssp CTSSSTSSSSSSCSCCCSSS
T ss_pred eCCCcccccccccCcCCCCC
Confidence 47889999999876665543
No 11
>cd01185 INT_Tn4399 Tn4399 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains. This CD includes various bacterial integrases, including cLV25, a Bacteroides fragilis chromosomal transfer factor integrase similar to the Bacteroides mobilizable transposon, Tn4399, integrase.
Probab=55.92 E-value=34 Score=27.49 Aligned_cols=68 Identities=16% Similarity=0.247 Sum_probs=43.7
Q ss_pred hhhHHHHHHHhcCC--CcccCCCCccchhhhhhhhccCCceeeecccccccCCCCCCCCCCCchhhhcchhHHHHHHHHH
Q 029917 47 DWNTFGQYLRNQRP--PVALSQCNSNHVLDFLRYLDQFGKTKVHLQGCVFFGQPEPPGPCSCPLKQAWGSLDALIGRLRA 124 (185)
Q Consensus 47 dwntf~qyL~n~rP--Plsl~~cs~~hVleFL~ylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQAwGSLDALIGRLRA 124 (185)
..+.|..||....+ .+.+..-+..||.+|+.|+-+.. ...-.++...++-||+
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 67788888999999999972110 1223456667777777
Q ss_pred HHHHh--CCCCCCCCcc
Q 029917 125 AYEEN--GGLPETNPFA 139 (185)
Q Consensus 125 afeE~--Gg~pE~NPF~ 139 (185)
+|.-. .+.-..|||.
T Consensus 99 ~~~~a~~~~~i~~np~~ 115 (299)
T cd01185 99 LLKIAYRDKGLRDNPFA 115 (299)
T ss_pred HHHHHHHCcCccCCCcc
Confidence 77642 2333356764
No 12
>PRK10529 DNA-binding transcriptional activator KdpE; Provisional
Probab=51.32 E-value=13 Score=28.06 Aligned_cols=17 Identities=29% Similarity=0.485 Sum_probs=13.5
Q ss_pred hhHHHHHHHHHHHHHhC
Q 029917 114 SLDALIGRLRAAYEENG 130 (185)
Q Consensus 114 SLDALIGRLRAafeE~G 130 (185)
+||.+|.|||.-+++.+
T Consensus 191 ~~~~~i~rlR~kl~~~~ 207 (225)
T PRK10529 191 YLRIYMGHLRQKLEQDP 207 (225)
T ss_pred CHHHHHHHHHHHhccCC
Confidence 58899999999887544
No 13
>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=48.74 E-value=8.7 Score=23.39 Aligned_cols=16 Identities=56% Similarity=1.271 Sum_probs=13.7
Q ss_pred ccccccCCCCCCCCCC
Q 029917 90 QGCVFFGQPEPPGPCS 105 (185)
Q Consensus 90 ~~C~ffg~p~ppapC~ 105 (185)
.+|.|||.|..-..|.
T Consensus 7 ~~CgF~G~~~t~~~Cs 22 (26)
T smart00259 7 PGCGFFGNPATEGLCS 22 (26)
T ss_pred CCCCCcCChhhcccCH
Confidence 6999999998877774
No 14
>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=45.96 E-value=3.4 Score=31.60 Aligned_cols=20 Identities=50% Similarity=0.772 Sum_probs=15.2
Q ss_pred CCCCCcc---chhHHHHHHHHhH
Q 029917 133 PETNPFA---SGAIRIYLREVRD 152 (185)
Q Consensus 133 pE~NPF~---araVR~YLReVRd 152 (185)
...|||+ ||-+|+||||=-|
T Consensus 4 ~k~NPfr~aiARKaRiyLr~Gld 26 (82)
T PF05528_consen 4 SKDNPFRGAIARKARIYLREGLD 26 (82)
T ss_pred cccCchhhhhhhheeeeeecCCc
Confidence 3479995 7889999997443
No 15
>PF00486 Trans_reg_C: Transcriptional regulatory protein, C terminal; InterPro: IPR001867 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain that is almost always found associated with the response regulator receiver domain (see IPR001789 from INTERPRO). It may play a role in DNA binding [].; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2K4J_A 2JPB_A 1ODD_A 1OPC_A 1KGS_A 2PMU_E 2JZY_A 1GXP_B 1QQI_A 2Z33_A ....
Probab=43.18 E-value=24 Score=23.24 Aligned_cols=21 Identities=52% Similarity=0.782 Sum_probs=18.2
Q ss_pred chhHHHHHHHHHHHHHhCCCC
Q 029917 113 GSLDALIGRLRAAYEENGGLP 133 (185)
Q Consensus 113 GSLDALIGRLRAafeE~Gg~p 133 (185)
-+||.+|-|||..++..|..+
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 489999999999999987544
No 16
>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional
Probab=42.89 E-value=18 Score=27.39 Aligned_cols=24 Identities=29% Similarity=0.542 Sum_probs=18.0
Q ss_pred Cchhhhcc--------hhHHHHHHHHHHHHHh
Q 029917 106 CPLKQAWG--------SLDALIGRLRAAYEEN 129 (185)
Q Consensus 106 CPlRQAwG--------SLDALIGRLRAafeE~ 129 (185)
--+++.|| +||.+|.|||.-+++.
T Consensus 173 ~l~~~~w~~~~~~~~~~v~~~i~rLR~kl~~~ 204 (223)
T PRK10816 173 SLMLQLYPDAELRESHTIDVLMGRLRKKIQAQ 204 (223)
T ss_pred HHHHHhcCCCCCCCcCCHHHHHHHHHHHhccC
Confidence 34556776 7899999999888764
No 17
>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=42.76 E-value=33 Score=27.84 Aligned_cols=26 Identities=23% Similarity=0.360 Sum_probs=20.2
Q ss_pred chhHHHHHHHHHHHHH---hCCCCCCCCcc
Q 029917 113 GSLDALIGRLRAAYEE---NGGLPETNPFA 139 (185)
Q Consensus 113 GSLDALIGRLRAafeE---~Gg~pE~NPF~ 139 (185)
-++...+..|+++|+- +|..+ .|||.
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 45444 89985
No 18
>cd08800 Death_UNC5A Death domain found in Uncoordinated-5A. Death Domain (DD) found in Uncoordinated-5A (UNC5A). UNC5A is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a critical role in neuronal development and differentiation, as well as axon-guidance. It also plays a role in regulating apoptosis in non-neuronal cells as a downstream target of p53. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathway
Probab=42.03 E-value=15 Score=27.97 Aligned_cols=17 Identities=24% Similarity=0.274 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHhCCC
Q 029917 116 DALIGRLRAAYEENGGL 132 (185)
Q Consensus 116 DALIGRLRAafeE~Gg~ 132 (185)
|.-|+.|.++++|+|+.
T Consensus 60 ~g~l~~L~~~l~emGR~ 76 (84)
T cd08800 60 NGNLNQLAAVVAEIGKQ 76 (84)
T ss_pred CCcHHHHHHHHHHhCch
Confidence 44589999999999974
No 19
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=41.60 E-value=25 Score=25.55 Aligned_cols=35 Identities=29% Similarity=0.442 Sum_probs=30.8
Q ss_pred CCCCchhhhcc----hhHHHHHHHHHHHHHhCCCCCCCC
Q 029917 103 PCSCPLKQAWG----SLDALIGRLRAAYEENGGLPETNP 137 (185)
Q Consensus 103 pC~CPlRQAwG----SLDALIGRLRAafeE~Gg~pE~NP 137 (185)
-|+|-|+..-+ +++.|=-+|..+++||......+|
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 999999999999999988787777
No 20
>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=40.59 E-value=26 Score=25.52 Aligned_cols=23 Identities=26% Similarity=0.400 Sum_probs=19.0
Q ss_pred hhcc---hhHHHHHHHHHHHHHhCCC
Q 029917 110 QAWG---SLDALIGRLRAAYEENGGL 132 (185)
Q Consensus 110 QAwG---SLDALIGRLRAafeE~Gg~ 132 (185)
.-|. +-|.-|+.|..+++|+|+.
T Consensus 51 ~~We~~~~~~~tv~~L~~~L~~mgr~ 76 (83)
T cd08781 51 DLWEARHRDDGALNDLAQILEEMGRT 76 (83)
T ss_pred HHHHhcCCCcchHHHHHHHHHHcCcH
Confidence 4574 4589999999999999975
No 21
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=39.54 E-value=26 Score=23.55 Aligned_cols=54 Identities=15% Similarity=0.297 Sum_probs=32.2
Q ss_pred hhhhHHHHHHHhcCCCcccCCCCccchhhhhhhhccCCceeeecccccccCCCCCCCCCCCchhhhcchhHHHHHHHHHH
Q 029917 46 RDWNTFGQYLRNQRPPVALSQCNSNHVLDFLRYLDQFGKTKVHLQGCVFFGQPEPPGPCSCPLKQAWGSLDALIGRLRAA 125 (185)
Q Consensus 46 rdwntf~qyL~n~rPPlsl~~cs~~hVleFL~ylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQAwGSLDALIGRLRAa 125 (185)
...+.|.+|+.+. ++...+..||.+||.||-..- ..+..++...+.-||..
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 455567889999999976221 14556777777777777
Q ss_pred HHH
Q 029917 126 YEE 128 (185)
Q Consensus 126 feE 128 (185)
|+-
T Consensus 75 f~~ 77 (85)
T PF13495_consen 75 FRW 77 (85)
T ss_dssp HHC
T ss_pred HHH
Confidence 763
No 22
>PF13276 HTH_21: HTH-like domain
Probab=37.62 E-value=52 Score=21.65 Aligned_cols=29 Identities=21% Similarity=0.308 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHhCCCCCCCCccchhHHHHHHH
Q 029917 116 DALIGRLRAAYEENGGLPETNPFASGAIRIYLRE 149 (185)
Q Consensus 116 DALIGRLRAafeE~Gg~pE~NPF~araVR~YLRe 149 (185)
|+|+-.++++|+++.+ =||.+-|..+|+.
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 23
>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=37.41 E-value=34 Score=22.40 Aligned_cols=20 Identities=40% Similarity=0.604 Sum_probs=17.6
Q ss_pred cchhHHHHHHHHHHHHHhCC
Q 029917 112 WGSLDALIGRLRAAYEENGG 131 (185)
Q Consensus 112 wGSLDALIGRLRAafeE~Gg 131 (185)
-.+|+.+|-|||..+++.|+
T Consensus 44 ~~~l~~~i~~LR~~l~~~~~ 63 (78)
T smart00862 44 DNTLDVHISRLRKKLEDDGA 63 (78)
T ss_pred cchHHHHHHHHHHHHhcCCC
Confidence 36799999999999998765
No 24
>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=36.11 E-value=25 Score=22.15 Aligned_cols=13 Identities=31% Similarity=0.756 Sum_probs=10.5
Q ss_pred hhHHHHHHHHhHH
Q 029917 141 GAIRIYLREVRDS 153 (185)
Q Consensus 141 raVR~YLReVRd~ 153 (185)
-+|++||++|+..
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 25
>PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=34.69 E-value=1.2e+02 Score=23.59 Aligned_cols=36 Identities=22% Similarity=0.367 Sum_probs=26.6
Q ss_pred hhhhhHHHHHHHhcCCCcccCCCCccchhhhhhhhcc
Q 029917 45 RRDWNTFGQYLRNQRPPVALSQCNSNHVLDFLRYLDQ 81 (185)
Q Consensus 45 rrdwntf~qyL~n~rPPlsl~~cs~~hVleFL~ylDq 81 (185)
+.+|+.|..|+..... ..+..-+..||.+||.++-+
T Consensus 32 ~~~~~~~~~~~~~~~~-~~~~~i~~~~i~~~~~~~~~ 67 (297)
T PRK00236 32 RRDLRAFLAFLEEHGI-SSLQDLDAADLRSFLARRRR 67 (297)
T ss_pred HHHHHHHHHHHHHcCC-CchhhCCHHHHHHHHHHHHh
Confidence 4577889899887543 45666678899999988643
No 26
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair]
Probab=34.00 E-value=29 Score=31.75 Aligned_cols=44 Identities=27% Similarity=0.551 Sum_probs=36.7
Q ss_pred CCCchhhhhhhhhhhHHHHHHHhcCCCc-ccCCCCccchhhhhhhhccCCc
Q 029917 35 APLSRYESQKRRDWNTFGQYLRNQRPPV-ALSQCNSNHVLDFLRYLDQFGK 84 (185)
Q Consensus 35 ~~~srYesQKrrdwntf~qyL~n~rPPl-sl~~cs~~hVleFL~ylDqfGk 84 (185)
-+.+-| |||-+.|.+||..+- + +|...+..||.+||.++-.+|.
T Consensus 25 nTl~sY----rrDL~~f~~~L~~~~--~~~l~~~~~~di~~yl~~l~~~g~ 69 (300)
T COG4974 25 NTLSSY----RRDLEDFREWLEERG--ITDLADATEADIREYLTELAEQGL 69 (300)
T ss_pred hhHHHH----HHHHHHHHHHHHhcC--CCChhhcCHHHHHHHHHHHHhCCc
Confidence 355566 689999999999886 4 6777889999999999999983
No 27
>KOG4670 consensus Uncharacterized conserved membrane protein [Function unknown]
Probab=33.61 E-value=26 Score=34.85 Aligned_cols=59 Identities=27% Similarity=0.397 Sum_probs=42.9
Q ss_pred hhhhhhhH------------HHHHHHhcCCCcccCCCCccchhhhhhhhccCCcee-----ee-cccccccCCCCCC
Q 029917 43 QKRRDWNT------------FGQYLRNQRPPVALSQCNSNHVLDFLRYLDQFGKTK-----VH-LQGCVFFGQPEPP 101 (185)
Q Consensus 43 QKrrdwnt------------f~qyL~n~rPPlsl~~cs~~hVleFL~ylDqfGkTk-----VH-~~~C~ffg~p~pp 101 (185)
-|+|.|++ ||-||..|.+|..+--=...---.||+-+++.-++. || ...|.+-.-.+||
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 57788875 999999999998776422223356788888887665 55 4578888777774
No 28
>PF10865 DUF2703: Domain of unknown function (DUF2703); InterPro: IPR021219 This family of protein has no known function.
Probab=32.13 E-value=19 Score=28.62 Aligned_cols=43 Identities=26% Similarity=0.342 Sum_probs=32.8
Q ss_pred hhhhhhhhccCCceeeecccccccCCCCCCCCCCCchhhhcchhHHHHHHHHHHHHHhCCCCC
Q 029917 72 VLDFLRYLDQFGKTKVHLQGCVFFGQPEPPGPCSCPLKQAWGSLDALIGRLRAAYEENGGLPE 134 (185)
Q Consensus 72 VleFL~ylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQAwGSLDALIGRLRAafeE~Gg~pE 134 (185)
+|+|+ |||..|+| |. +| ...+.+|+..+-+|+.+|+..|..++
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 47886 55555776 43 22 47788999999999999999998654
No 29
>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=31.99 E-value=41 Score=27.21 Aligned_cols=36 Identities=22% Similarity=0.537 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHhCCCCC---C---CC-ccchhHHHHHHHHhH
Q 029917 117 ALIGRLRAAYEENGGLPE---T---NP-FASGAIRIYLREVRD 152 (185)
Q Consensus 117 ALIGRLRAafeE~Gg~pE---~---NP-F~araVR~YLReVRd 152 (185)
.-|-+|+..|++.|...+ . ++ -.+..++.||||.-+
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 367889999999755
No 30
>KOG4405 consensus GDP dissociation inhibitor [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=31.72 E-value=17 Score=35.60 Aligned_cols=79 Identities=29% Similarity=0.460 Sum_probs=59.9
Q ss_pred HHHHHHHhcCCCcccCCC--------Ccc---------chhhhhhhhccCCceeeecccccccCCCCCCCCCCCchhhhc
Q 029917 50 TFGQYLRNQRPPVALSQC--------NSN---------HVLDFLRYLDQFGKTKVHLQGCVFFGQPEPPGPCSCPLKQAW 112 (185)
Q Consensus 50 tf~qyL~n~rPPlsl~~c--------s~~---------hVleFL~ylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQAw 112 (185)
+|.+||+.++=+-.|.+| +.. -...||..+.+||.|- --=|.||+-+.| -|-|-+--..
T Consensus 224 ~F~EyL~~~rltp~lqs~vl~aIaM~~~~~~tt~eGm~at~~fl~slGrfgntp---fLfPlYGqGELp-QcFCRlcAVf 299 (547)
T KOG4405|consen 224 PFSEYLKTMRLTPKLQSIVLHAIAMLSESQLTTIEGMDATKNFLTSLGRFGNTP---FLFPLYGQGELP-QCFCRLCAVF 299 (547)
T ss_pred cHHHHHHhcCCChhhHHHHHHHHHhcCcccccHHHHHHHHHHHHHHhhccCCCc---ceeeccCCCcch-HHHHHHHHHh
Confidence 999999999988777654 221 2457999999999997 334667887765 6888777777
Q ss_pred ch------------hHHHHHHHHHHHHHhCCC
Q 029917 113 GS------------LDALIGRLRAAYEENGGL 132 (185)
Q Consensus 113 GS------------LDALIGRLRAafeE~Gg~ 132 (185)
|+ ||..+++..|+.+.+|-+
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 577778888999999864
No 31
>smart00243 GAS2 Growth-Arrest-Specific Protein 2 Domain. GROWTH-ARREST-SPECIFIC PROTEIN 2 Domain
Probab=30.18 E-value=34 Score=25.75 Aligned_cols=15 Identities=33% Similarity=0.829 Sum_probs=13.3
Q ss_pred hhhHHHHHHHhcCCC
Q 029917 47 DWNTFGQYLRNQRPP 61 (185)
Q Consensus 47 dwntf~qyL~n~rPP 61 (185)
-|.||.+||..|.|=
T Consensus 55 GW~tL~~fL~khDPC 69 (73)
T smart00243 55 GWETLDEYLLKHDPC 69 (73)
T ss_pred cHHHHHHHHHhCCCc
Confidence 499999999999883
No 32
>PF06252 DUF1018: Protein of unknown function (DUF1018); InterPro: IPR009363 This family consists of several bacterial and phage proteins, related to Gp16 of phage Mu, of unknown function.
Probab=29.40 E-value=1.7e+02 Score=22.11 Aligned_cols=74 Identities=15% Similarity=0.111 Sum_probs=50.6
Q ss_pred hhhHHHHHHHhcCCCcccCCCCccchhhhhhhhccCCceeeecccccccCCCCCCCCCCCchhhhcchhHHHHHHHHHHH
Q 029917 47 DWNTFGQYLRNQRPPVALSQCNSNHVLDFLRYLDQFGKTKVHLQGCVFFGQPEPPGPCSCPLKQAWGSLDALIGRLRAAY 126 (185)
Q Consensus 47 dwntf~qyL~n~rPPlsl~~cs~~hVleFL~ylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQAwGSLDALIGRLRAaf 126 (185)
|..++..+|.+...=-|...++-....++|..+.+.|-. +..+.=.+-. .|.. ...+.+.+|+|..
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 456778888888877788888888888888888887742 1111111111 1111 1788999999999
Q ss_pred HHhCCCCC
Q 029917 127 EENGGLPE 134 (185)
Q Consensus 127 eE~Gg~pE 134 (185)
.++|....
T Consensus 68 ~~~~~~~~ 75 (119)
T PF06252_consen 68 KQLGKPGA 75 (119)
T ss_pred HHhhccCC
Confidence 99997655
No 33
>cd04436 DEP_fRgd2 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGAP (GTPase-activator protein) Rgd2-like proteins. Rgd2-like proteins share a common domain architecture, containing, beside the RhoGAP domain, a DEP and a FCH (Fes/CIP4 homology) domain. Yeast Rgd2 is a GAP protein for Cdc42 and Rho5.
Probab=29.10 E-value=28 Score=26.50 Aligned_cols=40 Identities=25% Similarity=0.414 Sum_probs=29.6
Q ss_pred hHHHHHHHhcCCCcccCCC--Cccchh--hhhhhhccCCceeee
Q 029917 49 NTFGQYLRNQRPPVALSQC--NSNHVL--DFLRYLDQFGKTKVH 88 (185)
Q Consensus 49 ntf~qyL~n~rPPlsl~~c--s~~hVl--eFL~ylDqfGkTkVH 88 (185)
.++++||..++|=-++..+ -|.|++ .|||+.+..|.|-++
T Consensus 33 ~~Iv~~L~~n~~~~s~~~aE~fGQdLv~~gfir~~g~vG~~F~n 76 (84)
T cd04436 33 SEIVSWLQENMPEKDLDAAEAFGQDLLNQGFLRLVGGVGSTFVN 76 (84)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHHHHhCchHHHhcccCcceec
Confidence 4677888888777666666 466664 499999999987664
No 34
>PF04221 RelB: RelB antitoxin; InterPro: IPR007337 Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. Several toxin/antitoxin pairs may occur in a single species. RelE and RelB form a toxin-antitoxin system; RelE represses translation, probably through binding ribosomes [, ]. RelB stably binds RelE, presumably deactivating it.; PDB: 2KC8_B 2K29_A.
Probab=28.65 E-value=1e+02 Score=22.03 Aligned_cols=39 Identities=31% Similarity=0.492 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHhCCCCCCCCccchhHHHHHHHHhHHHhhhhCCchhhh
Q 029917 117 ALIGRLRAAYEENGGLPETNPFASGAIRIYLREVRDSQAKARGIPYKKK 165 (185)
Q Consensus 117 ALIGRLRAafeE~Gg~pE~NPF~araVR~YLReVRd~QAkArgi~y~kk 165 (185)
.|--+..++|+++|-.+ +-||++||+.| +..+|||++-+
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 44578888654
No 35
>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=28.21 E-value=96 Score=31.00 Aligned_cols=42 Identities=19% Similarity=0.139 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHHhCCC-------------------------CCCCCc-cchhHHHHH----HHHhHHHhhh
Q 029917 116 DALIGRLRAAYEENGGL-------------------------PETNPF-ASGAIRIYL----REVRDSQAKA 157 (185)
Q Consensus 116 DALIGRLRAafeE~Gg~-------------------------pE~NPF-~araVR~YL----ReVRd~QAkA 157 (185)
|.+.-.+|.+++.++++ .|.||| |.|.||+|| .++=+.|.+|
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 55556777777776543 378996 789999999 5566666655
No 36
>PLN02837 threonine-tRNA ligase
Probab=27.77 E-value=35 Score=32.79 Aligned_cols=15 Identities=33% Similarity=0.558 Sum_probs=11.8
Q ss_pred hhhcchhHHHHHHHH
Q 029917 109 KQAWGSLDALIGRLR 123 (185)
Q Consensus 109 RQAwGSLDALIGRLR 123 (185)
|-.|||+|.|||-|-
T Consensus 489 ~~~~G~~eRlia~Li 503 (614)
T PLN02837 489 RAILGSLERFFGVLI 503 (614)
T ss_pred cCCccCHHHHHHHHH
Confidence 677999999887553
No 37
>PF09958 DUF2192: Uncharacterized protein conserved in archaea (DUF2192); InterPro: IPR018693 This family of various hypothetical archaeal proteins has no known function.
Probab=27.43 E-value=53 Score=29.16 Aligned_cols=21 Identities=43% Similarity=0.567 Sum_probs=18.5
Q ss_pred hhHHHHHHHHHHHHHhCCCCC
Q 029917 114 SLDALIGRLRAAYEENGGLPE 134 (185)
Q Consensus 114 SLDALIGRLRAafeE~Gg~pE 134 (185)
+=+.||.-||..|+++|..|=
T Consensus 27 ~R~~lv~~L~~~Y~~~gIeP~ 47 (231)
T PF09958_consen 27 DREELVELLREVYEENGIEPF 47 (231)
T ss_pred CHHHHHHHHHHHHHHcCCCcC
Confidence 458899999999999999864
No 38
>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=27.39 E-value=1.2e+02 Score=22.12 Aligned_cols=39 Identities=36% Similarity=0.656 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHhCCCCCCCCccchhHHHHHHHHhHHHhhhhCCchhhh
Q 029917 117 ALIGRLRAAYEENGGLPETNPFASGAIRIYLREVRDSQAKARGIPYKKK 165 (185)
Q Consensus 117 ALIGRLRAafeE~Gg~pE~NPF~araVR~YLReVRd~QAkArgi~y~kk 165 (185)
.|--..-++|+++|..+ +.|||++|+.| ++-+|||++-+
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 34455677889999875 56999999876 44578887754
No 39
>PF08544 GHMP_kinases_C: GHMP kinases C terminal ; InterPro: IPR013750 This domain is found in homoserine kinases (2.7.1.39 from EC), galactokinases (2.7.1.6 from EC) and mevalonate kinases (2.7.1.36 from EC). These kinases make up the GHMP kinase superfamily of ATP-dependent enzymes []. These enzymes are involved in the biosynthesis of isoprenes and amino acids as well as in carbohydrate metabolism. The C-terminal domain of homoserine kinase has a central alpha-beta plait fold and an insertion of four helices, which, together with the N-terminal fold, create a novel nucleotide binding fold [].; PDB: 2R3V_C 4EMD_A 4DXL_A 4ED4_A 2GS8_A 1K47_E 3GON_A 3K17_B 1PIE_A 2AJ4_A ....
Probab=27.38 E-value=8.3 Score=25.89 Aligned_cols=72 Identities=15% Similarity=0.243 Sum_probs=43.9
Q ss_pred hhhhhhHHHHHHHhcCC--CcccCCCCccchhhhhhhhccCC--ceee-ec--ccccccCCCCCCCCCCCchhhhcchhH
Q 029917 44 KRRDWNTFGQYLRNQRP--PVALSQCNSNHVLDFLRYLDQFG--KTKV-HL--QGCVFFGQPEPPGPCSCPLKQAWGSLD 116 (185)
Q Consensus 44 Krrdwntf~qyL~n~rP--Plsl~~cs~~hVleFL~ylDqfG--kTkV-H~--~~C~ffg~p~ppapC~CPlRQAwGSLD 116 (185)
++.||..|.+.+.+..- |.....+...+|.+.+.++-+.| -+++ .. .+|.|- |=.--...|
T Consensus 6 ~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~Ga~~~~~sGsG~G~~v~~------------l~~~~~~~~ 73 (85)
T PF08544_consen 6 AEGDLELLGELMNENQENEPENYREVLTPEIDELKEAAEENGALGAKMSGSGGGPTVFA------------LCKDEDDAE 73 (85)
T ss_dssp HTTCHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHTTESEEEEETTSSSSEEEE------------EESSHHHHH
T ss_pred HCcCHHHHHHHHHHhhhhcchHHHHHcCHHHHHHHHHHHHCCCCceecCCCCCCCeEEE------------EECCHHHHH
Confidence 46899999999995443 44455566678888888887777 3333 22 333321 112223566
Q ss_pred HHHHHHHHHHH
Q 029917 117 ALIGRLRAAYE 127 (185)
Q Consensus 117 ALIGRLRAafe 127 (185)
.++-+|++.|+
T Consensus 74 ~v~~~l~~~~~ 84 (85)
T PF08544_consen 74 RVAEALREHYK 84 (85)
T ss_dssp HHHHHHHHHTH
T ss_pred HHHHHHHHhCC
Confidence 67777777664
No 40
>PTZ00398 phosphoenolpyruvate carboxylase; Provisional
Probab=27.21 E-value=98 Score=32.22 Aligned_cols=43 Identities=16% Similarity=0.285 Sum_probs=32.0
Q ss_pred hcchhHHHHHHHHHHHHHhCC------------------CCCCCCccc-------------hhHHHHHHHHhHH
Q 029917 111 AWGSLDALIGRLRAAYEENGG------------------LPETNPFAS-------------GAIRIYLREVRDS 153 (185)
Q Consensus 111 AwGSLDALIGRLRAafeE~Gg------------------~pE~NPF~a-------------raVR~YLReVRd~ 153 (185)
-|-.+=.+..+|..+++++|+ .=++|||.. .|+++|+++|++.
T Consensus 263 l~~aiP~~~~~l~~al~~~~~~~~~~~~~~i~fGSWiGGDRDGNP~VTaevT~~~l~~~r~~al~~Y~~~l~~L 336 (974)
T PTZ00398 263 IFDALPNFIRYIDNVLYEYNLDPLPPTKKLFTFSSWVGGDRDGNPFVTAEVTRQVVYFNRIRACELFIHMIEKL 336 (974)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCCCCCceeccCCCCCCCCCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 355666788899999988764 234999984 4678899998764
No 41
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=26.93 E-value=1.2e+02 Score=22.71 Aligned_cols=37 Identities=38% Similarity=0.526 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHhCCCCCCCCccchhHHHHHHHHhHHHhhhhCCchh
Q 029917 117 ALIGRLRAAYEENGGLPETNPFASGAIRIYLREVRDSQAKARGIPYK 163 (185)
Q Consensus 117 ALIGRLRAafeE~Gg~pE~NPF~araVR~YLReVRd~QAkArgi~y~ 163 (185)
.|--..-++|+++|-.+ +.||++||+.| ++-+|||++
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 57999999887 445788877
No 42
>cd00383 trans_reg_C Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase.
Probab=26.52 E-value=57 Score=22.15 Aligned_cols=20 Identities=30% Similarity=0.443 Sum_probs=17.2
Q ss_pred chhHHHHHHHHHHHHHhCCC
Q 029917 113 GSLDALIGRLRAAYEENGGL 132 (185)
Q Consensus 113 GSLDALIGRLRAafeE~Gg~ 132 (185)
.+|+.+|=|||..+.+.|+.
T Consensus 62 ~~l~~~I~rLRkkl~~~~~~ 81 (95)
T cd00383 62 RTVDVHISRLRKKLEDDPSN 81 (95)
T ss_pred ccHHHHHHHHHHHhccCCCC
Confidence 57999999999999987653
No 43
>PF09674 DUF2400: Protein of unknown function (DUF2400); InterPro: IPR014127 Members of this uncharacterised protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighbourhoods show little conservation.
Probab=25.86 E-value=62 Score=28.16 Aligned_cols=25 Identities=24% Similarity=0.369 Sum_probs=23.5
Q ss_pred hhhcchhHHHHHHHHHHHHHhCCCC
Q 029917 109 KQAWGSLDALIGRLRAAYEENGGLP 133 (185)
Q Consensus 109 RQAwGSLDALIGRLRAafeE~Gg~p 133 (185)
-.|||.+..+|-.|..+|+.+|..|
T Consensus 24 ~lAyG~~~~I~~~~~~ll~~~~~~P 48 (232)
T PF09674_consen 24 LLAYGNRKQIIKKLERLLDLMGPSP 48 (232)
T ss_pred HHHccCHHHHHHHHHHHHHHhCCCH
Confidence 4799999999999999999999986
No 44
>KOG1452 consensus Predicted Rho GTPase-activating protein [Signal transduction mechanisms]
Probab=25.76 E-value=40 Score=32.23 Aligned_cols=31 Identities=35% Similarity=0.511 Sum_probs=23.2
Q ss_pred HHHHHHHHhCCC--------CCCCCccchhHHHHHHHHhH
Q 029917 121 RLRAAYEENGGL--------PETNPFASGAIRIYLREVRD 152 (185)
Q Consensus 121 RLRAafeE~Gg~--------pE~NPF~araVR~YLReVRd 152 (185)
-||++||-||+. |+.|= -+..++.||||+=|
T Consensus 233 mLR~~fe~n~r~~el~~E~iPD~nv-Itg~~kD~lrElpE 271 (442)
T KOG1452|consen 233 MLRRDFEPNGRDFELGAESIPDYNV-ITGDSKDELRELPE 271 (442)
T ss_pred HHHHHhccCCcccccccccCCCcce-eecccHhHHHhCCC
Confidence 589999999984 33443 45589999999743
No 45
>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=25.49 E-value=70 Score=29.99 Aligned_cols=53 Identities=36% Similarity=0.497 Sum_probs=35.0
Q ss_pred cchhhhhhhhccCC-ceeeecccccccCCCCCCCCCCCchhhhcchh--HH----HHHHHHHHHHHhCCCCC
Q 029917 70 NHVLDFLRYLDQFG-KTKVHLQGCVFFGQPEPPGPCSCPLKQAWGSL--DA----LIGRLRAAYEENGGLPE 134 (185)
Q Consensus 70 ~hVleFL~ylDqfG-kTkVH~~~C~ffg~p~ppapC~CPlRQAwGSL--DA----LIGRLRAafeE~Gg~pE 134 (185)
..-++||..|.+.| |.+|+ ..-.|-.+.+. |..+ |. .--||..||+++|..|.
T Consensus 49 ~agl~f~e~l~~~gakv~Vp----------TTlNp~~~D~~--w~~~gvd~~f~~~q~~i~~ay~~mG~~~t 108 (389)
T cd01355 49 DAGLEFLERLADQGAKVAVP----------TTLNPISMDLH--WRELGVDEEFAEKQARLVKAYKAMGVDPT 108 (389)
T ss_pred hhhHHHHHHHHhCCCeEeec----------CccCCcccCcc--hhhcCCCHHHHHHHHHHHHHHHHcCCccc
Confidence 34479999887666 34443 23456666766 8755 32 34477899999999765
No 46
>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=25.36 E-value=39 Score=29.01 Aligned_cols=14 Identities=43% Similarity=0.696 Sum_probs=11.2
Q ss_pred hhhhHHHHHHHhcC
Q 029917 46 RDWNTFGQYLRNQR 59 (185)
Q Consensus 46 rdwntf~qyL~n~r 59 (185)
=|.|+|.|||...+
T Consensus 141 VDR~EFdQYLn~~~ 154 (197)
T PF12067_consen 141 VDRTEFDQYLNSSR 154 (197)
T ss_pred hhHHHHHHHhcccc
Confidence 46899999999644
No 47
>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=24.58 E-value=61 Score=28.94 Aligned_cols=64 Identities=22% Similarity=0.340 Sum_probs=46.8
Q ss_pred CCchhhhhhhhhhhHHHHHHHhcCCCccc--CCCCccchhhhhhh-----------------hccCCceeeecccccccC
Q 029917 36 PLSRYESQKRRDWNTFGQYLRNQRPPVAL--SQCNSNHVLDFLRY-----------------LDQFGKTKVHLQGCVFFG 96 (185)
Q Consensus 36 ~~srYesQKrrdwntf~qyL~n~rPPlsl--~~cs~~hVleFL~y-----------------lDqfGkTkVH~~~C~ffg 96 (185)
.-.+|-++=|..-.+|.+||+.+.|-... ..-....|.+||.. ....|..++|.-+=..|.
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 34678888899999999999999987721 12245678899986 345777788887777777
Q ss_pred CCC
Q 029917 97 QPE 99 (185)
Q Consensus 97 ~p~ 99 (185)
+++
T Consensus 227 ~~g 229 (312)
T PF11709_consen 227 RTG 229 (312)
T ss_pred CCc
Confidence 665
No 48
>COG0745 OmpR Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=24.29 E-value=61 Score=27.19 Aligned_cols=37 Identities=30% Similarity=0.478 Sum_probs=26.5
Q ss_pred CCCCCCCCCCchhhhcc--------hhHHHHHHHHHHHHHhCCCC
Q 029917 97 QPEPPGPCSCPLKQAWG--------SLDALIGRLRAAYEENGGLP 133 (185)
Q Consensus 97 ~p~ppapC~CPlRQAwG--------SLDALIGRLRAafeE~Gg~p 133 (185)
+|+....-.--+.+.|| +||..|.|||.-.+..+..+
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 49
>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=24.03 E-value=81 Score=30.36 Aligned_cols=36 Identities=25% Similarity=0.339 Sum_probs=28.0
Q ss_pred hhHHHHHHHHHHHHHhCCC---------------------CCCCCc-cchhHHHHHHH
Q 029917 114 SLDALIGRLRAAYEENGGL---------------------PETNPF-ASGAIRIYLRE 149 (185)
Q Consensus 114 SLDALIGRLRAafeE~Gg~---------------------pE~NPF-~araVR~YLRe 149 (185)
+.|...-..|.+.+.++++ .|.||| |-|+||+||..
T Consensus 308 ~e~eq~~~y~~i~~~~~~~pv~iRtlDig~DK~~~~~~~~~E~NP~LG~RgiR~~l~~ 365 (565)
T TIGR01417 308 TEEEQFAAYKTVLEAMESDAVIVRTLDIGGDKELPYLNFPKEENPFLGYRAIRLALER 365 (565)
T ss_pred CHHHHHHHHHHHHHHhCCCceEEECCCCCCcccccccCCCCCCCccccchhhhhcccC
Confidence 4467777788888888764 379996 78999999964
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=24.01 E-value=38 Score=23.00 Aligned_cols=20 Identities=30% Similarity=0.504 Sum_probs=16.6
Q ss_pred CCccchhhhhhhhccCCcee
Q 029917 67 CNSNHVLDFLRYLDQFGKTK 86 (185)
Q Consensus 67 cs~~hVleFL~ylDqfGkTk 86 (185)
.|=+-++-+|.|+|+.|-|+
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 35567899999999999997
No 51
>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=23.88 E-value=5.3e+02 Score=23.12 Aligned_cols=24 Identities=21% Similarity=0.296 Sum_probs=19.9
Q ss_pred hhhhhhhhhhHHHHHHHhcCCCcc
Q 029917 40 YESQKRRDWNTFGQYLRNQRPPVA 63 (185)
Q Consensus 40 YesQKrrdwntf~qyL~n~rPPls 63 (185)
-.++.|+.|+.|.++.+.+.+|++
T Consensus 166 ~~n~~r~~~~~~~~l~~~~p~pit 189 (377)
T TIGR03190 166 VCDENRRLLRELFDYRKEADPKVT 189 (377)
T ss_pred HHHHHHHHHHHHHHHHccCCCCcC
Confidence 346788999999999888888886
No 52
>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=23.67 E-value=30 Score=21.03 Aligned_cols=16 Identities=44% Similarity=1.161 Sum_probs=10.6
Q ss_pred cccccccCCCCCCCCC
Q 029917 89 LQGCVFFGQPEPPGPC 104 (185)
Q Consensus 89 ~~~C~ffg~p~ppapC 104 (185)
..+|.|||.+..-.-|
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 5789999988755544
No 53
>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=23.64 E-value=46 Score=33.82 Aligned_cols=26 Identities=31% Similarity=0.484 Sum_probs=19.9
Q ss_pred CCCCCCc-cchhHHHHH--HHHhHHHhhh
Q 029917 132 LPETNPF-ASGAIRIYL--REVRDSQAKA 157 (185)
Q Consensus 132 ~pE~NPF-~araVR~YL--ReVRd~QAkA 157 (185)
..|.||| +.|.||+|| .++=+.|.+|
T Consensus 651 ~~E~NP~LG~RGiRl~l~~pei~~~QlrA 679 (856)
T TIGR01828 651 LHEVNPMLGHRGCRLGITYPEIYEMQVRA 679 (856)
T ss_pred CCCCCCccccchhhhccCChHHHHHHHHH
Confidence 3599997 679999999 5566666655
No 54
>PRK12435 ferrochelatase; Provisional
Probab=23.58 E-value=1.5e+02 Score=26.27 Aligned_cols=16 Identities=31% Similarity=0.723 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHhCCC
Q 029917 117 ALIGRLRAAYEENGGL 132 (185)
Q Consensus 117 ALIGRLRAafeE~Gg~ 132 (185)
.+|.+++..|+..||.
T Consensus 37 ~~l~~~~~~Y~~iGG~ 52 (311)
T PRK12435 37 EMLQDLKDRYEAIGGI 52 (311)
T ss_pred HHHHHHHHHHHHhCCc
Confidence 6778899999999874
No 55
>PF10520 Kua-UEV1_localn: Kua-ubiquitin conjugating enzyme hybrid localisation domain; InterPro: IPR019547 This entry represents part of the transcript of the fusion of two genes, the UEV1. UEV1 is an enzymatically inactive variant of the E2 ubiquitin-conjugating enzymes that regulate non-canonical elongation of ubiquitin chains, and Kua, an otherwise unknown gene. UEV1A is a nuclear protein, whereas both Kua and Kua-UEV localise to cytoplasmic structures, indicating that the addition of a Kua domain to UEV confers new biological properties. UEV1-Kua carries the B domain with its characteristic double histidine motif, and it is probably this domain which determines the cytoplasmic localisation. It is postulated that this hybrid transcript could preferentially direct the variant polyubiquitination of substrates closely associated with the cytoplasmic face of the endoplasmic reticulum, possibly, although not necessarily, in conjunction with membrane-bound ubiquitin-conjugating enzymes [].
Probab=23.55 E-value=39 Score=28.51 Aligned_cols=24 Identities=33% Similarity=0.697 Sum_probs=21.7
Q ss_pred hcchhHH-HHHHHHHHHHHhCCCCC
Q 029917 111 AWGSLDA-LIGRLRAAYEENGGLPE 134 (185)
Q Consensus 111 AwGSLDA-LIGRLRAafeE~Gg~pE 134 (185)
-|||+|- +||+.-++|.||-..|-
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 89999999999999885
No 56
>PF02187 GAS2: Growth-Arrest-Specific Protein 2 Domain; InterPro: IPR003108 The growth-arrest-specific protein 2 domain is found associated with the spectrin repeat, calponin homology domain and EF hand in many proteins. It is found among others in the growth arrest-specific protein 2 [].; GO: 0007050 cell cycle arrest; PDB: 1V5R_A.
Probab=23.54 E-value=20 Score=26.74 Aligned_cols=13 Identities=38% Similarity=1.091 Sum_probs=11.1
Q ss_pred hhHHHHHHHhcCC
Q 029917 48 WNTFGQYLRNQRP 60 (185)
Q Consensus 48 wntf~qyL~n~rP 60 (185)
|.||..||..|.|
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 57
>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=23.47 E-value=29 Score=27.44 Aligned_cols=37 Identities=24% Similarity=0.396 Sum_probs=29.9
Q ss_pred hhhhhHHHHHHHh---cCCCcccCCCCccchhhhhhhhcc
Q 029917 45 RRDWNTFGQYLRN---QRPPVALSQCNSNHVLDFLRYLDQ 81 (185)
Q Consensus 45 rrdwntf~qyL~n---~rPPlsl~~cs~~hVleFL~ylDq 81 (185)
...|..|++|+-. ..-|-.+.++.+.++.+||.-+|.
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 3478899998876 455777788999999999998874
No 58
>COG4865 Glutamate mutase epsilon subunit [Amino acid transport and metabolism]
Probab=23.39 E-value=55 Score=31.61 Aligned_cols=23 Identities=35% Similarity=0.589 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHhCCCCCCCCccc
Q 029917 118 LIGRLRAAYEENGGLPETNPFAS 140 (185)
Q Consensus 118 LIGRLRAafeE~Gg~pE~NPF~a 140 (185)
+|.||.-+|||||.+=...||+-
T Consensus 196 YVDRL~G~YeE~Gi~INREpFgP 218 (485)
T COG4865 196 YVDRLMGMYEEHGIRINREPFGP 218 (485)
T ss_pred HHHHHHhHHHhcCeeeccccCCC
Confidence 45677779999999877777763
No 59
>PF00667 FAD_binding_1: FAD binding domain; InterPro: IPR003097 This domain is found in sulphite reductase, NADPH cytochrome P450 reductase, nitric oxide synthase and methionine synthase reductase. Flavoprotein pyridine nucleotide cytochrome reductases [] (FPNCR) catalyse the interchange of reducing equivalents between one-electron carriers and the two-electron-carrying nicotinamide dinucleotides. The enzymes include ferredoxin:NADP+reductases (FNR) [], plant and fungal NAD(P)H:nitrate reductases [, ], NADH:cytochrome b5 reductases [], NADPH:P450 reductases [], NADPH:sulphite reductases [], nitric oxide synthases [], phthalate dioxygenase reductase [], and various other flavoproteins.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3QFR_B 3FJO_A 3QFC_B 3QE2_B 3QFS_A 3QFT_A 2B5O_B 2QTZ_A 2QTL_A 2BPO_B ....
Probab=23.20 E-value=72 Score=26.04 Aligned_cols=45 Identities=20% Similarity=0.175 Sum_probs=33.2
Q ss_pred ccchhhhhhhhccCCceeeecccccccCCCCCCCCCCCchhhhcc
Q 029917 69 SNHVLDFLRYLDQFGKTKVHLQGCVFFGQPEPPGPCSCPLKQAWG 113 (185)
Q Consensus 69 ~~hVleFL~ylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQAwG 113 (185)
.++|-+||..+.-.+.+.|......-.....+|.|.+|.++++--
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 457888888888888787766655533555677889999988753
No 60
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=23.18 E-value=42 Score=23.09 Aligned_cols=12 Identities=42% Similarity=0.775 Sum_probs=10.4
Q ss_pred cchhHHHHHHHH
Q 029917 112 WGSLDALIGRLR 123 (185)
Q Consensus 112 wGSLDALIGRLR 123 (185)
|-.||.||.+|.
T Consensus 37 f~~lD~li~~l~ 48 (49)
T PF07535_consen 37 FKELDSLISQLQ 48 (49)
T ss_pred HHHHHHHHHHhc
Confidence 779999999884
No 61
>PRK13197 pyrrolidone-carboxylate peptidase; Provisional
Probab=22.84 E-value=2.6e+02 Score=23.60 Aligned_cols=84 Identities=21% Similarity=0.241 Sum_probs=51.0
Q ss_pred CCchhhhhhhhhhhHHHHHHHhcCCCcccCCCCccchhhhhhh-----hccCCc-ee---eecccccccCCCCCCCCCCC
Q 029917 36 PLSRYESQKRRDWNTFGQYLRNQRPPVALSQCNSNHVLDFLRY-----LDQFGK-TK---VHLQGCVFFGQPEPPGPCSC 106 (185)
Q Consensus 36 ~~srYesQKrrdwntf~qyL~n~rPPlsl~~cs~~hVleFL~y-----lDqfGk-Tk---VH~~~C~ffg~p~ppapC~C 106 (185)
.|..|.+ .-+...+.+.|++.--|..+|.=-|.-|++|+=| +.+.+. ++ ||.|..+--....+..| .+
T Consensus 108 gp~~~~t--~Lp~~~l~~~l~~~gip~~~S~dAG~YlCN~i~Y~sl~~~~~~~~~~~a~FIHvP~~~~~~~~~~~~p-~~ 184 (215)
T PRK13197 108 GPAAYFS--TLPIKAMVKAIREAGIPASVSNTAGTFVCNHVMYGLLHLLDKKYPNIRAGFIHIPYLPEQAVNKPGTP-SM 184 (215)
T ss_pred CCceeEc--CCCHHHHHHHHHHcCCCceeccCCCceeehHHHHHHHHHHHhcCCCceeEEEEcCCchhhhhcCCCCC-Cc
Confidence 3445553 3456777888888888999999999999999544 444443 33 78886543321111111 22
Q ss_pred chhhhcchhHHHHHHHHHHHHHh
Q 029917 107 PLKQAWGSLDALIGRLRAAYEEN 129 (185)
Q Consensus 107 PlRQAwGSLDALIGRLRAafeE~ 129 (185)
+++.++.-+|++-++.
T Consensus 185 -------~~~~~~~av~~~i~~~ 200 (215)
T PRK13197 185 -------SLEDIVRGLELAIEAI 200 (215)
T ss_pred -------cHHHHHHHHHHHHHHH
Confidence 3666666666655543
No 62
>PF06480 FtsH_ext: FtsH Extracellular; InterPro: IPR011546 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This domain is found in the FtsH family of proteins that include FtsH a membrane-bound ATP-dependent protease universally conserved in prokaryotes []. The FtsH peptidases, which belong to MEROPS peptidase family M41 (clan MA(E)), efficiently degrade proteins that have a low thermodynamic stability - e.g. they lack robust unfoldase activity. This feature may be key and implies that this could be a criterion for degrading a protein. In Oenococcus oeni (Leuconostoc oenos) FtsH is involved in protection against environmental stress [], and shows increased expression under heat or osmotic stress. These two lines of evidence suggest that it is a fundamental prokaryotic self-protection mechanism that checks if proteins are correctly folded. The precise function of this N-terminal region is unclear. ; GO: 0004222 metalloendopeptidase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0016021 integral to membrane; PDB: 2LNA_A.
Probab=22.78 E-value=1.1e+02 Score=20.86 Aligned_cols=26 Identities=31% Similarity=0.203 Sum_probs=18.8
Q ss_pred cchhHHHHHHHHHHHHHhCCCCCCCC
Q 029917 112 WGSLDALIGRLRAAYEENGGLPETNP 137 (185)
Q Consensus 112 wGSLDALIGRLRAafeE~Gg~pE~NP 137 (185)
++++|.+.=+|..+-+|+|..+++.|
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 63
>PRK11173 two-component response regulator; Provisional
Probab=22.70 E-value=67 Score=24.75 Aligned_cols=18 Identities=28% Similarity=0.532 Sum_probs=15.5
Q ss_pred hhHHHHHHHHHHHHHhCC
Q 029917 114 SLDALIGRLRAAYEENGG 131 (185)
Q Consensus 114 SLDALIGRLRAafeE~Gg 131 (185)
+||..|.|||.-+++.+.
T Consensus 200 ~~~~~i~rlR~kl~~~~~ 217 (237)
T PRK11173 200 TVDVTIRRIRKHFESTPD 217 (237)
T ss_pred cHHHHHHHHHHHhccCCC
Confidence 899999999999986543
No 64
>cd04383 RhoGAP_srGAP RhoGAP_srGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in srGAPs. srGAPs are components of the intracellular part of Slit-Robo signalling pathway that is important for axon guidance and cell migration. srGAPs contain an N-terminal FCH domain, a central RhoGAP domain and a C-terminal SH3 domain; this SH3 domain interacts with the intracellular proline-rich-tail of the Roundabout receptor (Robo). This interaction with Robo then activates the rhoGAP domain which in turn inhibits Cdc42 activity. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific group
Probab=22.38 E-value=86 Score=25.42 Aligned_cols=35 Identities=23% Similarity=0.609 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHhCCCC---CCCC----ccchhHHHHHHHHhH
Q 029917 117 ALIGRLRAAYEENGGLP---ETNP----FASGAIRIYLREVRD 152 (185)
Q Consensus 117 ALIGRLRAafeE~Gg~p---E~NP----F~araVR~YLReVRd 152 (185)
+-|..||..|+. |..+ +.+. -.+..++.||||..+
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 1222 258899999999754
No 65
>PF01663 Phosphodiest: Type I phosphodiesterase / nucleotide pyrophosphatase; InterPro: IPR002591 This family consists of phosphodiesterases, including human plasma-cell membrane glycoprotein PC-1 / alkaline phosphodiesterase I / nucleotide pyrophosphatase (nppase). These enzymes catalyse the cleavage of phosphodiester and phosphosulphate bonds in NAD, deoxynucleotides and nucleotide sugars []. Another member of this family is ATX an autotaxin, tumor cell motility-stimulating protein which exhibits type I phosphodiesterases activity []. The alignment encompasses the active site [, ]. Also present within this family is 60 kDa Ca2+-ATPase from Myroides odoratus []. This signature also hits a number of ethanolamine phosphate transferase involved in glycosylphosphatidylinositol-anchor biosynthesis.; GO: 0003824 catalytic activity; PDB: 2XRG_A 2XR9_A 3T02_A 3T01_A 3SZZ_A 3SZY_A 3T00_A 3NKM_A 3NKN_A 3NKR_A ....
Probab=22.23 E-value=69 Score=26.26 Aligned_cols=27 Identities=41% Similarity=0.671 Sum_probs=23.0
Q ss_pred hhhhcchhHHHHHHHHHHHHHhCCCCC
Q 029917 108 LKQAWGSLDALIGRLRAAYEENGGLPE 134 (185)
Q Consensus 108 lRQAwGSLDALIGRLRAafeE~Gg~pE 134 (185)
.+.+.-.+|..||+|.+++++.|...+
T Consensus 208 ~~~~~~~~D~~ig~l~~~l~~~~~~~~ 234 (365)
T PF01663_consen 208 IEDAYRRIDQAIGRLLEALDENGLLED 234 (365)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTT-TTT
T ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCc
Confidence 578999999999999999999976544
No 66
>PF06947 DUF1290: Protein of unknown function (DUF1290); InterPro: IPR009709 This family consists of several bacterial small basic proteins of around 100 residues in length. The function of this family is unknown.
Probab=22.17 E-value=77 Score=24.62 Aligned_cols=17 Identities=35% Similarity=0.743 Sum_probs=15.1
Q ss_pred chhHHHHHHHHHHHHHh
Q 029917 113 GSLDALIGRLRAAYEEN 129 (185)
Q Consensus 113 GSLDALIGRLRAafeE~ 129 (185)
..||++.|-+||..|++
T Consensus 16 AaLDsvfGgiRA~le~~ 32 (88)
T PF06947_consen 16 AALDSVFGGIRASLEDK 32 (88)
T ss_pred HHHHHHHHHHHHHHHhh
Confidence 46999999999999975
No 67
>cd04379 RhoGAP_SYD1 RhoGAP_SYD1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in SYD-1_like proteins. Syd-1, first identified and best studied in C.elegans, has been shown to play an important role in neuronal development by specifying axonal properties. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=22.05 E-value=80 Score=26.31 Aligned_cols=36 Identities=33% Similarity=0.470 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHhCCCCCC------CCc-cchhHHHHHHHHhH
Q 029917 117 ALIGRLRAAYEENGGLPET------NPF-ASGAIRIYLREVRD 152 (185)
Q Consensus 117 ALIGRLRAafeE~Gg~pE~------NPF-~araVR~YLReVRd 152 (185)
+.|..|+..|+..+...+- ++. .|..++.||||.-+
T Consensus 47 ~~i~~L~~~~d~~~~~~~l~~~~~~dvh~vA~lLK~fLReLPe 89 (207)
T cd04379 47 AKKKELRDAFERNSAAVELSEELYPDINVITGVLKDYLRELPE 89 (207)
T ss_pred HHHHHHHHHHcCCCCcCCCChhhcccHHHHHHHHHHHHHhCCC
Confidence 3599999999986542221 222 58899999999654
No 68
>PRK09468 ompR osmolarity response regulator; Provisional
Probab=22.04 E-value=73 Score=24.43 Aligned_cols=16 Identities=50% Similarity=0.686 Sum_probs=12.2
Q ss_pred hhHHHHHHHHHHHHHh
Q 029917 114 SLDALIGRLRAAYEEN 129 (185)
Q Consensus 114 SLDALIGRLRAafeE~ 129 (185)
+||..|.|||.-++..
T Consensus 201 ~l~~~i~~LR~kl~~~ 216 (239)
T PRK09468 201 SIDVQISRLRRLIEED 216 (239)
T ss_pred CHHHHHHHHHHHhccC
Confidence 6888888888887643
No 69
>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=21.82 E-value=48 Score=23.17 Aligned_cols=31 Identities=19% Similarity=0.536 Sum_probs=24.0
Q ss_pred hhHHHHHHHhcCCCcccCCCCccchhhhhhhhccCC
Q 029917 48 WNTFGQYLRNQRPPVALSQCNSNHVLDFLRYLDQFG 83 (185)
Q Consensus 48 wntf~qyL~n~rPPlsl~~cs~~hVleFL~ylDqfG 83 (185)
-+.|.+=|++.+|-|+ .+||..|..|-.+||
T Consensus 32 ~~DF~~Al~~~kpSVs-----~~dl~~ye~w~~~FG 62 (62)
T PF09336_consen 32 MEDFEEALKKVKPSVS-----QEDLKKYEEWTKEFG 62 (62)
T ss_dssp HHHHHHHHHTCGGSS------HHHHHHHHHHHHHTS
T ss_pred HHHHHHHHHHcCCCCC-----HHHHHHHHHHHHHcC
Confidence 3557777888887654 569999999999998
No 70
>PRK05084 xerS site-specific tyrosine recombinase XerS; Reviewed
Probab=21.53 E-value=1.2e+02 Score=25.42 Aligned_cols=67 Identities=13% Similarity=0.233 Sum_probs=42.7
Q ss_pred hhhhHHHHHHHhcCC-----Cc-----ccCCCCccchhhhhhhhccCCceeeecccccccCCCCCCCCCCCchhhhcchh
Q 029917 46 RDWNTFGQYLRNQRP-----PV-----ALSQCNSNHVLDFLRYLDQFGKTKVHLQGCVFFGQPEPPGPCSCPLKQAWGSL 115 (185)
Q Consensus 46 rdwntf~qyL~n~rP-----Pl-----sl~~cs~~hVleFL~ylDqfGkTkVH~~~C~ffg~p~ppapC~CPlRQAwGSL 115 (185)
++...|.+||..+.. +. .|..-+..||.+|+.|+.+.-.. + ++.+ +...+..|+
T Consensus 43 ~~l~~f~~~l~~~~~~~~~~~~~~~~~~l~~lt~~~i~~f~~~l~~~~~~------~---~~~~-------~~~~s~~Ti 106 (357)
T PRK05084 43 TEYRRFFNWLISEGLSDASKIKDIPLSTLENLTKKDVEAFILYLRERPLL------N---GHST-------KKGNSQTTI 106 (357)
T ss_pred HHHHHHHHHHHHcCCCCcCCcccCCHHHHHhhhHHHHHHHHHHHHhcccc------c---cccc-------ccchhHHHH
Confidence 456678888876532 11 24566899999999998542100 0 0000 013467889
Q ss_pred HHHHHHHHHHHHH
Q 029917 116 DALIGRLRAAYEE 128 (185)
Q Consensus 116 DALIGRLRAafeE 128 (185)
...++-||++|.-
T Consensus 107 ~~~l~~l~~~~~~ 119 (357)
T PRK05084 107 NRTLSALKSLFKY 119 (357)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999999984
No 71
>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=20.66 E-value=1.4e+02 Score=26.57 Aligned_cols=38 Identities=29% Similarity=0.194 Sum_probs=29.7
Q ss_pred cchhHHHHHHHHHHHHHhCCC----------------------CCCCCc-cchhHHHHHHH
Q 029917 112 WGSLDALIGRLRAAYEENGGL----------------------PETNPF-ASGAIRIYLRE 149 (185)
Q Consensus 112 wGSLDALIGRLRAafeE~Gg~----------------------pE~NPF-~araVR~YLRe 149 (185)
+=+.+.+...++.+.+.++++ .|.||| |-|+||+||..
T Consensus 58 ~p~e~eq~~~y~~i~~~~~~~pV~iRtlD~g~dK~l~~~~~~~~E~NP~LG~RGiR~~l~~ 118 (293)
T PF02896_consen 58 PPSEEEQYEIYRKIAEAMGGKPVTIRTLDIGGDKPLPYLSREPKEENPALGLRGIRRSLAH 118 (293)
T ss_dssp HHHHHHHHHHHHHHHHHTTTSEEEEE---SBCCCGSCSSHHCH--SSGGGSSBTHHHHHHS
T ss_pred CchHHHHHHHHHHHHHHhccCcEEEEecCCCCCccCCcccccccccccccccccccccccc
Confidence 446788888899999888774 569994 77999999975
No 72
>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=20.52 E-value=56 Score=27.61 Aligned_cols=17 Identities=29% Similarity=0.602 Sum_probs=12.4
Q ss_pred hhhhcchhHHHHHHHHH
Q 029917 108 LKQAWGSLDALIGRLRA 124 (185)
Q Consensus 108 lRQAwGSLDALIGRLRA 124 (185)
-+-.||+++.+||=|-+
T Consensus 244 h~~~~g~~~R~i~ali~ 260 (261)
T cd00778 244 HQTSWGISTRLIGAIIM 260 (261)
T ss_pred EEecccHHHHHHHHHHh
Confidence 45669988888886644
No 73
>PHA03019 hypothetical protein; Provisional
Probab=20.31 E-value=69 Score=24.27 Aligned_cols=22 Identities=23% Similarity=0.400 Sum_probs=18.3
Q ss_pred hhhhhhHHHHHHHhcCCCcccC
Q 029917 44 KRRDWNTFGQYLRNQRPPVALS 65 (185)
Q Consensus 44 Krrdwntf~qyL~n~rPPlsl~ 65 (185)
--+--|+|.+|++||.|-+.|.
T Consensus 44 nd~~in~~ld~~knh~~nidli 65 (77)
T PHA03019 44 NDHCINKFLDFKKNHEPNIDLI 65 (77)
T ss_pred hHHHHHHHHHHHHccCCCccee
Confidence 3456799999999999988875
Done!